Sample records for bottlenecks population differentiation

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

    Barker, J.S.F.; Frydenberg, Jane; González, J.; Davies, H.I.; Ruiz, A; Sørensen, Jesper Givskov; Loeschcke, Volker


    original population simply due to genetic drift. Disentangling the effects of founder drift and selection after colonization is crucial to understanding the adaptive process. Drosophila buzzatii colonized Australia some 600-700 generations ago, and spread rapidly over a wide geographical range. Genetic......Species colonizing new areas disjunct from their original habitat may be subject to novel selection pressures, and exhibit adaptive genetic changes. However, if colonization occurs through a small number of founders, the genetic composition of the colonized population may differ from that of the...

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

    Zeng, Dong-Fang; Chen, Bin


    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

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

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


    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...

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

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


    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

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

    Mariette Stéphanie


    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.

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

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N; Hoffmann, Ary A


    desiccation resistance in the rain forest-restricted fly Drosophila bunnanda. After one generation of single-pair mating, additive genetic variance for desiccation resistance increased to a significant level, on average higher than for the control lines. Line crosses revealed that both dominance and epistatic......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 for...

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

    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.

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

    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.

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

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


    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

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

    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.

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

    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.

  12. Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

    Johannes A. Lenstra


    Full Text Available 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 have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

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

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


    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

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

    Frédéric Fabre


    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.

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

    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.


    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

  16. Logistics bottlenecks



    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.

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

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


    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

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

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


    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

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

    Berry Jaeker, Jillian Alexandra; Tucker, Anita Lynn


    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...

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

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


    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

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

    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.

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

    Sanichwankul Kittipong


    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.

  3. A Structured Population Model of Cell Differentiation

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


    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...

  4. 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.

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


    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

  5. When is a bottleneck a bottleneck?

    Schadschneider, Andreas; Popkov, Vladislav


    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.

  6. 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.

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


    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

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

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


    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.

  8. Genetic Differentiation between Geographically Distant Populations of DROSOPHILA MELANOGASTER

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


    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...

  9. Economic analysis of production bottlenecks

    Lawrence Stephen R.


    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.

  10. Different level of population differentiation among human genes

    Zhang Ya-Ping


    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.

  11. Uncorking the bottleneck



    CoeClerici Logistics' floating terminals have helped clients all over the world overcome a variety of infrastructure bottlenecks including limited draft or insufficient storage capacity. The vessel 'Bulk Irony' is a self-propelled 13,000 dwt transhipper built for Lucchini Steel's mill at Piombino, Italy for import of coal, coke and ores and export of steel products. The large 'Bulk Wayuu' coal terminal in the Lake of Maracaibo, Venezuela serves Carbones del Guasare, Venezuela's largest coal producer.

  12. Population Size, Structural Differentiation, and Human Behavior

    Sadalla, Edward K.


    Reviews evidence which indicates that the sheer size of an urban center has important social and psychological consequences. Available literature suggests that size combined with structural differentiation is related to psychological and behavioral variables such as anomymity, deindividuation, deviance, personality development, and…

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

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


    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

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

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


    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

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

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


    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

  16. Analysis of Microsatellite DNA Markers Reveals no Genetic Differentiation between Wild and Hatchery Populations of Pacific Threadfin in Hawaii

    Gang Pan, Jinzeng Yang


    Full Text Available Pacific threadfin, Polydactylus sexfilis, is popular fish in recreational fishing, as well as aquaculture in Hawaii. Its natural population has been continuously declining in the past several decades. Microsatellite DNA markers are useful DNA-based tool for monitoring Pacific threadfin populations. In this study, fifteen Microsatellite (MS DNA markers were identified from a partial genomic Pacific threadfin DNA library enriched in CA repeats, and six highly-polymorphic microsatellite loci were employed to analyze genetic similarity and differences between the wild population and hatchery population in Oahu Island. A total of 37 alleles were detected at the six MS loci in the two populations. Statistical analysis of fixation index (FST and analysis of molecular variance (AMOVA showed no genetic differentiation between the wild and hatchery populations (FST=0.001, CI95%= -0.01-0.021. Both high genetic diversity (Ho=0.664-0.674 and He=0.710-0.715 and Hardy-Weinberg equilibrium were observed in the wild and hatchery populations. Results of genetic bottleneck analysis indicated that the hatchery was founded with sufficient numbers of brooders as inbreeding coefficient is very low (FIS=0.052-0.072 in both wild and hatchery populations. Further studies are needed for comprehensive determinations of genetic varieties of primary founder broodstocks and successive offspring of the hatchery and wild populations with increased number of Pacific threadfin sample collections.

  17. Impacts of genetic bottlenecks on soybean genome diversity

    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


    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...

  18. The Constrained Bottleneck Transportation Problem

    Peerayuth Charnsethikul; Saeree Svetasreni


    Two classes of the bottleneck transportation problem with an additional budget constraint are introduced. An exact approach was proposed to solve both problem classes with proofs of correctness and complexity. Moreover, the approach was extended to solve a class of multi-commodity transportation network with a special case of the multi-period constrained bottleneck assignment problem.

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

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


    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

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

    Alicia R Martin


    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

  1. Periodic solutions of nonautonomous differential systems modeling obesity population

    Arenas, Abraham J. [Departamento de Matematicas y Estadistica, Universidad de Cordoba Monteria (Colombia)], E-mail:; Gonzalez-Parra, Gilberto [Departamento de Calculo, Universidad de los Andes, Merida (Venezuela, Bolivarian Republic of)], E-mail:; Jodar, Lucas [Instituto de Matematica Multidisciplinar, Universidad Politecnica de Valencia Edificio 8G, 2o, 46022 Valencia (Spain)], E-mail:


    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.

  2. Genetic differentiation between Atlantic salmon populations in the Windermere catchment

    Hartley, S.E.; Pickering, A.D.


    Genetic analysis, using single locus probes for genomic DNA, revealed that the juvenile Atlantic salmon populations in the Rivers Leven, Rothay and Troutbeck were related but genetically distinct. This genetic differentiation is greater than might be expected (by comparison with other salmon populations in the UK) and it is recommended that no action is taken which might promote genetic exchange between the three rivers. Thus, future fisheries management practices should treat the salmon from...

  3. Parameter Estimates in Differential Equation Models for Population Growth

    Winkel, Brian J.


    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,…

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

    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....

  5. Where do they come from? Flow connectivity detects landscape bottlenecks

    Alessandro Ferrarini


    Full Text Available In this paper, bottleneck flow connectivity is first introduced. A landscape bottleneck is defined here as the portion of an arbitrary study area which inevitably tunnels a specimen towards the point where it has been detected in situ. In other words, a bottleneck delimits the portion of the study area which forces the specimen to pass through the detected point of presence with, at most, a tolerance distance equal to an a priori defined uncertainty. There is one precise reason for the introduction of bottleneck flow connectivity: when a specimen is detected through in situ observations or GPS devices, it should be possible to derive the portion of the landscape where it can come from. In fact, the detected specimen is usually just one individual of an entire population that is moving somewhere in the landscape. Hence, such specimen can work as a tracker of the whole population if we have the proper methodological tools to turn its detected position into a map where the landscape bottleneck of the detected location is delineated. In case of a species of conservation interest, the application of bottleneck flow connectivity is useful for the individuation and then the conservation of such population. In case of an exotic undesired species, bottleneck flow connectivity can help individuate the location of the population that should be eradicated, starting from few field observations. An applicative example for wolf in the Ceno Valley (Italy is provided. Bottleneck flow connectivity has thus interesting implications both for the conservation of species of interest, but also for the management of undesired exotic species.

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

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


    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.

  7. 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

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


    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...... elephant (mean He 0.68-0.72). We interpret these results in terms of varying poaching pressure in the different parks, susceptibility of different species to poaching and differences in effective population sizes at the mitochondrial and nuclear loci....

  8. Insect population differentiation in response to enviromental thermal stress

    CHEN Bing; KANG Le


    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.

  9. Analysis of pharmacogenomic variants associated with population differentiation.

    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

  10. Effects of Bottlenecks in Vehicle Traffic

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


    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.

  11. Effects of Bottlenecks on Vehicle Traffic

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


    Traffic congestion is usually observed at the upper streams of bottlenecks such as 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 speed reduction in the bottleneck controls the emergence of stop-and-go waves. A phenomenological theory of bottleneck effects is constructed.

  12. Bottlenecks to coral recovery in the Seychelles

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


    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

  13. Narrower bottlenecks could be more efficient for concentrating choanoflagellates

    Sparacino, J.; Miño, G.; Koehl, M. A. R.; King, N.; Stocker, R.; Banchio, A. J.; Marconi, V. I.


    In evolutionary biology choanoflagellates are broadly investigated as the closest living relatives of the animal ancestors. Under diverse environmental cues, choanoflagellate Salpingoeca rosetta can differentiate in two types of solitary swimming cells: slow and fast microswimmers. Here we present a first phenomenological 2D-model for the choanoflagellates dynamics confined into a flat device divided by a wall of asymmetric microconstrictions. The model allow us to optimize the geometry of the microchannels for directing and concentrating cell populations under strict control. We solve our set of dynamical equations using Langevin dynamics. Experimental parameters for the motility of the slow and fast cells were measured and used for our numerical estimations of the directed transport efficiency, otherwise we have no adjustable parameters. We find remarkable differences in the rectification results for slow and fast choanoflagellates, which give us a strategy to develop a suitable microfluidic sorting device. For a given population velocity, narrower bottlenecks, of similar size to the cell dimension, show to be more efficient as concentrator of populations. Experiments and simulations are in good agreement.

  14. Nomenclature for clusters of differentiation (CD) of antigens defined on human leukocyte populations*


    Evaluation of 139 monoclonal antibodies detecting human leukocyte differentiation antigens during the First International Workshop on Human Leucocyte Differentiation Antigens in 1982 permitted the designation of a nomenclature for the Clusters of Differentiation of antigens defined on human leukocyte populations.

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

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


    from F(ST)-based analysis of genic and nongenic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps...... reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to the HLA-G gene on chromosome 6. Evidence of the sweep extends over a 8-Mb/3.5-cM region. Overall, the results illustrate the power of dense genotype and sample...

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

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


    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......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....... In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel...

  17. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    and relationship of Mongolian cattle populations with breeds from neighboring countries and exotic breeds, data from the ILRI cattle genotyping database were included. More particularly, we used previously obtained data from Asian taurine (Hanwoo, Yanbian and Japanese Black), two European taurine (Friesian and Charolais), two African taurine (Baoule and N'Dama) and two zebu breeds (Sahiwal and Ongole). For each breed, observed (Ho) and expected (He) heterozygosities as well as the mean number of alleles (MNA) across the nine loci were calculated between pairs of populations were also estimated and a UPGMA tree was constructed. The heterozygosities (Ho and He) in Mongolian cattle populations are similar to those obtained in Northeast Asian taurine breeds but the values are higher compared to the ones obtained for the European and African taurine breeds. The Mongol cattle in North Hangay has the highest corrected MNA value (all animals or 28 animals only). The UPGMA tree, built with the Reynolds' genetic distances, shows all six Northeast Asian cattle populations clustering into one group linked to the two European taurine breed. Interestingly, the two populations of the Mongol cattle are not closely related to each other. However, bootstrap values between the Northeast Asian taurine breeds, with the exception of the bootstrap value between Yanbian and Hanwoo, are relatively low, therefore the relationship between the Northeast Asian populations should be taken with caution. Fst values between the three Mongolian cattle populations are significant (P < 0.01), with the Govi Altay population being more differentiated from the North Hangay population than from the Khalkhun Golun breed (data not shown). Our data suggest that the traditional classification of Govi Altay and North Hangay populations as one breed, the Mongol cattle, should be revisited

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

    Zhiying JIA; Yuyong ZHANG; Shuqiang CHEN; Lianyu SHI


    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.


    ZUO Yan; GU Hanyu; XI Yugeng


    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.

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

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


    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.

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

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


    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

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

    Witten, Matthew


    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

  3. Global population structure and migration patterns suggest significant population differentiation among isolates of Pyrenophora tritici-repentis.

    Gurung, S; Short, D P G; Adhikari, T B


    The global population structure and migration patterns of foliar wheat pathogen Pyrenophora tritici-repentis (PTR) were determined using 12 microsatellite loci. Analysis of 439 single-spore isolates of PTR from five continents (18 wheat-producing countries) showed high level of genetic diversity, and moderate to high population differentiation between continents. A high level of gene diversity (H(S)=0.31 to 0.56) was observed within each population. Allelic richness indicated the European and the North American population have a high effective population size. Bayesian analyses showed five clusters where the inferred clusters did not represent geographical populations. Corrected standardized fixation index (G(ST)(″)) estimates ranged from 0.042 to 0.265 between populations, indicating low to high genetic differentiation exists between populations. We found migration (gene flow) between old world (Europe) and new world (Americas) population; however, little migration was observed among other continents. The European population was the major source of immigrants for the North American, South American, Australian and the Asian populations. Significant (PAustralian and the South American populations. In contrast, non-significant (P<0.001) LD values were observed in the Asian, European and the North American populations. Overall, our findings demonstrate the population differentiation exits among the global populations and strict quarantine measures should be applied to prevent the accelerated global spread of this pathogen. PMID:23376549


    Yongcai WANG; Qianchuan ZHAO; Dazhong ZHENG


    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.

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

    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


    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

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


    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.

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

    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

  8. Population Genomics of Early Events in the Ecological Differentiation of Bacteria

    Shapiro, B. Jesse; Friedman, Jonathan; Cordero, Otto X.; Preheim, Sarah P.; Timberlake, Sonia C.; Szabó, Gitta; Polz, Martin F.; Alm, Eric J.


    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...

  9. Exposure to a novel environment in conjunction with serial bottlenecks increases phenotypic and additive variation of a quantitative trait

    T.E. Callicrate


    Full Text Available Demographic bottlenecks were replicated in laboratory conditions using Tribolium castaneum in order to determine how additive genetic variance, and therefore adaptive potential, may be affected by a novel environment. A two-level bottleneck was imposed. The first level was a 100-individual bottleneck (five replicates. After three generations at population size 100, the second bottleneck consisted of a single mating pair (15 sub-replicates stemming from each first-level replicate. Two growth media (environments, standard (wheat flour or novel (wheat bran, were used in the sub-replicates to simulate translocation to an environment with a different foraging substrate. Sub-replicates were managed for slow population growth during six generations to population size 50 and were thus maintained for nine additional generations. Variance in pupa weight in generation 16 was affected by drift from the first and second-level bottlenecks (flour: N=382, bran: N=470 pupae, both P < 0.0001 at each bottleneck level. Total phenotypic variance was determined from the progeny of the single pair matings and was larger for bottlenecks occurring in bran than in flour, P < 0.01 (F469,381 = 1.29. Additive variance was also larger in bran than flour bottlenecks, P < 0.01 (F469,381 = 1.38. These results indicate that bottlenecks occurring in a novel environment could potentially increase the effectiveness of selection by bolstering additive variance.

  10. Analytical approach to continuous and intermittent bottleneck flows

    Helbing, D.; Johansson, A.; Mathiesen, Joachim Kaj; Jensen, M.H.; Hansen, A.


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

  11. Cloud Technology May Widen Genomic Bottleneck - TCGA

    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.

  12. Differential response of two sourgrass populations to glyphosate

    São Paulo State University, Jaboticabal, SP, Brazil


    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.

  13. Differential drought tolerance in tree populations from contrasting elevations

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


    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...

  14. The bottleneck of second language acquisition

    Slabakova, Roumyana


    Explaining why some linguistic features and constructions are easy or difficult to acquire in a second language has become a prominent current concern in generative second language acquisition (SLA) research. Based on a comparison of findings on the L2 acquisition of functional morphology, syntax, semantics and pragmatics, the Bottleneck Hypothesis argues that functional morphemes and their features are the bottleneck of L2 acquisition; acquisition of universal syntax, semantics and pragmatic...

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

    Winter, David J


    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

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

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


    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.

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

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


    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

  18. Differentiation of Effector CD4 T Cell Populations*

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


    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...

  19. Genetic and phenotypic differentiation of an Andean intermediate altitude population

    Eichstaedt, Christina A; Antão, Tiago; Cardona, Alexia; Pagani, Luca; Kivisild, Toomas; Mormina, Maru


    Highland populations living permanently under hypobaric hypoxia have been subject of extensive research because of the relevance of their physiological adaptations for the understanding of human health and disease. In this context, what is considered high altitude is a matter of interpretation and while the adaptive processes at high altitude (above 3000 m) are well documented, the effects of moderate altitude (below 3000 m) on the phenotype are less well established. In this study, we compar...

  20. Tracing Road Network Bottleneck by Data Driven Approach

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


    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

  1. Tracing Road Network Bottleneck by Data Driven Approach.

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


    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

  2. Tracing Road Network Bottleneck by Data Driven Approach.

    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.

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

    Alexander, Gigi; Cebula, Richard; Koch, James


    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.

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

    Puentes Tellez, Pilar; van Elsas, Jan Dirk


    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

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

    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

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

    Jolivet, Céline; Bernasconi, Giorgina


    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...

  7. Identification and optimization of traffic bottleneck with signal timing

    Shaoxin Yuan; Xiangmo Zhao; Yisheng An


    In urban transportation network, traffic congestion is likely to occur at traffic bottlenecks. The signal timing at intersections together with static properties of left-turn and straight-through lanes of roads are two significant factors causing traffic bottlenecks. A discrete-time model of traffic bottleneck is hence developed to analyze these two factors, and a bottleneck indicator is introduced to estimate the comprehensive bottleneck degree of individual road in regional transportation n...

  8. Potential performance bottleneck in Linux TCP

    Wu, Wenji; Crawford, Matt; /Fermilab


    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.

  9. New insights into pedestrian flow through bottlenecks

    Seyfried, A; Klingsch, W; Passon, O; Rupprecht, T; Steffen, B; Boltes, Maik; Klingsch, Wolfram; Passon, Oliver; Rupprecht, Tobias; Seyfried, Armin; Steffen, Bernhard


    Capacity estimation is an important tool for the design and dimensioning of pedestrian facilities. The literature contains different procedures and specifications which show considerable differences with respect to the estimated flow values. Moreover do new experimental data indicate a stepwise growing of the capacity with the width and thus challenge the validity of the specific flow concept. To resolve these differences we have studied experimentally the unidirectional pedestrian flow through bottlenecks under laboratory conditions. The time development of quantities like individual velocities, density and individual time gaps in bottlenecks of different width is presented. The data show a linear growth of the flow with the width. The comparison of the results with experimental data of other authors indicates that the basic assumption of the capacity estimation for bottlenecks has to be revised. In contradiction with most planning guidelines our main result is, that a jam occurs even if the incoming flow do...

  10. Gene variation, population differentiation, and sociogenetic structure of nests of Partamona seridoensis (Hymenoptera: Apidae, Meliponini).

    Fernandes, Carlo Rivero Moura; Martins, Celso Feitosa; Ferreira, Kátia Maria; Del Lama, Marco Antonio


    Gene variation and the differentiation of two populations of Partamona seridoensis (Hymenoptera: Apidae: Meliponini) from the Caatinga biome, a semiarid ecosystem unique to Brazil, were estimated through allozymic and microsatellite analyses. These populations exhibited similar low degrees of enzyme gene variation. Observed genotype frequencies at the allozyme and microsatellite loci were in accordance with Hardy-Weinberg equilibrium in the two populations. Both markers demonstrated that the two populations are not genetically homogeneous and must be considered distinct populations. The occurrence of private alleles at the allozyme and microsatellite loci corroborates this differentiation, sustaining the hypothesis of a low level of interpopulation gene flow. The phenotypic segregations clearly demonstrated that the progeny inside each nest were the result of mating between the queen of the colony and only one male. PMID:21938561

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

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


    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

  12. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants

    Genetic bottlenecks are stochastic events that narrow variation in a population. We compared bottlenecks during the systemic infection of Cucumber mosaic virus (CMV) in four host plants. We mechanically inoculated an artificial population of twelve CMV mutants to young leaves of tomato, pepper, Nicotiana benthamiana, and squash. The inoculated leaves and primary and secondary systemically infected leaves were sampled at 2, 10, and 15 days post-inoculation. All twelve mutants were detected in all of the inoculated leaves. The number of mutants recovered from the systemically infected leaves of all host species was reduced significantly, indicating bottlenecks in systemic movement. The recovery frequencies of a few of the mutants were significantly different in each host probably due to host-specific selective forces. These results have implications for the differences in virus population variation that is seen in different host plants.

  13. Differential effects of chronic monocyte depletion on macrophage populations

    The administration of the bone-seeking isotope, 89Sr, 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 89Sr treatment. Stem cell enumeration showed that a 90% fall in bone marrow macrophage colony-forming cells after 89Sr was accompanied by a 10-fold rise in splenic M-CFC. Splenectomy performed before 89Sr 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 89Sr. Four days later only a 2-fold increase in labeled peritoneal M luminal diameter was found in the 89Sr-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 89Sr 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

  14. Shear bands as bottlenecks in force transmission

    Tordesillas, Antoinette; Pucilowski, Sebastian; Tobin, Steven; Kuhn, Matthew R.; Andò, Edward; Viggiani, Gioacchino; Druckrey, Andrew; Alshibli, Khalid


    The formation of shear bands is a key attribute of degradation and failure in soil, rocks, and many other forms of amorphous and crystalline materials. Previous studies of dense sand under triaxial compression and two-dimensional analogues from simulations have shown that the ultimate shear band pattern may be detected in the nascent stages of loading, well before the band's known nucleation point (i.e., around peak stress ratio), as reported in the published literature. Here we construct a network flow model of force transmission to identify the bottlenecks in the contact networks of dense granular media: triaxial compression of Caicos ooid and Ottawa sand and a discrete element simulation of simple shear. The bottlenecks localise in the nascent stages of loading —in the location where the persistent shear band ultimately forms. This corroborates recent findings on vortices that suggest localised failure is a progressive process of degradation, initiating early in the loading history at sites spanning the full extent, yet confined to a subregion, of the sample. Bottlenecks are governed by the local and global properties of the sample fabric and the grain kinematics. Grains with large rotations and/or contacts having minimal load-bearing capacities per se do not identify the bottlenecks early in the loading history.

  15. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits.

    Szulkin, M; Gagnaire, P-A; Bierne, N; Charmantier, A


    Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12 106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting < 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment. PMID:26800038

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

    LI Zhongbao; LI Shaojing; WANG Guizhong


    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.

  17. Breaking the biomass bottleneck of the fossil free society

    Wenzel, Henrik

    for heat and power services as well as for transportation fuels and as feedstock for chemicals and materials – i.e. in practice all sectors today being dependant on fossil fuels. At the same time, unfortunately, the food sector is also in growing demand for agricultural crops. World population is still...... demand on food prices, namely the food crisis in 2007 – 2008. During this period, market prices on food and feed crops increased by almost a factor of 2, and the part of the world population suffering from hunger and starvation increased from 800 million to 900 million people. The amount of biomass...... 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...

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

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


    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.

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

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


    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.

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

    Glössl Josef


    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.

  1. Performance Bottlenecks in Digital Movie Systems

    Keller, Ralf; Effelsberg, Wolfgang; Lamparter, Bernd


    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...

  2. Teleworking and Congestion: A Dynamic Bottleneck Analysis

    Gubins, Sergejs; Verhoef, Erik T.


    We analyze the welfare effects of part-day teleworking on road traffic congestion in the context of Vickrey's dynamic bottleneck model. Endogenous decisions to become equipped with a teleworking-enabling technology change the scheduling of arrival times at work for equipped drivers and, due to congestion externalities, affects travel costs of all drivers. We show that even costless teleworking might be marginally welfare reducing, after reaching the optimal penetration level, as an equipped d...

  3. Individual Microscopic Results Of Bottleneck Experiments

    Bukáček, Marek; Krbálek, Milan


    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.




    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...

  5. Deep Bottleneck Feature for Image Classification

    Song, Yan; McLoughlin, Ian Vince; Dai, Lirong


    Effective image representation plays an important role for image classification and retrieval. Bag-of-Features (BoF) is well known as an effective and robust visual representation. However, on large datasets, convolutional neural networks (CNN) tend to perform much better, aided by the availability of large amounts of training data. In this paper, we propose a bag of Deep Bottleneck Features (DBF) for image classification, effectively combining the strengths of a CNN within a BoF framework. T...

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

    Hanna Wożakowska-Natkaniec


    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.

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

    Peris Ketty


    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.

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

    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.

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

    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

  10. A theory of traffic congestion at moving bottlenecks

    Kerner, Boris S.; Klenov, Sergey L.


    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.

  11. A theory of traffic congestion at moving bottlenecks

    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.

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

    Karmin, Monika


    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.

  13. Low genetic differentiation in a sedentary bird: house sparrow population genetics in a contiguous landscape

    Kekkonen, J; Seppä, P.; Hanski, I K; Jensen, H; Väisänen, R A; Brommer, J. E.


    The house sparrow Passer domesticus has been declining in abundance in many localities, including Finland. We studied the genetic diversity and differentiation of the house sparrow populations across Finland in the 1980s, at the onset of the species' decline in abundance. We genotyped 472 adult males (the less dispersive sex) from 13 locations in Finland (covering a range of 400 × 800 km) and one in Sweden (Stockholm) for 13 polymorphic microsatellite markers. Our analysis of Finnish ringing ...

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

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


    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...

  15. Analysis of bottleneck motion using Voronoi diagrams

    Liddle, Jack; Steffen, Bernhard


    Standard definitions of the density exhibit large fluctuations when the size of the measurement area is comparable with the size of a pedestrian. An alternative measurement method exists where a personal space, calculated through the Voronoi diagram, is assigned to each pedestrian. In this contribution this method is applied to an experiment studying motion through a bottleneck and the reduced fluctuations demonstrated. The integrated density also permits examination on much smaller spatial scales than the standard definition, the insights into the pedestrian motion this provides are discussed.

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

    Aleksandr Anatolyevich Kuklin


    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.

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

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


    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].

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

    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

  19. Where do they come from? Flow connectivity detects landscape bottlenecks

    Alessandro Ferrarini


    In this paper, bottleneck flow connectivity is first introduced. A landscape bottleneck is defined here as the portion of an arbitrary study area which inevitably tunnels a specimen towards the point where it has been detected in situ. In other words, a bottleneck delimits the portion of the study area which forces the specimen to pass through the detected point of presence with, at most, a tolerance distance equal to an a priori defined uncertainty. There is one precise reason for the introd...

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

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


    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....

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

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


    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.

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


    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.

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

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


    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.

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

    Getto, Philipp; Waurick, Marcus


    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.

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

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


    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

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

    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

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

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


    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

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

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


    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

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

    Achee Nicole L


    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

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

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


    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

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

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


    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

  12. Differential fertilization success between two populations of eastern oyster, Crassostrea virginica.

    Zhang, Haibin; Scarpa, John; Hare, Matthew P


    Identification of mechanisms promoting prezygotic reproductive isolation and their prevalence are key goals in evolutionary biology because of their potential role in speciation. In marine broadcast-spawning species, molecular interactions between gamete surface proteins are more important than mating behavior for determining reproductive compatibility. Evidence for differential fertilization capacity has been reported from experiments utilizing competing sperm from two males sampled within populations and between species, but to our knowledge conspecific populations that might have diverged in allopatry have never been tested on the basis of sperm competition. In the present study, the gametic compatibility and embryo survivorship from matings between two allopatric populations of Crassostrea virginica, the eastern oyster, on either side of a genetic step cline were investigated. Fertilization success, embryo survival, and paternity data all indicated an absence of strong reproductive barriers between the two oyster populations, implicating other mechanisms for maintenance of the cline step. Sperm from northern male oysters showed a tendency to produce more larvae than expected when competing with sperm from southern male oysters. Although the northern male advantage was not strong, the trend implies that long-distance dispersal across the step cline might more successfully result in north-to-south gene flow than the reverse, providing a mechanistic hypothesis explaining the asymmetric cline shape. PMID:20972259

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

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


    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

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

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


    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

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

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


    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

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

    ZHANG Hanbo; REN Weimin; SHAO Qiyong; DUAN Changqun


    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.

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

    WANG Li; YANG Juan; GUO Jing; ZHAO Guifang


    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

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

    Marc Ciosi


    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.

  19. Bimodal mesoporous silica with bottleneck pores.

    Reber, M J; Brühwiler, D


    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

  20. Bottleneck Management in Discrete Batch Production

    Ferenčíková Denisa


    Full Text Available Today, production planning and scheduling becomes very important part of production management because companies have to react to dynamic market conditions and rising customers´ requirements for shorter delivery times, lower prices and better quality and services. They can use a lot of sophisticated methods and approaches to make their planning processes more efficient and thus meet growing customers´ requirements. However, using these new approaches is not so easy in all types of production systems. This paper deals with production planning and scheduling in discrete batch production that is just an example of very complicated production system. This type of production process is susceptible to demand fluctuation and facility exceptions and this implies bottleneck shifting. Therefore it is quite difficult to implement methods such as Theory of Constraints (TOC for production planning improvement in the standard way. One part of this paper is a case study wherecurrent production planning and scheduling in real factory is improved just through the use TOC principles.

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

    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.

  2. Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

    Background: Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection...

  3. Endothelial Progenitor Cell Fraction Contained in Bone Marrow-Derived Mesenchymal Stem Cell Populations Impairs Osteogenic Differentiation

    Fabian Duttenhoefer


    Full Text Available In bone tissue engineering (TE endothelial cell-osteoblast cocultures are known to induce synergies of cell differentiation and activity. Bone marrow mononucleated cells (BMCs are a rich source of mesenchymal stem cells (MSCs able to develop an osteogenic phenotype. Endothelial progenitor cells (EPCs are also present within BMC. In this study we investigate the effect of EPCs present in the BMC population on MSCs osteogenic differentiation. Human BMCs were isolated and separated into two populations. The MSC population was selected through plastic adhesion capacity. EPCs (CD34+ and CD133+ were removed from the BMC population and the resulting population was named depleted MSCs. Both populations were cultured over 28 days in osteogenic medium (Dex+ or medium containing platelet lysate (PL. MSC population grew faster than depleted MSCs in both media, and PL containing medium accelerated the proliferation for both populations. Cell differentiation was much higher in Dex+ medium in both cases. Real-time RT-PCR revealed upregulation of osteogenic marker genes in depleted MSCs. Higher values of ALP activity and matrix mineralization analyses confirmed these results. Our study advocates that absence of EPCs in the MSC population enables higher osteogenic gene expression and matrix mineralization and therefore may lead to advanced bone neoformation necessary for TE constructs.

  4. A theory of traffic congestion at heavy bottlenecks

    Spatiotemporal features and physics of vehicular traffic congestion occurring due to heavy highway bottlenecks caused for example by bad weather conditions or accidents are found based on simulations in the framework of three-phase traffic theory. A model of a heavy bottleneck is presented. Under a continuous non-limited increase in bottleneck strength, i.e., when the average flow rate within a congested pattern allowed by the heavy bottleneck decreases continuously up to zero, the evolution of the traffic phases in congested traffic, synchronized flow and wide moving jams, is studied. It is found that at a small enough flow rate within the congested pattern, the pattern exhibits a non-regular structure: a pinch region of synchronized flow within the pattern disappears and appears randomly over time; wide moving jams upstream of the pinch region exhibit a complex non-regular dynamics in which the jams appear and disappear randomly. At greater bottleneck strengths, wide moving jams merge onto a mega-wide moving jam (mega-jam) within which low-speed patterns with a complex non-regular spatiotemporal dynamics occur. We show that when the bottleneck strength is great enough, only the mega-jam survives and synchronized flow remains only within its downstream front separating free flow and congested traffic. Theoretical results presented can explain why no sequence of wide moving jams can often be distinguished in non-homogeneous traffic congestion measured at very heavy bottlenecks caused by bad weather conditions or accidents

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

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


    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....

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

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


    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. PMID:25269000

  7. Deep bottleneck features for spoken language identification.

    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.

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

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


    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

  9. Genetic variation and differentiation in wide ranging populations of razor clam ( Sinonovacula constricta) inferred from AFLP markers

    Wang, Jingbo; Li, Qi; Kong, Lingfeng


    The genetic variation and differentiation of the razor clam Sinonovacula constricta distributed along the coast of China were studied through amplified fragment length polymorphism (AFLP) analysis. Six primer combinations generated 193 fragments. The H e values varied from 0.322 to 0.463 and the percentage of polymorphic loci ranged from 74.1% to 98.4%, which indicates a high level of genetic diversity. Cluster analysis by Nei’s pairwise distance grouped all specimens by geographical origins. AMOVA consistently showed that genetic variation among populations was 8.71%, and most of the variation came from the genetic variation within populations (91.29%). Genetic differentiation among the six populations was moderate; pairwise F ST ranged from 0.0282 to 0.1480, which indicated that S. constricta populations along the coast of China are genetically connected. Among all the six populations, the Beihai population is the mostly differentiated from the others, suggesting that Hainan Island and Leizhou Peninsula act as barriers to gene flow. All populations abide isolation by distance model as indicated by Mantel test, except for ZS (Zhoushan) and YQ (Yueqing) populations. Information obtained in this study will provide guidelines for conservation and fishery management of this species in the future.

  10. [Genetic diversity and differentiation between populations of Glyptothorax zanaensis in the middle and lower reaches of the Nujiang River].

    Liu, Shao-Ping; Wang, Ke; Yuan, Xi-Ping; Wang, Deng-Qiang; Yue, Xing-Jian; Chen, Da-Qing


    The development of hydroelectricity in the Nujiang River would have adverse impacts on the populations of Glyptothorax zanaensis. In order to assess the genetic diversity and differentiation of this species, we sequenced the cytochrome b gene of the mitochondria in 102 individuals of the fish collected from 6 sampling sites (Gongshan, Gudeng and Lushui in the Nujiang Prefectural District and Daojie, Mengnuo and Mucheng in the Baoshan Municipal District). A total of 87 variation sites were detected in the fragment of 1 137 bp in length, with which the 102 samples were defined as 36 haplotypes. The haplotype diversity (h) and the nucleotide diversity (pi) of total samples were 0.851+/-0.028 and 0.01356+/-0.0008, respectively. Therefore, the genetic diversity of G. zanaensis was relatively low. However, the genetic diversity of the Nujiang population was significantly higher than that of the Baoshan population. The pairwise Fst value between the populations (0.475-0.846) was higher than that within the population (0.002-0.108), which implied that the Fst value was positively related to geographic distance. Analysis of molecular variance (AMOVA) showed that the genetic differentiation between the populations and within the populations were 53.65% and 46.35%, respectively. The fixation index (Fst value) was 0.5365, indicating that there existed significant differentiation between the Nujiang population and the Baoshan population. The phylogentic tree and networks of the haplotypes of G. zanaensis showed that there were two separate lineages: the Nujiang lineage and the Baoshan lineage. Each lineage represents at least one separated management unit, or belongs to an evolutionary significant unit. It was suggested that in the construction of hydroelectric projects the measures for protecting G. zanaensis should be adopted in fully considering the populations of G. zanaensis and the status quo of their population structure to avoid the occurrence of gene exchange among

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



    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.

  12. Celebrity Suicides and Their Differential Influence on Suicides in the General Population: A National Population-Based Study in Korea

    Myung, Woojae; Won, Hong-Hee; Fava, Maurizio; Mischoulon, David; Yeung, Albert; Lee, Dongsoo; Kim, Doh Kwan; Jeon, Hong Jin


    Objective: Although evidence suggests that there is an increase in suicide rates in the general population following celebrity suicide, the rates are heterogeneous across celebrities and countries. It is unclear which is the more vulnerable population according to the effect sizes of celebrity suicides to general population. Methods: All suicide victims in the general population verified by the Korea National Statistical Office and suicides of celebrity in South Korea were included for 7 year...

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


    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...

  14. Systemic administration of RANKL overcomes the bottleneck of oral vaccine delivery through microfold cells in ileum.

    Maharjan, Sushila; Singh, Bijay; Jiang, Tao; Yoon, So-Yeon; Li, Hui-Shan; Kim, Girak; Gu, Min Jeong; Kim, Soo Ji; Park, Ok-Jin; Han, Seung Hyun; Kang, Sang-Kee; Yun, Cheol-Heui; Choi, Yun-Jaie; Cho, Chong-Su


    A successful delivery of antigen through oral route requires to overcome several barriers, such as enzymatic barrier of gastrointestinal tract and epithelial barrier that constitutes of microfold cells (M cells) for antigen uptake. Although each barrier represents a critical step in determining the final efficiency of antigen delivery, the transcytosis of antigen by M cells in the follicle-associated epithelium (FAE) to Peyer's patches appears to be a major bottleneck. Considering the systemic administration of receptor activator of nuclear factor (NF)-ĸB ligand (RANKL) induces differentiation of receptor activator of nuclear factor (NF)-ĸB (RANK)-expressing enterocytes into M cells, here, we illustrated a promising approach of antigen delivery using full length transmembrane RANKL (mRANKL). The results showed that the intraperitoneal injection of mRANKL increased the population of dendritic cells and macrophages in mesenteric lymph nodes and spleen. Subsequently, systemic administration of mRANKL resulted in significantly higher number of functional GP2(+) M cells leading higher transcytosis of fluorescent beads through them. To corroborate the effect of mRANKL in antigen delivery through M cells, we orally delivered microparticulate antigen to mice treated with mRANKL. Oral immunization induced strong protective IgA and systemic IgG antibody responses against orally delivered antigen in mRANKL-treated mice. The higher antibody responses are attributed to the higher transcytosis of antigens through M cells. Ultimately, the higher memory B cells and effector memory CD4 T cells after oral immunization in RANKL-treated mice confirmed potency of RANKL-mediated antigen delivery. To the best of our knowledge, this is the first study to demonstrate significant induction of mucosal and humoral immune responses to M cell targeted oral vaccines after the systemic administration of RANKL. PMID:26851393

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

    Antonio C.B. Bergamaschi


    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.

  16. Bottleneck management in the German and European electricity supply

    This publication describes how bottlenecks in the German and European electricity supply pose a danger to the realization of the European internal market in electricity, the transition to electricity production from renewable resources and to the safeguarding of grid availability and security of supply. Bottlenecks at cross-border interconnectors between member states of the European Union are hampering cross-border trade in electricity, posing an impediment to EU-wide competition among electricity production and electricity trading companies. Grid bottlenecks at cross-border interconnectors isolate national markets from one another, with the result that it is not always possible in the European Union to have the most competitive power plant produce electricity. This amounts to a loss of welfare compared with what it would be in the case of an electricity supply without bottlenecks. Furthermore, bottlenecks make it impossible for green electricity that would be eligible for promotion for reasons of climate and environmental protection to be transmitted unimpeded from the most suitable site to the consumer regions. Thus the transmission of electricity produced from wind power in Northern Germany to the industrial centres in Southern Germany is impeded by bottlenecks along the north-south lines of the national transmission network. Today some of the German electricity supply networks already have to be operated near the limits of their capacity, especially during high wind episodes. This poses a growing danger to network availability and security of supply. Since the installation, expansion and conversion of electricity supply networks in Germany and other member states of the European Union is no longer progressing at the required speed, growing importance attaches to the management of bottlenecks. The goal of bottleneck management is to resolve conflicts over network use such as can occur in overload situations with as little discrimination and as little

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

    Manegold, Stefan; Boncz, Peter; Kersten, Martin


    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...

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

    Boncz, Peter; Manegold, Stefan; Kersten, Martin


    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...

  19. Genetic diversity and differentiation of central European freshwater pearl mussel (Margaritifera margaritifera L.) populations: implications for conservation and management.

    Geist, Juergen; Kuehn, Ralph


    Despite the fact that mollusc species play an important role in many aquatic ecosystems, little is known about their biodiversity and conservation genetics. Freshwater pearl mussel (Margaritifera margaritifera L.) populations are seriously declining all over Europe and a variety of conservation programs are being established to support the remaining endangered central European populations. In order to provide guidelines for conservation strategies and management programs, we investigated the genetic structure of 24 freshwater pearl mussel populations originating from five major central European drainages including Elbe, Danube, Rhine, Maas and Weser, representing the last and most important populations in this area. We present a nondestructive sampling method of haemolymph for DNA analyses, which is applicable for endangered bivalves. The analyses of nine microsatellite loci with different levels of polymorphism revealed a high degree of fragmented population structure and very different levels of genetic diversity within populations. These patterns can be explained by historical and demographic effects and have been enforced by anthropogenic activities. Even within drainages, distinct conservation units were detected, as revealed from high F(ST) values, private alleles and genetic distance measures. Populations sampled close to contact zones between main drainage systems showed lowest levels of correct assignment to present-day drainage systems. Populations with high priority for conservation should not only be selected by means of census population size and geographical distance to other populations. Instead, detailed genetic analyses are mandatory for revealing differentiation and diversity parameters, which should be combined with ecological criteria for sustainable conservation and recovery programs. PMID:15660935

  20. Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel.

    Bučková, Jana; Cerný, Viktor; Novelletto, Andrea


    The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past. PMID:23460272

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

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


    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

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

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


    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

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

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


    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

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

    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


    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

  5. Steady State of Pedestrian Flow in Bottleneck Experiments

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


    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 ...

  6. Research of Cruise Industry Development Bottlenecks In China

    Ping Zhou


    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.

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

    Anna Siedlewska


    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.

  8. Bottleneck Paths and Trees and Deterministic Graphical Games

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


    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...

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

    HUANG Deshuang


    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.

  10. Fast Approximation Algorithm for Restricted Euclidean Bottleneck Steiner Tree Problem

    Zimao Li


    Full Text Available Bottleneck Steiner tree problem asks to find a Steiner tree for n terminals with at most k Steiner points such that the length of the longest edge in the tree is minimized. The problem has applications in the design of wireless communication networks. In this paper we study a restricted version of the bottleneck Steiner tree problem in the Euclidean plane which requires that only degree-2 Steiner points are possibly adjacent in the optimal solution. We first show that the problem is NP-hard and cannot be approximated within unless P=NP, and provide a fast polynomial time deterministic approximation algorithm with performance ratio .




    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.

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

    Rosser, Natalie L


    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

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

    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.

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

    Chopra, Aditya; Lineweaver, Charles H


    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

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

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


    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

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

    Geraldine Verplancke


    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.

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

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


    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

  18. Population differentiation in a Mediterranean relict shrub: the potential role of local adaptation for coping with climate change.

    Lázaro-Nogal, Ana; Matesanz, Silvia; Hallik, Lea; Krasnova, Alisa; Traveset, Anna; Valladares, Fernando


    Plants can respond to climate change by either migrating, adapting to the new conditions or going extinct. Relict plant species of limited distribution can be especially vulnerable as they are usually composed of small and isolated populations, which may reduce their ability to cope with rapidly changing environmental conditions. The aim of this study was to assess the vulnerability of Cneorum tricoccon L. (Cneoraceae), a Mediterranean relict shrub of limited distribution, to a future drier climate. We evaluated population differentiation in functional traits related to drought tolerance across seven representative populations of the species' range. We measured morphological and physiological traits in both the field and the greenhouse under three water availability levels. Large phenotypic differences among populations were found under field conditions. All populations responded plastically to simulated drought, but they differed in mean trait values as well as in the slope of the phenotypic response. Particularly, dry-edge populations exhibited multiple functional traits that favored drought tolerance, such as more sclerophyllous leaves, strong stomatal control but high photosynthetic rates, which increases water use efficiency (iWUE), and an enhanced ability to accumulate sugars as osmolytes. Although drought decreased RGR in all populations, this reduction was smaller for populations from the dry edge. Our results suggest that dry-edge populations of this relict species are well adapted to drought, which could potentially mitigate the species' extinction risk under drier scenarios. Dry-edge populations not only have a great conservation value but can also change expectations from current species' distribution models. PMID:26662734

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

    Cinthya Cristina Bulhões Arruda


    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.

  20. Population stochastic modelling (PSM)--an R package for mixed-effects models based on stochastic differential equations.

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode; Overgaard, Rune Viig; Madsen, Henrik


    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(1)) (2005) 109-141; C.W. Tornøe, R.V. Overgaard, H. Agersø, 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. Tornøe, 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 likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODEs) with an observation link that incorporates noise. This state-space formulation only allows for observation noise and not for system noise. Extending to SDEs allows for a Wiener noise component in the system equations. This additional noise component enables handling of autocorrelated residuals originating from natural variation or systematic model error. Autocorrelated residuals are often partly ignored in PK/PD modelling although violating the hypothesis for many standard statistical tests. This article presents a package for the statistical program R that is able to handle SDEs in a mixed-effects setting. The estimation method implemented is the FOCE(1) approximation to the population likelihood which is generated from the individual likelihoods that are approximated using the Extended Kalman Filter's one-step predictions. PMID:19268387

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

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


    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

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

    von Dassow Peter


    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

  3. Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event

    Plath Martin


    Full Text Available Abstract Background Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration before and after the flood. Results Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave, but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre. By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. Conclusions The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little

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

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


    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

  5. Low biochemical variability in European fallow deer (Dama dama L.): natural bottlenecks and the effects of domestication.

    Randi, E; Apollonio, M


    Tissue and blood samples from 180 fallow deer (Dama dama L.) belonging to an Italian free-ranging population were studied for biochemical variability by means of cellulose acetate and polyacrylamide gel electrophoresis. The 51 putative genetic loci successfully resolved showed a very low level of variability (P = 0.020, H = 0.006) in accordance with previously reported data on British and West German populations. That low biochemical polymorphism in European fallow deer populations is discussed taking into account the effects of natural bottlenecks and of domestication. PMID:3230030

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

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


    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...... (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, FST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results...

  7. A novel population of local pericyte precursor cells in tumor stroma that require Notch signaling for differentiation.

    Patenaude, Alexandre; Woerher, Stefan; Umlandt, Patricia; Wong, Fred; Ibrahim, Rawa; Kyle, Alastair; Unger, Sandy; Fuller, Megan; Parker, Jeremy; Minchinton, Andrew; Eaves, Connie J; Karsan, Aly


    Pericytes are perivascular support cells, the origin of which in tumor tissue is not clear. Recently, we identified a Tie1(+) precursor cell that differentiates into vascular smooth muscle, in a Notch-dependent manner. To understand the involvement of Notch in the ontogeny of tumor pericytes we used a novel flow immunophenotyping strategy to define CD146(+)/CD45(-)/CD31(-/lo) pericytes in the tumor stroma. This strategy combined with ex vivo co-culture experiments identified a novel pericyte progenitor cell population defined as Sca1(hi)/CD146(-)/CD45(-)/CD31(-). The differentiation of these progenitor cells was stimulated by co-culture with endothelial cells. Overexpression of the Notch ligand Jagged1 in endothelial cells further stimulated the differentiation of Sca1(hi)/CD146(-)/CD45(-)/CD31(-) cells into pericytes, while inhibition of Notch signaling with a γ-secretase inhibitor reduced this differentiation. However, Notch inhibition specifically in Tie1-expressing cells did not change the abundance of pericytes in tumors, suggesting that the pericyte precursor is distinct from the vascular smooth muscle cell precursor. Transplant experiments showed that the bone marrow contributes minimally to tumor pericytes. Immunophenotyping revealed that Sca1(hi)/CD146(-)/CD45(-)/CD31(-) cells have greater potential to differentiate into pericytes and have increased expression of classic mesenchymal stem cell markers (CD13, CD44, Nt5e and Thy-1) compared to Sca1(-/lo)/CD146(-)/CD45(-)/CD31(-) cells. Our results suggest that a local Sca1(hi)/CD146(-)/CD45(-)/CD31(-) pericyte progenitor resides in the tumor microenvironment and requires Notch signaling for differentiation into mature pericytes. PMID:26092680

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

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


    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

  9. [Genetic Differentiation of Populations of Baikal Endemic Sergentia baicalensis Tshern. (Diptera, Chironomidae)].

    Kravtsova, L S; Bukin, Yu S; Peretolchina, T E; Shcherbakov, D Yu


    The population structure of endemic species Sergentia baicalensis (Diptera, Chironomidae) from Lake Baikal was studied using the first subunit of the cytochrome C oxidase mitochondrial gene (Col). Two populations inhabiting different basins of this lake, the southern-central and northern, were detected. It was confirmed that the divergence time of this species was dated to Late Miocene (9.53 ± 3.9 Mya), during the period when geographically separated basins existed in the Baikal rift zone. PMID:26410937

  10. Aging and differentiation in yeast populations: elders with different properties and functions

    Palková, Z.; Wilkinson, D.; Váchová, Libuše


    Roč. 14, č. 1 (2014), s. 96-108. ISSN 1567-1356 R&D Projects: GA ČR GA13-08605S Institutional support: RVO:61388971 Keywords : yeast colonies * stationary-phase liquid cultures * comparison of differentiated cell subpopulations Subject RIV: EE - Microbiology, Virology Impact factor: 2.818, year: 2014

  11. Building the mammalian testis: origins, differentiation, and assembly of the component cell populations

    Svingen, Terje; Koopman, Peter


    Testis development in the mammalian embryo requires the formation and assembly of several cell types that allow these organs to achieve their roles in male reproduction and endocrine regulation. In this review, Svingen and Koopman focus on the issues of cell differentiation and development of the testis architecture and highlight the questions that remain to be explored.

  12. Towards a microscopic understanding of the phonon bottleneck

    Garanin, D. A.


    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.

  13. Nearly Optimal Solution for Restricted Euclidean Bottleneck Steiner Tree Problem

    Zimao Li


    Full Text Available A variation of the traditional Steiner tree problem, the bottleneck Steiner tree problem is considered in this paper, which asks to find a Steiner tree for n terminals with at most k Steiner points such that the length of the longest edge in the tree is minimized. The problem has applications in the design of WDM optical networks, design of wireless communication networks and reconstruction of phylogenetic tree in biology. We study a restricted version of the bottleneck Steiner tree problem in the Euclidean plane which requires that only degree-2 Steiner points are possibly adjacent in the optimal solution. The problem is known to be MAX-SNP hard and cannot be approximated within unless P=NP, we propose a nearly optimal randomized polynomial time approximation algorithm with performance ratio +e, where e is a positive number.

  14. Bottleneck Non-Crossing Matching in the Plane

    Abu-Affash, A Karim; Katz, Matthew J; Trabelsi, Yohai


    Let $P$ be a set of $2n$ points in the plane, and let $M_{\\rm C}$ (resp., $M_{\\rm NC}$) denote a bottleneck matching (resp., a bottleneck non-crossing matching) of $P$. We study the problem of computing $M_{\\rm NC}$. We first prove that the problem is NP-hard and does not admit a PTAS. Then, we present an $O(n^{1.5}\\log^{0.5} n)$-time algorithm that computes a non-crossing matching $M$ of $P$, such that $bn(M) \\le 2\\sqrt{10} \\cdot bn(M_{\\rm NC})$, where $bn(M)$ is the length of a longest edge in $M$. An interesting implication of our construction is that $bn(M_{\\rm NC})/bn(M_{\\rm C}) \\le 2\\sqrt{10}$.

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

    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.

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

    Piersma, T


    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...

  17. Health Care Reform and the Primary Care Workforce Bottleneck

    Schwartz, Mark D


    To establish and sustain the high-performing health care system envisioned in the Affordable Care Act (ACA), current provisions in the law to strengthen the primary care workforce must be funded, implemented, and tested. However, the United States is heading towards a severe primary care workforce bottleneck due to ballooning demand and vanishing supply. Demand will be fueled by the “silver tsunami” of 80 million Americans retiring over the next 20 years and the expanded insurance coverage fo...

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

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


    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...

  19. Congestion costs in bottleneck equilibrium with stochastic capacity and demand

    Fosgerau, Mogens


    I analyse congestion costs in the Vickrey bottleneck model of a congestible facility with a peak load in demand. The shape of the peak is endogenous, being the sum of individual scheduling decisions. Capacity and demand are random, which introduces uncertainty into the individual scheduling choices. These are essential features of actual peak loads. Based on work by Arnott, de Palma and Lindsey, I derive the expected marginal and total congestion costs and compare to the case with fixed capac...

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

    Endress, Ansgar D; Katzir, Roni


    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

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

    ZHANG Xin-min


    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.

  2. Time minimizing transportation problem with fractional bottleneck objective function

    Jain Madhuri; Saksena P.K.


    This paper is aimed at studying the Time Minimizing Transportation Problem with Fractional Bottleneck Objective Function (TMTP-FBOF). TMTP-FBOF is related to a Lexicographic Fractional Time Minimizing Transportation Problem (LFTMTP), which will be solved by a lexicographic primal code. An algorithm is also developed to determine an initial efficient basic solution to this TMTP-FBOF. The developed TMTP-FBOF Algorithm is supported by a real life example of Military Transportation Problem ...

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

    Salii, Y.


    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...

  4. Clogging transition of many-particle systems flowing through bottlenecks

    Iker Zuriguel; Daniel Ricardo Parisi; Raúl Cruz Hidalgo; Celia Lozano; Alvaro Janda; Paula Alejandra Gago; Juan Pablo Peralta; Luis Miguel Ferrer; Luis Ariel Pugnaloni; Eric Clément; Diego Maza; Ignacio Pagonabarraga; Angel Garcimartín


    When a large set of discrete bodies passes through a bottleneck, the flow may become intermittent due to the development of clogs that obstruct the constriction. Clogging is observed, for instance, in colloidal suspensions, granular materials and crowd swarming, where consequences may be dramatic. Despite its ubiquity, a general framework embracing research in such a wide variety of scenarios is still lacking. We show that in systems of very different nature and scale -including sheep herds, ...

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

    Thomas Meredith M


    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

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

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


    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, 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

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


    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.

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



    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.

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

    Banguera-Hinestroza, E.


    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.

  10. Populism

    Abts, Koenraad; van Kessel, Stijn


    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,...

  11. Differentiation of ovarian development and the evolution of fecundity in rapidly diverging exotic beetle populations.

    Macagno, Anna L M; Beckers, Oliver M; Moczek, Armin P


    Fecundity is a fundamental determinant of fitness, yet the proximate developmental and physiological mechanisms that enable its often rapid evolution in natural populations are poorly understood. Here, we investigated two populations of the dung beetle Onthophagus taurus that were established in exotic ranges in the early 1970s. These populations are subject to drastically different levels of resource competition in the field, and have diverged dramatically in female fecundity. Specifically, Western Australian O. taurus experience high levels of resource competition, and exhibit greatly elevated reproductive output compared to beetles from the Eastern US, where resource competition is minimal and female fecundity is low. We compared patterns of ovarian maturation, relative investment into and timing of egg production, and potential trade-offs between ovarian investment and the duration of larval development and adult body size between populations representative of both exotic ranges. We found that the rapid divergence in fecundity between exotic populations is associated with striking differences in several aspects of ovarian development: (1) Western Australian females exhibit accelerated ovarian development, (2) produce more eggs, (3) bigger eggs, and (4) start laying eggs earlier compared to their Eastern US counterparts. At the same time, divergence in ovarian maturation patterns occurred alongside changes in (5) larval developmental time, and (6) adult body size, and (7) mass. Western Australian females take longer to complete larval development and, surprisingly, emerge into smaller yet heavier adults than size-matched Eastern US females. We discuss our results in the context of the evolutionary developmental biology of fecundity in exotic populations. PMID:26300520

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

    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.

  13. Identification of a unique hepatocellular carcinoma line, Li-7, with CD13(+) cancer stem cells hierarchy and population change upon its differentiation during culture and effects of sorafenib

    Yamada, Takeshi; Abei, Masato; Danjoh, Inaho; Shirota, Ryoko; Yamashita, Taro; Hyodo, Ichinosuke; Nakamura, Yukio


    Backgrounds Cancer stem cell (CSC) research has highlighted the necessity of developing drugs targeting CSCs. We investigated a hepatocellular carcinoma (HCC) cell line that not only has CSC hierarchy but also shows phenotypic changes (population changes) upon differentiation of CSC during culture and can be used for screening drugs targeting CSC. Methods Based on a hypothesis that the CSC proportion should decrease upon its differentiation into progenitors (population change), we tested HCC ...

  14. Population genetic differentiation of height and body mass index across Europe

    Robinson, Matthew R.; Hemani, Gibran; Medina-Gomez, Carolina; Mezzavilla, Massimo; Esko, Tonu; Shakhbazov, Konstantin; Powell, Joseph E.; Vinkhuyzen, Anna; Berndt, Sonja I.; Gustafsson, Stefan; Pers, Tune Hannes; Werge, Thomas M.


    Across-nation differences in the mean values for complex traits are common(1-8), but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European...

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

    Yusuf Özşensoy


    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.

  16. Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

    C. MAGGI


    Full Text Available Parastichopus regalis (Cuvier, 1817 is the most expensive seafood product on the catalonian market (NE Spain, with prices around 130 €/Kg (fresh weight. Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia. We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST, AMOVA and correspondence analysis (CA based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1 an accurate assessment of the stocks status along the Spanish coasts; 2 the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3 the founding of protected areas (i.e. not take zones to conserve healthy populations and favour the recruitment on the nearby areas.

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

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


    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

  18. Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

    Friess, Daniel A.; Krauss, Ken W.; Horstman, Erik M.; Balke, Thorsten; Bouma, Tjeerd J.; Galli, Demis; Webb, Edward L.


    Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

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

    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

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

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


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

    María José Quero Gervilla


    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.

  2. Genetic Differentiation among Populations and Color Variants of Sea Cucumbers (Stichopus Japonicus) from Korea and China

    Kang, Jung-Ha; Kim, Yi-Kyong; Kim, Mi-Jung; Park, Jung-Yeon; An, Chul-Min; Kim, Bong-Seok; Jun, Je-Cheon; Kim, Sang-Kyu


    The Far Eastern sea cucumber, Stichopus japonicus, is a favored food in Eastern Asia, including Korea, Japan, and China. Aquaculture production of this species has increased because of recent declines in natural stocks and government-operated stock release programs are ongoing. Therefore, the analyses of genetic structure in wild and hatchery populations are necessary to maintain the genetic diversity of this valuable marine resource. In addition, given that sea cucumber color affects market ...

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

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


    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...

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

    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

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

    Bongoh Kye; Erika Arenas; Graciela Teruel; Luis Rubalcava


    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...

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

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


    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...

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

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


    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 ...

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

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


    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 ...

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

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


    © 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...

  10. Juvenile Myelomonocytic Leukemia (JMML Cells Spontaneously Differentiate into Dendritic-Cell Like Populations in vitro

    Parviz Shayan


    Full Text Available Objective: Juvenile myelomonocytic leukemia (JMML is a rare myelodysplastic/ myeloproliferative malignancy of early childhood, characterized by monocytosis, hepatosplenomegaly and an aggressive clinical course. Methods: In semi-solid culture JMML progenitor cells proliferate spontaneously into colony forming units. In order to study the mechanisms of proliferation and differentiation of JMML cells we developed a suspension culture system without additional exogenous growth factor supplement. Mononuclear cells (MNC from peripheral blood, bone marrow or spleen of 14 patients with JMML and 24 controls were studied. Findings: JMML cells expressed higher levels of the proliferation marker Ki67 (median 24% [7-39%] vs a median of 3.5% in controls. 90% of JMML cells were CD68-positive (vs 35% in controls and by day 7 all JMML samples contained CD1a- positive cells. Electron microscopy demonstrated cytoplasmic vesicular structures resembling multilamellar MHC II compare­timents, which together with the expression of CD1a - support a dendritic cell (DC-phenotype. Conclusion: Differentiation into CD1a-positive DC seems to be a frequent phenomenon in cultured JMML MNC, which in vivo may contribute to clinical characteristics such as skin and organ infiltration.

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

    Liang LENG; De-Xing ZHANG


    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

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

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


    characterized 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...

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

    Comfort O. AFOLAYAN


    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.

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

    Jason Munshi-South


    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.

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

    Laves, Kevin S.; Loeb, Susan C.


    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.

  16. The bottleneck effect in three-dimensional turbulence simulations

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


    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.

  17. A lexisearch Algorithm for the Bottleneck Traveling Salesman Problem

    Zakir H. Ahmed


    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.

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

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


    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...

  19. Bottlenecks in molecular testing for rare genetic diseases.

    Willems, Patrick J


    Despite the impressive progress in our understanding of the genetic causes of genetic diseases over the past decade, molecular diagnosis for rare genetic disorders is still in its infancy, being slow, expensive, unreliable, insufficient, and ill-organized in many countries. This leaves the gap between the hype of the current genomic research and the hope for a simple genetic diagnosis too large for patients and families affected with genetic disease. The bottlenecks in the molecular testing for rare genetic disorders are discussed below. PMID:18412107

  20. Orphan drug development across Europe: bottlenecks and opportunities.

    Heemstra, Harald E; de Vrueh, Remco L A; van Weely, Sonja; Büller, Hans A; Leufkens, Hubert G M


    With the assignment of the 500th European Union orphan drug designation in 2007, the Regulation on Orphan Medicinal Products truly begins to show its potential for delivering new medicines to patients with rare diseases. Here, we analysed European orphan drug development at a national level and unveil a strong relationship between orphan drug development and pharmaceutical innovation performance in Europe. Moreover, we identify gaps in transition from science into orphan drug development as important bottlenecks that exist in several European countries. Our findings underline the importance of innovation-based policies to enhance the development of orphan drugs in Europe. PMID:18583178

  1. Asymmetric exclusion processes on a closed network with bottlenecks

    We study the generic nonequilibrium steady states in asymmetric exclusion processes on a closed network with bottlenecks. To this end we propose and study closed simple networks with multiple-connected non-identical junctions. Depending upon the parameters that define the network junctions and the particle number density, the models display phase transitions with both static and moving density inhomogeneities. The currents in the models can be tuned by the junction parameters. Our models highlight how extended and point defects may affect the density profiles in a closed directed network. Phenomenological implications of our results are discussed. (paper)

  2. 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.

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


    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

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

    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.


    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.

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

    Tøttrup, Anders Peter; Thorup, Kasper


    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...... all studied species. Males show more synchronous migration patterns compared to females and, hence, first arriving females followed males more closely than later arriving individuals. However, we found no inter-sexual differences in arrival trends as both sexes advance spring arrival over time with...... climatic 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...

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

    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

  6. Genetic Differentiation among Populations and Color Variants of Sea Cucumbers (Stichopus Japonicus from Korea and China

    Jung-Ha Kang, Yi-Kyong Kim, Mi-Jung Kim, Jung-Yeon Park, Chul-Min An, Bong-Seok Kim, Je-Cheon Jun, Sang-Kyu Kim


    Full Text Available The Far Eastern sea cucumber, Stichopus japonicus, is a favored food in Eastern Asia, including Korea, Japan, and China. Aquaculture production of this species has increased because of recent declines in natural stocks and government-operated stock release programs are ongoing. Therefore, the analyses of genetic structure in wild and hatchery populations are necessary to maintain the genetic diversity of this valuable marine resource. In addition, given that sea cucumber color affects market price, with the rare, possibly reproductively isolated, red type being the most valuable, an understanding of the genetic structure and diversity in color variation of green and red types is necessary. We analyzed the genetic structure of wild and hatchery-produced green type S. japonicus from Korea and China, and wild red type from Korea using 9 microsatellite makers. The number of alleles per locus ranged from 11 to 29 across all populations. The mean allele numbers of the green types from Korea (10.6 and China (10.1 were similar, but differed slightly from that of the red type (9.1. Pairwise multilocus FST and genetic distance estimations showed no significant differences between the green types from Korea and China, whereas the differences between the green and red types were significant. This was clearly illustrated by a UPGMA dendrogram, in which the two close subclusters of green types were completely separated from the red type. In addition, the allele frequencies of the green and red types were significantly different. Assignment tests correctly assigned 100% (quality index 99.97% of individuals to their original color types and demonstrated the feasibility of microsatellite analysis for discrimination between color types.

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

    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. A bottleneck model of set-specific capture.

    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.

  9. Efficacy of sorafenib in advanced differentiated and medullary thyroid cancer: experience in a Turkish population

    Benekli, Mustafa; Yalcin, Suayib; Ozkan, Metin; Elkiran, Emin Tamer; Sevinc, Alper; Cabuk, Devrim; Coskun, Hasan Senol; Oksuzoglu, Berna; Bayar, Banu; Akbulat, Akif; Ozet, Ahmet


    Background Antivascular endothelial growth factor tyrosine kinase inhibitors have been used recently in the treatment of advanced differentiated thyroid cancer (DTC) and medullary thyroid cancer (MTC). Off-label sorafenib is used in Turkey with special permission by the Ministry of Health for this indication. Patients and methods Patients with advanced DTC and MTC were retrospectively identified from the Turkish Ministry of Health database. Data on these patients were prospectively collected before permission is granted to use sorafenib. Results Thirty patients with complete data were analyzed: 14 DTC (papillary number [n] =10; follicular n=4) and 16 MTC. The median age of the patients was 57 years (range: 28–79 years), and there were 18 males and 12 females. All DTC patients were iodine refractory and had received a median three doses of radioactive iodine (range: 1–7 doses). Sorafenib was used for a median of 12 months (range: 1–49 months). The overall response rate was 20%, all partial responses, with no complete response. The overall response rate was 14% in DTC and 25% in MTC patients. The median progression-free survival (PFS) was 17.1 months (95% confidence interval [CI]: 7.3–26.8) and overall survival (OS) was not reached. The 2-year PFS and OS were 39% and 68%, respectively. DTC and MTC patients had similar survival outcomes: median PFS of 21.3 months (95% CI: 5.8–36.7) versus 14.5 months (95% CI: 3.7–25.2), respectively (P=0.36), with the median OS not reached in either group (P=0.17). Tumor marker levels did not have any prognostic or predictive role. The toxicity profile was similar to that of other sorafenib trials. Conclusion Sorafenib is an effective and well-tolerated treatment in advanced thyroid cancers. PMID:25548522

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

    Damien C Tully


    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.