WorldWideScience

Sample records for bottlenecks population differentiation

  1. Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii

    DEFF Research Database (Denmark)

    Barker, J.S.F.; Frydenberg, Jane; González, J.;

    2009-01-01

    variation for 15 microsatellite loci in each of nine populations in eastern Australia was used to estimate the size of the bottleneck, and to determine if any of these microsatellites marked genomic regions subject to recent selection. We estimate that on its introduction to Australia, D. buzzatii went...... through a moderate bottleneck (approximately 30-40 founders). Linkage disequilibrium was common, both intrachromosomal and between loci on different chromosomes. Of the 15 loci, 2 showed evidence of selection, one exhibiting local adaptation in different populations and the other balancing selection. We...

  2. Reliability of genetic bottleneck tests for detecting recent population declines

    NARCIS (Netherlands)

    Peery, M. Zachariah; Kirby, Rebecca; Reid, Brendan N.; Stoelting, Ricka; Doucet-Beer, Elena; Robinson, Stacie; Vasquez-Carrillo, Catalina; Pauli, Jonathan N.; Palsboll, Per J.

    2012-01-01

    The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popula

  3. Genetic variability and bottleneck detection of four Tricholoma matsutake populations from northeastern and southwestern China.

    Science.gov (United States)

    Zeng, Dong-Fang; Chen, Bin

    2015-08-01

    The excessive commercial collection of matsutake mushrooms can lead to extreme reduction of population size, which may cause genetic bottleneck and decrease genetic diversity of Tricholoma matsutake. Here, six polymorphic microsatellite loci markers were used to examine the genetic diversity of four natural T. matsutake populations from two main producing regions of China. The minimum combinations of four loci were able to discriminate total 86 sampled individuals with distinctive multilocus genotypes. Our analysis of molecular variance (AMOVA) revealed that about 80% and 20% of the overall genetic variation were respectively partitioned within and among populations. The principal-coordinate analyses (PCA) distinguished the four tested populations into three genetic clusters, each of which was correlated with respective endemic host plants on a geographical basis. The AMOVA, PCA and pairwise population FST estimates consistently displayed the same genetic divergence patterns and spatial structure of T. matsutake mediated by host plants in China. The significant heterozygosity excesses demonstrated that a recent genetic bottleneck occurred in each population tested. The complementary M-ratio test indicated past genetic bottleneck events over longer periods. Only four individuals were identified as putative first generation migrants within northeastern China, which implies restricted interpopulation gene flow in T. matsutake. We discuss that the significant genetic differentiation among populations of T. matsutake is most likely a function of host adaptation, host specificity, genetic bottleneck, limited dispersal and habitat fragmentation. PMID:25682708

  4. Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness.

    OpenAIRE

    Novella, I S; Elena, S F; Moya, A.; Domingo, E; Holland, J J

    1995-01-01

    Genetic bottlenecks are important events in the genetic diversification of organisms and colonization of new ecological niches. Repeated bottlenecking of RNA viruses often leads to fitness losses due to the operation of Muller's ratchet. Herein we use vesicular stomatitis virus to determine the transmission population size which leads to fitness decreases of virus populations. Remarkably, the effective size of a genetic bottleneck associated with fitness loss is greater when the fitness of th...

  5. Fixation times in differentiation and evolution in the presence of bottlenecks, deserts, and oases.

    Science.gov (United States)

    Chou, Tom; Wang, Yu

    2015-05-01

    Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be quantified by their population at a corresponding node within a network of states. Their dynamics across the state-space network involve genotypic or phenotypic transitions that can occur upon cell division, such as during symmetric or asymmetric cell differentiation, or upon spontaneous mutation. Here, we use a general multi-type branching processes to study first passage time statistics for a single cell to appear in a specific state. Our approach readily allows for nonexponentially distributed waiting times between transitions, reflecting, e.g., the cell cycle. For simplicity, we restrict most of our detailed analysis to exponentially distributed waiting times (Poisson processes). We present results for a sequential evolutionary process in which L successive transitions propel a population from a "wild-type" state to a given "terminally differentiated," "resistant," or "cancerous" state. Analytic and numeric results are also found for first passage times across an evolutionary chain containing a node with increased death or proliferation rate, representing a desert/bottleneck or an oasis. Processes involving cell proliferation are shown to be "nonlinear" (even though mean-field equations for the expected particle numbers are linear) resulting in first passage time statistics that depend on the position of the bottleneck or oasis. Our results highlight the sensitivity of stochastic measures to cell division fate and quantify the limitations of using certain approximations (such as the fixed-population and mean-field assumptions) in evaluating fixation times.

  6. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

    Science.gov (United States)

    Phillips, Robyn L.; Gifford, Danna R.; MacLean, R. Craig

    2016-01-01

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions. PMID:27466449

  7. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution.

    Science.gov (United States)

    Vogwill, Tom; Phillips, Robyn L; Gifford, Danna R; MacLean, R Craig

    2016-07-27

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions. PMID:27466449

  8. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N;

    2008-01-01

    According to neutral quantitative genetic theory, population bottlenecks are expected to decrease standing levels of additive genetic variance of quantitative traits. However, some empirical and theoretical results suggest that, if nonadditive genetic effects influence the trait, bottlenecks may...... actually increase additive genetic variance. This has been an important issue in conservation genetics where it has been suggested that small population size might actually experience an increase rather than a decrease in the rate of adaptation. Here we test if bottlenecks can break a selection limit...... effects were responsible for the divergence in desiccation resistance between the original control and a bottlenecked line exhibiting increased additive genetic variance for desiccation resistance. However, when bottlenecked lines were selected for increased desiccation resistance, there was only a small...

  9. Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus

    Directory of Open Access Journals (Sweden)

    Mariette Stéphanie

    2010-08-01

    Full Text Available Abstract Background Domestication and breeding involve the selection of particular phenotypes, limiting the genomic diversity of the population and creating a bottleneck. These effects can be precisely estimated when the location of domestication is established. Few analyses have focused on understanding the genetic consequences of domestication and breeding in fruit trees. In this study, we aimed to analyse genetic structure and changes in the diversity in sweet cherry Prunus avium L. Results Three subgroups were detected in sweet cherry, with one group of landraces genetically very close to the analysed wild cherry population. A limited number of SSR markers displayed deviations from the frequencies expected under neutrality. After the removal of these markers from the analysis, a very limited bottleneck was detected between wild cherries and sweet cherry landraces, with a much more pronounced bottleneck between sweet cherry landraces and modern sweet cherry varieties. The loss of diversity between wild cherries and sweet cherry landraces at the S-locus was more significant than that for microsatellites. Particularly high levels of differentiation were observed for some S-alleles. Conclusions Several domestication events may have happened in sweet cherry or/and intense gene flow from local wild cherry was probably maintained along the evolutionary history of the species. A marked bottleneck due to breeding was detected, with all markers, in the modern sweet cherry gene pool. The microsatellites did not detect the bottleneck due to domestication in the analysed sample. The vegetative propagation specific to some fruit trees may account for the differences in diversity observed at the S-locus. Our study provides insights into domestication events of cherry, however, requires confirmation on a larger sampling scheme for both sweet cherry landraces and wild cherry.

  10. On the prospect of identifying adaptive loci in recently bottlenecked populations.

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    Yu-Ping Poh

    Full Text Available Identifying adaptively important loci in recently bottlenecked populations - be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed - remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.

  11. Circulating virus load determines the size of bottlenecks in viral populations progressing within a host.

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    Serafín Gutiérrez

    Full Text Available For any organism, population size, and fluctuations thereof, are of primary importance in determining the forces driving its evolution. This is particularly true for viruses--rapidly evolving entities that form populations with transient and explosive expansions alternating with phases of migration, resulting in strong population bottlenecks and associated founder effects that increase genetic drift. A typical illustration of this pattern is the progression of viral disease within a eukaryotic host, where such demographic fluctuations are a key factor in the emergence of new variants with altered virulence. Viruses initiate replication in one or only a few infection foci, then move through the vasculature to seed secondary infection sites and so invade distant organs and tissues. Founder effects during this within-host colonization might depend on the concentration of infectious units accumulating and circulating in the vasculature, as this represents the infection dose reaching new organs or "territories". Surprisingly, whether or not the easily measurable circulating (plasma virus load directly drives the size of population bottlenecks during host colonization has not been documented in animal viruses, while in plants the virus load within the sap has never been estimated. Here, we address this important question by monitoring both the virus concentration flowing in host plant sap, and the number of viral genomes founding the population in each successive new leaf. Our results clearly indicate that the concentration of circulating viruses directly determines the size of bottlenecks, which hence controls founder effects and effective population size during disease progression within a host.

  12. Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican parrot

    Science.gov (United States)

    Beissenger, S.R.; Wunderle, J.M.; Meyers, J.M.; Saether, B.-E.; Engen, S.

    2008-01-01

    The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk analysis, then examine evidence for the importance of specific processes maintaining the bottleneck using the multiple competing hypotheses approach, and finally integrate these results through a sensitivity analysis of a demographic model using life-stage simulation analysis (LSA) to determine the relative importance of genetic, demographic, environmental, and catastrophic processes on population growth. Annual population growth has been slow and variable (1.0 6 5.2 parrots per year, or an average k?1.05 6 0.19) from 16 parrots (1973) to a high of 40-42 birds (1997-1998). A risk analysis based on population prediction intervals (PPI) indicates great risk and large uncertainty, with a range of 22?83 birds in the 90% PPI only five years into the future. Four primary factors (reduced hatching success due to inbreeding, failure of adults to nest, nest failure due to nongenetic causes, and reduced survival of adults and juveniles) were responsible for maintaining the bottleneck. Egghatchability rates were low (70.6% per egg and 76.8% per pair), and hatchability increased after mate changes, suggesting inbreeding effects. Only an average of 34% of the population nested annually, which was well below the percentage of adults that should have reached an age of first breeding (41-56%). This chronic failure to nest appears to have been caused primarily by environmental and/or behavioral factors, and not by nest-site scarcity or a skewed sex ratio. Nest failure rates from nongenetic causes (i.e., predation, parasitism, and wet cavities) were low (29%) due to active management (protecting nests and fostering

  13. Variation at innate immunity Toll-like receptor genes in a bottlenecked population of a New Zealand robin.

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    Catherine E Grueber

    Full Text Available Toll-like receptors (TLRs are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (Petroica australis rakiura, for which reduced microsatellite diversity was previously observed. We genotyped 17-24 birds from a reintroduced island population (including the 12 founders for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (TLR1LB showed evidence of past directional selection. Results also confirmed a passerine duplication of TLR7. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.

  14. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima).

    Science.gov (United States)

    Nabholz, Benoit; Sarah, Gautier; Sabot, François; Ruiz, Manuel; Adam, Hélène; Nidelet, Sabine; Ghesquière, Alain; Santoni, Sylvain; David, Jacques; Glémin, Sylvain

    2014-05-01

    The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.

  15. Population aging and migrant workers: bottlenecks in tuberculosis control in rural China.

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    Sumedh Bele

    Full Text Available BACKGROUND: Tuberculosis is a serious global health problem. Its paradigms are shifting through time, especially in rapidly developing countries such as China. Health providers in China are at the forefront of the battle against tuberculosis; however, there are few empirical studies on health providers' perspectives on the challenges they face in tuberculosis control at the county level in China. This study was conducted among health providers to explore their experiences with tuberculosis control in order to identify bottlenecks and emerging challenges in controlling tuberculosis in rural China. METHODS: A qualitative approach was used. Semi-structured, in-depth interviews were conducted with 17 health providers working in various positions within the health system of one rural county (ZJG of China. Data were analyzed based on thematic content analysis using MAXQDA 10 qualitative data analysis software. RESULTS: Health providers reported several problems in tuberculosis control in ZJG county. Migrant workers and the elderly were repeatedly documented as the main obstacles in effective tuberculosis control in the county. At a personal level, doctors showed their frustration with the lack of new drugs for treating tuberculosis patients, and their opinions varied regarding incentives for referring patients. CONCLUSION: The results suggest that several problems still remain for controlling tuberculosis in rural China. Tuberculosis control efforts need to make reaching the most vulnerable populations a priority and encourage local health providers to adopt innovative practices in the local context based on national guidelines to achieve the best results. Considerable changes in China's National Tuberculosis Control Program are needed to tackle these emerging challenges faced by health workers at the county level.

  16. Limited population structure, genetic drift and bottlenecks characterise an endangered bird species in a dynamic, fire-prone ecosystem.

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    Sarah M Brown

    Full Text Available Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.

  17. Genetic Evidence of a Population Bottleneck and Inbreeding in the Endangered New Zealand Sea Lion, Phocarctos hookeri.

    Science.gov (United States)

    Osborne, Amy J; Negro, Sandra S; Chilvers, B Louise; Robertson, Bruce C; Kennedy, Martin A; Gemmell, Neil J

    2016-09-01

    The New Zealand sea lion (NZSL) is of high conservation concern due to its limited distribution and its declining population size. Historically, it occupied most of coastal New Zealand, but is now restricted to a few coastal sites in southern mainland New Zealand and the sub-Antarctic Islands. NZSLs have experienced a recent reduction in population size due to sealing in the 1900s, which is expected to have resulted in increased inbreeding and a loss of genetic variation, potentially reducing the evolutionary capacity of the species and negatively impacting on its long-term prospects for survival. We used 17 microsatellite loci, previously shown to have cross-species applications in pinnipeds, to determine locus- and population-specific statistics for 1205 NZSLs from 7 consecutive breeding seasons. We show that the NZSL population has a moderate level of genetic diversity in comparison to other pinnipeds. We provide genetic evidence for a population reduction, likely caused by historical sealing, and a measure of allele sharing/parental relatedness (internal relatedness) that is suggestive of increased inbreeding in pups that died during recent epizootic episodes. We hypothesize that population bottlenecks and nonrandom mating have impacted on the population genetic architecture of NZSLs, affecting its population recovery. PMID:26995741

  18. Ancient DNA reveals substantial genetic diversity in the California Condor (Gymnogyps californianus) prior to a population bottleneck

    Science.gov (United States)

    D'Elia, Jesse; Haig, Susan M.; Mullins, Thomas D.; Miller, Mark P.

    2016-01-01

    Critically endangered species that have undergone severe population bottlenecks often have little remaining genetic variation, making it difficult to reconstruct population histories to apply in reintroduction and recovery strategies. By using ancient DNA techniques, it is possible to combine genetic evidence from the historical population with contemporary samples to provide a more complete picture of a species' genetic variation across its historical range and through time. Applying this approach, we examined changes in the mitochondrial DNA (mtDNA) control region (526 base pairs) of the endangered California Condor (Gymnogyps californianus). Results showed a >80% reduction in unique haplotypes over the past 2 centuries. We found no spatial sorting of haplotypes in the historical population; the periphery of the range contained haplotypes that were common throughout the historical range. Direct examination of mtDNA from California Condor museum specimens provided a new window into historical population connectivity and genetic diversity showing: (1) a substantial loss of haplotypes, which is consistent with the hypothesis that condors were relatively abundant in the nineteenth century, but declined rapidly as a result of human-caused mortality; and (2) no evidence of historical population segregation, meaning that the available genetic data offer no cause to avoid releasing condors in unoccupied portions of their historical range.

  19. Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), and its implications for reintroduction.

    Science.gov (United States)

    Friar, E A; Ladoux, T; Roalson, E H; Robichaux, R H

    2000-12-01

    The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.

  20. Narrow bottlenecks affect Pea seedborne mosaic virus populations during vertical seed transmission but not during leaf colonization.

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    Frédéric Fabre

    2014-01-01

    Full Text Available The effective size of populations (Ne determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV colonizing leaves of pea plants (Pisum sativum L. during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence.

  1. Consequences of extreme life history traits on population persistence: do short-lived gobies face demographic bottlenecks?

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    Lefèvre, Carine D.; Nash, Kirsty L.; González-Cabello, Alonso; Bellwood, David R.

    2016-06-01

    The majority of coral reef goby species are short-lived, with some highly abundant species living less than 100 d. To understand the role and consequences of this extreme life history in shaping coral reef fish populations, we quantitatively documented the structure of small reef fish populations over a 26-month period (>14 short-lived fish generations) at an inshore reef on the Great Barrier Reef, Australia. Most species with life spans >1 yr, such as pomacentrids, exhibited a peak in recruitment during the austral summer, driving seasonal changes in the small fish community composition. In contrast, there were no clear changes in goby community composition, despite the abundance of short-lived, high turnover species. Species of Eviota, the most abundant gobiid genus observed, showed remarkably similar demographic profiles year-round, with consistent densities of adults as well as recently recruited juveniles. Our results demonstrate ongoing recruitment of these small cryptic fishes, which appears to compensate for an exceptionally short life span on the reef. Our results suggest that gobiid populations are able to overcome demographic limitations, and by maintaining reproduction, larval survival and recruitment throughout the year, they may avoid population bottlenecks. These findings also underline the potential trophodynamic importance of these small species; because of this constant turnover, Eviota species and other short-lived fishes may be particularly valuable contributors to the flow of energy on coral reefs, underpinning the year-round trophic structure.

  2. Meta-Analysis of mitochondrial DNA reveals several population bottlenecks during worldwide migrations of cattle

    NARCIS (Netherlands)

    Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Beja-Pereira, Albano; Bollongino, Ruth; Bradley, Daniel G.; Colli, Licia; De Gaetano, Anna; Edwards, Ceiridwen J.; Felius, Marleen; Ferretti, Luca; Ginja, Catarina; Hristov, Peter; Kantanen, Juha; Lirón, Juan Pedro; Magee, David A.; Negrini, Riccardo; Radoslavov, Georgi A.

    2014-01-01

    Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle ha

  3. Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research.

    Science.gov (United States)

    Chesler, Elissa J

    2014-02-01

    The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation.

  4. Logistics bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-09-15

    Many of the vulnerabilities to Energy Access, Energy Security, and Environmental Sustainability result from impediments to reaching a global demand-supply balance, as well as local balances, for various energy sources and carriers. Vulnerabilities result from multiple reasons: regional imbalances of energy production and consumption, the bulky character of the majority of energy fuels, the virtual necessity of electricity consumption following its production, among others. To detect and prioritize respective 'bottlenecks' across energy carriers, they have to be measured. In this report, production, consumption, exports, and imports were measured across all major energy carriers for seven key regions of the world for three time frames-2008, 2020, and 2050. Imbalances between production and consumption form bottlenecks in each region.

  5. Demographic and genetic factors in the recovery or demise of ex situ populations following a severe bottleneck in fifteen species of Hawaiian tree snails.

    Science.gov (United States)

    Price, Melissa R; Sischo, David; Pascua, Mark-Anthony; Hadfield, Michael G

    2015-01-01

    Wild populations of endangered Hawaiian tree snails have declined precipitously over the last century due to introduced predators and other human impacts. Life history traits, such as very low fecundity (species were collected from the wild to initiate captive-reared populations as a hedge against extinction. This small number of founders resulted in a severe bottleneck in each of the captive-reared populations. We identified key demographic parameters that predicted population recovery from this bottleneck. Species with captive populations that produced between two and four offspring per adult per year and had 20-50% of those offspring survive to maturity recovered to numbers above 100 individuals, and maintained viable populations following a decline that occurred between 2009 and 2014. Those populations that had less than two offspring per adult per year and less than 20% survival to maturity did not reach 100 individuals in captivity, and many of these populations died out during the recent decline. We suggest that small reductions in fitness may contribute to extirpation in taxa with inherently low fecundity, by keeping populations below a threshold number essential to long-term recovery. Future ex situ populations should be founded with no less than 15 adults, and maintained in conditions closely approximating the temperature and humidity of source locations to optimize fitness. Permanent translocations of wild populations for conservation purposes will be more likely to succeed with greater than 100 adults, and should be limited to locations with a similar climate to source locations. PMID:26587358

  6. Genetic differentiation in geographically close populations of the water rat Nectomys squamipes (Rodentia, Sigmodontinae from the Brazilian Atlantic Forest

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    Maroja L.S.

    2003-01-01

    Full Text Available We examined the genetic structure and the effects of a bottleneck in populations of the water rat Nectomys squamipes, a primary host of Schistosoma mansoni. Eight microsatellite loci were studied in 7 populations from the Sumidouro region of the Brazilian state of Rio de Janeiro. Our data, covering a four-year period during which a bottleneck occurred, revealed substantial variation (6-31 alleles per locus and high levels of both observed (0.718-0.789 and expected (0.748-0.832 heterozygosity. Most populations were in Hardy-Weinberg equilibrium without linkage disequilibrium between loci. Overall average genetic differentiation between populations (estimated with the F ST (q and R ST (r analogues was 0.037 for q and 0.060 for r. There was significant allelic and genotypic differentiation between populations, especially in pairwise comparisons that included the most geographically isolated population. Direct migration estimates showed a low rate of migration, indicating that infected N. squamipes populations had a limited ability to spread S. mansoni. When the pre- and post-bottleneck populations were compared there was no detectable reduction in heterozygosity or allele number, although a significant excess of heterozygosity was detected in the post-bottleneck population.

  7. Maintenance of genetic diversity in an introduced island population of guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation.

    Science.gov (United States)

    González, Benito A; Orozco-Terwengel, Pablo; von Borries, Rainer; Johnson, Warren E; Franklin, William L; Marín, Juan C

    2014-01-01

    Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10-20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation. PMID:24663026

  8. Hurry Up and Wait: Differential Impacts of Congestion, Bottleneck Pressure, and Predictability on Patient Length of Stay

    OpenAIRE

    Berry Jaeker, Jillian Alexandra; Tucker, Anita Lynn

    2012-01-01

    High work load, from high inventory levels, impacts unit processing times, but prior operations management studies have found conflicting results regarding direction. Thus, it is difficult to predict inventory’s effects on productivity a priori, inhibiting effective capacity management in high load systems. We categorize load into in-process inventory (congestion) and incoming inventory, decomposing the latter into its levels of bottleneck (BN) pressure and predictability, and quantify the ma...

  9. Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source-sink metapopulation structure, founder events and population bottlenecks.

    Science.gov (United States)

    Barson, N J; Cable, J; Van Oosterhout, C

    2009-03-01

    Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation-drift equilibrium. Dominant downstream migration over both short- and long-time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source-sink metapopulation, with the tributary furthest downstream representing a 'super sink', receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.

  10. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis).

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J; Robertson, Bruce C

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines. PMID:25719752

  11. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis.

    Directory of Open Access Journals (Sweden)

    Nicolas Dussex

    Full Text Available The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis. Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410, historical (n = 15 and fossil samples (n = 4 showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  12. Demographic changes and marker properties affect detection of human population differentiation

    Directory of Open Access Journals (Sweden)

    Sanichwankul Kittipong

    2007-05-01

    Full Text Available Abstract Background Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats. Results Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African while both successfully distinguished Hmong from Thai and Chinese. Conclusion Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.

  13. A Structured Population Model of Cell Differentiation

    CERN Document Server

    Doumic, Marie; Perthame, Benoit; Zubelli, Jorge P

    2010-01-01

    We introduce and analyze several aspects of a new model for cell differentiation. It assumes that differentiation of progenitor cells is a continuous process. From the mathematical point of view, it is based on partial differential equations of transport type. Specifically, it consists of a structured population equation with a nonlinear feedback loop. This models the signaling process due to cytokines, which regulate the differentiation and proliferation process. We compare the continuous model to its discrete counterpart, a multi-compartmental model of a discrete collection of cell subpopulations recently proposed by Marciniak-Czochra et al. in 2009 to investigate the dynamics of the hematopoietic system. We obtain uniform bounds for the solutions, characterize steady state solutions, and analyze their linearized stability. We show how persistence or extinction might occur according to values of parameters that characterize the stem cells self-renewal. We also perform numerical simulations and discuss the q...

  14. Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region.

    Science.gov (United States)

    Fu, Yong-Bi

    2012-02-01

    Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima's D were not significant, but a significant (P domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.

  15. The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck.

    Science.gov (United States)

    Zucker, Marc R; Harvey, Michael G; Oswald, Jessica A; Cuervo, Andrés; Derryberry, Elizabeth; Brumfield, Robb T

    2016-08-01

    Simultaneous examination of evolutionary history in island forms and closely related mainland relatives can provide reciprocal insight into the evolution of island and mainland faunas. The Cocos Flycatcher (Nesotriccus ridgwayi) is a small tyrant flycatcher (Tyrannidae) endemic to Cocos Island, an oceanic island in the eastern Pacific Ocean. We first established its close relationship to the mainland species Mouse-colored Tyrannulet (Phaeomyias murina) using a phylogeny from genome-wide ultraconserved elements and exons. We then used mitochondrial DNA to explore the relationships between Nesotriccus and Phaeomyias populations from across its distribution in Central and South America. We found that Nesotriccus is nested within the Phaeomyias evolutionary tree, and that Phaeomyias represents a complex of at least four evolutionarily distinct species that differ in plumage, voice, and habitat association. Nesotriccus underwent a population bottleneck subsequent to its divergence from Central American and northern South American Phaeomyias populations in the middle Pleistocene. The 46 UCE loci containing alleles that are fixed between the two species are widely distributed across the genome, which suggests that selective or neutral processes responsible for divergence have occurred genome-wide. Overall, our simultaneous examination of Phaeomyias and Nesotriccus revealed divergent levels of genetic diversity and evolutionary histories between island and mainland forms. PMID:27126184

  16. When is a bottleneck a bottleneck?

    CERN Document Server

    Schadschneider, Andreas; Popkov, Vladislav

    2015-01-01

    Bottlenecks, i.e. local reductions of capacity, are one of the most relevant scenarios of traffic systems. The asymmetric simple exclusion process (ASEP) with a defect is a minimal model for such a bottleneck scenario. One crucial question is "What is the critical strength of the defect that is required to create global effects, i.e. traffic jams localized at the defect position". Intuitively one would expect that already an arbitrarily small bottleneck strength leads to global effects in the system, e.g. a reduction of the maximal current. Therefore it came as a surprise when, based on computer simulations, it was claimed that the reaction of the system depends in non-continuous way on the defect strength and weak defects do not have a global influence on the system. Here we reconcile intuition and simulations by showing that indeed the critical defect strength is zero. We discuss the implications for the analysis of empirical and numerical data.

  17. Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

    Science.gov (United States)

    Wang, Wen-Ting; Xu, Bing; Zhang, Da-Yong; Bai, Wei-Ning

    2016-09-01

    The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity. PMID:27346642

  18. Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

    Science.gov (United States)

    Wang, Wen-Ting; Xu, Bing; Zhang, Da-Yong; Bai, Wei-Ning

    2016-09-01

    The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity.

  19. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Sifa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  20. Genetic Differentiation between Geographically Distant Populations of DROSOPHILA MELANOGASTER

    OpenAIRE

    Rama S Singh; Hickey, Donal A; David, Jean

    1982-01-01

    We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and sou...

  1. Economic analysis of production bottlenecks

    Directory of Open Access Journals (Sweden)

    Lawrence Stephen R.

    1995-01-01

    Full Text Available The management of bottlenecks has become a central topic in the planning and control of production systems. In this paper, we critically analyze bottlenecks from an economic perspective. Using a queueing network model, we demonstrate that bottlenecks are inevitable when there are differences in job arrival rates, processing rates, or costs of productive resources. These differences naturally lead to the creation of bottlenecks both for facilities design and demand planning problems. To evaluate bottlenecks from an economic perspective, we develop the notion of an “economic bottleneck,” which defines resources as bottlenecks based on economic, rather than physical, characteristics.

  2. Bottleneck flows in networks

    CERN Document Server

    Punnen, Abraham P

    2007-01-01

    The bottleneck network flow problem (BNFP) is a generalization of several well-studied bottleneck problems such as the bottleneck transportation problem (BTP), bottleneck assignment problem (BAP), bottleneck path problem (BPP), and so on. In this paper we provide a review of important results on this topic and its various special cases. We observe that the BNFP can be solved as a sequence of $O(\\log n)$ maximum flow problems. However, special augmenting path based algorithms for the maximum flow problem can be modified to obtain algorithms for the BNFP with the property that these variations and the corresponding maximum flow algorithms have identical worst case time complexity. On unit capacity network we show that BNFP can be solved in $O(\\min \\{{m(n\\log n)}^{{2/3}}, m^{{3/2}}\\sqrt{\\log n}\\})$. This improves the best available algorithm by a factor of $\\sqrt{\\log n}$. On unit capacity simple graphs, we show that BNFP can be solved in $O(m \\sqrt {n \\log n})$ time. As a consequence we have an $O(m \\sqrt {n \\l...

  3. Different level of population differentiation among human genes

    Directory of Open Access Journals (Sweden)

    Zhang Ya-Ping

    2011-01-01

    Full Text Available Abstract Background During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Results Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Conclusion Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

  4. Bayesian analysis of genetic differentiation between populations.

    Science.gov (United States)

    Corander, Jukka; Waldmann, Patrik; Sillanpää, Mikko J

    2003-01-01

    We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs. PMID:12586722

  5. Evolutionary forces shaping genomic islands of population differentiation in humans

    Directory of Open Access Journals (Sweden)

    Hofer Tamara

    2012-03-01

    Full Text Available Abstract Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM. A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i as much as 20% of islands are in non-genic regions ii these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii most loci are

  6. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.E.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58°N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of common accl

  7. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58 degrees N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of com

  8. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.E.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58_N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of common accl

  9. Genetic analysis of population differentiation and adaptation in Leuciscus waleckii.

    Science.gov (United States)

    Chang, Yumei; Tang, Ran; Sun, Xiaowen; Liang, Liqun; Chen, Jinping; Huang, Jinfeng; Dou, Xinjie; Tao, Ran

    2013-12-01

    Demographic events and natural selection both influence animal phenotypic and genetic variation; exploring the effects of demography and selection on population divergence is of great significance in evolutionary biology. To uncover the causes behind the patterns of genetic differentiation and adaptation among six populations of Leuciscus waleckii from Dali Basin (two populations, alkaline vs. freshwater) and Amur Basin (four populations, freshwater rivers vs. alkaline lake), a set of 21 unlinked polymorphic microsatellite markers and two mitochondrial DNA sequences (Cytb and D-loop) were applied to examine whether populations from different environments or habitats have distinct genetic differentiation and whether alkalinity is the major factor that caused population divergence. Bayesian analysis and principal component analysis as well as haplotype network analysis showed that these populations are primarily divided into two groups, which are congruent with geographic separation but not inconsistent with the habitat environment (alkalinity). Using three different approaches, outlier detection indicated that one locus, HLJYL017, may be under directional selection and involved in local adaptation processes. Overall, this study suggested that demographic events and selection of local environmental conditions including of alkalinity are jointly responsible for population divergence. These findings constitute an important step towards the understanding of the genetic basis of differentiation and adaptation, as well as towards the conservation of L. waleckii.

  10. Impacts of genetic bottlenecks on soybean genome diversity

    OpenAIRE

    Hyten, David L; Song, Qijian; Zhu, Youlin; Choi, Ik-Young; Nelson, Randall L.; Costa, Jose M.; Specht, James E; Shoemaker, Randy C.; Cregan, Perry B

    2006-01-01

    Soybean has undergone several genetic bottlenecks. These include domestication in Asia to produce numerous Asian landraces, introduction of relatively few landraces to North America, and then selective breeding over the past 75 years. It is presumed that these three human-mediated events have reduced genetic diversity. We sequenced 111 fragments from 102 genes in four soybean populations representing the populations before and after genetic bottlenecks. We show that soybean has lost many rare...

  11. High and distinct range-edge genetic diversity despite local bottlenecks.

    Science.gov (United States)

    Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Serrão, Ester Alvares

    2013-01-01

    The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines. PMID:23967038

  12. High and distinct range-edge genetic diversity despite local bottlenecks.

    Directory of Open Access Journals (Sweden)

    Jorge Assis

    Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

  13. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

    Directory of Open Access Journals (Sweden)

    Alicia R Martin

    2014-08-01

    Full Text Available Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP. The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and

  14. Periodic solutions of nonautonomous differential systems modeling obesity population

    Energy Technology Data Exchange (ETDEWEB)

    Arenas, Abraham J. [Departamento de Matematicas y Estadistica, Universidad de Cordoba Monteria (Colombia)], E-mail: aarenas@sinu.unicordoba.edu.co; Gonzalez-Parra, Gilberto [Departamento de Calculo, Universidad de los Andes, Merida (Venezuela, Bolivarian Republic of)], E-mail: gcarlos@ula.ve; Jodar, Lucas [Instituto de Matematica Multidisciplinar, Universidad Politecnica de Valencia Edificio 8G, 2o, 46022 Valencia (Spain)], E-mail: ljodar@imm.upv.es

    2009-10-30

    In this paper we study the periodic behaviour of the solutions of a nonautonomous model for obesity population. The mathematical model represented by a nonautonomous system of nonlinear ordinary differential equations is used to model the dynamics of obese populations. Numerical simulations suggest periodic behaviour of subpopulations solutions. Sufficient conditions which guarantee the existence of a periodic positive solution are obtained using a continuation theorem based on coincidence degree theory.

  15. Parameter Estimates in Differential Equation Models for Population Growth

    Science.gov (United States)

    Winkel, Brian J.

    2011-01-01

    We estimate the parameters present in several differential equation models of population growth, specifically logistic growth models and two-species competition models. We discuss student-evolved strategies and offer "Mathematica" code for a gradient search approach. We use historical (1930s) data from microbial studies of the Russian biologist,…

  16. Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington.

    Science.gov (United States)

    Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington. X. Wang and W. Chen. Washington State University, Pullman, WA, and USDA-ARS, Pullman, WA 99163 Sclerotinia sclerotiorum is the causal agent of white mold on lentils....

  17. Bottle-necks for restoration of the eel population, Anguilla anguilla (L.) of the river Yser basin (Flanders)

    OpenAIRE

    Denayer, B.; Belpaire, C.

    1996-01-01

    This paper describes some preliminary results on the status of eel populations in the river Yser and its tributaries. Data on glass eel migration at the river mouth during recent years are presented and compared with earlier observations. Populations of yellow eel were studied at several localities during 3 successive periods. Attention was given to all factors limiting development of normal eel stocks, especially migration obstruction to all stages. Suggestions for improving the aquatic habi...

  18. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    A. K. Gupta; M. Chauhan; S. N. Tandon; Sonia

    2005-12-01

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (± s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, $F_{\\text{IS}}$ (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode–shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

  19. Insect population differentiation in response to enviromental thermal stress

    Institute of Scientific and Technical Information of China (English)

    CHEN Bing; KANG Le

    2005-01-01

    Numerous studies reported the adaptation strategies adopted by ecthotherms to survive under environmental thermal stress. Geographic and seasonal variations in the thermal stress tolerance, which is closely associated with species' climatic adaptation and allopatric speciation, have been extensively investigated in insects. The variation patterns suggest directional selection for species' adaptive straits, and are used to predict the origin, distribution and dynamics of insect populations. These studies are becoming more and more important in the context of global warming. This paper discusses the process of adaptation to environmental thermal stress and the mechanisms underlying the differentiation in related adaptive straits of insect populations.

  20. Analysis of pharmacogenomic variants associated with population differentiation.

    Directory of Open Access Journals (Sweden)

    Bora Yeon

    Full Text Available In the present study, we systematically investigated population differentiation of drug-related (DR genes in order to identify common genetic features underlying population-specific responses to drugs. To do so, we used the International HapMap project release 27 Data and Pharmacogenomics Knowledge Base (PharmGKB database. First, we compared four measures for assessing population differentiation: the chi-square test, the analysis of variance (ANOVA F-test, Fst, and Nearest Shrunken Centroid Method (NSCM. Fst showed high sensitivity with stable specificity among varying sample sizes; thus, we selected Fst for determining population differentiation. Second, we divided DR genes from PharmGKB into two groups based on the degree of population differentiation as assessed by Fst: genes with a high level of differentiation (HD gene group and genes with a low level of differentiation (LD gene group. Last, we conducted a gene ontology (GO analysis and pathway analysis. Using all genes in the human genome as the background, the GO analysis and pathway analysis of the HD genes identified terms related to cell communication. "Cell communication" and "cell-cell signaling" had the lowest Benjamini-Hochberg's q-values (0.0002 and 0.0006, respectively, and "drug binding" was highly enriched (16.51 despite its relatively high q-value (0.0142. Among the 17 genes related to cell communication identified in the HD gene group, five genes (STX4, PPARD, DCK, GRIK4, and DRD3 contained single nucleotide polymorphisms with Fst values greater than 0.5. Specifically, the Fst values for rs10871454, rs6922548, rs3775289, rs1954787, and rs167771 were 0.682, 0.620, 0.573, 0.531, and 0.510, respectively. In the analysis using DR genes as the background, the HD gene group contained six significant terms. Five were related to reproduction, and one was "Wnt signaling pathway," which has been implicated in cancer. Our analysis suggests that the HD gene group from PharmGKB is

  1. Population differentiation of Phlebotomus perniciosus in Spain following postglacial dispersal.

    Science.gov (United States)

    Aransay, A M; Ready, P D; Morillas-Marquez, F

    2003-04-01

    Comparative sequencing of mitochondrial cytochrome b (Cyt b) and isoenzyme analyses have not resolved the population structure of the Iberian lineage of the sandfly Phlebotomus perniciosus, the most widespread vector of Leishmania infantum (Protozoa, Trypanosomatidae) to humans and dogs in the western Mediterranean subregion. Allelic variation at trinucleotide microsatellite loci was investigated in 13 Spanish populations of P. perniciosus. Four out of five loci showed significant differentiation between (pairwise F(ST)>0.23), but not within (pairwise F(ST)&Malta and Italy. The northeastern group of Spanish populations had a reduced number of microsatellite alleles (16 out of the 29 present in the southern populations), indicating its derivation as a peripheral isolate following the species' dispersal from a southern Ice Age refuge 8000-12 000 years ago. Pairwise F(ST) values did not increase with geographical distance between populations, over distances of 246-850 km (between regions) and 16-491 km (within regions). This suggests that the two regional groups of populations remain isolated, but that within each region there are no significant permanent barriers to gene flow between contiguous populations. These findings will help to predict the capacity of this sandfly to disperse, and originate new foci of leishmaniasis, in response to climate warming.

  2. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

    Science.gov (United States)

    Clowers, Katie J; Heilberger, Justin; Piotrowski, Jeff S; Will, Jessica L; Gasch, Audrey P

    2015-09-01

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.

  3. Effects of Bottlenecks in Vehicle Traffic

    CERN Document Server

    Yamamoto, S; Tadaki, S; Yamamoto, Syohei; Hieida, Yasuhiro; Tadaki, Shin-ichi

    2006-01-01

    Traffic congestion is usually observed at the upper streams of bottlenecks like tunnels. Congestion appears as stop-and-go waves and high density uniform flow. We perform simulations of traffic flow with a bottleneck using the coupled map optimal velocity model. The bottleneck is expressed as a road segment with speed reduction. The emergence of stop-and-go waves depends on the speed reduction in the bottleneck. A phenomenological theory of bottleneck effects is constructed.

  4. A recent bottleneck in the warthog and elephant populations of Queen Elizabeth National Park, revealed by a comparative study of four mammalian species in Uganda national parks

    DEFF Research Database (Denmark)

    Muwanika, Vincent B.; Siegismund, Hans Redlef; Okello, John Bosco A.;

    2003-01-01

    Until 1972, Uganda's national parks boasted of large numbers of large mammal species. Following the breakdown of law and order between 1972 and 1985, large-scale poaching led to an unprecedented decline in numbers of most large mammals in Uganda's national parks. However, the extent of decline...... microsatellite loci (for elephant and warthog populations) and mitochondrial control sequence variation in the warthogs, elephants, buffaloes and hippopotamuses. Queen Elizabeth National Park showed extreme reduction in nucleotide diversity for two species, the common warthog (p= 0.0%) and African elephant (p= 0...... varied in the different parks across different animal species. We have investigated the genetic effects of these reductions in four mammalian species (the common warthog, African savannah elephant, savannah buffalo and common river hippopotamus) from the three major parks of Uganda using both...

  5. Bottlenecks to coral recovery in the Seychelles

    Science.gov (United States)

    Chong-Seng, K. M.; Graham, N. A. J.; Pratchett, M. S.

    2014-06-01

    Processes that affect recovery of coral assemblages require investigation because coral reefs are experiencing a diverse array of more frequent disturbances. Potential bottlenecks to coral recovery include limited larval supply, low rates of settlement, and high mortality of new recruits or juvenile corals. We investigated spatial variation in local abundance of scleractinian corals in the Seychelles at three distinct life history stages (recruits, juveniles, and adults) on reefs with differing benthic conditions. Following widespread coral loss due to the 1998 bleaching event, some reefs are recovering (i.e., relatively high scleractinian coral cover: `coral-dominated'), some reefs have low cover of living macrobenthos and unconsolidated rubble substrates (`rubble-dominated'), and some reefs have high cover of macroalgae (`macroalgal-dominated'). Rates of coral recruitment to artificial settlement tiles were similar across all reef conditions, suggesting that larval supply does not explain differential coral recovery across the three reef types. However, acroporid recruits were absent on macroalgal-dominated reefs (0.0 ± 0.0 recruits tile-1) in comparison to coral-dominated reefs (5.2 ± 1.6 recruits tile-1). Juvenile coral colony density was significantly lower on macroalgal-dominated reefs (2.4 ± 1.1 colonies m-2), compared to coral-dominated reefs (16.8 ± 2.4 m-2) and rubble-dominated reefs (33.1 ± 7.3 m-2), suggesting that macroalgal-dominated reefs have either a bottleneck to successful settlement on the natural substrates or a high post-settlement mortality bottleneck. Rubble-dominated reefs had very low cover of adult corals (10.0 ± 1.7 %) compared to coral-dominated reefs (33.4 ± 3.6 %) despite no statistical difference in their juvenile coral densities. A bottleneck caused by low juvenile colony survivorship on unconsolidated rubble-dominated reefs is possible, or alternatively, recruitment to rubble-dominated reefs has only recently begun. This

  6. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Vieira, Filipe G.; Korneliussen, Thorfinn Sand;

    2013-01-01

    method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based...... on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled......Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data...

  7. Mitigating SDN controller performance bottlenecks

    DEFF Research Database (Denmark)

    Caba, Cosmin Marius; Soler, José

    2015-01-01

    proposes a new approach for addressing the performance bottlenecks that arise from limited computational resources at the SDNC. The proposed approach is based on optimally configuring the operating parameters of the components residing inside the SDNC (network control functions such as monitoring, routing...

  8. Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

    Institute of Scientific and Technical Information of China (English)

    Zhiying JIA; Yuyong ZHANG; Shuqiang CHEN; Lianyu SHI

    2012-01-01

    Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.

  9. Sales bottlenecks and their effect on profit

    NARCIS (Netherlands)

    Veltman, M.; Kooij, R.E.; Marban, S.

    2014-01-01

    This study introduces the term sales bottleneck, defined as a stage in a total production or service delivery process that limits sales. After analyzing the suitability of traditional methods to find sales bottlenecks, the study proposes the bottleneck accounting model as a method to determine sales

  10. MODIFIED BOTTLENECK-BASED PROCEDURE FOR LARGE-SCALE FLOW-SHOP SCHEDULING PROBLEMS WITH BOTTLENECK

    Institute of Scientific and Technical Information of China (English)

    ZUO Yan; GU Hanyu; XI Yugeng

    2006-01-01

    A new bottleneck-based heuristic for large-scale flow-shop scheduling problems with a bottleneck is proposed, which is simpler but more tailored than the shifting bottleneck (SB)procedure. In this algorithm, a schedule for the bottleneck machine is first constructed optimally and then the non-bottleneck machines are scheduled around the bottleneck schedule by some effective dispatching rules. Computational results show that the modified bottleneck-based procedure can achieve a tradeoff between solution quality and computational time comparing with SB procedure for medium-size problems. Furthermore it can obtain a good solution in quite short time for large-scale scheduling problems.

  11. Dynamic Prediction Method of Production Logistics Bottleneck Based on Bottleneck Index

    Institute of Scientific and Technical Information of China (English)

    LIU Mingzhou; TANG Juan; GE Maogen; JIANG Zengqiang; HU Jing; LING Lin

    2009-01-01

    In modern manufacturing pattern, there are many uncertain factors in the modern manufacturing process, such as changes of product attribute, changes of manufacturing resources' state, and so on, which cause production logistics bottleneck frequently shift, and make decisions of production planning and control based on formed bottleneck deviated from practical production process. Considering these factors, present researches mainly apply afterwards control to optimize production process to passively adapt to bottleneck changes. If the direction of bottleneck shifting can be accurately forecasted, the transition from afterwards control of chasing bottleneck to beforehand control can be realized. Therefore, aiming at the phenomenon of production logistics bottleneck shifting under uncertain manufacturing circumstances, this paper starts off with dynamic property of capability and requirement and then builds the concepts of bottleneck degree and bottleneck index to describe dynamic bottleneck characteristic of production unit;taken production capability, production load and quality assurance capability into consideration, mathematical model of bottleneck index is established to measure bottleneck degree accurately, consequently, quantitative research on mechanism of production logistics shifting is achieved. Based on bottleneck index, the prediction model of production logistics bottleneck is founded to predict dynamic change of bottleneck accurately. Finally, an example of forecasting and monitoring the production logistics bottleneck in one manufacturing shop is given to testify the validation and practicability of the prediction method.

  12. Breaking the biomass bottleneck of the fossil free society

    DEFF Research Database (Denmark)

    Wenzel, Henrik

    be converted to high-density fuels for mobility purposes, and it is a key source of carbon feedstock All in all, everything points to the fact, that biomass (and agricultural land) may be a severe bottleneck in the fossil free society and that excessive use can have severe consequences for the world’s forest...... resources, the food sector and the poorest part of the world population. We can, however, break this bottleneck. First of all, we must seek further energy savings. Secondly, we need to look for ways to de-carbonize society. There is a growing consensus among energy scientists and energy planners...... by hydrogenation and CCR, can approximately five-double our biomass potential for providing storable and high-density fuels and carbon feedstock compared to the presently applied technologies for converting biomass to fuels and feedstock. This can fully and effectively break the biomass bottleneck of the fossil...

  13. Hyperbolic partial differential equations populations, reactors, tides and waves theory and applications

    CERN Document Server

    Witten, Matthew

    1983-01-01

    Hyperbolic Partial Differential Equations, Volume 1: Population, Reactors, Tides and Waves: Theory and Applications covers three general areas of hyperbolic partial differential equation applications. These areas include problems related to the McKendrick/Von Foerster population equations, other hyperbolic form equations, and the numerical solution.This text is composed of 15 chapters and begins with surveys of age specific population interactions, populations models of diffusion, nonlinear age dependent population growth with harvesting, local and global stability for the nonlinear renewal eq

  14. Does local adaptation to resources explain genetic differentiation among Daphnia populations?

    Science.gov (United States)

    Allen, Michael R; Thum, Ryan A; Cáceres, Carla E

    2010-08-01

    Substantial genetic differentiation is frequently observed among populations of cyclically parthenogenetic zooplankton despite their high dispersal capabilities and potential for gene flow. Local adaptation has been invoked to explain population genetic differentiation despite high dispersal, but several neutral models that account for basic life history features also predict high genetic differentiation. Here, we study genetic differentiation among four populations of Daphnia pulex in east central Illinois. As with other studies of Daphnia, we demonstrate substantial population genetic differentiation despite close geographic proximity (explain genetic differentiation among these Daphnia populations and that other factors related to extinction/colonization dynamics, a long approach to equilibrium F(ST) or substantial genetic drift due to a low number of individuals hatching from the egg bank each season may explain genetic differentiation.

  15. A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae: Colias behrii).

    Science.gov (United States)

    Schoville, Sean D; Lam, Athena W; Roderick, George K

    2012-09-01

    Spatial and environmental heterogeneity are major factors in structuring species distributions in alpine landscapes. These landscapes have also been affected by glacial advances and retreats, causing alpine taxa to undergo range shifts and demographic changes. These nonequilibrium population dynamics have the potential to obscure the effects of environmental factors on the distribution of genetic variation. Here, we investigate how demographic change and environmental factors influence genetic variation in the alpine butterfly Colias behrii. Data from 14 microsatellite loci provide evidence of bottlenecks in all population samples. We test several alternative models of demography using approximate Bayesian computation (ABC), with the results favouring a model in which a recent bottleneck precedes rapid population growth. Applying independent calibrations to microsatellite loci and a nuclear gene, we estimate that this bottleneck affected both northern and southern populations 531-281 years ago, coinciding with a period of global cooling. Using regression approaches, we attempt to separate the effects of population structure, geographical distance and landscape on patterns of population genetic differentiation. Only 40% of the variation in F(ST) is explained by these models, with geographical distance and least-cost distance among meadow patches selected as the best predictors. Various measures of genetic diversity within populations are also decoupled from estimates of local abundance and habitat patch characteristics. Our results demonstrate that demographic change can have a disproportionate influence on genetic diversity in alpine species, contrasting with other studies that suggest landscape features control contemporary demographic processes in high-elevation environments. PMID:22849440

  16. BOTTLENECKS IN PRODUCTION NETWORKS: AN OVERVIEW

    Institute of Scientific and Technical Information of China (English)

    Yongcai WANG; Qianchuan ZHAO; Dazhong ZHENG

    2005-01-01

    Bottlenecks, the key ingredients for improving the performances of the production networks,have been profoundly studied during the last decade. Yet, because of the complexity of the research results, there is still a significant gap between theory and practice. In this paper, we review various bottleneck definitions, detection methods and the asymptotic results and provide a practical guidance for recognizing and utilizing the bottlenecks in production networks. Queueing theory works as the mathematical foundation in our study. Various definitions of the bottlenecks are classified as either Performance in Processing (PIP) based or sensitivity based definitions, which reflect the preferences of the managers. Detection methods are surveyed closely based on the definitions. These methods are used to recognize the bottlenecks and to provide diagnosis results to managers. Comparisons show that different detection methods may lead to vastly different conclusions. The recognition of the bottlenecks has another advantage: the ultimate phenomena of the bottlenecks can greatly reduce the computation complexity in calculating the system performances. Bottlenecks based approximation and asymptotic results are studied to exhibit the contribution of bottlenecks in performance estimation and theoretical analysis.

  17. Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

    Science.gov (United States)

    Manni, Mosè; Lima, Kátia Manuela; Guglielmino, Carmela Rosalba; Lanzavecchia, Silvia Beatriz; Juri, Marianela; Vera, Teresa; Cladera, Jorge; Scolari, Francesca; Gomulski, Ludvik; Bonizzoni, Mariangela; Gasperi, Giuliano; Silva, Janisete Gomes; Malacrida, Anna Rodolfa

    2015-01-01

    Abstract We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area. PMID:26798258

  18. Geographic after-tax real income differentials and population growth rates.

    Science.gov (United States)

    Alexander, G; Cebula, R J; Koch, J V

    1990-03-01

    "The purpose of this [one-page] note is to empirically investigate the impact of geographic after-tax real income differentials on geographic population growth rate differentials. The focus is on population growth rates in Florida's 67 counties over the period 1980-88." The authors conclude that "even after allowing for a variety of other location-influencing factors, including coastal access, after-tax real income differentials exercise a positive and significant impact on population growth rate differentials among Florida's counties."

  19. Phenotypic plasticity and population differentiation in an ongoing species invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available The ability to succeed in diverse conditions is a key factor allowing introduced species to successfully invade and spread across new areas. Two non-exclusive factors have been suggested to promote this ability: adaptive phenotypic plasticity of individuals, and the evolution of locally adapted populations in the new range. We investigated these individual and population-level factors in Polygonum cespitosum, an Asian annual that has recently become invasive in northeastern North America. We characterized individual fitness, life-history, and functional plasticity in response to two contrasting glasshouse habitat treatments (full sun/dry soil and understory shade/moist soil in 165 genotypes sampled from nine geographically separate populations representing the range of light and soil moisture conditions the species inhabits in this region. Polygonum cespitosum genotypes from these introduced-range populations expressed broadly similar plasticity patterns. In response to full sun, dry conditions, genotypes from all populations increased photosynthetic rate, water use efficiency, and allocation to root tissues, dramatically increasing reproductive fitness compared to phenotypes expressed in simulated understory shade. Although there were subtle among-population differences in mean trait values as well as in the slope of plastic responses, these population differences did not reflect local adaptation to environmental conditions measured at the population sites of origin. Instead, certain populations expressed higher fitness in both glasshouse habitat treatments. We also compared the introduced-range populations to a single population from the native Asian range, and found that the native population had delayed phenology, limited functional plasticity, and lower fitness in both experimental environments compared with the introduced-range populations. Our results indicate that the future spread of P. cespitosum in its introduced range will likely be

  20. Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis were examined by means of electrophoresis technique. Analysis of 9 enzyme systems including 16 loci showed that all the three natural populations of the pine were high in genetic diversity but low in inter -population genetic differentiation. The proportion of polymorphic loci is 0.667 , with eachlocus holding 2.13 alleles, averagely. The average expected and obse rved heterozygosity was 0.288 and 0.197, respectively. The gene differentiation among populations was 0.052, but the mean genetic distance was only 0.015.

  1. Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex.

    Directory of Open Access Journals (Sweden)

    Bengt Hansson

    Full Text Available Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene

  2. Differential response of two sourgrass populations to glyphosate

    Directory of Open Access Journals (Sweden)

    São Paulo State University, Jaboticabal, SP, Brazil

    2013-02-01

    Full Text Available The repetitive use of glyphosate may cause increase on the resistance of sourgrass (Digitaria insularis through mechanisms of natural selection. The aim of this study was to verify the response of two populations of sourgrass (one collected from nonagricultural area and the other one from area suspected of glyphosate resistance to increasing doses of glyphosate. The experimental design was completely randomized with four repetitions. For both populations, glyphosate was sprayed at 10 doses (0D, D/16, D/8, D/4, D/2, D, 2D, 4D, 8D, and 16D; so that D is the dose of 1.08 kg e.a. ha-1. The treatments were sprayed when the plants had shown 3-5 tillers. The population collected in the nonagricultural area was slightly more sensible to the herbicide glyphosate than the population originated from an area where the herbicide application is common, not indicating glyphosate resistance.

  3. Differential drought tolerance in tree populations from contrasting elevations

    OpenAIRE

    Ma, Fei; Xu, Ting Ting; Ji, Ming Fei; Zhao, Chang Ming

    2014-01-01

    To predict the ecological consequences of climate change for a widely distributed tree species, it is essential to develop a deep understanding of the ecophysiological responses of populations from contrasting climates to varied soil water availabilities. In the present study, we focused on Pinus tabuliformis, one of the most economically and ecologically important tree species in China. In a greenhouse experiment, we exposed trees from high-elevation (HP) and low-elevation (LP) populations t...

  4. Estimation of the bottleneck size in Florida panthers

    Science.gov (United States)

    Culver, M.; Hedrick, P.W.; Murphy, K.; O'Brien, S.; Hornocker, M.G.

    2008-01-01

    We have estimated the extent of genetic variation in museum (1890s) and contemporary (1980s) samples of Florida panthers Puma concolor coryi for both nuclear loci and mtDNA. The microsatellite heterozygosity in the contemporary sample was only 0.325 that in the museum samples although our sample size and number of loci are limited. Support for this estimate is provided by a sample of 84 microsatellite loci in contemporary Florida panthers and Idaho pumas Puma concolor hippolestes in which the contemporary Florida panther sample had only 0.442 the heterozygosity of Idaho pumas. The estimated diversities in mtDNA in the museum and contemporary samples were 0.600 and 0.000, respectively. Using a population genetics approach, we have estimated that to reduce either the microsatellite heterozygosity or the mtDNA diversity this much (in a period of c. 80years during the 20th century when the numbers were thought to be low) that a very small bottleneck size of c. 2 for several generations and a small effective population size in other generations is necessary. Using demographic data from Yellowstone pumas, we estimated the ratio of effective to census population size to be 0.315. Using this ratio, the census population size in the Florida panthers necessary to explain the loss of microsatellite variation was c .41 for the non-bottleneck generations and 6.2 for the two bottleneck generations. These low bottleneck population sizes and the concomitant reduced effectiveness of selection are probably responsible for the high frequency of several detrimental traits in Florida panthers, namely undescended testicles and poor sperm quality. The recent intensive monitoring both before and after the introduction of Texas pumas in 1995 will make the recovery and genetic restoration of Florida panthers a classic study of an endangered species. Our estimates of the bottleneck size responsible for the loss of genetic variation in the Florida panther completes an unknown aspect of this

  5. MMOD: an R library for the calculation of population differentiation statistics.

    Science.gov (United States)

    Winter, David J

    2012-11-01

    MMOD is a library for the R programming language that allows the calculation of the population differentiation measures D(est), G″(ST) and φ'(ST). R provides a powerful environment in which to conduct and record population genetic analyses but, at present, no R libraries provide functions for the calculation of these statistics from standard population genetic files. In addition to the calculation of differentiation measures, mmod can produce parametric bootstrap and jackknife samples of data sets for further analysis. By integrating with and complimenting the existing libraries adegenet and pegas, mmod extends the power of R as a population genetic platform. PMID:22883857

  6. Analytical approach to continuous and intermittent bottleneck flows

    DEFF Research Database (Denmark)

    Helbing, D.; Johansson, A.; Mathiesen, Joachim Kaj;

    2006-01-01

    Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20......Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20...

  7. Approximation of solutions to retarded differential equations with applications to population dynamics

    Directory of Open Access Journals (Sweden)

    D. Bahuguna

    2005-01-01

    Full Text Available We consider a retarded differential equation with applications to population dynamics. We establish the convergence of a finite-dimensional approximations of a unique solution, the existence and uniqueness of which are also proved in the process.

  8. Cloud Technology May Widen Genomic Bottleneck - TCGA

    Science.gov (United States)

    Computational biologist Dr. Ilya Shmulevich suggests that renting cloud computing power might widen the bottleneck for analyzing genomic data. Learn more about his experience with the Cloud in this TCGA in Action Case Study.

  9. Anticipation Behavior Upstream of a Bottleneck

    NARCIS (Netherlands)

    Duives, D.C.; Daamen, W.; Hoogendoorn, S.P.

    2014-01-01

    Whether pedestrian movements do or do not follow similar patterns as vehicular traffic while experiencing congestion is not entirely understood. Using data gathered during bottleneck experiments under laboratory conditions, the phenomenon of anticipation before entering congestion is studied. This p

  10. Geographical structure and differential natural selection among North European populations

    DEFF Research Database (Denmark)

    McEvoy, Brian P; Montgomery, Grant W; McRae, Allan F;

    2009-01-01

    the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and European-American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogeneous region. There is evidence...

  11. Regional differentiation among populations of the Diamondback terrapin (Malaclemys terrapin)

    Science.gov (United States)

    Hart, Kristen M.; Hunter, Margaret E.; King, Tim L.

    2014-01-01

    The Diamondback terrapin (Malaclemys terrapin) is a brackish-water turtle species whose populations have been fragmented due to anthropogenic activity such as development of coastal habitat and entrapment in commercial blue crab (Callinectes sapidus) fishing gear. Genetic analyses can improve conservation efforts for the long-term protection of the species. We used microsatellite DNA analysis to investigate levels of gene flow among and genetic variability within 21 geographically separate collections of the species distributed from Massachusetts to Texas. Quantified levels of genetic variability (allelic diversity, genotypic frequencies, and heterozygosity) revealed three zones of genetic discontinuity, resulting in four discrete populations: Northeast Atlantic, Coastal Mid-Atlantic, Florida and Texas/Louisiana. The average number of alleles and expected heterozygosity for the four genetic clusters were NA = 6.54 and HE = 0.050, respectively. However, the geographic boundaries of the populations did not correspond to accepted terrapin subspecies limits. Our results illuminate not only the need to sample terrapins in additional sites, specifically in the southeast, but also the necessity for allowing uninterrupted gene flow among population groupings to preserve current levels of genetic diversity.

  12. Genetic evidence for population expansion in Hydrotaea irritans (Fallèn) (Diptera: Muscidae)

    DEFF Research Database (Denmark)

    Loeschcke, V.; Nielsen, B. O.; Pedersen, A. Aa.;

    2004-01-01

    geographic variation, F-statistics, allozyme electrophoresis, skewed allele frequencies, bottleneck, population expansion......geographic variation, F-statistics, allozyme electrophoresis, skewed allele frequencies, bottleneck, population expansion...

  13. Urban traffic congestion propagation and bottleneck identification

    Institute of Scientific and Technical Information of China (English)

    LONG JianCheng; GAO ZiYou; REN HuaLing; LIAN AiPing

    2008-01-01

    Bottlenecks in urban traffic network are sticking points in restricting network col-lectivity traffic efficiency.To identify network bottlenecks effectively is a founda-tional work for improving network traffic condition and preventing traffic conges-tion.In this paper,a congestion propagation model of urban network traffic is proposed based on the cell transmission model (CTM).The proposed model in-cludes a link model,which describes flow propagation on links,and a node model,which represents link-to-link flow propagation.A new method of estimating average journey velocity (AJV) of both link and network is developed to identify network congestion bottlenecks.A numerical example is studied in Sioux Falls urban traffic network.The proposed model is employed in simulating network traffic propaga-tion and congestion bottleneck identification under different traffic demands.The simulation results show that continual increase of traffic demand is an immediate factor in network congestion bottleneck emergence and increase as well as re-ducing network collectivity capability.Whether a particular link will become a bot-tleneck is mainly determined by its position in network,its traffic flow (attributed to different OD pairs) component,and network traffic demand.

  14. Differentiation of Effector CD4 T Cell Populations*

    OpenAIRE

    Zhu, Jinfang; Yamane, Hidehiro; Paul, William E.

    2010-01-01

    CD4 T cells play critical roles in mediating adaptive immunity to a variety of pathogens. They are also involved in autoimmunity, asthma, and allergic responses as well as in tumor immunity. During TCR activation in a particular cytokine milieu, naive CD4 T cells may differentiate into one of several lineages of T helper (Th) cells, including Th1, Th2, Th17, and iTreg, as defined by their pattern of cytokine production and function. In this review, we summarize the discovery, functions, and r...

  15. Genetic Differentiation of Different Geographical Populations of Bemisia tabaci (Gennadius) Complex

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; LIU Guo-xia; FAN Zhong-xue; TAO Yun-li; ZHANG You-jun

    2007-01-01

    Bemisia tabaci (Gennadius) is a species complex, which includes different geographical populations with genetic differentiation. The recent progress on the genetic differentiation of various geographical populations of B. tabaci complex was introduced. The genetic differentiation was further analyzed on the basis of the sequences of mtDNA COI and rDNA ITSl recorded in the world's GenBank. Five groups are defined on the basis of mtDNA COI and rDNA ITS1, including the Asia group, America group, Africa group, Australia group, and Biotype B/Mediterranean/Middle East/ Northern Africa/Biotype Ms group. There are several ungrouped geographical classifications, such as the Uganda population, Ivory Coast population, and Taiwan population. Geographical isolation may be the most important factor that contributed to the genetic differentiation of various geographical populations of B. tabaci. Many populations with biological advantages invaded new regions and caused severe economic losses within human activity. It is necessary to strengthen the research of B. tabaci biotype to prevent the spread of invaded populations and the invasion of potentially dangerous populations.

  16. Population genetic structure of Bombus terrestris in Europe: Isolation and genetic differentiation of Irish and British populations.

    Science.gov (United States)

    Moreira, António S; Horgan, Finbarr G; Murray, Tomás E; Kakouli-Duarte, Thomais

    2015-07-01

    The genetic structure of the earth bumblebee (Bombus terrestris L.) was examined across 22 wild populations and two commercially reared populations using eight microsatellite loci and two mitochondrial genes. Our study included wild bumblebee samples from six populations in Ireland, one from the Isle of Man, four from Britain and 11 from mainland Europe. A further sample was acquired from New Zealand. Observed levels of genetic variability and heterozygosity were low in Ireland and the Isle of Man, but relatively high in continental Europe and among commercial populations. Estimates of Fst revealed significant genetic differentiation among populations. Bayesian cluster analysis indicated that Irish populations were highly differentiated from British and continental populations, the latter two showing higher levels of admixture. The data suggest that the Irish Sea and prevailing south westerly winds act as a considerable geographical barrier to gene flow between populations in Ireland and Britain; however, some immigration from the Isle of Man to Ireland was detected. The results are discussed in the context of the recent commercialization of bumblebees for the European horticultural industry. PMID:25958977

  17. More precisely biased : increasing the number of markers is not a silver bullet in genetic bottleneck testing

    NARCIS (Netherlands)

    Peery, M. Zachariah; Reid, Brendan N.; Kirby, Rebecca; Stoelting, Ricka; Doucet-Beer, Elena; Robinson, Stacie; Vasquez-Carrillo, Catalina; Pauli, Jonathan N.; Palsboll, Per J.

    2013-01-01

    In response to our review of the use of genetic bottleneck tests in the conservation literature (Peery etal. 2012, Molecular Ecology, 21, 3403-3418), Hoban etal. (2013, Molecular Ecology, in press) conducted population genetic simulations to show that the statistical power of genetic bottleneck test

  18. Differential stress resistance and metabolic traits underlie coexistence in a sympatrically evolved bacterial population

    NARCIS (Netherlands)

    Puentes Tellez, Pilar; van Elsas, Jan Dirk

    2015-01-01

    Following intermittent batch growth in Luria-Bertani (LB) broth for about 1000 generations, differentially evolved forms were found in a population of Escherichia coli cells. Studies on this population revealed the emergence of key polymorphisms, as evidenced by analysis of both whole genome sequenc

  19. Geographic After-Tax Real Income Differentials and Population Growth Rates

    OpenAIRE

    Alexander, Gigi; Cebula, Richard; Koch, James

    1989-01-01

    This empirical note investigates the impact of geographic after-tax real, as opposed to nominal, income differentials on geographic population growth rates. The focus is on Florida's 67 counties and the 1980-88 time period. The empirical results imply that the population growth rate in Florida counties was of after-tax real income.

  20. Patterns of genetic and reproductive traits differentiation in Mainland vs. Corsican populations of bumblebees.

    Directory of Open Access Journals (Sweden)

    Thomas Lecocq

    Full Text Available Populations on islands often exhibit lower levels of genetic variation and ecomorphological divergence compared to their mainland relatives. While phenotypic differentiation in characters, such as size or shape among insular organisms, has been well studied, insular differentiation in quantitative reproductive traits involved in chemical communication has received very little attention to date. Here, we investigated the impact of insularity on two syntopic bumblebee species pairs: one including species that are phylogenetically related (Bombus terrestris and B. lucorum, and the other including species that interact ecologically (B. terrestris and its specific nest inquiline B. vestalis. For each bumblebee species, we characterized the patterns of variation and differentiation of insular (Corsican vs. mainland (European populations (i with four genes (nuclear and mitochondrial, 3781 bp and (ii in the chemical composition of male marking secretions (MMS, a key trait for mate attraction in bumblebees, by gas chromatography-mass spectrometry (GC-MS. Our results provide evidence for genetic differentiation in Corsican bumblebees and show that, contrary to theoretical expectations, island populations of bumblebees exhibit levels of genetic variation similar to the mainland populations. Likewise, our comparative chemical analyses of MMS indicate that Corsican populations of bumblebees are significantly differentiated from the mainland yet they hold comparative levels of within-population MMS variability compared to the mainland. Therefore, insularity has led Corsican populations to diverge both genetically and chemically from their mainland relatives, presumably through genetic drift, but without a decrease of genetic diversity in island populations. We hypothesize that MMS divergence in Corsican bumblebees was driven by a persistent lack of gene flow with mainland populations and reinforced by the preference of Corsican females for sympatric (Corsican

  1. Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

    Science.gov (United States)

    Adkison, M.D.

    1995-01-01

    Morphological, behavioral, and life-history differences between Pacific salmon (Oncorhynchus spp.) populations are commonly thought to reflect local adaptation, and it is likewise common to assume that salmon populations separated by small distances are locally adapted. Two alternatives to local adaptation exist: random genetic differentiation owing to genetic drift and founder events, and genetic homogeneity among populations, in which differences reflect differential trait expression in differing environments. Population genetics theory and simulations suggest that both alternatives are possible. With selectively neutral alleles, genetic drift can result in random differentiation despite many strays per generation. Even weak selection can prevent genetic drift in stable populations; however, founder effects can result in random differentiation despite selective pressures. Overlapping generations reduce the potential for random differentiation. Genetic homogeneity can occur despite differences in selective regimes when straying rates are high. In sum, localized differences in selection should not always result in local adaptation. Local adaptation is favored when population sizes are large and stable, selection is consistent over large areas, selective diffeentials are large, and straying rates are neither too high nor too low. Consideration of alternatives to local adaptation would improve both biological research and salmon conservation efforts.

  2. Molecular and Quantitative Genetic Differentiation in European Populations of Silene latifolia (Caryophyllaceae)

    OpenAIRE

    Jolivet, Céline; Bernasconi, Giorgina

    2009-01-01

    Background and Aims: Among-population differentiation in phenotypic traits and allelic variation is expected as a consequence of isolation, drift, founder effects and local selection. Therefore, investigating molecular and quantitative genetic divergence is a pre-requisite for studies of local adaptation in response to selection under variable environmental conditions. Methods: Among- and within-population variation were investigated in six geographically separated European populations of t...

  3. Population genomics of early events in the ecological differentiation of bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Shapiro, Jesse B. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Broad Inst., Cambridge, MA (United States); Friedman, Jonatan [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Cordero, Otto X. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Preheim, Sarah P.. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Timberlake, Sonia C. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Szabo, Gitta [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Polz, Martin F. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Alm, Eric J. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Broad Inst., Cambridge, MA (United States)

    2012-04-06

    Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.

  4. Gender differentiation by finger ridge count among South Indian population.

    Science.gov (United States)

    Nithin, M D; Manjunatha, B; Preethi, D S; Balaraj, B M

    2011-02-01

    The goal of this study is to determine the gender based on finger ridge count within a well-defined area. Rolled fingerprints were taken from 550 subjects (275 men and 275 women) belonging to South Indian population all within the age range of 18-65 years. Results show that women have a significantly higher ridge count than men. Application of Baye's theorem suggests that a fingerprint possessing ridge density 14 ridges/25 mm(2) are most likely to be of female origin. These results are helpful as a tool for fingerprint experts as they can be used as a presumptive indicator of gender based on the degree of ridge density. PMID:21315302

  5. Tracing Road Network Bottleneck by Data Driven Approach

    Science.gov (United States)

    Qi, Hongsheng; Liu, Meiqi; Zhang, Lihui; Wang, Dianhai

    2016-01-01

    Urban road congestions change both temporally and spatially. They are essentially caused by network bottlenecks. Therefore, understanding bottleneck dynamics is critical in the goal of reasonably allocating transportation resources. In general, a typical bottleneck experiences the stages of formation, propagation and dispersion. In order to understand the three stages of a bottle neck and how the bottleneck moves on a road network, traffic flow data can be used to reconstruct these dynamics. However, raw traffic flow data is usually flawed in many ways. For instance some portion of data may be missing due to the failure of data collection devices, or some random factors in the data make it hard to identify real bottlenecks. In this paper a “user voting method” is proposed to deal with such raw-data-related issues. In this method, road links are ranked according to the weighed sum of certain performance measures and the links that are ranked relatively high are regarded as recurrent bottlenecks in a network, and several bottlenecks form a bottleneck area. A series of bottleneck parameters can be defined based on the identified bottleneck areas, such as bottleneck coverage, bottleneck link length, etc. Identifying bottleneck areas and calculating the bottleneck parameters for each time interval can reflect the evolution of the bottlenecks and also help trace how the bottlenecks move. PMID:27228150

  6. Tracing Road Network Bottleneck by Data Driven Approach.

    Science.gov (United States)

    Qi, Hongsheng; Liu, Meiqi; Zhang, Lihui; Wang, Dianhai

    2016-01-01

    Urban road congestions change both temporally and spatially. They are essentially caused by network bottlenecks. Therefore, understanding bottleneck dynamics is critical in the goal of reasonably allocating transportation resources. In general, a typical bottleneck experiences the stages of formation, propagation and dispersion. In order to understand the three stages of a bottle neck and how the bottleneck moves on a road network, traffic flow data can be used to reconstruct these dynamics. However, raw traffic flow data is usually flawed in many ways. For instance some portion of data may be missing due to the failure of data collection devices, or some random factors in the data make it hard to identify real bottlenecks. In this paper a "user voting method" is proposed to deal with such raw-data-related issues. In this method, road links are ranked according to the weighed sum of certain performance measures and the links that are ranked relatively high are regarded as recurrent bottlenecks in a network, and several bottlenecks form a bottleneck area. A series of bottleneck parameters can be defined based on the identified bottleneck areas, such as bottleneck coverage, bottleneck link length, etc. Identifying bottleneck areas and calculating the bottleneck parameters for each time interval can reflect the evolution of the bottlenecks and also help trace how the bottlenecks move. PMID:27228150

  7. Tracing Road Network Bottleneck by Data Driven Approach.

    Directory of Open Access Journals (Sweden)

    Hongsheng Qi

    Full Text Available Urban road congestions change both temporally and spatially. They are essentially caused by network bottlenecks. Therefore, understanding bottleneck dynamics is critical in the goal of reasonably allocating transportation resources. In general, a typical bottleneck experiences the stages of formation, propagation and dispersion. In order to understand the three stages of a bottle neck and how the bottleneck moves on a road network, traffic flow data can be used to reconstruct these dynamics. However, raw traffic flow data is usually flawed in many ways. For instance some portion of data may be missing due to the failure of data collection devices, or some random factors in the data make it hard to identify real bottlenecks. In this paper a "user voting method" is proposed to deal with such raw-data-related issues. In this method, road links are ranked according to the weighed sum of certain performance measures and the links that are ranked relatively high are regarded as recurrent bottlenecks in a network, and several bottlenecks form a bottleneck area. A series of bottleneck parameters can be defined based on the identified bottleneck areas, such as bottleneck coverage, bottleneck link length, etc. Identifying bottleneck areas and calculating the bottleneck parameters for each time interval can reflect the evolution of the bottlenecks and also help trace how the bottlenecks move.

  8. Population differentiation and selective constraints in Pelargonium line pattern virus.

    Science.gov (United States)

    Castaño, Aurora; Ruiz, Leticia; Elena, Santiago F; Hernández, Carmen

    2011-01-01

    The genomic structure of Pelargonium line pattern virus (PLPV), a tentative member of a proposed new genus within the family Tombusviridae, has been recently determined. However, little is known about the genetic variability and population structure of this pathogen. Here, we have investigated the heterogeneity of PLPV isolates from different origins by sequence analysis of a 1817nt fragment encompassing the movement (p7 and p9.7) and coat protein genes as well as flanking segments including the complete 3' untranslated region. We have evaluated the selective pressures operating on both viral proteins and RNA genome in order to assess the relative functional and/or structural relevance of different amino acid or nucleotide sites. The results of the study have revealed that distinct protein domains are under different selective constraints and that maintenance of certain primary and/or secondary structures in RNA regulatory sequences might be an important factor limiting viral heterogeneity. We have also performed covariation analyses to uncover potential dependencies among amino acid sites of the same protein or of different proteins. The detection of linked amino acid substitutions has permitted to draw a putative network of intra- and interprotein interactions that are likely required to accomplish the different steps of the infection cycle. Finally, we have obtained phylogenetic trees that support geographical segregation of PLPV sequences.

  9. Rapid differentiation of sexual signals in invasive toads: call variation among populations.

    Science.gov (United States)

    Yasumiba, Kiyomi; Duffy, Richard L; Parsons, Scott A; Alford, Ross A; Schwarzkopf, Lin

    2016-01-01

    Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls from four populations of different ages since invasion, and analysed the geographic differentiation of seven call parameters. Our comparisons indicate that the calls of R. marina differ among Australian populations. The signal variation was not simply clinal with respect to population age, climate, or morphological differentiation. We suggest that selection on signalling among populations has been idiosyncratic and may reflect local female preferences or adaptation to environmental factors that are not clinal such as energy availability. PMID:27328666

  10. Differential effects of chronic monocyte depletion on macrophage populations

    Energy Technology Data Exchange (ETDEWEB)

    Volkman, A.; Chang, N.C.; Strausbauch, P.H.; Morahan, P.S.

    1983-09-01

    The administration of the bone-seeking isotope, /sup 89/Sr, to mice results in severe monocytopenia without any apparent effect on the numbers of resident peritoneal macrophages (M luminal diameter). An explanation for this dichotomy was sought by determining whether the residual blood monocytes were still an effective source of M luminal diameter after /sup 89/Sr treatment. Stem cell enumeration showed that a 90% fall in bone marrow macrophage colony-forming cells after /sup 89/Sr was accompanied by a 10-fold rise in splenic M-CFC. Splenectomy performed before /sup 89/Sr treatment, however, resulted in little additional monocytopenia and had no affect on the numbers of resident peritoneal M luminal diameter even when sampling was extended to 31 days, an interval beyond the accepted half-time for peritoneal M luminal diameter. Intraperitoneal injections of thioglycollate or Corynebacterium parvum elicited few or no monocyte-M luminal diameter during respective intervals of 4 and 7 days. Elicitation with thioglycollate was attempted in tritiated thymidine-labeled mice 26 days after /sup 89/Sr. Four days later only a 2-fold increase in labeled peritoneal M luminal diameter was found in the /sup 89/Sr-treated mice compared with a 150-fold increase in the controls. Studies of the ectoenzymes 5'-nucleotidase, alkaline phosphodiesterase I, and leucine aminopeptidase in such elicitation experiments suggested that the observed changes in activities reflected the direct stimulation of resident M luminal diameter rather than monocyte immigration. Overall, the results indicate that treatment with /sup 89/Sr distinguishes two large populations of M luminal diameter on the basis of their dependence on bone marrow. M luminal diameter of inflammation reflect the monocytopenia and are severely and rapidly depleted by such treatment.

  11. The Simulation Utilization for the Bottleneck Identification

    Directory of Open Access Journals (Sweden)

    Petra Vegnerová

    2009-12-01

    Full Text Available Advancing globalization increasingly leads to the creation of delivery systems. Increasing competition forces companies to reduce costs permanently. Both of these trends lead to the need to control material and information flows precisely. The target of this article is to describe and show one of ways of bottleneck determination in the supply system. This study deals with the computer simulation and its utilization for assessment of bottleneck. The foundation of the work is created a model of the supply system, it is used to compare the costs associated with the existence of stocks and stock levels in the individual partner of the system, depending on the location of the bottleneck. This article is published as a part of the research intention MSM 6046137306.

  12. Potential performance bottleneck in Linux TCP

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenji; Crawford, Matt; /Fermilab

    2006-12-01

    TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system to its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.

  13. Epigenetic differentiation persists after male gametogenesis in natural populations of the perennial herb Helleborus foetidus (Ranunculaceae.

    Directory of Open Access Journals (Sweden)

    Carlos M Herrera

    Full Text Available Despite the importance of assessing the stability of epigenetic variation in non-model organisms living in real-world scenarios, no studies have been conducted on the transgenerational persistence of epigenetic structure in wild plant populations. This gap in knowledge is hindering progress in the interpretation of natural epigenetic variation. By applying the methylation-sensitive amplified fragment length polymorphism (MSAP technique to paired plant-pollen (i.e., sporophyte-male gametophyte DNA samples, and then comparing methylation patterns and epigenetic population differentiation in sporophytes and their descendant gametophytes, we investigated transgenerational constancy of epigenetic structure in three populations of the perennial herb Helleborus foetidus (Ranunculaceae. Single-locus and multilocus analyses revealed extensive epigenetic differentiation between sporophyte populations. Locus-by-locus comparisons of methylation status in individual sporophytes and descendant gametophytes showed that ~75% of epigenetic markers persisted unchanged through gametogenesis. In spite of some epigenetic reorganization taking place during gametogenesis, multilocus epigenetic differentiation between sporophyte populations was preserved in the subsequent gametophyte stage. In addition to illustrating the efficacy of applying the MSAP technique to paired plant-pollen DNA samples to investigate epigenetic gametic inheritance in wild plants, this paper suggests that epigenetic differentiation between adult plant populations of H. foetidus is likely to persist across generations.

  14. Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation.

    Science.gov (United States)

    Safran, R J; Scordato, E S C; Wilkins, M R; Hubbard, J K; Jenkins, B R; Albrecht, T; Flaxman, S M; Karaardıç, H; Vortman, Y; Lotem, A; Nosil, P; Pap, P; Shen, S; Chan, S-F; Parchman, T L; Kane, N C

    2016-08-01

    Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as 'isolation by adaptation' (IBA). IBA can be complementary to the well-known pattern of 'isolation by distance' (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole-genome sequence for H. rustica, to which we aligned a set of 9493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behaviour and sexual signalling, as well as geographic distance, together explain over 70% of genome-wide divergence among populations. Controlling for IBD, we find 42% of genomewide divergence is attributable to IBA through pairwise differences in traits related to migratory behaviour and sexual signalling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population-level differentiation in this group of closely related populations. PMID:27357267

  15. Properties of Bottleneck on Complex Networks

    Institute of Scientific and Technical Information of China (English)

    WANG Chao-Yang; WU Jian-Jun; GAO Zi-You

    2011-01-01

    The traffic bottleneck plays a key role in most of the natural and artificial network.Here we present a simply model for bottleneck dynamical characteristics consideration the reliability on the complex network by taking into account the network topology characteristics and system size.We find that there is a critical rate of flow generation below which the network traffic is free but above which traffic congestion occurs.Also, it is found that random networks have larger critical flow generating rate than scale free ones.Analytical results may be practically useful for designing networks, especially for the urban traffic network.

  16. Role of phenotypic plasticity and population differentiation in adaptation to novel environmental conditions.

    Science.gov (United States)

    Volis, Sergei; Ormanbekova, Danara; Yermekbayev, Kanat

    2015-09-01

    Species can adapt to new environmental conditions either through individual phenotypic plasticity, intraspecific genetic differentiation in adaptive traits, or both. Wild emmer wheat, Triticum dicoccoides, an annual grass with major distribution in Eastern Mediterranean region, is predicted to experience in the near future, as a result of global climate change, conditions more arid than in any part of the current species distribution. To understand the role of the above two means of adaptation, and the effect of population range position, we analyzed reaction norms, extent of plasticity, and phenotypic selection across two experimental environments of high and low water availability in two core and two peripheral populations of this species. We studied 12 quantitative traits, but focused primarily on the onset of reproduction and maternal investment, which are traits that are closely related to fitness and presumably involved in local adaptation in the studied species. We hypothesized that the population showing superior performance under novel environmental conditions will either be genetically differentiated in quantitative traits or exhibit higher phenotypic plasticity than the less successful populations. We found the core population K to be the most plastic in all three trait categories (phenology, reproductive traits, and fitness) and most successful among populations studied, in both experimental environments; at the same time, the core K population was clearly genetically differentiated from the two edge populations. Our results suggest that (1) two means of successful adaptation to new environmental conditions, phenotypic plasticity and adaptive genetic differentiation, are not mutually exclusive ways of achieving high adaptive ability; and (2) colonists from some core populations can be more successful in establishing beyond the current species range than colonists from the range extreme periphery with conditions seemingly closest to those in the new

  17. Patterns of post-glacial genetic differentiation in marginal populations of a marine microalga.

    Directory of Open Access Journals (Sweden)

    Pia Tahvanainen

    Full Text Available This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS sequences and Amplified Fragment Length Polymorphism (AFLP of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F(ST between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms.

  18. Genetic diversity and differentiation of mud crab Scylla serrata populations from southeastern China

    Institute of Scientific and Technical Information of China (English)

    LI Zhongbao; LI Shaojing; WANG Guizhong

    2004-01-01

    The genetic diversity and differentiation of 6 mud crab Scylla serrata populations from southeastern China are investigated using allozyme electrophoresis. The mean number of alleles per locus population is 1.3 ± 0.1; the percentage of polymorphic loci per population is 27.3; the observed heterozygosity ranges from ( 0.195 ± 0.083)to ( 0.241 ± 0.090) and the expected heterozygosity ranges from ( 0.105 ± 0.043 ) to ( 0.131 ± 0.047 ). The coefficient of gene differentiation among populations is low (Fst =0.032), indicating that only 3.2 % of the total genetic diversity comes from inter-population, while the remaining 96.8 % comes from intra-population differences.The genetic distance among populations is 0.000~0.008 (the average is 0.002). Gene flow among the populations is large (Nm= 7.56).Genetic structure is very similar among 6 Scylla serrata populations.

  19. Analysis of the genetic diversity and differentiation of Fenneropenaeus penicillatus populations using AFLP technology

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guiling; CAO Yuanyu; LI Zhongbao; CHEN Jin; ZHAO Binli; LEI Guanggao; WANG Zhanlin

    2012-01-01

    Fenneropenaeus penicillatus (redtail shrimp) is an important marine commercial animal in China.Recently,its resources have been depleted rapidly as a result of,for example,over-exploitation and environmental degradation of spawning grounds.Therefore,we analyzed the genetic diversity and differentiation of nine wild populations of F.penicillatus of China (Ningde,Lianjiang,Putian,Xiamen,Quanzhou,Zhangpu,Dongshan,Nanao,and Shenzhen populations) by amplified fragment length polymorphism (AFLP) technology,to provide genetic information necessary for resource protection,rejuvenation,artificial breeding,and sustainable use of the resource.Eight AFLP primer pairs were used for amplification,and 508 bands were detected among the populations.The results show that the percentage of polymorphic loci (P) ranged from 41.34% to 63.58%; the Nei's gene diversity (H) of the populations was 0.119 4-0.230 5; and Sharnon's Information Index (I) was 0.184 1-0.342 5.These genetic data indicate that the genetic diversity of F.penicillatus was high.The genetic differentiation coefficient (Gsr=0.216 2) and gene flow (Nm=1.812 4) show that there was a high level of genetic differentiation and a moderate level of gene flow among populations.More studies on the genetic differentiation mechanism of F.penicillatus along the south-eastern coast of China need to be conducted to find more effective scientific protection strategies for the conservation ofF.penicillatus genetic resources.

  20. Microgeographic and Temporal Genetic Differentiation in Natural Populations of DROSOPHILA SUBOBSCURA

    OpenAIRE

    Cabrera, V M; González, A M; M Hernández; Larruga, J. M.; Martell, M

    1985-01-01

    Evidence of microgeographic and temporal genetic differentiation in natural populations of Drosophila subobscura is presented. The alcohol dehydrogenease locus was used as a genetic marker. Behavioral differences among the sexes and genotypes may explain these observations, although the molecular basis remains obscure.

  1. Strategic behavior and social outcomes in a bottleneck queue: experimental evidence

    DEFF Research Database (Denmark)

    Breinbjerg, Jesper Breinbjerg; Sebald, Alexander Christopher; Østerdal, Lars Peter

    2016-01-01

    We theoretically and experimentally study the differential incentive effects of three well known queue disciplines in a strategic environment in which a bottleneck facility opens and impatient players decide when to arrive. For a class of three-player games, we derive equilibrium arrivals under...

  2. Molecular differentiation of commercial varieties and feral populations of oilseed rape (Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Glössl Josef

    2010-03-01

    Full Text Available Abstract Background For assessing the risk of escape of transgenes from cultivation, the persistence of feral populations of crop plants is an important aspect. Feral populations of oilseed rape, Brassica napus, are well known, but only scarce information is available on their population dynamics, particularly in Central Europe. To investigate genetic diversity, origin and persistence of feral oilseed rape in Austria, we compared variation at nine polymorphic microsatellite loci in eight feral populations with 19 commercial varieties. Results Overall, commercial varieties and feral populations showed a similar pattern of genetic variation and a similar level of observed heterozygosity. The two groups, however, shared less than 50% of the alleles and no multilocus genotype. A significant among-group (commercial varieties versus feral populations component of genetic variation was observed (AMOVA: FCT = 0.132. Pairwise comparisons between varieties and feral populations showed moderate to very high genetic differentiation (FST = 0.209 - 0.900. The software STRUCTURE also demonstrated a clear separation between commercial varieties and feral samples: out of 17 identified genetic clusters, only one comprised plants from both a commercial variety and feral sites. Conclusions The results suggest that feral oilseed rape is able to maintain persistent populations. The feral populations may have derived from older cultivars that were not included in our analyses or perhaps have already hybridised with related crops or wild relatives. Feral populations therefore have to be considered in ecological risk assessment and future coexistence measures as a potential hybridisation partner of transgenic oilseed rape.

  3. Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

    Energy Technology Data Exchange (ETDEWEB)

    Adkison, M.D. [Washington Univ., Seattle, WA (United States). Coll. of Fisheries

    1995-12-01

    The effects of local adaptation among Pacific salmon populations were discussed. Morphological and behavioural differences between Pacific salmon are believed to be a result of local adaptation. Two alternatives were recognized: (1) random genetic differentiation owing to genetic drift and founder events, and (2) genetic homogeneity among populations. In general, local adaptation is favoured when population sizes are large and stable, when selection is consistent over large areas, when selective differentials are large, and straying rates are neither too high nor too low. Since there are definite limits to local adaptation, particularly on fine spatial scales, consideration of alternatives to local adaptation could improve both basic science and conservation efforts. 127 refs., 2 tabs., 3 figs.

  4. Genetic differentiation among Maconellicoccus hirsutus (Hemiptera: Pseudococcidae) populations living on different host plants.

    Science.gov (United States)

    Rosas-García, Ninfa M; Sarmiento-Benavides, Sandra L; Villegas-Mendoza, Jesús M; Hernández-Delgado, Sanjuana; Mayek-Pérez, Netzahualcoyotl

    2010-06-01

    The pink hibiscus mealybug Maconellicoccus hirsutus (Green) is a dangerous pest that damages a wide variety of agricultural, horticultural, and forestry crops. Amplified fragment length polymorphism (AFLP) fingerprints were used to characterize the genetic variation of 11 M. hirsutus populations infesting three plant species in Nayarit, Mexico. Analysis was carried out using four primers combinations, producing 590 polymorphic bands. Cluster analysis, as well as bootstrap dendrogram and nonmetric multidimensional scaling analysis, grouped M. hirsutus populations according to their host plant. The estimated F(ST) values indicated a high differentiation in M. hirsutus populations among the three host plant species. These results were also supported by a Bayesian analysis, which indicated a population clustering robustness according to their host plant. Genetic variation among populations is not caused by geographic distances, as shown by a Mantel test.

  5. Ecological differentiation of Lemna minor L. and Spirodela polyrrhiza (L. Schleiden populations

    Directory of Open Access Journals (Sweden)

    Hanna Wożakowska-Natkaniec

    2015-05-01

    Full Text Available The subject of thep resent study are 19 natural, ecological populations of Lemna minor and Spirodela polyrrhiza coming from sixteen habitats in Lower Silesia. The study showed the essential differences between ecological populations of both species, conditioned on chemistry (pH, level N, P, K, Ca, Mg and Fe and the natural water radioactivity. It was shown experimentally that these populations, in nature, establish a set of ecotypes or ecophene variability. Ecotypic differentiation of populations of Lemna minor and Spirodela polyrrhiza is based upon individual features and population characteristics such as: shape and size of plants, plant frequency of two, three, and four fronds, the ratio of right- to left-handed plants, and the dynamics of growth and biomass production.

  6. Nucleotide diversity and population differentiation of the Melanocortin 1 Receptor gene, MC1R

    Directory of Open Access Journals (Sweden)

    Peris Ketty

    2008-04-01

    Full Text Available Abstract Background The melanocortin 1 receptor gene (MC1R is responsible for normal pigment variation in humans and is highly polymorphic with numerous population-specific alleles. Some MC1R variants have been associated with skin cancer risk. Results Allele frequency data were compiled on 55 single nucleotide polymorphisms from seven geographically distinct human populations (n = 2306 individuals. MC1R nucleotide diversity, π, was much higher (10.1 × 10-4 than in other genes for all subjects. A large degree of population differentiation, determined by FST, was also present, particularly between Asia and all other populations, due to the p.R163Q (c.488 G>A polymorphism. The least amount of differentiation was between the United States, Northern Europe, and Southern Europe. Tajima's D statistic suggested the presence of positive selection in individuals from Europe. Conclusion This study further quantifies the degree of population-specific genetic variation and suggests that positive selection may be present in European populations in MC1R.

  7. Local environment but not genetic differentiation influences biparental care in ten plover populations.

    Directory of Open Access Journals (Sweden)

    Orsolya Vincze

    Full Text Available Social behaviours are highly variable between species, populations and individuals. However, it is contentious whether behavioural variations are primarily moulded by the environment, caused by genetic differences, or a combination of both. Here we establish that biparental care, a complex social behaviour that involves rearing of young by both parents, differs between closely related populations, and then test two potential sources of variation in parental behaviour between populations: ambient environment and genetic differentiation. We use 2904 hours behavioural data from 10 geographically distinct Kentish (Charadrius alexandrinus and snowy plover (C. nivosus populations in America, Europe, the Middle East and North Africa to test these two sources of behavioural variation. We show that local ambient temperature has a significant influence on parental care: with extreme heat (above 40 °C total incubation (i.e. % of time the male or female incubated the nest increased, and female share (% female share of incubation decreased. By contrast, neither genetic differences between populations, nor geographic distances predicted total incubation or female's share of incubation. These results suggest that the local environment has a stronger influence on a social behaviour than genetic differentiation, at least between populations of closely related species.

  8. Performance Bottlenecks in Digital Movie Systems

    OpenAIRE

    Keller, Ralf; Effelsberg, Wolfgang; Lamparter, Bernd

    1993-01-01

    Digital movie systems offer great perspectives for multimedia applications. But the large amounts of data involved and the demand for isochronous transmission and playback are also great challenges for the designers of a new generation of file systems, database systems, operating systems, window systems, video encoder/decoder and networks. Today's research prototypes of digital movie systems suffer from severe performance bottlenecks, resulting in small movie windows, low frame rates or bad i...

  9. DYNAMIC BOTTLENECKS IN HANDLING AND STORAGE SYSTEMS

    OpenAIRE

    PANOVA YULIA; HILMOLA OLLI-PEKKA

    2015-01-01

    The development of industrial engineering and production systems is manifested under the demand of Russian customers in the current economic and political situation, e.g. deprivation from several import markets. In these circumstances, issues related to the formation of process systems are gaining their importance. The article considers the objective of reaching the smooth and continuous material flow in the handling and storage system of the plant, as well as the problems of bottlenecks opti...

  10. Individual Microscopic Results Of Bottleneck Experiments

    CERN Document Server

    Bukáček, Marek; Krbálek, Milan

    2016-01-01

    This contribution provides microscopic experimental study of pedestrian motion in front of the bottleneck, explains the high variance of individual travel time by the statistical analysis of trajectories. The analysis shows that this heterogeneity increases with increasing occupancy. Some participants were able to reach lower travel time due more efficient path selection and more aggressive behavior within the crowd. Based on this observations, linear model predicting travel time with respect to the aggressiveness of pedestrian is proposed.

  11. Quantitative single cell analysis of cell population dynamics during submandibular salivary gland development and differentiation

    Directory of Open Access Journals (Sweden)

    Deirdre A. Nelson

    2013-04-01

    Epithelial organ morphogenesis involves reciprocal interactions between epithelial and mesenchymal cell types to balance progenitor cell retention and expansion with cell differentiation for evolution of tissue architecture. Underlying submandibular salivary gland branching morphogenesis is the regulated proliferation and differentiation of perhaps several progenitor cell populations, which have not been characterized throughout development, and yet are critical for understanding organ development, regeneration, and disease. Here we applied a serial multiplexed fluorescent immunohistochemistry technology to map the progressive refinement of the epithelial and mesenchymal cell populations throughout development from embryonic day 14 through postnatal day 20. Using computational single cell analysis methods, we simultaneously mapped the evolving temporal and spatial location of epithelial cells expressing subsets of differentiation and progenitor markers throughout salivary gland development. We mapped epithelial cell differentiation markers, including aquaporin 5, PSP, SABPA, and mucin 10 (acinar cells; cytokeratin 7 (ductal cells; and smooth muscle α-actin (myoepithelial cells and epithelial progenitor cell markers, cytokeratin 5 and c-kit. We used pairwise correlation and visual mapping of the cells in multiplexed images to quantify the number of single- and double-positive cells expressing these differentiation and progenitor markers at each developmental stage. We identified smooth muscle α-actin as a putative early myoepithelial progenitor marker that is expressed in cytokeratin 5-negative cells. Additionally, our results reveal dynamic expansion and redistributions of c-kit- and K5-positive progenitor cell populations throughout development and in postnatal glands. The data suggest that there are temporally and spatially discreet progenitor populations that contribute to salivary gland development and homeostasis.

  12. Population based model of human embryonic stem cell (hESC differentiation during endoderm induction.

    Directory of Open Access Journals (Sweden)

    Keith Task

    Full Text Available The mechanisms by which human embryonic stem cells (hESC differentiate to endodermal lineage have not been extensively studied. Mathematical models can aid in the identification of mechanistic information. In this work we use a population-based modeling approach to understand the mechanism of endoderm induction in hESC, performed experimentally with exposure to Activin A and Activin A supplemented with growth factors (basic fibroblast growth factor (FGF2 and bone morphogenetic protein 4 (BMP4. The differentiating cell population is analyzed daily for cellular growth, cell death, and expression of the endoderm proteins Sox17 and CXCR4. The stochastic model starts with a population of undifferentiated cells, wherefrom it evolves in time by assigning each cell a propensity to proliferate, die and differentiate using certain user defined rules. Twelve alternate mechanisms which might describe the observed dynamics were simulated, and an ensemble parameter estimation was performed on each mechanism. A comparison of the quality of agreement of experimental data with simulations for several competing mechanisms led to the identification of one which adequately describes the observed dynamics under both induction conditions. The results indicate that hESC commitment to endoderm occurs through an intermediate mesendoderm germ layer which further differentiates into mesoderm and endoderm, and that during induction proliferation of the endoderm germ layer is promoted. Furthermore, our model suggests that CXCR4 is expressed in mesendoderm and endoderm, but is not expressed in mesoderm. Comparison between the two induction conditions indicates that supplementing FGF2 and BMP4 to Activin A enhances the kinetics of differentiation than Activin A alone. This mechanistic information can aid in the derivation of functional, mature cells from their progenitors. While applied to initial endoderm commitment of hESC, the model is general enough to be applicable

  13. Differential expression of the chemosensory transcriptome in two populations of the stemborer Sesamia nonagrioides.

    Science.gov (United States)

    Glaser, Nicolas; Gallot, Aurore; Legeai, Fabrice; Harry, Myriam; Kaiser, Laure; Le Ru, Bruno; Calatayud, Paul-André; Jacquin-Joly, Emmanuelle

    2015-10-01

    Among the proposed mechanisms of local adaptation to different ecological environments, transcriptional changes may play an important role. In this study, we investigated whether such variability occurred within the chemosensory organs of a herbivorous insect, for which chemosensation guides most of its host preferences. A European and an African population of the noctuid Sesamia nonagrioides that display significant differences in their ecological preferences were collected on Zea mays and Typha domingensis, respectively. RNAseq were used between the two populations for digital expression profiling of chemosensory organs from larval antennae and palps. Preliminary data on adult female antennae and ovipositors were also collected. We found 6,550 differentially expressed transcripts in larval antennae and palps. Gene ontology enrichment analyses suggested that transcriptional activity was overrepresented in the French population and that virus and defense activities were overrepresented in the Kenyan population. In addition, we found differential expression of a variety of cytochrome P450s, which may be linked to the different host-plant diets. Looking at olfactory genes, we observed differential expression of numerous candidate odorant-binding proteins, chemosensory proteins, and one olfactory receptor, suggesting that differences in olfactory sensitivity participate in insect adaptation. PMID:26316282

  14. Genetic diversity and differentiation of three populations of Penaeus monodon Fabricus

    Institute of Scientific and Technical Information of China (English)

    WANG Guizhong; TAN Shuhua; LI shaojing; YE Haihui

    2008-01-01

    Genetic diversity of two wild Penaeus monodon populations sampled from the coastal waters of Qinglan ( Hainan Province of China, HN) and Malaysia (KD),and the F1 generation of a Thailand broodstock population (CP) were examined by vertical polyacryl- amide gel electrophoresis.Of 21 loci encoded by ten enzymes,11 were polymorphic.The mean proportions of polymorphic loci of HN,KD and CP were 36.36%,45.45% and 50.00%,with the average heterezygosities of 0.135,0.181 and 0.191,and the effective numbers of alleles per loci were 1.300,1.330 and 1.329,respectively.The divergent indexes of HN,KD and CP were 0.023,0.124,and 0.117,respectively.The genetic distance between the two wild populations was 0.005,and the gene differ- entiation coefficient was also very low (0.014).The results indicated that the F1 generation population had a higher genetic di- versity than the two wild populations,and that the HN population had the lowest one.There was no significant differentiation be- tween HN and KD populations and all populations existed with a slight heterozygote excess.

  15. Periodic solutions of first-order functional differential equations in population dynamics

    CERN Document Server

    Padhi, Seshadev; Srinivasu, P D N

    2014-01-01

    This book provides cutting-edge results on the existence of multiple positive periodic solutions of first-order functional differential equations. It demonstrates how the Leggett-Williams fixed-point theorem can be applied to study the existence of two or three positive periodic solutions of functional differential equations with real-world applications, particularly with regard to the Lasota-Wazewska model, the Hematopoiesis model, the Nicholsons Blowflies model, and some models with Allee effects. Many interesting sufficient conditions are given for the dynamics that include nonlinear characteristics exhibited by population models. The last chapter provides results related to the global appeal of solutions to the models considered in the earlier chapters. The techniques used in this book can be easily understood by anyone with a basic knowledge of analysis. This book offers a valuable reference guide for students and researchers in the field of differential equations with applications to biology, ecology, a...

  16. Differential Exploitation of Atlantic Salmon Populations by a Rod Fishery on the River Spey, Scotland

    OpenAIRE

    Thorley, Joseph L.; Youngson, Alan F.; Laughton, Robert

    2004-01-01

    Due to heritable population differences in run-timing, Atlantic salmon (Salmo salar) enter Scottish rivers throughout the year. Maintenance of this diversity is vital for the continued commercial and recreational value of the associated rod fisheries, which extend on most rivers from February to September. However, as the data we present demonstrate, management of the rod fishery on the River Spey, Scotland, is complicated by differential exploitation of the Atlantic salmon from the various r...

  17. Differentiation of population income and poverty problem (based on the data of Tyumen region

    Directory of Open Access Journals (Sweden)

    Aleksandr Anatolyevich Kuklin

    2011-03-01

    Full Text Available The results of differentiation analysis of money income in the Tyumen region are presented in this paper. Analysis of differentiation was performed using Foster-Greer-Torbeke class indicators by areas included in Tyumen region: autonomous areas (Khanty-Mansiysk and Yamal-Nenets and the southern part of the region. It is shown that, along with increasing interterritorial income differentiation, income differentiation within these regions is also growing. Based on the results of an assessment carried out during the last ten years in the social policy, the package of measures aimed at improving the situation of the poor population is proposed. Thus, it is shown that the advancement of the poor population may be the result of a comprehensive social policy aimed at reducing income inequality by eliminating the strain distribution in the relationship. The emphasis of the regional authorities should be given to programs that go beyond the narrow definition of social protection: programs to improve labour market efficiency, quality of workforce and education etc.

  18. Clonal, self-renewing and differentiating human and porcine urothelial cells, a novel stem cell population.

    Directory of Open Access Journals (Sweden)

    Hans M Larsson

    Full Text Available Although urothelial progenitor-like cells have been described in the human urinary tract, the existence of stem cells remains to be proven. Using a culture system that favors clonogenic epithelial cell growth, we evaluated and characterized clonal human urothelial cells. We isolated human urothelial cells that were clonogenic, capable of self-renewal and could develop into fully differentiated urothelium once re-implanted into the subcapsular space of nude mice. In addition to final urothelial cell differentiation, spontaneous formation of bladder-like microstructures was observed. By examining an epithelial stem cell signature marker, we found p63 to correlate with the self-renewal capacity of the isolated human urothelial clonal populations. Since a clinically relevant, long-term model for functional reconstitution of human cells does not exist, we sought to establish a culture method for porcine urothelial cells in a clinically relevant porcine model. We isolated cells from porcine ureter, urethra and bladder that were clonogenic and capable of self-renewal and differentiation into fully mature urothelium. In conclusion, we could isolate human and porcine cell populations, behaving as urothelial stem cells and showing clonogenicity, self-renewal and, once re-implanted, morphological differentiation.

  19. A theory of traffic congestion at moving bottlenecks

    Science.gov (United States)

    Kerner, Boris S.; Klenov, Sergey L.

    2010-10-01

    The physics of traffic congestion occurring at a moving bottleneck on a multi-lane road is revealed based on the numerical analyses of vehicular traffic with a discrete stochastic traffic flow model in the framework of three-phase traffic theory. We find that there is a critical speed of a moving bottleneck at which traffic breakdown, i.e. a first-order phase transition from free flow to synchronized flow, occurs spontaneously at the moving bottleneck, if the flow rate upstream of the bottleneck is great enough. The greater the flow rate, the higher the critical speed of the moving bottleneck. A diagram of congested traffic patterns at the moving bottleneck is found, which shows regions in the flow-rate-moving-bottleneck-speed plane in which congested patterns emerge spontaneously or can be induced through large enough disturbances in an initial free flow. A comparison of features of traffic breakdown and resulting congested patterns at the moving bottleneck with known ones at an on-ramp (and other motionless) bottleneck is made. Nonlinear features of complex interactions and transformations of congested traffic patterns occurring at on- and off-ramp bottlenecks due to the existence of the moving bottleneck are found. The physics of the phenomenon of traffic congestion due to 'elephant racing' on a multi-lane road is revealed.

  20. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Institute of Scientific and Technical Information of China (English)

    Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU

    2011-01-01

    Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species.Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China.Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation.Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population.The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve.Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations.All individuals from the same subpopulation were assigned to one cluster.This indicates high gene flow between subpopulations.F statistic analyses revealed a low Fls-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR.Additionally,our data show a high level of genetic diversity for the Tangjiahe population.Mean allele number (A),Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangiiahe population was 5.9,5.173 and 0.703,respectively.This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6):717-724,2011].

  1. Genetic Diversity and Population Differentiation of Guignardia mangiferae from “Tahiti” Acid Lime

    Directory of Open Access Journals (Sweden)

    Ester Wickert

    2012-01-01

    Full Text Available Among the citrus plants, “Tahiti” acid lime is known as a host of G. mangiferae fungi. This species is considered endophytic for citrus plants and is easily isolated from asymptomatic fruits and leaves. G. mangiferae is genetically related and sometimes confused with G. citricarpa which causes Citrus Black Spot (CBS. “Tahiti” acid lime is one of the few species that means to be resistant to this disease because it does not present symptoms. Despite the fact that it is commonly found in citric plants, little is known about the populations of G. mangiferae associated with these plants. Hence, the objective of this work was to gain insights about the genetic diversity of the G. mangiferae populations that colonize “Tahiti” acid limes by sequencing cistron ITS1-5.8S-ITS2. It was verified that “Tahiti” acid lime plants are hosts of G. mangiferae and also of G. citricarpa, without presenting symptoms of CBS. Populations of G. mangiferae present low-to-moderate genetic diversity and show little-to-moderate levels of population differentiation. As gene flow was detected among the studied populations and they share haplotypes, it is possible that all populations, from citrus plants and also from the other known hosts of this fungus, belong to one great panmictic population.

  2. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    KAUST Repository

    Karmin, Monika

    2015-04-30

    It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

  3. Genomic diversity and differentiation of a managed island wild boar population

    DEFF Research Database (Denmark)

    Iacolina, Laura; Scandura, Massimo; J. Goedbloed, Daniel;

    2016-01-01

    The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed...... since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number...... of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (FST=0.126–0.138), and from DP (FST=0...

  4. Genetic Diversity and Population Differentiation of the Causal Agent of Citrus Black Spot in Brazil

    Directory of Open Access Journals (Sweden)

    Ester Wickert

    2012-01-01

    Full Text Available One of the most important diseases that affect sweet orange orchards in Brazil is the Citrus Black Spot that is caused by the fungus Guignardia citricarpa. This disease causes irreparable losses due to the premature falling of fruit, as well as its severe effects on the epidermis of ripe fruit that renders them unacceptable at the fresh fruit markets. Despite the fact that the fungus and the disease are well studied, little is known about the genetic diversity and the structure of the fungi populations in Brazilian orchards. The objective of this work was study the genetic diversity and population differentiation of G. citricarpa associated with four sweet orange varieties in two geographic locations using DNA sequence of ITS1-5.8S-ITS2 region from fungi isolates. We observed that different populations are closely related and present little genetic structure according to varieties and geographic places with the highest genetic diversity distributed among isolates of the same populations. The same haplotypes were sampled in different populations from the same and different orange varieties and from similar and different origins. If new and pathogenic fungi would become resistant to fungicides, the observed genetic structure could rapidly spread this new form from one population to others.

  5. Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula.

    Directory of Open Access Journals (Sweden)

    Eva Graciá

    Full Text Available The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70's. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus. In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species' demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species' pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals

  6. Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula.

    Science.gov (United States)

    Graciá, Eva; Ortego, Joaquín; Godoy, José Antonio; Pérez-García, Juan Manuel; Blanco, Guillermo; Delgado, María del Mar; Penteriani, Vincenzo; Almodóvar, Irene; Botella, Francisco; Sánchez-Zapata, José Antonio

    2015-01-01

    The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70's. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus). In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species' demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species' pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals on the species

  7. Low genetic differentiation across three major ocean populations of the whale shark, Rhincodon typus.

    Directory of Open Access Journals (Sweden)

    Jennifer V Schmidt

    Full Text Available BACKGROUND: Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated populations. Genetic analysis of population structure is one essential component of the baseline data required for whale shark conservation. METHODOLOGY/PRINCIPAL FINDINGS: We have identified 8 polymorphic microsatellites in the whale shark and used these markers to assess genetic variation and population structure in a panel of whale sharks covering a broad geographic region. This is the first record of microsatellite loci in the whale shark, which displayed an average of 9 alleles per locus and mean H(o = 0.66 and H(e = 0.69. All but one of the eight loci meet the expectations of Hardy-Weinberg equilibrium. Analysis of these loci in whale sharks representing three major portions of their range, the Pacific (P, Caribbean (C, and Indian (I Oceans, determined that there is little population differentiation between animals sampled in different geographic regions, indicating historical gene flow between populations. F(ST values for inter-ocean comparisons were low (PxC = 0.0387, CxI = 0.0296 and PxI = -0.0022, and only CxI approached statistical significance (p = 0.0495. CONCLUSIONS/SIGNIFICANCE: We have shown only low levels of genetic differentiation between geographically distinct whale shark populations. Existing satellite tracking data have revealed both regional and long-range migration of whale sharks throughout their range, which supports the finding of gene flow between populations. Whale sharks traverse geographic and political boundaries during their

  8. Herbivory at marginal populations: Consequences for maternal fitness and vegetative differentiation

    Science.gov (United States)

    Castilla, Antonio R.; Alonso, Conchita; Herrera, Carlos M.

    2013-05-01

    Margins of distribution of plant species constitute natural areas where the impact of the antagonistic interactions is expected to be higher and where changes in the dynamics of plant-herbivore coevolution could promote intraspecific differentiation in (co)evolving plant traits. In the present study, we investigated how differences in the average herbivory level affect maternal fitness in core continuous and marginal disjunct populations of Daphne laureola in an effort to assess the role of herbivores limiting plant distribution. Furthermore, we investigated intraspecific differentiation in vegetative traits and their potential connection to divergent selection by herbivores in both groups of populations. Our results did not support increased herbivory at the species margin but did support a difference in the effect of herbivory on maternal fitness between core continuous and marginal disjunct populations of D. laureola. In addition, herbivores did not exert phenotypic selection consistent with the geographic variation in studied plant traits. Therefore, the geographic variation of vegetative traits of D. laureola seems to be consequence of environmental heterogeneity more than result of geographically divergent selection by herbivores.

  9. Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by salmonella.

    Directory of Open Access Journals (Sweden)

    Chee Han Lim

    2014-07-01

    Full Text Available Vaccination represents an important instrument to control typhoid fever in humans and protects mice from lethal infection with mouse pathogenic serovars of Salmonella species. Mixed infections with tagged Salmonella can be used in combination with probabilistic models to describe the dynamics of the infection process. Here we used mixed oral infections with tagged Salmonella strains to identify bottlenecks in the infection process in naïve and vaccinated mice. We established a next generation sequencing based method to characterize the composition of tagged Salmonella strains which offers a fast and reliable method to characterise the composition of genome-tagged Salmonella strains. We show that initial colonization of Salmonella was distinguished by a non-Darwinian selection of few bacteria setting up the infection independently in gut associated lymphoid tissue and systemic compartments. Colonization of Peyer's patches fuels the sustained spread of bacteria into mesenteric lymph nodes via dendritic cells. In contrast, infection of liver and spleen originated from an independent pool of bacteria. Vaccination only moderately reduced invasion of Peyer's patches but potently uncoupled bacterial populations present in different systemic compartments. Our data indicate that vaccination differentially skews the capacity of Salmonella to colonize systemic and gut immune compartments and provide a framework for the further dissection of infection dynamics.

  10. Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by salmonella.

    Science.gov (United States)

    Lim, Chee Han; Voedisch, Sabrina; Wahl, Benjamin; Rouf, Syed Fazle; Geffers, Robert; Rhen, Mikael; Pabst, Oliver

    2014-07-01

    Vaccination represents an important instrument to control typhoid fever in humans and protects mice from lethal infection with mouse pathogenic serovars of Salmonella species. Mixed infections with tagged Salmonella can be used in combination with probabilistic models to describe the dynamics of the infection process. Here we used mixed oral infections with tagged Salmonella strains to identify bottlenecks in the infection process in naïve and vaccinated mice. We established a next generation sequencing based method to characterize the composition of tagged Salmonella strains which offers a fast and reliable method to characterise the composition of genome-tagged Salmonella strains. We show that initial colonization of Salmonella was distinguished by a non-Darwinian selection of few bacteria setting up the infection independently in gut associated lymphoid tissue and systemic compartments. Colonization of Peyer's patches fuels the sustained spread of bacteria into mesenteric lymph nodes via dendritic cells. In contrast, infection of liver and spleen originated from an independent pool of bacteria. Vaccination only moderately reduced invasion of Peyer's patches but potently uncoupled bacterial populations present in different systemic compartments. Our data indicate that vaccination differentially skews the capacity of Salmonella to colonize systemic and gut immune compartments and provide a framework for the further dissection of infection dynamics.

  11. A differential equation with state-dependent delay from cell population biology

    Science.gov (United States)

    Getto, Philipp; Waurick, Marcus

    2016-04-01

    We analyze a differential equation, describing the maturation of a stem cell population, with a state-dependent delay, which is implicitly defined via the solution of an ODE. We elaborate smoothness conditions for the model ingredients, in particular vital rates, that guarantee the existence of a local semiflow and allow to specify the linear variational equation. The proofs are based on theoretical results of Hartung et al. combined with implicit function arguments in infinite dimensions. Moreover we elaborate a criterion for global existence for differential equations with state-dependent delay. To prove the result we adapt a theorem by Hale and Lunel to the C1-topology and use a result on metric spaces from Diekmann et al.

  12. Genetic diversity and population differentiation in the cockle Cerastoderma edule estimated by microsatellite markers

    Science.gov (United States)

    Martínez, L.; Méndez, J.; Insua, A.; Arias-Pérez, A.; Freire, R.

    2013-03-01

    The edible cockle Cerastoderma edule is a marine bivalve commercially fished in several European countries that have lately suffered a significant decrease in production. Despite its commercial importance, genetic studies in this species are scarce. In this work, genetic diversity and population differentiation of C. edule has been assessed using 11 microsatellite markers in eight locations from the European Atlantic coast. All localities showed similar observed and expected heterozygosity values, but displayed differences in allelic richness, with lowest values obtained for localities situated farther north. Global Fst value revealed the existence of significant genetic structure; all but one locality from the Iberian Peninsula were genetically homogeneous, while more remote localities from France, The Netherlands, and Scotland were significantly different from all other localities. A combined effect of isolation by distance and the existence of barriers that limit gene flow may explain the differentiation observed.

  13. Genetic Differentiation between Sympatric Populations of Bacillus cereus and Bacillus thuringiensis

    Science.gov (United States)

    Vilas-Boas, Gislayne; Sanchis, Vincent; Lereclus, Didier; Lemos, Manoel Victor F.; Bourguet, Denis

    2002-01-01

    Little is known about genetic exchanges in natural populations of bacteria of the spore-forming Bacillus cereus group, because no population genetics studies have been performed with local sympatric populations. We isolated strains of Bacillus thuringiensis and B. cereus from small samples of soil collected at the same time from two separate geographical sites, one within the forest and the other at the edge of the forest. A total of 100 B. cereus and 98 B. thuringiensis strains were isolated and characterized by electrophoresis to determine allelic composition at nine enzymatic loci. We observed genetic differentiation between populations of B. cereus and B. thuringiensis. Populations of a given Bacillus species—B. thuringiensis or B. cereus—were genetically more similar to each other than to populations of the other Bacillus species. Hemolytic activity provided further evidence of this genetic divergence, which remained evident even if putative clones were removed from the data set. Our results suggest that the rate of gene flow was higher between strains of the same species, but that exchanges between B. cereus and B. thuringiensis were nonetheless possible. Linkage disequilibrium analysis revealed sufficient recombination for B. cereus populations to be considered panmictic units. In B. thuringiensis, the balance between clonal proliferation and recombination seemed to depend on location. Overall, our data indicate that it is not important for risk assessment purposes to determine whether B. cereus and B. thuringiensis belong to a single or two species. Assessment of the biosafety of pest control based on B. thuringiensis requires evaluation of the extent of genetic exchange between strains in realistic natural conditions. PMID:11872495

  14. Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes.

    Science.gov (United States)

    Congdon, B C; Piatt, J F; Martin, K; Friesen, V L

    2000-06-01

    Mechanisms of population differentiation in highly vagile species such as seabirds are poorly understood. Previous studies of marbled murrelets (Brachyramphus marmoratus; Charadriiformes: Alcidae) found significant population genetic structure, but could not determine whether this structure is due to historical vicariance (e.g., due to Pleistocene glaciers), isolation by distance, drift or selection in peripheral populations, or nesting habitat selection. To discriminate among these possibilities, we analyzed sequence variation in nine nuclear introns from 120 marbled murrelets sampled from British Columbia to the western Aleutian Islands. Mismatch distributions indicated that murrelets underwent at least one population expansion during the Pleistocene and probably are not in genetic equilibrium. Maximum-likelihood analysis of allele frequencies suggested that murrelets from "mainland" sites (from the Alaskan Peninsula east) are genetically different from those in the Aleutians and that these two lineages diverged prior to the last glaciation. Analyses of molecular variance, as well as estimates of gene flow derived using coalescent theory, indicate that population genetic structure is best explained by peripheral isolation of murrelets in the Aleutian Islands, rather than by selection associated with different nesting habitats. No isolation-by-distance effects could be detected. Our results are consistent with a rapid expansion of murrelets from a single refugium during the early-mid Pleistocene, subsequent isolation and divergence in two or more refugia during the final Pleistocene glacial advance, and secondary contact following retreat of the ice sheets. Population genetic structure now appears to be maintained by distance effects combined with small populations and a highly fragmented habitat in the Aleutian Islands. PMID:10937270

  15. Differential effects of weather and natural enemies on coexisting aphid populations.

    Science.gov (United States)

    Alyokhin, Andrei; Drummond, Francis A; Sewell, Gary; Storch, Richard H

    2011-06-01

    Study of mechanisms responsible for regulating populations of living organisms is essential for a better comprehension of the structure of biological communities and evolutionary forces in nature. Aphids (Hemiptera: Sternorrhyncha) comprise a large and economically important group of phytophagous insects distributed worldwide. Previous studies determined that density-dependent mechanisms play an important role in regulating their populations. However, only a few of those studies identified specific factors responsible for the observed regulation. Time series data used in this study originated from the untreated control plots that were a part of potato (Solanum tuberosum L.) insecticide trials in northern Maine from 1971 to 2004. The data set contained information on population densities of three potato-colonizing aphid species (buckthorn aphid, Aphis nasturtii; potato aphid, Macrosiphum euphorbiae; and green peach aphid, Myzus persicae) and their natural enemies. We used path analysis to explore effects of weather and natural enemies on the intrinsic growth rates of aphid populations. Weather factors considered in our analyses contributed to the regulation of aphid populations, either directly or through natural enemies. However, direct weather effects were in most cases detectable only at P ≤ 0.10. Potato aphids were negatively affected by both fungal disease and predators, although buckthorn aphids were negatively affected by predators only. Parasitoids did not have a noticeable effect on the growth of any of the three aphid species. Growth of green peach aphid populations was negatively influenced by interspecific interactions with the other two aphid species. Differential population regulation mechanisms detected in the current study might at least partially explain coexistence of three ecologically similar aphid species sharing the same host plant.

  16. Microsatellite data suggest significant population structure and differentiation within the malaria vector Anopheles darlingi in Central and South America

    Directory of Open Access Journals (Sweden)

    Achee Nicole L

    2008-03-01

    Full Text Available Abstract Background Anopheles darlingi is the most important malaria vector in the Neotropics. An understanding of A. darlingi's population structure and contemporary gene flow patterns is necessary if vector populations are to be successfully controlled. We assessed population genetic structure and levels of differentiation based on 1,376 samples from 31 localities throughout the Peruvian and Brazilian Amazon and Central America using 5–8 microsatellite loci. Results We found high levels of polymorphism for all of the Amazonian populations (mean RS = 7.62, mean HO = 0.742, and low levels for the Belize and Guatemalan populations (mean RS = 4.3, mean HO = 0.457. The Bayesian clustering analysis revealed five population clusters: northeastern Amazonian Brazil, southeastern and central Amazonian Brazil, western and central Amazonian Brazil, Peruvian Amazon, and the Central American populations. Within Central America there was low non-significant differentiation, except for between the populations separated by the Maya Mountains. Within Amazonia there was a moderate level of significant differentiation attributed to isolation by distance. Within Peru there was no significant population structure and low differentiation, and some evidence of a population expansion. The pairwise estimates of genetic differentiation between Central America and Amazonian populations were all very high and highly significant (FST = 0.1859 – 0.3901, P DA and FST distance-based trees illustrated the main division to be between Central America and Amazonia. Conclusion We detected a large amount of population structure in Amazonia, with three population clusters within Brazil and one including the Peru populations. The considerable differences in Ne among the populations may have contributed to the observed genetic differentiation. All of the data suggest that the primary division within A. darlingi corresponds to two white gene genotypes between Amazonia (genotype 1

  17. Coherent population trapping magnetometer by differential detecting magneto-optic rotation effect

    Science.gov (United States)

    Zhang, Fan; Tian, Yuan; Zhang, Yi; Gu, Si-Hong

    2016-09-01

    A pocket coherent population trapping (CPT) atomic magnetometer scheme that uses a vertical cavity surface emitting laser as a light source is proposed and experimentally investigated. Using the differential detecting magneto-optic rotation effect, a CPT spectrum with the background canceled and a high signal-to-noise ratio is obtained. The experimental results reveal that the sensitivity of the proposed scheme can be improved by half an order, and the ability to detect weak magnetic fields is extended one-fold. Therefore, the proposed scheme is suited to realize a pocket-size CPT magnetometer. Project supported by the National Natural Science Foundation of China (Grant Nos. 11304362 and 61434005).

  18. Sex-differentiated migration patterns, protandry and phenology in North European songbird populations

    DEFF Research Database (Denmark)

    Tøttrup, Anders Peter; Thorup, Kasper

    2008-01-01

    changes may influence subsequent mating decisions, with subsequent feedbacks on population dynamics such as reproductive success and individual fitness. However, during decades of consistent earlier spring arrival in all phases of migration we found no evidence of inter-sexual phenological differences.......This study aims to investigate causes and mechanisms controlling protandrous migration patterns (the earlier breeding area arrival of males relative to females) and inter-sexual differences in timing of migration in relation to the recent climate-driven changes in phenology. Using standardised...... ringing data from a single site for eight North European migratory passerines collected throughout 22 years, we analysed sex-differentiated migration patterns, protandry and phenology of the entire populations. Our results show protandrous patterns for the first as well as later arriving individuals...

  19. Pronounced population genetic differentiation in the rock bream Oplegnathus fasciatus inferred from mitochondrial DNA sequences.

    Science.gov (United States)

    Xiao, Yongshuang; Li, Jun; Ren, Guijing; Ma, Daoyuan; Wang, Yanfeng; Xiao, ZhiZhong; Xu, Shihong

    2016-05-01

    The population genetic structure of the rock bream (Oplegnathus fasciatus) along the coastal waters of China was estimated based on three mtDNA fragments (D-loop, COI, and Cytb). A total of 112 polymorphic sites were checked, which defined 63 haplotypes. A pattern with high levels of haplotype diversity (hCOI = 0.886 ± 0.034, hCytb = 0.874 ± 0.023) and low levels of nucleotide diversity (лCOI = 0.009 ± 0.005, лCytb = 0.006 ± 0.003) was detected based on the COI and Cytb fragments, and high levels of genetic diversity (hD-loop = 0.995 ± 0.007, лD-loop = 0.021 ± 0.011) were detected from the mtDNA D-loop. The population genetic diversity of O. fasciatus in south China was significantly higher than those of north China. Three genealogical clades were checked in the O. fasciatus populations based on the NJ and MST analyses of mtDNA COI gene sequence, and the genetic distances among the clades ranged from 0.018 to 0.025. Significant population genetic differentiation was also checked based on the Fst (0.331, p = 0.000) and exact p (0.000) test analyses. No significant population differentiations were checked based on mtDNA D-loop and Cytb fragments. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidences, we inferred that the genetic make-up of extant populations of O. fasciatus was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (neutrality tests, mismatch distribution analysis, and Bayesian skyline analyses) showed that the species along coastline of China has experienced population expansions originated in its most recent history at about 169-175 kya before present. PMID:25427804

  20. Modified bottleneck-based heuristic for large-scale job-shop scheduling problems with a single bottleneck

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A modified bottleneck-based (MB) heuristic for large-scale job-shop scheduling problems with a welldefined bottleneck is suggested,which is simpler but more tailored than the shifting bottleneck (SB) procedure.In this algorithm,the bottleneck is first scheduled optimally while the non-bottleneck machines are subordinated around the solutions of the bottleneck schedule by some effective dispatching rules.Computational results indicate that the MB heuristic can achieve a better tradeoff between solution quality and computational time compared to SB procedure for medium-size problems.Furthermore,it can obtain a good solution in a short time for large-scale job-shop scheduling problems.

  1. Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci

    OpenAIRE

    Garine-Wichatitsky de, M.; De Meeûs, Thierry; Chevillon, Christine; BERTHIER, D.; Barre, N.; Thevenon, S.; Maillard, J.C.

    2009-01-01

    Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms....

  2. Genetic variability in four Alouatta species measured by means of nine DNA microsatellite markers: genetic structure and recent bottlenecks.

    Science.gov (United States)

    Ruiz-Garcia, M; Escobar-Armel, P; Alvarez, D; Mudry, M; Ascunce, M; Gutierrez-Espeleta, G; Shostell, J M

    2007-01-01

    We used microsatellite DNA to study the population genetics of 4 Alouatta species from Central and South America. Our main findings include the following: (1) A. seniculus had the highest level of microsatellite variability while A. caraya and A. palliata had the lowest mean number of alleles per locus and the lowest expected heterozygosity, respectively; (2) the samples of A. seniculus and A. palliata came from different regions and were not in Hardy-Weinberg equilibrium (HWE) which may indicate a Wahlund effect and differentiated gene pools -- in contrast, A. macconnelli and A. caraya were in HWE; (3) the microsatellite genetic heterogeneity of the 4 Alouatta species was similar to the karyotype divergence found among these Alouatta species; the species pair with the lowest level of heterogeneity (genetic differentiation) was A. seniculus/A. caraya, while the Central American species, A. palliata, was highly differentiated from the other 3 South American species; (4) we recommend the establishment of a conservation plan to help protect A. caraya because the Cornuet and Luikart procedure demonstrated a recent bottleneck for this species. PMID:17303937

  3. Genetic differentiation of the Cabo Verde archipelago population analysed by STR polymorphisms.

    Science.gov (United States)

    Fernandes, A T; Velosa, R; Jesus, J; Carracedo, A; Brehm, A

    2003-07-01

    Allele frequencies for 17 STR loci were analyzed in a sample of unrelated males from the Cabo Verde Archipelago. The samples were gathered in such a way that the origin of the subjects was perfectly identified, and they could be included in one of the leeward or windward groups of islands. This study reveals that there are significant differences between both groups of islands, and between Cabo Verdeans and other populations from sub-Sahara Africa including the Guineans, the most probable source population for Cabo Verdeans. This study confirms mtDNA data and, together with HLA and Y chromosome data already published, shows that the Cabo Verde population is sub-structured and atypical, diverging substantially from mainland sub-Saharan populations. Overall these differences are most probably due to admixture between sub-Saharan slaves brought into the islands and other settlers of European origin. In the absence of a clear indication of a different ethnic composition of the first sub-Saharan settlers of Cabo Verde, the differentiation exhibited in both groups of islands can be most probably be attributed to genetic drift. PMID:12914568

  4. Life history trait differentiation and local adaptation in invasive populations of Ambrosia artemisiifolia in China.

    Science.gov (United States)

    Li, Xiao-Meng; She, Deng-Ying; Zhang, Da-Yong; Liao, Wan-Jin

    2015-03-01

    Local adaptation has been suggested to play an important role in range expansion, particularly among invasive species. However, the extent to which local adaptation affects the success of an invasive species and the factors that contribute to local adaptation are still unclear. This study aimed to investigate a case of population divergence that may have contributed to the local adaptation of invasive populations of Ambrosia artemisiifolia in China. Common garden experiments in seven populations indicated clinal variations along latitudinal gradients, with plants from higher latitudes exhibiting earlier flowering and smaller sizes at flowering. In reciprocal transplant experiments, plants of a northern Beijing origin produced more seeds at their home site than plants of a southern Wuhan origin, and the Wuhan-origin plants had grown taller at flowering than the Beijing-origin plants in Wuhan, which is believed to facilitate pollen dispersal. These results suggest that plants of Beijing origin may be locally adapted through female fitness and plants from Wuhan possibly locally adapted through male fitness. Selection and path analysis suggested that the phenological and growth traits of both populations have been influenced by natural selection and that flowering time has played an important role through its direct and indirect effects on the relative fitness of each individual. This study evidences the life history trait differentiation and local adaptation during range expansion of invasive A. artemisiifolia in China. PMID:25362583

  5. Evidence of ecotypic differentiation between populations of the tree species Parapiptadenia rigida due to flooding.

    Science.gov (United States)

    Silva, D C G; Carvalho, M C C G; Ruas, P M; Ruas, C F; Medri, M E

    2010-01-01

    The tree species Parapiptadenia rigida, native to southern South America, is frequently used in reforestation of riverbanks in Brazil. This tree is also a source of gums, tannins and essential oils, and it has some medicinal uses. We investigated flooding tolerance and genetic diversity in two populations of P. rigida; one of them was naturally exposed to flooding. Plants derived from seeds collected from each population were submitted to variable periods of experimental waterlogging and submergence. Waterlogging promoted a decrease in biomass and structural adjustments, such as superficial roots with aerenchyma and hypertrophied lenticels, that contribute to increase atmospheric oxygen intake. Plants that were submerged had an even greater reduction in biomass and a high mortality rate (40%). The two populations varied significantly in their RAPD marker profiles, in their ability to produce aerenchyma when waterlogged and to survive when submerged, suggesting ecotypic differentiation between them. Hence, the seasonal flooding that has been challenging the tropical riparian forest appears to be genetically modifying the P. rigida populations exposed to it by selecting individuals with increased ability to live under this condition. PMID:20449813

  6. Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system.

    Directory of Open Access Journals (Sweden)

    Ganeshprasad Arunkumar

    Full Text Available Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined with a shared genetic heritage dating back to the late Pleistocene (10-30 Kya, suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4-6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.

  7. Differentiation of four Indian aboriginal cattle populations revealed by STR markers.

    Science.gov (United States)

    Sharma, R; Maitra, A; Pandey, A K; Mishra, B P

    2012-06-01

    Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjharpuri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD-IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 +/- 0.04 in Binjharpuri to 0.664 +/- 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 +/- 0.02 and 0.720 +/- 0.01, respectively. In the overall population, the homozygote excess (F(IT)) of 0.132 +/- 0.03, was partly due to the genetic differentiation among breeds (F(ST) = 0.044 +/- 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F(IS) = 0.094 +/- 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei's Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership. PMID:22946330

  8. The strength and timing of the mitochondrial bottleneck in salmon suggests a conserved mechanism in vertebrates.

    Directory of Open Access Journals (Sweden)

    Jonci N Wolff

    Full Text Available In most species mitochondrial DNA (mtDNA is inherited maternally in an apparently clonal fashion, although how this is achieved remains uncertain. Population genetic studies show not only that individuals can harbor more than one type of mtDNA (heteroplasmy but that heteroplasmy is common and widespread across a diversity of taxa. Females harboring a mixture of mtDNAs may transmit varying proportions of each mtDNA type (haplotype to their offspring. However, mtDNA variants are also observed to segregate rapidly between generations despite the high mtDNA copy number in the oocyte, which suggests a genetic bottleneck acts during mtDNA transmission. Understanding the size and timing of this bottleneck is important for interpreting population genetic relationships and for predicting the inheritance of mtDNA based disease, but despite its importance the underlying mechanisms remain unclear. Empirical studies, restricted to mice, have shown that the mtDNA bottleneck could act either at embryogenesis, oogenesis or both. To investigate whether the size and timing of the mitochondrial bottleneck is conserved between distant vertebrates, we measured the genetic variance in mtDNA heteroplasmy at three developmental stages (female, ova and fry in chinook salmon and applied a new mathematical model to estimate the number of segregating units (N(e of the mitochondrial bottleneck between each stage. Using these data we estimate values for mtDNA Ne of 88.3 for oogenesis, and 80.3 for embryogenesis. Our results confirm the presence of a mitochondrial bottleneck in fish, and show that segregation of mtDNA variation is effectively complete by the end of oogenesis. Considering the extensive differences in reproductive physiology between fish and mammals, our results suggest the mechanism underlying the mtDNA bottleneck is conserved in these distant vertebrates both in terms of it magnitude and timing. This finding may lead to improvements in our understanding of

  9. Genetic differentiation of Arthrobacter population from heavy metal-contaminated environment

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hanbo; REN Weimin; SHAO Qiyong; DUAN Changqun

    2007-01-01

    Six samples containing extremely high concentration of Pb,Zn,and Cd were obtained from the layers of 5-10 cm and 25-30 cm three tailing piles,with ages of about 10,20 and more than 80 years,respectively.Then,48 bacterial strains were obtained from these samples,and subsequently their phylogenetic positions were determined by analysis on the partial sequence of 16S rRNA gene (fragment length ranging from 474 to 708 bp).These isolates were members of the Arthrobacter genus,phylogenetically close to A.keyseri and A.ureafaciens,with sequence ranging from 99.1%to 100%.Furthermore,genetic variation between subpopulations from different samples was revealed by analysis on their randomly amplified polymorphic DNA profile.Nei genetic distance showed that the greatest differentiation occurred between subpopulation A and C.Notably,either genetic distance between subpopulations from the layers of 5-10 cm and 25-30 cm of each tailing pile or between same layers of different tailing pile increased with the history of tailings.Moreover,correlation analysis showed that soluble Pb has a significantly negative relationship with Nei'gene diversity of subpopulation.It was assumed that soluble Pb may be responsible for the reduced genetic diversity of the Arthrobacter population.Our data provided evidence that genetic differentiation of microbial populations was consistent with the changes of environmental factors,particularly heavy metals.

  10. Genetic structure and differentiation of Psathyrostachys huashanica populations detected with RAPD markers

    Institute of Scientific and Technical Information of China (English)

    WANG Li; YANG Juan; GUO Jing; ZHAO Guifang

    2007-01-01

    Psathyrostachys huashanica Keng is a perennial grass and belongs to genus Psathyrostachys under Triticeae.sathyrostachys is found in the center of Middle Asia and the Caucasus Mountain,while P.huashanica,a species endemic to China,is only located in Mt.Hua in the Shaanxi province,China.At present,the population of this species is decreasing,and reaching the edge of extinction.Due to the limitation in distribution and the importance as breeding material for germplasm storage,it has been considered as first class among the national protected rare plants.For this reason,the present study is significant in probing plant flora,origin and evolution of Triticeae,and crop breeding.Randomly amplified polymorphic DNA (RAPD)markers were used to analyze the genetic structure and differentiation of P.huashanica populations sampled in three valleys (Huangpu,Xian,and Huashan Valleys)in Mr.Hua.One hundred and twenty-two RAPDfragments were obtained in all 266 individuals with 20 primers with a mean of 6.1 (2-10)fragments per primer.The percentage of polymorphic loci (PPB)was 60.66%in Huangpu Valley,90.98%in Xian Valley,95.08%in Huashan Valley,and the total PPB was 95.08%,which indicated a highly genetic variability of P.huashanica.The Shannon's Information index and GST were 0.3306 and 0.3263,respectively,indicating that there were more genetic variations within the subpopulations than those among the subpopulations.The gene flow among the subpopulations of P.huashanica (Nm=1.0322)was much less than that of the common anemophytes (Nm=5.24).Mean genetic distance is 0.1571(range:0.0022-0.2901).The highest value of genetic distance was found between the subpopulation (hp1)of Huangpu Valley and the highest altitude subpopulation (h8)of Huashan Valley.Correlation analysis detected significant correlation between genetic distance and vertical distance of altitude.Clustering analysis and principal coordinate analysis revealed the genetic differentiation among the populations of P.huashanica.Differentiation

  11. The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird.

    Science.gov (United States)

    Bertrand, J A M; Delahaie, B; Bourgeois, Y X C; Duval, T; García-Jiménez, R; Cornuault, J; Pujol, B; Thébaud, C; Milá, B

    2016-04-01

    Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variations among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using 11 microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST ) and phenotypic differentiation (PST ) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact midway up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients. PMID:26779843

  12. Differential Impact of Tobacco Control Policies on Youth Sub-Populations

    Directory of Open Access Journals (Sweden)

    John A. Tauras

    2013-09-01

    Full Text Available Background: While previous studies have demonstrated the efficacy of tobacco control interventions in reducing tobacco use among youth overall, there have been very few studies that examine the potential differential impact of tobacco control policies on various youth subgroups, defined by socio-economic status (SES, race/ethnicity, and gender. Objective: We examined the relationship between state-level cigarette prices and smoke-free air laws and youth smoking prevalence and intensity for various youth sub-populations in the United States. Methods: We estimated a 2-part model of cigarette demand using data from the 1991 through 2010 nationally representative surveys of 8th-, 10th-, and 12th-grade students as part of the Monitoring the Future project. Findings: We found that real cigarette prices are strong determinants of youth smoking. Blacks, females, Hispanics, and low-SES subpopulations are found to have a larger price response with respect to smoking prevalence than the full sample. Smoke-free air laws are found to have a negative effect on smoking prevalence for the full sample and for the male, white, and high-SES sub-populations. Conclusions: This research concludes that higher cigarette prices will reduce smoking prevalence rates of Blacks, Hispanics, females, and low-SES subpopulations faster than the overall youth population and other youth sub-populations. Moreover, this research concludes that smoke-free air laws will reduce smoking prevalence for the overall youth population with the largest reductions in high SES and male subpopulations.

  13. Bulinus globosus (Planorbidae; Gastropoda) populations in the Lake Victoria basin and coastal Kenya show extreme nuclear genetic differentiation

    DEFF Research Database (Denmark)

    Nyakaana, Silvester; Stothard, J. Russell; Nalugwa, Allen;

    2013-01-01

    and quantified using FST statistics and Bayesian clustering algorithms. The four loci used in this study contained sufficient statistical power to detect low levels of population genetic differentiation and were highly polymorphic with the number of alleles per locus across populations ranging from 16 to 22...

  14. The Limited Utility of Multiunit Data in Differentiating Neuronal Population Activity.

    Directory of Open Access Journals (Sweden)

    Corey J Keller

    Full Text Available To date, single neuron recordings remain the gold standard for monitoring the activity of neuronal populations. Since obtaining single neuron recordings is not always possible, high frequency or 'multiunit activity' (MUA is often used as a surrogate. Although MUA recordings allow one to monitor the activity of a large number of neurons, they do not allow identification of specific neuronal subtypes, the knowledge of which is often critical for understanding electrophysiological processes. Here, we explored whether prior knowledge of the single unit waveform of specific neuron types is sufficient to permit the use of MUA to monitor and distinguish differential activity of individual neuron types. We used an experimental and modeling approach to determine if components of the MUA can monitor medium spiny neurons (MSNs and fast-spiking interneurons (FSIs in the mouse dorsal striatum. We demonstrate that when well-isolated spikes are recorded, the MUA at frequencies greater than 100Hz is correlated with single unit spiking, highly dependent on the waveform of each neuron type, and accurately reflects the timing and spectral signature of each neuron. However, in the absence of well-isolated spikes (the norm in most MUA recordings, the MUA did not typically contain sufficient information to permit accurate prediction of the respective population activity of MSNs and FSIs. Thus, even under ideal conditions for the MUA to reliably predict the moment-to-moment activity of specific local neuronal ensembles, knowledge of the spike waveform of the underlying neuronal populations is necessary, but not sufficient.

  15. Bimodal mesoporous silica with bottleneck pores.

    Science.gov (United States)

    Reber, M J; Brühwiler, D

    2015-11-01

    Bimodal mesoporous silica consisting of two sets of well-defined mesopores is synthesized by a partial pseudomorphic transformation of an ordered mesoporous starting material (SBA-15 type). The introduction of a second set of smaller mesopores (MCM-41 type) establishes a pore system with bottlenecks that restricts the access to the core of the bimodal mesoporous silica particles. The particle size and shape of the starting material are retained, but micropores present in the starting material disappear during the transformation, leading to a true bimodal mesoporous product. A varying degree of transformation allows the adjustment of the pore volume contribution of the two mesopore domains. Information on the accessibility of the mesopores is obtained by the adsorption of fluorescence-labeled poly(amidoamine) dendrimers and imaging by confocal laser scanning microscopy. This information is correlated with nitrogen sorption data to provide insights regarding the spatial distribution of the two mesopore domains. The bimodal mesoporous materials are excellent model systems for the investigation of cavitation effects in nitrogen desorption isotherms. PMID:26399172

  16. Coherent population trapping magnetometer by differential detecting magneto–optic rotation effect

    Science.gov (United States)

    Zhang, Fan; Tian, Yuan; Zhang, Yi; Gu, Si-Hong

    2016-09-01

    A pocket coherent population trapping (CPT) atomic magnetometer scheme that uses a vertical cavity surface emitting laser as a light source is proposed and experimentally investigated. Using the differential detecting magneto–optic rotation effect, a CPT spectrum with the background canceled and a high signal-to-noise ratio is obtained. The experimental results reveal that the sensitivity of the proposed scheme can be improved by half an order, and the ability to detect weak magnetic fields is extended one-fold. Therefore, the proposed scheme is suited to realize a pocket-size CPT magnetometer. Project supported by the National Natural Science Foundation of China (Grant Nos. 11304362 and 61434005).

  17. Lack of population genetic differentiation of a marine ovoviviparous fish Sebastes schlegelii in Northwestern Pacific.

    Science.gov (United States)

    Zhang, Hui; Yanagimoto, Takashi; Zhang, Xiumei; Song, Na; Gao, Tianxiang

    2016-05-01

    Sebastes schlegelii is one of the fishes that aggregate around drifting seaweed during early development. To examine the population genetic structure of S. schlegelii, a 452-bp fragment of the mtDNA control region was sequenced and used to interpret life history characteristics and larval dispersal strategy. Two-hundred and twenty-one individuals from 13 sites across the entire range of S. schlegelii in China, Japan and Korea were analyzed. A neighbor-joining tree and network showed that there were no significant genealogical structures corresponding to sampling locations. AMOVA, pair-wise FST and exact test revealed no significant genetic differentiation among locations. The migration rate among locations was high based on the result of LAMARC. We conclude that larval dispersal with drifting seaweed and the current environmental factors may play an important role in shaping the contemporary phylogeographic pattern and genetic homogeneity of S. schlegelii.

  18. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon

    DEFF Research Database (Denmark)

    Tartally, András; Kelager, Andreas; Fürst, Matthias A.;

    2016-01-01

    The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are...... usually spatially distinct, but at R€scruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, fiardu. Our results showed that while the two forms are...... different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow....

  19. Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes.

    Directory of Open Access Journals (Sweden)

    Marc Ciosi

    2014-02-01

    Full Text Available BACKGROUND: The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations. METHODOLOGY/PRINCIPAL FINDINGS: We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC. There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population. CONCLUSIONS/SIGNIFICANCE: All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology.

  20. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    Science.gov (United States)

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism.

  1. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    Science.gov (United States)

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism. PMID:27306555

  2. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection.

    Directory of Open Access Journals (Sweden)

    Rowena A Bull

    2011-09-01

    Full Text Available Hepatitis C is a pandemic human RNA virus, which commonly causes chronic infection and liver disease. The characterization of viral populations that successfully initiate infection, and also those that drive progression to chronicity is instrumental for understanding pathogenesis and vaccine design. A comprehensive and longitudinal analysis of the viral population was conducted in four subjects followed from very early acute infection to resolution of disease outcome. By means of next generation sequencing (NGS and standard cloning/Sanger sequencing, genetic diversity and viral variants were quantified over the course of the infection at frequencies as low as 0.1%. Phylogenetic analysis of reassembled viral variants revealed acute infection was dominated by two sequential bottleneck events, irrespective of subsequent chronicity or clearance. The first bottleneck was associated with transmission, with one to two viral variants successfully establishing infection. The second occurred approximately 100 days post-infection, and was characterized by a decline in viral diversity. In the two subjects who developed chronic infection, this second bottleneck was followed by the emergence of a new viral population, which evolved from the founder variants via a selective sweep with fixation in a small number of mutated sites. The diversity at sites with non-synonymous mutation was higher in predicted cytotoxic T cell epitopes, suggesting immune-driven evolution. These results provide the first detailed analysis of early within-host evolution of HCV, indicating strong selective forces limit viral evolution in the acute phase of infection.

  3. Karyotype differentiation and reproductive isolation among natural populations of Drosophila lacertosa

    Institute of Scientific and Technical Information of China (English)

    LI PING HE; HIDE AKI WATABE; YA PING ZHANG; TADASHI AOTSUKA

    2003-01-01

    Drosophila lacertosa is widely distributed from northern India to Far East of Russia throughout China.We have studied geographical distributions of three kinds of chromosomal karyotypes,type D(2n=10,4 pairs of V-shaped metacentric chromosomes and a pair of micro-chromosomes),type L(2n= 10,5V with a pair of large-sized heterochromatic autosomes)and type M(2n=10,5V with middle-sized ones).Type D was found exclusively in local populations of D.lacertosa distributed in Yun-Gui Plateau,southwestern China.Both type L and M have a wide range of distribution,and the former occurred in subtropical regions of China including Taiwan Island,whereas the latter in cool temperate regions of East Asia covering Far East of Russia,Korea and the Japan Islands.A strong premating isolation was detected between flies with type D and those with type L or M.These data demonstrate that genetic differentiation leading to cryptic speciation might have occurred in natural populations of Drosophila lacertosa.

  4. Allozyme variation in Pinus cembra and P. sibirica: differentiation between populations and species

    Directory of Open Access Journals (Sweden)

    D.V. Politov

    2013-12-01

    Full Text Available Two closely related Eurasian species of 5-needle pines, Swiss stone pine(Pinus cembra L. and Siberian stone pine (P. sibirica Du Tour occupy two disjunctive parts of the formerly common range in Europe andSiberia, respectively. These forms show so close morphological and genetic similarity that in some classifications they are treated as subspecies. Using a set of 29 allozyme loci (Adh-1,-2, Fdh, Fest-2, Gdh, Got-1,-2,-3, Idh, Lap- 2,-3, Mdh-1,-2,-3,-4, Mnr-1, Pepca, 6-Pgd-1,-2,-3, Pgi-1,-2, Pgm-1,-2, Skdh-1,-2, Sod-2,-3,- 4 we analyzed genetic differentiation within the Alpine-Carpathian part of the range (P.cembra and found relatively low genetic diversity for conifers (HE=0,08 and moderate level of differentiation (FST=7,4%. For thesame loci set within Siberian populations (P. sibirica genic diversity was higher (0,14, while differentiation was lower (3%. The factthat differentiation within the highly fragmented range of Swiss stone pine is just 2.5 times higher than in widespread closely related P.sibirica makes us consider factors other than unlimited gene flow responsible for uniformity of allelic frequencies. Among these factors the leading role belongs to balancing selection.Heterozygote superiority leads to both (i increasing of heterozygosity in course of stand development and (ii through balancing selectionto stable equilibrium state. Under this equilibrium, virtually the same genetic structure is maintained, even when remote and isolatedparts of the species' ranges are compared. For many studied loci, Swiss and Siberian stone pines have the same allelic profiles despite the fact that gene flow among them ceased a long time ago. According to one point of view fragmentation of the formerly united range might take place in the Atlantic time of the Holocene (about 5000 years BC, however, an alternative hypothesis refers to a much earlierPleistocene glacial time. Analysis of a combined data set (P. cembra

  5. IGF1 stimulates crypt expansion via differential activation of 2 intestinal stem cell populations.

    Science.gov (United States)

    Van Landeghem, Laurianne; Santoro, M Agostina; Mah, Amanda T; Krebs, Adrienne E; Dehmer, Jeffrey J; McNaughton, Kirk K; Helmrath, Michael A; Magness, Scott T; Lund, P Kay

    2015-07-01

    Insulin-like growth factor 1 (IGF1) has potent trophic effects on normal or injured intestinal epithelium, but specific effects on intestinal stem cells (ISCs) are undefined. We used Sox9-enhanced green fluorescent protein (EGFP) reporter mice that permit analyses of both actively cycling ISCs (Sox9-EGFP(Low)) and reserve/facultative ISCs (Sox9-EGFP(High)) to study IGF1 action on ISCs in normal intestine or during crypt regeneration after high-dose radiation-induced injury. We hypothesized that IGF1 differentially regulates proliferation and gene expression in actively cycling and reserve/facultative ISCs. IGF1 was delivered for 5 days using subcutaneously implanted mini-pumps in uninjured mice or after 14 Gy abdominal radiation. ISC numbers, proliferation, and transcriptome were assessed. IGF1 increased epithelial growth in nonirradiated mice and enhanced crypt regeneration after radiation. In uninjured and regenerating intestines, IGF1 increased total numbers of Sox9-EGFP(Low) ISCs and percentage of these cells in M-phase. IGF1 increased percentages of Sox9-EGFP(High) ISCs in S-phase but did not expand this population. Microarray revealed that IGF1 activated distinct gene expression signatures in the 2 Sox9-EGFP ISC populations. In vitro IGF1 enhanced enteroid formation by Sox9-EGFP(High) facultative ISCs but not Sox9-EGFP(Low) actively cycling ISCs. Our data provide new evidence that IGF1 activates 2 ISC populations via distinct regulatory pathways to promote growth of normal intestinal epithelium and crypt regeneration after irradiation.

  6. Deep bottleneck features for spoken language identification.

    Directory of Open Access Journals (Sweden)

    Bing Jiang

    Full Text Available A key problem in spoken language identification (LID is to design effective representations which are specific to language information. For example, in recent years, representations based on both phonotactic and acoustic features have proven their effectiveness for LID. Although advances in machine learning have led to significant improvements, LID performance is still lacking, especially for short duration speech utterances. With the hypothesis that language information is weak and represented only latently in speech, and is largely dependent on the statistical properties of the speech content, existing representations may be insufficient. Furthermore they may be susceptible to the variations caused by different speakers, specific content of the speech segments, and background noise. To address this, we propose using Deep Bottleneck Features (DBF for spoken LID, motivated by the success of Deep Neural Networks (DNN in speech recognition. We show that DBFs can form a low-dimensional compact representation of the original inputs with a powerful descriptive and discriminative capability. To evaluate the effectiveness of this, we design two acoustic models, termed DBF-TV and parallel DBF-TV (PDBF-TV, using a DBF based i-vector representation for each speech utterance. Results on NIST language recognition evaluation 2009 (LRE09 show significant improvements over state-of-the-art systems. By fusing the output of phonotactic and acoustic approaches, we achieve an EER of 1.08%, 1.89% and 7.01% for 30 s, 10 s and 3 s test utterances respectively. Furthermore, various DBF configurations have been extensively evaluated, and an optimal system proposed.

  7. Deep bottleneck features for spoken language identification.

    Science.gov (United States)

    Jiang, Bing; Song, Yan; Wei, Si; Liu, Jun-Hua; McLoughlin, Ian Vince; Dai, Li-Rong

    2014-01-01

    A key problem in spoken language identification (LID) is to design effective representations which are specific to language information. For example, in recent years, representations based on both phonotactic and acoustic features have proven their effectiveness for LID. Although advances in machine learning have led to significant improvements, LID performance is still lacking, especially for short duration speech utterances. With the hypothesis that language information is weak and represented only latently in speech, and is largely dependent on the statistical properties of the speech content, existing representations may be insufficient. Furthermore they may be susceptible to the variations caused by different speakers, specific content of the speech segments, and background noise. To address this, we propose using Deep Bottleneck Features (DBF) for spoken LID, motivated by the success of Deep Neural Networks (DNN) in speech recognition. We show that DBFs can form a low-dimensional compact representation of the original inputs with a powerful descriptive and discriminative capability. To evaluate the effectiveness of this, we design two acoustic models, termed DBF-TV and parallel DBF-TV (PDBF-TV), using a DBF based i-vector representation for each speech utterance. Results on NIST language recognition evaluation 2009 (LRE09) show significant improvements over state-of-the-art systems. By fusing the output of phonotactic and acoustic approaches, we achieve an EER of 1.08%, 1.89% and 7.01% for 30 s, 10 s and 3 s test utterances respectively. Furthermore, various DBF configurations have been extensively evaluated, and an optimal system proposed. PMID:24983963

  8. Critical Bottleneck Size for Jamless Particle Flows in Two Dimensions

    Science.gov (United States)

    Masuda, Takumi; Nishinari, Katsuhiro; Schadschneider, Andreas

    2014-04-01

    We propose a simple microscopic model for arching phenomena at bottlenecks. The dynamics of particles in front of a bottleneck is described by a one-dimensional stochastic cellular automaton on a semicircular geometry. The model reproduces oscillation phenomena due to the formation and collapsing of arches. It predicts the existence of a critical bottleneck size for continuous particle flows. The dependence of the jamming probability on the system size is approximated by the Gompertz function. The analytical results are in good agreement with simulations.

  9. Mapping enteroendocrine cell populations in transgenic mice reveals an unexpected degree of complexity in cellular differentiation within the gastrointestinal tract

    OpenAIRE

    1990-01-01

    The gastrointestinal tract is lined with a monolayer of cells that undergo perpetual and rapid renewal. Four principal, terminally differentiated cell types populate the monolayer, enterocytes, goblet cells, Paneth cells, and enteroendocrine cells. This epithelium exhibits complex patterns of regional differentiation, both from crypt- to-villus and from duodenum-to-colon. The "liver" fatty acid binding protein (L-FABP) gene represents a useful model for analyzing the molecular basis for intes...

  10. Gene variation and genetic differentiation among populations of the solitary mud dauber wasp Trypoxylon (Trypargilum albitarse Fabricius 1804 (Hymenoptera, Crabronidae

    Directory of Open Access Journals (Sweden)

    Antonio C.B. Bergamaschi

    2015-01-01

    Full Text Available Abstract Trypoxylon is a genus of solitary crabronid wasps whose population genetics is poorly known. The purpose of the present study was to investigate the genetic variation and differentiation among five populations of Trypoxylon albitarse, a species widely distributed throughout the Neotropics, with records from Panama to northern Argentina. Eight species-specific microsatellite loci were used for genotyping 96 adult wasps (one female per nest sampled at five sites in Brazil. The analysis of allelic richness and private alleles indicated high genetic diversity in the populations sampled. Pairwise comparisons using the Fst and Dest indices revealed significant differentiation for all, but one pair of populations. Fst, Dest, AMOVA and assignment test values pointed to inter-population differentiation. Additionally, the analysis of population structure using Bayesian and PCA methods characterized two alternative genetic groups. The Mantel test indicated no correlation between genetic and geographic distances. Despite evidence of considerable dispersal capacity for T. albitarse, the data indicate low to moderate population structuring in this species.

  11. Genetic diversity and differentiation of sea trout (Salmo trutta) populations in Lithuanian rivers assessed by microsatellite DNA variation.

    Science.gov (United States)

    Samuiloviene, Aurelija; Kontautas, Antanas; Gross, Riho

    2009-11-01

    The genetic diversity and differentiation of sea trout were studied in three river basins in Lithuania: Akmena-Dane, Bartuva, and Nemunas. A total of 282 individuals were genotyped at eight microsatellite loci. A similar level of genetic diversity was found in all of the populations studied: mean allelic richness ranged from 3.64 to 5.03, and average expected heterozygosity ranged from 0.588 to 0.721. Significant genetic divergence was observed among the different river basins as well as between populations within the drainages. All pairwise F (ST) values were highly significant, ranging from 0.027 to 0.197. The analysis of molecular variance showed rather weak hierarchical population structuring within the Nemunas basin, which may be explained by extensive gene flow among different river basins or, alternatively, reflect the influence of artificial breeding. Information on genetic diversity and differentiation of the Lithuanian sea trout populations will be useful for future management decisions.

  12. Diversity and stability of Aleutian mink disease virus during bottleneck transitions resulting from eradication in domestic mink in Denmark

    DEFF Research Database (Denmark)

    Christensen, Laurids Siig; Hansen, Lene Gram; Chriél, Mariann;

    2011-01-01

    cluster compared with Swedish, Finnish and Dutch isolates and seem to represent a minor fraction of the genetic diversity previously found in Denmark. Stability of nucleoide deviations reveals that the purifying selection of bottlenecks imposed on the AMDV population in Denmark by the stamping out policy...

  13. Optimizing Database Architecture for the New Bottleneck: Memory Access

    OpenAIRE

    Manegold, Stefan; Boncz, Peter; Kersten, Martin

    2000-01-01

    In the past decade, advances in speed of commodity CPUs have far out-paced advances in memory latency. Main-memory access is therefore increasingly a performance bottleneck for many computer applications, including database systems. In this article, we use a simple scan test to show the severe impact of this bottleneck. The insights gained are translated into guidelines for database architecture; in terms of both data structures and algorithms. We discuss how vertically fragmented data struct...

  14. Database architecture optimized for the new bottleneck: Memory access

    OpenAIRE

    Boncz, Peter; Manegold, Stefan; Kersten, Martin

    1999-01-01

    In the past decade, advances in speed of commodity CPUs have far out-paced advances in memory latency. Main-memory access is therefore increasingly a performance bottleneck for many computer applications, including database systems. In this article, we use a simple scan test to show the severe impact of this bottleneck. The insights gained are translated into guidelines for database architecture; in terms of both data structures and algorithms. We discuss how vertically fragmented data struct...

  15. Differentiation and Gene Flow among European Populations of Leishmania infantum MON-1

    Science.gov (United States)

    Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A.; Schönian, Gabriele

    2008-01-01

    Background Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. Methodology/Principal Findings We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups—MON-1 and non-MON-1—could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands–Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. Conclusion In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological

  16. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Directory of Open Access Journals (Sweden)

    Katrin Kuhls

    Full Text Available BACKGROUND: Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. METHODOLOGY/PRINCIPAL FINDINGS: We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1 Greece; (2 Spain islands-Majorca/Ibiza; (3 mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. CONCLUSION: In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further

  17. Digital IIR filters design using differential evolution algorithm with a controllable probabilistic population size.

    Directory of Open Access Journals (Sweden)

    Wu Zhu

    Full Text Available Design of a digital infinite-impulse-response (IIR filter is the process of synthesizing and implementing a recursive filter network so that a set of prescribed excitations results a set of desired responses. However, the error surface of IIR filters is usually non-linear and multi-modal. In order to find the global minimum indeed, an improved differential evolution (DE is proposed for digital IIR filter design in this paper. The suggested algorithm is a kind of DE variants with a controllable probabilistic (CPDE population size. It considers the convergence speed and the computational cost simultaneously by nonperiodic partial increasing or declining individuals according to fitness diversities. In addition, we discuss as well some important aspects for IIR filter design, such as the cost function value, the influence of (noise perturbations, the convergence rate and successful percentage, the parameter measurement, etc. As to the simulation result, it shows that the presented algorithm is viable and comparable. Compared with six existing State-of-the-Art algorithms-based digital IIR filter design methods obtained by numerical experiments, CPDE is relatively more promising and competitive.

  18. Genetic Differentiation of Japanese Sardinella (Sardinella zunasi)Populations in the Northwest Pacific Revealed by ISSR Analysis

    Institute of Scientific and Technical Information of China (English)

    YING Yiping; GAO Tianxiang; MIAO Zhenqing

    2011-01-01

    Knowledge of population genetic structure plays an important role in fisheries management.In this research,Inter-Simple-Sequence-Repeat (ISSR) markers were employed to evaluate the genetic structure of Japanese sardinella (Sardinella zunasi) populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic primers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was detected between the Chinese and Japanese populations by both AMOVA and pairwise Fsr analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.

  19. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China.

    Science.gov (United States)

    Diao, Yongzhao; Zhang, Can; Xu, Jianping; Lin, Dong; Liu, Li; Mtung'e, Olivo G; Liu, Xili

    2015-01-01

    Colletotrichum truncatum is an extremely important fungal pathogen. It can cause diseases both in humans and in over 460 plant species. However, little is known about its genetic diversity within and among populations. One of the major plant hosts of C. truncatum is pepper, and China is one of the main pepper-producing countries in the world. Here, we propose the hypotheses that geography has a major influence on the relationships among populations of C. truncatum in China and that infections in different populations need to be managed differently. To test these hypotheses, we obtained and analyzed 266 C. truncatum isolates from 13 regions representing the main pepper-growing areas throughout China. The analysis based on nine microsatellite markers identified high intrapopulation genetic diversity, evidence of sexual recombination, and geographic differentiation. The genetic differentiation was positively correlated with geographic distance, with the southern and northern China populations grouped in two distinct clusters. Interestingly, isolates collected from the pepper-breeding center harbored the most private alleles. The results suggest that the geographic populations of C. truncatum on peppers in China are genetically differentiated and should be managed accordingly. Our study also provides a solid foundation from which to further explore the global genetic epidemiology of C. truncatum in both plants and humans. PMID:25667606

  20. Genetic differentiation among populations of the beetle Bolitophagus reticulatus (Coleoptera: tenebrionidae) in a fragmented and a continuous landscape.

    Science.gov (United States)

    Knutsen, H; Rukke, B A; Jorde, P E; Ims, R A

    2000-06-01

    The effect of habitat fragmentation on genetic differentiation among local populations of the fungivorous beetle Bolitophagus reticulatus (Coleoptera: Tenebrionidae) was studied in two contrasting landscapes: one heavily fragmented with forest fragments of variable size surrounded by inhabitable agricultural fields, the other an old forest providing a continuous habitat. The genetic structure of the beetle within each of the two contrasting areas was investigated by means of protein electrophoresis, screening four polymorphic loci in 20 populations from each area. In both areas there were significant genetic differences among local populations, but on average differentiation in the fragmented area was three times greater than in the continuous one, strongly indicating a genetic isolation effect of habitat fragmentation. These genetic results are in accordance with previous studies on dispersal in this species. PMID:10886382

  1. Hindu-Muslim differentials in fertility and population growth in India: role of proximate variables.

    Science.gov (United States)

    Balasubramanian, K

    1984-09-01

    In India, Hindu and Muslim differentials in fertility were examined using census data and the findings of 11 surveys. An explanation of the fertility differences was offered. The proportion of Muslims in the population increased and the proportion of Hindus decreased, both before and after partition of the country. After partition, and between 1951-71, the proportion of Muslims increased from 9.9%-11.2% while the proportion of Hindus decreased from 84.9%-82.7%. An examination of mortality and migration data suggests that these proportional changes cannot be attributed to differences in migration or mortality; therefore, they must be due to differences in fertility. Census and survey data provide considerable evidence that fertility is higher among Muslims than among Hindus. According to the 1971 census data, the total marital fertility rate for Muslim women was 11% higher in urban areas and 20% higher in rural areas than the rate for Hindus. Even when education was controlled, the Muslim rate remained higher. The findings of 11 demographic surveys consistently revealed higher fertility rates for Muslims compared to Hindus. Several studies demonstrated that these differences narrowed but remained significant when education and socioeconomic factors were controlled. Investigators generally offer 1 of 3 hypotheses to explain the differences. The 1st hypothesis attributes the fertility differences to differences in the background or socioeconomic characteristics of the 2 populations. This explanation is not supported by studies which have introduced socioeconomic controls. The 2nd hypothesis states that minority status itself is a sufficient cause of high fertility. There is considerable evidence with which to refute this hypothesis. For example, in predominantly Muslim countries, Hindu minorities tend to have lower fertility than Muslims. The 3rd hypothesis attributed the fertility differences to religious beliefs concerning reproduction. Both Islam and Hinduism are

  2. Genetic analysis of scattered populations of the Indian eri silkworm, Samia cynthia ricini Donovan: Differentiation of subpopulations.

    Science.gov (United States)

    Pradeep, Appukuttannair R; Jingade, Anuradha H; Singh, Choba K; Awasthi, Aravind K; Kumar, Vikas; Rao, Guruprasad C; Prakash, N B Vijaya

    2011-07-01

    Deforestation and exploitation has led to the fragmentation of habitats and scattering of populations of the economically important eri silkworm, Samia cynthia ricini, in north-east India. Genetic analysis of 15 eri populations, using ISSR markers, showed 98% inter-population, and 23% to 58% intra-population polymorphism. Nei's genetic distance between populations increased significantly with altitude (R(2) = 0.71) and geographic distance (R(2) = 0.78). On the dendrogram, the lower and upper Assam populations were clustered separately, with intermediate grouping of those from Barpathar and Chuchuyimlang, consistent with geographical distribution. The Nei's gene diversity index was 0.350 in total populations and 0.121 in subpopulations. The genetic differentiation estimate (Gst) was 0.276 among scattered populations. Neutrality tests showed deviation of 118 loci from Hardy-Weinberg equilibrium. The number of loci that deviated from neutrality increased with altitude (R(2) = 0.63). Test of linkage disequilibrium showed greater contribution of variance among eri subpopulations to total variance. D('2)IS exceeded D('2)ST, showed significant contribution of random genetic drift to the increase in variance of disequilibrium in subpopulations. In the Lakhimpur population, the peripheral part was separated from the core by a genetic distance of 0.260. Patchy habitats promoted low genetic variability, high linkage disequilibrium and colonization by new subpopulations. Increased gene flow and habitat-area expansion are required to maintain higher genetic variability and conservation of the original S. c. ricini gene pool. PMID:21931526

  3. Genetic Diversity and Differentiation in Urban and Indigenous Populations of Mexico: Patterns of Mitochondrial DNA and Y-Chromosome Lineages.

    Science.gov (United States)

    González-Sobrino, Blanca Z; Pintado-Cortina, Ana P; Sebastián-Medina, Leticia; Morales-Mandujano, Fabiola; Contreras, Alejandra V; Aguilar, Yasnaya E; Chávez-Benavides, Juan; Carrillo-Rodríguez, Aurelio; Silva-Zolezzi, Irma; Medrano-González, Luis

    2016-01-01

    Aside from the admixture between indigenous people and people from overseas, populations in Mexico changed drastically after the Spanish conquest of the sixteenth century, forming an intricate history that has been underutilized in understanding the genetic population structure of Mexicans. To infer historical processes of isolation, dispersal, and assimilation, we examined the phylogeography of mitochondrial (mt) DNA and Y-chromosome lineages in 3,026 individuals from 10 urban and nine indigenous populations by identifying single nucleotide polymorphisms. A geographic array with a predominance of Amerindian lineages was observed for mtDNA, with northern indigenous populations being divergent from the central and southern indigenous populations; urban populations showed low differentiation with isolation by distance. Y-chromosome variation distinguished urban and indigenous populations through the Amerindian haplogroup Q frequency. The MtDNA and the Y-chromosome together primarily distinguished urban and indigenous populations, with different geographic arrays for both. Gene flow across geographical distance and between the urban and indigenous realms appears to have altered the pre-Hispanic phylogeography in central and southern Mexico, mainly by displacement of women, while maintaining the indigenous isolation in the north, southeast, and Zapotec regions. Most Amerindian mtDNA diversity currently occurs in urban populations and appears to be reduced among indigenous people. PMID:27050033

  4. Genetic analysis of scattered populations of the Indian eri silkworm, Samia cynthia ricini Donovan: differentiation of subpopulations

    Directory of Open Access Journals (Sweden)

    Appukuttannair R. Pradeep

    2011-01-01

    Full Text Available Deforestation and exploitation has led to the fragmentation of habitats and scattering of populations of the economically important eri silkworm, Samia cynthia ricini, in north-east India. Genetic analysis of 15 eri populations, using ISSR markers, showed 98% inter-population, and 23% to 58% intra-population polymorphism. Nei's genetic distance between populations increased significantly with altitude (R² = 0.71 and geographic distance (R² = 0.78. On the dendrogram, the lower and upper Assam populations were clustered separately, with intermediate grouping of those from Barpathar and Chuchuyimlang, consistent with geographical distribution. The Nei's gene diversity index was 0.350 in total populations and 0.121 in subpopulations. The genetic differentiation estimate (Gst was 0.276 among scattered populations. Neutrality tests showed deviation of 118 loci from Hardy-Weinberg equilibrium. The number of loci that deviated from neutrality increased with altitude (R² = 0.63. Test of linkage disequilibrium showed greater contribution of variance among eri subpopulations to total variance. D'2IS exceeded D'2ST, showed significant contribution of random genetic drift to the increase in variance of disequilibrium in subpopulations. In the Lakhimpur population, the peripheral part was separated from the core by a genetic distance of 0.260. Patchy habitats promoted low genetic variability, high linkage disequilibrium and colonization by new subpopulations. Increased gene flow and habitat-area expansion are required to maintain higher genetic variability and conservation of the original S. c. ricini gene pool.

  5. Isoenzymatic differentiation in putative hybrid swarm population (Pinus mugo Turra x P. sylvestris L. from "Torfowisko Zieleniec" peat-bog

    Directory of Open Access Journals (Sweden)

    Anna Siedlewska

    2014-02-01

    Full Text Available Isoenzyme variability of eight groups of individuals from different parts of putative hybrid swarm population (P. mugo Turra x P. sylvestris L. from "Torfowisko Zieleniec" peat-bog complex was studied at ten enzymatic loci. Differences in allelic frequencies distribution among particular samples of the Zieleniec population were statistically significant at 9 loci, as shown by G2- statistics. Chi-square test indicated that in each of studied subpopulations frequencies of alleles at some loci (2-5 differed significantly from frequencies expected for a homogeneous population. Heterozygosity values and also a genotypic polymorphism in studied population confirmed the existence of large genetic variation. Wright's fixation indices (F showed some excess of homozygotes in majority studied groups of individuals, notably higher in some subpopulations. Gene diversity coefficient for 8 subpopulations was high (GST=9.4%. However, when MDH C locus was excluded from the calculation, its value decreased to 2.8%. Presented data demonstrated notable differentiation of subpopulations within studied pine population, comparable with the differentiation among different populations of coniferous species.

  6. The Levels of Genetic Differentiation of Small-Tailed Han Sheep and Tan Sheep Populations Using Structural Loci

    Institute of Scientific and Technical Information of China (English)

    LU Sheng-xia; CHANG Hong; JI De-jun; Tsunoda Kenji; REN Zhan-jun; REN Xiang-lian; SUN Wei; YANG Zhang-ping; CHANG Guo-bin

    2006-01-01

    Using the method of "random sampling in typical colonies of the central area of the habitat" and several electrophoresis techniques, the variations of 17 structural loci encoding blood proteins in 60 Small-Tailed Han sheep and 73 Tan sheep were examined and compared with those of 14 other sheep populations in China and other countries to investigate their levels of genetic differentiation. The average heterozygosities of Small-Tailed Han sheep and Tan sheep were 0.2360 and 0.2587, respectively. The average polymorphic information content values were 0.1974 and 0.2102, respectively. The average effective numbers of alleles were 1.5723 and 1.5751, respectively. The coefficients of gene differentiation in the four groups (including 4, 6, 13, and 16 sheep populations, respectively) were 0.049323, 0.059987, 0.1728, and 0.201256,respectively, indicating that the degree of gene differentiation at the structural loci was the least in Hu sheep, Tong sheep,Small-Tailed Han sheep, and Tan sheep; followed by the above-mentioned four sheep populations and two Mongolian sheep populations; and was the highest in sheep populations belonging to the Mongolian sheep group, South Asian sheep, and European sheep. The earlier researchers' conclusions that both Small-Tailed Han sheep and Tan sheep evolved from Mongolian sheep were further verified by the results of this study. Hu sheep, Tong sheep, Small-Tailed Han sheep, and Tan sheep were decreasingly affected by the bloodline of Mongolian sheep to different degrees. The relationships among sheep populations were not closely related to the geographical distances among sheep populations.

  7. Bottlenecks in serial production lines: A system-theoretic approach

    Directory of Open Access Journals (Sweden)

    C.-T. Kuo

    1996-01-01

    Full Text Available In this work, a new definition of production systems bottlenecks is formulated and analyzed. Specifically, a machine is defined as the bottleneck if the sensitivity of the system's performance index to this machine's production rate in isolation is the largest. Although appealing from the systems point of view, this definition suffers a deficiency due to the fact that the sensitivities involved cannot be either measured on-line or efficiently calculated off-line. To avoid this, the paper develops a method based on indirect but real-time data. From this point of view, the main result of the work is as follows: The bottleneck machine in a serial production line can be identified by analyzing relationships between the so-called manufacturing blockage and manufacturing starvation of each machine. This leads to a simple rule for bottleneck identification. The rule requires neither the calculation of the production rate sensitivities nor the production rate itself. When the probabilities of manufacturing blockages and starvations are not available from on-line measurements, the paper presents their analytical estimates which, under certain conditions, can be used for bottleneck identification. Finally, a case study at an automotive component plant is described.

  8. Within-population genetic diversity of Taraxacum officinale (Asteraceae): differential genotype response and effect on interspecific competition.

    Science.gov (United States)

    Vavrek, M

    1998-07-01

    Clonal offspring of five morphologically distinct individuals of Taraxacum officinale were planted in a greenhouse experiment with each of three competitors, Plantago major, Poa pratensis and Trifolium pratense. The competitors were chosen to represent a series of competitive environments experienced by a natural population of T. officinale through the year. Differences in size, morphology, and response to the competitive environments were found among clones and support classification of the five individuals as distinct genotypes. Both differential competitive responses (alteration in performance) and competitive effects (impediment by competitor performance) were exhibited among genotypes. The differential response by the T. officinale genotypes to the competitors indicates that the biotic environment may influence the genetic structure of a population. The biotic environment in this case is determined by the sequential appearance and dominance of competitors in a field rather than the spatial distribution of these competitors. Since competitors change in relative dominance across seasons, competition is likely to be a component of the genotype by season interaction that had been observed in the natural population. Thus, differential responses among genotypes to a temporally and spatially fluctuating biotic environment may contribute to the maintenance of within-population genetic diversity. PMID:21684978

  9. GENETIC DIFFERENTIATION BETWEEN NOBLE CRAYFISH, ASTACUS ASTACUS (L., POPULATIONS DETECTED BY MICROSATELLITE LENGTH VARIATION IN THE RDNA ITS1 REGION

    Directory of Open Access Journals (Sweden)

    EDSMAN L.

    2002-07-01

    Full Text Available The Internal Transcribed Spacer (ITS region of the nuclear ribosomal repeat was investigated in the search for a suitable genetic marker for population studies of the noble crayfish Astacus astacus (L.. DNA sequencing revealed the presence of two microsatellite insertions in ITS1. By designing highly specific PCR primers, adjacent to one of the insertions, we were able to use fragment analysis to explore the variation of the insertion in 642 specimens from 17 populations of crayfish from Sweden and former Yugoslavia. A new statistical test, the Population Divergence Test, was developed to assess statistical significance of divergence between populations. This test does not assume Mendelian inheritance. Our results demonstrate that different populations often produce characteristic fragment patterns, and that most, but not all, populations are genetically distinct, with high significance. The populations that cannot be significantly differentiated are situated in close geographic proximity to each other and belong to the same main river system, probably reflecting that these populations have had recent contact and that gene flow has occurred.

  10. Steady State of Pedestrian Flow in Bottleneck Experiments

    CERN Document Server

    Liao, Weichen; Seyfried, Armin; Chraibi, Mohcine; Drzycimski, Kevin; Zheng, Xiaoping; Zhao, Ying

    2015-01-01

    Experiments with pedestrians could depend strongly on initial conditions. Comparisons of the results of such experiments require to distinguish carefully between transient state and steady state. In this work, a feasible algorithm - Cumulative Sum Control Chart - is proposed and improved to automatically detect steady states from density and speed time series of bottleneck experiments. The threshold of the detection parameter in the algorithm is calibrated using an autoregressive model. Comparing the detected steady states with previous manually selected ones, the modified algorithm gives more reproducible results. For the applications, three groups of bottleneck experiments are analysed and the steady states are detected. The study about pedestrian flow shows that the difference between the flows in all states and in steady state mainly depends on the ratio of pedestrian number to bottleneck width. When the ratio is higher than a critical value (approximately 115 persons/m), the flow in all states is almost ...

  11. Research of Cruise Industry Development Bottlenecks In China

    Directory of Open Access Journals (Sweden)

    Ping Zhou

    2014-08-01

    Full Text Available Cruise industry is a comprehensive new industry, which has a strong impetus to the development of other industries. In recent years, as the explosive growth in cruise market, China has become a global rapidly-growing emerging cruise market. The cruise industry has begun transiting from infancy to the development phase, in all likelihood facing a number of bottlenecks problem. In this paper, the development trend of the cruise industry is first analyzed, then the bottlenecks of cruise industry are studied and finally some reasonable countermeasures and suggestions are put forward. By perfecting policy and legal, expanding industrial chain, diversifying investment mode, cultivating the market of consumer subjects, and establishing a scientific talents training mode of enterprise, the bottlenecks of cruise industry can be solved. This will consequently promote healthy and rapid development in cruise tourism industry, and give full play to the role of joint economy.

  12. Statistical guidelines for detecting past population shifts using ancient DNA

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon; Gilbert, M Thomas P;

    2012-01-01

    quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast...... post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our...

  13. A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences.

    Science.gov (United States)

    Guo, Juan; Wang, Yunsheng; Song, Chi; Zhou, Jianfeng; Qiu, Lijuan; Huang, Hongwen; Wang, Ying

    2010-09-01

    Background and Aims It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean. Methods The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck. Key Results Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K' = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years. Conclusions As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be approximately 2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in

  14. Demographic history and asynchronous spawning shape genetic differentiation among populations of the hard coral Acropora tenuis in Western Australia.

    Science.gov (United States)

    Rosser, Natalie L

    2016-05-01

    Genetic subdivision within populations can ultimately lead to the evolution of new species, and in populations of broadcast-spawners a potential facilitator of genetic subdivision is asynchronous reproduction. However, the factors that shape genetic variation in marine systems are complex and ambiguous, and ecological genetic structure may be influenced by the overriding signature of past demographic events. Here, the relative roles of the timing of reproduction and historical geography on the partitioning of genetic variation were examined in seven populations of the broadcast-spawning coral Acropora tenuis over 12° of latitude. The analysis of multiple loci (mitochondrial control region, two nuclear introns and six microsatellites) revealed significant genetic division between the most northern reef and all other reefs, suggesting that WA reefs were re-colonized from two different sources after the Pleistocene glaciation. Accompanying this pattern was significant genetic differentiation associated with different breeding seasons (spring and autumn), which was greatest in PaxC, in which there were two divergent lineages (ΦST=0.98). This is the second study to find divergent clades of PaxC associated with spring and autumn spawners, strengthening the suggestion of some selective connection to timing of reproduction in corals. This study reiterates the need to incorporate reproductive timing into population genetic studies of corals because it facilitates genetic differentiation; however, careful analysis of population genetic data is required to separate ecological and evolutionary processes. PMID:26876640

  15. A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus)

    DEFF Research Database (Denmark)

    Ferchaud, Anne-Laure; Pedersen, Susanne H.; Bekkevold, Dorte;

    2014-01-01

    Background: The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine......: RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional...... have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene...

  16. Bottleneck Paths and Trees and Deterministic Graphical Games

    OpenAIRE

    Chechik, Shiri; Kaplan, Haim; Thorup, Mikkel; Zamir, Or; Zwick, Uri

    2016-01-01

    Gabow and Tarjan showed that the Bottleneck Path (BP) problem, i.e., finding a path between a given source and a given target in a weighted directed graph whose largest edge weight is minimized, as well as the Bottleneck spanning tree (BST) problem, i.e., finding a directed spanning tree rooted at a given vertex whose largest edge weight is minimized, can both be solved deterministically in O(m * log^*(n)) time, where m is the number of edges and n is the number of vertices in the graph. We p...

  17. Kinetic description of bottleneck effects in traffic flow

    Institute of Scientific and Technical Information of China (English)

    Peng ZHANG; Dong-yan WU; S. C. WONG; Yi-zhou TAO

    2009-01-01

    This paper deals with the effects of traffic bottlenecks using an extended Lighthill-Whitham-Richards (LWR) model. The solution structure is analytically indi-cated by the study of the Riemann problem characterized by a discontinuous flux. This leads to a typical solution describing a queue upstream of the bottleneck and its width and height, and informs the design of a 5-mapping algorithm. More significantly, it is found that the kinetic model is able to reproduce stop-and-go waves for a triangular fun-damental diagram. Some simulation examples, which are in agreement with the analytical solutions, are given to support these conclusions.

  18. The "Bottleneck" Behaviours in Linear FNNCs and Their Breakthrough

    Institute of Scientific and Technical Information of China (English)

    HUANG Deshuang

    1999-01-01

    The classification mechanisms of linear feed forward neural network classifiers (FNNC), whose hidden layer performs the Fisher lineartrans formation of the input patterns, under the supervision of outer-supervised signals are investigated. The "bottleneck" behavioursin linear FNNCs are observed and analyzed. In addition, the structure stabilities of the linear FNNCs are also discussed. It is pointed out that the key point to break through the "bottleneck" behaviours forlinear FNNCs is to change linear hidden neurons into nonlinear hiddenones. Finally, the experimental results, taking the parity 3 problem asexample, are given.

  19. Effect of anthropogenic landscape features on population genetic differentiation of Przewalski's gazelle: main role of human settlement.

    Directory of Open Access Journals (Sweden)

    Ji Yang

    Full Text Available Anthropogenic landscapes influence evolutionary processes such as population genetic differentiation, however, not every type of landscape features exert the same effect on a species, hence it is necessary to estimate their relative effect for species management and conservation. Przewalski's gazelle (Procapra przewalskii, which inhabits a human-altered area on Qinghai-Tibet Plateau, is one of the most endangered antelope species in the world. Here, we report a landscape genetic study on Przewalski's gazelle. We used skin and fecal samples of 169 wild gazelles collected from nine populations and thirteen microsatellite markers to assess the genetic effect of anthropogenic landscape features on this species. For comparison, the genetic effect of geographical distance and topography were also evaluated. We found significant genetic differentiation, six genetic groups and restricted dispersal pattern in Przewalski's gazelle. Topography, human settlement and road appear to be responsible for observed genetic differentiation as they were significantly correlated with both genetic distance measures [F(ST/(1-F(ST and F'(ST/(1-F'(ST] in Mantel tests. IBD (isolation by distance was also inferred as a significant factor in Mantel tests when genetic distance was measured as F(ST/(1-F(ST. However, using partial Mantel tests, AIC(c calculations, causal modeling and AMOVA analysis, we found that human settlement was the main factor shaping current genetic differentiation among those tested. Altogether, our results reveal the relative influence of geographical distance, topography and three anthropogenic landscape-type on population genetic differentiation of Przewalski's gazelle and provide useful information for conservation measures on this endangered species.

  20. High genetic differentiation of Aegla longirostri (Crustacea, Decapoda, Anomura) populations in southern Brazil revealed by multi-loci microsatellite analysis.

    Science.gov (United States)

    Bartholomei-Santos, M L; Roratto, P A; Santos, S

    2011-01-01

    Species with a broad distribution rarely have the same genetic make-up throughout their entire range. In some cases, they may constitute a cryptic complex consisting of a few species, each with a narrow distribution, instead of a single-, widely distributed species. These differences can have profound impacts for biodiversity conservation planning. The genetic differentiation of four populations of Aegla longirostri, a freshwater crab found in two geographically isolated basins in Rio Grande do Sul State, Brazil, was investigated by analyzing pentanucleotide multi-loci microsatellites in a heteroduplex assay. Although no morphological differences were evident, we found significant genetic differentiation among the four populations, based on F(ST) values and clustering analysis. This high level of differentiation may be indicative of cryptic species in these populations. If this hypothesis is correct, then the species occurring in the Ibicuí-Mirim River, at the southern limit of the Atlantic Rain Forest, would be under threat, considering its very restricted distribution. PMID:22179994

  1. Differential marking, investigation and motor activity in presence of conspecific odours differing on their population of origin in bank voles

    Directory of Open Access Journals (Sweden)

    Geraldine Verplancke

    2011-06-01

    Full Text Available Odours emitted by rodent species convey cues about their overall body conditions and provide valuable information intervening in many aspects of their social relationships such as territorial and mating activities. Although bank vole is one of the primary models for studying chemical communication in wild rodents, literature is scarce about its reactivity to odours of conspecifics from its population compared to those of conspecifics from a different population. Here we tested the effect of the population of origin on the behaviour of wild bank voles (Myodes glareolus through 30min tests in laboratory. We observed both males and females differential marking (i.e. by urine or glandular secretions, motor activity and investigation (i.e. sniffing events in presence of conspecific whole body odours coming from either the Same Population of Origin (SPO or from a Different Population of Origin (DPO. Our results showed that both male and female bank voles react differently to odours of conspecifics according to the population of origin of the latter. Both motor activity and marking were more important when voles were confronted to odours from DPO donors than SPO ones. These effects were independent of the sex of the subjects. Moreover, male subjects tended to investigate more odours from DPO conspecifics than odours from SPO ones. Causes underlying apparent between-populations differences in the bank voles' body odours are discussed.

  2. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    Science.gov (United States)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ΦST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  3. Progress and bottleneck in induced pluripotency

    Directory of Open Access Journals (Sweden)

    Zhang Zhen-Ning

    2012-07-01

    Full Text Available Abstract With their capability to undergo unlimited self-renewal and to differentiate into all cell types in the body, induced pluripotent stem cells (iPSCs, reprogrammed from somatic cells of individual patients with defined factors, have unlimited potential in cell therapy and in modeling complex human diseases. Significant progress has been achieved to improve the safety of iPSCs and the reprogramming efficiency. To avoid the cancer risk and spontaneous reactivation of the reprogramming factors associated with the random integration of viral vectors into the genome, several approaches have been established to deliver the reprogramming factors into the somatic cells without inducing genetic modification. In addition, a panel of small molecule compounds, many of which targeting the epigenetic machinery, have been identified to increase the reprogramming efficiency. Despite these progresses, recent studies have identified genetic and epigenetic abnormalities of iPSCs as well as the immunogenicity of some cells derived from iPSCs. In addition, due to the oncogenic potential of the reprogramming factors and the reprogramming-induced DNA damage, the critical tumor suppressor pathways such as p53 and ARF are activated to act as the checkpoints that suppress induced pluripotency. The inactivation of these tumor suppression pathways even transiently during reprogramming processes could have significant adverse impact on the genome integrity. These safety concerns must be resolved to improve the feasibility of the clinic development of iPSCs into human cell therapy.

  4. Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791): A bivalve with planktonic larval dispersion

    Science.gov (United States)

    2009-01-01

    Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe) and both H5 and H9 (Prainha and Acupe). Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted. PMID:21637701

  5. Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791: a bivalve with planktonic larval dispersion

    Directory of Open Access Journals (Sweden)

    Cinthya Cristina Bulhões Arruda

    2009-01-01

    Full Text Available Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe and both H5 and H9 (Prainha and Acupe. Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted.

  6. Assessing the genetic influence of ancient sociopolitical structure: micro-differentiation patterns in the population of Asturias (Northern Spain).

    Science.gov (United States)

    Pardiñas, Antonio F; Roca, Agustín; García-Vazquez, Eva; López, Belén

    2012-01-01

    The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as "micro-differentiation". It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions.

  7. Assessing the genetic influence of ancient sociopolitical structure: micro-differentiation patterns in the population of Asturias (Northern Spain.

    Directory of Open Access Journals (Sweden)

    Antonio F Pardiñas

    Full Text Available The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as "micro-differentiation". It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions.

  8. Energetic bottlenecks and other design constraints in avian annual cycles

    NARCIS (Netherlands)

    Piersma, T

    2002-01-01

    The flexible phenotypes of birds and mammals often appear to represent adjustments to alleviate some energetic bottleneck or another. By increasing the size of the organs involved in digestion and assimilation of nutrients (gut and liver), an individual bird can increase its ability to process nutri

  9. The Case for a Gaian Bottleneck: The Biology of Habitability.

    Science.gov (United States)

    Chopra, Aditya; Lineweaver, Charles H

    2016-01-01

    The prerequisites and ingredients for life seem to be abundantly available in the Universe. However, the Universe does not seem to be teeming with life. The most common explanation for this is a low probability for the emergence of life (an emergence bottleneck), notionally due to the intricacies of the molecular recipe. Here, we present an alternative Gaian bottleneck explanation: If life emerges on a planet, it only rarely evolves quickly enough to regulate greenhouse gases and albedo, thereby maintaining surface temperatures compatible with liquid water and habitability. Such a Gaian bottleneck suggests that (i) extinction is the cosmic default for most life that has ever emerged on the surfaces of wet rocky planets in the Universe and (ii) rocky planets need to be inhabited to remain habitable. In the Gaian bottleneck model, the maintenance of planetary habitability is a property more associated with an unusually rapid evolution of biological regulation of surface volatiles than with the luminosity and distance to the host star.

  10. The bottleneck may be the solution, not the problem.

    Science.gov (United States)

    Lotem, Arnon; Kolodny, Oren; Halpern, Joseph Y; Onnis, Luca; Edelman, Shimon

    2016-01-01

    As a highly consequential biological trait, a memory "bottleneck" cannot escape selection pressures. It must therefore co-evolve with other cognitive mechanisms rather than act as an independent constraint. Recent theory and an implemented model of language acquisition suggest that a limit on working memory may evolve to help learning. Furthermore, it need not hamper the use of language for communication. PMID:27562516

  11. Bottlenecks reduction using superconductors in high voltage transmission lines

    Directory of Open Access Journals (Sweden)

    Daloub Labib

    2016-01-01

    Full Text Available Energy flow bottlenecks in high voltage transmission lines known as congestions are one of the challenges facing power utilities in fast developing countries. Bottlenecks occur in selected power lines when transmission systems are operated at or beyond their transfer limits. In these cases, congestions result in preventing new power supply contracts, infeasibility in existing contracts, price spike and market power abuse. The “Superconductor Technology” in electric power transmission cables has been used as a solution to solve the problem of bottlenecks in energy transmission at high voltage underground cables and overhead lines. The increase in demand on power generation and transmission happening due to fast development and linked to the intensive usage of transmission network in certain points, which in turn, lead to often frequent congestion in getting the required power across to where it is needed. In this paper, a bottleneck in high voltage double overhead transmission line with Aluminum Conductor Steel Reinforced was modeled using conductor parameters and replaced by Gap-Type Superconductor to assess the benefit of upgrading to higher temperature superconductor and obtain higher current carrying capacity. This proved to reduce the high loading of traditional aluminum conductors and allow more power transfer over the line using superconductor within the same existing right-of-way, steel towers, insulators and fittings, thus reducing the upgrade cost of building new lines.

  12. The Case for a Gaian Bottleneck: The Biology of Habitability.

    Science.gov (United States)

    Chopra, Aditya; Lineweaver, Charles H

    2016-01-01

    The prerequisites and ingredients for life seem to be abundantly available in the Universe. However, the Universe does not seem to be teeming with life. The most common explanation for this is a low probability for the emergence of life (an emergence bottleneck), notionally due to the intricacies of the molecular recipe. Here, we present an alternative Gaian bottleneck explanation: If life emerges on a planet, it only rarely evolves quickly enough to regulate greenhouse gases and albedo, thereby maintaining surface temperatures compatible with liquid water and habitability. Such a Gaian bottleneck suggests that (i) extinction is the cosmic default for most life that has ever emerged on the surfaces of wet rocky planets in the Universe and (ii) rocky planets need to be inhabited to remain habitable. In the Gaian bottleneck model, the maintenance of planetary habitability is a property more associated with an unusually rapid evolution of biological regulation of surface volatiles than with the luminosity and distance to the host star. PMID:26789354

  13. Congestion in a city with a central bottleneck

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Palma, André de

    2012-01-01

    We consider dynamic congestion in an urban setting where trip origins are spatially distributed. All travelers must pass through a downtown bottleneck in order to reach their destination in the CBD. Each traveler chooses departure time to maximize general concave scheduling utility. We find that...

  14. Mitigating the controller performance bottlenecks in Software Defined Networks

    DEFF Research Database (Denmark)

    Caba, Cosmin Marius; Soler, José

    2016-01-01

    proposes a new approach for addressing the performance bottlenecks that arise from limited computational resources at the SDNC. The proposed approach is based on optimally configuring the operating parameters of the components residing inside the SDNC (network control functions such as monitoring, routing...

  15. Congestion in a city with a central bottleneck

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Palma, André de

    2010-01-01

    We consider dynamic congestion in an urban setting where trip origins are spatially distributed. All travelers must pass through a downtown bottleneck in order to reach their destination in the CBD. Each traveler chooses departure time to maximize general concave scheduling utility. At equilibrium...

  16. On the inefficiency of equilibria in linear bottleneck congestion games

    NARCIS (Netherlands)

    Keijzer, B. de; Schäfer, G.; Telelis, O.; Kontogiannis, S.; Koutsoupias, E.; Spirakis, P.G.

    2010-01-01

    We study the inefficiency of equilibrium outcomes in bottleneck congestion games. These games model situations in which strategic players compete for a limited number of facilities. Each player allocates his weight to a (feasible) subset of the facilities with the goal to minimize the maximum (weigh

  17. Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta

    Directory of Open Access Journals (Sweden)

    von Dassow Peter

    2010-01-01

    Full Text Available Abstract Background Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. Results All isolates from the more regionally-localized population (population 2 possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1. The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. Conclusions The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is

  18. Genetic differentiation in red-bellied piranha populations (Pygocentrus nattereri, Kner, 1858) from the Solimões-Amazonas River.

    Science.gov (United States)

    Dos Santos, Carlos Henrique Dos A; de Sá Leitão, Carolina S; Paula-Silva, Maria de N; Almeida-Val, Vera Maria F

    2016-06-01

    Red-bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões-Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red-bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red-bellied piranha populations collected at different locations of Solimões-Amazonas River system. We collected 234 red-bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões-Amazonas River system, with significant genetic differentiation between them. The red-bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing. PMID:27516875

  19. Feather isotope analysis reveals differential patterns of habitat and resource use in populations of white-winged doves

    Science.gov (United States)

    Carleton, Scott A.; Martinez Del Rio, Carlos; Robinson, Timothy J.

    2015-01-01

    The white-winged dove (Zenaida asiatica) serves an important ecological role as a diurnal pollinator of the saguaro cactus in the Sonoran desert and an economic role as a highly sought after game bird in North America. White-winged doves are intimately linked to anthropogenic changes on the landscape and because of this, have experienced dramatic population fluctuations over the last 75 years in response, both positively and negatively, to anthropogenic changes on the landscape. To understand the factors driving population growth and decline of migratory species like the white-winged dove, it is imperative we study resource use on both their breeding and wintering grounds. To understand how populations are distributed on the wintering grounds, we tested an alternative to band recovery approaches by using stable isotope analysis. Before we could use isotope analysis to link breeding and wintering locations for this species, we first needed to determine if hydrogen (δ2H) and carbon (δ13C) stable isotopes in feather tissue (δ2Hf and δ13Cf, respectively) could differentiate among populations of white-winged doves across their breeding range in Texas, New Mexico, and Arizona. δ2Hf and δ13Cf not only differentiated between populations of white-winged doves that breed in the United States, but δ2Hf also provided further differentiation in white-winged doves that breed in native Sonoran Desert and agricultural habitats in the western portion of their range. Ecological processes associated with desert resources and anthropogenic influences, specifically saguaro cacti and irrigated crops, largely determined δ2Hf in some white-winged doves in Arizona whereas δ2H of precipitation (δ2Hp) largely determined δ2Hfof doves in New Mexico and Texas. This study highlights the usefulness of stable isotope analysis to differentiate populations of animals across the landscape and the insight isotopes can provide into habitat and resource use. Published 2015. This article

  20. Marked Genetic Differentiation between Western Iberian and Italic Populations of the Olive Fly: Southern France as an Intermediate Area.

    Directory of Open Access Journals (Sweden)

    Barbara van Asch

    Full Text Available The olive fly, Bactrocera oleae, is the most important pest affecting the olive industry, to which it is estimated to cause average annual losses in excess of one billion dollars. As with other insects with a wide distribution, it is generally accepted that the understanding of B. oleae population structure and dynamics is fundamental for the design and implementation of effective monitoring and control strategies. However, and despite important advances in the past decade, a clear picture of B. oleae's population structure is still lacking. In the Mediterranean basin, where more than 95% of olive production is concentrated, evidence from several studies suggests the existence of three distinct sub-populations, but the geographical limits of their distributions, and the level of interpenetration and gene flow among them remain ill-characterized. Here we use mitochondrial haplotype analysis to show that one of the Mediterranean mitochondrial lineages displays geographically correlated substructure and demonstrate that Italic populations, though markedly distinct from their Iberian and Levantine counterparts are more diverse than previously described. Finally, we show that this distinction does not result from extant hypothetical geographic limits imposed by the Alps or the Pyrenees nor, more generally, does it result from any sharp boundary, as intermixing is observed in a broad area, albeit at variable levels. Instead, Bayesian phylogeographic analysis suggests the interplay between isolation-mediated differentiation during glacial periods and bi-directional dispersal and population intermixing in the interglacials has played a major role in shaping current olive fly population structure.

  1. Marked Genetic Differentiation between Western Iberian and Italic Populations of the Olive Fly: Southern France as an Intermediate Area.

    Science.gov (United States)

    van Asch, Barbara; Pereira-Castro, Isabel; Rei, Fernando Trindade; da Costa, Luís Teixeira

    2015-01-01

    The olive fly, Bactrocera oleae, is the most important pest affecting the olive industry, to which it is estimated to cause average annual losses in excess of one billion dollars. As with other insects with a wide distribution, it is generally accepted that the understanding of B. oleae population structure and dynamics is fundamental for the design and implementation of effective monitoring and control strategies. However, and despite important advances in the past decade, a clear picture of B. oleae's population structure is still lacking. In the Mediterranean basin, where more than 95% of olive production is concentrated, evidence from several studies suggests the existence of three distinct sub-populations, but the geographical limits of their distributions, and the level of interpenetration and gene flow among them remain ill-characterized. Here we use mitochondrial haplotype analysis to show that one of the Mediterranean mitochondrial lineages displays geographically correlated substructure and demonstrate that Italic populations, though markedly distinct from their Iberian and Levantine counterparts are more diverse than previously described. Finally, we show that this distinction does not result from extant hypothetical geographic limits imposed by the Alps or the Pyrenees nor, more generally, does it result from any sharp boundary, as intermixing is observed in a broad area, albeit at variable levels. Instead, Bayesian phylogeographic analysis suggests the interplay between isolation-mediated differentiation during glacial periods and bi-directional dispersal and population intermixing in the interglacials has played a major role in shaping current olive fly population structure.

  2. Genetic diversity, structure and individual assignment of Casta Navarra cattle: a well-differentiated fighting bull population.

    Science.gov (United States)

    Sanz, A; Martin-Burriel, I; Cons, C; Reta, M; Poblador, A; Rodellar, C; Zaragoza, P

    2014-02-01

    The Casta Navarra lineage was one of the populations used to establish the fighting bull (FB) breed, and it has also been reproductively isolated from the others FBs. A total of 1284 individuals from two generations of 16 Casta Navarra herds were sampled to analyse their diversity, their genetic structure and the ability of 28 microsatellite markers to assign individuals to closely related populations. These animals were compared with closely related phylogenetic (FB) or geographical (Pirenaica and Monchina) populations. Hardy-Weinberg equilibrium analysis showed that 82% of the loci had a significant heterozygote deficit as a consequence of the Wahlund effect. The average proportion of genetic variation explained by farm differences was 9% by Wright's FST index. A phylogenetic tree constructed with a neighbour-joining method based on Reynolds genetic distances and a Bayesian Markov chain Monte Carlo clustering approach revealed clear differences between farm groups that generally corresponded to historical information and could unambiguously differentiate Casta Navarra cattle from the other populations. The percentage of animals correctly assigned to the Casta Navarra population was 91.78% for a q threshold of >0.9. Admixture was only detected in 4.45% (q < 0.8) of the cattle. These results are relevant for the maintenance and development of diversity and conservation in the Casta Navarra population.

  3. Reproductive Allochrony in Seasonally Sympatric Populations Maintained by Differential Response to Photoperiod: Implications for Population Divergence and Response to Climate Change.

    Science.gov (United States)

    Fudickar, Adam M; Greives, Timothy J; Atwell, Jonathan W; Stricker, Craig A; Ketterson, Ellen D

    2016-04-01

    Reproductive allochrony presents a potential barrier to gene flow and is common in seasonally sympatric migratory and sedentary birds. Mechanisms mediating reproductive allochrony can influence population divergence and the capacity of populations to respond to environmental change. We asked whether reproductive allochrony in seasonally sympatric birds results from a difference in response to supplementary or photoperiodic cues and whether the response varies in relation to the distance separating breeding and wintering locations as measured by stable isotopes. We held seasonally sympatric migratory and sedentary male dark-eyed juncos (Junco hyemalis) in a common garden in early spring under simulated natural changes in photoperiod and made measurements of reproductive and migratory physiology. On the same dates and photoperiods, sedentary juncos had higher testosterone (initial and gonadotropin-releasing hormone induced), more developed cloacal protuberances, and larger testes than migrants. In contrast, migratory juncos had larger fat reserves (fuel for migration). We found a negative relationship between testis mass and feather hydrogen isotope ratios, indicating that testis growth was more delayed in migrants making longer migrations. We conclude that reproductive allochrony in seasonally sympatric migratory and sedentary birds can result from a differential response to photoperiodic cues in a common garden, and as a result, gene flow between migrants and residents may be reduced by photoperiodic control of reproductive development. Further, earlier breeding in response to future climate change may currently be constrained by differential response to photoperiodic cues. PMID:27028072

  4. Reproductive allochrony in seasonally sympatric populations maintained by differential response to photoperiod: Implications for population divergence and response to climate change

    Science.gov (United States)

    Fudickar, A.M.; Grieves, T.J.; Atwell, Jonathan W.; Stricker, Craig A.; Ketterson, Ellen D.

    2016-01-01

    Reproductive allochrony presents a potential barrier to gene flow and is common in seasonally sympatric migratory and sedentary birds. Mechanisms mediating reproductive allochrony can influence population divergence and the capacity of populations to respond to environmental change. We asked whether reproductive allochrony in seasonally sympatric birds results from a difference in response to supplementary or photoperiodic cues and whether the response varies in relation to the distance separating breeding and wintering locations as measured by stable isotopes. We held seasonally sympatric migratory and sedentary male dark-eyed juncos (Junco hyemalis) in a common garden in early spring under simulated natural changes in photoperiod and made measurements of reproductive and migratory physiology. On the same dates and photoperiods, sedentary juncos had higher testosterone (initial and gonadotropin-releasing hormone induced), more developed cloacal protuberances, and larger testes than migrants. In contrast, migratory juncos had larger fat reserves (fuel for migration). We found a negative relationship between testis mass and feather hydrogen isotope ratios, indicating that testis growth was more delayed in migrants making longer migrations. We conclude that reproductive allochrony in seasonally sympatric migratory and sedentary birds can result from a differential response to photoperiodic cues in a common garden, and as a result, gene flow between migrants and residents may be reduced by photoperiodic control of reproductive development. Further, earlier breeding in response to future climate change may currently be constrained by differential response to photoperiodic cues.

  5. Differential response to ocean acidification in physiological traits of Concholepas concholepas populations

    Science.gov (United States)

    Lardies, Marco A.; Arias, María Belén; Poupin, María Josefina; Manríquez, Patricio H.; Torres, Rodrigo; Vargas, Cristian A.; Navarro, Jorge M.; Lagos, Nelson A.

    2014-07-01

    Phenotypic adaptation to environmental fluctuations frequently occurs by preexisting plasticity and its role as a major component of variation in physiological diversity is being widely recognized. Few studies have considered the change in phenotypic flexibility among geographic populations in marine calcifiers to ocean acidification projections, despite the fact that this type of study provides understanding about how the organism may respond to this chemical change in the ocean. We examined the geographic variation in CO2 seawater concentrations in the phenotype and in the reaction norm of physiological traits using a laboratory mesocosm approach with short-term acclimation in two contrasting populations (Antofagasta and Calfuco) of the intertidal snail Concholepas concholepas. Our results show that elevated pCO2 conditions increase standard metabolic rates in both populations of the snail juveniles, likely due to the higher energy cost of homeostasis. Juveniles of C. concholepas in the Calfuco (southern) population showed a lower increment of metabolic rate in high-pCO2 environments concordant with a lesser gene expression of a heat shock protein with respect to the Antofagasta (northern) population. Combined these results indicate a negative effect of ocean acidification on whole-organism functioning of C. concholepas. Finally, the significant Population × pCO2 level interaction in both studied traits indicates that there is variation between populations in response to high-pCO2 conditions.

  6. Development of microsatellite markers to genetically differentiate populations of Octopus minor from Korea and China.

    Science.gov (United States)

    Kang, Jung-Ha; Kim, Yi-Kyung; Park, Jung-Youn; An, Chel-Min; Jun, Je-Chun

    2012-08-01

    Of the more than 300 octopus species, Octopus minor is one of the most popular and economically important species in Eastern Asia, including Korea, along with O. vulgaris, O. ocellatus, and O. aegina. We developed 19 microsatellite markers from Octopus minor and eight polymorphic markers were developed to analyze the genetic diversity and relationships among four octopus populations from Korea and three from China. The number of alleles per locus varied from 10 to 49, and allelic richness per locus ranged from 2 to 16.4 across all populations. The average allele number among the populations was 11.1, with a minimum of 8.3 and a maximum of 13.6. The mean allelic richness was 8.7 in all populations. The Hardy-Weinberg equilibrium (HWE) test revealed significant deviation in 19 of the 56 single-locus sites, and null alleles were presumed in five of eight loci. The pairwise F ( ST ) values between populations from Korea and China differed significantly in all pairwise comparisons. The genetic distances between the China and Korea samples ranged from 0.161 to 0.454. The genetic distances among the populations from Korea ranged from 0.033 to 0.090, with an average of 0.062; those among populations from China ranged from 0.191 to 0.316, with an average of 0.254. The populations from Korea and China formed clearly separated into clusters via an unweighted pair group method with arithmetic mean dendrogram. Furthermore, a population from muddy flats on the western coast of the Korean Peninsula and one from a rocky area on Jeju Island formed clearly separated subclusters. An assignment test based on the allele distribution discriminated between the Korean and Chinese origins with 96.9 % accuracy.

  7. Population differentiation of the Chagas disease vector Triatoma maculata (Erichson, 1848) from Colombia and Venezuela.

    Science.gov (United States)

    Monsalve, Yoman; Panzera, Francisco; Herrera, Leidi; Triana-Chávez, Omar; Gómez-Palacio, Andrés

    2016-06-01

    The emerging vector of Chagas disease, Triatoma maculata (Hemiptera, Reduviidae), is one of the most widely distributed Triatoma species in northern South America. Despite its increasing relevance as a vector, no consistent picture of the magnitude of genetic and phenetic diversity has yet been developed. Here, several populations of T. maculata from eleven Colombia and Venezuela localities were analyzed based on the morphometry of wings and the mitochondrial NADH dehydrogenase subunit 4 (ND4) gene sequences. Our results showed clear morphometric and genetic differences among Colombian and Venezuelan populations, indicating high intraspecific diversity. Inter-population divergence is suggested related to East Cordillera in Colombia. Analyses of other populations from Colombia, Venezuela, and Brazil from distinct eco-geographic regions are still needed to understand its systematics and phylogeography as well as its actual role as a vector of Chagas disease. PMID:27232127

  8. Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses

    Science.gov (United States)

    Li, Jianfang; Yang, Yuchen; Chen, Qipian; Fang, Lu; He, Ziwen; Guo, Wuxia; Qiao, Sitan; Wang, Zhengzhen; Guo, Miaomiao; Zhong, Cairong; Zhou, Renchao; Shi, Suhua

    2016-01-01

    Systematically investigating the impacts of Pleistocene sea-level fluctuations on mangrove plants may provide a better understanding of their demographic history and useful information for their conservation. Therefore, we conducted population genomic analyses of 88 nuclear genes to explore the population dynamics of a mangrove tree Lumnitzera racemosa across the Indo-West Pacific region. Our results revealed pronounced genetic differentiation in this species between the populations from the Indian Ocean and the Pacific Ocean, which may be attributable to the long-term isolation between the western and eastern coasts of the Malay Peninsula during sea-level drops in the Pleistocene glacial periods. The mixing of haplotypes from the two highly divergent groups was identified in a Cambodian population at almost all 88 nuclear genes, suggesting genetic admixture of the two lineages at the boundary region. Similar genetic admixture was also found in other populations from Southeast Asia based on the Bayesian clustering analysis of six nuclear genes, which suggests extensive and recent secondary contact of the two divergent lineages in Southeast Asia. Computer simulations indicated substantial migration from the Indian Ocean towards the South China Sea, which likely results in the genetic admixture in Southeast Asia. PMID:27380895

  9. Behavioral, ecological and genetic differentiation in an open environment--a study of a mysid population in the Baltic Sea.

    Directory of Open Access Journals (Sweden)

    Martin Ogonowski

    Full Text Available Diel vertical migration (DVM is often assumed to encompass an entire population. However, bimodal nighttime vertical distributions have been observed in various taxa. Mysid shrimp populations also display this pattern with one group concentrated in the pelagia and the other near the bottom. This may indicate alternative migratory strategies, resembling the seasonal partial migrations seen in birds, fishes and amphibians, where only a subset of the population migrates. To assess the persistence of these alternative strategies, we analyzed the nitrogen and carbon stable isotope signatures (as proxies for diet, biochemical indices (as proxies for growth condition, and genetic population divergence in the Baltic mysid Mysis salemaai collected at night in the pelagia and close to the bottom. Stable isotope signatures were significantly different between migrants (pelagic samples and residents (benthic samples, indicating persistent diet differences, with pelagic mysids having a more uniform and carnivorous diet. Sequencing of the mitochondrial cytochrome subunit I (COI gene showed genetic differentiation attributable to geographic location but not between benthic and pelagic groups. Divergent migration strategies were however supported by significantly lower gene flow between benthic populations indicating that these groups have a lower predisposition for horizontal migrations compared to pelagic ones. Different migration strategies did not convey measurable growth benefits as pelagic and benthic mysids had similar growth condition indices. Thus, the combination of ecological, biochemical and genetic markers indicate that this partial migration may be a plastic behavioral trait that yields equal growth benefits.

  10. Label-free detection of neuronal differentiation in cell populations using high-throughput live-cell imaging of PC12 cells.

    Directory of Open Access Journals (Sweden)

    Sebastian Weber

    Full Text Available Detection of neuronal cell differentiation is essential to study cell fate decisions under various stimuli and/or environmental conditions. Many tools exist that quantify differentiation by neurite length measurements of single cells. However, quantification of differentiation in whole cell populations remains elusive so far. Because such populations can consist of both proliferating and differentiating cells, the task to assess the overall differentiation status is not trivial and requires a high-throughput, fully automated approach to analyze sufficient data for a statistically significant discrimination to determine cell differentiation. We address the problem of detecting differentiation in a mixed population of proliferating and differentiating cells over time by supervised classification. Using nerve growth factor induced differentiation of PC12 cells, we monitor the changes in cell morphology over 6 days by phase-contrast live-cell imaging. For general applicability, the classification procedure starts out with many features to identify those that maximize discrimination of differentiated and undifferentiated cells and to eliminate features sensitive to systematic measurement artifacts. The resulting image analysis determines the optimal post treatment day for training and achieves a near perfect classification of differentiation, which we confirmed in technically and biologically independent as well as differently designed experiments. Our approach allows to monitor neuronal cell populations repeatedly over days without any interference. It requires only an initial calibration and training step and is thereafter capable to discriminate further experiments. In conclusion, this enables long-term, large-scale studies of cell populations with minimized costs and efforts for detecting effects of external manipulation of neuronal cell differentiation.

  11. Postglacial colonisation of western Central Europe by Polyommatus coridon (Poda 1761) (Lepidoptera: Lycaenidae): evidence from population genetics.

    Science.gov (United States)

    Schmitt, T; Giessl, A; Seitz, A

    2002-01-01

    The genetic population structure of Polyommatus coridon (Poda 1761) over large regions of France, Italy and Germany was studied by allozyme electrophoresis. The genetic diversity within populations was high for all parameters analysed (number of alleles 2.72; observed and expected heterozygosity 19.6% and 20.3%, respectively; percentage of polymorphic loci: total: 76.4% and, with polymorphism if the frequency of the commonest allele is below 95%: 53.1%), whereas genetic differentiation between populations was comparatively low (FST = 0.021 +/- 0.002). The mean number of alleles declined significantly from southern to northern populations (r = -0.53, P = 0.0005). Similar effects were found also for other parameters of genetic diversity. This is interpreted as a loss of genetic diversity during postglacial expansion. However, samples from France and Italy had similar patterns of genetic diversity indicating no significant loss in this region. Populations from southern Germany were genetically uniform, well differentiated from French populations and showed a significant loss of genetic diversity. Probably, this is due to a bottleneck during passing through the Burgundian Gap, which is a migration corridor from north-eastern France to southern Germany. In contrast to southern German populations, western German populations were not well differentiated from French populations. Nevertheless, they were genetically impoverished, probably as a result from local bottlenecks and post-expansion phenomena.

  12. Effect of estradiol on proliferation and differentiation of side population stem/progenitor cells from murine endometrium

    Directory of Open Access Journals (Sweden)

    Xu Jing

    2011-07-01

    Full Text Available Abstract Background In our previous study, endometrium side population cells (SP cells were isolated from postpartum murine uterus, and characterized by a heterogeneous population of stem/progenitor cells. In this study, we investigated the effect of estrogen on the proliferation and differentiation of SP cells. Methods SP and non-SP cells of postpartum murine endometrium were isolated by DNA dye Hoechst 33342. The expression of estrogen receptor 1 (ESR1 was measured by reverse transcription polymerase chain reaction (RT-PCR, Real-time PCR, Western blot, immunofluorescence and immunohistochemistry. The proliferation and differentiation of SP cells treated with different concentrations [10(-8 M-10(-6 M] of estradiol (E2 and E2+ ICI182780 (Faslodex, inhibitor of ESR1 were measured by 3-(4, 5-dimethylthiazoly1-2-2,5-diphenyltetrazolium bromide(MTT and clonogenic assays. Results (1 SP cells expressed ESR1 at a higher level than non-SP cells. (2 The level of E2 in the serum and the expression of ESR1 in the uterus of postpartum murine changed in the same manner with the ratio of SP cells to total uterus cells at a different postpartum time point. ESR1, as ABCG2 is also predominantly located in the stroma and the glandular epithelium of the uterus. (3 10(-6 M E2 notably promoted the proliferation of SP cells after treatment for 24 h. This effect could be inhibited by ICI182780. E2 at the concentration of 10(-7 M or 10(-8 M was sent to impair the large cloning efficiency (CE of SP cells. Conclusions The effect of estrogen on the proliferation and differentiation of endometrium SP cells via ESR1 was observed and it was in a concentration dependent fashion. Clearly, more work is needed to understand the in vivo effect of E2 at the physiological concentration on the differentiation of SP cells.

  13. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

    Directory of Open Access Journals (Sweden)

    Thomas Meredith M

    2009-10-01

    Full Text Available Abstract Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity

  14. Physiological basis of differential zinc and copper tolerance of Verbascum populations from metal-contaminated and uncontaminated areas.

    Science.gov (United States)

    Morina, Filis; Jovanović, Ljubinko; Prokić, Ljiljana; Veljović-Jovanović, Sonja

    2016-05-01

    Metal contamination represents a strong selective pressure favoring tolerant genotypes and leading to differentiation between plant populations. We investigated the adaptive capacity of early-colonizer species of Verbascum recently exposed to Zn- and Cu-contaminated soils (10-20 years). Two Verbascum thapsus L. populations from uncontaminated sites (NMET1, NMET2), one V. thapsus from a zinc-contaminated site (MET1), and a Verbascum lychnitis population from an open-cast copper mine (MET2) were exposed to elevated Zn or Cu in hydroponic culture under glasshouse conditions. MET populations showed considerably higher tolerance to both Zn and Cu than NMET populations as assessed by measurements of growth and net photosynthesis, yet they accumulated higher tissue Zn concentrations in the shoot. Abscisic acid (ABA) concentration increased with Zn and Cu treatment in the NMET populations, which was correlated to stomatal closure, decrease of net photosynthesis, and nutritional imbalance, indicative of interference with xylem loading and divalent-cation homeostasis. At the cellular level, the sensitivity of NMET2 to Zn and Cu was reflected in significant metal-induced ROS accumulation and ion leakage from roots as well as strong induction of peroxidase activity (POD, EC 1.11.1.7), while Zn had no significant effect on ABA concentration and POD activity in MET1. Interestingly, MET2 had constitutively higher root ABA concentration and POD activity. We propose that ABA distribution between shoots and roots could represent an adaptive mechanism for maintaining low ABA levels and unaffected stomatal conductance. The results show that metal tolerance can occur in Verbascum populations after relatively short time of exposure to metal-contaminated soil, indicating their potential use for phytostabilization. PMID:26865485

  15. Genetic Differentiations among the Populations of Salvia japonica (Lamiaceae and Its Related Species

    Directory of Open Access Journals (Sweden)

    SUDARMONO

    2008-03-01

    Full Text Available Morphological and genetic variations within Salvia japonica (Lamiaceae and its related species in Japan were analyzed for clarifying their taxonomic significance. The genetic variations were explored through chloroplast and nuclear ribosomal DNA sequences and allozyme polymorphisms. Since chromosome numbers characterized the genus of Salvia, we also examined whether the karyotypes were different. We examined 58 populations of S. japonica and 14 populations of others species of Salvia. Among the populations of S. japonica represented four forms (f. japonica, f. longipes, f. lanuginosa and f. albiflora. The size of chromosomes were various among Salvia spp. Based on the allozyme as well as the DNA sequence, the populations of S. japonica separated from the others Salvia species. The populations of S. japonica exhibited four combinations of the morphological characters. However, these combinations did not correlate to the four forms of S. japonica. In addition, the morphological variations did not correlate to the allozyme and DNA sequences. It is suggested that the four morphological variations as well as the four form of S. japonica should not considered to be a taxonomic unit; accordingly, S. japonica were considered to be still at the early stage of speciation process.

  16. The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by(δμ)2 and DA distances, and the divergence times between populations were estimated by (δμ)2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles (10), whereas,Bohai black and Buffalo had the smallest number of private alleles (2). Chinese Holstein showed the highest genetic variability. Its observed number of alleles (Na), mean effective number of alleles (MNA), and mean heterozygosity (He) were 7.7500, 4.9722, and 0.7719,respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first,followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations.Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago (MYA), however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600MYA, respectively.

  17. Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

    Directory of Open Access Journals (Sweden)

    Jian Li

    Full Text Available Although copy number variation (CNV has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip(R Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01. After merging overlapping CNVs, 1135 copy number variation regions (CNVRs, covering approximately 439 Mb (14.3% of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.

  18. Mutational meltdown in laboratory yeast populations

    NARCIS (Netherlands)

    Zeyl, C.; Mizesko, M.; Visser, de J.A.G.M.

    2001-01-01

    In small or repeatedly bottlenecked populations, mutations are expected to accumulate by genetic drift, causing fitness declines. In mutational meltdown models, such fitness declines further reduce population size, thus accelerating additional mutation accumulation and leading to extinction. Because

  19. Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck.

    Science.gov (United States)

    Wilson, Ian J; Carling, Phillipa J; Alston, Charlotte L; Floros, Vasileios I; Pyle, Angela; Hudson, Gavin; Sallevelt, Suzanne C E H; Lamperti, Costanza; Carelli, Valerio; Bindoff, Laurence A; Samuels, David C; Wonnapinij, Passorn; Zeviani, Massimo; Taylor, Robert W; Smeets, Hubert J M; Horvath, Rita; Chinnery, Patrick F

    2016-03-01

    With a combined carrier frequency of 1:200, heteroplasmic mitochondrial DNA (mtDNA) mutations cause human disease in ∼1:5000 of the population. Rapid shifts in the level of heteroplasmy seen within a single generation contribute to the wide range in the severity of clinical phenotypes seen in families transmitting mtDNA disease, consistent with a genetic bottleneck during transmission. Although preliminary evidence from human pedigrees points towards a random drift process underlying the shifting heteroplasmy, some reports describe differences in segregation pattern between different mtDNA mutations. However, based on limited observations and with no direct comparisons, it is not clear whether these observations simply reflect pedigree ascertainment and publication bias. To address this issue, we studied 577 mother-child pairs transmitting the m.11778G>A, m.3460G>A, m.8344A>G, m.8993T>G/C and m.3243A>G mtDNA mutations. Our analysis controlled for inter-assay differences, inter-laboratory variation and ascertainment bias. We found no evidence of selection during transmission but show that different mtDNA mutations segregate at different rates in human pedigrees. m.8993T>G/C segregated significantly faster than m.11778G>A, m.8344A>G and m.3243A>G, consistent with a tighter mtDNA genetic bottleneck in m.8993T>G/C pedigrees. Our observations support the existence of different genetic bottlenecks primarily determined by the underlying mtDNA mutation, explaining the different inheritance patterns observed in human pedigrees transmitting pathogenic mtDNA mutations. PMID:26740552

  20. Towards a microscopic understanding of the phonon bottleneck

    Science.gov (United States)

    Garanin, D. A.

    2007-03-01

    The problem of the phonon bottleneck in the relaxation of two-level systems (spins) to a narrow group of resonant phonons via emission-absorption processes is investigated from first principles. It is shown that the kinetic approach based on the Pauli master equation is invalid because of the narrow distribution of the phonons exchanging their energy with the spins. This results in a long-memory effect that can be best taken into account by introducing an additional dynamical variable corresponding to the nondiagonal matrix elements responsible for spin-phonon correlation. The resulting system of dynamical equations describes the phonon-bottleneck plateau in the spin excitation, as well as a gap in the spin-phonon spectrum, for any finite concentration of spins. On the other hand, it does not accurately render the line shape of emitted phonons and still needs improving.

  1. Reservoir computing and the Sooner-is-Better bottleneck.

    Science.gov (United States)

    Frank, Stefan L; Fitz, Hartmut

    2016-01-01

    Prior language input is not lost but integrated with the current input. This principle is demonstrated by "reservoir computing": Untrained recurrent neural networks project input sequences onto a random point in high-dimensional state space. Earlier inputs can be retrieved from this projection, albeit less reliably so as more input is received. The bottleneck is therefore not "Now-or-Never" but "Sooner-is-Better."

  2. Energetic bottlenecks and other design constraints in avian annual cycles

    OpenAIRE

    Piersma, T

    2002-01-01

    The flexible phenotypes of birds and mammals often appear to represent adjustments to alleviate some energetic bottleneck or another. By increasing the size of the organs involved in digestion and assimilation of nutrients (gut and liver), an individual bird can increase its ability to process nutrients, for example to quickly store fuel for onward flight. Similarly, an increase in the exercise organs (pectoral muscles and heart) enables a bird to increase its metabolic power for sustained fl...

  3. Linguistics, cognitive psychology, and the Now-or-Never bottleneck.

    Science.gov (United States)

    Endress, Ansgar D; Katzir, Roni

    2016-01-01

    Christiansen & Chater (C&C)'s key premise is that "if linguistic information is not processed rapidly, that information is lost for good" (sect. 1, para. 1). From this "Now-or-Never bottleneck" (NNB), C&C derive "wide-reaching and fundamental implications for language processing, acquisition and change as well as for the structure of language itself" (sect. 2, para. 10). We question both the premise and the consequentiality of its purported implications.

  4. Restricted Dynamic Programming Heuristic for Precedence Constrained Bottleneck Generalized TSP

    OpenAIRE

    Salii, Y.

    2015-01-01

    We develop a restricted dynamical programming heuristic for a complicated traveling salesman problem: a) cities are grouped into clusters, resp. Generalized TSP; b) precedence constraints are imposed on the order of visiting the clusters, resp. Precedence Constrained TSP; c) the costs of moving to the next cluster and doing the required job inside one are aggregated in a minimax manner, resp. Bottleneck TSP; d) all the costs may depend on the sequence of previously visited clusters, resp. Seq...

  5. Natural language processing and the Now-or-Never bottleneck.

    Science.gov (United States)

    Gómez-Rodríguez, Carlos

    2016-01-01

    Researchers, motivated by the need to improve the efficiency of natural language processing tools to handle web-scale data, have recently arrived at models that remarkably match the expected features of human language processing under the Now-or-Never bottleneck framework. This provides additional support for said framework and highlights the research potential in the interaction between applied computational linguistics and cognitive science. PMID:27561430

  6. Linguistics, cognitive psychology, and the Now-or-Never bottleneck.

    Science.gov (United States)

    Endress, Ansgar D; Katzir, Roni

    2016-01-01

    Christiansen & Chater (C&C)'s key premise is that "if linguistic information is not processed rapidly, that information is lost for good" (sect. 1, para. 1). From this "Now-or-Never bottleneck" (NNB), C&C derive "wide-reaching and fundamental implications for language processing, acquisition and change as well as for the structure of language itself" (sect. 2, para. 10). We question both the premise and the consequentiality of its purported implications. PMID:27561603

  7. Nonlocal bottleneck effect in two-dimensional turbulence

    OpenAIRE

    Biskamp, D.; Celani, A; E. Schwarz

    1998-01-01

    The bottleneck pileup in the energy spectrum is investigated for several two-dimensional (2D) turbulence systems by numerical simulation using high-order diffusion terms to amplify the effect, which is weak for normal diffusion. For 2D magnetohydrodynamic (MHD) turbulence, 2D electron MHD (EMHD) turbulence and 2D thermal convection, which all exhibit direct energy cascades, a nonlocal behavior is found resulting in a logarithmic enhancement of the spectrum.

  8. Metaheuristic procedures for the lexicographic bottleneck assembly line balancing problem

    OpenAIRE

    Pastor Moreno, Rafael; García Villoria, Alberto; Laguna, Manuel; Martí Cunquero, Rafael

    2015-01-01

    The goal of this work is to develop an improved procedure for the solution of the lexicographic bottleneck variant of the assembly line balancing problem (LB-ALBP). The objective of the LB-ALBP is to minimize the workload of the most heavily loaded workstation, followed by the workload of the second most heavily loaded workstation and so on. This problem-recently introduced to the literature (Pastor, 2011)-has practical relevance to manufacturing facilities. We design, implement and fine-tune...

  9. Bottleneck on Supply Chain of Organic Agricultural Products and Countermeasures

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xin-min

    2012-01-01

    Organic agriculture is one of successful models of low-carbon agriculture, and plays an important role in alleviating and adapting to climate change. However, the development of supply chain of organic agricultural products lags behind, which seriously restricts development of organic agricultural product market. In this paper, major models and bottleneck of supply chain of organic agricultural products are analyzed, and finally countermeasures are put forward.

  10. Spatial differentiation of population development in a declining region: the case of Saarland

    NARCIS (Netherlands)

    J.J. Hoekveld

    2015-01-01

    We increasingly understand the causes of urban population decline: these can be, among others, processes of deindustrialisation, decreasing fertility or the succession of a city through the stages of urban life as the city matures. However, we are still insufficiently able to explain why differences

  11. A Macro Model for Traffic Flow with Consideration of Static Bottleneck

    Institute of Scientific and Technical Information of China (English)

    唐铁桥; 李鹏; 吴永洪; 黄海军

    2012-01-01

    In this paper, we develop a macro model for traffic flow with consideration of static bottleneck to explore the impacts of static bottleneck on traffic flow. The analytical and numerical results show that the proposed model can qualitatively describe the equilibrium flux, uniform flow and small perturbation under the action of a static bottleneck.

  12. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    DEFF Research Database (Denmark)

    Monika, Karmin; Saag, Lauri; Vicente, Mario;

    2015-01-01

    the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males....

  13. ON THE BOTTLENECK CAPACITY EXPANSION PROBLEMS ON NETWORKS

    Institute of Scientific and Technical Information of China (English)

    Yang Chao; Zhang Jianzhong

    2006-01-01

    This article considers a class of bottleneck capacity expansion problems. Such problems aim to enhance bottleneck capacity to a certain level with minimum cost. Given a network G(V, A,(-C)) consisting of a set of nodes V = {v1, v2,………, vn}, a set of arcs A(∪-){(vi, vj) | i = 1, 2,………, n; j = 1, 2,………, n} and a capacity vector (-C). The component (-C)ij of (-C) is the capacity of arc (vi, vj). Define the capacity of a subset A' of A as the minimum capacity of the arcs in A, the capacity of a family F of subsets of A is the maximum capacity of its members. There axe two types of expanding models. In the arc-expanding model, the unit cost to increase the capacity of arc (vi, vj) is wij. In the node-expanding model, it is assumed that the capacities of all arcs (vi, vi) which start at the same node vi should be increased by the same amount and that the unit cost to make such expansion is wi. This article considers three kinds of bottleneck capacity expansion problems (path,spanning arborescence and maximum flow) in both expanding models. For each kind of expansion problems, this article discusses the characteristics of the problems and presents several results on the complexity of the problems.

  14. Clonal Evolution of Enterocytozoon bieneusi Populations in Swine and Genetic Differentiation in Subpopulations between Isolates from Swine and Humans.

    Science.gov (United States)

    Wan, Qiang; Xiao, Lihua; Zhang, Xichen; Li, Yijing; Lu, Yixin; Song, Mingxin; Li, Wei

    2016-08-01

    Enterocytozoon bieneusi is a widespread parasite with high genetic diversity among hosts. Its natural reservoir remains elusive and data on population structure are available only in isolates from primates. Here we describe a population genetic study of 101 E. bieneusi isolates from pigs using sequence analysis of the ribosomal internal transcribed spacer (ITS) and four mini- and microsatellite markers. The presence of strong linkage disequilibrium (LD) and limited genetic recombination indicated a clonal structure for the population. Bayesian inference of phylogeny, structural analysis, and principal coordinates analysis separated the overall population into three subpopulations (SP3 to SP5) with genetic segregation of the isolates at some geographic level. Comparative analysis showed the differentiation of SP3 to SP5 from the two known E. bieneusi subpopulations (SP1 and SP2) from primates. The placement of a human E. bieneusi isolate in pig subpopulation SP4 supported the zoonotic potential of some E. bieneusi isolates. Network analysis showed directed evolution of SP5 to SP3/SP4 and SP1 to SP2. The high LD and low number of inferred recombination events are consistent with the possibility of host adaptation in SP2, SP3, and SP4. In contrast, the reduced LD and high genetic diversity in SP1 and SP5 might be results of broad host range and adaptation to new host environment. The data provide evidence of the potential occurrence of host adaptation in some of E. bieneusi isolates that belong to the zoonotic ITS Group 1. PMID:27563718

  15. Investigating population differentiation in a major African agricultural pest: evidence from geometric morphometrics and connectivity suggests high invasion potential.

    Science.gov (United States)

    Karsten, M; Addison, P; Jansen van Vuuren, B; Terblanche, J S

    2016-07-01

    The distribution, spatial pattern and population dynamics of a species can be influenced by differences in the environment across its range. Spatial variation in climatic conditions can cause local populations to undergo disruptive selection and ultimately result in local adaptation. However, local adaptation can be constrained by gene flow and may favour resident individuals over migrants-both are factors critical to the assessment of invasion potential. The Natal fruit fly (Ceratitis rosa) is a major agricultural pest in Africa with a history of island invasions, although its range is largely restricted to south east Africa. Across Africa, C. rosa is genetically structured into two clusters (R1 and R2), with these clusters occurring sympatrically in the north of South Africa. The spatial distribution of these genotypic clusters remains unexamined despite their importance for understanding the pest's invasion potential. Here, C. rosa, sampled from 22 South African locations, were genotyped at 11 polymorphic microsatellite loci and assessed morphologically using geometric morphometric wing shape analyses to investigate patterns of population structure and determine connectedness of pest-occupied sites. Our results show little to no intraspecific (population) differentiation, high population connectivity, high effective population sizes and only one morphological type (R2) within South Africa. The absence of the R1 morphotype at sites where it was previously found may be a consequence of differences in thermal niches of the two morphotypes. Overall, our results suggest high invasion potential of this species, that area-wide pest management should be undertaken on a country-wide scale, and that border control is critical to preventing further invasions. PMID:27085997

  16. The impact of share wave elastography in differentiation of hepatic hemangioma from malignant liver tumors in pediatric population

    International Nuclear Information System (INIS)

    Highlights: • We evaluated the impact of share wave elastography technique in differentiation hepatic hemangiomas from malignant liver tumors in pediatric population. • Share wave technique can increase the diagnostic capability of conventional ultrasonography in the differential diagnosis of liver tumors in children. • Share wave elastography is a potential adjunctive diagnostic technique for pediatric liver tumors. - Abstract: Objective: In children it is crucial to differentiate malignant liver tumors from the most common benign tumor, hepatic hemangiomas since the treatment strategies are quite different. We aimed to evaluate the efficiency of shear wave elastography (SWE) technique in differentiation of malignant hepatic tumors and hepatic hemangiomas. Methods: Twenty patients with hepatic tumor were included in our study. Two radiologists performed SWE for 13 patients with malignant hepatic tumors including hepatoblastoma (n = 7), hepatocellular carcinoma (n = 3), metastasis (n = 2), embryonal sarcoma (n = 1) and 7 patients with hepatic hemangioma. All of our patients were between the age of 1 and 192 months (mean age: 56.88 months). Receiver operating characteristic analysis was achieved to evaluate the diagnostic accuracy of SWE and to determine the optimal cut-off value in differentiation hepatic hemangioma from malignant hepatic tumors. Results: The mean SWE values (in kPa) for the first observer were 46.94 (13.8–145) and 22.38 (6.6–49.6) and those for the second observer were 57.91 (11–237) and 23.87 (6.4–57.5), respectively for malignant hepatic tumors and hepatic hemangiomas. The SWE values of malignant hepatic tumors were significantly higher than those of hepatic hemangioma (p = 0.02). The inter-observer agreement was almost perfect (0.81). The area under the receiver operating characteristic curve of SWE for differentiating the hepatic hemangioma from malignant hepatic tumors was 0.77 with a sensitivity of 72.7% and a specificity of 66

  17. Digital IIR filters design using differential evolution algorithm with a controllable probabilistic population size

    OpenAIRE

    Wu Zhu; Jian-an Fang; Yang Tang; Wenbing Zhang; Wei Du

    2012-01-01

    Design of a digital infinite-impulse-response (IIR) filter is the process of synthesizing and implementing a recursive filter network so that a set of prescribed excitations results a set of desired responses. However, the error surface of IIR filters is usually non-linear and multi-modal. In order to find the global minimum indeed, an improved differential evolution (DE) is proposed for digital IIR filter design in this paper. The suggested algorithm is a kind of DE variants with a controlla...

  18. Genetic Diversity and Differentiation of the Orange-Spotted Grouper (Epinephelus coioides Between and Within Cultured Stocks and Wild Populations Inferred from Microsatellite DNA Analysis

    Directory of Open Access Journals (Sweden)

    Haoran Lin

    2011-07-01

    Full Text Available In the present study, we employed microsatellite DNA markers to analyze the genetic diversity and differentiation between and within cultured stocks and wild populations of the orange-spotted grouper originating from the South China Sea and Southeast Asia. Compared to wild populations, genetic changes including reduced genetic diversity and significant differentiation have taken place in cultured grouper stocks, as shown by allele richness and heterozygosity studies, pairwise Fst, structure, molecular variance analysis, as well as multidimensional scaling analysis. Although two geographically adjacent orange-spotted grouper populations in China showed negligible genetic divergence, significant population differentiation was observed in wild grouper populations distributed in a wide geographical area from China, through Malaysia to Indonesia. However, the Mantel test rejected the isolation-by-distance model of genetic structure, which indicated the genetic differentiation among the populations could result from the co-effects of various factors, such as historical dispersal, local environment, ocean currents, river flows and island blocks. Our results demonstrated that microsatellite markers could be suitable not only for genetic monitoring cultured stocks but also for revealing the population structuring of wild orange-spotted grouper populations. Meanwhile, our study provided important information for breeding programs, management of cultured stocks and conservation of wild populations of the orange-spotted grouper.

  19. Populism

    OpenAIRE

    Abts, Koenraad; van Kessel, Stijn

    2015-01-01

    Populism is a concept applied to a wide range of political movements and actors across the globe. There is, at the same time, considerable confusion about the attributes and manifestation of populism, as well as its impact on democracy. This contribution identifies the defining elements of the populist ideology and discusses the varieties in which populism manifests itself, for instance as a component of certain party families. We finally discuss various normative interpretations of populism,...

  20. SSR Marker Analysis on indica-japonica Differentiation of Natural Population of Oryza rufipogon in Yuanjiang, Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    LI Ya-li; YANG Xiao-xi; ZHAO Feng-ping; XU Ming-hui

    2006-01-01

    By using 19 pairs of primers that could identify two subspecies (indica and japonica) of cultivated rice (Oryza sativa L.), the indica-japonica differentiation of 56 individuals from the natural population of common wild rice (Oryza rufipogon Griff.) in Yuanjiang was analyzed by SSR (microsatellite DNAs, or simple sequence repeat). Of the 19 pairs of primers, 17 pairs (89.47%) could amplify only one kind of band type among ail of the individuals, but primers RM251 and RM18 could amplify polymorphic band types. The bands amplified by 16 pairs of primers (84.21%) were identical to the indica-japonica diagnostic bands of relevant locus in cultivated rice, including 11 japonica-like loci and 4 indica-like loci. The bands amplified by the other three pairs of primers (RM18, RM202,RM205) were different from indica or japonica diagnostic bands of cultivated rice. The results showed that according to 19 loci analyzed, 84.21% of SSR loci in genomic DNA of common wild rice in Yuanjiang displayed indica-japonica differentiation and 13.79% of the loci still kept primitive, and most of the detected loci were homogenetic in the natural population.

  1. Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range.

    Directory of Open Access Journals (Sweden)

    Jean-Baptiste Lamy

    Full Text Available BACKGROUND: Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. METHODOLOGY: We assessed cavitation resistance (P(50, growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F(ST and quantitative genetic differentiation (Q(ST, for retrospective identification of the evolutionary forces acting on these traits. RESULTS/DISCUSSION: In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h(2 (ns = 0.43±0.18, CV(A = 4.4%. Q(ST was significantly lower than F(ST, indicating uniform selection for P(50, rather than genetic drift. Putative mechanisms underlying Q(ST

  2. Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

    KAUST Repository

    Banguera-Hinestroza, E.

    2014-02-27

    Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact. © 2014 Springer Science+Business Media Dordrecht.

  3. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.

    Science.gov (United States)

    Fernandes, Andrew D; Macklaim, Jean M; Linn, Thomas G; Reid, Gregor; Gloor, Gregory B

    2013-01-01

    Experimental variance is a major challenge when dealing with high-throughput sequencing data. This variance has several sources: sampling replication, technical replication, variability within biological conditions, and variability between biological conditions. The high per-sample cost of RNA-Seq often precludes the large number of experiments needed to partition observed variance into these categories as per standard ANOVA models. We show that the partitioning of within-condition to between-condition variation cannot reasonably be ignored, whether in single-organism RNA-Seq or in Meta-RNA-Seq experiments, and further find that commonly-used RNA-Seq analysis tools, as described in the literature, do not enforce the constraint that the sum of relative expression levels must be one, and thus report expression levels that are systematically distorted. These two factors lead to misleading inferences if not properly accommodated. As it is usually only the biological between-condition and within-condition differences that are of interest, we developed ALDEx, an ANOVA-like differential expression procedure, to identify genes with greater between- to within-condition differences. We show that the presence of differential expression and the magnitude of these comparative differences can be reasonably estimated with even very small sample sizes.

  4. Explicative Factors for Entrepreneurial Intention in Women: Gender Differentials Amongst the University Population

    Directory of Open Access Journals (Sweden)

    María José Quero Gervilla

    2013-01-01

    Full Text Available The aim of this research project is to shed some light on the reasons why women are less likely to get involved in the processes of setting up businesses. To do this, a structural equations model has been developed, identifying a series of variables that can explain entrepreneurial intention amongst the potentially entrepreneurial population. The model has been validated by carrying out a survey amongst 1,222 students studying 12 different degree courses at the University of Malaga, Spain. In applying the model to both the male and female populations, significant differences have been found in the patterns of behaviour of the two sexes, with women undergoing a more complex process than men, and requiring external support.

  5. Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America

    OpenAIRE

    Fabian, Daniel K; Kapun, Martin; Nolte, Viola; Kofler, Robert; Schmidt, Paul S; Schlötterer, Christian; Flatt, Thomas

    2012-01-01

    Abstract Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. Drosophila melanogaster, an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome-wide next-generation sequencing of DNA pools ('pool-seq') from three populations collected along the North America...

  6. Rapid differentiation of sexual signals in invasive toads: call variation among populations

    OpenAIRE

    Kiyomi Yasumiba; Duffy, Richard L.; Parsons, Scott A.; Ross A Alford; Lin Schwarzkopf

    2016-01-01

    Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls ...

  7. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

    Directory of Open Access Journals (Sweden)

    Rodrick J Chiodini

    Full Text Available Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem

  8. Education, Elderly Health, and Differential Population Aging in South Korea: A Demographic Approach

    OpenAIRE

    Bongoh Kye; Erika Arenas; Graciela Teruel; Luis Rubalcava

    2014-01-01

    Background: Population aging proceeds with other socioeconomic developments, including educational expansion. Improvements in educational attainment lead to changes in demographic behaviors such as assortative mating, fertility, and the intergenerational transmission of education, which change the health of the elderly and the education of their offspring generation. Objective: We examine such a jointly-changing process in South Korea. Methods: We apply a recursive demographic model (Ma...

  9. Fmr1 KO and Fenobam Treatment Differentially Impact Distinct Synapse Populations of Mouse Neocortex

    OpenAIRE

    Wang, Gordon X.; Smith, Stephen J.; MOURRAIN, PHILIPPE

    2014-01-01

    Cognitive deficits in fragile X syndrome (FXS) are attributed to molecular abnormalities of the brain’s vast and heterogeneous synapse populations. Unfortunately, the density of synapses coupled with their molecular heterogeneity presents formidable challenges in understanding the specific contribution of synapse changes in FXS. We demonstrate powerful new methods for the large-scale molecular analysis of individual synapses that allow quantification of numerous specific changes in synapse po...

  10. Low Genetic Differentiation across Three Major Ocean Populations of the Whale Shark, Rhincodon typus

    OpenAIRE

    Schmidt, Jennifer V.; Claudia L Schmidt; Fusun Ozer; Robin E Ernst; Feldheim, Kevin A; Ashley, Mary V.; Marie Levine

    2009-01-01

    BACKGROUND: Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated ...

  11. The differential effects of increasing frequency and magnitude of extreme events on coral populations

    OpenAIRE

    Fabina, NS; Baskett, ML; Gross, K.

    2015-01-01

    © 2015 by the Ecological Society of America. Extreme events, which have profound ecological consequences, are changing in both frequency and magnitude with climate change. Because extreme temperatures induce coral bleaching, we can explore the relative impacts of changes in frequency and magnitude of high temperature events on coral reefs. Here, we combined climate projections and a dynamic population model to determine how changing bleaching regimes influence coral persistence. We additional...

  12. Density regulation in toad populations (Epidalea calamita, Bufotes viridis) by differential winter survival of juveniles.

    Science.gov (United States)

    Sinsch, Ulrich; Schäfer, Alena M

    2016-01-01

    The size of amphibian populations varies considerably between years, so that systematic trends in dynamics are difficult to detect. Informed conservation management of presumably declining populations requires the identification of the most sensitive life stage. In temperate-zone anurans there is growing evidence that juveniles hibernating for the first time suffer from substantial winter losses. In two syntopic toads (Epidalea calamita, Bufotes viridis) we monitored survival of such juveniles during four consecutive winters in the natural habitat and in four temperature treatments (3°, 5 °C, 10°/15 °C or 20 °C, natural light-dark cycle) in temperature-controlled chambers during winter. Specifically, we tested the hypotheses that (1) winter mortality of juvenile toads which hibernate for the first time in their life is an important component of population dynamics, and that (2) mortality rates differed between the two species. Parameters quantified were size-dependent winter mortality and body condition of pre- and post-hibernating juveniles. Field data provided evidence for the important role of winter mortality of first-hibernators in population dynamics. Choice of hibernacula differed in E. calamita between small and medium-sized individuals and also between the two species suggesting distinct mortality risks. The inability of small E. calamita to reach frost-proof hibernacula by burrowing, and the exposure of small B. viridis to predators are the most probable causes of size-assortative winter mortality. In conclusion, E. calamita juveniles may benefit from rising average winter temperatures in the future by decreased risk of freezing to death, whereas predator-caused winter mortality of B. viridis juveniles will also depend on the effects of climate warming on predator phenology.

  13. Selective isolation and differentiation of a stromal population of human embryonic stem cells with osteogenic potential

    DEFF Research Database (Denmark)

    Harkness, Linda M; Mahmood, Amer; Ditzel, Nicholas;

    2011-01-01

    The derivation of osteogenic cells from human embryonic stem cells (hESC) has been hampered by the absence of easy and reproducible protocols. hESC grown in feeder-free conditions, often show a sub population of fibroblast-like, stromal cells growing between the colonies. Thus, we examined...... the possibility that these cells represent a population of stromal (mesenchymal) stem cells (hESC-stromal). Two in house derived hES cell lines (Odense3 and KMEB3) as well as an externally derived cell line (Hues8) were transitioned to feeder-free conditions. A sub population of fibroblast-like cells established...... between the hESC colonies were isolated by selective adherence to hyaluronic acid-coated plates (100μg/ml) and were characterized using a combination of FACS analysis and staining. The cells were CD44(+), CD29(+), CD73(+), CD166(+), CD146(+), and CD105(+); and, Oct4(-), CD34(-), CD45(-) and CXCR4(-). When...

  14. Philopatry drives genetic differentiation in an island archipelago: comparative population genetics of Galapagos Nazca boobies (Sula granti) and great frigatebirds (Fregata minor).

    Science.gov (United States)

    Levin, Iris I; Parker, Patricia G

    2012-11-01

    Seabirds are considered highly mobile, able to fly great distances with few apparent barriers to dispersal. However, it is often the case that seabird populations exhibit strong population genetic structure despite their potential vagility. Here we show that Galapagos Nazca booby (Sula granti) populations are substantially differentiated, even within the small geographic scale of this archipelago. On the other hand, Galapagos great frigatebird (Fregata minor) populations do not show any genetic structure. We characterized the genetic differentiation by sampling five colonies of both species in the Galapagos archipelago and analyzing eight microsatellite loci and three mitochondrial genes. Using an F-statistic approach on the multilocus data, we found significant differentiation between nearly all island pairs of Nazca booby populations and a Bayesian clustering analysis provided support for three distinct genetic clusters. Mitochondrial DNA showed less differentiation of Nazca booby colonies; only Nazca boobies from the island of Darwin were significantly differentiated from individuals throughout the rest of the archipelago. Great frigatebird populations showed little to no evidence for genetic differentiation at the same scale. Only two island pairs (Darwin - Wolf, N. Seymour - Wolf) were significantly differentiated using the multilocus data, and only two island pairs had statistically significant φ(ST) values (N. Seymour - Darwin, N. Seymour - Wolf) according to the mitochondrial data. There was no significant pattern of isolation by distance for either species calculated using both markers. Seven of the ten Nazca booby migration rates calculated between island pairs were in the south or southeast to north or northwest direction. The population differentiation found among Galapagos Nazca booby colonies, but not great frigatebird colonies, is most likely due to differences in natal and breeding philopatry.

  15. Time matters: Some interesting properties of the population differentiation measures GST and D overlooked in the equilibrium perspective

    Institute of Scientific and Technical Information of China (English)

    Liang LENG; De-Xing ZHANG

    2013-01-01

    Genetic differentiation of populations has been traditionally quantified by Wright's F-statistics,typically assuming mutation-migration-drift equilibrium.However,the equilibrium perspective can be unrealistic as many natural populations are likely not yet in equilibrium.Therefore,understanding the behaviors,robustness,and power of the differentiation indexes under non-equilibrium conditions has important implications.Here,we report an extensive examination of the properties of two major indexes GsT and D under non-equilibrium conditions by theoretical deduction under the infinite allele model (IAM) and simulation under the stepwise mutation model (SMM).Several properties of GST and D valid under both SMM and IAM,which have not been recognized under the equilibrium perspective,were unveiled.First,ifgene flow is very weak (e.g.,m < 10 4),GsT,like D,also takes a fairly long time to reach equilibrium if mutation rate is not very large.When GST (D) is in equilibrium depends on when Hs and HT are both in equilibrium.Under IAM and complete isolation,this is determined by the product ofμ and t:GsT will not approach equilibrium as long as μt < 1.Under SMM,10-4 appears to be the rough threshold migration rate; when m < 10-4,GsT approaches equilibrium much slower and later than Hs,whereas the opposite is true when m > 10 4.Second,contrary to the popular belief,μ < m is neither an obligatory request for GST to be an effective differentiation measure nor a sufficient condition for using GST to estimate gene flow level (Nm),if GST is not yet approaching equilibrium.Third,under SMM (but not IAM) and complete isolation,when population size is large (e.g.,> 1000),mutation rate shows a great impact on GST but only a mild influence on D; hence D can be much less sensitive to mutation rate heterogeneity than GST in certain situations.Fourth,whatever the level of gene flow,drift plays a dominant role on GST,whereas gene flow appears to have a stronger influence on D when

  16. Genetic diversity of native Turkish cattle breeds: Mantel, AMOVA and bottleneck analysis

    Directory of Open Access Journals (Sweden)

    Yusuf Özşensoy

    2014-09-01

    Full Text Available This study was conducted to evaluate potential extinction risk of Turkish native cattle breeds using Mantel and AMOVA tests and Bottleneck analysis. A total of 271 DNA samples were isolated from Anatolian Black, Anatolian Grey, South Anatolian Red, Native Southern Anatolian Yellow, East Anatolian Red, and Zavot cattle. In this study, genotypes of 20 microsatellites were determined by capillary electrophoresis and fragment analysis. A total of 269 different alleles were detected. The maximum and minimum numbers of total alleles were observed in TGLA122 (n=26 and INRA005 (n=7 loci, respectively. The highest average observed and expected heterozygosity values were determined as 0.619–0.852 and 0.669–0.877, respectively. The average FIS value was 0.068. Results of AMOVA and Mantel tests illustrated statistically significant differences in populations (p<0.001 and correlation (p<0.01. Bottleneck analysis revealed a normal distribution of L–shaped curve indicating that there was no recent risk of extinction for these breeds.

  17. Genetic Differentiation of Archachatina marginata Populations from Three Vegetation Zones Using Radom Amplified Polymorphic DNA Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Comfort O. AFOLAYAN

    2015-09-01

    Full Text Available The genetic differentiation of Archachatina marginata populations from three different zones of Nigeria was studied with a view to delimiting them into sub-species. One hundred and nineteen (119 snail specimens were collected, comprising of forty (40 specimens from Yenagoa (Mangrove forest and from Kabba (Guinea Savanna and thirty nine (39 specimens were from Ile-Ife (Rainforest. Eight parameters of the shell specimens of A. marginata which included height of shell, width of shell, aperture height, aperture width, spire length, spire width, penultimate whorl length and first whorl length were subjected to Principal Component Analysis (PCA and Canonical Variates Analysis (CVA to delimit the populations into sub-species. DNA of the various populations was extracted from the foot muscle using CTAB (Cetyl Trimethyl Ammonium Bromide method, which was subjected to RAPD analysis. The RAPD studies employed five (5 oligonucleotide primers (OPB – 17, OPH – 12, OPH – 17, OPI – 06 and OPU – 14 to amplify DNA from 27 samples of A. marginata selected. All five primers produced different band patterns, and the number of fragments amplified per primer varied. Among them, OPB- 17 gave DNA profiles with more numerous bands than the others primers. Both PCA and CVA produced overlapped clusters of A. marginata specimens from the three vegetation zones. The height of shell was observed to be the most variable feature and preferably the most suitable parameter for population grouping. Analysis of the proportions of polymorphic loci and band sharing based on similarity indices for A. marginata samples indicated a relatively high level of genetic variation in the populations from the three areas.

  18. Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

    Science.gov (United States)

    In population genetic studies, growing awareness has been raised on non-neutral markers which can provide more estimates of evolutionary differentiation caused by different selections among populations, even though neutral genetic markers have provided unbiased estimates of divergence time and the a...

  19. Differential exposure of the urban population to vehicular air pollution in Hong Kong.

    Science.gov (United States)

    Fan, Xiaopeng; Lam, Kin-che; Yu, Qi

    2012-06-01

    This study aims to characterize the spatial variations in, and examine the influence of socio-economic class on, the exposure of urban population of Hong Kong to air pollution from vehicular sources. Hong Kong provides a unique and interesting case for an in-depth study of environmental inequality because of its dense environment and housing provision mechanism through which about half of the population is accommodated in public housing estates provided by the government. To estimate the exposure of the urban population to vehicular air pollution, the IMMIS(net) air dispersion model developed for city-wide air quality assessment was used. The annual mean concentrations of CO, NO(x), SO(2) and PM(10) were estimated for various assessment points of 275 public and 295 private building groups. The results show more pronounced inequality among residents living in private than in public housing estates. Elderly people and those of lower socio-economic status were found to be exposed to relatively higher levels of vehicular air pollution compared with groups of higher socio-economic status. However, when all the residents in Hong Kong were pooled together for analysis, no distinct class-biased patterns were found. This could be ascribed to the housing provision mechanism, in which less well-off people are accommodated in public housing estates where the air quality is relatively better. This study highlights the importance of government intervention in housing provision, through which the deprived groups in Hong Kong are inadvertently more protected from air pollution exposure.

  20. Differential Estimates of Southern Flying Squirrel (Glaucomys volans) Population Structure Based on Capture Method.

    Energy Technology Data Exchange (ETDEWEB)

    Laves, Kevin S.; Loeb, Susan C.

    2006-01-01

    ABSTRACT.—It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucomys volans) using two methods to study their effect on red-cockaded woodpecker (Picoides borealis) reproductive success. Southern flying squirrels were captured at and removed from 30 red-cockaded woodpecker cluster sites during March to July 1994 and 1995 using Sherman traps placed in a grid encompassing a red-cockaded woodpecker nest tree and by hand from red-cockaded woodpecker cavities. Totals of 195 (1994) and 190 (1995) red-cockaded woodpecker cavities were examined at least three times each year. Trappability of southern flying squirrels in Sherman traps was significantly greater in 1995 (1.18%; 22,384 trap nights) than in 1994 (0.42%; 20,384 trap nights), and capture rate of southern flying squirrels in cavities was significantly greater in 1994 (22.7%; 502 cavity inspections) than in 1995 (10.8%; 555 cavity inspections). However, more southern flying squirrels were captured per cavity inspection than per Sherman trap night in both years. Male southern flying squirrels were more likely to be captured from cavities than in Sherman traps in 1994, but not in 1995. Both male and female juveniles were more likely to be captured in cavities than in traps in both years. In 1994 males in reproductive condition were more likely to be captured in cavities than in traps and in 1995 we captured significantly more reproductive females in cavities than in traps. Our data suggest that population estimates based solely on one trapping method may not represent true population size or structure of southern flying squirrels.

  1. [Differential expression of DTSsa4 Tc1-like transposons in closely related populations of Baikal ciscoes].

    Science.gov (United States)

    Bychenko, O S; Sukhanova, L V; Azhikina, T L; Sverdlov, E D

    2009-01-01

    Two representatives of Baikal ciscoes - lake cisco and omul - diverged from a common ancestor as recently as 10-20 thousand years ago. We have found an increasing expression level of DTSsa4 Tc1-like DNA transposons in cisco and omul brains. The mapping of the sequences of these transposons from Salmo salar and Danio rerio genomes has shown that in some cases, these transposons are located in the 5' and 3' regions, as well as in the promoter regions of various genes. Probably, Tc1-like transposons affect the activity of neighboring genes, providing the adaptive divergence of the cisco population.

  2. Assortative mating and differential male mating success in an ash hybrid zone population

    Directory of Open Access Journals (Sweden)

    Frascaria-Lacoste Nathalie

    2006-11-01

    Full Text Available Abstract Background The structure and evolution of hybrid zones depend mainly on the relative importance of dispersal and local adaptation, and on the strength of assortative mating. Here, we study the influence of dispersal, temporal isolation, variability in phenotypic traits and parasite attacks on the male mating success of two parental species and hybrids by real-time pollen flow analysis. We focus on a hybrid zone population between the two closely related ash species Fraxinus excelsior L. (common ash and F. angustifolia Vahl (narrow-leaved ash, which is composed of individuals of the two species and several hybrid types. This population is structured by flowering time: the F. excelsior individuals flower later than the F. angustifolia individuals, and the hybrid types flower in-between. Hybrids are scattered throughout the population, suggesting favorable conditions for their local adaptation. We estimate jointly the best-fitting dispersal kernel, the differences in male fecundity due to variation in phenotypic traits and level of parasite attack, and the strength of assortative mating due to differences in flowering phenology. In addition, we assess the effect of accounting for genotyping error on these estimations. Results We detected a very high pollen immigration rate and a fat-tailed dispersal kernel, counter-balanced by slight phenological assortative mating and short-distance pollen dispersal. Early intermediate flowering hybrids, which had the highest male mating success, showed optimal sex allocation and increased selfing rates. We detected asymmetry of gene flow, with early flowering trees participating more as pollen donors than late flowering trees. Conclusion This study provides striking evidence that long-distance gene flow alone is not sufficient to counter-act the effects of assortative mating and selfing. Phenological assortative mating and short-distance dispersal can create temporal and spatial structuring that appears

  3. Differentiation of Soil Fauna Populations in Conventional Tillage and No—Tillage Red Soil Ecosystems

    Institute of Scientific and Technical Information of China (English)

    HUFENG; LIHUIXIN; 等

    1997-01-01

    In a field experiment ,the popultions of major soil fauna groups including earthworms,enchytraeids,arthropods and nematodes were examined in conventional tillage(CT) and no-tillage(NT) red soil ecosystems to evaluate their responses to tillage disturbance.Earthworms,macro- and micro-arthropods were stimulated under NT with earthworms showing the highest population increase by four times ,while enchytraeids and nematodes favored CT system predicting certain adaptability of these animals to plow-disturbed soil envi-ronment ,On the basis of relative response index it was found that soil fauna was more sensitive to tillage than soil resource base(C and N pools) and microflora.The population structure of soil fauna was also affected by tillage treatments.Analysis on nematode trophic groups showed that bacteria-feeding and plant parasitic nematodes were more abundant in CT soil whereas the proportions of fungivores and onmivore-predators increased in NT soil.Possible reasons for the differentiaion in both size and structure of the fauna populaion were discussed and the ecological significance involved in these changes was emphasized.

  4. Diets of differentially processed wheat alter ruminal fermentation parameters and microbial populations in beef cattle.

    Science.gov (United States)

    Jiang, S Z; Yang, Z B; Yang, W R; Li, Z; Zhang, C Y; Liu, X M; Wan, F C

    2015-11-01

    The influences of differently processed wheat products on rumen fermentation, microbial populations, and serum biochemistry profiles in beef cattle were studied. Four ruminally cannulated Limousin × Luxi beef cattle (400 ± 10 kg) were used in the experiment with a 4 × 4 Latin square design. The experimental diets contained (on a DM basis) 60% corn silage as a forage source and 40% concentrate with 4 differently processed wheat products (extruded, pulverized, crushed, and rolled wheat). Concentrations of ruminal NH-N and microbial protein (MCP) in cattle fed crushed and rolled wheat were greater ( cattle fed pulverized and extruded wheat. Ruminal concentrations of total VFA and acetate and the ratio of acetate to propionate decreased ( cattle fed extruded wheat had the lowest concentrations of total VFA and acetate among all treatments. The relative abundance of , , ciliated protozoa, and was lower in cattle fed the pulverized wheat diet than in the other 3 diets ( cattle fed extruded wheat compared with cattle fed crushed and rolled wheat ( 0.05). Our findings suggest that the method of wheat processing could have a significant effect on ruminal fermentation parameters and microbial populations in beef cattle and that crushed and rolled processing is better in terms of ruminal NH-N and MCP content, acetate-to-propionate ratio, and relative abundance of rumen microorganisms.

  5. Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo.

    Science.gov (United States)

    Zhang, Y; Vankan, D; Zhang, Y; Barker, J S F

    2011-08-01

    Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral Bubalus arnee (possibly with some river-type introgression). Relationships among the swamp populations (D(A) genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo. PMID:21749419

  6. Application of ILO classification to a population without industrial exposure: findings to be differentiated from pneumoconiosis

    International Nuclear Information System (INIS)

    The International Labour Office (ILO) classification for radiographs of pneumoconiosis is a standard means of assessing the presence or absence of pneumoconiosis in workers exposed to mineral dusts. Using this classification, 200 admission chest radiographs were reviewed on hospitalized patients in an urban university medical center to determine the prevalence and possible significance of ''small opacities'' in a population without known industrial exposure. Seventy-one men and 129 women were screened with the mean age of 44.2 years (range, 15-84). Thirty-six (18%) of the 200 patients had small opacities at profusion level 1/0 or greater, and this constituted the ''positive radiographs'' group. Twenty-two patients (11%) with positive radiographs had no documentable dust exposure or other specific medical etiology that would explain the presence of their lung opacities. The high prevalence of small opacities in ''normal'' older individuals has important implications in the assessment of patients with suspected pneumoconiosis

  7. Larval Environment Alters Amphibian Immune Defenses Differentially across Life Stages and Populations.

    Directory of Open Access Journals (Sweden)

    Katherine L Krynak

    Full Text Available Recent global declines, extirpations and extinctions of wildlife caused by newly emergent diseases highlight the need to improve our knowledge of common environmental factors that affect the strength of immune defense traits. To achieve this goal, we examined the influence of acidification and shading of the larval environment on amphibian skin-associated innate immune defense traits, pre and post-metamorphosis, across two populations of American Bullfrogs (Rana catesbeiana, a species known for its wide-ranging environmental tolerance and introduced global distribution. We assessed treatment effects on 1 skin-associated microbial communities and 2 post-metamorphic antimicrobial peptide (AMP production and 3 AMP bioactivity against the fungal pathogen Batrachochytrium dendrobatidis (Bd. While habitat acidification did not affect survival, time to metamorphosis or juvenile mass, we found that a change in average pH from 7 to 6 caused a significant shift in the larval skin microbial community, an effect which disappeared after metamorphosis. Additionally, we found shifts in skin-associated microbial communities across life stages suggesting they are affected by the physiological or ecological changes associated with amphibian metamorphosis. Moreover, we found that post-metamorphic AMP production and bioactivity were significantly affected by the interactions between pH and shade treatments and interactive effects differed across populations. In contrast, there were no significant interactions between treatments on post-metamorphic microbial community structure suggesting that variation in AMPs did not affect microbial community structure within our study. Our findings indicate that commonly encountered variation in the larval environment (i.e. pond pH and degree of shading can have both immediate and long-term effects on the amphibian innate immune defense traits. Our work suggests that the susceptibility of amphibians to emerging diseases could be

  8. Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus in New York City

    Directory of Open Access Journals (Sweden)

    Jason Munshi-South

    2013-04-01

    Full Text Available Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five remnant urban populations of dusky salamanders in NYC. These genetic measures provide information on isolation, prevalence of inbreeding, long-term prospects for population persistence, and potential for evolutionary responses to future environmental change. All populations were genetically differentiated from each other, and the most isolated populations in Manhattan have maintained very little genetic variation (i.e. <20% heterozygosity. A majority of the populations also exhibited evidence of genetic bottlenecks. These findings contrast with published estimates of high genetic variation within and lack of structure between populations of other desmognathine salamanders sampled over similar or larger spatial scales. Declines in genetic variation likely resulted from population extirpations and the degradation of stream and terrestrial paths for dispersal in NYC. Loss of genetic variability in populations isolated by human development may be an underappreciated cause and/or consequence of the decline of this species in urbanized areas of the northeast USA.

  9. The bottleneck effect in three-dimensional turbulence simulations

    CERN Document Server

    Dobler, W; Yousef, T A; Brandenburg, A; Dobler, Wolfgang; Haugen, Nils Erland L.; Yousef, Tarek A.; Brandenburg, Axel

    2003-01-01

    At numerical resolutions around $512^3$ and above, three-dimensional energy spectra from turbulence simulations begin to show noticeably shallower spectra than $k^{-5/3}$ near the Kolmogorov dissipation wavenumber (`bottleneck effect'). This effect is shown to be significantly weaker in one-dimensional spectra like those obtained in wind tunnel turbulence. The difference can be understood in terms of the transformation between one-dimensional and three-dimensional energy spectra under the assumption that the turbulent velocity field is isotropic. Transversal and longitudinal energy spectra are similar and can both accurately be computed from the full three-dimensional spectra.

  10. Bottlenecks to vibrational energy flow in OCS: Structures and mechanisms

    CERN Document Server

    Paškauskas, R; Uzer, T

    2008-01-01

    Finding the causes for the nonstatistical vibrational energy relaxation in the planar carbonyl sulfide (OCS) molecule is a longstanding problem in chemical physics: Not only is the relaxation incomplete long past the predicted statistical relaxation time, but it also consists of a sequence of abrupt transitions between long-lived regions of localized energy modes. We report on the phase space bottlenecks responsible for this slow and uneven vibrational energy flow in this Hamiltonian system with three degrees of freedom. They belong to a particular class of two-dimensional invariant tori which are organized around elliptic periodic orbits. We relate the trapping and transition mechanisms with the linear stability of these structures.

  11. Give or take? Rewards vs. Charges for a Congested Bottleneck

    OpenAIRE

    Rouwendal, Jan; Erik T. Verhoef; Knockaert, Jasper

    2010-01-01

    This discussion paper resulted in a publication in 'Regional Science and Urban Economics', 42(1-2), 166-76.This paper analyzes the possibilities to relieve congestion using rewards instead of taxes, as well as combinations of rewards and taxes. The model considers a Vickrey-ADL model of bottleneck congestion with endogenous scheduling. With inelastic demand, a fine (time-varying) reward is equivalent to a fine toll, and to a continuum of combinations of time-varying tolls and rewards (includi...

  12. A lexisearch Algorithm for the Bottleneck Traveling Salesman Problem

    Directory of Open Access Journals (Sweden)

    Zakir H. Ahmed

    2010-02-01

    Full Text Available The Bottleneck Traveling Salesman Problem (BTSP is a variation of the well-known Traveling Salesman Problem in which the objective is to minimize the maximum lap (arc length in the tour of the salesman. In this paper, a lexisearch algorithm using adjacency representation for a tour has been developed for obtaining exact optimal solution to the problem. Then a comparative study has been carried out to show the efficiency of the algorithm as against existing exact algorithm for some randomly generated and TSPLIB instances of different sizes.

  13. A cellular automaton model for a bridge traffic bottleneck

    Institute of Scientific and Technical Information of China (English)

    Shifa Xiao; Lingjiang Kong; Muren Liu

    2005-01-01

    A cellular automaton (CA) model is proposed in this paper to analyze a bridge traffic bottleneck. The simulation results with this model show that there are several phase transitions in the traffic average density, velocity and flow for each lane under a periodic boundary condition. An unstable phase in the traffic average density and velocity for the upstream and downstream lanes of the bridge is shown in a range of initial traffic densities. The critical points of the phase transitions and the phenomenon of the unstable phase found in the simulation are also explained with the mean-field theory.

  14. OPTIMISATION OF JOB SHOP SCHEDULING USING SHIFTING BOTTLENECK TECHNIQUE

    Directory of Open Access Journals (Sweden)

    Katuru Phani Raja Kumar

    2013-07-01

    Full Text Available In manufacturing system the problem of scheduling machines is a difficult task to reach the due date of the productivity. The Job Shop Scheduling have been solved by different algorithms and methods based on the sequence operation constraints and processing times for small size problems. The JSSP with m machines and n jobs is represented to determine an optimal solution by using the shortest processing time technique and Gantt chart is drawn to visually represent the total makespan. The shifting bottleneck method has been used to reduce the total flow time of the JSSP and arrive at an optimal solution.

  15. The Plasmodium bottleneck: malaria parasite losses in the mosquito vector

    Directory of Open Access Journals (Sweden)

    Ryan C Smith

    2014-08-01

    Full Text Available Nearly one million people are killed every year by the malaria parasite Plasmodium. Although the disease-causing forms of the parasite exist only in the human blood, mosquitoes of the genus Anopheles are the obligate vector for transmission. Here, we review the parasite life cycle in the vector and highlight the human and mosquito contributions that limit malaria parasite development in the mosquito host. We address parasite killing in its mosquito host and bottlenecks in parasite numbers that might guide intervention strategies to prevent transmission.

  16. Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

    Directory of Open Access Journals (Sweden)

    Brunner Sylvia

    2008-05-01

    Full Text Available Abstract Background Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation. Results We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation. Conclusion Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

  17. The differential effects of increasing frequency and magnitude of extreme events on coral populations.

    Science.gov (United States)

    Fabina, Nicholas S; Baskett, Marissa L; Gross, Kevin

    2015-09-01

    Extreme events, which have profound ecological consequences, are changing in both frequency and magnitude with climate change. Because extreme temperatures induce coral bleaching, we can explore the relative impacts of changes in frequency and magnitude of high temperature events on coral reefs. Here, we combined climate projections and a dynamic population model to determine how changing bleaching regimes influence coral persistence. We additionally explored how coral traits and competition with macroalgae mediate changes in bleaching regimes. Our results predict that severe bleaching events reduce coral persistence more than frequent bleaching. Corals with low adult mortality and high growth rates are successful when bleaching is mild, but bleaching resistance is necessary to persist when bleaching is severe, regardless of frequency. The existence of macroalgae-dominated stable states reduces coral persistence and changes the relative importance of coral traits. Building on previous studies, our results predict that management efforts may need to prioritize protection of "weaker" corals with high adult mortality when bleaching is mild, and protection of "stronger" corals with high bleaching resistance when bleaching is severe. In summary, future reef projections and conservation targets depend on both local bleaching regimes and biodiversity. PMID:26552262

  18. The Effects of Juvenile Competitive Bottleneck on Dynamic Behavior%幼年竞争瓶颈对动力学行为的影响

    Institute of Scientific and Technical Information of China (English)

    唐光耀

    2011-01-01

    The effect of juvenile competitive bottlenecks on population dynamics is investigated by formulating food web models with a nonlinear maturation rate.The food web system consists of a resource (R),an intermediate consumer (N) and a predator (P).Our results show,with weak bottlenecks,that a juvenile bottleneck in the predator's life history has a larger impact than a bottleneck in the consumer.In the food web model with bottleneck for the predator,there are two possible internal steady states,and the system can exhibit consumer-predator equilibrium and consumer equilibrium as two alternative stable states,as well as the consumer equilibrium and predator equilibrium as two alternative stable states.No bistable phenomenon induced by bottleneck can be detected,and nothing new happens in system with consumer bottlenecks.Further,we show that a bottleneck can change the net effect of the intermediate consumer on predator from facilitation to inhibition or from inhibition to facilitation,which case occurs depends on both the choice of bottleneck and the initial states of systems.%通过建立具有非线性成熟率的食物网模型研究了幼年竞争瓶颈对种群动力学行为的影响,结论显示当竞争瓶颈比较弱的时,捕食者生活史中的幼年瓶颈对系统的影响要大于成年.模型存在两种可能的共存态或双稳定性,即消费者-捕食者和消费者平衡态共存,但是瓶颈不能诱导系统的双稳定性.进一步研究说明了选择不同的瓶颈或初始条件,瓶颈能够改变次级消费者对捕食者的净影响.

  19. Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure

    Science.gov (United States)

    Echelle, A.A.; Hackler, J.C.; Lack, Justin B.; Ballard, S. R.; Roman, J.; Fox, S. F.; Leslie,, David M., Jr.; Van Den Bussche, Ronald A.

    2010-01-01

    A previous mtDNA study indicated that female-mediated gene flow was extremely rare among alligator snapping turtle populations in different drainages of the Gulf of Mexico. In this study, we used variation at seven microsatellite DNA loci to assess the possibility of male-mediated gene flow, we augmented the mtDNA survey with additional sampling of the large Mississippi River System, and we evaluated the hypothesis that the consistently low within-population mtDNA diversity reflects past population bottlenecks. The results show that dispersal between drainages of the Gulf of Mexico is rare (F STmsat  = 0.43, ΦSTmtDNA = 0.98). Past range-wide bottlenecks are indicated by several genetic signals, including low diversity for microsatellites (1.1–3.9 alleles/locus; H e = 0.06–0.53) and mtDNA (h = 0.00 for most drainages; π = 0.000–0.001). Microsatellite data reinforce the conclusion from mtDNA that the Suwannee River population might eventually be recognized as a distinct taxonomic unit. It was the only population showing fixation or near fixation for otherwise rare microsatellite alleles. Six evolutionarily significant units are recommended on the basis of reciprocal mtDNA monophyly and high levels of microsatellite DNA divergence.

  20. A bottleneck model of set-specific capture.

    Directory of Open Access Journals (Sweden)

    Katherine Sledge Moore

    Full Text Available Set-specific contingent attentional capture is a particularly strong form of capture that occurs when multiple attentional sets guide visual search (e.g., "search for green letters" and "search for orange letters". In this type of capture, a potential target that matches one attentional set (e.g. a green stimulus impairs the ability to identify a temporally proximal target that matches another attentional set (e.g. an orange stimulus. In the present study, we investigated whether set-specific capture stems from a bottleneck in working memory or from a depletion of limited resources that are distributed across multiple attentional sets. In each trial, participants searched a rapid serial visual presentation (RSVP stream for up to three target letters (T1-T3 that could appear in any of three target colors (orange, green, or lavender. The most revealing findings came from trials in which T1 and T2 matched different attentional sets and were both identified. In these trials, T3 accuracy was lower when it did not match T1's set than when it did match, but only when participants failed to identify T2. These findings support a bottleneck model of set-specific capture in which a limited-capacity mechanism in working memory enhances only one attentional set at a time, rather than a resource model in which processing capacity is simultaneously distributed across multiple attentional sets.

  1. A bottleneck model of set-specific capture.

    Science.gov (United States)

    Moore, Katherine Sledge; Weissman, Daniel H

    2014-01-01

    Set-specific contingent attentional capture is a particularly strong form of capture that occurs when multiple attentional sets guide visual search (e.g., "search for green letters" and "search for orange letters"). In this type of capture, a potential target that matches one attentional set (e.g. a green stimulus) impairs the ability to identify a temporally proximal target that matches another attentional set (e.g. an orange stimulus). In the present study, we investigated whether set-specific capture stems from a bottleneck in working memory or from a depletion of limited resources that are distributed across multiple attentional sets. In each trial, participants searched a rapid serial visual presentation (RSVP) stream for up to three target letters (T1-T3) that could appear in any of three target colors (orange, green, or lavender). The most revealing findings came from trials in which T1 and T2 matched different attentional sets and were both identified. In these trials, T3 accuracy was lower when it did not match T1's set than when it did match, but only when participants failed to identify T2. These findings support a bottleneck model of set-specific capture in which a limited-capacity mechanism in working memory enhances only one attentional set at a time, rather than a resource model in which processing capacity is simultaneously distributed across multiple attentional sets.

  2. Whole-body MRI in generalized cystic lymphangiomatosis in the pediatric population: diagnosis, differential diagnoses, and follow-up

    Energy Technology Data Exchange (ETDEWEB)

    Herruela-Suffee, Cecile; Warin, Mathilde; Castier-Amouyel, Melody; Dallery, Florine; Bonnaire, Bruno; Constans, Jean-Marc [CHU Amiens-Picardie, Service de Radiologie, Amiens Cedex 1 (France)

    2016-02-15

    Generalized cystic lymphangiomatosis is a particularly rare disease with variable involvement of skeletal and extraskeletal sites. The key role of imaging in the diagnosis of this disease is no longer in doubt. The aim of our study was to demonstrate the contribution of whole-body magnetic resonance imaging (WB-MRI) at the diagnostic stage and during the follow-up in the pediatric population. Three children were included from 2008. The inclusion criteria were radiological images (conventional radiographs, computed tomography, and MRI) compatible with histological confirmation. Each child included received WB-MRI at the diagnosis stage and during follow-up. WB-MRI detected multiple hypointense T1 and hyperintense T2-STIR cystic bony lesions. One unnoticed mass in the retroperitoneum on computed tomography was easily detected by MRI. Mediastinal involvement was observed in one asymptomatic case. Histology was contributory in all cases. Preventive intramedullary nailings was done in one case. Follow-up WB-MRI detected new asymptomatic lesions in all cases. One child presented a third episode of lymphangitis of the right thigh during follow-up. Due to its high sensitivity to diagnose, ability to eliminate differential diagnoses and make exhaustive lesions assessment, and its non-radiating character for long-term follow-up, WB-MRI is highly recommended for generalized cystic lymphangiomatosis in the pediatric population. (orig.)

  3. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

    Science.gov (United States)

    Tully, Damien C.; Ogilvie, Colin B.; Batorsky, Rebecca E.; Bean, David J.; Power, Karen A.; Ghebremichael, Musie; Bedard, Hunter E.; Gladden, Adrianne D.; Seese, Aaron M.; Amero, Molly A.; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B.; Tinsley, Jake; Lennon, Niall J.; Henn, Matthew R.; Brumme, Zabrina L.; Norris, Philip J.; Rosenberg, Eric S.; Mayer, Kenneth H.; Jessen, Heiko; Kosakovsky Pond, Sergei L.; Walker, Bruce D.; Altfeld, Marcus; Carlson, Jonathan M.; Allen, Todd M.

    2016-01-01

    Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic “signatures” within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission. PMID:27163788

  4. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Directory of Open Access Journals (Sweden)

    Damien C Tully

    2016-05-01

    Full Text Available Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU, we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

  5. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Science.gov (United States)

    Tully, Damien C; Ogilvie, Colin B; Batorsky, Rebecca E; Bean, David J; Power, Karen A; Ghebremichael, Musie; Bedard, Hunter E; Gladden, Adrianne D; Seese, Aaron M; Amero, Molly A; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B; Tinsley, Jake; Lennon, Niall J; Henn, Matthew R; Brumme, Zabrina L; Norris, Philip J; Rosenberg, Eric S; Mayer, Kenneth H; Jessen, Heiko; Kosakovsky Pond, Sergei L; Walker, Bruce D; Altfeld, Marcus; Carlson, Jonathan M; Allen, Todd M

    2016-05-01

    Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission. PMID:27163788

  6. Relationship between hierarchic - spatial differentiation of social structure and population size of municipalities in turkey: Evidence from the election case of local administration in 2004

    Directory of Open Access Journals (Sweden)

    Murat Çiftçi

    2011-07-01

    Full Text Available Turkey, whose population is young and dynamic, is a country where social change has a high acceleration. This circumstance has led to a spatial heterogeneity of social structure in the scale of campuses. Almost all the municipalities differ significantly from each other. In results of statistical applications, it was possible to conclude that there is a relationship between spatial differentiation of social structure indicators (PDI, PIDI and population sizes in municipalities. This relationship also supports that there was a differentiation of graded spatial social structure among municipalities in the Turkey of 2004. It is possible to make contact with this to the spatial differentiation that moves in parallel with population size and is in transition degree from a community to a society.

  7. Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina.

    Science.gov (United States)

    Anello, M; Daverio, M S; Romero, S R; Rigalt, F; Silbestro, M B; Vidal-Rioja, L; Di Rocco, F

    2016-02-01

    The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.

  8. Traffic Flow States in a Freeway with Bottleneck

    Institute of Scientific and Technical Information of China (English)

    PENG Zi-Hui; SUN Gang; ZHU Jing-Yi

    2009-01-01

    The system of mixture of single lane and double lane is studied by a cellular automata model, which is developed by us based on the Nagel and Schreckenberg's models. We justify that the model can reach a stable states quickly. The density distributions of the stable state is presented for several cases, which illustrate the manner of the congestion. The relationship between the outflow rate and the total number of vehicles and that between the outflow rate and the density just before the bottleneck are both given. Comparing with the relationship that occurring in the granular flow, we conclude that the transition from the free traffic flow to the congested traffic flow can also be attributed to the abrupt variation through unstable flow state, which can naturally explain the discontinuities and the complex time variation behavior observed in the traffic flow experiments.

  9. Queuing model of a traffic bottleneck with bimodal arrival rate

    Science.gov (United States)

    Woelki, Marko

    2016-06-01

    This paper revisits the problem of tuning the density in a traffic bottleneck by reduction of the arrival rate when the queue length exceeds a certain threshold, studied recently for variants of totally asymmetric simple exclusion process (TASEP) and Burgers equation. In the present approach, a simple finite queuing system is considered and its contrasting “phase diagram” is derived. One can observe one jammed region, one low-density region and one region where the queue length is equilibrated around the threshold. Despite the simplicity of the model the physics is in accordance with the previous approach: The density is tuned at the threshold if the exit rate lies in between the two arrival rates.

  10. New ideas about genetic differentiation of Chilo suppressalis (Lepidoptera: Pyralidae) populations in China based on the mtDNA cytochrome b gene.

    Science.gov (United States)

    Tang, Xiao-Tian; Zheng, Fu-Shan; Lu, Ming-Xing; Du, Yu-Zhou

    2016-01-01

    The striped stem borer, Chilo suppressalis (Walker), is an important pest of rice in China and other parts of the world. To further explore the population genetic structure and genetic differentiation of C. suppressalis populations found on rice in China, we amplified 432 bp fragments of the cytochrome b (cyt b) gene for 44 C. suppressalis populations. Nineteen variable sites in the mtDNA gene were observed, and 16 haplotypes were identified. Nucleotide diversity (π) and haplotype diversity (h) ranged from 0.00274 to 0.00786 and 0.72297 to 0.87604, respectively, while genetic structure analysis found significant genetic differentiation to be present among the five regions in China - northern China (NC), northeastern China (NEC), central China (CC), southern China (SC) and southwestern China (SWC) - where C. suppresalis was collected. In addition, molecular variance (AMOVA) showed that a relatively high proportion (57.6%) of the total genetic variance was attributable to variation within the populations. N(m) and F(ST) analyses suggested that the differentiation was not significantly different between NEC and NC, CC and SC, and SC and SWC regions, but was significant between NEC and CC, SC and SWC regions, corresponding well with the geographical distribution of the sampled populations. Phylogenetic analysis divided the populations into two indistinct clades: a NEC-NC-CC clade and a CC-SC-SWC clade, while CC region acted as a transition zone between north and south China, a finding different from previous work.

  11. Automatic Differentiation Variational Inference

    OpenAIRE

    Kucukelbir, Alp; Tran, Dustin; Ranganath, Rajesh; Gelman, Andrew; Blei, David M.

    2016-01-01

    Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist on...

  12. Genetic variation of mini- and microsatellites and a clonal structure in Enterocytozoon bieneusi population in foxes and raccoon dogs and population differentiation of the parasite between fur animals and humans.

    Science.gov (United States)

    Li, Wei; Wan, Qiang; Yu, Qinlei; Yang, Yuqi; Tao, Wei; Jiang, Yanxue; Xiao, Lihua

    2016-07-01

    Enterocytozoon bieneusi is an obligate intracellular protozoan parasite that infects a wide range of mammal hosts and birds. Previous genotypic surveys were limited to measure the polymorphisms at the ribosomal internal transcribed spacer (ITS) that evolved slowly. Data on population structure are available only on E. bieneusi isolates from primates. This study explored the genotypic and phylogenetic characteristics of four mini- and microsatellites and performed a population genetic analysis in 39 E. bieneusi isolates of potentially zoonotic ITS genotype D from farmed foxes and raccoon dogs in China. Sequence polymorphisms facilitated determination of six, two, four, and five genotypes at markers MS1, MS3, MS4, and MS7, respectively. Patterns of phylogeny revealed different levels of diversity within and among the genetic markers. Clear genotypic and phylogenetic divergences between E. bieneusi isolates of ITS genotype D from fur animals and humans were observed at individual markers. Complete linkage disequilibrium and very limited recombination in subsequent population genetic analysis supported a clonal structure for E. bieneusi population from fur animals (FID). Phylogenetic analysis, genetic network, and measures of F ST and gene flow demonstrated population differentiation of FID from two known human E. bieneusi populations HID (with a clonal structure) and HIA (with an epidemic structure). The data indicated an ideal resolving power of MLST compared to the previously widely used ITS genotyping and confirmed the clonal nature and population differentiation of E. bieneusi in various hosts. PMID:27095568

  13. Adaptation in isolated populations: when does it happen and when can we tell?

    Science.gov (United States)

    Crisci, Jessica L; Dean, Matthew D; Ralph, Peter

    2016-08-01

    Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here, we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affect the ability of outlier scans for selection to identify adaptive alleles using both single-site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur and yet the adaptive variants are most likely to derive from a single ancestor (a 'hard' selective sweep); in this zone, four commonly used statistics detect selection with high power. Real-world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole-genome sequencing of differentiated populations. PMID:27297514

  14. Bottleneck Analysis of the Minimum Coat Problem for the Generalized Network Based on Augmented Forest Structure

    Institute of Scientific and Technical Information of China (English)

    江永亨; 王军; 等

    2003-01-01

    The bottleneck analysis of the minimum coat problem for the generalized netwok(MCPGN) is discussed.The analysis is based on the network simplex algorithm,which gains negative cost graphs by constructing augmented forest structure,then augments flows on the negative cost graphs until the optimal revolution is gained Bottleneck structure is presented after analyzing the augmented forest structure.The negative cost augmented graphs are constructed with the bottleneck structure.The arcs that block the negative cost augmented graph are the elements of the bottleneck.The bottleneck analysis for the generalized circulation problem,the minimum circulation problem and the circulation problem are discussed respectively as the basal problems,then that for MCPGN is achieved.An example is presented at the end.

  15. Bottlenecks of motion processing during a visual glance: the leaky flask model.

    Directory of Open Access Journals (Sweden)

    Haluk Öğmen

    Full Text Available Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic memory, visual short-term memory (VSTM, and long-term memory (LTM. It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing.

  16. Inducible nitric oxide synthase polymorphism is associated with the increased risk of differentiated gastric cancer in a Japanese population

    Institute of Scientific and Technical Information of China (English)

    Yasuyuki Goto; Takafumi Ando; Mariko Naito; Hidemi Goto; Nobuyuki Hamajima

    2006-01-01

    AIM: To examine the association of inducible nitric oxide synthase (iNOS) C150T polymorphism with gastric cancer, as well as with gastric atrophy and H pylori seropositivity.METHODS: A single nucleotide polymorphism of iNOS C150T was examined for 454 Japanese health checkup examinees (126 males and 328 females) aged 35 to 85 years without a history of cancer and 202 gastric cancer patients (134 males and 68 females) aged 33 to 94 years with pathologically confirmed diagnosis of gastric adenocarcinoma.RESULTS: The iNOS C150T polymorphism was not associated with gastric atrophy or with H pylori seropositivity. The odds ratio (OR) of the C/T +T/T for gastric cancer was increased without statistical significance (OR=1.19, 95% confidence interval (CI):0.68-2.08). In the differentiated subgroup (n = 113),however, the OR of the C/T genotype for gastric cancer was significant (OR = 2.02, 95% CI: 1.04-3.92) relative to the C/C genotype. In addition, considering the location of gastric cancer (n = 105), there were significant differences between the controls and non-cardia group with the OR of 2.13 (95% CI: 1.08-4.18) for C/T and 1.94(95% CI: 1.00-3.78) for C/T + T/T.CONCLUSION: The iNOS C150T polymorphism is associated with the risk of H pylori-related gastric cancer in a Japanese population. This polymorphism may play an important role in increasing the risk of gastric cancer in Asian countires with the highest rates of gastric cancer.

  17. Unravelling the differential functions and regulation of striatal neuron sub-populations in motor control, reward and motivational processes

    Directory of Open Access Journals (Sweden)

    Sabrina eEna

    2011-07-01

    Full Text Available The striatum, the major input structure of the basal ganglia, is critically involved in motor control and learning of habits and skills, and is also involved in motivational and reward processes. The dorsal striatum, caudate-putamen, is primarily implicated in motor functions whereas the ventral striatum, the nucleus accumbens, is essential for motivation and drug reinforcement. Severe basal ganglia dysfunction occurs in movement disorders as Parkinson’s and Huntington’s disease, and in psychiatric disorders such as schizophrenia and drug addiction. The striatum is essentially composed of GABAergic medium-sized spiny neurons (MSNs that are output neurons giving rise to the so-called direct and indirect pathways and are targets of the cerebral cortex and mesencephalic dopaminergic neurons. Although the involvement of striatal sub-areas in motor control and motivation has been thoroughly characterized, major issues remained concerning the specific and respective functions of the two MSNs sub-populations, D2R-striatopallidal (dopamine D2 receptor-positive and D1R-striatonigral (dopamine D1 receptor-positive neurons, as well as their specific regulation. Here, we review recent advances that gave new insight in the understanding of the differential roles of striatopallidal and striatonigral neurons in the basal ganglia circuit. We discuss innovative techniques developed in the last decade which allowed a much precise evaluation of molecular pathways implicated in motivational processes and functional roles of striatopallidal and striatonigral neurons in motor control and in the establishment of reward-associated behaviour.

  18. Childhood osteomyelitis-incidence and differentiation from other acute onset musculoskeletal features in a population-based study

    Directory of Open Access Journals (Sweden)

    Reiseter Tor

    2008-10-01

    Full Text Available Abstract Background Osteomyelitis can be difficult to diagnose and there has previously not been a prospective approach to identify all children in a defined geographic area. The aim of this study was to assess the annual incidence of osteomyelitis in children, describe the patient and disease characteristics in those with acute ( Methods In a population-based Norwegian study physicians were asked to refer all children with suspected osteomyelitis. Children with osteomyelitis received follow-up at six weeks, six months and thereafter as long as clinically needed. Results The total annual incidence rate of osteomyelitis was 13 per 100 000 (acute osteomyelitis 8 and subacute osteomyelitis 5 per 100 000. The incidence was higher in patients under the age of 3 than in older children (OR 2.9, 95%: CI 2.3–3.7. The incidence of non-vertebral osteomyelitis was higher than the incidence of vertebral osteomyelitis (10 vs. 3 per 100 000; p = .002. Vertebral osteomyelitis was more frequent in girls than in boys (OR 7.0, 95%: CI 3.3–14.7. ESR ≥ 40 mm/hr had the highest positive predictive laboratory value to identify osteomyelitis patients at 26% and MRI had a positive predictive value of 85%. Long-bone infection was found in 16 (43% patients. ESR, CRP, white blood cell count, neutrophils and platelet count were higher for patients with acute osteomyelitis than for patients with subacute osteomyelitis. Subacute findings on MRI and doctor's delay were more common in subacute osteomyelitis than in acute osteomyelitis patients. Blood culture was positive in 26% of the acute osteomyelitis patients and was negative in all the subacute osteomyelitis patients. Conclusion The annual incidence of osteomyelitis in Norway remains high. ESR values and MRI scan may help to identify osteomyelitis patients and differentiate acute and subacute osteomyelitis.

  19. Genetic differentiation of hypothalamus parentally biased transcripts in populations of the house mouse implicate the Prader-Willi syndrome imprinted region as a possible source of behavioral divergence.

    Science.gov (United States)

    Lorenc, Anna; Linnenbrink, Miriam; Montero, Inka; Schilhabel, Markus B; Tautz, Diethard

    2014-12-01

    Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the Western house mouse (Mus musculus domesticus). Here, we ask whether this could be mediated by genomically imprinted transcripts that are subject to fast differentiation between these populations. We focus on three organs that are of special relevance for mate choice and behavior: The vomeronasal organ (VNO), the hypothalamus, and the liver. To first identify candidate transcripts at a genome-wide scale, we used reciprocal crosses between M. m. domesticus and M. m. musculus inbred strains and RNA sequencing of the respective tissues. Using a false discovery cutoff derived from mock reciprocal cross comparisons, we find a total of 66 imprinted transcripts, 13 of which have previously not been described as imprinted. The largest number of imprinted transcripts were found in the hypothalamus; fewer were found in the VNO, and the least were found in the liver. To assess molecular differentiation and imprinting in the wild-derived M. m. domesticus populations, we sequenced the RNA of the hypothalamus from individuals of these populations. This confirmed the presence of the above identified transcripts also in wild populations and allowed us to search for those that show a high genetic differentiation between these populations. Our results identify the Ube3a-Snrpn imprinted region on chromosome 7 as a region that encompasses the largest number of previously not described transcripts with paternal expression bias, several of which are at the same time highly differentiated. For four of these, we confirmed their imprinting status via single nucleotide polymorphism-specific pyrosequencing assays with RNA from reciprocal crosses. In addition, we find the

  20. Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions.

    Science.gov (United States)

    Volis, S; Ormanbekova, D; Shulgina, I

    2016-04-01

    Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean. In a multiyear reciprocal transplant experiment, the plants of desert and Mediterranean origin demonstrated home advantage, and population differentiation in several phenotypic traits related to reproduction exceeded neutral predictions, as determined by comparisons of QST values with theoretical FST distributions. Thus, variation in these traits likely resulted from local adaptation to desert and Mediterranean environments. The two separate common garden experiments conducted with different experimental design revealed that two population comparisons, in contrast to multi-population comparisons, are likely to detect population differences in virtually every trait, but many of these differences reflect effects of local rather than regional environment. We detected a general reduction in neutral (SSR) genetic variation but not in adaptive quantitative trait variation in peripheral desert as compared with Mediterranean core populations. On the other hand, the molecular data indicated intensive gene flow from the Mediterranean core towards desert periphery. Although species range position in our study (edge vs. interior) was confounded with climate (desert vs. Mediterranean), the results suggest that the gene flow from the species core does not have negative consequences for either performance of the peripheral plants or their adaptive potential.

  1. Eye shape and the nocturnal bottleneck of mammals.

    Science.gov (United States)

    Hall, Margaret I; Kamilar, Jason M; Kirk, E Christopher

    2012-12-22

    Most vertebrate groups exhibit eye shapes that vary predictably with activity pattern. Nocturnal vertebrates typically have large corneas relative to eye size as an adaptation for increased visual sensitivity. Conversely, diurnal vertebrates generally demonstrate smaller corneas relative to eye size as an adaptation for increased visual acuity. By contrast, several studies have concluded that many mammals exhibit typical nocturnal eye shapes, regardless of activity pattern. However, a recent study has argued that new statistical methods allow eye shape to accurately predict activity patterns of mammals, including cathemeral species (animals that are equally likely to be awake and active at any time of day or night). Here, we conduct a detailed analysis of eye shape and activity pattern in mammals, using a broad comparative sample of 266 species. We find that the eye shapes of cathemeral mammals completely overlap with nocturnal and diurnal species. Additionally, most diurnal and cathemeral mammals have eye shapes that are most similar to those of nocturnal birds and lizards. The only mammalian clade that diverges from this pattern is anthropoids, which have convergently evolved eye shapes similar to those of diurnal birds and lizards. Our results provide additional evidence for a nocturnal 'bottleneck' in the early evolution of crown mammals.

  2. HIV/AIDS: global trends, global funds and delivery bottlenecks

    Directory of Open Access Journals (Sweden)

    Hadingham Jacqui

    2005-08-01

    Full Text Available Abstract Globalisation affects all facets of human life, including health and well being. The HIV/AIDS epidemic has highlighted the global nature of human health and welfare and globalisation has given rise to a trend toward finding common solutions to global health challenges. Numerous international funds have been set up in recent times to address global health challenges such as HIV. However, despite increasingly large amounts of funding for health initiatives being made available to poorer regions of the world, HIV infection rates and prevalence continue to increase world wide. As a result, the AIDS epidemic is expanding and intensifying globally. Worst affected are undoubtedly the poorer regions of the world as combinations of poverty, disease, famine, political and economic instability and weak health infrastructure exacerbate the severe and far-reaching impacts of the epidemic. One of the major reasons for the apparent ineffectiveness of global interventions is historical weaknesses in the health systems of underdeveloped countries, which contribute to bottlenecks in the distribution and utilisation of funds. Strengthening these health systems, although a vital component in addressing the global epidemic, must however be accompanied by mitigation of other determinants as well. These are intrinsically complex and include social and environmental factors, sexual behaviour, issues of human rights and biological factors, all of which contribute to HIV transmission, progression and mortality. An equally important factor is ensuring an equitable balance between prevention and treatment programmes in order to holistically address the challenges presented by the epidemic.

  3. Information bottleneck based incremental fuzzy clustering for large biomedical data.

    Science.gov (United States)

    Liu, Yongli; Wan, Xing

    2016-08-01

    Incremental fuzzy clustering combines advantages of fuzzy clustering and incremental clustering, and therefore is important in classifying large biomedical literature. Conventional algorithms, suffering from data sparsity and high-dimensionality, often fail to produce reasonable results and may even assign all the objects to a single cluster. In this paper, we propose two incremental algorithms based on information bottleneck, Single-Pass fuzzy c-means (spFCM-IB) and Online fuzzy c-means (oFCM-IB). These two algorithms modify conventional algorithms by considering different weights for each centroid and object and scoring mutual information loss to measure the distance between centroids and objects. spFCM-IB and oFCM-IB are used to group a collection of biomedical text abstracts from Medline database. Experimental results show that clustering performances of our approaches are better than such prominent counterparts as spFCM, spHFCM, oFCM and oHFCM, in terms of accuracy. PMID:27260783

  4. Photonic ADC: overcoming the bottleneck of electronic jitter.

    Science.gov (United States)

    Khilo, Anatol; Spector, Steven J; Grein, Matthew E; Nejadmalayeri, Amir H; Holzwarth, Charles W; Sander, Michelle Y; Dahlem, Marcus S; Peng, Michael Y; Geis, Michael W; DiLello, Nicole A; Yoon, Jung U; Motamedi, Ali; Orcutt, Jason S; Wang, Jade P; Sorace-Agaskar, Cheryl M; Popović, Miloš A; Sun, Jie; Zhou, Gui-Rong; Byun, Hyunil; Chen, Jian; Hoyt, Judy L; Smith, Henry I; Ram, Rajeev J; Perrott, Michael; Lyszczarz, Theodore M; Ippen, Erich P; Kärtner, Franz X

    2012-02-13

    Accurate conversion of wideband multi-GHz analog signals into the digital domain has long been a target of analog-to-digital converter (ADC) developers, driven by applications in radar systems, software radio, medical imaging, and communication systems. Aperture jitter has been a major bottleneck on the way towards higher speeds and better accuracy. Photonic ADCs, which perform sampling using ultra-stable optical pulse trains generated by mode-locked lasers, have been investigated for many years as a promising approach to overcome the jitter problem and bring ADC performance to new levels. This work demonstrates that the photonic approach can deliver on its promise by digitizing a 41 GHz signal with 7.0 effective bits using a photonic ADC built from discrete components. This accuracy corresponds to a timing jitter of 15 fs - a 4-5 times improvement over the performance of the best electronic ADCs which exist today. On the way towards an integrated photonic ADC, a silicon photonic chip with core photonic components was fabricated and used to digitize a 10 GHz signal with 3.5 effective bits. In these experiments, two wavelength channels were implemented, providing the overall sampling rate of 2.1 GSa/s. To show that photonic ADCs with larger channel counts are possible, a dual 20-channel silicon filter bank has been demonstrated. PMID:22418205

  5. Photonic ADC: overcoming the bottleneck of electronic jitter.

    Science.gov (United States)

    Khilo, Anatol; Spector, Steven J; Grein, Matthew E; Nejadmalayeri, Amir H; Holzwarth, Charles W; Sander, Michelle Y; Dahlem, Marcus S; Peng, Michael Y; Geis, Michael W; DiLello, Nicole A; Yoon, Jung U; Motamedi, Ali; Orcutt, Jason S; Wang, Jade P; Sorace-Agaskar, Cheryl M; Popović, Miloš A; Sun, Jie; Zhou, Gui-Rong; Byun, Hyunil; Chen, Jian; Hoyt, Judy L; Smith, Henry I; Ram, Rajeev J; Perrott, Michael; Lyszczarz, Theodore M; Ippen, Erich P; Kärtner, Franz X

    2012-02-13

    Accurate conversion of wideband multi-GHz analog signals into the digital domain has long been a target of analog-to-digital converter (ADC) developers, driven by applications in radar systems, software radio, medical imaging, and communication systems. Aperture jitter has been a major bottleneck on the way towards higher speeds and better accuracy. Photonic ADCs, which perform sampling using ultra-stable optical pulse trains generated by mode-locked lasers, have been investigated for many years as a promising approach to overcome the jitter problem and bring ADC performance to new levels. This work demonstrates that the photonic approach can deliver on its promise by digitizing a 41 GHz signal with 7.0 effective bits using a photonic ADC built from discrete components. This accuracy corresponds to a timing jitter of 15 fs - a 4-5 times improvement over the performance of the best electronic ADCs which exist today. On the way towards an integrated photonic ADC, a silicon photonic chip with core photonic components was fabricated and used to digitize a 10 GHz signal with 3.5 effective bits. In these experiments, two wavelength channels were implemented, providing the overall sampling rate of 2.1 GSa/s. To show that photonic ADCs with larger channel counts are possible, a dual 20-channel silicon filter bank has been demonstrated.

  6. Analysis of registered CDM projects: potential removal of evidenced bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    Agosto, D.; Bombard, P.; Gostinelli, F.

    2007-07-01

    The Clean Development Mechanism (CDM) has developed during its first period of implementation, a distinctive set of patterns. The authors thought of concentrating on the CDM analysis in order to highlight potential remedies or reasons for given bottlenecks. In order to establish a sort of extensive SWOT analysis for CDMs, all the 356 projects actually (November 2006) registered at UNFCCC were examined, together with all the about 1000 PDDs presented to the UNFCCC but not registered yet. The CDM projects have been studied trying to cluster projects according to relevant characteristics, both from a technical and an economic point of view. Chosen indicators are meant to identify: more convenient/more diffused energy system for a CDM; reasons for a geographical distribution of different types of projects; potentials for a future exploitation of lower used technologies in CDM. Conclusions are drawn and appropriate tables and graphs presented. (1) the Baseline Emission Factor, combined to economic patterns, is the pivotal factor that characterizes both choices of host country and technology; (2) some technologies can exploit appropriately CDM scheme, whilst other technologies, are constrained by it. (3) there are still some important weak points: grouping of non Annex I countries; crediting period; criteria for the evaluation of sustainable development. (auth)

  7. Resistance of virus to extinction on bottleneck passages: Study of a decaying and fluctuating pattern of fitness loss

    Science.gov (United States)

    Lázaro, Ester; Escarmís, Cristina; Pérez-Mercader, Juan; Manrubia, Susanna C.; Domingo, Esteban

    2003-01-01

    RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern. PMID:12960384

  8. Population differentiation and phylogeographic pattern of a relict species, Conandron ramondioides (Gesneriaceae), revealed from sequence polymorphism and haplotypes of the CYCLOIDEA gene

    Institute of Scientific and Technical Information of China (English)

    Li-Hong XIAO; Zhi LI; Rui WANG; yin-Zheng WANG

    2012-01-01

    Historical events are expected to affect population genetic differentiation and DNA molecular evolution,but the impact of these effects remains a matter of debate.Here,for Conandron ramondioides (Gesneriaceae),we analyzed the genetic structure and phylogeographical pattern of 248 individuals from 13 populations,distributed in mainland China and Taiwan Island,based on the nucleotide sequence and haplotype of the coding sequence of CYCLOIDEA1 (GCYC1).Among the populations,we found a high level of haplotype diversity (h =0.831) and a relatively low level of nucleotide diversity (Dij =0.004).Both the haplotype network and the neighbor-joining tree constructed from GCYC1 haplotypes suggest two major geographical groupings,one on the mainland and the other on Taiwan.Consistently,AMOVA analysis revealed high genetic differentiation between these groupings,with 84.65% variation partitioning the two regions,and the two groupings shared no haplotype.On the mainland,population genetic differentiation was correlated with more recent events,presumably Pleistocene glaciations and human activities since the Neolithic.In addition,C.ramondioides GCYC1 rapidly accumulated neutral mutations,consistent with this gene being silenced or down-regulated in actinomorphic lineages of the Lamiales,such as Conandron.

  9. Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations.

    Science.gov (United States)

    Munshi-South, Jason; Zolnik, Christine P; Harris, Stephen E

    2016-04-01

    Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns. PMID:27099621

  10. Genetic diversity of and differentiation among five populations of blunt snout bream (Megalobrama amblycephala revealed by SRAP markers: implications for conservation and management.

    Directory of Open Access Journals (Sweden)

    Wei Ji

    Full Text Available The blunt snout bream (Megalobrama amblycephala is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian and one genetic strain ('Pujiang No. 1' of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei's gene diversity (h and Shannon's information index (I values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>'Pujiang No. 1'>Yuni Lake. Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations, Nanxian and 'Pujiang No. 1' (cultured population and genetically selected strain, and Yuni Lake (natural population. Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA, with more genetic divergence existing among populations (55.49%, than within populations (44.51%. This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish.

  11. Allozyme variation in Czech populations of the invasive spiny-cheek crayfish Orconectes limosus (Cambaridae

    Directory of Open Access Journals (Sweden)

    L. Filipová

    2009-01-01

    Full Text Available The North American spiny-cheek crayfish, Orconectes limosus, was most probably introduced into Europe only once, in 1890. The size of the founding population was just 90 individuals. Low genetic variability resulting from a bottleneck effect during introduction might therefore be supposed in European spiny-cheek crayfish populations. On the other hand, the fast spread of O. limosus in Europe and colonisation of various habitats suggest that this species does not suffer from inbreeding depression due to an introduction bottleneck. We analysed 14 O. limosus populations from the Czech Republic using allozyme electrophoresis to evaluate the level of intra- and among-population genetic variation. Out of eight well-scoring allozyme loci chosen for detailed analysis, six were variable in studied populations, suggesting that sufficient variability was maintained during the introduction. Genetic differentiation of Czech populations of the spiny-cheek crayfish was relatively low and did not show any clear geographic pattern, probably due to long-range translocations by humans.

  12. Genetic variation and population differentiation of Michelia formosana (Magnoliaceae) based on cpDNA variation and RAPD fingerprints: relevance to post-Pleistocene recolonization.

    Science.gov (United States)

    Lu, Sheng-You; Hong, Kuo-Hsiang; Liu, Show-Ling; Cheng, Yu-Pin; Wu, Wen-Luan; Chiang, Tzen-Yuh

    2002-06-01

    We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis to assess the phylogeographic pattern of Michelia formosana, a species restricted to Taiwan and the Ryukyus. In total, 31 haplotypes were identified and clustered into four major chlorotypes. Genetic composition of nearly all populations was heterogeneous and paraphyletic phylogenetically. Although the apportionment of cpDNA variation hardly revealed a geographic pattern due to the coancestry of dominant sequences, some chlorotypes were restrictedly distributed. According to the patterns of clade dispersion and displacement, a reconstructed minimum spanning network revealed that historical events of past fragmentation and range expansion, associated with glaciation, may have shaped the phylogeographic patterns of M. formosana. Four possible refugia were identified: the Iriomote and Ishigaki Islands (the southern Ryukyus), Wulai (northern Taiwan), and Nanjen (southern Taiwan), on the basis of the interior positions of their haplotypes in the network and the high level of nucleotide diversity. Given insufficient time for coalescence at the cpDNA locus since the late Pleistocene recolonization, lineage sorting led to low levels of genetic differentiation among populations. In contrast, hierarchical examination of the random amplified polymorphic DNA (RAPD) data scored from six populations across three geographical regions, using an analysis of molecular variance (AMOVA), indicated high genetic differentiation both among populations (Phi(ST) = 0.471) and among regions (Phi(CT) = 0.368). An unweighted pair group method with arithmetic mean (UPGMA) tree of the RAPD fingerprints revealed that populations of two offshore islands of eastern Taiwan ( M. formosana var. kotoensis) were clustered with geographically remote populations of the Ryukyus instead of those in southern Taiwan, suggesting some historical division due to geographic barriers of the central mountain range. In

  13. Population stochastic modelling (PSM)-An R package for mixed-effects models based on stochastic differential equations

    DEFF Research Database (Denmark)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode;

    2009-01-01

    The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model...... development, J. Pharmacokinet. Pharmacodyn. 32 (February(l)) (2005) 109-141; C.W. Tornoe, R.V Overgaard, H. Agerso, H.A. Nielsen, H. Madsen, E.N. Jonsson, Stochastic differential equations in NONMEM: implementation, application, and comparison with ordinary differential equations, Pharm. Res. 22 (August(8......)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornoe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum...

  14. Is integration and survival of newborn neurons the bottleneck for effective neural repair by endogenous neural precursor cells?

    Directory of Open Access Journals (Sweden)

    Ann eTurnley

    2014-02-01

    Full Text Available After two decades of research the existence of adult neural precursor cells and the phenomenon of adult neurogenesis is well established. However, there has been little or no effective harnessing of these endogenous cells to promote functional neuronal replacement following neural injury or disease. Neural precursor cells can respond to neural damage by proliferating, migrating to the site of injury and differentiating into neuronal or glial lineages. However, after a month or so, very few or no newborn neurons can be detected, suggesting that even though neuroblasts are generated, they generally fail to survive as mature neurons and contribute to the local circuitry. Is this lack of survival and integration one of the major bottlenecks that inhibits effective neuronal replacement and subsequent repair of the nervous system following injury or disease? In this perspective article the possibility that this bottleneck can be targeted to enhance the integration and subsequent survival of newborn neurons will be explored and will suggest some possible mechanisms that may need to be modulated for this to occur.

  15. Differences in Strength and Timing of the mtDNA Bottleneck between Zebrafish Germline and Non-germline Cells

    Directory of Open Access Journals (Sweden)

    Auke B.C. Otten

    2016-07-01

    Full Text Available We studied the mtDNA bottleneck in zebrafish to elucidate size, timing, and variation in germline and non-germline cells. Mature zebrafish oocytes contain, on average, 19.0 × 106 mtDNA molecules with high variation between oocytes. During embryogenesis, the mtDNA copy number decreases to ∼170 mtDNA molecules per primordial germ cell (PGC, a number similar to that in mammals, and to ∼50 per non-PGC. These occur at the same developmental stage, implying considerable variation in mtDNA copy number in (non-PGCs of the same female, dictated by variation in the mature oocyte. The presence of oocytes with low mtDNA numbers, if similar in humans, could explain how (de novo mutations can reach high mutation loads within a single generation. High mtDNA copy numbers in mature oocytes are established by mtDNA replication during oocyte development. Bottleneck differences between germline and non-germline cells, due to early differentiation of PGCs, may account for different distribution patterns of familial mutations.

  16. Lonely populations in the deep: genetic structure of red gorgonians at the heads of submarine canyons in the north-western Mediterranean Sea

    Science.gov (United States)

    Pérez-Portela, Rocío; Cerro-Gálvez, Elena; Taboada, Sergi; Tidu, Carlo; Campillo-Campbell, Carolina; Mora, Joan; Riesgo, Ana

    2016-09-01

    The red gorgonian Paramuricea clavata plays a central role in coralligenous ecosystems of the Mediterranean Sea, being relatively abundant in shallow habitats (5-35 m depth). Recently, deeper populations have been discovered at the heads of submarine canyons in the north-western Mediterranean Sea, between 50 and 70 m deep. Colonies from some of these deeper populations were exceptionally large (>1 m high), contrasting with the general prevalence of smaller size classes in shallower populations. Importantly, the high pressure of trawling activities on the nearby continental shelf could threaten these populations of large and old colonies. Although the genetic diversity and structure of populations in shallow habitats is relatively well known, very little is known about deeper populations. We aimed to assess the genetic structure, connectivity and potential demographic decline of six deep populations of P. clavata located at the heads of La Fonera, Blanes and Arenys de Mar submarine canyons, as well as potential gene flow between those and the two nearest shallow populations. A total of 188 individuals were genotyped using nine microsatellite loci. Results showed strong genetic differentiation among populations in different submarine canyons, among populations within one of the canyons and between shallow and deep populations. Gene flow among populations was very limited, estimates of effective population size in some populations were small, and evidence of recent population reductions (bottlenecks) was detected in several populations. The large genetic differentiation in populations of P. clavata among canyons is related to limited effective dispersal.

  17. Genetic Differentiation within the Puccinia triticina Population in South America and Comparison with the North American Population Suggests Common Ancestry and Intercontinental Migration

    Science.gov (United States)

    Leaf rust, caused by Puccinia triticina is the most prevalent and widespread disease of wheat in South America. The objective of this study was to determine the number of genetically differentiated groups of P. triticina that are currently present in South America, and to compare the South American ...

  18. Differentiation of muscle, fat, cartilage, and bone from progenitor cells present in a bone-derived clonal cell population: effect of dexamethasone

    OpenAIRE

    1988-01-01

    RCJ 3.1, a clonally derived cell population isolated from 21-d fetal rat calvaria, expresses the osteoblast-associated characteristics of polygonal morphology, a cAMP response to parathyroid hormone, synthesis of predominantly type I collagen, and the presence of 1,25- dihydroxyvitamin D3-regulated alkaline phosphatase activity. When cultured in the presence of ascorbic acid, sodium beta- glycerophosphate, and the synthetic glucocorticoid dexamethasone, this clone differentiated in a time-dep...

  19. Is Dementia Differentially Distributed? A Study on the Prevalence of Dementia in Migrant, Urban, Rural, and Tribal Elderly Population of Himalayan Region in Northern India

    Directory of Open Access Journals (Sweden)

    Sunil Kumar Raina

    2014-01-01

    Full Text Available Background: Throughout the world, a large number of surveys have been carried out to find the prevalence of dementia with variable results. Aims: This study was to generate data on the prevalence of dementia and to generate a hypothesis on the differential distribution across populations. Materials and Methods: Four settings identified for the purpose of this study included a migrant, urban, rural, and tribal. The study was conducted in two phases: 1 A screening phase and 2 a clinical phase, on 2,000 individuals above 60 years of age. To complete the required sample of 2,000 elderly individuals, 500 individuals were approached from each site. Nobody refused to participate. Results: A total of 32/2,000 (1.6% elderly individuals were classified as demented. No case of dementia was reported from tribal population. A look at sex differential reveals that majority (21/32; 66% of individuals identified as demented were females. As age advanced scores on cognitive screen decreased with elders above 80 years of age showing lowest scores. Out of 32, 18 (56% of patients classified as demented were more than 80 years of age. Conclusion: The findings of this study are in agreement with previous studies which point towards differential distribution of dementia across populations.

  20. Colonization and persistence of urban ant populations as revealed by joint estimation of kinship and population genetic parameters.

    Science.gov (United States)

    Yamamoto, Junpei; Uchida, Kei; Takami, Yasuoki

    2013-01-01

    The decrease in biodiversity due to increasing urbanization has been well documented, but the processes of colonization and maintenance of wildlife populations in urban areas remain poorly understood. We address this issue using 462 individuals from 10 urban populations of the ant Formica japonica in Kobe City, Japan. We sampled workers regardless of colony identity, genotyped them using 6 microsatellite loci, and estimated allele frequencies and genotypes of reproductive individuals, together with other population genetic parameters, by estimating kinship structure using a likelihood method. Estimated genetic diversity and effective size of populations were not associated with environmental parameters, suggesting that populations are unaffected by urbanization. However, effective population sizes were small, and frequent population bottlenecks were detected. These results suggest that urban F. japonica populations are unstable, and the possibility of frequent extinctions and recolonizations in urban habitats. Populations were moderately differentiated without isolation by distance, suggesting a strong dispersal ability that enables colonization of urban habitats. Dispersal was male biased. Collectively, F. japonica was regarded as an urban adapter, which can colonize urban habitats by virtue of its preference for open ground and high dispersal ability but can persist in urban populations for only a short time, showing a tendency as a temporary urban inhabitant.

  1. Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks.

    Science.gov (United States)

    Haidari, Leila A; Connor, Diana L; Wateska, Angela R; Brown, Shawn T; Mueller, Leslie E; Norman, Bryan A; Schmitz, Michelle M; Paul, Proma; Rajgopal, Jayant; Welling, Joel S; Leonard, Jim; Claypool, Erin G; Weng, Yu-Ting; Chen, Sheng-I; Lee, Bruce Y

    2013-01-01

    Although vaccine supply chains in many countries require additional stationary storage and transport capacity to meet current and future needs, international donors tend to donate stationary storage devices far more often than transport equipment. To investigate the impact of only adding stationary storage equipment on the capacity requirements of transport devices and vehicles, we used HERMES (Highly Extensible Resource for Modeling Supply Chains) to construct a discrete event simulation model of the Niger vaccine supply chain. We measured the transport capacity requirement for each mode of transport used in the Niger vaccine cold chain, both before and after adding cold rooms and refrigerators to relieve all stationary storage constraints in the system. With the addition of necessary stationary storage, the average transport capacity requirement increased from 88% to 144% for cold trucks, from 101% to 197% for pickup trucks, and from 366% to 420% for vaccine carriers. Therefore, adding stationary storage alone may worsen or create new transport bottlenecks as more vaccines flow through the system, preventing many vaccines from reaching their target populations. Dynamic modeling can reveal such relationships between stationary storage capacity and transport constraints.

  2. Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks.

    Science.gov (United States)

    Haidari, Leila A; Connor, Diana L; Wateska, Angela R; Brown, Shawn T; Mueller, Leslie E; Norman, Bryan A; Schmitz, Michelle M; Paul, Proma; Rajgopal, Jayant; Welling, Joel S; Leonard, Jim; Claypool, Erin G; Weng, Yu-Ting; Chen, Sheng-I; Lee, Bruce Y

    2013-01-01

    Although vaccine supply chains in many countries require additional stationary storage and transport capacity to meet current and future needs, international donors tend to donate stationary storage devices far more often than transport equipment. To investigate the impact of only adding stationary storage equipment on the capacity requirements of transport devices and vehicles, we used HERMES (Highly Extensible Resource for Modeling Supply Chains) to construct a discrete event simulation model of the Niger vaccine supply chain. We measured the transport capacity requirement for each mode of transport used in the Niger vaccine cold chain, both before and after adding cold rooms and refrigerators to relieve all stationary storage constraints in the system. With the addition of necessary stationary storage, the average transport capacity requirement increased from 88% to 144% for cold trucks, from 101% to 197% for pickup trucks, and from 366% to 420% for vaccine carriers. Therefore, adding stationary storage alone may worsen or create new transport bottlenecks as more vaccines flow through the system, preventing many vaccines from reaching their target populations. Dynamic modeling can reveal such relationships between stationary storage capacity and transport constraints. PMID:23903398

  3. Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

    Directory of Open Access Journals (Sweden)

    A. K. Thiruvenkadan

    2014-09-01

    Full Text Available Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders. Materials and Methods: Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM, stepwise mutation model (SMM and two-phase model (TPM and the observed gene diversity (He and expected equilibrium gene diversity (Heq were estimated under different models of microsatellite evolution. Results: The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008 to 17 (BM64444 with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively. Conclusion: All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed

  4. Low temperature during winter elicits differential responses among populations of the Mediterranean evergreen cork oak (Quercus suber).

    Science.gov (United States)

    Aranda, I; Castro, L; Alía, R; Pardos, J A; Gil, L

    2005-08-01

    Populations of cork oak (Quercus suber L.) were assessed for seasonal and inter-population variability in, and temperature responses of, the ratio between light-induced variable and maximum fluorescence of chlorophyll, Fv/Fm, considered a surrogate for the maximum photochemical efficiency of photosystem II (PSII). Seedlings from 10 populations throughout the distribution range of Q. suber in the Mediterranean basin were grown in a common garden in central Spain. The Fv/Fm ratio of dark-adapted leaves was measured at dawn every month for 2 years. Air temperature was recorded at a nearby climatic station. During the summer, when maximum air temperatures reached 40 degrees C, there were no significant differences in Fv/Fm among populations, but significant differences were seen during the winter. In colder months, Fv/Fm ranged in all populations between 0.5-0.6 and 0.2-0.3 in 2001 and 2002, respectively. The variance explained by the population effect was greatest during winter months, especially in 2002, reaching a peak value of 10% when minimum air temperature was below -10 degrees C. Populations originating from warmer sites showed the largest decline in Fv/Fm between the end of 2001 and the beginning of 2002. Thus, a negative linear relationship was established between mean annual temperature at the population source and population mean Fv/Fm recorded in the coldest month in 2002 and normalized by the Fv/Fm spring measurement.

  5. Development of control strategy of variable speed limits for improving traffic operations at freeway bottlenecks

    Institute of Scientific and Technical Information of China (English)

    李志斌; 刘攀; 王炜; 徐铖铖

    2014-01-01

    A control strategy of variable speed limits (VSL) was developed to reduce the travel time at freeway recurrent bottleneck areas. The proposed control strategy particularly focused on preventing the capacity drop and increasing the discharge flow. A cell transmission model (CTM) was developed to evaluate the effects of the proposed VSL control strategy on the traffic operations. The results show that the total travel time is reduced by 25.5% and the delay is reduced by 56.1%. The average travel speed is increased by 34.3% and the queue length is reduced by 31.0%. The traffic operation is improved by the proposed VSL control strategy. The way to use the proposed VSL control strategy in different types of freeway bottlenecks was also discussed by considering different traffic flow characteristics. It is concluded that the VSL control strategy is effective for merge bottlenecks but is less effective for diverge bottlenecks.

  6. Circuit model for spin-bottleneck resistance in magnetic-tunnel-junction devices

    OpenAIRE

    Jungwirth, T.; MacDonald, A. H.

    1998-01-01

    Spin-bottlenecks are created in magnetic-tunnel-junction devices by spatial inhomogeneity in the relative resistances for up and down spins. We propose a simple electrical circuit model for these devices which incorporates spin-bottleneck effects and can be used to calculate their overall resistance and magnetoresistance. The model permits a simple understanding of the dependence of device magnetoresistance on spin diffusion lengths, tunneling magnetoresistance, and majority and minority spin...

  7. On the Accurate Identification of Network Paths Having a Common Bottleneck

    Directory of Open Access Journals (Sweden)

    Muhammad Murtaza Yousaf

    2013-01-01

    Full Text Available We present a new mechanism for detecting shared bottlenecks between end-to-end paths in a network. Our mechanism, which only needs one-way delays from endpoints as an input, is based on the well-known linear algebraic approach: singular value decomposition (SVD. Clusters of flows which share a bottleneck are extracted from SVD results by applying an outlier detection method. Simulations with varying topologies and different network conditions show the high accuracy of our technique.

  8. A Framework for Accelerating Bottlenecks in GPU Execution with Assist Warps

    OpenAIRE

    Vijaykumar, Nandita; Pekhimenko, Gennady; Jog, Adwait; Ghose, Saugata; Bhowmick, Abhishek; Ausavarangnirun, Rachata; Das, Chita; Kandemir, Mahmut; Mowry, Todd C.; Mutlu, Onur

    2016-01-01

    Modern Graphics Processing Units (GPUs) are well provisioned to support the concurrent execution of thousands of threads. Unfortunately, different bottlenecks during execution and heterogeneous application requirements create imbalances in utilization of resources in the cores. For example, when a GPU is bottlenecked by the available off-chip memory bandwidth, its computational resources are often overwhelmingly idle, waiting for data from memory to arrive. This work describes the Core-Assist...

  9. Analysis of the pedestrian arching at bottleneck based on a bypassing behavior model

    Science.gov (United States)

    Tang, Ming; Jia, Hongfei; Ran, Bin; Li, Jun

    2016-07-01

    A bypassing behavior model was proposed, in which the local optimal decision behavior in the strategy level was modeled in velocity-time domain, to describe how pedestrians bypass the local obstacles considering the relative speed. The model contains (1) pedestrian visual and contact information acquisition; (2) motion state prediction of the local obstacles based on the visual and contact information; (3) pedestrian bypass strategy modeling in the velocity-time domain; (4) moving and overlapping solution. In the numerical solution, velocity domain was divided into n equal angle, the value of n ranges from 2 to infinity, the Manhattan space was refined gradually to Euclid Space accordingly, in which the movement of pedestrians was described. The model was applied to the analysis of pedestrian arching at the bottleneck in the emergent evacuation situation. (1) The results showed that the formation of the pedestrian arching at the bottleneck was deformation pressure, because many pedestrians try to pass through the bottleneck simultaneously, even in the absence of friction, the pedestrian arching still occurs; (2) In the emergent situation, we are more concerned about the bottleneck attribution of resistance to form the arching, the calculation and simulation results showed that the probability of an arching and the bottleneck width is an exponential function relationship, so when the stampede occurs in the middle of the bottleneck, the probability of arching will increase exponentially.

  10. The genetic structure of a relict population of wood frogs

    Science.gov (United States)

    Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

    2012-01-01

    Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

  11. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history. PMID:24102001

  12. Thermodynamic modelling predicts energetic bottleneck for seabirds wintering in the northwest Atlantic.

    Science.gov (United States)

    Fort, Jérôme; Porter, Warren P; Grémillet, David

    2009-08-01

    Studying the energetics of marine top predators such as seabirds is essential to understand processes underlying adult winter survival and its impact on population dynamics. Winter survival is believed to be the single most important life-history trait in long-lived species but its determinants are largely unknown. Seabirds are inaccessible during this season, so conventional metabolic studies are extremely challenging and new approaches are needed. This paper describes and uses a state-of-the-art mechanistic model, Niche Mapper, to predict energy expenditure and food requirements of the two main seabird species wintering in the northwest Atlantic. We found that energy demand increased throughout the winter phase in both species. Across this period, mean estimated daily energy requirements were 1306 kJ day(-1) for Brünnich's guillemots (Uria lomvia) and 430 kJ day(-1) for little auks (Alle alle) wintering off Greenland and Newfoundland. Mean estimated daily food requirements were 547 g wet food day(-1) for Brünnich's guillemots, and 289 g wet food day(-1) for little auks. For both species and both wintering sites, our model predicts a sharp increase in energy expenditure between November and December, primarily driven by climatic factors such as air temperature and wind speed. These findings strongly suggest the existence of an energetic bottleneck for North Atlantic seabirds towards the end of the year, a challenging energetic phase which might explain recurrent events of winter mass-mortality, so called 'seabird winter wrecks'. Our study therefore emphasizes the relevance of thermodynamics/biophysical modelling for investigating the energy balance of wintering marine top predators and its interplay with survival and population dynamics in the context of global change. PMID:19617442

  13. Epigeic Earthworms Exert a Bottleneck Effect on Microbial Communities through Gut Associated Processes

    Science.gov (United States)

    Gómez-Brandón, María; Aira, Manuel; Lores, Marta; Domínguez, Jorge

    2011-01-01

    Background Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. Methodology To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (fluorescein diacetate hydrolysis) in the earthworm casts derived from three types of animal manure (cow, horse and pig manure), which differed in microbial composition. Principal Findings The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. Conclusions/Significance Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions within the decomposer

  14. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

    Directory of Open Access Journals (Sweden)

    María Gómez-Brandón

    Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

  15. [Genetic variability and differentiation of three Russian populations of yellow potato cyst nematode Globodera rostochiensis as revealed by nuclear markers].

    Science.gov (United States)

    Khrisanfova, G G; Kharchevnikov, D A; Popov, I O; Zinov'eva, S V; Semenova, S K

    2008-05-01

    Genetic variability of yellow potato cyst nematode G. rostochiensis from three Russian populations (Karelia, Vladimir oblast, and Moscow oblast) was investigated using two types of nuclear markers. Using RAPD markers identified with the help of six random primers (P-29, OPA-10, OPT-14, OPA-11, OPB-11, and OPH-20), it was possible to distinguish Karelian population from the group consisting of the populations from two adjacent regions (Moscow oblast and Vladimir oblast). Based on the combined matrix, containing 294 RAPD fragments, dendrogram of genetic differences was constructed, and the indices of genetic divergence and partition (P, H, and G(st)), as well as the gene flow indices N(m) between the nematode samples examined, were calculated. The dendrogram structure, genetic diversity indices, and variations of genetic distances between single individuals in each population from Karelia and Central Russia pointed to genetic isolation and higher genetic diversity of the nematodes from Karelia. Based on polymorphism of rDNA first intergenic spacer ITS1, attribution of all populations examined to the species G. rostochiensis was proved. Small variations of the ITS1 sequence in different geographic populations of nematodes from different regions of the species world range did not allow isolation of separate groups within the species. Possible factors (including interregional transportations of seed potato) affecting nematode population structure in Russia are discussed. PMID:18672794

  16. Post-fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source-sink population network.

    Science.gov (United States)

    Husemann, M; Cousseau, L; Callens, T; Matthysen, E; Vangestel, C; Hallmann, C; Lens, L

    2015-03-01

    The impact of demographic parameters on the genetic population structure and viability of organisms is a long-standing issue in the study of fragmented populations. Demographic and genetic tools are now readily available to estimate census and effective population sizes and migration and gene flow rates with increasing precision. Here we analysed the demography and genetic population structure over a recent 15-year time span in five remnant populations of Cabanis's greenbul (Phyllastrephus cabanisi), a cooperative breeding bird in a severely fragmented cloud forest habitat. Contrary to our expectation, genetic admixture and effective population sizes slightly increased, rather than decreased between our two sampling periods. In spite of small effective population sizes in tiny forest remnants, none of the populations showed evidence of a recent population bottleneck. Approximate Bayesian modelling, however, suggested that differentiation of the populations coincided at least partially with an episode of habitat fragmentation. The ratio of meta-Ne to meta-Nc was relatively low for birds, which is expected for cooperative breeding species, while Ne /Nc ratios strongly varied among local populations. While the overall trend of increasing population sizes and genetic admixture may suggest that Cabanis's greenbuls increasingly cope with fragmentation, the time period over which these trends were documented is rather short relative to the average longevity of tropical species. Furthermore, the critically low Nc in the small forest remnants keep the species prone to demographic and environmental stochasticity, and it remains open if, and to what extent, its cooperative breeding behaviour helps to buffer such effects.

  17. Genetic population structure of European sprat (Sprattus sprattus L.): differentiation across a steep environmental gradient in a small pelagic fish

    DEFF Research Database (Denmark)

    Limborg, Morten; Pedersen, Jes S.; Hansen, Jakob Hemmer;

    2009-01-01

    locations in and around the North- and Baltic Sea area and from a geographically distant population from the Adriatic Sea. Analyses of nine microsatellite loci revealed a sharp genetic division separating samples from the Northeastern Atlantic and the Baltic Sea (pairwise θ = 0.019–0.035), concurring...... population structure resembles that of most other marine fishes studied in the North/Baltic Sea areas. Nevertheless, spatially explicit differences are observed among species, likely reflecting specific life-histories. Such fine-scale population structure should be taken into account, e.g. in ecosystem......Factors such as oceanographic retention, isolation by distance and secondary contact zones have, among others, been suggested to explain the low, but statistically significant, neutral population structure observed in many marine fishes. European sprat Sprattus sprattus is not known to display...

  18. Comparison of haplotype frequencies differentiate fall armyworm (Lepidoptera: Noctuidae) corn-strain populations from Florida and Brazil.

    Science.gov (United States)

    Nagoshi, Rod N; Silvie, Pierre; Meagher, Robert L

    2007-06-01

    Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a major economic pest throughout the Western Hemisphere. Populations can be subdivided into two morphologically identical but genetically distinct strains (corn-strain and rice-strain) that differ in their host plant preferences. These strains can be distinguished by using polymorphisms in the mitochondrial cytochrome oxidase 1 gene. Additional sequence analysis of this locus identified two sites that were highly polymorphic in the corn-strain population and that produced four different haplotype subgroups. Comparisons of the frequency distribution of these haplotypes found no seasonal or plant host specificities, but they did demonstrate that the Brazil corn-strain population is different from corn-strain fall armyworm found in Florida. The development of a rapid means of distinguishing fall armyworm populations originating from Brazil versus Florida provides an opportunity for investigating and comparing the genetic complexity and long-range movements of this important agricultural pest.

  19. Phylogeography of two parthenogenetic sawfly species (Hymenoptera: Tenthredinidae): relationship of population genetic differentiation to host plant distribution

    NARCIS (Netherlands)

    Müller, C.; Barker, A.; Boevé, J.L.; Jong, de P.W.; Vos, de H.; Brakefield, P.M.

    2004-01-01

    This study compares the population genetic structure of two obligate parthenogenetic sawfly species, Aneugmenus padi (L.) Zhelochovtsev and Eurhadinoceraea ventralis (Panzer) Enslin (Hymenoptera: Tenthredinidae). Allozymes were used to detect genetic differences in larvae collected at different site

  20. Stocking impact and temporal stability of genetic composition in a brackish northern pike population ( Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples

    DEFF Research Database (Denmark)

    Larsen, Peter Foged; Hansen, Michael Møller; Eg Nielsen, Einar;

    2005-01-01

    the three populations used for stocking. Despite large numbers of stocked fry, the results from both individual and population level admixture analyses demonstrated extremely poor performance and 250), but there were indications of bottlenecks in all samples and populations. We ascribe this finding...... to historical rather than recent bottlenecks, possibly dating back to founder events associated with postglacial recolonisation....

  1. Isoenzymatic differentiation in putative hybrid swarm population (Pinus mugo Turra x P. sylvestris L.) from "Torfowisko Zieleniec" peat-bog

    OpenAIRE

    Anna Siedlewska

    2014-01-01

    Isoenzyme variability of eight groups of individuals from different parts of putative hybrid swarm population (P. mugo Turra x P. sylvestris L.) from "Torfowisko Zieleniec" peat-bog complex was studied at ten enzymatic loci. Differences in allelic frequencies distribution among particular samples of the Zieleniec population were statistically significant at 9 loci, as shown by G2- statistics. Chi-square test indicated that in each of studied subpopulations frequencies of alleles at some loci ...

  2. Water-Price Differential and the Efficient Population Size and Urban-Rural Composition of a Distant, Large, Arid Island

    OpenAIRE

    Levy, Amnon; Zamani, Reza

    2004-01-01

    A low population density and a large distance from civilization centres present a high degree of isolation to the island's residents. Immigration can reduce the mental and material costs of isolation for the veteran residents, but at the expense of cultural and national cohesion and social harmony; and, in the case of an arid land, also at the expense of the amount and price of water allocated to agriculture. An expected-net-benefit-maximisation model for determining population size and its e...

  3. Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics

    OpenAIRE

    Larmuseau, Maarten HD; Ottoni, Claudio; Raeymaekers, Joost AM; Vanderheyden, Nancy; Larmuseau, Hendrik FM; Decorte, Ronny

    2011-01-01

    The pattern of population genetic variation and allele frequencies within a species are unstable and are changing over time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome (Y-chr) genotyping to disentangle signals of historical population genetic structures because of the exponential increase in genetic genealogical data. To test this approach, we studied the temporal pattern of the ‘autochthon...

  4. Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins in north-western Australia.

    Science.gov (United States)

    Brown, Alexander M; Kopps, Anna M; Allen, Simon J; Bejder, Lars; Littleford-Colquhoun, Bethan; Parra, Guido J; Cagnazzi, Daniele; Thiele, Deborah; Palmer, Carol; Frère, Celine H

    2014-01-01

    Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins ('snubfin' and 'humpback dolphins', hereafter) of north-western Australia. While both species are listed as 'near threatened' by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (FST = 0.05-0.09; Pdolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for the first documented case of hybridisation between a female snubfin dolphin and a male humpback dolphin.

  5. Postenrichment population differentials using buffered Listeria enrichment broth: implications of the presence of Listeria innocua on Listeria monocytogenes in food test samples.

    Science.gov (United States)

    Keys, Ashley L; Dailey, Rachel C; Hitchins, Anthony D; Smiley, R Derike

    2013-11-01

    The recovery of low levels of Listeria monocytogenes from foods is complicated by the presence of competing microorganisms. Nonpathogenic species of Listeria pose a particular problem because variation in growth rate during the enrichment step can produce more colonies of these nontarget cells on selective and/or differential media, resulting in a preferential recovery of nonpathogens, especially Listeria innocua. To gauge the extent of this statistical barrier to pathogen recovery, 10 isolates each of L. monocytogenes and L. innocua were propagated together from approximately equal initial levels using the current U. S. Food and Drug Administration's enrichment procedure. In the 100 isolate pairs, an average 1.3-log decrease was found in the 48-h enrichment L. monocytogenes population when L. innocua was present. In 98 of the 100 isolate pairs, L. innocua reached higher levels at 48 h than did L. monocytogenes, with a difference of 0.2 to 2.4 log CFU/ml. The significance of these population differences was apparent by an increase in the difficulty of isolating L. monocytogenes by the streak plating method. L. monocytogenes went completely undetected in 18 of 30 enrichment cultures even after colony isolation was attempted on Oxoid chromogenic Listeria agar. This finding suggests that although both Listeria species were present on the plate, the population differential between them restricted L. monocytogenes to areas of the plate with confluent growth and that isolated individual colonies were only L. innocua.

  6. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps

    OpenAIRE

    Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R.; Morton, Newton E.

    2004-01-01

    Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Popu...

  7. Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms.

    Science.gov (United States)

    Dussex, Nicolas; Chuah, Aaron; Waters, Jonathan M

    2016-01-01

    Insect flight loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in codistributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain range. We find that winged populations (altitude 200-500 m; Zelandoperla decorata) show no genetic structuring within or among streams, suggesting substantial dispersal mediated by flight. By contrast, wingless populations (Zelandoperla fenestrata; altitude 200-1100 m) exhibit distinct genetic clusters associated with each stream, and additional evidence of isolation by distance within streams. Our data support the hypothesis that wing-loss can initiate diversification in alpine insect populations over small spatial scales. The often deep phylogenetic placement of lowland Z. fenestrata within their stream-specific clades suggests the possibility of independent alpine colonization events for each stream. Additionally, the detection of winged, interspecific hybrid individuals raises the intriguing possibility that a previously flightless lineage could reacquire flight via introgression. PMID:26614689

  8. Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms.

    Science.gov (United States)

    Dussex, Nicolas; Chuah, Aaron; Waters, Jonathan M

    2016-01-01

    Insect flight loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in codistributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain range. We find that winged populations (altitude 200-500 m; Zelandoperla decorata) show no genetic structuring within or among streams, suggesting substantial dispersal mediated by flight. By contrast, wingless populations (Zelandoperla fenestrata; altitude 200-1100 m) exhibit distinct genetic clusters associated with each stream, and additional evidence of isolation by distance within streams. Our data support the hypothesis that wing-loss can initiate diversification in alpine insect populations over small spatial scales. The often deep phylogenetic placement of lowland Z. fenestrata within their stream-specific clades suggests the possibility of independent alpine colonization events for each stream. Additionally, the detection of winged, interspecific hybrid individuals raises the intriguing possibility that a previously flightless lineage could reacquire flight via introgression.

  9. Raptor mortality in wind farms of southern Spain: mitigation measures on a major migration bottleneck area

    Energy Technology Data Exchange (ETDEWEB)

    Gallego, Antonio-Roman Munoz; Lucas, Manuela De; Casado, Eva; Ferrer, Miguel

    2011-07-01

    Full text: To assess and monitor the impact of wind farms on fauna is crucial if we want to achieve ecologically sustainable development of this renewable energy resource. Today there are clear evidences that the probability of raptor collision depends critically on species behaviour and weather conditions, and the topographic factors related to each windmill. In our study area EIA were not able to predict this differential risk and in these circumstances mitigating the causes of bird mortality becomes a task of major importance, especially to those wind farms located in the Strait of Gibraltar, a water crossing of 14 km at its shortest distance acting as a major migration bottleneck for Paleo-African soaring migrants. We collected all available information on raptor collision from 1992, when the first wind farm was installed, and from 2005 until present a total of 262 turbines, grouped into 20 wind farms, were surveyed in a daily basis through a surveillance program with the main goal of register the actual mortality of birds. A total of 1291 raptors of 19 species were found of which 78.5% correspond to two species, the griffon vulture (Gyps fulvus) and the kestrel (Falco tinnunculus). In order to mitigate the impact on raptors, and particularly on the griffon vulture, in 2007 a program based on selective stopping of turbines was imposed, in collaboration with the environmental competent authority, on new approved projects. During 2008 there was a reduction in mortality by 48%, which remained in 2009 with a remarkably lower economic cost. An analysis of the temporal collision patterns will be presented and discussed, with special attention to those species suffering higher mortality rate, and to those who have some degree of threat. (Author)

  10. Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni and Indo-Pacific humpback (Sousa chinensis dolphins in north-western Australia.

    Directory of Open Access Journals (Sweden)

    Alexander M Brown

    Full Text Available Little is known about the Australian snubfin (Orcaella heinsohni and Indo-Pacific humpback (Sousa chinensis dolphins ('snubfin' and 'humpback dolphins', hereafter of north-western Australia. While both species are listed as 'near threatened' by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32 and Roebuck Bays (n = 25, and humpback dolphins from the Dampier Archipelago (n = 19 and the North West Cape (n = 18. All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins and 13 (for humpback dolphins microsatellite loci (FST = 0.05-0.09; P<0.001 and a 422 bp sequence of the mitochondrial control region (FST = 0.50-0.70; P<0.001. The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00-0.06 to 0.13 (0.03-0.24. These are the first estimates of genetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for

  11. Central as well as peripheral attentional bottlenecks in dual-task performance activate lateral prefrontal cortices

    Directory of Open Access Journals (Sweden)

    Andre J Szameitat

    2016-03-01

    Full Text Available Human information processing suffers from severe limitations in parallel processing. In particular, when required to respond to two stimuli in rapid succession, processing bottlenecks may appear at central and peripheral stages of task processing. Importantly, it has been suggested that executive functions are needed to resolve the interference arising at such bottlenecks. The aims of the present study were to test whether central attentional limitations (i.e., bottleneck at the decisional response selection stage as well as peripheral limitations (i.e., bottleneck at response initiation both demand executive functions located in the lateral prefrontal cortex. For this, we re-analysed two previous studies, in which a total of 33 participants performed a dual-task according to the paradigm of the psychological refractory period (PRP during fMRI. In one study (N=17, the PRP task consisted of two two-choice response tasks known to suffer from a central bottleneck (CB group. In the other study (N=16, the PRP task consisted of two simple-response tasks known to suffer from a peripheral bottleneck (PB group. Both groups showed considerable dual-task costs in form of slowing of the second response in the dual-task (PRP effect. Imaging results are based on the subtraction of both single-tasks from the dual-task within each group. In the CB group, the bilateral middle frontal gyri and inferior frontal gyri were activated. Higher activation in these areas was associated with lower dual-task costs. In the PB group, the right middle frontal and inferior frontal gyrus were activated. Here, higher activation was associated with higher dual-task costs. In conclusion we suggest that central and peripheral bottlenecks both demand executive functions located in lateral prefrontal cortices. Differences between the CB and PB groups with respect to the exact prefrontal areas activated and the correlational patterns suggest that the executive functions resolving

  12. High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life.

    Science.gov (United States)

    Karafet, Tatiana M; Osipova, Ludmila P; Gubina, Marina A; Posukh, Olga L; Zegura, Stephen L; Hammer, Michael F

    2002-12-01

    We examined genetic variation on the nonrecombining portion of the Y chromosome (NRY) to investigate the paternal population structure of indigenous Siberian groups and to reconstruct the historical events leading to the peopling of Siberia. A set of 62 biallelic markers on the NRY were genotyped in 1432 males representing 18 Siberian populations, as well as nine populations from Central and East Asia and one from European Russia. A subset of these markers defines the 18 major NRY haplogroups (A-R) recently described by the Y Chromosome Consortium (YCC 2002). While only four of these 18 major NRY haplogroups accounted for -95% of Siberian Y-chromosome variation, native Siberian populations differed greatly in their haplogroup composition and exhibited the highest phiST value for any region of the world. When we divided our Siberian sample into four geographic regions versus five major linguistic groupings, analyses of molecular variance (AMOVA) indicated higher phiST and phiCT values for linguistic groups than for geographic groups. Mantel tests also supported the existence of NRY genetic patterns that were correlated with language, indicating that language affiliation might be a better predictor of the genetic affinity among Siberians than their present geographic position. The combined results, including those from a nested cladistic analysis, underscored the important role of directed dispersals, range expansions, and long-distance colonizations bound by common ethnic and linguistic affiliation in shaping the genetic landscape of Siberia. The Siberian pattern of reduced haplogroup diversity within populations combined with high levels of differentiation among populations may be a general feature characteristic of indigenous groups that have small effective population sizes and that have been isolated for long periods of time.

  13. Tertiary origin and pleistocene diversification of dragon blood tree (Dracaena cambodiana-Asparagaceae populations in the Asian tropical forests.

    Directory of Open Access Journals (Sweden)

    Jian-Li Zhao

    Full Text Available BACKGROUND: The origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests. METHODS: WE ANALYZED NUCLEOTIDE SEQUENCE DATA OF TWO CHLOROPLAST DNA (CPDNA: atpB-rbcL and trnD-trnT regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa and BEAST software programs. RESULTS: A significant phylogeographic structure (N ST = 0.876, G ST = 0.796, F ST-SSR = 0.329, R ST = 0.449; N ST>G ST, R ST>F ST-SSR, P<0.05 and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period. CONCLUSIONS: The results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction

  14. Predictive performance for population models using stochastic differential equations applied on data from an oral glucose tolerance test

    DEFF Research Database (Denmark)

    Møller, Jonas Bech; Overgaard, R.V.; Madsen, Henrik;

    2010-01-01

    Several articles have investigated stochastic differential equations (SDEs) in PK/PD models, but few have quantitatively investigated the benefits to predictive performance of models based on real data. Estimation of first phase insulin secretion which reflects beta-cell function using models of ...... obtained from the glucose tolerance tests. Since, the estimation time of extended models was not heavily increased compared to basic models, the applied method is concluded to have high relevance not only in theory but also in practice....

  15. Genetic structure and population differentiation of the Mediterranean pioneer spiny broom Calicotome villosa across the Strait of Gibraltar

    DEFF Research Database (Denmark)

    Arroyo, Juan; Aparicio, Abelardo; Albadalejo, Rafael G.;

    2008-01-01

    differentiation. Consequently, extensive historical gene flow appears to be the rule for this species in this area. According to the natural history traits of C. villosa (pollination, dispersal, and colonization ability), we hypothesize that gene flow must be strongly influenced by seed dispersal because pollen...... the Strait of Gibraltar. It is stressed that colonization ability, which depends upon seed dispersal and life form, can be a more critical factor in gene flow than pollination....

  16. Population genetic structure of gray wolves (Canis lupus) in a marine archipelago suggests island-mainland differentiation consistent with dietary niche

    DEFF Research Database (Denmark)

    Stronen, Astrid Vik; Navid, Erin L; Quinn, Michael S;

    2014-01-01

    Background Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores. On the central coast of British Columbia, Canada, wolf (Canis lupus L., 1758) dietary niche and......) might contribute to genetic differentiation. Accordingly, this working hypothesis presents an exciting avenue for future research where marine resources or other components of ecological heterogeneity are present.......Background Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores. On the central coast of British Columbia, Canada, wolf (Canis lupus L., 1758) dietary niche...... and parasite prevalence data indicate strong ecological divergence between marine-oriented wolves inhabiting islands and individuals on the coastal mainland that interact primarily with terrestrial prey. Local holders of traditional ecological knowledge, who distinguish between mainland and island wolf forms...

  17. Stem cell-like differentiation potentials of endometrial side population cells as revealed by a newly developed in vivo endometrial stem cell assay.

    Directory of Open Access Journals (Sweden)

    Kaoru Miyazaki

    Full Text Available BACKGROUND: Endometrial stem/progenitor cells contribute to the cyclical regeneration of human endometrium throughout a woman's reproductive life. Although the candidate cell populations have been extensively studied, no consensus exists regarding which endometrial population represents the stem/progenitor cell fraction in terms of in vivo stem cell activity. We have previously reported that human endometrial side population cells (ESP, but not endometrial main population cells (EMP, exhibit stem cell-like properties, including in vivo reconstitution of endometrium-like tissues when xenotransplanted into immunodeficient mice. The reconstitution efficiency, however, was low presumably because ESP cells alone could not provide a sufficient microenvironment (niche to support their stem cell activity. The objective of this study was to establish a novel in vivo endometrial stem cell assay employing cell tracking and tissue reconstitution systems and to examine the stem cell properties of ESP through use of this assay. METHODOLOGY/PRINCIPAL FINDINGS: ESP and EMP cells isolated from whole endometrial cells were infected with lentivirus to express tandem Tomato (TdTom, a red fluorescent protein. They were mixed with unlabeled whole endometrial cells and then transplanted under the kidney capsule of ovariectomized immunodeficient mice. These mice were treated with estradiol and progesterone for eight weeks and nephrectomized. All of the grafts reconstituted endometrium-like tissues under the kidney capsules. Immunofluorescence revealed that TdTom-positive cells were significantly more abundant in the glandular, stromal, and endothelial cells of the reconstituted endometrium in mice transplanted with TdTom-labeled ESP cells than those with TdTom-labeled EMP cells. CONCLUSIONS/SIGNIFICANCE: We have established a novel in vivo endometrial stem cell assay in which multi-potential differentiation can be identified through cell tracking during in vivo

  18. A double-blind, randomized quantitative comparison of calcitriol ointment and calcipotriol ointment on epidermal cell populations, proliferation and differentiation.

    NARCIS (Netherlands)

    Korver, J.E.M.; Vissers, W.H.P.M.; Rens, D.W.A. van; Pasch, M.C.; Erp, P.E.J. van; Boezeman, J.B.M.; Kerkhof, P.C.M. van de

    2007-01-01

    BACKGROUND: Calcitriol and calcipotriol are widely used in the topical treatment of psoriasis. However, studies comparing both treatment modalities are scarce. Especially, there are almost no studies comparing the effects on epidermal cell populations in a quantitative manner. OBJECTIVES: The aim of

  19. Men's and Women's Health Beliefs Differentially Predict Coronary Heart Disease Incidence in a Population-Based Sample

    Science.gov (United States)

    Korin, Maya Rom; Chaplin, William F.; Shaffer, Jonathan A.; Butler, Mark J.; Ojie, Mary-Jane; Davidson, Karina W.

    2013-01-01

    Objective: To examine gender differences in the association between beliefs in heart disease preventability and 10-year incidence of coronary heart disease (CHD) in a population-based sample. Methods: A total of 2,688 Noninstitutionalized Nova Scotians without prior CHD enrolled in the Nova Scotia Health Study (NSHS95) and were followed for 10…

  20. Mitochondrial analysis of a Byzantine population reveals the differential impact of multiple historical events in South Anatolia.

    Science.gov (United States)

    Ottoni, Claudio; Ricaut, François-X; Vanderheyden, Nancy; Brucato, Nicolas; Waelkens, Marc; Decorte, Ronny

    2011-05-01

    The archaeological site of Sagalassos is located in Southwest Turkey, in the western part of the Taurus mountain range. Human occupation of its territory is attested from the late 12th millennium BP up to the 13th century AD. By analysing the mtDNA variation in 85 skeletons from Sagalassos dated to the 11th-13th century AD, this study attempts to reconstruct the genetic signature potentially left in this region of Anatolia by the many civilizations, which succeeded one another over the centuries until the mid-Byzantine period (13th century BC). Authentic ancient DNA data were determined from the control region and some SNPs in the coding region of the mtDNA in 53 individuals. Comparative analyses with up to 157 modern populations allowed us to reconstruct the origin of the mid-Byzantine people still dwelling in dispersed hamlets in Sagalassos, and to detect the maternal contribution of their potential ancestors. By integrating the genetic data with historical and archaeological information, we were able to attest in Sagalassos a significant maternal genetic signature of Balkan/Greek populations, as well as ancient Persians and populations from the Italian peninsula. Some contribution from the Levant has been also detected, whereas no contribution from Central Asian population could be ascertained. PMID:21224890

  1. The spatial genetic differentiation of the legume pod borer, Maruca vitrata F. (Lepidoptera: Pyralidae) populations in West Africa

    Science.gov (United States)

    The legume pod borer, Maruca vitrata, is an endemic insect pest that causes significant yield loss to the cowpea crop in West Africa, and contributes to food shortages and malnutrition in native human populations. The genetic structure of Maruca vitrata was investigated among five sites from Burkin...

  2. Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean.

    Science.gov (United States)

    Thompson, K F; Patel, S; Baker, C S; Constantine, R; Millar, C D

    2016-03-01

    Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat. PMID:26626574

  3. A size-structured simulation model for evaluating management strategies in gillnet fisheries exploiting spatially differentiated populations.

    NARCIS (Netherlands)

    Pet, J.S.; Machiels, M.A.M.; Densen, van W.L.T.

    1996-01-01

    A length-structured simulation model is presented as a tool in decision making for gillnet fisheries management. The analytical model simulates the fish population dynamics and impact of the fisheries, taking into account size-dependent spatial distribution patterns and migration of the fish. The da

  4. Systematic review of differential inorganic arsenic exposure in minority, low-income, and indigenous populations in the United States

    Science.gov (United States)

    Inorganic arsenic (iAs) is carcinogenic in humans and also associated with cardiovascular, respiratory, and skin diseases. Natural and anthropogenic sources contribute to low concentrations of iAs in water, food, soil, and air. Minority and low income populations are often at hig...

  5. Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium

    Energy Technology Data Exchange (ETDEWEB)

    McDermott, Jason E.; Taylor, Ronald C.; Yoon, Hyunjin; Heffron, Fred

    2009-02-01

    Recent advances in experimental methods have provided sufficient data to consider systems as large networks of interconnected components. High-throughput determination of protein-protein interaction networks has led to the observation that topological bottlenecks, that is proteins defined by high centrality in the network, are enriched in proteins with systems-level phenotypes such as essentiality. Global transcriptional profiling by microarray analysis has been used extensively to characterize systems, for example, cellular response to environmental conditions and genetic mutations. These transcriptomic datasets have been used to infer regulatory and functional relationship networks based on co-regulation. We use the context likelihood of relatedness (CLR) method to infer networks from two datasets gathered from the pathogen Salmonella typhimurium; one under a range of environmental culture conditions and the other from deletions of 15 regulators found to be essential in virulence. Bottleneck nodes were identified from these inferred networks and we show that these nodes are significantly more likely to be essential for virulence than their non-bottleneck counterparts. A network generated using Pearson correlation did not display this behavior. Overall this study demonstrates that topology of networks inferred from global transcriptional profiles provides information about the systems-level roles of bottleneck genes. Analysis of the differences between the two CLR-derived networks suggests that the bottleneck nodes are either mediators of transitions between system states or sentinels that reflect the dynamics of these transitions.

  6. Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium.

    Science.gov (United States)

    McDermott, Jason E; Taylor, Ronald C; Yoon, Hyunjin; Heffron, Fred

    2009-02-01

    Recent advances in experimental methods have provided sufficient data to consider systems as large networks of interconnected components. High-throughput determination of protein-protein interaction networks has led to the observation that topological bottlenecks, proteins defined by high centrality in the network, are enriched in proteins with systems-level phenotypes such as essentiality. Global transcriptional profiling by microarray analysis has been used extensively to characterize systems, for example, examining cellular response to environmental conditions and effects of genetic mutations. These transcriptomic datasets have been used to infer regulatory and functional relationship networks based on co-regulation. We use the context likelihood of relatedness (CLR) method to infer networks from two datasets gathered from the pathogen Salmonella typhimurium: one under a range of environmental culture conditions and the other from deletions of 15 regulators found to be essential in virulence. Bottleneck and hub genes were identified from these inferred networks, and we show for the first time that these genes are significantly more likely to be essential for virulence than their non-bottleneck or non-hub counterparts. Networks generated using simple similarity metrics (correlation and mutual information) did not display this behavior. Overall, this study demonstrates that topology of networks inferred from global transcriptional profiles provides information about the systems-level roles of bottleneck genes. Analysis of the differences between the two CLR-derived networks suggests that the bottleneck nodes are either mediators of transitions between system states or sentinels that reflect the dynamics of these transitions.

  7. Study on traffic characteristics for a typical expressway on-ramp bottleneck considering various merging behaviors

    Science.gov (United States)

    Sun, Jie; Li, Zhipeng; Sun, Jian

    2015-12-01

    Recurring bottlenecks at freeway/expressway are considered as the main cause of traffic congestion in urban traffic system while on-ramp bottlenecks are the most significant sites that may result in congestion. In this paper, the traffic bottleneck characteristics for a simple and typical expressway on-ramp are investigated by the means of simulation modeling under the open boundary condition. In simulations, the running behaviors of each vehicle are described by a car-following model with a calibrated optimal velocity function, and lane changing actions at the merging section are modeled by a novel set of rules. We numerically derive the traffic volume of on-ramp bottleneck under different upstream arrival rates of mainline and ramp flows. It is found that the vehicles from the ramp strongly affect the pass of mainline vehicles and the merging ratio changes with the increasing of ramp vehicle, when the arrival rate of mainline flow is greater than a critical value. In addition, we clarify the dependence of the merging ratio of on-ramp bottleneck on the probability of lane changing and the length of the merging section, and some corresponding intelligent control strategies are proposed in actual traffic application.

  8. Genetic differentiation, structure, and a transition zone among populations of the pitcher plant moth Exyra semicrocea: implications for conservation.

    Directory of Open Access Journals (Sweden)

    Jessica D Stephens

    Full Text Available Pitcher plant bogs, or carnivorous plant wetlands, have experienced extensive habitat loss and fragmentation throughout the southeastern United States Coastal Plain, resulting in an estimated reduction to <3% of their former range. This situation has lead to increased management attention of these habitats and their carnivorous plant species. However, conservation priorities focus primarily on the plants since little information currently exists on other community members, such as their endemic arthropod biota. Here, we investigated the population structure of one of these, the obligate pitcher plant moth Exyra semicrocea (Lepidoptera: Noctuidae, using mitochondrial cytochrome c oxidase subunit I (COI gene sequences. Examination of 221 individuals from 11 populations across eight southeastern US states identified 51 unique haplotypes. These haplotypes belonged to one of two divergent (∼1.9-3.0% lineages separated by the Mississippi alluvial plain. Populations of the West Gulf Coastal Plain exhibited significant genetic structure, contrasting with similarly distanced populations east of the Mississippi alluvial plain. In the eastern portion of the Coastal Plain, an apparent transition zone exists between two regionally distinct population groups, with a well-established genetic discontinuity for other organisms coinciding with this zone. The structure of E. semicrocea appears to have been influenced by patchy pitcher plant bog habitats in the West Gulf Coastal Plain as well as impacts of Pleistocene interglacials on the Apalachicola-Chattahoochee-Flint River Basin. These findings, along with potential extirpation of E. semicrocea at four visited, but isolated, sites highlight the need to consider other endemic or associated community members when managing and restoring pitcher plant bog habitats.

  9. Selectivity of fish ladders: a bottleneck in Neotropical fish movement

    Directory of Open Access Journals (Sweden)

    Carlos Sérgio Agostinho

    2007-01-01

    their proportions in the downriver stretch: fish samples in the ladder were clearly dominated by a few species, including some that do not need to be translocated. Thus, selectivity constitutes an important bottleneck to initiatives for translocating fish aimed at conserving their stocks or biodiversity. It is urgent to review the decision-making process for the construction of fish passages and to evaluate the functioning of those already operating.Dezenas de escadas de peixes foram construídas em barragens de reservatórios brasileiros, mas são raros os estudos acerca de suas eficiências como instrumentos de conservação da ictiofauna Neotropical, em especial de espécies migradoras. Neste contexto, o presente estudo teve como objetivo avaliar a seletividade específica no ingresso e ascensão de peixes na escada localizada junto à barragem de Lajeado (UHE Luis Eduardo Magalhães, rio Tocantins. Amostragens foram realizadas mensalmente de novembro de 2002 a outubro de 2003 nos tanques de descanso da escada, utilizando tarrafas, e no trecho a jusante, utilizando redes de espera. A avaliação da seletividade no ingresso da escada foi realizada através da comparação da ocorrência, abundância relativa, dominância e congruência dos ranks de abundância de espécies migradoras e não migradoras na escada e no trecho imediatamente a jusante. A riqueza e abundância específica nos diferentes tanques de descanso foram utilizadas para avaliar a seletividade ao longo da escada. Os efeitos das variações temporais do nível hidrométrico de jusante e da velocidade de fluxo na seletividade foram também analisados. Das 130 espécies registradas a jusante, 63,2% foram capturadas na escada, com claro favorecimento das espécies migradoras. Entretanto, mais de 2/3 das capturas pertenceram a apenas três espécies (Rhaphiodon vulpinus, Psectrogaster amazonica e Oxydoras niger. Embora a maioria das espécies que ingressa na escada possa alcançar seu topo, constatou

  10. How Population Growth Affects Linkage Disequilibrium

    OpenAIRE

    Alan R Rogers

    2014-01-01

    The “LD curve” relates the linkage disequilibrium (LD) between pairs of nucleotide sites to the distance that separates them along the chromosome. The shape of this curve reflects natural selection, admixture between populations, and the history of population size. This article derives new results about the last of these effects. When a population expands in size, the LD curve grows steeper, and this effect is especially pronounced following a bottleneck in population size. When a population ...

  11. IDENTIFYING BOTTLENECKS FOR APPROPRIATE INFANT FEEDING IN URBAN SLUMS, ALIGARH CITY.

    Directory of Open Access Journals (Sweden)

    Saira Mehnaz

    2012-04-01

    Full Text Available Introduction: Urban population is increasing rapidly. Majority of these families are poor or landless farmers and labourers, who settle down in peri-urban areas, creating slums. Urban slums are thus growing at an alarming rate. The present study was carried out with the general objective of identifying factors which prevent access to health services. Objectives: 1. To determine the prevalence of stunting, wasting, and underweight in infants and young children. 2. To determine presence of certain micro-environmental and socioeconomic factors associated with poor nutritional status of infants and children. Methodology: Baseline study was carried out in Oct –Nov 2009 (as a part of another ongoing study and data was collected in 110 Mothers who had delivered children during the last one month. In Oct 2010 these families were visited again the infants were followed up. 39 families had shifted to another location or emigrated back to their parent state or village mostly in search of seasonal employment as reported by neighbours. One family refused to cooperate. . Two infants had died. Remaining 68 Mothers were interviewed in friendly informal manner after taking consent for study. Results: (35.4% study subjects had migrated to other areas, as reported by neighbours. Of the 68 mothers interviewed during follow up visit, previous baseline record showed that a majority were 20-30 years of age. , only 2 mothers (2.9% had exclusively breastfed for 6 months. 46 (67.6% said they had not been contacted by any health worker during the last 3 months. All 68 children were malnourished. Immunization status was poor and 94.1% children had suffered from some illness in the last one month. Conclusion: Migration is a problem which makes it difficult for providers to give continuity of care. Capacity building of the community can reduce the the bottlenecks leading to marginalization and exclusion of slum mothers from the mainstream urban health services.

  12. Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

    Science.gov (United States)

    Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

    2015-01-01

    Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

  13. A population of human brain cells expressing phenotypic markers of more than one lineage can be induced in vitro to differentiate into mesenchymal cells

    International Nuclear Information System (INIS)

    Proliferating astrocytic cells from germinal, as well as mature areas of brain parenchyma, have the characteristics of neural stem/progenitor cells and are capable of generating both neurons and glia. We previously reported that primary fetal human brain cells, designated as Normal Human Astrocytes (NHA), expressed, in addition to GFAP, Vimentin and Nestin, low levels of βIII-Tubulin, an early neuronal marker, and differentiated into neurons and astrocytes in vitro. Here, we showed that primary NHA cells co-express low levels of mesenchymal markers Fibronectin and Collagen-1 in culture. These cells transitioned into mesenchymal-like cells when cultured in adherent conditions in serum containing media. The mesenchymal-like derivatives of these cells were characterized based on their morphological changes, high expression of Vimentin and extracellular matrix (ECM) proteins, Collagen-1 and Fibronectin, and decline of neural markers. When incubated in osteogenic and adipogenic induction media, the mesenchymal-like cells differentiated into osteoblasts and adipocytes. Furthermore, NHA cells express markers of neural crest cells, SOX-10 and p75. These data support the idea of ectoderm-derived mesenchymal lineages. These findings suggest that a population of primitive fetal brain cells with neural/neural crest/mesenchymal phenotype, resembles the remarkable phenotypic plasticity of neural crest cells, and differentiates into adipocytes and osteocytes under the influence of environmental factors

  14. Herbivory Differentially Affects Plant Fitness in Three Populations of the Perennial Herb Lythrum salicaria along a Latitudinal Gradient

    OpenAIRE

    Lina Lehndal; Jon Ågren

    2015-01-01

    Herbivory can negatively and selectively affect plant fitness by reducing growth, survival and reproductive output, thereby influencing plant population dynamics and evolution. Latitudinal variation in intensity of herbivory is common, but the extent to which it translates into corresponding variation in effects on plant performance is still poorly known. We tested the hypothesis that variation in the fitness-consequences of herbivory mirror differences in intensity of herbivory among three n...

  15. The spatial genetic differentiation of the legume pod borer, Maruca vitrata F. (Lepidoptera: Crambidae) populations in West Africa

    KAUST Repository

    Agunbiade, Tolulope A.

    2012-04-17

    The legume pod borer, Maruca vitrata, is an endemic insect pest that causes significant yield loss to the cowpea crop in West Africa. The application of population genetic tools is important in the management of insect pests but such data on M. vitrata is lacking. We applied a set of six microsatellite markers to assess the population structure of M. vitrata collected at five sites from Burkina Faso, Niger and Nigeria. Observed polymorphisms ranged from one (marker 3393) to eight (marker 32008) alleles per locus. Observed and expected heterozygosities ranged from 0.0 to 0.8 and 0.0 to 0.6, respectively. Three of the loci in samples from Nigeria and Burkina Faso deviated significantly from Hardy-Weinberg Equilibrium (HWE), whereas no loci deviated significantly in samples from Niger. Analysis of molecular variance (AMOVA) indicated that 67.3% level of the genetic variation was within individuals compared to 17.3% among populations. A global estimate of F ST=0.1 (ENA corrected F ST=0.1) was significant (Pa=0.05) and corroborated by pairwise F ST values that were significant among all possible comparisons. A significant correlation was predicted between genetic divergence and geographic distance between subpopulations (R2=0.6, P=0.04), and cluster analysis by the program STRUCTURE predicted that co-ancestry of genotypes were indicative of three distinct populations. The spatial genetic variance among M. vitrata in West Africa may be due to limited gene flow, south-north seasonal movement pattern or other reproductive barriers. This information is important for the cultural, chemical and biological control strategies for managing M. vitrata. Copyright © 2012 Cambridge University Press.

  16. Comparison of haplotype frequencies differentiate fall armyworm (Lepidoptera : Noctuidae) corn-strain populations from Florida and Brazil

    OpenAIRE

    Nagoshi, R. N.; Silvie, Pierre; Meagher, R.L.

    2007-01-01

    Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a major economic pest throughout the Western Hemisphere. Populations can be subdivided into two morphologically identical but genetically distinct strains (corn-strain and rice-strain) that differ in their host plant preferences. These strains can be distinguished by using polymorphisms in the mitochondrial cytochrome oxidase I gene. Additional sequence analysis of this locus identified two sites that were highly p...

  17. The spatial genetic differentiation of the legume pod borer, Maruca vitrata F. (Lepidoptera: Crambidae) populations in West Africa.

    Science.gov (United States)

    Agunbiade, T A; Coates, B S; Kim, K S; Forgacs, D; Margam, V M; Murdock, L L; Ba, M N; Binso-Dabire, C L; Baoua, I; Ishiyaku, M F; Tamò, M; Pittendrigh, B R

    2012-10-01

    The legume pod borer, Maruca vitrata, is an endemic insect pest that causes significant yield loss to the cowpea crop in West Africa. The application of population genetic tools is important in the management of insect pests but such data on M. vitrata is lacking. We applied a set of six microsatellite markers to assess the population structure of M. vitrata collected at five sites from Burkina Faso, Niger and Nigeria. Observed polymorphisms ranged from one (marker 3393) to eight (marker 32008) alleles per locus. Observed and expected heterozygosities ranged from 0.0 to 0.8 and 0.0 to 0.6, respectively. Three of the loci in samples from Nigeria and Burkina Faso deviated significantly from Hardy-Weinberg Equilibrium (HWE), whereas no loci deviated significantly in samples from Niger. Analysis of molecular variance (AMOVA) indicated that 67.3% level of the genetic variation was within individuals compared to 17.3% among populations. A global estimate of F ST=0.1 (ENA corrected F ST=0.1) was significant (P⩽0.05) and corroborated by pairwise F ST values that were significant among all possible comparisons. A significant correlation was predicted between genetic divergence and geographic distance between subpopulations (R2=0.6, P=0.04), and cluster analysis by the program STRUCTURE predicted that co-ancestry of genotypes were indicative of three distinct populations. The spatial genetic variance among M. vitrata in West Africa may be due to limited gene flow, south-north seasonal movement pattern or other reproductive barriers. This information is important for the cultural, chemical and biological control strategies for managing M. vitrata.

  18. Skull and limb morphology differentially track population history and environmental factors in the transition to agriculture in Europe

    OpenAIRE

    von Cramon-Taubadel, N.; Stock, J. T.; Pinhasi, R.

    2013-01-01

    The Neolithic transition in Europe was a complex mosaic spatio-temporal process, involving both demic diffusion from the Near East and the cultural adoption of farming practices by indigenous hunter–gatherers. Previous analyses of Mesolithic hunter–gatherers and Early Neolithic farmers suggest that cranial shape variation preserves the population history signature of the Neolithic transition. However, the extent to which these same demographic processes are discernible in the postcranium is p...

  19. 16S partial gene mitochondrial DNA and internal transcribed spacers ribosomal DNA as differential markers of Trichuris discolor populations.

    Science.gov (United States)

    Callejón, R; Halajian, A; de Rojas, M; Marrugal, A; Guevara, D; Cutillas, C

    2012-05-25

    Comparative morphological, biometrical and molecular studies of Trichuris discolor isolated from Bos taurus from Spain and Iran was carried out. Furthermore, Trichuris ovis isolated from B. taurus and Capra hircus from Spain has been, molecularly, analyzed. Morphological studies revealed clear differences between T. ovis and T. discolor isolated from B. taurus but differences were not observed between populations of T. discolor isolated from different geographical regions. Nevertheless, the molecular studies based on the amplification and sequencing of the internal transcribed spacers 1 and 2 ribosomal DNA and 16S partial gene mitochondrial DNA showed clear differences between both populations of T. discolor from Spain and Iran suggesting two cryptic species. Phylogenetic studies corroborated these data. Thus, phylogenetic trees based on ITS1, ITS2 and 16S partial gene sequences showed that individuals of T. discolor from B. taurus from Iran clustered together and separated, with high bootstrap values, of T. discolor isolated from B. taurus from Spain, while populations of T. ovis from B. taurus and C. hircus from Spain clustered together but separated with high bootstrap values of both populations of T. discolor. Furthermore, a comparative phylogenetic study has been carried out with the ITS1and ITS2 sequences of Trichuris species from different hosts. Three clades were observed: the first clustered all the species of Trichuris parasitizing herbivores (T. discolor, T. ovis, Trichuris leporis and Trichuris skrjabini), the second clustered all the species of Trichuris parasitizing omnivores (Trichuris trichiura and Trichuris suis) and finally, the third clustered species of Trichuris parasitizing carnivores (Trichuris muris, Trichuris arvicolae and Trichuris vulpis).

  20. Comparative population genetics of the German shepherd dog in South Africa

    Directory of Open Access Journals (Sweden)

    N. J. Coutts

    2010-01-01

    Full Text Available Modern breeding practices strive to achieve distinctive phenotypic uniformity in breeds of dogs, but these strategies are associated with the inevitable loss of genetic diversity. Thus, in parallel with the morphological variation displayed by breeds, purebred dogs commonly express genetic defects as a result of the inbreeding associated with artificial selection and the reduction of selection against disease phenotypes. Microsatellite marker analyses of 15 polymorphic canine loci were used to investigate measures of genetic diversity and population differentiation within and between German-bred and South African-bred German shepherd dogs. These data were quantified by comparison with typically outbred mongrel or crossbred dogs. Both the imported and locally-bred German shepherd dogs exhibited similar levels of genetic diversity. The breed is characterised by only a moderate loss of genetic diversity relative to outbred dogs, despite originating from a single founding sire and experiencing extensive levels of inbreeding throughout the history of the breed. Non-significant population differentiation between the ancestral German and derived South African populations indicates sufficient contemporary gene flow between these populations, suggesting that migration resulting from the importation of breeding stock has mitigated the effects of random genetic drift and a population bottleneck caused by the original founder event in South Africa. Significant differentiation between the combined German shepherd dog population and the outbred dogs illustrates the effects of selection and genetic drift on the breed since its establishment just over 100 years ago.

  1. Population Growth, Migration, and Changes in the Racial Differential in Imprisonment in the United States, 1940–1980

    Directory of Open Access Journals (Sweden)

    David J. Harding

    2016-07-01

    Full Text Available The proportion of U.S. prison inmates who were black increased dramatically between 1940 and 2000. While about two-thirds of the increase occurred between 1940 and 1970, most recent research analyzes the period after 1970, focusing on explanations such as the war on drugs, law-and-order politics, discrimination, inequality, and racial threat. We analyze the growth in the racial difference in incarceration between 1940 and 1980, focusing on the role of demographic processes, particularly population growth, migration, and urbanization. We implement three analyses to assess the role of these demographic processes: (1 a simple accounting model that decomposes the national trend into population growth, changes in arrests, and changes in sentencing; (2 a model of state variation in incarceration that decomposes the racial difference in incarceration into population change, migration between states with different incarceration rates, and other processes; and (3 race-specific models of within-state variation in incarceration rates using state characteristics coupled with a decomposition of the role of changes in state characteristics.

  2. Effects of speed bottleneck on traffic flow with feedback control signal

    Science.gov (United States)

    Zhu, Kangli; Bi, Jiantao; Wu, Jianjun; Li, Shubin

    2016-09-01

    Various car-following models (CMs) have been developed to capture the complex characteristics of microscopic traffic flow, among which the coupled map CM can better reveal and reflect various phenomena of practical traffic flow. Capacity change at bottleneck contributes to high-density traffic flow upstream the bottleneck and contains very complex dynamic behavior. In this paper, we analyze the effect of speed bottleneck on the spatial-temporal evolution characteristics of traffic flow, and propose a method to reduce traffic congestion with the feedback control signal based on CM. Simulation results highlight the potential of using the feedback signal to control the stop-and-go wave and furthermore to alleviate the traffic congestion effectively.

  3. Differentiation of Tetragenococcus populations occurring in products and manufacturing processes of puffer fish ovaries fermented with rice-bran.

    Science.gov (United States)

    Kobayashi, T; Kimura, B; Fujii, T

    2000-06-01

    Tetragenococcus strains isolated from the manufacturing process of Japanese puffer fish ovaries fermented with rice-bran were characterized and differentiated phenotypically and genotypically. A total of 413 Tetragenococcus isolates were evaluated. On the basis of five representative substrates, the isolates were grouped into seven groups. An RFLP (restriction fragment length polymorphisms) analysis of the 16S rRNA gene of representative strains of major groups revealed that they could be grouped into two groups: one was identified as the most prominent halophilic lactic acid coccus, Tetragenococcus halophilus, and the other as T. muriaticus, which has recently been added to the genus Tetragenococcus as a new species. Physiologically, the major differences between the two groups were found in the ability to grow in medium not supplemented with NaCl and the fermentation of L-arabinose, sucrose and D-mannitol, and several other carbohydrates. PMID:10857547

  4. Common variants at 9q22.33, 14q13.3, and ATM loci, and risk of differentiated thyroid cancer in the French Polynesian population.

    Directory of Open Access Journals (Sweden)

    Stéphane Maillard

    Full Text Available French Polynesia has one of the highest incidence rates of thyroid cancer worldwide. Relationships with the atmospheric nuclear weapons tests and other environmental, biological, or behavioral factors have already been reported, but genetic susceptibility has yet to be investigated. We assessed the contribution of polymorphisms at the 9q22.33 and 14q13.3 loci identified by GWAS, and within the DNA repair gene ATM, to the risk of differentiated thyroid cancer (DTC in 177 cases and 275 matched controls from the native population.For the GWAS SNP rs965513 near FOXE1, an association was found between genotypes G/A and A/A, and risk of DTC. A multiplicative effect of allele A was even noted. An excess risk was also observed in individuals carrying two long alleles of the poly-alanine tract expansion in FOXE1, while no association was observed with rs1867277 falling in the promoter region of the gene. In contrast, the GWAS SNP rs944289 (NKX2-1 did not show any significant association. Although the missense substitution D1853N (rs1801516 in ATM was rare in the population, carriers of the minor allele (A also showed an excess risk. The relationships between these five polymorphisms and the risk of DTC were not contingent on the body surface area, body mass index, ethnicity or dietary iodine intake. However, an interaction was evidenced between the thyroid radiation dose and rs944289.A clear link could not be established between the high incidence in French Polynesia and the studied polymorphisms, involved in susceptibility to DTC in other populations. Important variation in allele frequencies was observed in the Polynesian population as compared to the European populations. For FOXE1 rs965513, the direction of association and the effect size was similar to that observed in other populations, whereas for ATM rs1801516, the minor allele was associated to an increased risk in the Polynesian population and with a decreased risk in the European population.

  5. "BOTTLENECK" AND COUNTERMEASURE OF HIGH-TECHNOLOGIZATION OF MARINE INDUSTRY IN CHINA

    Institute of Scientific and Technical Information of China (English)

    LUAN Wei-xin

    2004-01-01

    This article deeply researched into the existent five problems and four main "bottlenecks" in the high-technologization of marine industry in China on the basis of analyzing the new trends in international marine problems and the necessity of implementing the strategy of developing China based on marine. This article brought up specific measures to the five "bottlenecks" according to the situations, and pointed out that new marine industry should be high-technologization and the traditional marine industry should be reformed by high-technique. The research results may provide the scientific basis for realizing the high-technologization of marine industry in China.

  6. Reducing the Analytical Bottleneck for Domain Scientists: Lessons from a Climate Data Visualization Case Study

    Energy Technology Data Exchange (ETDEWEB)

    Dasgupta, Aritra; Poco, Jorge; Bertini, Enrico; Silva, Claudio T.

    2016-01-31

    The gap between large-scale data production rate and the rate of generation of data-driven scientific insights has led to an analytical bottleneck in scientific domains like climate, biology, etc. This is primarily due to the lack of innovative analytical tools that can help scientists efficiently analyze and explore alternative hypotheses about the data, and communicate their findings effectively to a broad audience. In this paper, by reflecting on a set of successful collaborative research efforts between with a group of climate scientists and visualization researchers, we introspect how interactive visualization can help reduce the analytical bottleneck for domain scientists.

  7. Mechanical food properties and dental topography differentiate three populations of Lemur catta in southwest Madagascar.

    Science.gov (United States)

    Yamashita, Nayuta; Cuozzo, Frank P; Sauther, Michelle L; Fitzgerald, Emily; Riemenschneider, Andrea; Ungar, Peter S

    2016-09-01

    Determining the proximate causes of tooth wear remains a major focus of dental study. Here we compare the diets of three ring-tailed lemur (Lemur catta) populations and examine how different dietary components may contribute to patterns of wear-related tooth shape. Casts were made from dental impressions collected between 2003 and 2010 from lemurs in the gallery and spiny/mixed forests of the Bezá Mahafaly Special Reserve (BMSR; Parcels 1 and 2) and the spiny/mixed forests of Tsimanampesotse National Park (TNP), Madagascar. Tooth shape variables (occlusal relief and slope, angularity) were analyzed using dental topographic analysis. Focal observations and food mechanical properties (FMPs: toughness, hardness, elastic modulus) were conducted and tested, respectively, during wet and dry seasons from 2008 to 2012. We found that FMPs correlate with patterns of dental topography in these three populations. Specifically, food toughness and elastic modulus correlate with the dental variables, but hardness does not. Average food toughness and elastic modulus, but not hardness, are highest in BMSR Parcel 2, followed by BMSR Parcel 1 and TNP. Occlusal relief and slope, which serve as proxies for tooth wear, show the greatest wear in Parcel 2 and the least in TNP. Angularity is also more pronounced in TNP. Further, dental topographic patterns correspond to reliance on Tamarindus indica (tamarind) fruit. Both BMSR populations consume tamarind at high frequencies in the dry season, but the fruits are rare at TNP and only occasionally consumed. Thus, high seasonal tamarind consumption and its mechanical values help explain the low dental relief and slope among BMSR lemurs. By investigating the ecology of a single widespread species across a variety of habitats, we have been able to link specific components of diet to patterns of dental topography in this species. This provides a context for interpreting wear-related tooth shape changes more generally, illustrating that

  8. Research on polymorphism of production logistics bottleneck based on bottleneck index%基于瓶颈指数的生产物流瓶颈多态性研究

    Institute of Scientific and Technical Information of China (English)

    唐娟; 刘志

    2011-01-01

    Aiming at the shifting phenomenon of production logistics in the manufacturing shop under uncertain environments, the conceptual model which is composed of main bottleneck, second bottleneck, sensitive bottleneck and insensitive bottleneck is built;taken production capability,production load,quality assurance capability and production cost of manufacturing unit into con-sideration ,mathematical model of bottleneck index is established to measure bottleneck degree accurately;based on bottleneck in-dex, the prediction mechanism is established to identify bottleneck and non-bottleneck,main bottleneck and second bottleneck, then sensitive coefficient of bottleneck shifting is founded to accurately judge sensitive bottleneck and insensitive bottleneck of the manufacturing shop,which provide a method support for forecasting and monitoring the phenomenon of bottleneck shifting.%针对不确定性环境下制造车间生产物流瓶颈漂移现象,建立以主瓶颈、次瓶颈、灵敏型瓶颈和迟钝型瓶颈为主的瓶颈多态性概念模型;综合考虑制造单元的生产能力、生产负荷、质量保证能力和生产成本,构建瓶颈指数数学模型,以实现制造单元瓶颈度的准确度量;以瓶颈指数为基础,构建瓶颈及主次瓶颈的预测机制,并构建瓶颈漂移敏感系数,以实现制造车间生产物流瓶颈与非瓶颈、主瓶颈和次瓶颈、灵敏型瓶颈和迟钝型瓶颈的准确判别,进而为实现瓶颈漂移现象的预测和监控提供一种方法.

  9. Study of Differential Equation Application in the Forecast of Population Growth%差分方程在人口增长预测中的应用研究

    Institute of Scientific and Technical Information of China (English)

    曾维

    2011-01-01

    In the study of population growth forecast, the accuracy of common prediction model is somewhat low and the results lack of guidance. However, the hyperbolic model and the computational complexity of differential equation model are both complex in calculating and also difficult to solve. It is not convenient for use in the area with low technology. To solve these problems, based on the gray prediction model, a differential equation model of population growth has been built. The model simulates different ages, different types of demographic changes. It can accurately predict the structural changes, changes in sex ratio, urbanization, and so on. The model was applied to predict China's population. The result is consistent of the population development prediction in the study of national population development strategy. The calculation of residuals is less than 0.2 and the model predicts good results.%在人口增长预测的研究中,关于人口总数、性别、年龄结构等预测,一般预测模型准确性较低,预测结果缺乏指导意义;而双曲模型和微分方程模型计算复杂,很难求解,不便于科技水平较低地区使用.为解决上述问题,基于灰色预测模型,提出差分方程构建人口增长预测模型.模型能仿真出不同年龄、不同类型人口变化情况,能准确预测结构变化、性别比例变化、城镇化情况等.应用模型对中国人口进行仿真预测,得到结果与国家人口发展战略研究人口发展预测相符合,为人口增长提供了较好的预测模型.

  10. Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.

    Science.gov (United States)

    Gazave, Elodie; Tassone, Erica E; Ilut, Daniel C; Wingerson, Megan; Datema, Erwin; Witsenboer, Hanneke M A; Davis, James B; Grant, David; Dyer, John M; Jenks, Matthew A; Brown, Jack; Gore, Michael A

    2016-01-01

    The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

  11. Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.

    Science.gov (United States)

    Gazave, Elodie; Tassone, Erica E; Ilut, Daniel C; Wingerson, Megan; Datema, Erwin; Witsenboer, Hanneke M A; Davis, James B; Grant, David; Dyer, John M; Jenks, Matthew A; Brown, Jack; Gore, Michael A

    2016-01-01

    The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits. PMID:27148342

  12. Age, differential growth and mortality rates in unexploited populations of Florida gar, an apex predator in the Florida Everglades

    Science.gov (United States)

    Murie, D.J.; Parkyn, D.C.; Nico, L.G.; Herod, J.J.; Loftus, W.F.

    2009-01-01

    Florida gar, Lepisosteus platyrhincus DeKay, were sampled in two canal systems in south Florida during 2000-2001 to estimate age, growth and mortality as part of the Everglades ecosystem-restoration effort. Tamiami (C-4) and L-31W canal systems had direct connections to natural wetlands of the Everglades and harboured large Florida gar populations. Of 476 fish aged, maximum ages were 19 and 10years for females and males, respectively. Maximum sizes were also larger for females compared with males (817 vs 602 mm total length). Overall, female Florida gar from both Tamiami and L-31W were larger at age than males from L-31W that, in turn, were larger at any given age than males from Tamiami. Females also had lower rates of annual mortality (Z = 0.21) than males from L-31W (Z = 0.31) or males from Tamiami (Z = 0.54). As a large and long-lived apex predator in the Everglades, Florida gar may structure lower trophic levels. Regional- and sex-specific population parameters for Florida gar will contribute to the simulation models designed to evaluate Everglades restoration alternatives. ?? 2009 Blackwell Publishing Ltd.

  13. Divergence in morphology, but not habitat use, despite low genetic differentiation among insular populations of the lizard Anolis lemurinus in Honduras

    Science.gov (United States)

    Logan, M.L.; Montgomery, Chad E.; Boback, Scott M.; Reed, R.N.; Campbell, J.A.

    2012-01-01

    Studies of recently isolated populations are useful because observed differences can often be attributed to current environmental variation. Two populations of the lizard Anolis lemurinus have been isolated on the islands of Cayo Menor and Cayo Mayor in the Cayos Cochinos Archipelago of Honduras for less than 15 000 y. We measured 12 morphometric and 10 habitat-use variables on 220 lizards across these islands in 2 y, 2008 and 2009. The goals of our study were (1) to explore patterns of sexual dimorphism, and (2) to test the hypothesis that differences in environment among islands may have driven divergence in morphology and habitat use despite genetic homogeneity among populations. Although we found no differences among sexes in habitat use, males had narrower pelvic girdles and longer toe pads on both islands. Between islands, males differed in morphology, but neither males nor females differed in habitat use. Our data suggest that either recent selection has operated differentially on males despite low genetic dill'erentiation, or that they display phenotypic plasticity in response to environmental variation. We suggest that patterns may be driven by variation in intrapopulation density or differences in predator diversity among islands.

  14. Modest genetic differentiation among North American populations of Sarcocystic neurona may reflect expansion in its geographic range

    Science.gov (United States)

    Sundar, N.; Asmundsson, I.M.; Thomas, N.J.; Samuel, M.D.; Dubey, J.P.; Rosenthal, B.M.

    2008-01-01

    Sarcocystis neurona is an important cause of neurological disease in horses (equine protozoal myeloencephalitis, EPM) and sea otters in the United States. In addition, EPM-like disease has been diagnosed in several other land and marine mammals. Opossums are its only definitive hosts. Little genetic diversity among isolates of S. neurona from different hosts has been reported. Here, we used 11 microsatellites to characterize S. neurona DNA isolated from natural infections in 22 sea otters (Enhydra lutris) from California and Washington and in 11 raccoons (Procyon lotor) and 1 striped skunk (Mephitis mephitis) from Wisconsin. By jointly analyzing these 34 isolates with 26 isolates previously reported, we determined that geographic barriers may limit S. neurona dispersal and that only a limited subset of possible parasite genotypes may have been introduced to recently established opossum populations. Moreover, our study confirms that diverse intermediate hosts share a common infection source, the opossum (Didelphis virginiana).

  15. Differential effects of drugs targeting cancer stem cell (CSC) and non-CSC populations on lung primary tumors and metastasis.

    Science.gov (United States)

    Larzabal, Leyre; El-Nikhely, Nefertiti; Redrado, Miriam; Seeger, Werner; Savai, Rajkumar; Calvo, Alfonso

    2013-01-01

    Cancer stem cells (CSCs) are thought to be responsible for tumor initiation and recurrence after chemotherapy. Targeting CSCs and non-CSCs with specific compounds may be an effective approach to reduce lung cancer growth and metastasis. The aim of this study was to investigate the effect of salinomycin, a selective inhibitor of CSCs, with or without combination with paclitaxel, in a metastatic model. To evaluate the effect of these drugs in metastasis and tumor microenvironment we took advantage of the immunocompetent and highly metastatic LLC mouse model. Aldefluor assays were used to analyze the ALDH+/- populations in murine LLC and human H460 and H1299 lung cancer cells. Salinomycin reduced the proportion of ALDH+ CSCs in LLC cells, whereas paclitaxel increased such population. The same effect was observed for the H460 and H1299 cell lines. Salinomycin reduced the tumorsphere formation capacity of LLC by more than 7-fold, but paclitaxel showed no effect. In in vivo experiments, paclitaxel reduced primary tumor volume but increased the number of metastatic nodules (p<0.05), whereas salinomycin had no effect on primary tumors but reduced lung metastasis (p<0.05). Combination of both drugs did not improve the effect of single therapies. ALDH1A1, SOX2, CXCR4 and SDF-1 mRNA levels were higher in metastatic lesions than in primary tumors, and were significantly elevated in both locations by paclitaxel treatment. On the contrary, such levels were reduced (or in some cases did not change) when mice were administered with salinomycin. The number of F4/80+ and CD11b+ cells was also reduced upon administration of both drugs, but particularly in metastasis. These results show that salinomycin targets ALDH+ lung CSCs, which has important therapeutic effects in vivo by reducing metastatic lesions. In contrast, paclitaxel (although reducing primary tumor growth) promotes the selection of ALDH+ cells that likely modify the lung microenvironment to foster metastasis. PMID

  16. Differential effects of drugs targeting cancer stem cell (CSC and non-CSC populations on lung primary tumors and metastasis.

    Directory of Open Access Journals (Sweden)

    Leyre Larzabal

    Full Text Available Cancer stem cells (CSCs are thought to be responsible for tumor initiation and recurrence after chemotherapy. Targeting CSCs and non-CSCs with specific compounds may be an effective approach to reduce lung cancer growth and metastasis. The aim of this study was to investigate the effect of salinomycin, a selective inhibitor of CSCs, with or without combination with paclitaxel, in a metastatic model. To evaluate the effect of these drugs in metastasis and tumor microenvironment we took advantage of the immunocompetent and highly metastatic LLC mouse model. Aldefluor assays were used to analyze the ALDH+/- populations in murine LLC and human H460 and H1299 lung cancer cells. Salinomycin reduced the proportion of ALDH+ CSCs in LLC cells, whereas paclitaxel increased such population. The same effect was observed for the H460 and H1299 cell lines. Salinomycin reduced the tumorsphere formation capacity of LLC by more than 7-fold, but paclitaxel showed no effect. In in vivo experiments, paclitaxel reduced primary tumor volume but increased the number of metastatic nodules (p<0.05, whereas salinomycin had no effect on primary tumors but reduced lung metastasis (p<0.05. Combination of both drugs did not improve the effect of single therapies. ALDH1A1, SOX2, CXCR4 and SDF-1 mRNA levels were higher in metastatic lesions than in primary tumors, and were significantly elevated in both locations by paclitaxel treatment. On the contrary, such levels were reduced (or in some cases did not change when mice were administered with salinomycin. The number of F4/80+ and CD11b+ cells was also reduced upon administration of both drugs, but particularly in metastasis. These results show that salinomycin targets ALDH+ lung CSCs, which has important therapeutic effects in vivo by reducing metastatic lesions. In contrast, paclitaxel (although reducing primary tumor growth promotes the selection of ALDH+ cells that likely modify the lung microenvironment to foster

  17. Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe.

    Directory of Open Access Journals (Sweden)

    Elina Salmela

    Full Text Available BACKGROUND: Genome-wide data provide a powerful tool for inferring patterns of genetic variation and structure of human populations. PRINCIPAL FINDINGS: In this study, we analysed almost 250,000 SNPs from a total of 945 samples from Eastern and Western Finland, Sweden, Northern Germany and Great Britain complemented with HapMap data. Small but statistically significant differences were observed between the European populations (F(ST = 0.0040, p<10(-4, also between Eastern and Western Finland (F(ST = 0.0032, p<10(-3. The latter indicated the existence of a relatively strong autosomal substructure within the country, similar to that observed earlier with smaller numbers of markers. The Germans and British were less differentiated than the Swedes, Western Finns and especially the Eastern Finns who also showed other signs of genetic drift. This is likely caused by the later founding of the northern populations, together with subsequent founder and bottleneck effects, and a smaller population size. Furthermore, our data suggest a small eastern contribution among the Finns, consistent with the historical and linguistic background of the population. SIGNIFICANCE: Our results warn against a priori assumptions of homogeneity among Finns and other seemingly isolated populations. Thus, in association studies in such populations, additional caution for population structure may be necessary. Our results illustrate that population history is often important for patterns of genetic variation, and that the analysis of hundreds of thousands of SNPs provides high resolution also for population genetics.

  18. About the Role of the Bottleneck/Cork Interface on Oxygen Transfer.

    Science.gov (United States)

    Lagorce-Tachon, Aurélie; Karbowiak, Thomas; Paulin, Christian; Simon, Jean-Marc; Gougeon, Régis D; Bellat, Jean-Pierre

    2016-09-01

    The transfer of oxygen through a corked bottleneck was investigated using a manometric technique. First, the effect of cork compression on oxygen transfer was evaluated without considering the glass/cork interface. No significant effect of cork compression (at 23% strain, corresponding to the compression level of cork in a bottleneck for still wines) was noticeable on the effective diffusion coefficient of oxygen. The mean value of the effective diffusion coefficient is equal to 10(-8) m(2) s(-1), with a statistical distribution ranging from 10(-10) to 10(-7) m(2) s(-1), which is of the same order of magnitude as for the non-compressed cork. Then, oxygen transfer through cork compressed in a glass bottleneck was determined to assess the effect of the glass/cork interface. In the particular case of a gradient-imposed diffusion of oxygen through our model corked bottleneck system (dry cork without surface treatment; 200 and ∼0 hPa of oxygen on both sides of the sample), the mean effective diffusion coefficient is of 5 × 10(-7) m(2) s(-1), thus revealing the possible importance of the role of the glass/stopper interface in the oxygen transfer.

  19. Self-organized phenomena of pedestrian counterflow through a wide bottleneck in a channel

    Science.gov (United States)

    Dong, Li-Yun; Lan, Dong-Kai; Li, Xiang

    2016-09-01

    The pedestrian counterflow through a bottleneck in a channel shows a variety of flow patterns due to self-organization. In order to reveal the underlying mechanism, a cellular automaton model was proposed by incorporating the floor field and the view field which reflects the global information of the studied area and local interactions with others. The presented model can well reproduce typical collective behaviors, such as lane formation. Numerical simulations were performed in the case of a wide bottleneck and typical flow patterns at different density ranges were identified as rarefied flow, laminar flow, interrupted bidirectional flow, oscillatory flow, intermittent flow, and choked flow. The effects of several parameters, such as the size of view field and the width of opening, on the bottleneck flow are also analyzed in detail. The view field plays a vital role in reproducing self-organized phenomena of pedestrian. Numerical results showed that the presented model can capture key characteristics of bottleneck flows. Project supported by the National Basic Research Program of China (Grant No. 2012CB725404) and the National Natural Science Foundation of China (Grant Nos. 11172164 and 11572184).

  20. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

    DEFF Research Database (Denmark)

    Rebolledo-Jaramillo, Boris; Su, Marcia Shu-Wei; Stoler, Nicholas;

    2014-01-01

    The manifestation of mitochondrial DNA (mtDNA) diseases depends on the frequency of heteroplasmy (the presence of several alleles in an individual), yet its transmission across generations cannot be readily predicted owing to a lack of data on the size of the mtDNA bottleneck during oogenesis...

  1. Temperature dependence of the polariton relaxation bottleneck in a GaN microcavity

    Energy Technology Data Exchange (ETDEWEB)

    Stokker-Cheregi, F. [LENS and Department of Physics, University of Florence (Italy); NILPRP, Lasers Department, Magurele, Bucharest (Romania); Vinattieri, A.; Colocci, M.; Gurioli, M. [LENS and Department of Physics, University of Florence (Italy); Semond, F.; Leroux, M.; Massies, J. [CRHEA-CNRS, Valbonne (France); Sellers, I.R. [CRHEA-CNRS, Valbonne (France); Department of Physics, University of Buffalo, NY (United States)

    2008-07-01

    We present an experimental study aimed to investigate discuss the possible presence of a phonon bottleneck in a GaN bulk microcavity. Clear anticrossing between the lower (LP) and upper polariton (UP) branches has been observed up to room temperature in photoluminescence (PL) by angular measurements with a Rabi splitting of the order of 30 meV. In order to determine the presence of a relaxation bottleneck, angular PL measurements have been performed at different temperatures for negative detuning. At low T the PL shows a clear maximum, at the angle corresponding to the resonance between the exciton and the photon modes, which is an experimental demonstration of the presence of a relaxation bottleneck. The PL enhancement in resonance condition is suppressed with increasing T and it almost disappears at room temperature. We therefore demonstrate that the exciton-phonon interaction washes out the polariton bottleneck in GaN MCs at room temperature. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  2. Identifikasi Bottleneck pada Hasil Ekstraksi Proses Bisnis ERP dengan Membandingkan Algoritma Alpha++ dan Heuristics Miner

    Directory of Open Access Journals (Sweden)

    Laeila Mardhatillah

    2012-09-01

    Full Text Available Saat ini banyak perusahaan menggunakan sistem informasi untuk menunjang proses bisnis. Namun kenyataannya hanya beberapa perusahaan yang melakukan evaluasi untuk proses bisnis pada sistem informasi tersebut. Evaluasi ini didapat dari data Event log yang merupakan hasil proses ekstrasi ERP. Cara melakukan evaluasi yaitu dengan process mining. Process mining berfungsi untuk menggali proses transaksi sehingga terbentuk suatu workflow proses bisnis yang actual. Workflow proses bisnis ini akan digambarkan dalam bentuk Petri Net, selanjutnya dari Petri Net inilah akan dilakukan analisis untuk mengidentifikasi adanya BottleneckBottleneck merupakan peristiwa pada suatu transaksi yang memiliki waktu tunggu yang lebih lama dibandingkan transaksi lainnya dalam suatu proses bisnis. Dengan adanya PROM Tools maka penggambaran mengenai proses bisnis ERP dapat terbentuk. Penggambaran model tersebut menggunakan dua algoritma, yaitu Algoritma Alpha ++ dan Heuristics Miner. Kedua algoritma ini digunakan untuk mencari perbedaan bottleneck yang terjadi. Dari penelitian didapatkan  hasil bahwa algoritma sangat mempengaruhi letak bottleneck. Letak tersebut didasarkan pada perhitungan waktu token yang ada pada place (tempat antara dua transisi atau dua transaksi saat terbentuk model.

  3. Consequences of the Now-or-Never bottleneck for signed versus spoken languages.

    Science.gov (United States)

    Emmorey, Karen

    2016-01-01

    Signed and spoken languages emerge, change, are acquired, and are processed under distinct perceptual, motor, and memory constraints. Therefore, the Now-or-Never bottleneck has different ramifications for these languages, which are highlighted in this commentary. The extent to which typological differences in linguistic structure can be traced to processing differences provides unique evidence for the claim that structure is processing. PMID:27562833

  4. Evaluation of bottlenecks in the late stages of protein secretion in Bacillus subtilis

    NARCIS (Netherlands)

    Bolhuis, A; Tjalsma, H; Smith, H.E; Meima, R.; Venema, G; Bron, S; van Dijl, J.M

    1999-01-01

    Despite a high capacity for secretion of homologous proteins, the secretion of heterologous proteins by Bacillus subtilis is frequently inefficient. In the present studies, we have investigated and compared bottlenecks in the secretion of four heterologous proteins: Bacillus lichenifomis alpha-amyla

  5. About the Role of the Bottleneck/Cork Interface on Oxygen Transfer.

    Science.gov (United States)

    Lagorce-Tachon, Aurélie; Karbowiak, Thomas; Paulin, Christian; Simon, Jean-Marc; Gougeon, Régis D; Bellat, Jean-Pierre

    2016-09-01

    The transfer of oxygen through a corked bottleneck was investigated using a manometric technique. First, the effect of cork compression on oxygen transfer was evaluated without considering the glass/cork interface. No significant effect of cork compression (at 23% strain, corresponding to the compression level of cork in a bottleneck for still wines) was noticeable on the effective diffusion coefficient of oxygen. The mean value of the effective diffusion coefficient is equal to 10(-8) m(2) s(-1), with a statistical distribution ranging from 10(-10) to 10(-7) m(2) s(-1), which is of the same order of magnitude as for the non-compressed cork. Then, oxygen transfer through cork compressed in a glass bottleneck was determined to assess the effect of the glass/cork interface. In the particular case of a gradient-imposed diffusion of oxygen through our model corked bottleneck system (dry cork without surface treatment; 200 and ∼0 hPa of oxygen on both sides of the sample), the mean effective diffusion coefficient is of 5 × 10(-7) m(2) s(-1), thus revealing the possible importance of the role of the glass/stopper interface in the oxygen transfer. PMID:27564243

  6. South West Georgia: an important bottleneck for raptor migration during autumn

    NARCIS (Netherlands)

    B. Verhelst; J. Jansen; W. Vansteelant

    2011-01-01

    Counts of migrating raptors at Batumi, Georgia, revealed the eastern Black Sea coast to form one of the most important bottlenecks for raptor migration during autumn in the Eurasian-African migration system. Totals for 10 species (European Honey-buzzard Pernis apivorus, Steppe Buzzard Buteo buteo vu

  7. Dispersal and colonisation of plants in lowland streams: success rates and bottlenecks

    DEFF Research Database (Denmark)

    Riis, Tenna

    2008-01-01

    by releasing plant shoots and subsequently re-collecting the retained shoots in the study reach. The main bottleneck for plant colonisation in macrophyte-rich lowland streams is the primary colonisation (development of attached roots in the sediment from vegetative propagules or seedlings) of retained shoots...

  8. Steiner tree heuristic in the Euclidean d-space using bottleneck distances

    DEFF Research Database (Denmark)

    Lorenzen, Stephan Sloth; Winter, Pawel

    2016-01-01

    in a greedy fashion to obtain a low cost tree spanning all terminals. The weakness of this approach is that obtained solutions are topologically related to minimum spanning trees. To avoid this and to obtain even better solutions, bottleneck distances are utilized to determine good subsets of terminals...

  9. Avoiding the problem state bottleneck by strategic use of the environment

    NARCIS (Netherlands)

    Borst, Jelmer P.; Buwalda, Trudy A.; van Rijn, Hedderik; Taatgen, Niels A.

    2013-01-01

    We investigated whether environmental support can be used to circumvent the problem state bottleneck in human multitasking. Previously, it was shown that people can only maintain a single chunk of information in their problem state resource, the central part of working memory. Consequently, when the

  10. Bottleneck distances and Steiner trees in the Euclidean d-space

    DEFF Research Database (Denmark)

    Winter, Pawel; Lorenzen, Stephan Sloth

    fashion to obtain low cost trees spanning all terminals. The weakness of this approach is that obtained solutions are topologically related to minimum spanning trees. To obtain better solutions, bottleneck distances are utilized to determine good subsets of terminals without being constrained...

  11. The nocturnal bottleneck and the evolution of activity patterns in mammals

    NARCIS (Netherlands)

    Gerkema, Menno P.; Davies, Wayne I. L.; Foster, Russell G.; Menaker, Michael; Hut, Roelof A.

    2013-01-01

    In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals

  12. Achievements & bottlenecks in humanitarian demining EU-funded research: Final results from the EC DELVE project

    NARCIS (Netherlands)

    Sahli, H.; Bruschini, C.; Kempen, L. van; Schleijpen, H.M.A.; Breejen, E. den

    2008-01-01

    The EC DELVE Support Action project has analyzed the bottlenecks in the transfer of Humanitarian Demining (HD) technology from technology development to the use in the field, and drawn some lessons learned, basing itself on the assessment of the European Humanitarian Demining Research and Technology

  13. HIF-1alpha and HIF-2alpha are differentially activated in distinct cell populations in retinal ischaemia.

    Directory of Open Access Journals (Sweden)

    Freya M Mowat

    Full Text Available BACKGROUND: Hypoxia plays a key role in ischaemic and neovascular disorders of the retina. Cellular responses to oxygen are mediated by hypoxia-inducible transcription factors (HIFs that are stabilised in hypoxia and induce the expression of a diverse range of genes. The purpose of this study was to define the cellular specificities of HIF-1alpha and HIF-2alpha in retinal ischaemia, and to determine their correlation with the pattern of retinal hypoxia and the expression profiles of induced molecular mediators. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the tissue distribution of retinal hypoxia during oxygen-induced retinopathy (OIR in mice using the bio-reductive drug pimonidazole. We measured the levels of HIF-1alpha and HIF-2alpha proteins by Western blotting and determined their cellular distribution by immunohistochemistry during the development of OIR. We measured the temporal expression profiles of two downstream mediators, vascular endothelial growth factor (VEGF and erythropoietin (Epo by ELISA. Pimonidazole labelling was evident specifically in the inner retina. Labelling peaked at 2 hours after the onset of hypoxia and gradually declined thereafter. Marked binding to Müller glia was evident during the early hypoxic stages of OIR. Both HIF-1alpha and HIF-2alpha protein levels were significantly increased during retinal hypoxia but were evident in distinct cellular distributions; HIF-1alpha stabilisation was evident in neuronal cells throughout the inner retinal layers whereas HIF-2alpha was restricted to Müller glia and astrocytes. Hypoxia and HIF-alpha stabilisation in the retina were closely followed by upregulated expression of the downstream mediators VEGF and EPO. CONCLUSIONS/SIGNIFICANCE: Both HIF-1alpha and HIF-2alpha are activated in close correlation with retinal hypoxia but have contrasting cell specificities, consistent with differential roles in retinal ischaemia. Our findings suggest that HIF-2alpha activation

  14. Contrasting patterns of genetic variation in core and peripheral populations of highly outcrossing and wind pollinated forest tree species.

    Science.gov (United States)

    Wójkiewicz, Błażej; Litkowiec, Monika; Wachowiak, Witold

    2016-01-01

    Gene flow tends to have a homogenising effect on a species' background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine-a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species' putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average FST = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management programs

  15. Gender differentials in the evolution of cigarette smoking habits in a general European adult population from 1993–2003

    Directory of Open Access Journals (Sweden)

    Lopez Alan D

    2006-05-01

    Full Text Available Abstract Background Describe the recent evolution of cigarette smoking habits by gender in Geneva, where incidence rates of lung cancer have been declining in men but increasing in women. Methods Continuous cross-sectional surveillance of the general adult (35–74 yrs population of Geneva, Switzerland for 11 years (1993–2003 using a locally-validated smoking questionnaire, yielding a representative random sample of 12,271 individuals (6,164 men, 6,107 women. Results In both genders, prevalence of current cigarette smoking was stable over the 11-year period, at about one third of men and one quarter of women, even though smoking began at an earlier age in more recent years. Older men were more likely to be former smokers than older women. Younger men, but not women, tended to quit smoking at an earlier age. Conclusion This continuous (1993–2003 risk factor surveillance system, unique in Europe, shows stable prevalence of smoking in both genders. However, sharp contrasts in age-specific prevalence of never and former smoking and of ages at smoking initiation indicate that smoking continues a long-term decline in men but has still not reached its peak in women.

  16. Chromosome mapping of 5S rRNA genes differentiates Brazilian populations of Leporellus vittatus (Anostomidae, Characiformes

    Directory of Open Access Journals (Sweden)

    Cecilia Teixeira de Aguilar

    2008-01-01

    Full Text Available Among the anostomid fishes, the genus Leporellus is represented by only three species: L. nattereri, endemic of the Amazon River, L. retropinnis, endemic of the Piracicaba River, and L. vittatus, widely distributed in rivers from Peru, Colombia, Guianas, and different major hydrographic basins of Brazil. A cytogenetic study carried out on specimens of Leporellus vittatus from three major Brazilian hydrographic basins evidenced a karyotype of 54 metacentric and submetacentric chromosomes. C-banding analysis revealed the presence of large pericentromeric heterochromatic segments in all chromosomes and a telomeric block coincident with the NOR sites. Ag, CMA3 or MM staining, and FISH with ribosomal probes located the 45S ribosomal genes on the terminal region of the long arm of the 12th chromosome pair of all populations. Nevertheless, in the specimens from the Paraná and São Francisco Basins the 5S rDNA clusters were interstitially located by FISH on the long arm of the 2nd chromosome pair, while in the specimens from the Tocantins-Araguaia Basin these sites were observed on the long arm of the 9th chromosome pair and on the short arm of the 17th chromosome pair. These data suggest that the species currently named Leporellus vittatus may comprise a complex of cryptic species.

  17. The effects of differential reddening and stellar rotation on the appearance of multiple populations in star clusters: the case of Trumpler 20

    CERN Document Server

    Platais, I; Quinn, S N; Clem, J L; de Mink, S E; Dotter, A; Kozhurina-Platais, V; Latham, D W; Bellini, A

    2012-01-01

    We present a detailed analysis of the upper main sequence of the 1.3 Gyr old open cluster Trumpler 20. High accuracy BV photometry combined with the Very Large Telescope/FLAMES medium-resolution spectroscopy of 954 stars is essential to understanding the unusual appearance of the color-magnitude diagram (CMD), initially suggesting multiple populations in Trumpler 20. We show that differential reddening is a dominant contributor to the apparent splitting/widening of the main-sequence turnoff region. At its extreme, the excess differential reddening reaches Delta(B-V)=0.1 while the adopted minimum reddening for the cluster is E(B-V)=0.36. A unique sample of measured projected rotational velocities indicates that stellar rotation is high near the main-sequence turnoff, reaching vsin i=180 km/s. By dividing the upper main-sequence stars into equal groups of slow and fast rotators, we find that fast rotators have a marginal blueshift of delta(V-I)=-0.01, corresponding to a difference in the median vsin i of 60 km/...

  18. Fungal specificity bottlenecks during orchid germination and development.

    Science.gov (United States)

    Bidartondo, Martin I; Read, David J

    2008-08-01

    Fungus-subsidized growth through the seedling stage is the most critical feature of the life history for the thousands of mycorrhizal plant species that propagate by means of 'dust seeds.' We investigated the extent of specificity towards fungi shown by orchids in the genera Cephalanthera and Epipactis at three stages of their life cycle: (i) initiation of germination, (ii) during seedling development, and (iii) in the mature photosynthetic plant. It is known that in the mature phase, plants of these genera can be mycorrhizal with a number of fungi that are simultaneously ectomycorrhizal with the roots of neighbouring forest trees. The extent to which earlier developmental stages use the same or a distinctive suite of fungi was unclear. To address this question, a total of 1500 packets containing orchid seeds were buried for up to 3 years in diverse European forest sites which either supported or lacked populations of helleborine orchids. After harvest, the fungi associated with the three developmental stages, and with tree roots, were identified via cultivation-independent molecular methods. While our results show that most fungal symbionts are ectomycorrhizal, differences were observed between orchids in the representation of fungi at the three life stages. In Cephalanthera damasonium and C. longifolia, the fungi detected in seedlings were only a subset of the wider range seen in germinating seeds and mature plants. In Epipactis atrorubens, the fungi detected were similar at all three life stages, but different fungal lineages produced a difference in seedling germination performance. Our results demonstrate that there can be a narrow checkpoint for mycorrhizal range during seedling growth relative to the more promiscuous germination and mature stages of these plants' life cycle.

  19. Hierarchical genetic analysis of German cockroach (Blattella germanica) populations from within buildings to across continents.

    Science.gov (United States)

    Vargo, Edward L; Crissman, Jonathan R; Booth, Warren; Santangelo, Richard G; Mukha, Dmitry V; Schal, Coby

    2014-01-01

    Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species. PMID:25020136

  20. Hierarchical genetic analysis of German cockroach (Blattella germanica populations from within buildings to across continents.

    Directory of Open Access Journals (Sweden)

    Edward L Vargo

    Full Text Available Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city than at larger spatial scales (within and between continents. About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species.

  1. Interlimb coupling from the arms to legs is differentially specified for populations of motor units comprising the compound H-reflex during "reduced" human locomotion.

    Science.gov (United States)

    Mezzarane, Rinaldo A; Klimstra, Marc; Lewis, Allen; Hundza, Sandra R; Zehr, E Paul

    2011-01-01

    Recent experiments have identified neuromechanical interactions between the arms and legs during human locomotor movement. Previous work reported that during the rhythmic movement of all four limbs, the influence of the arms on reflex expression in the legs was superimposed on the dominant effect of the legs. This evidence was based upon studies using cutaneous and H-reflex modulation as indices of neuronal activity related to locomotion. The earlier H-reflex study was restricted to one phase of movement and to only a fixed H-reflex amplitude. Also, all four limbs were actively engaged in locomotor movement, and this led to the speculation that the effect from the arms could be underestimated by "swamping" of the conditioning during movement of the test limb. Work from the cat suggests that descending locomotor drive may be differentially specified for different motor unit populations in the hindlimb. Accordingly, details of interlimb coordination between the arms and legs in humans require further characterization and an examination of different populations of motor units as can be obtained from H-reflex recruitment curve (RC) parameters. Using modulation of H-reflex amplitudes across the entire ascending limb as neural probes for interlimb coupling, the present study evaluated the separated influences of rhythmic activity of the arms and leg on neuronal excitability of a stationary "test leg". This three-limb "reduced" locomotion approach was applied using a stepping ergometer during the performance of three rhythmic movement tasks: arms (A); contralateral leg (L); and arms and contralateral leg (AL). Data were sampled at four different phases of the stepping cycle (using the moving leg as reference): start power (SP); end power (EP); start recovery (SR); and end recovery (ER). The main result was a large and significant influence of rhythmic AL activity on RC parameters of the H-reflex at EP and SP phases. However, the parameters (and thus motor unit populations

  2. "Use of Random Amplified Polymorphic DNA Polymerase Chain Reaction (RAPD-PCR and ITS2 PCR assays for differentiation of populations and putative sibling species of Anopheles fluviatilis (Diptera: Culicidae in Iran"

    Directory of Open Access Journals (Sweden)

    SR Naddaf Dezfouli

    2002-09-01

    Full Text Available Anopheles fluviatilis complex is known to be a vector of malaria in Iran. Since mosquitoes of this species cover a wide geographical range in Iran, they might have evolved into different separated populations. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR assay was used to differentiate geographic populations of this species. DNA was extracted from individual mosquitoes from 8 localities in 4 south and southeast provinces and amplified in PCR reactions using 18 single primers of arbitrary nucleotide sequence. Results of RAPD-PCR showed that Kazeroun populations could simply be differentiated from other populations using a diagnostic fragment amplified with primer UBC-306. But other populations could not be differentiated either visually or by means of statistical analysis. Moreover ITS2 fragments of some selected specimens were amplified using a pair of universal primer and sequenced as a key standard for detection of putative sibling species. Sequence analysis of the ITS2 fragments revealed a very high (100% homology among the populations. These findings are crucial in epidemiological studies concerning relatedness of geographic populations and vector movement in the region. Results of RAPD-PCR and ITS2 analysis suggest that this taxon in Iran comprises of only one species with a low genetic variation among geographic populations.

  3. 基于瓶颈多态性的生产物流瓶颈闭环预测方法%Close-loop prediction method of logistics bottleneck based on bottleneck polymorphism

    Institute of Scientific and Technical Information of China (English)

    刘志; 唐娟; 费志敏

    2012-01-01

    针对不确定性环境下的生产物流瓶颈漂移预测问题,提出一种基于瓶颈多态性的瓶颈闭环预测方法。建立灵敏型瓶颈、迟钝型瓶颈、渐向型瓶颈和渐离型瓶颈的概念,以定性描述制造系统的物流瓶颈多态性;以瓶颈指数为基础,以制造单元时问和质量为参数,构建瓶颈漂移指数数学模型,并以此为依据构建瓶颈多态性判定机制,以实现瓶颈多态性的定量描述,进而为瓶颈漂移规律的研究提供技术支持;构建包含数据统计分析、瓶颈预测机制、瓶颈多态性分析和瓶颈指数迭代预测四项内容的瓶颈闭环预测方法,以实现生产物流瓶颈的动态连续预测。通过对某汽车装配车间生产物流瓶颈的动态预测和监控,验证了该方法的有效性和准确性。%Aiming at the prediction problem of production logistics bottleneck shifting under uncertain environment, a closed-loop prediction method of bottleneck was proposed based on bottleneck polymorphisrrL The concepts of sensi- tive bottleneck, obtuse bottleneck, growing bottleneck and decreasing bottleneck were formulated to describe the lo- gistics bottleneck polymorphism of manufacturing system qualitatively. Based on bottleneck index, mathematical model of bottleneck shifting index was established by taking time and quality of manufacturing unit as parameters. Decision mechanism of bottleneck polymorphism was constructed to realize bottleneck polymorphism description on the basis of bottleneck shifting index quantitatively, which provided technological support for studying on bottleneck shifting rule. The bottleneck closed-loop prediction method which was composed of data statistic analysis, bottle- neck prediction mechanism, bottleneck polymorphism analysis and bottleneck index iterative prediction was founded to realize dynamic and continuous prediction of production logistics bottleneck. An example of dynamically forecas- ting

  4. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations.

    Science.gov (United States)

    Hume, David A; Summers, Kim M; Raza, Sobia; Baillie, J Kenneth; Freeman, Thomas C

    2010-06-01

    Very large microarray datasets showing gene expression across multiple tissues and cell populations provide a window on the transcriptional networks that underpin the differences in functional activity between biological systems. Clusters of co-expressed genes provide lineage markers, candidate regulators of cell function and, by applying the principle of guilt by association, candidate functions for genes of currently unknown function. We have analysed a dataset comprising pure cell populations from hemopoietic and non-hemopoietic cell types (http://biogps.gnf.org). Using a novel network visualisation and clustering approach, we demonstrate that it is possible to identify very tight expression signatures associated specifically with embryonic stem cells, mesenchymal cells and hematopoietic lineages. Selected examples validate the prediction that gene function can be inferred by co-expression. One expression cluster was enriched in phagocytes, which, alongside endosome-lysosome constituents, contains genes that may make up a 'pathway' for phagocyte differentiation. Promoters of these genes are enriched for binding sites for the ETS/PU.1 and MITF families. Another cluster was associated with the production of a specific extracellular matrix, with high levels of gene expression shared by cells of mesenchymal origin (fibroblasts, adipocytes, osteoblasts and myoblasts). We discuss the limitations placed upon such data by the presence of alternative promoters with distinct tissue specificity within many protein-coding genes.

  5. 基于两种瓶颈度的制造车间多瓶颈动态预测方法%Dynamic Prediction Method of Multi-bottleneck in Manufacturing Shop Based on Two Bottleneck Degrees

    Institute of Scientific and Technical Information of China (English)

    刘志; 蒋增强; 龚本刚

    2014-01-01

    针对制造车间多瓶颈预测问题,提出一种基于两种瓶颈度的多瓶颈动态预测方法,以在合理认定瓶颈责任的前提下实现系统多瓶颈的连续准确预测。首先,建立综合瓶颈度和独立瓶颈度的概念模型,并以时间、质量和成本为参数,构建其数学模型;然后,构建包含多瓶颈双层预测机制、瓶颈多态性分析和瓶颈指数迭代预测模型的多瓶颈动态预测方法;最后,将多瓶颈动态预测方法、单瓶颈度法和PBM 法运用至某汽车产品总装线,以验证该方法有效性。%Aiming at the prediction problem of multi-bottleneck in complex manufacturing shop , a dynamic prediction method of multi-bottleneck was proposed based on two bottleneck degrees ,which can forecast bottleneck accurately under conditions that bottleneck responsibility was verified reasona-bly .Firstly ,conceptual models about general bottleneck degree and independent bottleneck degree were built ,and then taking time ,quality and cost as parameters ,their mathematical models were es-tablished .Secondly ,one dynamic prediction method of multi-bottleneck was come up with ,which con-tained dual-layer multi-bottleneck prediction mechanism ,bottleneck polymorphism analysis and the it-erative prediction of bottleneck index .Finally ,it is proved to be superior and credible by comparison to the method of single bottleneck degree and the method of PBM for production bottleneck prediction problem of one vehicle assembly line .

  6. Differential Item Functioning in the SF-36 Physical Functioning and Mental Health Sub-Scales: A Population-Based Investigation in the Canadian Multicentre Osteoporosis Study.

    Directory of Open Access Journals (Sweden)

    Lisa M Lix

    Full Text Available Self-reported health status measures, like the Short Form 36-item Health Survey (SF-36, can provide rich information about the overall health of a population and its components, such as physical, mental, and social health. However, differential item functioning (DIF, which arises when population sub-groups with the same underlying (i.e., latent level of health have different measured item response probabilities, may compromise the comparability of these measures. The purpose of this study was to test for DIF on the SF-36 physical functioning (PF and mental health (MH sub-scale items in a Canadian population-based sample.Study data were from the prospective Canadian Multicentre Osteoporosis Study (CaMos, which collected baseline data in 1996-1997. DIF was tested using a multiple indicators multiple causes (MIMIC method. Confirmatory factor analysis defined the latent variable measurement model for the item responses and latent variable regression with demographic and health status covariates (i.e., sex, age group, body weight, self-perceived general health produced estimates of the magnitude of DIF effects.The CaMos cohort consisted of 9423 respondents; 69.4% were female and 51.7% were less than 65 years. Eight of 10 items on the PF sub-scale and four of five items on the MH sub-scale exhibited DIF. Large DIF effects were observed on PF sub-scale items about vigorous and moderate activities, lifting and carrying groceries, walking one block, and bathing or dressing. On the MH sub-scale items, all DIF effects were small or moderate in size.SF-36 PF and MH sub-scale scores were not comparable across population sub-groups defined by demographic and health status variables due to the effects of DIF, although the magnitude of this bias was not large for most items. We recommend testing and adjusting for DIF to ensure comparability of the SF-36 in population-based investigations.

  7. Association with Spontaneous Hepatitis C Viral Clearance and Genetic Differentiation of IL28B/IFNL4 Haplotypes in Populations from Mexico

    Science.gov (United States)

    Gonzalez-Aldaco, Karina; Rebello Pinho, João R.; Roman, Sonia; Gleyzer, Ketti; Fierro, Nora A.; Oyakawa, Leticia; Ramos-Lopez, Omar; Ferraz Santana, Rubia A.; Sitnik, Roberta; Panduro, Arturo

    2016-01-01

    Aim To analyze the genetic heterogeneity of the Amerindian and admixed population (Mestizos) based on the IL28B (rs12979860, rs8099917) and IFNL4 (rs368234815) haplotypes, and their association with spontaneous clearance (SC) and liver damage in patients with hepatitis C infection from West Mexico. Methods A total of 711 subjects from West Mexico (181 Amerindians and 530 Mestizos) were studied for the prevalence of IL28B (rs12979860C/T, rs8099917G/T) and IFNL4 (rs368234815∆G/TT) genotypes. A case-control study was performed in 234 treatment-naïve HCV Mestizos (149 chronic hepatitis C and 85 with SC) for the association of haplotypes with SC and liver damage. A real-time PCR assay was used for genotyping, and transitional elastography staged liver damage. Results Significant Fst-values indicated differentiation between the studied populations. The frequencies of the protective C, T, TT alleles were significantly lower in the Amerindians than in Mestizos (p<0.05). The r2 measure of linkage disequilibrium was significant for all variants and the T/G/ΔG risk haplotype predominated in Amerindians and secondly in Mestizos. The protective C/T/TT haplotype was associated with SC (OR = 0.46, 95% IC 0.22–0.95, p = 0.03) and less liver damage (OR = 0.32, 95% IC 0.10–0.97, p = 0.04) in chronic patients. The Structure software analysis demonstrated no significant differences in ancestry among SC and chronic patients. Conclusions West Mexico´s population is genetically heterogeneous at the IL28B/IFNL4 polymorphisms. The T/G/ΔG high-risk haplotype predominated in Amerindians and the beneficial alternative haplotype in Mestizos. The C/T/TT haplotype was associated with SC and less liver damage in chronically infected Mestizo patients. PMID:26741362

  8. Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci.

    Science.gov (United States)

    de Garine-Wichatitsky, M; de Meeûs, T; Chevillon, C; Berthier, D; Barré, N; Thévenon, S; Maillard, J-C

    2009-12-01

    Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms. The genetic structure of farmed and wild populations differed significantly. There was a significant isolation by distance for wild populations, whereas farmed populations were significantly differentiated between farms independently from their geographical proximity. Wild rusa deer consisted of small populations (with effective population sizes ranging between 7 and 19 individuals depending on the methods used), with a low parent-offspring dispersion range (0.20-2.02 km). Genetic tools and direct observations provided congruent estimates of dispersion and population sizes. We discuss the relevance of our results for management purposes. PMID:19680748

  9. Genetic diversity in population of largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry) from Yangtze River determined by microsatellite DNA analysis.

    Science.gov (United States)

    Zhang, Futie; Tan, Deqing

    2010-01-01

    Largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry 1874), one of the endemic fish species in the upper reaches of the Yangtze River in China, is a benthic and potamodromous fish that is typically found in rivers with torrential flow. Three dams in the Yangtze River, Ertan Dam, Three Gorges Dam and Gezhouba Dam, may have had vital impacts on the habitat and spawning behaviors of largemouth bronze gudgeon, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of C. guichenoti samples collected at seven sites (JH, GLP, BX, HJ, MD, SDP and XB) within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 11 polymorphic microsatellite loci. A high genetic diversity among these largemouth bronze gudgeon populations was indicated by the number of microsatellite alleles (A) and the expected heterozygosity (HE). No significant population variation occurred among GLP, BX, HJ and MD populations, but dramatic population differentiation was observed among JH and XB, two dam-blocked populations, versus other populations. Tests for bottlenecks did not indicate recent dramatic population declines and concurrent losses of genetic diversity in any largemouth bronze gudgeon populations. To the contrary, we found that dams accelerated the population differentiation of this fish. PMID:21317547

  10. Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly.

    Directory of Open Access Journals (Sweden)

    Sofie Vandewoestijne

    Full Text Available BACKGROUND: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history. We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient. METHODOLOGY/PRINCIPAL FINDINGS: Populations (23 along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494 than between woodland populations (4.183, and significantly higher genetic differentiation between agricultural (0.050 than woodland (0.034 pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra- and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional

  11. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.

    Science.gov (United States)

    Cai, Xiaoyun; Qin, Zhendong; Wen, Bo; Xu, Shuhua; Wang, Yi; Lu, Yan; Wei, Lanhai; Wang, Chuanchao; Li, Shilin; Huang, Xingqiu; Jin, Li; Li, Hui

    2011-01-01

    Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK) and Hmong-Mien (HM) speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape), with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia. PMID:21904623

  12. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.

    Directory of Open Access Journals (Sweden)

    Xiaoyun Cai

    Full Text Available Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK and Hmong-Mien (HM speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape, with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia.

  13. Effects of Changes in Food Supply at the Time of Sex Differentiation on the Gonadal Transcriptome of Juvenile Fish. Implications for Natural and Farmed Populations

    Science.gov (United States)

    Díaz, Noelia; Ribas, Laia; Piferrer, Francesc

    2014-01-01

    Background Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish. Methods and Findings This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1) 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2) testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i) sustained fast growth, ii) sustained slow growth, iii) accelerated growth, iv) decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish. Conclusions Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis. Thus, fish are able to recover transcriptionally their testes if they are provided with enough food

  14. Effects of changes in food supply at the time of sex differentiation on the gonadal transcriptome of juvenile fish. Implications for natural and farmed populations.

    Directory of Open Access Journals (Sweden)

    Noelia Díaz

    Full Text Available Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish.This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2 testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i sustained fast growth, ii sustained slow growth, iii accelerated growth, iv decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish.Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis. Thus, fish are able to recover transcriptionally their testes if they are provided with enough food supply during sex

  15. Zero-temperature quantum annealing bottlenecks in the spin-glass phase

    Science.gov (United States)

    Knysh, Sergey

    2016-08-01

    A promising approach to solving hard binary optimization problems is quantum adiabatic annealing in a transverse magnetic field. An instantaneous ground state--initially a symmetric superposition of all possible assignments of N qubits--is closely tracked as it becomes more and more localized near the global minimum of the classical energy. Regions where the energy gap to excited states is small (for instance at the phase transition) are the algorithm's bottlenecks. Here I show how for large problems the complexity becomes dominated by O(log N) bottlenecks inside the spin-glass phase, where the gap scales as a stretched exponential. For smaller N, only the gap at the critical point is relevant, where it scales polynomially, as long as the phase transition is second order. This phenomenon is demonstrated rigorously for the two-pattern Gaussian Hopfield model. Qualitative comparison with the Sherrington-Kirkpatrick model leads to similar conclusions.

  16. Note: Inhibiting bottleneck corrosion in electrical calcium tests for ultra-barrier measurements

    Science.gov (United States)

    Nehm, F.; Müller-Meskamp, L.; Klumbies, H.; Leo, K.

    2015-12-01

    A major failure mechanism is identified in electrical calcium corrosion tests for quality assessment of high-end application moisture barriers. Accelerated calcium corrosion is found at the calcium/electrode junction, leading to an electrical bottleneck. This causes test failure not related to overall calcium loss. The likely cause is a difference in electrochemical potential between the aluminum electrodes and the calcium sensor, resulting in a corrosion element. As a solution, a thin, full-area copper layer is introduced below the calcium, shifting the corrosion element to the calcium/copper junction and inhibiting bottleneck degradation. Using the copper layer improves the level of sensitivity for the water vapor transmission rate (WVTR) by over one order of magnitude. Thin-film encapsulated samples with 20 nm of atomic layer deposited alumina barriers this way exhibit WVTRs of 6 × 10-5 g(H2O)/m2/d at 38 °C, 90% relative humidity.

  17. Squeezing through the Now-or-Never bottleneck: Reconnecting language processing, acquisition, change, and structure.

    Science.gov (United States)

    Chater, Nick; Christiansen, Morten H

    2016-01-01

    If human language must be squeezed through a narrow cognitive bottleneck, what are the implications for language processing, acquisition, change, and structure? In our target article, we suggested that the implications are far-reaching and form the basis of an integrated account of many apparently unconnected aspects of language and language processing, as well as suggesting revision of many existing theoretical accounts. With some exceptions, commentators were generally supportive both of the existence of the bottleneck and its potential implications. Many commentators suggested additional theoretical and linguistic nuances and extensions, links with prior work, and relevant computational and neuroscientific considerations; some argued for related but distinct viewpoints; a few, though, felt traditional perspectives were being abandoned too readily. Our response attempts to build on the many suggestions raised by the commentators and to engage constructively with challenges to our approach.

  18. Understanding of empty container movement: A study on a bottleneck at an off-dock depot

    Science.gov (United States)

    Zain, Rosmaizura Mohd; Rahman, Mohd Nizam Ab; Nopiah, Zulkifli Mohd; Saibani, Nizaroyani

    2014-09-01

    Port not only function as connections between marine and land transportation but also as core business areas. In a port terminal, available space is limited, but the influx of container is growing. The off-dock depot is one of the key supply chain players that hold empty containers in the inventory. Therefore, this paper aims to identify the main factors of bottlenecks or congestion that hinder the rapid movement of empty containers from the off-dock depot to the customers. Thirty interviews were conducted with individuals who are key players in the container supply chain. The data were analyzed using Atlas.ti software and the analytic hierarchy process to rank the priority factors of bottlenecks. Findings show that several pertinent factors act as barriers to the key players in the container movement in the day-to-day operations. In future studies, strategies to overcome fragmentation in the container supply chain and logistics must be determined.

  19. CO2 capture enhancement in InOF-1 via the bottleneck effect of confined ethanol.

    Science.gov (United States)

    Peralta, Ricardo A; Campos-Reales-Pineda, Alberto; Pfeiffer, Heriberto; Álvarez, J Raziel; Zárate, J Antonio; Balmaseda, Jorge; González-Zamora, Eduardo; Martínez, Ana; Martínez-Otero, Diego; Jancik, Vojtech; Ibarra, Ilich A

    2016-08-11

    CO2 capture of InOF-1 was enhanced 3.6-fold, at 1 bar and 30 °C, by confining EtOH within its pores. Direct visualisation by single crystal X-ray diffraction revealed that EtOH divides InOF-1 channels in wide sections separated by "bottlenecks" caused by EtOH molecules bonded to the μ2-OH functional groups of InOF-1. PMID:27469274

  20. Why don’t we see changes?: The role of attentional bottlenecks and limited visual memory

    OpenAIRE

    Jeremy M Wolfe; Reinecke, Andrea; BRAWN, PETER

    2006-01-01

    Seven experiments explore the role of bottlenecks in selective attention and access to visual short-term memory in the failure of observers to identify clearly visible changes in otherwise stable visual displays. Experiment One shows that observers fail to register a color change in an object even if they are cued to the location of the object by a transient at that location as the change is occurring. Experiment Two shows the same for orientation change. In Experiments Three and Four, attent...

  1. An assessment of The Capacity Drops at The Bottleneck Segments: A review on the existing methodologies

    Directory of Open Access Journals (Sweden)

    Sugiarto Sugiarto

    2015-08-01

    Full Text Available The term of capacity is very useful to quantify the ability of transport facilities in terms of carrying traffic. The capacity of the road is an essential ingredient in the planning, design, and operation of roadways. It is desirable for traffic analyst to be able to predict the time and places where congestion will occur and the volumes to be expected. Most of urbanized areas have been experiencing of traffic congestion problems particularly at urban arterial systems. High traffic demand and limited supply of roadways are always the main factors produced traffic congestion. However, there are other sources of local and temporal congestion, such as uncontrolled access point, median opening and on-street parking activities, which are caused a reduction of roadway capacity during peak operations. Those locations could result in reduction of travel speed and road, as known as hidden bottlenecks. This is bottleneck which is without any changes in geometric of the segments. The Indonesian Highway Capacity Manual (IHCM, 1997 is used to assess urban arterial systems till current days. IHCM provides a static method for examining the capacityand does not systematically take into account of bottleneck activities. However, bottleneck activities create interruption smooth traffic flow along arterial streets, which in turns stimulate related problems, such as, excessive air pollution, additional energy consumption and driver’s frustration due to traffic jammed. This condition could happen simultaneously; mostly repetitive and predictable in same peak hour demands. Therefore, this paper carefully summarize on the existing methodologies considering required data, handled data processing and expected output of each proposed of analysis. We further notice that dynamic approach could be more appropriated for analyzing temporal congestion segments (median opening, on street parking, etc.. Method of oblique cumulative plot seems to be more applicable in terms of

  2. Bottleneck of Farmers’ Quality in New Socialist Countryside Construction and Countermeasures

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    We analyzed problems of farmers’ quality in the new socialist countryside construction,including low educational level,poor specialized skills,and low ideological and ethical quality.These problems become bottleneck of the socialist countryside construction.In view of these problems,we put forward following countermeasures:speeding up urbanization development,consolidating rural basic education,strengthening rural vocational education,and developing new approaches to improve farmers’ ideological and ethical quality.

  3. Emerging from the bottleneck: Benefits of the comparative approach to modern neuroscience

    OpenAIRE

    Brenowitz, Eliot A.; Zakon, Harold H.

    2015-01-01

    Neuroscience historically exploited a wide diversity of animal taxa. Recently, however, research focused increasingly on a few model species. This trend accelerated with the genetic revolution, as genomic sequences and genetic tools became available for a few species, which formed a bottleneck. This coalescence on a small set of model species comes with several costs often not considered, especially in the current drive to use mice explicitly as models for human diseases. Comparative studies ...

  4. Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae).

    Science.gov (United States)

    Boys, Jacquelyn; Cherry, Marilyn; Dayanandan, Selvadurai

    2005-05-01

    Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28-35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine. PMID:21652464

  5. The nocturnal bottleneck and the evolution of activity patterns in mammals.

    Science.gov (United States)

    Gerkema, Menno P; Davies, Wayne I L; Foster, Russell G; Menaker, Michael; Hut, Roelof A

    2013-08-22

    In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.

  6. Incident and Traffic-Bottleneck Detection Algorithm in High-Resolution Remote Sensing Imagery

    Directory of Open Access Journals (Sweden)

    S.M.M. Kahaki

    2012-09-01

    Full Text Available One of the most important methods to solve traffic congestion is to detect the incident state of a roadway. This paper describes the development of a method for road traffic monitoring aimed at the acquisition and analysis of remote sensing imagery. We propose a strategy for road extraction, vehicle detection and incident detection from remote sensing imagery using techniques based on neural networks, Radon transform for angle detection and traffic-flow measurements. Traffic-bottleneck detection is another method that is proposed for recognizing incidents in both offline and real-time mode. Traffic flows and incidents are extracted from aerial images of bottleneck zones. The results show that the proposed approach has a reasonable detection performance compared to other methods. The best performance of the learning system was a detection rate of 87% and a false alarm rate of less than 18% on 45 aerial images of roadways. The performance of the traffic-bottleneck detection method had a detection rate of 87.5%.

  7. Managing bottlenecks in manual automobile assembly systems using discrete event simulation

    Directory of Open Access Journals (Sweden)

    Dewa, M.

    2013-08-01

    Full Text Available Batch model lines are quite handy when the demand for each product is moderate. However, they are characterised by high work-in-progress inventories, lost production time when changing over models, and reduced flexibility when it comes to altering production rates as product demand changes. On the other hand, mixed model lines can offer reduced work-in-progress inventory and increased flexibility. The object of this paper is to illustrate that a manual automobile assembling system can be optimised through managing bottlenecks by ensuring high workstation utilisation, reducing queue lengths before stations and reducing station downtime. A case study from the automobile industry is used for data collection. A model is developed through the use of simulation software. The model is then verified and validated before a detailed bottleneck analysis is conducted. An operational strategy is then proposed for optimal bottleneck management. Although the paper focuses on improving automobile assembly systems in batch mode, the methodology can also be applied in single model manual and automated production lines.

  8. Potential and bottlenecks of the carbon market: The case of a developing country, Nepal

    International Nuclear Information System (INIS)

    The majority of clean development mechanism (CDM) projects are confined to a few countries. For many developing nations, entry into the carbon market, either through CDM or others, has been difficult. Thus, rationalizing CDM projects and the carbon market as a tool for sustainable development is often questioned. Many developing countries, such as Nepal, lack a quantification of CO2 reduction potential and an assessment of bottlenecks necessary for the carbon market. In this context, this paper assesses the potential emission reductions from major sectors of Nepal and the accompanying bottlenecks of the carbon market. The analyses provide indications of the type and scale of the carbon mitigation opportunities in key sectors such as waste management, biogas utilization, promotion of electric vehicles, rice cultivation, bio-energy utilization, brick making, hydropower development and a few others. These might be helpful to decision-makers in Nepal as well as to the process of re-orienting CDM and other carbon markets to better understand the bottlenecks of developing countries.

  9. Mine production index (MPI)-extension of OEE for bottleneck detection in mining

    Institute of Scientific and Technical Information of China (English)

    Amol Arun Lanke; Seyed Hadi Hoseinie; Behzad Ghodrati

    2016-01-01

    Although mining production depends on various equipments, significant amount of production loss can be attributed a specific equipment or fleet. Bottleneck is defined not only by production loss but also by our satisfaction from the equipment. The user satisfaction could be measured as machine effectiveness. Mining literatures on performance improvement and optimization of equipment operations assert importance of availability, utilization and production performance as key parameters. These three param-eters are useful for evaluating effectiveness of equipment. Mine production index (MPI), which can rep-resent the effect of these factors, has been applied for continuous operation in mining. MPI uses Fuzzy Delphi Analytical Hierarchy Process to determine importance of each three parameter for individual equipment. A case study in a Swedish open pit mine was done to evaluate the field application of MPI. The results reveal that crusher is the bottleneck equipment in studied mine. As a methodical approach, an algorithm which uses MPI and detects bottleneck in continuous mining operation has been proposed.

  10. Lagrangian-averaged model for magnetohydrodynamic turbulence and the absence of bottlenecks.

    Science.gov (United States)

    Pietarila Graham, Jonathan; Mininni, Pablo D; Pouquet, Annick

    2009-07-01

    We demonstrate that, for the case of quasiequipartition between the velocity and the magnetic field, the Lagrangian-averaged magnetohydrodynamics (LAMHD) alpha model reproduces well both the large-scale and the small-scale properties of turbulent flows; in particular, it displays no increased (superfilter) bottleneck effect with its ensuing enhanced energy spectrum at the onset of the subfilter scales. This is in contrast to the case of the neutral fluid in which the Lagrangian-averaged Navier-Stokes alpha model is somewhat limited in its applications because of the formation of spatial regions with no internal degrees of freedom and subsequent contamination of superfilter-scale spectral properties. We argue that, as the Lorentz force breaks the conservation of circulation and enables spectrally nonlocal energy transfer (associated with Alfvén waves), it is responsible for the absence of a viscous bottleneck in magnetohydrodynamics (MHD), as compared to the fluid case. As LAMHD preserves Alfvén waves and the circulation properties of MHD, there is also no (superfilter) bottleneck found in LAMHD, making this method capable of large reductions in required numerical degrees of freedom; specifically, we find a reduction factor of approximately 200 when compared to a direct numerical simulation on a large grid of 1536;{3} points at the same Reynolds number. PMID:19658812

  11. Modeling the Impact of Border Crossing Bottlenecks on Supply Chain Disruption Risk

    Directory of Open Access Journals (Sweden)

    Shaheen Sardar

    2015-04-01

    Full Text Available In order to remain competitive, companies outsource the manufacturing process to global markets. Globalization requires shipping of goods across borders. Cross border movement of goods faces diverse difficulties and creates bottlenecks in the supply chain. Complex products involve numerous parts and complications in the assembly process, resulting in multiple border-crossings with varying level of complexity across multiple countries before reaching to the customers. This activity contributes to the supply chain disruption risk. Border crossing is unavoidable in global supply chains, and how to integrate border crossing complexity in supply chain models is an unresolved issue. This paper suggests an approach to quantify the border crossing complexity and its impact on the supply chain disruption risk in the global outsourcing environment. Results show that key factors which contribute to border crossing complexity include product complexity, trade procedures, and various bottlenecks at each bordercrossing. Based on results drawn from the quantitative analysis, we propose several strategies to manage the impact of border crossing bottlenecks. The focus of this research is the manufacturing companies which are involved in managing the global supply chains.

  12. 1. Fertility differentials by incidence of marriage and their reproductive wastage in a Muslim population from rural north-east India

    Directory of Open Access Journals (Sweden)

    Anjali Haloi

    2014-01-01

    Full Text Available :The study strives to assess the fertility differentials by women's present age, influence of incidence of marriage (whether once or more than once married /consanguineous or non-consanguineous marriage, their reproductive wastage and the effect of socio-economic factors on reproductive wastage of women in a rural Muslim population of North-East India. Data for the present study were collected on 1034 married women (15-49 years through structured schedule by cross sectional method and then presented in terms of percentage, mean, and standard error. Student's t-test and ANOVA test were also applied to see the significant difference. The multiple regression analysis was used to predict whether or not reproductive wastage depends on some other independent variables. . The present study reveals that mean live births (fertility are directly proportional to the advancement of age of women, which is probably due to the fact that higher number of pregnancies in older women results from a lack of education and antenatal care leading to concomitant miscarriages and stillbirths. Marriage among the Assamese Muslims was found to be very 'stable' as only 12 females (1.17% of all married individuals reportedly changed their mates. There are 23.73% women, whose marriage is consanguineous while 77.27% women have non-consanguineous marriage. In the former group, 38 (3.7% women have given birth to physically deformed children while not a single case of physically deformed children was reported among the mothers of the latter group. The frequency of reproductive wastage, of all the pregnancies considered in this study, was found to be 14.32%. Further the study shows that women's age, maternal education, type of family, household income and antenatal care are important factors in regulating the fertility and reproductive wastage of a population.

  13. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication.

    Science.gov (United States)

    Akagi, Takashi; Hanada, Toshio; Yaegaki, Hideaki; Gradziel, Thomas M; Tao, Ryutaro

    2016-06-01

    Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops. PMID:27085183

  14. Genetic polymorphism analyses of 30 InDels in Chinese Xibe ethnic group and its population genetic differentiations with other groups.

    Science.gov (United States)

    Meng, Hao-Tian; Zhang, Yu-Dang; Shen, Chun-Mei; Yuan, Guo-Lian; Yang, Chun-Hua; Jin, Rui; Yan, Jiang-Wei; Wang, Hong-Dan; Liu, Wen-Juan; Jing, Hang; Zhu, Bo-Feng

    2015-01-01

    In the present study, we obtained population genetic data and forensic parameters of 30 InDel loci in Chinese Xibe ethnic group from northwestern China and studied the genetic relationships between the studied Xibe group and other reference groups. The observed heterozygosities ranged from 0.1704 at HLD118 locus to 0.5247 at HLD92 locus while the expected heterozygosities ranged from 0.1559 at HLD118 locus to 0.4997 at HLD101 locus. The cumulative power of exclusion and total probability of discrimination power in the studied group were 0.9867 and 0.9999999999902 for the 30 loci, respectively. Analyses of structure, PCA, interpopulation differentiations and phylogenetic tree revealed that the Xibe group had close genetic relationships with South Korean, Beijing Han and Guangdong Han groups. The results indicated that these 30 loci should only be used as a complement for autosomal STRs in paternity cases but could provide an acceptable level of discrimination in forensic identification cases in the studied Xibe group. Further studies should be conducted for better understanding of the Xibe genetic background. PMID:25651970

  15. High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco.

    Science.gov (United States)

    El Mousadik, A; Petit, R J

    1996-05-01

    Genetic diversity at nine isozyme loci was surveyed in an endangered tree species, the argan tree, endemic to south-western Morocco. The species is highly diverse (3.6 alleles/locus) with populations strongly differentiated from each other (F ST=0.25). This example is used to illustrate a method for standardizing measures of allelic richness in samples of unequal sample sizes, which was developed for the estimation of the number of species and relies on the technique of rarefaction. In addition, it is shown that the measure of subdivision, θ ST, obtained when allelic richness is used in place ofh (Nei's index of diversity), is much larger than the F ST [e.g. θ ST(40)=0.52, where (40) indicates the specified sample used to estimate the allelic richness]. This suggests that rare alleles (which strongly influence measures of allelic richness) have a more scattered distribution than more frequent ones, a result which raises special conservation issues for the argan tree. PMID:24166548

  16. Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation in Nothofagus dombeyi (Mirb.) Oerst. in Chile

    Science.gov (United States)

    González, Jorge; Fuentes, Glenda; Alarcón, Diego; Ruiz, Eduardo

    2016-01-01

    Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation. Nothofagus dombeyi (Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories in Nothofagus dombeyi requires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species. PMID:27446942

  17. Influence of drift and admixture on population structure of American black bears (Ursus americanus) in the Central Interior Highlands, USA, 50 years after translocation.

    Science.gov (United States)

    Puckett, Emily E; Kristensen, Thea V; Wilton, Clay M; Lyda, Sara B; Noyce, Karen V; Holahan, Paula M; Leslie, David M; Beringer, Jeff; Belant, Jerrold L; White, Don; Eggert, Lori S

    2014-05-01

    Bottlenecks, founder events, and genetic drift often result in decreased genetic diversity and increased population differentiation. These events may follow abundance declines due to natural or anthropogenic perturbations, where translocations may be an effective conservation strategy to increase population size. American black bears (Ursus americanus) were nearly extirpated from the Central Interior Highlands, USA by 1920. In an effort to restore bears, 254 individuals were translocated from Minnesota, USA, and Manitoba, Canada, into the Ouachita and Ozark Mountains from 1958 to 1968. Using 15 microsatellites and mitochondrial haplotypes, we observed contemporary genetic diversity and differentiation between the source and supplemented populations. We inferred four genetic clusters: Source, Ouachitas, Ozarks, and a cluster in Missouri where no individuals were translocated. Coalescent models using approximate Bayesian computation identified an admixture model as having the highest posterior probability (0.942) over models where the translocation was unsuccessful or acted as a founder event. Nuclear genetic diversity was highest in the source (AR = 9.11) and significantly lower in the translocated populations (AR = 7.07-7.34; P = 0.004). The Missouri cluster had the lowest genetic diversity (AR = 5.48) and served as a natural experiment showing the utility of translocations to increase genetic diversity following demographic bottlenecks. Differentiation was greater between the two admixed populations than either compared to the source, suggesting that genetic drift acted strongly over the eight generations since the translocation. The Ouachitas and Missouri were previously hypothesized to be remnant lineages. We observed a pretranslocation remnant signature in Missouri but not in the Ouachitas.

  18. The effect of recurrent floods on genetic composition of marble trout populations.

    Directory of Open Access Journals (Sweden)

    José Martin Pujolar

    Full Text Available A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global F(ST of 0.716, which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3-4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change.

  19. Population structure of Squatina guggenheim (Squatiniformes, Squatinidae) from the south-western Atlantic Ocean.

    Science.gov (United States)

    Garcia, G; Pereyra, S; Gutierrez, V; Oviedo, S; Miller, P; Domingo, A

    2015-01-01

    Population genetic analyses based on both mitochondrial cytochrome b and the internal transcribed spacer 2 of recombinant (r)DNA genes were implemented to examine hypotheses of population differentiation in the angular angel shark Squatina guggenheim, one of the four most-widespread endemic species inhabiting coastal ecosystems in the south-western Atlantic Ocean. A total of 82 individuals of S. guggenheim from 10 sampling sites throughout the Río de la Plata mouth, its maritime front, the outer shelf at the subtropical confluence and the coastal areas of the south-west Atlantic Ocean, were included. The analysis of molecular variance (AMOVA) based on the second internal transcribed spacer (its-2) region supports that the samples from the outer shelf represent an isolated group from other sites. Historical gene flow in a coalescent-based approach revealed significant immigration and emigration asymmetry between sampling sites. Based on the low level of genetic diversity, the existence of a long-term population decline or a past recent population expansion following a population bottleneck could be proposed in S. guggenheim. This demographic differentiation suggests a degree of vulnerability to overexploitation in this endemic and endangered south-west Atlantic Ocean shark, given its longevity and low reproductive potential. PMID:25424738