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Sample records for populations feedback structures

  1. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    PubMed

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  2. Demography and population dynamics of the mouse opossum (Thylamys elegans) in semi-arid Chile: seasonality, feedback structure and climate.

    PubMed Central

    Lima, M.; Stenseth, N. C.; Yoccoz, N. G.; Jaksic, F. M.

    2001-01-01

    Here we present, to the authors' knowledge for the very first time for a small marsupial, a thorough analysis of the demography and population dynamics of the mouse opossum (Thylamys elegans) in western South America. We test the relative importance of feedback structure and climatic factors (rainfall and the Southern Oscillation Index) in explaining the temporal variation in the demography of the mouse opossum. The demographic information was incorporated into a stage-structured population dynamics model and the model's predictions were compared with observed patterns. The mouse opossum's capture rates showed seasonal (within-year) and between-year variability, with individuals having higher capture rates during late summer and autumn and lower capture rates during winter and spring. There was also a strong between-year effect on capture probabilities. The reproductive (the fraction of reproductively active individuals) and recruitment rates showed a clear seasonal and a between-year pattern of variation with the peak of reproductive activity occuring during winter and early spring. In addition, the fraction of reproductive individuals was positively related to annual rainfall, while population density and annual rainfall positively influenced the recruitment rate. The survival rates were negatively related to annual rainfall. The average finite population growth rate during the study period was estimated to be 1.011 +/- 0.0019 from capture-recapture estimates. While the annual growth rate estimated from the seasonal linear matrix models was 1.026, the subadult and adult survival and maturation rates represent between 54% (winter) and 81% (summer) of the impact on the annual growth rate. PMID:11571053

  3. Optical feedback structures and methods of making

    DOEpatents

    Snee, Preston T; Chan, Yin Thai; Nocera, Daniel G; Bawendi, Moungi G

    2014-11-18

    An optical resonator can include an optical feedback structure disposed on a substrate, and a composite including a matrix including a chromophore. The composite disposed on the substrate and in optical communication with the optical feedback structure. The chromophore can be a semiconductor nanocrystal. The resonator can provide laser emission when excited.

  4. World population projections and possible ecological feedbacks.

    PubMed

    Lutz, W; Prinz, C; Langgassner, J

    1993-01-01

    The aim of this article was to define population scenarios between 1990 and 2030 for 12 regions in the world. Future paths of fertility, mortality, and migration are affected by the size, age structure, and regional distribution of the world's population and are responsive to social, economic, and environmental factors. A scenario approach puts emphasis on "if-then" calculations; makes all assumptions explicit; addresses all components of change separately, giving reasons for an invariant measure; and may include a number of scenario options. The assumptions in the scenarios chosen were taken from several background papers in recent ILASA and Council of Europe publications. The 12 regions allowed for grouping by level of development, continents, or other homogenous units. Assumptions for the scenarios were that fertility would range between 1.1 and 2.1 for developed countries and 1.7 and 3.00 for developing countries. African fertility was assumed differently at 4.0 to 5.0. Mortality was derived from UN and Coale and Guo model life tables adjusted to UN life expectancies. Improvement in life expectancy was expected to be the same by sex and to increase per decade. Nonproportional mortality change was assumed. Age patterns of migrants were taken from model migration schedules of Rogers and Castro. Population was expected to begin in 1990 at 5 billion and reach at least 8 billion over 40-50 years. Under high fertility and low mortality assumptions, population size was expected to reach 35 billion by 2100. Under low fertility and high mortality assumptions, there could be a rise and then a decline to 1990 levels. Africa's share of the population would increase from 12% in 1990 to 19% by 2030 and 35% by 2100. The mean age of world population would be 36 years in 1990, 40 years in 2030 under high fertility and high mortality assumptions, and 60 years by 2100 under low fertility, low mortality, and low migration assumptions: evidence of the rapid aging process. Age

  5. Effects of Active galactic nuclei feedback in galaxy population

    NASA Astrophysics Data System (ADS)

    Lagos, C.; Cora, S.; Padilla, N.

    We analyze the effects of feedback from Active Galactic Nuclei (AGN) on the formation and evolution of galaxies, which is assumed to quench cooling flows in massive halos. With this aim we use an hybrid model that combines a cosmological Lambda CDM simulation with a semi-analytic model of galaxy formation. We consider the semi-analytic model described by Cora (2006) (SAMC06) which has been improved by including AGNs, which are associated with the presence of supermassive black holes (BHs). Modellization of BH includes gas accretion during merger-driven starbursts and black hole mergers (Malbon et al., 2006), accretion during starbursts triggered by disk instabilities (Bower et al. 2006), and accretion of cooling gas from quasi-hydrostatically cooling haloes (Croton et al. 2006); Eddington limit is applied in all accretion processes. It is assumed that feedback from AGNs operates in the later case. We show that this new model can simultaneously explain: (i) the bright-end of the galaxy luminosity function (LF); (ii) the observed older population of stars in massive galaxies, thus reproducing the stellar mass function (SMF); (iii) a star formation rate (SFR) seemingly showing an anti-hierarchical galaxy growth. The success of our model is mainly due to the ability of AGN feedback to suppress further cooling and SF in the most massive structures.

  6. Feedback strategies for visual search in airframe structural inspection.

    PubMed

    Gramopadhye, A K; Drury, C G; Sharit, J

    1997-05-01

    Feedback of information has consistently shown positive results in human inspection, provided it is given in a timely and appropriate manner. Feedback serves as the basis of most training schemes; traditionally this has been performance feedback. Other forms of feedback which provide strategy information rather than performance information may have a role in improving inspection. This study compared performance feedback and cognitive feedback in a realistic simulation of an aircraft structural inspection task. Performance (time, errors) feedback showed the greatest improvements in performance measures. Cognitive feedback enhanced efficiency measures of search strategy. When cognitive feedback consisted of visual representations of the path and the coverage of the search sequence, subjects also were able to use this task information to improve their search performance.

  7. Eco-evolutionary feedbacks can rescue cooperation in microbial populations

    PubMed Central

    Moreno-Fenoll, Clara; Cavaliere, Matteo; Martínez-García, Esteban; Poyatos, Juan F.

    2017-01-01

    Bacterial populations whose growth depends on the cooperative production of public goods are usually threatened by the rise of cheaters that do not contribute but just consume the common resource. Minimizing cheater invasions appears then as a necessary mechanism to maintain these populations. However, that invasions result instead in the persistence of cooperation is a prospect that has yet remained largely unexplored. Here, we show that the demographic collapse induced by cheaters in the population can actually contribute to the rescue of cooperation, in a clear illustration of how ecology and evolution can influence each other. The effect is made possible by the interplay between spatial constraints and the essentiality of the shared resource. We validate this result by carefully combining theory and experiments, with the engineering of a synthetic bacterial community in which the public compound allows survival to a lethal stress. The characterization of the experimental system identifies additional factors that can matter, like the impact of the lag phase on the tolerance to stress, or the appearance of spontaneous mutants. Our work explains the unanticipated dynamics that eco-evolutionary feedbacks can generate in microbial communities, feedbacks that reveal fundamental for the adaptive change of ecosystems at all scales. PMID:28211914

  8. Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

    PubMed Central

    Sanchez, Alvaro; Gore, Jeff

    2013-01-01

    The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate

  9. HIGHER EDUCATION--A POPULATION FLOW FEEDBACK MODEL.

    ERIC Educational Resources Information Center

    REISMAN, ARNOLD

    A MATHEMATICAL MODEL IS DEVELOPED TO STUDY THE PRODUCTION OF DOCTORAL, MASTER'S, AND BACHELOR'S DEGREES AND THEIR FEEDBACK INTO HIGHER EDUCATION. FEEDBACK IS DETERMINED BY A SET OF "BASIC BALANCE EQUATIONS" WHICH STATE THAT THE TOTAL RATE OF FLOW INTO A CATEGORY LESS THE RATE OF OUTFLOW IS EQUAL TO THE RATE OF ACCUMULATION OR GROWTH IN A GIVEN…

  10. Compensatory density feedback of Oncomelania hupensis populations in two different environmental settings in China

    PubMed Central

    2011-01-01

    Background The most recent strategy for schistosomiasis control in the People's Republic of China aims to reduce the likelihood of environmental contamination of schistosome eggs. Despite considerable progress, it is believed that achievements would be further consolidated with additional intermediate host snail control measures. We provide an empirical framework for discerning the relative contribution of intrinsic effects (density feedback) from other extrinsic drivers of snail population dynamics. Methods We set up experiments in two study locations to collect reproduction data of Oncomelania hupensis, the intermediate host snail of Schistosoma japonicum. We applied a set of four population dynamic models that have been widely used to study phenomenological time-series data to examine the properties of demographic density feedback patterns from abundance data. We also contrasted the obtained results with the component feedback of density on survival rate to determine whether adult survival was the principal driver of the demographic feedback observed. Results Demographic density feedback models (Ricker- and Gompertz-logistic) accounted for > 99% of Akaike's information criterion model weight, with the Gompertz ranking highest in all O. hupensis population groups. We found some evidence for stronger compensatory feedback in the O. hupensis population from Sichuan compared to a Jiangsu population. Survival rates revealed strong component feedback, but the log-linear relationships (i.e. Gompertz) had less support in the demographic feedback analysis. Conclusions Our findings indicate that integrated schistosomiasis control measures must continue to reduce parasite abundance further because intermediate host snail populations tend to grow exponentially at low densities, especially O. hupensis populations in mountainous regions. We conclude that density feedback in adult survival is the principal component contribution to the demographic phenomenon observed in the

  11. Effectiveness of Structural Feedback Provided by Pathfinder Networks

    ERIC Educational Resources Information Center

    Trumpower, David L.; Sarwar, Gul Shahzad

    2010-01-01

    Within the field of education, there has been an increasing recognition of the importance of formative assessment and of structural knowledge. In an effort to fill needs in each of these areas, this article describes an innovative feedback strategy intended to improve students' structural knowledge. Twenty-four high school physics students were…

  12. Local environment and density-dependent feedbacks determine population growth in a forest herb.

    PubMed

    Dahlgren, Johan P; Ostergård, Hannah; Ehrlén, Johan

    2014-12-01

    Linking spatial variation in environmental factors to variation in demographic rates is essential for a mechanistic understanding of the dynamics of populations. However, we still know relatively little about such links, partly because feedbacks via intraspecific density make them difficult to observe in natural populations. We conducted a detailed field study and investigated simultaneous effects of environmental factors and the intraspecific density of individuals on the demography of the herb Lathyrus vernus. In regression models of vital rates we identified effects associated with spring shade on survival and growth, while density was negatively correlated with these vital rates. Density was also negatively correlated with average individual size in the study plots, which is consistent with self-thinning. In addition, average plant sizes were larger than predicted by density in plots that were less shaded by the tree canopy, indicating an environmentally determined carrying capacity. A size-structured integral projection model based on the vital rate regressions revealed that the identified effects of shade and density were strong enough to produce differences in stable population sizes similar to those observed in the field. The results illustrate how the local environment can determine dynamics of populations and that intraspecific density may have to be more carefully considered in studies of plant demography and population viability analyses of threatened species. We conclude that demographic approaches incorporating information about both density and key environmental factors are powerful tools for understanding the processes that interact to determine population dynamics and abundances.

  13. Real-time feedback from iterative electronic structure calculations.

    PubMed

    Vaucher, Alain C; Haag, Moritz P; Reiher, Markus

    2016-04-05

    Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm used and the necessity to provide data in fixed and short time intervals for real-time rendering. We introduce the concept of a mediator as a component able to deal with infrequent and unpredictable reference data to generate reliable feedback. In the context of real-time quantum chemistry, the mediator takes the form of a surrogate potential that has the same local shape as the first-principles potential and can be evaluated efficiently to deliver atomic forces as real-time feedback. The surrogate potential is updated continuously by electronic structure calculations and guarantees to provide a reliable response to the operator for any molecular structure. To demonstrate the application of iterative electronic structure methods in real-time reactivity exploration, we implement self-consistent semiempirical methods as the data source and apply the surrogate-potential mediator to deliver reliable real-time feedback.

  14. Integrated Control with Structural Feedback to Enable Lightweight Aircraft

    NASA Technical Reports Server (NTRS)

    Taylor, Brian R.

    2011-01-01

    This presentation for the Fundamental Aeronautics Program Technical Conference covers the benefits of active structural control, related research areas, and focuses on the use of optimal control allocation for the prevention of critical loads. Active control of lightweight structures has the potential to reduce aircraft weight and fuel burn. Sensor, control law, materials, control effector, and system level research will be necessary to enable active control of lightweight structures. Optimal control allocation with structural feedback has been shown in simulation to be feasible in preventing critical loads and is one example of a control law to enable future lightweight aircraft.

  15. Feedback enhancement of the amplitude of dynamically excited coherent population trapping resonance in Rb vapour

    NASA Astrophysics Data System (ADS)

    Radnatarov, Daba; Khripunov, Sergey; Kobtsev, Sergey; Taichenachev, Alexey; Yudin, Valery; Basalaev, Maxim; Popkov, Ivan; Andryushkov, Valeriy; Steschenko, Tatiana

    2016-11-01

    This work reports on possibilities of contrast enhancement of dynamically excited coherent population trapping (CPT) resonance in 87Rb vapour arising from application of feedback methods. Controlling the bichromatic pump radiation power through a feedback loop that stabilises Rb atom luminescence when scanning the frequency difference of the bichromatic pump radiation resulted in a more than an order-or-magnitude improvement in the amplitude of the CPT resonance at scanning frequencies over 100 Hz. It is established that the excursion of the pump radiation power controlled by the feedback loop under dynamic excitation is by an order of magnitude smaller than that under quasistationary excitation at scan frequencies < 1 Hz.

  16. Dose-structured population dynamics.

    PubMed

    Ginn, Timothy R; Loge, Frank J

    2007-07-01

    Applied population dynamics modeling is relied upon with increasing frequency to quantify how human activities affect human and non-human populations. Current techniques include variously the population's spatial transport, age, size, and physiology, but typically not the life-histories of exposure to other important things occurring in the ambient environment, such as chemicals, heat, or radiation. Consequently, the effects of such 'abiotic' aspects of an ecosystem on populations are only currently addressed through individual-based modeling approaches that despite broad utility are limited in their applicability to realistic ecosystems [V. Grimm, Ten years of individual-based modeling in ecology: what have we learned and what could we learn in the future? Ecol. Model. 115 (1999) 129-148][1]. We describe a new category of population dynamics modeling, wherein population dynamical states of the biotic phases are structured on dose, and apply this framework to demonstrate how chemical species or other ambient aspects can be included in population dynamics in three separate examples involving growth suppression in fish, inactivation of microorganisms with ultraviolet irradiation, and metabolic lag in population growth. Dose-structuring is based on a kinematic approach that is a simple generalization of age-structuring, views the ecosystem as a multi-component mixture with reacting biotic/abiotic components. The resulting model framework accommodates (a) different memories of exposure as in recovery from toxic ambient conditions, (b) differentiation between exogenous and endogenous sources of variation in population response, and (c) quantification of acute or sub-acute effects on populations arising from life-history exposures to abiotic species. Classical models do not easily address the very important fact that organisms differ and have different experiences over their life cycle. The dose structuring is one approach to incorporate some of these elements into the

  17. Robust Feedback Control of Flow Induced Structural Radiation of Sound

    NASA Technical Reports Server (NTRS)

    Heatwole, Craig M.; Bernhard, Robert J.; Franchek, Matthew A.

    1997-01-01

    A significant component of the interior noise of aircraft and automobiles is a result of turbulent boundary layer excitation of the vehicular structure. In this work, active robust feedback control of the noise due to this non-predictable excitation is investigated. Both an analytical model and experimental investigations are used to determine the characteristics of the flow induced structural sound radiation problem. The problem is shown to be broadband in nature with large system uncertainties associated with the various operating conditions. Furthermore the delay associated with sound propagation is shown to restrict the use of microphone feedback. The state of the art control methodologies, IL synthesis and adaptive feedback control, are evaluated and shown to have limited success for solving this problem. A robust frequency domain controller design methodology is developed for the problem of sound radiated from turbulent flow driven plates. The control design methodology uses frequency domain sequential loop shaping techniques. System uncertainty, sound pressure level reduction performance, and actuator constraints are included in the design process. Using this design method, phase lag was added using non-minimum phase zeros such that the beneficial plant dynamics could be used. This general control approach has application to lightly damped vibration and sound radiation problems where there are high bandwidth control objectives requiring a low controller DC gain and controller order.

  18. Endogenous field feedback promotes the detectability for exogenous electric signal in the hybrid coupled population

    SciTech Connect

    Wei, Xile; Zhang, Danhong; Wang, Jiang; Yu, Haitao; Lu, Meili; Che, Yanqiu

    2015-01-15

    This paper presents the endogenous electric field in chemical or electrical synaptic coupled networks, aiming to study the role of endogenous field feedback in the signal propagation in neural systems. It shows that the feedback of endogenous fields to network activities can reduce the required energy of the noise and enhance the transmission of input signals in hybrid coupled populations. As a common and important nonsynaptic interactive method among neurons, particularly, the endogenous filed feedback can not only promote the detectability of exogenous weak signal in hybrid coupled neural population but also enhance the robustness of the detectability against noise. Furthermore, with the increasing of field coupling strengths, the endogenous field feedback is conductive to the stochastic resonance by facilitating the transition of cluster activities from the no spiking to spiking regions. Distinct from synaptic coupling, the endogenous field feedback can play a role as internal driving force to boost the population activities, which is similar to the noise. Thus, it can help to transmit exogenous weak signals within the network in the absence of noise drive via the stochastic-like resonance.

  19. Laplacian eigenfunctions learn population structure.

    PubMed

    Zhang, Jun; Niyogi, Partha; McPeek, Mary Sara

    2009-12-01

    Principal components analysis has been used for decades to summarize genetic variation across geographic regions and to infer population migration history. More recently, with the advent of genome-wide association studies of complex traits, it has become a commonly-used tool for detection and correction of confounding due to population structure. However, principal components are generally sensitive to outliers. Recently there has also been concern about its interpretation. Motivated from geometric learning, we describe a method based on spectral graph theory. Regarding each study subject as a node with suitably defined weights for its edges to close neighbors, one can form a weighted graph. We suggest using the spectrum of the associated graph Laplacian operator, namely, Laplacian eigenfunctions, to infer population structure. In simulations and real data on a ring species of birds, Laplacian eigenfunctions reveal more meaningful and less noisy structure of the underlying population, compared with principal components. The proposed approach is simple and computationally fast. It is expected to become a promising and basic method for population genetics and disease association studies.

  20. Genealogical histories in structured populations.

    PubMed

    Kumagai, Seiji; Uyenoyama, Marcy K

    2015-06-01

    In genealogies of genes sampled from structured populations, lineages coalesce at rates dependent on the states of the lineages. For migration and coalescence events occurring on comparable time scales, for example, only lineages residing in the same deme of a geographically subdivided population can have descended from a common ancestor in the immediately preceding generation. Here, we explore aspects of genealogical structure in a population comprising two demes, between which migration may occur. We use generating functions to obtain exact densities and moments of coalescence time, number of mutations, total tree length, and age of the most recent common ancestor of the sample. We describe qualitative features of the distribution of gene genealogies, including factors that influence the geographical location of the most recent common ancestor and departures of the distribution of internode lengths from exponential.

  1. Feedback magnetization of ultra-low index irradiative structure

    NASA Astrophysics Data System (ADS)

    Rybin, Oleg; Shulga, Sergey

    2015-10-01

    Ultra-low refractive index irradiative structure is considered. The structure consists of a patch antenna with the metamaterial slab located on top of the antenna, as superstrate. In this study, ultra-low index phenomenon of the irradiative system is associated with improving the directivity of the patch antenna by putting the metamaterial slab on top of the antenna. The last phenomenon, in turn, is associated with the feedback partial magnetization of Iron inclusions of the slab caused by the radiation from the antenna. Mathematical model for evaluating the complex effective relative permittivity of the irradiative structure is developed. Numerical calculations for complex effective relative permittivity of the irradiative structure and real part of the complex effective relative permeability of the metamaterial slab are done in the study.

  2. Microbial population and community dynamics on plant roots and their feedbacks on plant communities.

    PubMed

    Bever, James D; Platt, Thomas G; Morton, Elise R

    2012-01-01

    The composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology.

  3. Multivariable feedback active structural acoustic control using adaptive piezoelectric sensoriactuators.

    PubMed

    Vipperman, J S; Clark, R L

    1999-01-01

    An experimental implementation of a multivariable feedback active structural acoustic control system is demonstrated on a piezostructure plate with pinned boundary conditions. Four adaptive piezoelectric sensoriactuators provide an array of truly colocated actuator/sensor pairs to be used as control transducers. Radiation filters are developed based on the self- and mutual-radiation efficiencies of the structure and are included into the performance cost of an H2 control law which minimizes total radiated sound power. In the cost function, control effort is balanced with reductions in radiated sound power. A similarity transform which produces generalized velocity states that are required as inputs to the radiation filters is presented. Up to 15 dB of attenuation in radiated sound power was observed at the resonant frequencies of the piezostructure.

  4. Positive and Negative Feedbacks and Free-Scale Pattern Distribution in Rural-Population Dynamics

    PubMed Central

    Alados, Concepción L.; Errea, Paz; Gartzia, Maite; Saiz, Hugo; Escós, Juan

    2014-01-01

    Depopulation of rural areas is a widespread phenomenon that has occurred in most industrialized countries, and has contributed significantly to a reduction in the productivity of agro-ecological resources. In this study, we identified the main trends in the dynamics of rural populations in the Central Pyrenees in the 20th C and early 21st C, and used density independent and density dependent models and identified the main factors that have influenced the dynamics. In addition, we investigated the change in the power law distribution of population size in those periods. Populations exhibited density-dependent positive feedback between 1960 and 2010, and a long-term positive correlation between agricultural activity and population size, which has resulted in a free-scale population distribution that has been disrupted by the collapse of the traditional agricultural society and by emigration to the industrialized cities. We concluded that complex socio-ecological systems that have strong feedback mechanisms can contribute to disruptive population collapses, which can be identified by changes in the pattern of population distribution. PMID:25474704

  5. Population structure of Streptococcus oralis

    PubMed Central

    Do, Thuy; Jolley, Keith A.; Maiden, Martin C. J.; Gilbert, Steven C.; Clark, Douglas; Wade, William G.; Beighton, David

    2009-01-01

    Streptococcus oralis is a member of the normal human oral microbiota, capable of opportunistic pathogenicity; like related oral streptococci, it exhibits appreciable phenotypic and genetic variation. A multilocus sequence typing (MLST) scheme for S. oralis was developed and the resultant data analysed to examine the population structure of the species. Analysis of 113 isolates, confirmed as belonging to the S. oralis/mitis group by 16S rRNA gene sequencing, characterized the population as highly diverse and undergoing inter- and intra-species recombination with a probable clonal complex structure. ClonalFrame analysis of these S. oralis isolates along with examples of Streptococcus pneumoniae, Streptococcus mitis and Streptococcus pseudopneumoniae grouped the named species into distinct, coherent populations and did not support the clustering of S. pseudopneumoniae with S. mitis as reported previously using distance-based methods. Analysis of the individual loci suggested that this discrepancy was due to the possible hybrid nature of S. pseudopneumoniae. The data are available on the public MLST website (http://pubmlst.org/soralis/). PMID:19423627

  6. Range-Expanding Populations of a Globally Introduced Weed Experience Negative Plant-Soil Feedbacks

    PubMed Central

    Andonian, Krikor; Hierro, José L.; Khetsuriani, Liana; Becerra, Pablo; Janoyan, Grigor; Villarreal, Diego; Cavieres, Lohengrin; Fox, Laurel R.; Callaway, Ragan M.

    2011-01-01

    Background Biological invasions are fundamentally biogeographic processes that occur over large spatial scales. Interactions with soil microbes can have strong impacts on plant invasions, but how these interactions vary among areas where introduced species are highly invasive vs. naturalized is still unknown. In this study, we examined biogeographic variation in plant-soil microbe interactions of a globally invasive weed, Centaurea solstitialis (yellow starthistle). We addressed the following questions (1) Is Centaurea released from natural enemy pressure from soil microbes in introduced regions? and (2) Is variation in plant-soil feedbacks associated with variation in Centaurea's invasive success? Methodology/Principal Findings We conducted greenhouse experiments using soils and seeds collected from native Eurasian populations and introduced populations spanning North and South America where Centaurea is highly invasive and noninvasive. Soil microbes had pervasive negative effects in all regions, although the magnitude of their effect varied among regions. These patterns were not unequivocally congruent with the enemy release hypothesis. Surprisingly, we also found that Centaurea generated strong negative feedbacks in regions where it is the most invasive, while it generated neutral plant-soil feedbacks where it is noninvasive. Conclusions/Significance Recent studies have found reduced below-ground enemy attack and more positive plant-soil feedbacks in range-expanding plant populations, but we found increased negative effects of soil microbes in range-expanding Centaurea populations. While such negative feedbacks may limit the long-term persistence of invasive plants, such feedbacks may also contribute to the success of invasions, either by having disproportionately negative impacts on competing species, or by yielding relatively better growth in uncolonized areas that would encourage lateral spread. Enemy release from soil-borne pathogens is not sufficient to

  7. Pseudomonas aeruginosa Population Structure Revisited

    PubMed Central

    Pirnay, Jean-Paul; Bilocq, Florence; Pot, Bruno; Cornelis, Pierre; Zizi, Martin; Van Eldere, Johan; Deschaght, Pieter; Vaneechoutte, Mario; Jennes, Serge; Pitt, Tyrone; De Vos, Daniel

    2009-01-01

    At present there are strong indications that Pseudomonas aeruginosa exhibits an epidemic population structure; clinical isolates are indistinguishable from environmental isolates, and they do not exhibit a specific (disease) habitat selection. However, some important issues, such as the worldwide emergence of highly transmissible P. aeruginosa clones among cystic fibrosis (CF) patients and the spread and persistence of multidrug resistant (MDR) strains in hospital wards with high antibiotic pressure, remain contentious. To further investigate the population structure of P. aeruginosa, eight parameters were analyzed and combined for 328 unrelated isolates, collected over the last 125 years from 69 localities in 30 countries on five continents, from diverse clinical (human and animal) and environmental habitats. The analysed parameters were: i) O serotype, ii) Fluorescent Amplified-Fragment Length Polymorphism (FALFP) pattern, nucleotide sequences of outer membrane protein genes, iii) oprI, iv) oprL, v) oprD, vi) pyoverdine receptor gene profile (fpvA type and fpvB prevalence), and prevalence of vii) exoenzyme genes exoS and exoU and viii) group I pilin glycosyltransferase gene tfpO. These traits were combined and analysed using biological data analysis software and visualized in the form of a minimum spanning tree (MST). We revealed a network of relationships between all analyzed parameters and non-congruence between experiments. At the same time we observed several conserved clones, characterized by an almost identical data set. These observations confirm the nonclonal epidemic population structure of P. aeruginosa, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise. One of these clones is the renown and widespread MDR serotype O12 clone. On the other hand, we found no evidence for a widespread CF transmissible clone. All but one of the 43 analysed CF strains belonged to a ubiquitous P

  8. How to control chaotic behaviour and population size with proportional feedback

    NASA Astrophysics Data System (ADS)

    Liz, Eduardo

    2010-01-01

    We study the control of chaos in one-dimensional discrete maps as they often occur in modelling population dynamics. For managing the population, we seek to suppress any possible chaotic behavior, leading the system to a stable equilibrium. In this Letter, we make a rigorous analysis of the proportional feedback method under certain conditions fulfilled by a wide family of maps. We show that it is possible to stabilize the chaotic dynamics towards a globally stable positive equilibrium, that can be chosen among a broad range of possible values. In particular, the size of the population can be enhanced by control in form of population reduction. This paradoxical phenomenon is known as the hydra effect, and it has important implications in the design of strategies in such areas as fishing, pest management, and conservation biology.

  9. Factors shaping e-feedback utilization following electronic Objective Structured Clinical Examinations.

    PubMed

    Ashby, Samantha E; Snodgrass, Suzanne H; Rivett, Darren A; Russell, Trevor

    2016-09-01

    The development of student-practitioners' practical clinical skills is essential in health professional education. Objective Structured Clinical Examinations are central to the assessment of students performing clinical procedures on simulated patients (actors). While feedback is considered core to learning providing timely, individualised student OSCE feedback is difficult. This study explored the perceptions of students about the multiple factors which shape the utility of e-feedback following an electronic Objective Structured Clinical Examinations, which utilized iPad and specialised software. The e-feedback was trialled in four courses within occupational therapy and physiotherapy pre-professional programs with a cohort of 204 students. Evaluation of student perceptions about feedback was collected using two surveys and eight focus groups. This data showed three factors shaped perceptions of the utility of e- Objective Structured Clinical Examinations feedback: 1) timely accessibility within one day of the assessment, 2) feedback demonstrating examiners' academic literacy and 3) feedback orientated to ways of improving future performance of clinical skills. The study found training in the provision of feedback using IPads and software is needed for examiners to ensure e-feedback meets students' needs for specific, future-oriented e-feedback and institutional requirements for justification of grades.

  10. Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations.

    PubMed

    Haafke, Julia; Abou Chakra, Maria; Becks, Lutz

    2016-03-01

    Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here, we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated.

  11. Direct reciprocity in structured populations

    PubMed Central

    van Veelen, Matthijs; García, Julián; Rand, David G.; Nowak, Martin A.

    2012-01-01

    Reciprocity and repeated games have been at the center of attention when studying the evolution of human cooperation. Direct reciprocity is considered to be a powerful mechanism for the evolution of cooperation, and it is generally assumed that it can lead to high levels of cooperation. Here we explore an open-ended, infinite strategy space, where every strategy that can be encoded by a finite state automaton is a possible mutant. Surprisingly, we find that direct reciprocity alone does not lead to high levels of cooperation. Instead we observe perpetual oscillations between cooperation and defection, with defection being substantially more frequent than cooperation. The reason for this is that “indirect invasions” remove equilibrium strategies: every strategy has neutral mutants, which in turn can be invaded by other strategies. However, reciprocity is not the only way to promote cooperation. Another mechanism for the evolution of cooperation, which has received as much attention, is assortment because of population structure. Here we develop a theory that allows us to study the synergistic interaction between direct reciprocity and assortment. This framework is particularly well suited for understanding human interactions, which are typically repeated and occur in relatively fluid but not unstructured populations. We show that if repeated games are combined with only a small amount of assortment, then natural selection favors the behavior typically observed among humans: high levels of cooperation implemented using conditional strategies. PMID:22665767

  12. Predation risk suppresses the positive feedback between size structure and cannibalism.

    PubMed

    Kishida, Osamu; Trussell, Geoffrey C; Ohno, Ayaka; Kuwano, Shinya; Ikawa, Takuya; Nishimura, Kinya

    2011-11-01

    between cannibals and victims was similar in both risk treatments. These results suggest that dragonfly risk cues first suppress cannibalism among hatchlings and then prevent size variation from increasing through time. 5. We suggest that the positive feedback dynamics between size structure and cannibalism and their modification by predation risk may also operate in other systems to shape the population dynamics of cannibalistic prey species as well as overall community dynamics.

  13. Ordering structured populations in multiplayer cooperation games

    PubMed Central

    Peña, Jorge; Wu, Bin; Traulsen, Arne

    2016-01-01

    Spatial structure greatly affects the evolution of cooperation. While in two-player games the condition for cooperation to evolve depends on a single structure coefficient, in multiplayer games the condition might depend on several structure coefficients, making it difficult to compare different population structures. We propose a solution to this issue by introducing two simple ways of ordering population structures: the containment order and the volume order. If population structure is greater than population structure in the containment or the volume order, then can be considered a stronger promoter of cooperation. We provide conditions for establishing the containment order, give general results on the volume order, and illustrate our theory by comparing different models of spatial games and associated update rules. Our results hold for a large class of population structures and can be easily applied to specific cases once the structure coefficients have been calculated or estimated. PMID:26819335

  14. A cholinergic feedback circuit to regulate striatal population uncertainty and optimize reinforcement learning.

    PubMed

    Franklin, Nicholas T; Frank, Michael J

    2015-12-25

    Convergent evidence suggests that the basal ganglia support reinforcement learning by adjusting action values according to reward prediction errors. However, adaptive behavior in stochastic environments requires the consideration of uncertainty to dynamically adjust the learning rate. We consider how cholinergic tonically active interneurons (TANs) may endow the striatum with such a mechanism in computational models spanning three Marr's levels of analysis. In the neural model, TANs modulate the excitability of spiny neurons, their population response to reinforcement, and hence the effective learning rate. Long TAN pauses facilitated robustness to spurious outcomes by increasing divergence in synaptic weights between neurons coding for alternative action values, whereas short TAN pauses facilitated stochastic behavior but increased responsiveness to change-points in outcome contingencies. A feedback control system allowed TAN pauses to be dynamically modulated by uncertainty across the spiny neuron population, allowing the system to self-tune and optimize performance across stochastic environments.

  15. Isonymy structure of USA population.

    PubMed

    Barrai, I; Rodriguez-Larralde, A; Mamolini, E; Manni, F; Scapoli, C

    2001-02-01

    The isonymy structure of the 48 states of the continental United States of America was studied using the surname distributions of 18 million telephone users, distributed in 247 towns. The shortest linear distance between nearest neighbor towns included in the sample was 12.0 km. The largest distance was 4,577 km. The number of different surnames found in the whole analysis was 899,585. Lasker's distance was found to be significantly but weakly correlated with the geographic distance, with r = 0.21 +/- 0.01. A dendrogram of the 48 states was built from the matrix of isonymy distances: it divides the US into several clusters, in general correlated with geography. A notable exception is California and New Jersey, which cluster together. Wisconsin is separated from all other states. An important cluster is formed by Texas, Colorado, New Mexico, Nevada, and Arizona, together with Illinois and Florida. It was observed that Hispanic surnames are among the most frequent in Illinois, as they are in New Jersey and California. No main distinction among the states clearly attributable to surnames of French origin was detected; however, New Hampshire, Vermont, and Maine which have a considerable number of these surnames belong to the same northeastern cluster. From the present analysis, the great mobility of the US population emerges clearly, and it seems relevant that the practical absence of isolation by distance is seen also considering only small towns. It appears that groups of different origin are well-mixed over the whole area of the United States. The values of isonymy indicate that the south-central area of the USA has the highest level of inbreeding. In fact, the heterogeneity in surname composition is greater in the coastal areas, particularly on the East Coast, than anywhere else in the USA.

  16. Students' feedback of objectively structured clinical examination: a private medical college experience.

    PubMed

    Khursheed, Iram; Usman, Yaseen; Usman, Jawaid

    2007-03-01

    The aim of the study was to evaluate undergraduate students' perceptions regarding Objectively Structured Clinical Examination (OSCE) to be used as a feedback to improve the assessment technique. At the end of OSCE, students were provided with a feedback questionnaire related to OSCE to obtain their views and comments. The feedback was obtained from two consecutive batches of third year medical students and was utilized to incorporate the improvements in the process, wherever possible. A great majority of students (93% from group 'A' and 95% from group 'B') regarded OSCE as a practical and useful assessment tool in early years of medical education. In this study, students appreciated OSCE and offered constructive feedback on structure and organization of the process. However, at some stations they felt that instructions were ambiguous and time allocation was inadequate for the assigned tasks. The overall feedback was very useful and facilitated a critical review of the process.

  17. Structural Perturbations to Population Skeletons: Transient Dynamics, Coexistence of Attractors and the Rarity of Chaos

    PubMed Central

    Singh, Brajendra K.; Parham, Paul E.; Hu, Chin-Kun

    2011-01-01

    Background Simple models of insect populations with non-overlapping generations have been instrumental in understanding the mechanisms behind population cycles, including wild (chaotic) fluctuations. The presence of deterministic chaos in natural populations, however, has never been unequivocally accepted. Recently, it has been proposed that the application of chaos control theory can be useful in unravelling the complexity observed in real population data. This approach is based on structural perturbations to simple population models (population skeletons). The mechanism behind such perturbations to control chaotic dynamics thus far is model dependent and constant (in size and direction) through time. In addition, the outcome of such structurally perturbed models is [almost] always equilibrium type, which fails to commensurate with the patterns observed in population data. Methodology/Principal Findings We present a proportional feedback mechanism that is independent of model formulation and capable of perturbing population skeletons in an evolutionary way, as opposed to requiring constant feedbacks. We observe the same repertoire of patterns, from equilibrium states to non-chaotic aperiodic oscillations to chaotic behaviour, across different population models, in agreement with observations in real population data. Model outputs also indicate the existence of multiple attractors in some parameter regimes and this coexistence is found to depend on initial population densities or the duration of transient dynamics. Our results suggest that such a feedback mechanism may enable a better understanding of the regulatory processes in natural populations. PMID:21980342

  18. The ethics of feedback of HIV test results in population-based surveys of HIV infection.

    PubMed

    Maher, Dermot

    2013-12-01

    Population-based disease prevalence surveys raise ethical questions, including whether participants should be routinely told their test results. Ethical guidelines call for informing survey participants of any clinically relevant finding to enable appropriate management. However, in anonymous surveys of human immunodeficiency virus (HIV) infection, participants can "opt out" of being given their test results or are offered the chance to undergo voluntary HIV testing in local counselling and testing services. This is aimed at minimizing survey participation bias. Those who opt out of being given their HIV test results and who do not seek their results miss the opportunity to receive life-saving antiretroviral therapy. The justification for HIV surveys without routine feedback of results to participants is based on a public health utility argument: that the benefits of more rigorous survey methods - reduced participation bias - outweigh the benefits to individuals of knowing their HIV status. However, people with HIV infection have a strong immediate interest in knowing their HIV status. In consideration of the ethical value of showing respect for people and thereby alleviating suffering, an argument based on public health utility is not an appropriate justification. In anonymous HIV surveys as well as other prevalence surveys of treatable conditions in any setting, participation should be on the basis of routine individual feedback of results as an integral part of fully informed participation. Ensuring that surveys are ethically sound may stimulate participation, increase a broader uptake of HIV testing and reduce stigmatization of people who are HIV-positive.

  19. Consensus of population systems with community structures.

    PubMed

    Wang, Jing; Wu, Bin; Wang, Long; Fu, Feng

    2008-11-01

    Multicommunity population systems may reach a consensus state where the fractions of each species in different communities agree on a common value. In this paper, by analyzing the evolutionary dynamics based on an extended replicator equation incorporating community effects, the consensus problem of population systems with n communities is studied. In particular, the simple case of two communities is investigated in detail. In general, for n communities, a sufficient and necessary condition for population systems to reach a consensus of coexistent state is provided. Regarding the population dynamics for the four different types of games, whether the population systems can achieve consensus is determined. The dynamics of community-structured populations shows richer features than nonstructured populations, and some nontrivial phenomena arising from different community-structured population systems are illustrated with concrete numerical examples.

  20. Getting on the same page: The effect of normative feedback interventions on structured interview ratings.

    PubMed

    Hartwell, Christopher J; Campion, Michael A

    2016-06-01

    This study explores normative feedback as a way to reduce rating errors and increase the reliability and validity of structured interview ratings. Based in control theory and social comparison theory, we propose a model of normative feedback interventions (NFIs) in the context of structured interviews and test our model using data from over 20,000 interviews conducted by more than 100 interviewers over a period of more than 4 years. Results indicate that lenient and severe interviewers reduced discrepancies between their ratings and the overall normative mean rating after receipt of normative feedback, though changes were greater for lenient interviewers. When various waves of feedback were presented in later NFIs, the combined normative mean rating over multiple time periods was more predictive of subsequent rating changes than the normative mean rating from the most recent time period. Mean within-interviewer rating variance, along with interrater agreement and interrater reliability, increased after the initial NFI, but results from later NFIs were more complex and revealed that feedback interventions may lose effectiveness over time. A second study using simulated data indicated that leniency and severity errors did not impact rating validity, but did affect which applicants were hired. We conclude that giving normative feedback to interviewers will aid in minimizing interviewer rating differences and enhance the reliability of structured interview ratings. We suggest that interviewer feedback might be considered as a potential new component of interview structure, though future research is needed before a definitive conclusion can be drawn. (PsycINFO Database Record

  1. Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

    PubMed

    Turcotte, Martin M; Reznick, David N; Daniel Hare, J

    2013-05-01

    An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

  2. Evolution of cooperation in spatially structured populations

    PubMed

    Brauchli; Killingback; Doebeli

    1999-10-21

    Using a spatial lattice model of the Iterated Prisoner's Dilemma we studied the evolution of cooperation within the strategy space of all stochastic strategies with a memory of one round. Comparing the spatial model with a randomly mixed model showed that (1) there is more cooperative behaviour in a spatially structured population, (2) PAVLOV and generous variants of it are very successful strategies in the spatial context and (3) in spatially structured populations evolution is much less chaotic than in unstructured populations. In spatially structured populations, generous variants of PAVLOV are found to be very successful strategies in playing the Iterated Prisoner's Dilemma. The main weakness of PAVLOV is that it is exploitable by defective strategies. In a spatial context this disadvantage is much less important than the good error correction of PAVLOV, and especially of generous PAVLOV, because in a spatially structured population successful strategies always build clusters. Copyright 1999 Academic Press.

  3. A cholinergic feedback circuit to regulate striatal population uncertainty and optimize reinforcement learning

    PubMed Central

    Franklin, Nicholas T; Frank, Michael J

    2015-01-01

    Convergent evidence suggests that the basal ganglia support reinforcement learning by adjusting action values according to reward prediction errors. However, adaptive behavior in stochastic environments requires the consideration of uncertainty to dynamically adjust the learning rate. We consider how cholinergic tonically active interneurons (TANs) may endow the striatum with such a mechanism in computational models spanning three Marr's levels of analysis. In the neural model, TANs modulate the excitability of spiny neurons, their population response to reinforcement, and hence the effective learning rate. Long TAN pauses facilitated robustness to spurious outcomes by increasing divergence in synaptic weights between neurons coding for alternative action values, whereas short TAN pauses facilitated stochastic behavior but increased responsiveness to change-points in outcome contingencies. A feedback control system allowed TAN pauses to be dynamically modulated by uncertainty across the spiny neuron population, allowing the system to self-tune and optimize performance across stochastic environments. DOI: http://dx.doi.org/10.7554/eLife.12029.001 PMID:26705698

  4. Delayed feedback control experiments on some flexible structures

    NASA Astrophysics Data System (ADS)

    Cai, Guo-Ping; Chen, Long-Xiang

    2010-12-01

    In recent decades, studies on delayed system dynamics have attracted increasing attention and advances have been achieved in stability, nonlinearity, delay identification, delay elimination and application. However, most of the existing work is on the theoretical basis and little is on the experiment. This paper presents our experimental studies on delayed feedback control conducted in recent years with the focus on the discussion of a DSP-based delayed experiment system. Some phenomena in our delay experiments are discussed and a few topics of interest for further research are brought forward.

  5. (Genetic structure of natural populations)

    SciTech Connect

    Not Available

    1988-01-01

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

  6. Population Structure in Nontypeable Haemophilus influenzae

    PubMed Central

    LaCross, Nathan C.; Marrs, Carl F.; Gilsdorf, Janet R.

    2013-01-01

    Nontypeable Haemophilus influenzae (NTHi) frequently colonize the human pharynx asymptomatically, and are an important cause of otitis media in children. Past studies have identified typeable H. influenzae as being clonal, but the population structure of NTHi has not been extensively characterized. The research presented here investigated the diversity and population structure in a well-characterized collection of NTHi isolated from the middle ears of children with otitis media or the pharynges of healthy children in three disparate geographic regions. Multilocus sequence typing identified 109 unique sequence types among 170 commensal and otitis media-associated NTHi isolates from Finland, Israel, and the US. The largest clonal complex contained only five sequence types, indicating a high level of genetic diversity. The eBURST v3, ClonalFrame 1.1, and structure 2.3.3 programs were used to further characterize diversity and population structure from the sequence typing data. Little clustering was apparent by either disease state (otitis media or commensalism) or geography in the ClonalFrame phylogeny. Population structure was clearly evident, with support for eight populations when all 170 isolates were analyzed. Interestingly, one population contained only commensal isolates, while two others consisted solely of otitis media isolates, suggesting associations between population structure and disease. PMID:23266487

  7. The application of smart structures toward feedback suppression in amplified acoustic guitars

    NASA Astrophysics Data System (ADS)

    Griffin, Steve; Lane, Steven A.; Clark, Robert L.

    2003-06-01

    Smart structures technology can be applied to amplified acoustic guitars to prevent instability resulting from acoustic feedback. This work presents a coupled model of the guitar dynamics and the acoustic feedback mechanism, and explains how a simple control loop using a piezoelectric ceramic actuator can be used to reduce the effects of acoustic feedback. In addition to model simulations, experimental results using a real system and a simple controller are presented. The results show that a significantly higher (7 dB) guitar output can be achieved before instability, without detrimentally affecting the amplified and unamplified guitar response.

  8. Population genetic structure in Lahontan cutthroat trout

    USGS Publications Warehouse

    Nielsen, Jennifer L.; Sage, George K.

    2002-01-01

    We used 10 microsatellite loci to examine the genetic population structure of cutthroat trout Oncorhynchus clarki within the Lahontan Basin complex. Genetic diversity was analyzed for trout from Nevada, California, and Utah representing three putative subspecies: Lahontan O. c. henshawi, Paiute O. c. seleniris, and Humboldt (an unnamed subspecies) cutthroat trout. We found significant differences in microsatellite diversity among the three putative subspecies found in this area. Analysis of molecular variance partitioned microsatellite variation as 9.8% among subspecies, 27.7% among populations, and 62.5% within populations of Lahontan Basin cutthroat trout. Genetic distance analyses (Cavalli-Sforza-Edwards and F st) supported unique population structure in cutthroat trout from the Humboldt and Pilot Peak drainages. Pairwise F st values for Lahontan cutthroat trout were not significantly correlated with geographic distance between population pairs (r 2 = 0.008; P < 0.0001), suggesting that they are extremely isolated populations with small effective sizes that are vulnerable to extinction. Two extant hatchery strains of Lahontan cutthroat trout showed genetic associations with different geographic source populations. The Pyramid Lake hatchery strain was most closely associated genetically with fish from Summit Lake. The Pilot Peak hatchery strain was associated genetically with Pilot Peak wild trout (Utah) and Macklin Creek trout (California). The phylogeographic diversity depicted in this study supports unique population structure and suggests important evolutionary relationships needed to evaluate transplanted populations and hatchery supplementation within the basin.

  9. Structured populations with diffusion and Feller conditions.

    PubMed

    Bartomiejczyk, Agnieszka; Leszczynski, Henryk

    2016-04-01

    We prove a weak maximum principle for structured population models with dynamic boundary conditions. We establish existence and positivity of solutions of these models and investigate the asymptotic behaviour of solutions. In particular, we analyse so called size profile.

  10. Genetic Structure of the Spanish Population

    PubMed Central

    2010-01-01

    Background Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias. Results In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV) analyses, and have compared these estimates of the Spanish population with existing data from similar efforts. Conclusions In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community. PMID:20500880

  11. Distinguishing Recent Admixture from Ancestral Population Structure

    PubMed Central

    Slatkin, Montgomery

    2017-01-01

    We develop and test two methods for distinguishing between recent admixture and ancestral population structure as explanations for greater similarity of one of two populations to an outgroup population. This problem arose when Neanderthals were found to be slightly more similar to nonAfrican than to African populations. The excess similarity is consistent with both recent admixture from Neanderthals into the ancestors of nonAfricans and subdivision in the ancestral population. Although later studies showed that there had been recent admixture, distinguishing between these two classes of models will be important in other situations, particularly when high-coverage genomes cannot be obtained for all populations. One of our two methods is based on the properties of the doubly conditioned frequency spectrum combined with the unconditional frequency spectrum. This method does not require a linkage map and can be used when there is relatively low coverage. The second method uses the extent of linkage disequilibrium among closely linked markers. PMID:28186554

  12. Structural tailoring and feedback control synthesis - An interdisciplinary approach

    NASA Technical Reports Server (NTRS)

    Belvin, W. Keith; Park, K. C.

    1988-01-01

    Structural tailoring provides an attractive method to optimize the performance of actively controlled space structures. However, the simultaneous optimization of control gains and structural properties often becomes prohibitively expensive for large systems and physical insight is often lost in the resulting control law. This paper presents a method for optimization of the closed loop structural system using only structural tailoring. Optimal Linear Quadratic Regulator (LQR) control theory is used with weighting matrices chosen based on physical considerations. The LQR control law depends only on two scalar gains and the structural properties. Hence, the closed loop-performance can be expressed in terms of the structural parameters. Results are given for a beam and a truss-beam to show the simplicity of the method and the importance of structural tailoring to increase dynamic performance and to reduce the control effort.

  13. Genetic structure among Fijian island populations.

    PubMed

    Shipley, Gerhard P; Taylor, Diana A; Tyagi, Anand; Tiwari, Geetanjali; Redd, Alan J

    2015-02-01

    We examined nine Y chromosome short tandem repeats (Y-STRs) and the mitochondrial DNA (mtDNA) hypervariable segment 1 region in the Fijian island populations of Viti Levu, Vanua Levu, Kadavu, the Lau islands and Rotuma. We found significant genetic structure among these populations for the Y-STRs, both with and without the Rotumans, but not for the mtDNA. We also found that all five populations exhibited the sex-biased admixture associated with areas settled by Austronesian-speaking people, with paternal lineages more strongly associated with Melanesian populations and maternal lineages more strongly associated with Polynesian populations. We also found that the Rotumans in the north and the Lau Islanders in the east were genetically more similar to Polynesian populations than were the other Fijians, but only for the mtDNA. For the Y-STRs, the Rotumans and the Lau Islanders were genetically as similar to Melanesian populations as were the other three populations. Of the five populations, the Rotumans were the most different in almost every regard. Although past genetic studies treated the Fijians as being genetically homogenous despite known geographic, phenotypic, cultural and linguistic variation, our findings show significant genetic variation and a need for a closer examination of individual island populations within Fiji, particularly the Rotumans, in order to better understand the process of the peopling of Fiji and of the surrounding regions.

  14. Population structure of the Classic period Maya.

    PubMed

    Scherer, Andrew K

    2007-03-01

    This study examines the population structure of Classic period (A.D. 250-900) Maya populations through analysis of odontometric variation of 827 skeletons from 12 archaeological sites in Mexico, Guatemala, Belize, and Honduras. The hypothesis that isolation by distance characterized Classic period Maya population structure is tested using Relethford and Blangero's (Hum Biol 62 (1990) 5-25) approach to R matrix analysis for quantitative traits. These results provide important biological data for understanding ancient Maya population history, particularly the effects of the competing Tikal and Calakmul hegemonies on patterns of lowland Maya site interaction. An overall F(ST) of 0.018 is found for the Maya area, indicating little among-group variation for the Classic Maya sites tested. Principal coordinates plots derived from the R matrix analysis show little regional patterning in the data, though the geographic outliers of Kaminaljuyu and a pooled Pacific Coast sample did not cluster with the lowland Maya sites. Mantel tests comparing the biological distance matrix to a geographic distance matrix found no association between genetic and geographic distance. In the Relethford-Blangero analysis, most sites possess negative or near-zero residuals, indicating minimal extraregional gene flow. The exceptions were Barton Ramie, Kaminaljuyu, and Seibal. A scaled R matrix analysis clarifies that genetic drift is a consideration for understanding Classic Maya population structure. All results indicate that isolation by distance does not describe Classic period Maya population structure.

  15. Mycorrhizal symbioses drive temperate forest population dynamics through plant-soil feedbacks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Feedback with soil biota is a major driver of diversity within terrestrial plant communities. However, little is known about the factors regulating plant-soil feedback, which can vary from positive to negative among plant species. In a large-scale observational and experimental study involving 55 sp...

  16. Population structure of ice-breeding seals.

    PubMed

    Davis, Corey S; Stirling, Ian; Strobeck, Curtis; Coltman, David W

    2008-07-01

    The development of population genetic structure in ice-breeding seal species is likely to be shaped by a combination of breeding habitat and life-history characteristics. Species that return to breed on predictable fast-ice locations are more likely to exhibit natal fidelity than pack-ice-breeding species, which in turn facilitates the development of genetic differentiation between subpopulations. Other aspects of life history such as geographically distinct vocalizations, female gregariousness, and the potential for polygynous breeding may also facilitate population structure. Based on these factors, we predicted that fast-ice-breeding seal species (the Weddell and ringed seal) would show elevated genetic differentiation compared to pack-ice-breeding species (the leopard, Ross, crabeater and bearded seals). We tested this prediction using microsatellite analysis to examine population structure of these six ice-breeding species. Our results did not support this prediction. While none of the Antarctic pack-ice species showed statistically significant population structure, the bearded seal of the Arctic pack ice showed strong differentiation between subpopulations. Again in contrast, the fast-ice-breeding Weddell seal of the Antarctic showed clear evidence for genetic differentiation while the ringed seal, breeding in similar habitat in the Arctic, did not. These results suggest that the development of population structure in ice-breeding phocid seals is a more complex outcome of the interplay of phylogenetic and ecological factors than can be predicted on the basis of breeding substrate and life-history characteristics.

  17. Breathing FIRE: How Stellar Feedback Drives Radial Migration, Rapid Size Fluctuations, and Population Gradients in Low-mass Galaxies

    NASA Astrophysics Data System (ADS)

    El-Badry, Kareem; Wetzel, Andrew; Geha, Marla; Hopkins, Philip F.; Kereš, Dusan; Chan, T. K.; Faucher-Giguère, Claude-André

    2016-04-01

    We examine the effects of stellar feedback and bursty star formation on low-mass galaxies (Mstar = 2 × 106 - 5 × 1010 M⊙) using the Feedback in Realistic Environments (FIRE) simulations. While previous studies emphasized the impact of feedback on dark matter profiles, we investigate the impact on the stellar component: kinematics, radial migration, size evolution, and population gradients. Feedback-driven outflows/inflows drive significant radial stellar migration over both short and long timescales via two processes: (1) outflowing/infalling gas can remain star-forming, producing young stars that migrate ˜1 kpc within their first 100 Myr, and (2) gas outflows/inflows drive strong fluctuations in the global potential, transferring energy to all stars. These processes produce several dramatic effects. First, galaxies’ effective radii can fluctuate by factors of >2 over ˜200 Myr, and these rapid size fluctuations can account for much of the observed scatter in the radius at fixed Mstar. Second, the cumulative effects of many outflow/infall episodes steadily heat stellar orbits, causing old stars to migrate outward most strongly. This age-dependent radial migration mixes—and even inverts—intrinsic age and metallicity gradients. Thus, the galactic-archaeology approach of calculating radial star formation histories from stellar populations at z = 0 can be severely biased. These effects are strongest at Mstar ≈ 107-9.6 M⊙, the same regime where feedback most efficiently cores galaxies. Thus, detailed measurements of stellar kinematics in low-mass galaxies can strongly constrain feedback models and test baryonic solutions to small-scale problems in ΛCDM.

  18. BREATHING FIRE: HOW STELLAR FEEDBACK DRIVES RADIAL MIGRATION, RAPID SIZE FLUCTUATIONS, AND POPULATION GRADIENTS IN LOW-MASS GALAXIES

    SciTech Connect

    El-Badry, Kareem; Geha, Marla; Wetzel, Andrew; Hopkins, Philip F.; Kereš, Dusan; Chan, T. K.; Faucher-Giguère, Claude-André

    2016-04-01

    We examine the effects of stellar feedback and bursty star formation on low-mass galaxies (M{sub star} = 2 × 10{sup 6} − 5 × 10{sup 10} M{sub ⊙}) using the Feedback in Realistic Environments (FIRE) simulations. While previous studies emphasized the impact of feedback on dark matter profiles, we investigate the impact on the stellar component: kinematics, radial migration, size evolution, and population gradients. Feedback-driven outflows/inflows drive significant radial stellar migration over both short and long timescales via two processes: (1) outflowing/infalling gas can remain star-forming, producing young stars that migrate ∼1 kpc within their first 100 Myr, and (2) gas outflows/inflows drive strong fluctuations in the global potential, transferring energy to all stars. These processes produce several dramatic effects. First, galaxies’ effective radii can fluctuate by factors of >2 over ∼200 Myr, and these rapid size fluctuations can account for much of the observed scatter in the radius at fixed M{sub star}. Second, the cumulative effects of many outflow/infall episodes steadily heat stellar orbits, causing old stars to migrate outward most strongly. This age-dependent radial migration mixes—and even inverts—intrinsic age and metallicity gradients. Thus, the galactic-archaeology approach of calculating radial star formation histories from stellar populations at z = 0 can be severely biased. These effects are strongest at M{sub star} ≈ 10{sup 7–9.6} M{sub ⊙}, the same regime where feedback most efficiently cores galaxies. Thus, detailed measurements of stellar kinematics in low-mass galaxies can strongly constrain feedback models and test baryonic solutions to small-scale problems in ΛCDM.

  19. The evolution of structure and feedback with Arcus

    NASA Astrophysics Data System (ADS)

    Brenneman, Laura W.; Smith, Randall K.; Bregman, J.; Kaastra, J.; Brickhouse, N.; Allured, R.; Foster, A.; Wolk, S.; Wilms, J.; Valencic, L.; Willingale, R.; Grant, C.; Bautz, M.; Heilmann, R.; Huenemoerder, D.; Miller, E.; Nowak, M.; Schattenburg, M.; Schulz, N.; Burwitz, V.; Nandra, K.; Sanders, J.; Bookbinder, J.; Petre, R.; Ptak, A.; Smale, A.; Burrows, D.; Poppenhaeger, K.; Costantini, E.; DeRoo, C.; McEntaffer, R.; Mushotzky, R.; Miller, J. M.; Temi, P.

    2016-07-01

    Arcus is a NASA/MIDEX mission under development in response to the anticipated 2016 call for proposals. It is a freeflying, soft X-ray grating spectrometer with the highest-ever spectral resolution in the 8-51 Å (0.24 - 1.55 keV) energy range. The Arcus bandpass includes the most sensitive tracers of diffuse million-degree gas: spectral lines from O VII and O VIII, H- and He-like lines of C, N, Ne and Mg, and unique density- and temperature-sensitive lines from Si and Fe ions. These capabilities enable an advance in our understanding of the formation and evolution of baryons in the Universe that is unachievable with any other present or planned observatory. The mission will address multiple key questions posed in the Decadal Survey1 and NASA's 2013 Roadmap2: How do baryons cycle in and out of galaxies? How do black holes and stars influence their surroundings and the cosmic web via feedback? How do stars, circumstellar disks and exoplanet atmospheres form and evolve? Arcus data will answer these questions by leveraging recent developments in off-plane gratings and silicon pore optics to measure X-ray spectra at high resolution from a wide range of sources within and beyond the Milky Way. CCDs with strong Suzaku heritage combined with electronics based on the Swift mission will detect the dispersed X-rays. Arcus will support a broad astrophysical research program, and its superior resolution and sensitivity in soft X-rays will complement the forthcoming Athena calorimeter, which will have comparably high resolution above 2 keV.

  20. Dynamic behavior of time-delayed acceleration feedback controller for active vibration control of flexible structures

    NASA Astrophysics Data System (ADS)

    An, Fang; Chen, Wei-dong; Shao, Min-qiang

    2014-09-01

    This paper addresses the design problem of the controller with time-delayed acceleration feedback. On the basis of the reduction method and output state-derivative feedback, a time-delayed acceleration feedback controller is proposed. Stability boundaries of the closed-loop system are determined by using Hurwitz stability criteria. Due to the introduction of time delay into the controller with acceleration feedback, the proposed controller has the feature of not only changing the mass property but also altering the damping property of the controlled system in the sense of equivalent structural modification. With this feature, the closed-loop system has a greater logarithmic decrement than the uncontrolled one, and in turn, the control behavior can be improved. In this connection, the time delay in the acceleration feedback control is a positive factor when satisfying some given conditions and it could be actively utilized. On the ground of the analysis, the developed controller is implemented on a cantilever beam for different controller gain-delay combinations, and the control performance is evaluated with the comparison to that of pure acceleration feedback controller. Simulation and experimental results verify the ability of the controller to attenuate the vibration resulting from the dominant mode.

  1. Ocean currents help explain population genetic structure

    PubMed Central

    White, Crow; Selkoe, Kimberly A.; Watson, James; Siegel, David A.; Zacherl, Danielle C.; Toonen, Robert J.

    2010-01-01

    Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management. PMID:20133354

  2. Ocean currents help explain population genetic structure.

    PubMed

    White, Crow; Selkoe, Kimberly A; Watson, James; Siegel, David A; Zacherl, Danielle C; Toonen, Robert J

    2010-06-07

    Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management.

  3. The impact of stellar feedback on the density and velocity structure of the interstellar medium

    NASA Astrophysics Data System (ADS)

    Grisdale, Kearn; Agertz, Oscar; Romeo, Alessandro B.; Renaud, Florent; Read, Justin I.

    2017-04-01

    We study the impact of stellar feedback in shaping the density and velocity structure of neutral hydrogen (H I) in disc galaxies. For our analysis, we carry out ∼4.6 pc resolution N-body+adaptive mesh refinement hydrodynamic simulations of isolated galaxies, set up to mimic a Milky Way and a Large and Small Magellanic Cloud. We quantify the density and velocity structure of the interstellar medium using power spectra and compare the simulated galaxies to observed H I in local spiral galaxies from THINGS (The H I Nearby Galaxy Survey). Our models with stellar feedback give an excellent match to the observed THINGS H I density power spectra. We find that kinetic energy power spectra in feedback-regulated galaxies, regardless of galaxy mass and size, show scalings in excellent agreement with supersonic turbulence (E(k) ∝ k-2) on scales below the thickness of the H I layer. We show that feedback influences the gas density field, and drives gas turbulence, up to large (kpc) scales. This is in stark contrast to density fields generated by large-scale gravity-only driven turbulence. We conclude that the neutral gas content of galaxies carries signatures of stellar feedback on all scales.

  4. The Effects of the Timing of Corrective Feedback on the Acquisition of a New Linguistic Structure

    ERIC Educational Resources Information Center

    Li, Shaofeng; Zhu, Yan; Ellis, Rod

    2016-01-01

    The article reports on a study investigating the comparative effects of immediate and delayed corrective feedback in learning the English past passive construction, a linguistic structure of which the learners had little prior knowledge. A total of 120 learners of English as a foreign language (EFL) from 4 intact classes at a Chinese middle school…

  5. STRUCTURE AND FEEDBACK IN 30 DORADUS. II. STRUCTURE AND CHEMICAL ABUNDANCES

    SciTech Connect

    Pellegrini, E. W.; Baldwin, J. A.; Ferland, G. J.

    2011-09-01

    We use our new optical-imaging and spectrophotometric survey of key diagnostic emission lines in 30 Doradus, together with CLOUDY photoionization models, to study the physical conditions and ionization mechanisms along over 4000 individual lines of sight at points spread across the face of the extended nebula, out to a projected radius 75 pc from R136 at the center of the ionizing cluster NGC 2070. We focus on the physical conditions, geometry, and importance of radiation pressure on a point-by-point basis, with the aim of setting observational constraints on important feedback processes. We find that the dynamics and large-scale structure of 30 Dor are set by a confined system of X-ray bubbles in rough pressure equilibrium with each other and with the confining molecular gas. Although the warm (10,000 K) gas is photoionized by the massive young stars in NGC 2070, the radiation pressure does not currently play a major role in shaping the overall structure. The completeness of our survey also allows us to create a composite spectrum of 30 Doradus, simulating the observable spectrum of a spatially unresolved, distant giant extragalactic H II region. We find that the highly simplified models used in the 'strong line' abundance technique do in fact reproduce our observed line strengths and deduced chemical abundances, in spite of the more than one order of magnitude range in the ionization parameter and density of the actual gas in 30 Dor.

  6. Crystal structure of rat GTP cyclohydrolase I feedback regulatory protein, GFRP.

    PubMed

    Bader, G; Schiffmann, S; Herrmann, A; Fischer, M; Gütlich, M; Auerbach, G; Ploom, T; Bacher, A; Huber, R; Lemm, T

    2001-10-05

    Tetrahydrobiopterin, the cofactor required for hydroxylation of aromatic amino acids regulates its own synthesis in mammals through feedback inhibition of GTP cyclohydrolase I. This mechanism is mediated by a regulatory subunit called GTP cyclohydrolase I feedback regulatory protein (GFRP). The 2.6 A resolution crystal structure of rat GFRP shows that the protein forms a pentamer. This indicates a model for the interaction of mammalian GTP cyclohydrolase I with its regulator, GFRP. Kinetic investigations of human GTP cyclohydrolase I in complex with rat and human GFRP showed similar regulatory effects of both GFRP proteins.

  7. Familial identification: population structure and relationship distinguishability.

    PubMed

    Rohlfs, Rori V; Fullerton, Stephanie Malia; Weir, Bruce S

    2012-02-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.

  8. Familial Identification: Population Structure and Relationship Distinguishability

    PubMed Central

    Rohlfs, Rori V.; Fullerton, Stephanie Malia; Weir, Bruce S.

    2012-01-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States. PMID:22346758

  9. On the interaction structure of linear multi-input feedback control systems. M.S. Thesis; [problem solving, lattices (mathematics)

    NASA Technical Reports Server (NTRS)

    Wong, P. K.

    1975-01-01

    The closely-related problems of designing reliable feedback stabilization strategy and coordinating decentralized feedbacks are considered. Two approaches are taken. A geometric characterization of the structure of control interaction (and its dual) was first attempted and a concept of structural homomorphism developed based on the idea of 'similarity' of interaction pattern. The idea of finding classes of individual feedback maps that do not 'interfere' with the stabilizing action of each other was developed by identifying the structural properties of nondestabilizing and LQ-optimal feedback maps. Some known stability properties of LQ-feedback were generalized and some partial solutions were provided to the reliable stabilization and decentralized feedback coordination problems. A concept of coordination parametrization was introduced, and a scheme for classifying different modes of decentralization (information, control law computation, on-line control implementation) in control systems was developed.

  10. Spatial population structure of Yellowstone bison

    USGS Publications Warehouse

    Olexa, E.M.; Gogan, P.J.P.

    2007-01-01

    Increases in Yellowstone National Park, USA, bison (Bison bison) numbers and shifts in seasonal distribution have resulted in more frequent movements of bison beyond park boundaries and development of an interagency management plan for the Yellowstone bison population. Implementation of the plan under the adaptive management paradigm requires an understanding of the spatial and temporal structure of the population. We used polythetic agglomerative hierarchical cluster analysis of radiolocations obtained from free-ranging bison to investigate seasonal movements and aggregations. We classified radiolocations into 4 periods: annual, peak rut (15 Jul-15 Sep), extended rut (1 Jun-31 Oct), and winter (1 Nov-31 May). We documented spatial separation of Yellowstone bison into 2 segments, the northern and central herds, during all periods. The estimated year-round exchange rate (4.85-5.83%) of instrumented bison varied with the fusion strategy employed. We did not observe exchange between the 2 segments during the peak rut and it varied during the extended rut (2.15-3.23%). We estimated a winter exchange of 4.85-7.77%. The outcome and effectiveness of management actions directed at Yellowstone bison may be affected by spatial segregation and herd affinity within the population. Reductions based on total population size, but not applied to the entire population, may adversely affect one herd while having little effect on the other. Similarly, management actions targeting a segment of the population may benefit from the spatial segregation exhibited.

  11. Impact of structured verbal feedback module in medical education: A questionnaire- and test score-based analysis

    PubMed Central

    Aggarwal, Meenakshi; Singh, Sonia; Sharma, Anu; Singh, Poonam; Bansal, Priya

    2016-01-01

    Introduction: Feedback is a divalent bond between the supplier (teacher) and the recipient (student). The strength of the bond depends on the instructional design of the feedback. Feedback is central to medical education in promoting self-directed learning in students. In the present study, a structured verbal feedback module was prepared, implemented, and evaluated. Methods: The study was done on 280 students from four consecutive batches (2011 to 2014) of the 1st year MBBS students exposed to different types and modes of feedback. Analysis was done using student feedback questionnaire for the perception of students to verbal feedback. Quantitative analysis using post hoc test and ANOVA for the impact of type of feedback (verbal or written) and effect of modes (individual or group) of verbal feedback on test score performance were done. Result: In this study, ≥95% of the students preferred verbal feedback of both positive and negative attributes in student questionnaires. It was observed that verbal feedback sessions made a difference of up to 2–2.4 grade points in the mean score of batch when compared to the written feedback. The initial mean test score (T1) of 2011 + 2012 and 2013 + 2014 was not statistically significant (P = 0.113). But, in all subsequent tests (T2, T3, and T4), there was a statistically significant difference in the mean test scores (P = 0.000). Conclusion: (1) Students prefer verbal one-to-one feedback over written feedback. (2) Verbal feedback changes learning process and causes sustained improvement in learning strategies. PMID:27563592

  12. Positive feedback fishery: Population consequences of `crab-tiling' on the green crab Carcinus maenas

    NASA Astrophysics Data System (ADS)

    Sheehan, E. V.; Thompson, R. C.; Coleman, R. A.; Attrill, M. J.

    2008-11-01

    Collection of marine invertebrates for use as fishing bait is a substantial activity in many parts of the world, often with unknown ecological consequences. As new fisheries develop, it is critical for environmental managers to have high quality ecological information regarding the potential impacts, in order to develop sound management strategies. Crab-tiling is a largely unregulated and un-researched fishery, which operates commercially in the south-west UK. The target species is the green crab Carcinus maenas. Those crabs which are pre-ecdysis and have a carapace width greater than 40 mm are collected to be sold to recreational anglers as bait. Collection involves laying artificial structures on intertidal sandflats and mudflats in estuaries. Crabs use these structures as refugia and are collected during low tide. However, the effect that this fishery has on populations of C. maenas is not known. The impact of crab-tiling on C. maenas population structure was determined by sampling crabs from tiled estuaries and non-tiled estuaries using baited drop-nets. A spatially and temporarily replicated, balanced design was used to compare crab abundance, sizes and sex ratios between estuaries. Typically, fisheries are associated with a reduction in the abundance of the target species. Crab-tiling, however, significantly increased C. maenas abundance. This was thought to be a result of the extra habitat in tiled estuaries, which probably provides protection from natural predators, such as birds and fish. Although crabs were more abundant in tiled estuaries than non-tiled estuaries, the overall percentage of reproductively active crabs in non-tiled estuaries was greater than in tiled estuaries. As with most exploited fisheries stocks, crabs in exploited (tiled) estuaries tended to be smaller, with a modal carapace width of 20-29 mm rather than 30-39 mm in non-tiled estuaries. The sex ratio of crabs however; was not significantly different between tiled and non

  13. Efficient eigenvalue assignment by state and output feedback with applications for large space structures

    NASA Technical Reports Server (NTRS)

    Vannell, Eric C.; Kenny, Sean P.; Maghami, Peiman G.

    1995-01-01

    The erection and deployment of large flexible structures having thousands of degrees of freedom requires controllers based on new techniques of eigenvalue assignment that are computationally stable and more efficient. Scientists at NASA Langley Research Center have developed a novel and efficient algorithm for the eigenvalue assignment of large, time-invariant systems using full-state and output feedback. The objectives of this research were to improve upon the output feedback version of this algorithm, to produce a toolbox of MATLAB functions based on the efficient eigenvalue assignment algorithm, and to experimentally verify the algorithm and software by implementing controllers designed using the MATLAB toolbox on the phase 2 configuration of NASA Langley's controls-structures interaction evolutionary model, a laboratory model used to study space structures. Results from laboratory tests and computer simulations show that effective controllers can be designed using software based on the efficient eigenvalue assignment algorithm.

  14. Natural selection and age-structured populations.

    PubMed

    Demetrius, L

    1975-03-01

    This paper studies the properties of a new class of demographic parameters for age-structured populations and analyzes the effect of natural selection on these parameters. Two new demographic variables are introduced: the entropy of a population and the reproductive potential. The entropy of a population measures the variability of the contribution of the different age classes to the stationary population. The reproductive potential measures the mean of the contribution of the different age classes to the Malthusian parameter. The Malthusian parameter is precisely the difference between the entropy and the reproductive potential. The effect of these demographic variables on changes in gene frequency is discussed. The concept of entropy of a genotype is introduced and it is shown that in a random mating population in Hardy-Weinberg equilibrium and under slow selection, the rate of change of entropy is equal to the genetic variance in entropy minus the covariance in entropy and reproductive potential. This result is an information theoretic analog of Fisher's fundamental theorem of natural selection.

  15. Structural Basis for l-Lysine Feedback Inhibition of Homocitrate Synthase

    SciTech Connect

    Bulfer, Stacie L.; Scott, Erin M.; Pillus, Lorraine; Trievel, Raymond C.

    2010-09-02

    The {alpha}-aminoadipate pathway of lysine biosynthesis is modulated at the transcriptional and biochemical levels by feedback inhibition. The first enzyme in the {alpha}-aminoadipate pathway, homocitrate synthase (HCS), is the target of the feedback regulation and is strongly inhibited by L-lysine. Here we report the structure of Schizosaccharomyces pombe HCS (SpHCS) in complex with L-lysine. The structure illustrates that the amino acid directly competes with the substrate 2-oxoglutarate for binding within the active site of HCS. Differential recognition of the substrate and inhibitor is achieved via a switch position within the ({alpha}/{beta}){sub 8} TIM barrel of the enzyme that can distinguish between the C5-carboxylate group of 2-oxoglutarate and the {epsilon}-ammonium group of L-lysine. In vitro and in vivo assays demonstrate that mutations of the switch residues, which interact with the L-lysine {epsilon}-ammonium group, abrogate feedback inhibition, as do substitutions of residues within the C-terminal domain that were identified in a previous study of L-lysine-insensitive HCS mutants in Saccharomyces cerevisiae. Together, these results yield new insights into the mechanism of feedback regulation of an enzyme central to lysine biosynthesis.

  16. Global stability of a population dynamics model with inhibition and negative feedback.

    PubMed

    Vargas-De-Leóon, Cruz; Korobeinikov, Andrei

    2013-03-01

    Reactions or interactions with the rate which is inhibited by the product or a by-product of the reaction are fairly common in biology and chemical kinetics. Biological examples of such interactions include selfpoisoning of bacteria, the non-lytic immune response and the antiviral (and in particular antiretroviral) therapy. As a case study, in this notice, we consider global asymptotic properties for a simple model with negative feedback (the Wodarz model) where the interaction is inhibited by a by-product of the reaction. The objective of this notice is an extending of a technique that was developed during last decade for the global analysis of models with positive feedback to the systems, where the feedback is negative. Using the direct Lyapunov method with Volterra type Lyapunov functions, we establish conditions for the global stability of this model. This result enables us to evaluate the comparative impacts of the lytic and nonlytic components, the efficiency of the antiviral therapy and the possibility of self-poisoning for bacteria. The same approach can be successfully applied to more complex models with negative feedback.

  17. Acoustic Power Suppression of a Panel Structure Using H∞OUTPUT Feedback Control

    NASA Astrophysics Data System (ADS)

    SIVRIOGLU, S.; TANAKA, N.; YUKSEK, I.

    2002-01-01

    This paper presents a robust control system design for suppressing the radiated acoustic power emitted from a vibrating planar structure, and spillover effect caused by neglected high-frequency modes. A state-space model of a simply supported panel structure is derived and an output equation is formed based on the one-dimensional PVDF film sensors. An output feedback H∞control is designed by introducing a multiplicative perturbation which represents unmodelled high-frequency dynamics in the control system. The simulation and experimental results demonstrated significant decrease in sound radiation for the considered structural power modes in control.

  18. Structure of corrective feedback for selection of ineffective vegetable parenting practices for use in a simulation videogame

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A serious videogame is being developed to train parents of preschool children in selecting and using parenting practices that are likely to encourage their child to eat more vegetables. The structure of feedback to the parents on their selection may influence what they learn from the game. Feedback ...

  19. An L-Band Superconducting Traveling Wave Accelerating Structure With Feedback

    SciTech Connect

    Kanareykin, A.; Avrakhov, P.; Yakovlev, V. P.; Solyak, N.; Kazakov, S.

    2009-01-22

    The most severe problem of the International Linear Collider is its high cost, resulting in part from the enormous length of the collider. This length is determined mainly by the achievable accelerating gradient in the RF system of the ILC. In the ILC project the required accelerating gradient is higher than 30 MeV/m. Further improvement of the coupling to the beam may be achieved by using a Traveling Wave SC structure [1]. We have demonstrated that an additional gradient increase of up to 46% may be possible if a {pi}/2 TW SC structure is employed. However, a TW SC structure requires a SC feedback waveguide to return the few GW of circulating RF power from the structure output back to the structure input. The test cavity with feedback is designed to demonstrate the possibility of achieving a significantly higher gradient than existing SC structures. The double-coupler powering excitation and tuning have been studied numerically and the corresponding model results are presented. The proposed double-coupler powering scheme significantly reduces the tuning requirements as long as any of the partial modes of given magnitude and phase are excited independently, providing a clear traveling wave regime of structure operation.

  20. A PDE-based methodology for modeling, parameter estimation and feedback control in structural and structural acoustic systems

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Brown, D. E.; Metcalf, Vern L.; Silcox, R. J.; Smith, Ralph C.; Wang, Yun

    1994-01-01

    A problem of continued interest concerns the control of vibrations in a flexible structure and the related problem of reducing structure-borne noise in structural acoustic systems. In both cases, piezoceramic patches bonded to the structures have been successfully used as control actuators. Through the application of a controlling voltage, the patches can be used to reduce structural vibrations which in turn lead to methods for reducing structure-borne noise. A PDE-based methodology for modeling, estimating physical parameters, and implementing a feedback control scheme for problems of this type is discussed. While the illustrating example is a circular plate, the methodology is sufficiently general so as to be applicable in a variety of structural and structural acoustic systems.

  1. Reflecting on reflections: enhancement of medical education curriculum with structured field notes and guided feedback.

    PubMed

    Wald, Hedy S; Davis, Stephen W; Reis, Shmuel P; Monroe, Alicia D; Borkan, Jeffrey M

    2009-07-01

    The promotion of reflective capacity within the teaching of clinical skills and professionalism is posited as fostering the development of competent health practitioners. An innovative approach combines structured reflective writing by medical students and individualized faculty feedback to those students to augment instruction on reflective practice. A course for preclinical students at the Warren Alpert Medical School of Brown University, entitled "Doctoring," combined reflective writing assignments (field notes) with instruction in clinical skills and professionalism and early clinical exposure in a small-group format. Students generated multiple e-mail field notes in response to structured questions on course topics. Individualized feedback from a physician-behavioral scientist dyad supported the students' reflective process by fostering critical-thinking skills, highlighting appreciation of the affective domain, and providing concrete recommendations. The development and implementation of this innovation are presented, as is an analysis of the written evaluative comments of students taking the Doctoring course. Theoretical and clinical rationales for features of the innovation and supporting evidence of their effectiveness are presented. Qualitative analyses of students' evaluations yielded four themes of beneficial contributions to their learning experience: promoting deeper and more purposeful reflection, the value of (interdisciplinary) feedback, the enhancement of group process, and personal and professional development. Evaluation of the innovation was the fifth theme; some limitations are described, and suggestions for improvement are provided. Issues of the quality of the educational paradigm, generalizability, and sustainability are addressed.

  2. Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP.

    PubMed

    Maita, Nobuo; Okada, Kengo; Hatakeyama, Kazuyuki; Hakoshima, Toshio

    2002-02-05

    In the presence of phenylalanine, GTP cyclohydrolase I feedback regulatory protein (GFRP) forms a stimulatory 360-kDa complex with GTP cyclohydrolase I (GTPCHI), which is the rate-limiting enzyme in the biosynthesis of tetrahydrobiopterin. The crystal structure of the stimulatory complex reveals that the GTPCHI decamer is sandwiched by two GFRP homopentamers. Each GFRP pentamer forms a symmetrical five-membered ring similar to beta-propeller. Five phenylalanine molecules are buried inside each interface between GFRP and GTPCHI, thus enhancing the binding of these proteins. The complex structure suggests that phenylalanine-induced GTPCHI x GFRP complex formation enhances GTPCHI activity by locking the enzyme in the active state.

  3. Spectral characteristics of distributed feedback semiconductor laser and their improvements by corrugation-pitch-modulated structure

    NASA Astrophysics Data System (ADS)

    Okai, Makoto

    1994-01-01

    This paper presents a review of a theoretical analysis problems that occur with single-mode lasers, and a novel laser structure for superstable single-mode operation. Also presented is a new grating-fabrication technique termed photo-mask self-interference, to fabricate corrugation-pitch-modulated (CPM) structures, for enhancing the stability of the longitudinal single-mode operation in distributed feedback lasers (DFB). It is seen that the CPM-DFB laser developed for coherent transmission systems displays the narrowest spectral linewidth (56 kHz) reported so far for a semiconductor.

  4. Ecological feedbacks can reduce population-level efficacy of wildlife fertility control

    USGS Publications Warehouse

    Ransom, Jason I.; Powers, Jenny G.; Hobbs, N. Thompson; Baker, Dan L.

    2014-01-01

    1. Anthropogenic stress on natural systems, particularly the fragmentation of landscapes and the extirpation of predators from food webs, has intensified the need to regulate abundance of wildlife populations with management. Controlling population growth using fertility control has been considered for almost four decades, but nearly all research has focused on understanding effects of fertility control agents on individual animals. Questions about the efficacy of fertility control as a way to control populations remain largely unanswered. 2. Collateral consequences of contraception can produce unexpected changes in birth rates, survival, immigration and emigration that may reduce the effectiveness of regulating animal abundance. The magnitude and frequency of such effects vary with species-specific social and reproductive systems, as well as connectivity of populations. Developing models that incorporate static demographic parameters from populations not controlled by contraception may bias predictions of fertility control efficacy. 3. Many population-level studies demonstrate that changes in survival and immigration induced by fertility control can compensate for the reduction in births caused by contraception. The most successful cases of regulating populations using fertility control come from applications of contraceptives to small, closed populations of gregarious and easily accessed species. 4. Fertility control can result in artificial selection pressures on the population and may lead to long-term unintentional genetic consequences. The magnitude of such selection is dependent on individual heritability and behavioural traits, as well as environmental variation. 5. Synthesis and applications. Understanding species' life-history strategies, biology, behavioural ecology and ecological context is critical to developing realistic expectations of regulating populations using fertility control. Before time, effort and funding are invested in wildlife

  5. Ecological feedbacks can reduce population-level efficacy of wildlife fertility control.

    PubMed

    Ransom, Jason I; Powers, Jenny G; Thompson Hobbs, N; Baker, Dan L

    2014-02-01

    Anthropogenic stress on natural systems, particularly the fragmentation of landscapes and the extirpation of predators from food webs, has intensified the need to regulate abundance of wildlife populations with management. Controlling population growth using fertility control has been considered for almost four decades, but nearly all research has focused on understanding effects of fertility control agents on individual animals. Questions about the efficacy of fertility control as a way to control populations remain largely unanswered.Collateral consequences of contraception can produce unexpected changes in birth rates, survival, immigration and emigration that may reduce the effectiveness of regulating animal abundance. The magnitude and frequency of such effects vary with species-specific social and reproductive systems, as well as connectivity of populations. Developing models that incorporate static demographic parameters from populations not controlled by contraception may bias predictions of fertility control efficacy.Many population-level studies demonstrate that changes in survival and immigration induced by fertility control can compensate for the reduction in births caused by contraception. The most successful cases of regulating populations using fertility control come from applications of contraceptives to small, closed populations of gregarious and easily accessed species.Fertility control can result in artificial selection pressures on the population and may lead to long-term unintentional genetic consequences. The magnitude of such selection is dependent on individual heritability and behavioural traits, as well as environmental variation.Synthesis and applications. Understanding species' life-history strategies, biology, behavioural ecology and ecological context is critical to developing realistic expectations of regulating populations using fertility control. Before time, effort and funding are invested in wildlife contraception, managers may

  6. LQG and direct rate feedback control with model reduction on a flexible laboratory grid structure

    NASA Technical Reports Server (NTRS)

    Schamel, G. C., II; Haftka, R. T.

    1989-01-01

    This paper presents experimental and theoretical comparisons of three control laws applied to a complex laboratory structure. A reduced finite element model was generated for designing the control systems and then corrected based on measured mode shapes and frequencies. A standard time-invariant linear quadratic regulator with state estimation was investigated first. Two simple direct rate feedback control laws both guaranteeing stability were also designed using the reduced model. One minimizes the maximum control force and the other minimizes the same quadratic performance index as the linear quadratic regulator. The three control laws have comparable performance indices with the direct rate feedback designs having better spillover properties. Experimental results for all designs were obtained with digital implementation. It was shown that the performance of the control system designed on the basis of the corrected finite element model agreed better with experimental results than the performance of the control system designed on the basis of the uncorrected model.

  7. An open-structure electrowetting-based reflective display with a feedback system

    NASA Astrophysics Data System (ADS)

    Choi, Seungyul; Lee, Junghoon

    2015-11-01

    Electrowetting-based reflective displays have long been considered a promising display choice for electronic paper applications due to their fast operating speeds and high color contrasts. However, they still require several improvements in terms of their packaging process, color contrast, and reliability. This study investigates such enhancements via an open-structure design and a capacitive feedback system. It has a femto-farad level resolution and demonstrates a high operating speed (approximately 10 ms), effective ink dosing, and large color area change (approximately 92%). The feedback system for the precise control of the color area is verified by testing under a wide range of interfacial tension. The system reduces the deviation of color contrast by 85%. Working with high fidelity with large disturbances, which are represented by interfacial variations, the system shows robust performance against other disturbances, such as temperature variation and contact angle hysteresis.

  8. Output feedback model matching in linear impulsive systems with control feedthrough: a structural approach

    NASA Astrophysics Data System (ADS)

    Zattoni, Elena

    2017-01-01

    This paper investigates the problem of structural model matching by output feedback in linear impulsive systems with control feedthrough. Namely, given a linear impulsive plant, possibly featuring an algebraic link from the control input to the output, and given a linear impulsive model, the problem consists in finding a linear impulsive regulator that achieves exact matching between the respective forced responses of the linear impulsive plant and of the linear impulsive model, for all the admissible input functions and all the admissible sequences of jump times, by means of a dynamic feedback of the plant output. The problem solvability is characterized by a necessary and sufficient condition. The regulator synthesis is outlined through the proof of sufficiency, which is constructive.

  9. Performance limitations of joint variable-feedback controllers due to manipulator structural flexibility

    NASA Technical Reports Server (NTRS)

    Cetinkunt, Sabri; Book, Wayne J.

    1990-01-01

    The performance limitations of manipulators under joint variable-feedback control are studied as a function of the mechanical flexibility inherent in the manipulator structure. A finite-dimensional time-domain dynamic model of a two-link two-joint planar manipulator is used in the study. Emphasis is placed on determining the limitations of control algorithms that use only joint variable-feedback information in calculations of control decisions, since most motion control systems in practice are of this kind. Both fine and gross motion cases are studied. Results for fine motion agree well with previously reported results in the literature and are also helpful in explaining the performance limitations in fast gross motions.

  10. Inner structure detection by optical tomography technology based on feedback of microchip Nd:YAG lasers.

    PubMed

    Xu, Chunxin; Zhang, Shulian; Tan, Yidong; Zhao, Shijie

    2013-05-20

    We describe a new optical tomography technology based on feedback of microchip Nd:YAG lasers. In the case of feedback light frequency-shifted, light can be magnified by a fact of 10(6) in the Nd:YAG microchip lasers, which makes it possible to realize optical tomography with a greater depth than current optical tomography. The results of the measuring and imaging of kinds of samples are presented, which demonstrate the feasibility and potential of this approach in the inner structure detection. The system has a lateral resolution of ~1 μm, a vertical resolution of 15 μm and a longitudinal scanning range of over 10mm.

  11. Genetic structure of populations of Legionella pneumophila.

    PubMed Central

    Selander, R K; McKinney, R M; Whittam, T S; Bibb, W F; Brenner, D J; Nolte, F S; Pattison, P E

    1985-01-01

    The genetic structure of populations of Legionella pneumophila was defined by an analysis of electrophoretically demonstrable allelic variation at structural genes encoding 22 enzymes in 292 isolates from clinical and environmental sources. Nineteen of the loci were polymorphic, and 62 distinctive electrophoretic types (ETs), representing multilocus genotypes, were identified. Principal coordinates and clustering analyses demonstrated that isolates received as L. pneumophila were a heterogeneous array of genotypes that included two previously undescribed species. For 50 ETs of L. pneumophila (strict sense), mean genetic diversity per locus was 0.312, and diversity was equivalent in ETs represented by isolates recovered from clinical sources and those collected from environmental sources. Cluster analysis revealed four major groups or lineages of ETs in L. pneumophila. Genetic diversity among ETs of the same serotype was, on average, 93% of that in the total sample of ETs. Isolates marked by particular patterns of reactivity to a panel of nine monoclonal antibodies were also genetically heterogeneous, mean diversity within patterns being about 75% of the total. Both Pontiac fever and the pneumonic form of legionellosis may be caused by isolates of the same ET. The genetic structure of L. pneumophila is clonal, and many clones apparently are worldwide in distribution. The fact that L. pneumophila is only 60% as variable as Escherichia coli raises the possibility that isolates recovered from clinical cases and man-made environments are a restricted subset of all clones in the species as a whole. PMID:4030689

  12. Population inertia and its sensitivity to changes in vital rates and population structure

    USGS Publications Warehouse

    Koons, D.N.; Holmes, R.R.; Grand, J.B.

    2007-01-01

    Because the (st)age structure of a population may rarely be stable, studies of transient population dynamics and population momentum are becoming ever more popular. Yet, studies of "population momentum" are restricted in the sense that they describe the inertia of population size resulting from a demographic transition to the stationary population growth rate. Although rarely mentioned, inertia in population size is a general phenomenon and can be produced by any demographic transition or perturbation. Because population size is of central importance in demography, conservation, and management, formulas relating the sensitivity of population inertia to changes in underlying vital rates and population structure could provide much-needed insight into the dynamics of populations with unstable (st)age structure. Here, we derive such formulas, which are readily computable, and provide examples of their potential use in studies of life history and applied arenas of population study. ?? 2007 by the Ecological Society of America.

  13. Types of provincial structure and population health.

    PubMed

    Young, Frank W; Rodriguez, Eunice

    2005-01-01

    This paper explores the potential of using large administrative units for studies of population health within a country. The objective is to illustrate a new way of defining structural dimensions and to use them in examining variation in life expectancy rates. We use data from the 50 provinces of Spain as a case study. A factor analysis of organizational items such as schools, hotels and medical personnel is employed to define and generate "collective" measures for well-known provincial types, in this case: urban, commercial, industrial and tourist provinces. The scores derived from the factor analysis are then used in a regression model to predict life expectancy. The City-centered and Commercial provinces showed positive correlations with life expectancy while those for the Tourist provinces were negative. The industrial type was nonsignificant. Explanations of these correlations are proposed and the advantages and disadvantages of this exploratory technique are reviewed. The use of this technique for generating an overview of social organization and population health is discussed.

  14. Population Structure of Atlantic Mackerel (Scomber scombrus)

    PubMed Central

    Jansen, Teunis; Gislason, Henrik

    2013-01-01

    Atlantic mackerel (Scomber scombrus) occurs on both sides of the north Atlantic and has traditionally been grouped into 5 spawning components, some of which were thought to be isolated natal homing stocks. Previous studies have provided no evidence for cross Atlantic migration and no or weak support for isolated spawning components within either side of the North Atlantic. We question the de-facto accepted hypothesis of isolation between spawning components on the basis of spawning and age distribution data. The spawning intensities, proxied by larval abundances, are negatively correlated between the North Sea and Celtic Sea, which indicates that the two spawning components may be connected by straying individuals. This finding is based on unique larvae samples collected before the collapse of North Sea component, thus showing that the exchange is not a recent phenomenon due to the collapse. The analyses of old as well as more recent age distributions show that strong year classes spread into other areas where they spawn as adults (“twinning”). Our findings are in accordance with the lack of solid evidence for stock separation from previous analyses of tagging data, genetics, ectoparasite infections, otolith shapes, and blood phenotypes. Because no method has been able to identify the origin of spawning mackerel unequivocally from any of the traditional spawning components, and in the light of our results, we conclude that straying outweighs spatial segregation. We propose a new model where the population structure of mackerel is described as a dynamic cline, rather than as connected contingents. Temporal changes in hydrography and mackerel behavior may affect the steepness of the cline at various locations. The new interpretation of the population structure of Atlantic mackerel has important implications for research, assessment and management. PMID:23741381

  15. Population structure of Atlantic mackerel (Scomber scombrus).

    PubMed

    Jansen, Teunis; Gislason, Henrik

    2013-01-01

    Atlantic mackerel (Scomber scombrus) occurs on both sides of the north Atlantic and has traditionally been grouped into 5 spawning components, some of which were thought to be isolated natal homing stocks. Previous studies have provided no evidence for cross Atlantic migration and no or weak support for isolated spawning components within either side of the North Atlantic. We question the de-facto accepted hypothesis of isolation between spawning components on the basis of spawning and age distribution data. The spawning intensities, proxied by larval abundances, are negatively correlated between the North Sea and Celtic Sea, which indicates that the two spawning components may be connected by straying individuals. This finding is based on unique larvae samples collected before the collapse of North Sea component, thus showing that the exchange is not a recent phenomenon due to the collapse. The analyses of old as well as more recent age distributions show that strong year classes spread into other areas where they spawn as adults ("twinning"). Our findings are in accordance with the lack of solid evidence for stock separation from previous analyses of tagging data, genetics, ectoparasite infections, otolith shapes, and blood phenotypes. Because no method has been able to identify the origin of spawning mackerel unequivocally from any of the traditional spawning components, and in the light of our results, we conclude that straying outweighs spatial segregation. We propose a new model where the population structure of mackerel is described as a dynamic cline, rather than as connected contingents. Temporal changes in hydrography and mackerel behavior may affect the steepness of the cline at various locations. The new interpretation of the population structure of Atlantic mackerel has important implications for research, assessment and management.

  16. The prediction of EEG signals using a feedback-structured adaptive rational function filter.

    PubMed

    Kim, H S; Kim, T S; Choi, Y H; Park, S H

    2000-08-01

    In this article, we present a feedback-structured adaptive rational function filter based on a recursive modified Gram-Schmidt algorithm and apply it to the prediction of an EEG signal that has nonlinear and nonstationary characteristics. For the evaluation of the prediction performance, the proposed filter is compared with other methods, where a single-step prediction and a multi-step prediction are considered for a short-term prediction, and the prediction performance is assessed in normalized mean square error. The experimental results show that the proposed filter shows better performance than other methods considered for the short-term prediction of EEG signals.

  17. A stage structure pest management model with impulsive state feedback control

    NASA Astrophysics Data System (ADS)

    Pang, Guoping; Chen, Lansun; Xu, Weijian; Fu, Gang

    2015-06-01

    A stage structure pest management model with impulsive state feedback control is investigated. We get the sufficient condition for the existence of the order-1 periodic solution by differential equation geometry theory and successor function. Further, we obtain a new judgement method for the stability of the order-1 periodic solution of the semi-continuous systems by referencing the stability analysis for limit cycles of continuous systems, which is different from the previous method of analog of Poincarè criterion. Finally, we analyze numerically the theoretical results obtained.

  18. Global output feedback stabilisation of nonlinear systems with a unifying linear controller structure

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; Lin, Yan

    2014-02-01

    We investigate the problem of global stabilisation by linear output feedback for a class of uncertain nonlinear systems with zero-dynamics. Compared with the previous works, new dilation-based assumptions are introduced that allow the system nonlinearities and its bounding functions to be coupled with all the states. The nonlinear systems of this paper can be considered as an extended form of some low triangular and feedforward systems. Dynamic gain scaling technique is applied to the controller design and stability analysis. It is proved that with a unifying linear controller structure and flexible adaptive laws for the observer gain, global stabilisation of the nonlinear systems can be achieved.

  19. Bounded global Hopf branches for stage-structured differential equations with unimodal feedback

    NASA Astrophysics Data System (ADS)

    Shu, Hongying; Wang, Lin; Wu, Jianhong

    2017-03-01

    We consider a class of stage-structured differential equations with unimodal feedback. By using the time delay as a bifurcation parameter, we show that the number of local Hopf bifurcation values is finite. Furthermore, we analytically prove that these local Hopf bifurcation values are neatly paired, and each pair is jointed by a bounded global Hopf branch. We use the well-known Mackey-Glass equation with a stage structure as an illustrative example to demonstrate that bounded global Hopf branches can induce interesting and rich dynamics. As the delay increases over a finite interval, the stage-structured Mackey-Glass equation exhibits certain symmetric dynamic patterns: the solutions evolve from a stable equilibrium to sustained stable periodic oscillations, to chaotic-like aperiodic oscillations and back to sustained stable periodic oscillations, to a stable equilibrium.

  20. Self-organizing biochemical cycle in dynamic feedback with soil structure

    NASA Astrophysics Data System (ADS)

    Vasilyeva, Nadezda; Vladimirov, Artem; Smirnov, Alexander; Matveev, Sergey; Tyrtyshnikov, Evgeniy; Yudina, Anna; Milanovskiy, Evgeniy; Shein, Evgeniy

    2016-04-01

    In the present study we perform bifurcation analysis of a physically-based mathematical model of self-organized structures in soil (Vasilyeva et al., 2015). The state variables in this model included microbial biomass, two organic matter types, oxygen, carbon dioxide, water content and capillary pore size. According to our previous experimental studies, organic matter affinity to water is an important property affecting soil structure. Therefore, organic matter wettability was taken as principle distinction between organic matter types in this model. It considers general known biological feedbacks with soil physical properties formulated as a system of parabolic type non-linear partial differential equations with elements of discrete modeling for water and pore formation. The model shows complex behavior, involving emergence of temporal and spatial irregular auto-oscillations from initially homogeneous distributions. The energy of external impact on a system was defined by a constant oxygen level on the boundary. Non-linear as opposed to linear oxygen diffusion gives possibility of modeling anaerobic micro-zones formation (organic matter conservation mechanism). For the current study we also introduced population competition of three different types of microorganisms according to their mobility/feeding (diffusive, moving and fungal growth). The strongly non-linear system was solved and parameterized by time-optimized algorithm combining explicit and implicit (matrix form of Thomas algorithm) methods considering the time for execution of the evaluated time-step according to accuracy control. The integral flux of the CO2 state variable was used as a macroscopic parameter to describe system as a whole and validation was carried out on temperature series of moisture dependence for soil heterotrophic respiration data. Thus, soil heterotrophic respiration can be naturally modeled as an integral result of complex dynamics on microscale, arising from biological processes

  1. Developing STR databases on structured populations: the native South Siberian population versus the Russian population.

    PubMed

    Zhivotovsky, Lev A; Malyarchuk, Boris A; Derenko, Miroslava V; Wozniak, Marcin; Grzybowski, Tomasz

    2009-09-01

    Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of theta-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus i, Cyrillic AmpFlSTR Profiler Plus. The groups differentiate from each other with average theta-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on theta-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on theta-values.

  2. Auroral Current and Electrodynamics Structure (ACES) Observations of Ionospheric Feedback in the Alfven Resonator

    NASA Technical Reports Server (NTRS)

    Cohen, Ian J.; Lessard, Marc; Lund, Eric J.; Bounds, Scott R.; Kletzing, Craig; Kaeppler, Stephen R.; Sigsbee, Kristine M.; Streltsov, Anatoly V.; Labelle, James W.; Dombrowski, Micah P.; Pfaff, Robert F.; Rowland, Doug; Jones, Sarah; Anderson, Brian Jay; Heinselman, Craig J.; Gjerloev, Jesper W.; Dudok de Wit, Thierry

    2011-01-01

    In 2009, the Auroral Current and Electrodynamics Structure (ACES) High and Low sounding rockets were launched from the Poker Flat Rocket Range (PFRR) in Alaska, with the science objective of gathering in-situ data to quantify current closure in a discrete auroral arc. As ACES High crossed through the return current of an arc (that was monitored using an all sky camera from the ground at Fort Yukon), its instruments recorded clear Alfv nic signatures both poleward and equatorward of the return current region, but not within the main region of the return current itself. These data provide an excellent opportunity to study ionospheric feedback and how it interacts with the Alfv n resonator. We compare the observations with predictions and new results from a model of ionospheric feedback in the ionospheric Alfv n resonator (IAR) and report the significance and impact of these new data for the Magnetosphere-Ionosphere Coupling in the Alfv n Resonator (MICA) rocket mission to launch from PFRR this winter. MICA s primary science objectives specifically focus on better understanding the small-scale structure that the model predicts should exist within the return current region.

  3. Understanding cooperative behavior in structurally disordered populations

    NASA Astrophysics Data System (ADS)

    Xu, C.; Zhang, W.; Du, P.; Choi, C. W.; Hui, P. M.

    2016-06-01

    The effects of an inhomogeneous competing environment on the extent of cooperation are studied within the context of a site-diluted evolutionary snowdrift game on a square lattice, with the occupied sites representing the players, both numerically and analytically. The frequency of cooperation ℱ C generally shows a non-monotonic dependence on the fraction of occupied sites ρ, for different values of the payoff parameter r. Slightly diluting a lattice leads to a lower cooperation for small and high values of r. For a range of r, however, dilution leads to an enhanced cooperation. An analytic treatment is developed for ℱC I + ℱC II, with ℱC I emphasizing the importance of the small clusters of players especially for ℱC II from the other players is shown to be inadequate. A local configuration approximation (LCA) that treats the local competing configurations as the variables and amounts to include spatial correlation up to the neighborhood of a player's neighbors is developed. Results of ℱ C ( ρ) and the number of different local configurations from LCA are in good agreement with simulation results. A transparent physical picture of the dynamics stemming from LCA is also presented. The theoretical approach provides a framework that can be readily applied to competing agent-based models in structurally ordered and disordered populations.

  4. Structural vibration control of micro/macro-manipulator using feedforward and feedback approaches

    SciTech Connect

    Lew, J.Y.; Cannon, D.W.; Magee, D.P.; Book, W.J.

    1995-09-01

    Pacific Northwest Laboratory (PDL) researchers investigated the combined use of two control approaches to minimize micro/macro-manipulator structural vibration: (1) modified input shaping and (2) inertial force active damping control. Modified input shaping (MIS) is used as a feedforward controller to modify reference input by canceling the vibratory motion. Inertial force active damping (IFAD) is applied as a feedback controller to increase the system damping and robustness to unexpected disturbances. Researchers implemented both control schemes in the PNL micro/macro flexible-link manipulator testbed collaborating with Georgia Institute of Technology. The experiments successfully demonstrated the effectiveness of two control approaches in reducing structural vibration. Based on the results of the experiments, the combined use of two controllers is recommended for a micro/macro manipulator to achieve the fastest response to commands while canceling disturbances from unexpected forces.

  5. Failure of glucocorticoid feedback in males of a population of small marsupials (Antechinus swainsonii) during the period of mating.

    PubMed

    McDonald, I R; Lee, A K; Than, K A; Martin, R W

    1986-01-01

    In an investigation of the factors leading to the increase in the concentration of plasma free glucocorticoid, which results in immunosuppression and death after mating of all males in natural populations of a small shrew-like marsupial, the dusky antechinus (Antechinus swainsonii), the integrity of the glucocorticoid feedback control of the concentration of plasma cortisol was examined by use of dexamethasone-suppression tests. Injection of 0.2 mg dexamethasone/kg i.m. caused a marked fall in the concentration of plasma cortisol 17 h later, approximately 2 months and 2 weeks before the annual mating period in mid-July. However, the same dose had no significant effect on the increased concentration of plasma cortisol characteristic of the mid- to late July mating period. Injection of 100 i.u. ACTH/kg i.m. caused a significant increase in the concentration of plasma cortisol 6-7 h later on all occasions, indicating that the responsiveness of the adrenal cortex to ACTH did not change. Pretreatment with dexamethasone had no effect on the ACTH-stimulated cortisol concentration, ruling out a possible direct effect of dexamethasone on adrenocortical secretion in this species. Dexamethasone also reduced the concentration of plasma testosterone when the level was low, before the mating period, but not when the level was high, at the beginning of the mating period. It is concluded that, in association with a rapid increase in the concentration of plasma testosterone, an increase in aggression and intense mating activity, glucocorticoid feedback control of ACTH secretion is impaired.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion

    PubMed Central

    Kunert, James M.; Proctor, Joshua L.; Kutz, J. Nathan

    2017-01-01

    Using a computational model of the Caenorhabditis elegans connectome dynamics, we show that proprioceptive feedback is necessary for sustained dynamic responses to external input. This is consistent with the lack of biophysical evidence for a central pattern generator, and recent experimental evidence that proprioception drives locomotion. The low-dimensional functional response of the Caenorhabditis elegans network of neurons to proprioception-like feedback is optimized by input of specific spatial wavelengths which correspond to the spatial scale of real body shape dynamics. Furthermore, we find that the motor subcircuit of the network is responsible for regulating this response, in agreement with experimental expectations. To explore how the connectomic dynamics produces the observed two-mode, oscillatory limit cycle behavior from a static fixed point, we probe the fixed point’s low-dimensional structure using Dynamic Mode Decomposition. This reveals that the nonlinear network dynamics encode six clusters of dynamic modes, with timescales spanning three orders of magnitude. Two of these six dynamic mode clusters correspond to previously-discovered behavioral modes related to locomotion. These dynamic modes and their timescales are encoded by the network’s degree distribution and specific connectivity. This suggests that behavioral dynamics are partially encoded within the connectome itself, the connectivity of which facilitates proprioceptive control. PMID:28076347

  7. Structural Basis for Feedback and Pharmacological Inhibition of Saccharomyces cerevisiae Glutamate Cysteine Ligase

    SciTech Connect

    Biterova, Ekaterina I.; Barycki, Joseph J.

    2010-04-30

    Structural characterization of glutamate cysteine ligase (GCL), the enzyme that catalyzes the initial, rate-limiting step in glutathione biosynthesis, has revealed many of the molecular details of substrate recognition. To further delineate the mechanistic details of this critical enzyme, we have determined the structures of two inhibited forms of Saccharomyces cerevisiae GCL (ScGCL), which shares significant sequence identity with the human enzyme. In vivo, GCL activity is feedback regulated by glutathione. Examination of the structure of ScGCL-glutathione complex (2.5 A; R = 19.9%, R(free) = 25.1%) indicates that the inhibitor occupies both the glutamate- and the presumed cysteine-binding site and disrupts the previously observed Mg(2+) coordination in the ATP-binding site. l-Buthionine-S-sulfoximine (BSO) is a mechanism-based inhibitor of GCL and has been used extensively to deplete glutathione in cell culture and in vivo model systems. Inspection of the ScGCL-BSO structure (2.2 A; R = 18.1%, R(free) = 23.9%) confirms that BSO is phosphorylated on the sulfoximine nitrogen to generate the inhibitory species and reveals contacts that likely contribute to transition state stabilization. Overall, these structures advance our understanding of the molecular regulation of this critical enzyme and provide additional details of the catalytic mechanism of the enzyme.

  8. Population structure with localized haplotype clusters.

    PubMed

    Browning, Sharon R; Weir, Bruce S

    2010-08-01

    We propose a multilocus version of F(ST) and a measure of haplotype diversity using localized haplotype clusters. Specifically, we use haplotype clusters identified with BEAGLE, which is a program implementing a hidden Markov model for localized haplotype clustering and performing several functions including inference of haplotype phase. We apply this methodology to HapMap phase 3 data. With this haplotype-cluster approach, African populations have highest diversity and lowest divergence from the ancestral population, East Asian populations have lowest diversity and highest divergence, and other populations (European, Indian, and Mexican) have intermediate levels of diversity and divergence. These relationships accord with expectation based on other studies and accepted models of human history. In contrast, the population-specific F(ST) estimates obtained directly from single-nucleotide polymorphisms (SNPs) do not reflect such expected relationships. We show that ascertainment bias of SNPs has less impact on the proposed haplotype-cluster-based F(ST) than on the SNP-based version, which provides a potential explanation for these results. Thus, these new measures of F(ST) and haplotype-cluster diversity provide an important new tool for population genetic analysis of high-density SNP data.

  9. A feedback mechanism converts individual cell features into a supracellular ECM structure in Drosophila trachea.

    PubMed

    Öztürk-Çolak, Arzu; Moussian, Bernard; Araújo, Sofia J; Casanova, Jordi

    2016-02-02

    The extracellular matrix (ECM), a structure contributed to and commonly shared by many cells in an organism, plays an active role during morphogenesis. Here, we used the Drosophila tracheal system to study the complex relationship between the ECM and epithelial cells during development. We show that there is an active feedback mechanism between the apical ECM (aECM) and the apical F-actin in tracheal cells. Furthermore, we reveal that cell-cell junctions are key players in this aECM patterning and organisation and that individual cells contribute autonomously to their aECM. Strikingly, changes in the aECM influence the levels of phosphorylated Src42A (pSrc) at cell junctions. Therefore, we propose that Src42A phosphorylation levels provide a link for the ECM environment to ensure proper cytoskeletal organisation.

  10. Consensus positive position feedback control for vibration attenuation of smart structures

    NASA Astrophysics Data System (ADS)

    Omidi, Ehsan; Nima Mahmoodi, S.

    2015-04-01

    This paper presents a new network-based approach for active vibration control in smart structures. In this approach, a network with known topology connects collocated actuator/sensor elements of the smart structure to one another. Each of these actuators/sensors, i.e., agent or node, is enhanced by a separate multi-mode positive position feedback (PPF) controller. The decentralized PPF controlled agents collaborate with each other in the designed network, under a certain consensus dynamics. The consensus constraint forces neighboring agents to cooperate with each other such that the disagreement between the time-domain actuation of the agents is driven to zero. The controller output of each agent is calculated using state-space variables; hence, optimal state estimators are designed first for the proposed observer-based consensus PPF control. The consensus controller is numerically investigated for a flexible smart structure, i.e., a thin aluminum beam that is clamped at its both ends. Results demonstrate that the consensus law successfully imposes synchronization between the independently controlled agents, as the disagreements between the decentralized PPF controller variables converge to zero in a short time. The new consensus PPF controller brings extra robustness to vibration suppression in smart structures, where malfunctions of an agent can be compensated for by referencing the neighboring agents’ performance. This is demonstrated in the results by comparing the new controller with former centralized PPF approach.

  11. Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities

    PubMed Central

    Estrela, Sylvie; Brown, Sam P.

    2013-01-01

    Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities. Within these communities, microbial cells excrete a wide range of metabolites, setting the stage for interspecific metabolic interactions. The links, however, between metabolic and ecological interactions (functional relationships), and species spatial organization (structural relationships) are still poorly understood. Here, we use an individual-based modelling framework to simulate the growth of a two-species surface-attached community where food (resource) is traded for detoxification (service) and investigate how metabolic constraints of individual species shape the emergent structural and functional relationships of the community. We show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Specifically, we observed a striking and highly stable emergent lineage branching pattern, generating a persistent lineage mixing that was absent when the metabolic exchange was removed. These emergent community properties are driven by demographic feedbacks, such that aid from neighbouring cells directly enhances focal cell growth, which in turn feeds back to neighbour fecundity. In contrast, weak metabolic interdependence drives conflict (exploitation or competition), and in turn greater interspecific segregation. Together, these results support the idea that species structural and functional relationships represent the net balance of metabolic interdependencies. PMID:24385891

  12. Modeling Subducting Slabs: Structural Variations due to Thermal Models, Latent Heat Feedback, and Thermal Parameter

    NASA Astrophysics Data System (ADS)

    Marton, F. C.

    2001-12-01

    The thermal, mineralogical, and buoyancy structures of thermal-kinetic models of subducting slabs are highly dependent upon a number of parameters, especially if the metastable persistence of olivine in the transition zone is investigated. The choice of starting thermal model for the lithosphere, whether a cooling halfspace (HS) or plate model, can have a significant effect, resulting in metastable wedges of olivine that differ in size by up to two to three times for high values of the thermal parameter (ǎrphi). Moreover, as ǎrphi is the product of the age of the lithosphere at the trench, convergence rate, and dip angle, slabs with similar ǎrphis can show great variations in structures as these constituents change. This is especially true for old lithosphere, as the lithosphere continually cools and thickens with age for HS models, but plate models, with parameters from Parson and Sclater [1977] (PS) or Stein and Stein [1992] (GDH1), achieve a thermal steady-state and constant thickness in about 70 My. In addition, the latent heats (q) of the phase transformations of the Mg2SiO4 polymorphs can also have significant effects in the slabs. Including q feedback in models raises the temperature and reduces the extent of metastable olivine, causing the sizes of the metastable wedges to vary by factors of up to two times. The effects of the choice of thermal model, inclusion and non-inclusion of q feedback, and variations in the constituents of ǎrphi are investigated for several model slabs.

  13. Physical properties of simulated galaxy populations at z = 2 - I. Effect of metal-line cooling and feedback from star formation and AGN

    NASA Astrophysics Data System (ADS)

    Haas, Marcel R.; Schaye, Joop; Booth, C. M.; Dalla Vecchia, Claudio; Springel, Volker; Theuns, Tom; Wiersma, Robert P. C.

    2013-11-01

    We use hydrodynamical simulations from the OverWhelmingly Large Simulations (OWLS) project to investigate the dependence of the physical properties of galaxy populations at redshift 2 on metal-line cooling and feedback from star formation and active galactic nuclei (AGN). We find that if the sub-grid feedback from star formation is implemented kinetically, the feedback is only efficient if the initial wind velocity exceeds a critical value. This critical velocity increases with galaxy mass and also if metal-line cooling is included. This suggests that radiative losses quench the winds if their initial velocity is too low. If the feedback is efficient, then the star formation rate is inversely proportional to the amount of energy injected per unit stellar mass formed (which is proportional to the initial mass loading for a fixed wind velocity). This can be understood if the star formation is self-regulating, i.e. if the star formation rate (and thus the gas fraction) increases until the outflow rate balances the inflow rate. Feedback from AGN is efficient at high masses, while increasing the initial wind velocity with gas pressure or halo mass allows one to generate galaxy-wide outflows at all masses. Matching the observed galaxy mass function requires efficient feedback. In particular, the predicted faint-end slope is too steep unless we resort to highly mass loaded winds for low-mass objects. Such efficient feedback from low-mass galaxies (M* ≪ 1010 M⊙) also reduces the discrepancy with the observed specific star formation rates, which are higher than predicted unless the feedback transitions from highly efficient to inefficient just below M* ˜ 5 × 109 M⊙.

  14. Genetic structure of Tribolium castaneum (Coleptera: Tenebrionidae) populations in mills

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The red flour beetle, Tribolium castaneum, is primarily found associated with human structures such as wheat and rice mills, which are spatially isolated resource patches with apparently limited immigration that could produce genetically structured populations. We investigated genetic diversity and...

  15. Population structure and genetic diversity of moose in Alaska.

    PubMed

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P < 0.001) with F(ST) < 0.109 and R(ST) < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast.

  16. Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population.

    PubMed

    Aspi, J; Roininen, E; Ruokonen, M; Kojola, I; Vilà, C

    2006-05-01

    The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.

  17. Evolutionary dynamics of general group interactions in structured populations

    NASA Astrophysics Data System (ADS)

    Li, Aming; Broom, Mark; Du, Jinming; Wang, Long

    2016-02-01

    The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions.

  18. Disentangling the effects of feedback structure and climate on Poaceae annual airborne pollen fluctuations and the possible consequences of climate change.

    PubMed

    García de León, David; García-Mozo, Herminia; Galán, Carmen; Alcázar, Purificación; Lima, Mauricio; González-Andújar, José L

    2015-10-15

    Pollen allergies are the most common form of respiratory allergic disease in Europe. Most studies have emphasized the role of environmental processes, as the drivers of airborne pollen fluctuations, implicitly considering pollen production as a random walk. This work shows that internal self-regulating processes of the plants (negative feedback) should be included in pollen dynamic systems in order to give a better explanation of the observed pollen temporal patterns. This article proposes a novel methodological approach based on dynamic systems to investigate the interaction between feedback structure of plant populations and climate in shaping long-term airborne Poaceae pollen fluctuations and to quantify the effects of climate change on future airborne pollen concentrations. Long-term historical airborne Poaceae pollen data (30 years) from Cordoba city (Southern Spain) were analyzed. A set of models, combining feedback structure, temperature and actual evapotranspiration effects on airborne Poaceae pollen were built and compared, using a model selection approach. Our results highlight the importance of first-order negative feedback and mean annual maximum temperature in driving airborne Poaceae pollen dynamics. The best model was used to predict the effects of climate change under two standardized scenarios representing contrasting temporal patterns of economic development and CO2 emissions. Our results predict an increase in pollen levels in southern Spain by 2070 ranging from 28.5% to 44.3%. The findings from this study provide a greater understanding of airborne pollen dynamics and how climate change might impact the future evolution of airborne Poaceae pollen concentrations and thus the future evolution of related pollen allergies.

  19. Selection of Cooperation in Spatially Structured Populations

    NASA Astrophysics Data System (ADS)

    Yang, Hyunmo; Ghim, Cheol-Min

    The social dilemma games give rise to an emergence of cooperation in which altruistic individuals survive the natural selection at higher rate than random chance. We try to extend our understanding of this spatial reciprocity by including the impact of degree-degree correlation on the propensity toward prosocial behaviour in an otherwise well-mixed population. In a stochastic death-birth process with weak selection, we find that the disassortative degree mixing, or negative correlation between the degrees of neighbouring nodes significantly promotes the fixation of cooperators whereas the assortative mixing acts to suppress it. This is consistent with the fact that the spatial heterogeneity weakens the average tendency of a population to cooperate, which we describe in a unified scheme of the effective isothermality in coarse-grained networks. We also discuss the individual-level incentives that indirectly foster restructuring the social networks toward the more cooperative topologies.

  20. Feedback can be superior to observational training for both rule-based and information-integration category structures.

    PubMed

    Edmunds, C E R; Milton, Fraser; Wills, Andy J

    2015-01-01

    The effects of two different types of training on rule-based and information-integration category learning were investigated in two experiments. In observational training, a category label is presented, followed by an example of that category and the participant's response. In feedback training, the stimulus is presented, and the participant assigns it to a category and then receives feedback about the accuracy of that decision. Ashby, Maddox, and Bohil (2002. Observational versus feedback training in rule-based and information-integration category learning. Memory & Cognition, 30, 666-677) reported that feedback training was superior to observational training when learning information-integration category structures, but that training type had little effect on the acquisition of rule-based category structures. These results were argued to support the COVIS (competition between verbal and implicit systems) dual-process account of category learning. However, a number of nonessential differences between their rule-based and information-integration conditions complicate interpretation of these findings. Experiment 1 controlled between-category structures for participant error rates, category separation, and the number of stimulus dimensions relevant to the categorization. Under these more controlled conditions, rule-based and information-integration category structures both benefited from feedback training to a similar degree. Experiment 2 maintained this difference in training type when learning a rule-based category that had otherwise been matched, in terms of category overlap and overall performance, with the rule-based categories used in Ashby et al. These results indicate that differences in dimensionality between the category structures in Ashby et al. is a more likely explanation for the interaction between training type and category structure than the dual-system explanation that they offered.

  1. A Multi-Mode Blade Damping Control using Shunted Piezoelectric Transducers with Active Feedback Structure

    NASA Technical Reports Server (NTRS)

    Choi, Benjamin; Morrison, Carlos; Min, James

    2009-01-01

    The Structural Dynamics and. Mechanics branch (RXS) is developing smart adaptive structures to improve fan blade damping at resonances using piezoelectric (PE) transducers. In this presentation, only one shunted PE transducer was used to demonstrate active control of multi-mode blade resonance damping on a titanium alloy (Ti-6A1-4V) flat plate model, regardless of bending, torsion, and 2-stripe modes. This work would have a significant impact on the conventional passive shunt damping world because the standard feedback control design tools can now be used to design and implement electric shunt for vibration control. In other words, the passive shunt circuit components using massive inductors and. resistors for multi-mode resonance control can be replaced with digital codes. Furthermore, this active approach with multi patches can simultaneously control several modes in the engine operating range. Dr. Benjamin Choi presented the analytical and experimental results from this work at the Propulsion-Safety and. Affordable Readiness (P-SAR) Conference in March, 2009.

  2. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  3. Conditions for HD cooling in the first galaxies revisited: interplay between far-ultraviolet and cosmic ray feedback in Population III star formation

    NASA Astrophysics Data System (ADS)

    Nakauchi, Daisuke; Inayoshi, Kohei; Omukai, Kazuyuki

    2014-08-01

    HD dominates the cooing of primordial clouds with enhanced ionization, e.g. shock-heated clouds in structure formation or supernova remnants, relic H II regions of Pop III stars and clouds with cosmic ray (CR) irradiation. There, the temperature decreases to several 10 K and the characteristic stellar mass decreases to ˜10 M⊙, in contrast with first stars formed from undisturbed pristine clouds (˜100 M⊙). However, without CR irradiation, even weak far-ultraviolet (FUV) irradiation suppresses HD formation/cooling. Here, we examine conditions for HD cooling in primordial clouds including both FUV and CR feedback. At the beginning of collapse, the shock-compressed gas cools with its density increasing, while the relic H II region gas cools at a constant density. Moreover, shocks tend to occur in denser environments than H II regions. Owing to the higher column density and the more effective shielding, the critical FUV intensity for HD cooling in a shock-compressed gas becomes ˜10 times higher than that in relic H II regions. Consequently, in the shock-compressed gas, the critical FUV intensity exceeds the background level for most of the redshift we consider (6 ≲ z ≲ 15), while in relic H II regions, HD cooling becomes effective after the CR intensity increases enough at z ≲ 10. Our result suggests that less massive (˜10 M⊙) Pop III stars may be more common than previously considered and could be the dominant population of Pop III stars.

  4. Audio Feedback -- Better Feedback?

    ERIC Educational Resources Information Center

    Voelkel, Susanne; Mello, Luciane V.

    2014-01-01

    National Student Survey (NSS) results show that many students are dissatisfied with the amount and quality of feedback they get for their work. This study reports on two case studies in which we tried to address these issues by introducing audio feedback to one undergraduate (UG) and one postgraduate (PG) class, respectively. In case study one…

  5. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae)

    PubMed Central

    Multini, Laura Cristina; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

    Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city. PMID:27598889

  6. Determining population structure and hybridization for two iris species

    PubMed Central

    Hamlin, Jennafer A P; Arnold, Michael L

    2014-01-01

    Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species. PMID:24683457

  7. Evolution of extortion in structured populations

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games.

  8. Social and population structure in the ant Cataglyphis emmae.

    PubMed

    Jowers, Michael J; Leniaud, Laurianne; Cerdá, Xim; Alasaad, Samer; Caut, Stephane; Amor, Fernando; Aron, Serge; Boulay, Raphaël R

    2013-01-01

    Dispersal has consequences not only for individual fitness, but also for population dynamics, population genetics and species distribution. Social Hymenoptera show two contrasting colony reproductive strategies, dependent and independent colony foundation modes, and these are often associated to the population structures derived from inter and intra-population gene flow processes conditioned by alternative dispersal strategies. Here we employ microsatellite and mitochondrial markers to investigate the population and social genetic structure and dispersal patterns in the ant Cataglyphis emmae at both, local and regional scales. We find that C. emmae is monogynous and polyandrous. Lack of detection of any population viscosity and population structure with nuclear markers at the local scale suggests efficient dispersal, in agreement with a lack of inbreeding. Contrasting demographic differences before and during the mating seasons suggest that C. emmae workers raise sexuals in peripheric nest chambers to reduce intracolonial conflicts. The high genetic differentiation recovered from the mtDNA haplotypes, together with the significant correlation of such to geographic distance, and presence of new nuclear alleles between areas (valleys) suggest long-term historical isolation between these regions, indicative of limited dispersal at the regional scale. Our findings on the ecological, social and population structure of this species increases our understanding of the patterns and processes involved under independent colony foundation.

  9. Social and Population Structure in the Ant Cataglyphis emmae

    PubMed Central

    Jowers, Michael J.; Leniaud, Laurianne; Cerdá, Xim; Alasaad, Samer; Caut, Stephane; Amor, Fernando; Aron, Serge; Boulay, Raphaël R.

    2013-01-01

    Dispersal has consequences not only for individual fitness, but also for population dynamics, population genetics and species distribution. Social Hymenoptera show two contrasting colony reproductive strategies, dependent and independent colony foundation modes, and these are often associated to the population structures derived from inter and intra-population gene flow processes conditioned by alternative dispersal strategies. Here we employ microsatellite and mitochondrial markers to investigate the population and social genetic structure and dispersal patterns in the ant Cataglyphis emmae at both, local and regional scales. We find that C. emmae is monogynous and polyandrous. Lack of detection of any population viscosity and population structure with nuclear markers at the local scale suggests efficient dispersal, in agreement with a lack of inbreeding. Contrasting demographic differences before and during the mating seasons suggest that C. emmae workers raise sexuals in peripheric nest chambers to reduce intracolonial conflicts. The high genetic differentiation recovered from the mtDNA haplotypes, together with the significant correlation of such to geographic distance, and presence of new nuclear alleles between areas (valleys) suggest long-term historical isolation between these regions, indicative of limited dispersal at the regional scale. Our findings on the ecological, social and population structure of this species increases our understanding of the patterns and processes involved under independent colony foundation. PMID:24039827

  10. Ecological factors influence population genetic structure of European grey wolves.

    PubMed

    Pilot, Malgorzata; Jedrzejewski, Wlodzimierz; Branicki, Wojciech; Sidorovich, Vadim E; Jedrzejewska, Bogumila; Stachura, Krystyna; Funk, Stephan M

    2006-12-01

    Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal-habitat-biased dispersal as an underlying mechanism linking population ecology with population genetic structure.

  11. HOW POPULATION STRUCTURE SHAPES NEIGHBORHOOD SEGREGATION*

    PubMed Central

    Bruch, Elizabeth E.

    2014-01-01

    This study investigates how choices about social affiliation based on one attribute can exacerbate or attenuate segregation on another correlated attribute. The specific application is the role of racial and economic factors in generating patterns of racial residential segregation. I identify three population parameters—between-group inequality, within-group inequality, and relative group size—that determine how income inequality between race groups affects racial segregation. I use data from the Panel Study of Income Dynamics to estimate models of individual-level residential mobility, and incorporate these estimates into agent-based models. I then simulate segregation dynamics under alternative assumptions about: (1) the relative size of minority groups; and (2) the degree of correlation between race and income among individuals. I find that income inequality can have offsetting effects at the high and low ends of the income distribution. I demonstrate the empirical relevance of the simulation results using fixed-effects, metro-level regressions applied to 1980-2000 U.S. Census data. PMID:25009360

  12. Genetic Variation and Population Structure in Native Americans

    PubMed Central

    Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V; Molina, Julio A; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria Luiza; Tsuneto, Luiza T; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Feldman, Marcus W; Rosenberg, Noah A; Ruiz-Linares, Andrés

    2007-01-01

    We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. PMID:18039031

  13. Insights into the algebraic structure of Lorenz-like systems using feedback circuit analysis and piecewise affine models

    NASA Astrophysics Data System (ADS)

    Letellier, Christophe; Amaral, Gleison F. V.; Aguirre, Luis A.

    2007-06-01

    The characterization of chaotic attractors has been a widely addressed problem and there are now many different techniques to define their nature in a rather accurate way, at least in the case of a three-dimensional system. Nevertheless, the link between the structure of the ordinary differential equations and the topology of their solutions is still missing and only a few necessary conditions on the algebraic structure are known today. By using a feedback circuit analysis, it is shown that it is possible to identify the relevant terms of the equations, that is, the terms that really contribute to the structure of the phase portrait. Such analysis also provides some guidelines for constructing piecewise affine models. Moreover, equivalence classes can be defined on the basis of the active feedback circuits involved.

  14. Plasmodium vivax Diversity and Population Structure across Four Continents

    PubMed Central

    Koepfli, Cristian; Rodrigues, Priscila T.; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y. M.; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U.; Felger, Ingrid

    2015-01-01

    Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations. PMID:26125189

  15. Resource competition in stage-structured populations.

    PubMed

    Revilla, T A

    2000-05-21

    Two models are made to account for the dynamics of a consumer-resource system in which the consumers are divided into juveniles and adults. The resource grows logistically and a type II functional response is assumed for consumers. Resource levels determine fecundity and maturation rates in one model, and mortality rates in the other. The analysis of the models shows that the condition for establishment of consumers is that the product of per capita fecundity rate and maturation rates is higher than the product of juvenile and adult per capita decay rates at a resource level equal to its carrying capacity. This result imposes a minimal abundance of resource able to maintain the consumers. A second result shows an equilibrium stage structure, with a small instability when juveniles and adults mean saturation constants are different. The implications of these results for community dynamics are discussed.

  16. Statistical validation of structured population models for Daphnia magna.

    PubMed

    Adoteye, Kaska; Banks, H T; Cross, Karissa; Eytcheson, Stephanie; Flores, Kevin B; LeBlanc, Gerald A; Nguyen, Timothy; Ross, Chelsea; Smith, Emmaline; Stemkovski, Michael; Stokely, Sarah

    2015-08-01

    In this study we use statistical validation techniques to verify density-dependent mechanisms hypothesized for populations of Daphnia magna. We develop structured population models that exemplify specific mechanisms and use multi-scale experimental data in order to test their importance. We show that fecundity and survival rates are affected by both time-varying density-independent factors, such as age, and density-dependent factors, such as competition. We perform uncertainty analysis and show that our parameters are estimated with a high degree of confidence. Furthermore, we perform a sensitivity analysis to understand how changes in fecundity and survival rates affect population size and age-structure.

  17. Patterns of admixture and population structure in native populations of Northwest North America.

    PubMed

    Verdu, Paul; Pemberton, Trevor J; Laurent, Romain; Kemp, Brian M; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E; Shattuck, Milena R; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S; Rosenberg, Noah A; Malhi, Ripan S

    2014-08-01

    The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  18. Patterns of Admixture and Population Structure in Native Populations of Northwest North America

    PubMed Central

    Verdu, Paul; Pemberton, Trevor J.; Laurent, Romain; Kemp, Brian M.; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E.; Shattuck, Milena R.; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S.; Rosenberg, Noah A.; Malhi, Ripan S.

    2014-01-01

    The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas. PMID:25122539

  19. Amplification on Undirected Population Structures: Comets Beat Stars.

    PubMed

    Pavlogiannis, Andreas; Tkadlec, Josef; Chatterjee, Krishnendu; Nowak, Martin A

    2017-12-01

    The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.

  20. Spatial structuring within a reservoir fish population: implications for management

    USGS Publications Warehouse

    Stewart, David R.; Long, James M.; Shoup, Daniel E.

    2014-01-01

    Spatial structuring in reservoir fish populations can exist because of environmental gradients, species-specific behaviour, or even localised fishing effort. The present study investigated whether white crappie exhibited evidence of improved population structure where the northern more productive half of a lake is closed to fishing to provide waterfowl hunting opportunities. Population response to angling was modelled for each substock of white crappie (north (protected) and south (unprotected) areas), the entire lake (single-stock model) and by combining simulations of the two independent substock models (additive model). White crappie in the protected area were more abundant, consisting of larger, older individuals, and exhibited a lower total annual mortality rate than in the unprotected area. Population modelling found that fishing mortality rates between 0.1 and 0.3 resulted in sustainable populations (spawning potential ratios (SPR) >0.30). The population in the unprotected area appeared to be more resilient (SPR > 0.30) at the higher fishing intensities (0.35–0.55). Considered additively, the whole-lake fishery appeared more resilient than when modelled as a single-panmictic stock. These results provided evidence of spatial structuring in reservoir fish populations, and we recommend model assessments used to guide management decisions should consider those spatial differences in other populations where they exist.

  1. Genetic structure of North American wolverine (Gulo gulo) populations.

    PubMed

    Kyle, C J; Strobeck, C

    2001-02-01

    Wolverines (Gulo gulo) are found in low densities throughout their circumpolar distribution. They are also potentially susceptible to human-caused population fragmentation (development, recreation and fur harvesting). The combination of these factors has contributed to this species being listed as having either vulnerable or endangered status across much of its current range. The effects of inherently low densities and anthropogenic pressures on the genetic structure and variation of wolverine populations are, as yet, unknown. In this study, 461 individuals were typed at 12 microsatellite loci to investigate the population genetic structure of wolverines from north-western Alaska to eastern Manitoba. Levels of gene flow and population differentiation among the sampled regions were estimated via a genotype assignment test, pairwise F(ST), and two genetic distance measures. Our results suggest that wolverine populations from southernmost regions, in which anthropogenic factors are strongest, revealed more genetic structuring than did northern populations. Furthermore, these results suggest that reductions in this species' range may have led to population fragmentation in the extreme reaches of its southern distribution. The continued reduction of suitable habitat for this species may lead to more populations becoming isolated remnants of a larger distribution of northern wolverines, as documented in other North American carnivore species.

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

    PubMed Central

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

    2012-01-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients. PMID:22588131

  3. Revealing the full young stellar population in the Carina Nebula, the nearest laboratory of massive star feedback, with VISTA

    NASA Astrophysics Data System (ADS)

    Zeidler, Peter; Preibisch, Thomas; Ratzka, Thorsten; Gaczkowski, Benjamin; Roccatagliata, Veronica

    2013-07-01

    The Carina Nebula (NGC 3372) represents one of the most massive star forming regions in our Galaxy. With a distance of 2.3 kpc, it has the most extreme stellar population within a few kpc of the sun (at least 65 O-type stars). It is our best connection between the nearby star forming regions like the Orion Nebula and the even larger and extremer, but more distant regions like 30 Doradus in the Large Magellanic Cloud. Therefore it is a unique target and our richest nearby laboratory for detailed studies of violent massive star formation and its resulting feedback effects of cloud dispersal and triggered star formation. Our recent Herschel far-infrared survey of the Carina Nebula showed that the cloud complex extends over some 2 × 2.5 deg on the sky. Most of the recent investigations of the Carina Nebula had, however, been focused on the central, ≤ 1 square-degree area of the region, leaving the periphery of the cloud complex poorly studied. In order to solve this problem and to allow a characterization of the young stars throughout the entire extent of the complex, we have used the ESO Visible and Infrared Survey Telescope for Astronomy (VISTA) to map a ˜2 × 3 deg area around the Carina Nebula in the near-infrared J-, H-, Ks bands. Our NIR survey is large enough to cover the full spatial extent of the Carina Nebula complex and is deep enough to detect all young stars down to masses of 0.1 Msun through extinctions of at least Av = 10 mag. We detected in more than ˜ 4 million individual point sources. The data has a typical completeness limit of J ≃ 18, H ≃ 18, and Ks ≃ 17. In combination with a recent Chandra X-ray survey, Spitzer-IRAC, and Herschel observations we have now a sample of data, which reaches from X-ray to the FIR. It will allow us to distinguish between young stars and background contaminating objects and it will allow the identification and characterization of all X-ray selected young stars and the embedded young stellar objects revealed by

  4. Population genetic structure of Aedes albopictus in Penang, Malaysia.

    PubMed

    Zawani, M K N; Abu, H A; Sazaly, A B; Zary, S Y; Darlina, M N

    2014-10-07

    The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.

  5. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control.

  6. The spatial structure of stimuli shapes the timescale of correlations in population spiking activity.

    PubMed

    Litwin-Kumar, Ashok; Chacron, Maurice J; Doiron, Brent

    2012-01-01

    Throughout the central nervous system, the timescale over which pairs of neural spike trains are correlated is shaped by stimulus structure and behavioral context. Such shaping is thought to underlie important changes in the neural code, but the neural circuitry responsible is largely unknown. In this study, we investigate a stimulus-induced shaping of pairwise spike train correlations in the electrosensory system of weakly electric fish. Simultaneous single unit recordings of principal electrosensory cells show that an increase in the spatial extent of stimuli increases correlations at short (≈ 10 ms) timescales while simultaneously reducing correlations at long (≈ 100 ms) timescales. A spiking network model of the first two stages of electrosensory processing replicates this correlation shaping, under the assumptions that spatially broad stimuli both saturate feedforward afferent input and recruit an open-loop inhibitory feedback pathway. Our model predictions are experimentally verified using both the natural heterogeneity of the electrosensory system and pharmacological blockade of descending feedback projections. For weak stimuli, linear response analysis of the spiking network shows that the reduction of long timescale correlation for spatially broad stimuli is similar to correlation cancellation mechanisms previously suggested to be operative in mammalian cortex. The mechanism for correlation shaping supports population-level filtering of irrelevant distractor stimuli, thereby enhancing the population response to relevant prey and conspecific communication inputs.

  7. Stage-Structured Population Dynamics of AEDES AEGYPTI

    NASA Astrophysics Data System (ADS)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

    Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

  8. Effects of structured written feedback by cards on medical students’ performance at Mini Clinical Evaluation Exercise (Mini-CEX) in an outpatient clinic

    PubMed Central

    HAGHANI, FARIBA; HATEF KHORAMI, MOHAMMAD; FAKHARI, MOHAMMAD

    2016-01-01

    Introduction Feedback cards are recommended as a feasible tool for structured written feedback delivery in clinical education while effectiveness of this tool on the medical students’ performance is still questionable.  The purpose of this study was to compare the effects of structured written feedback by cards as well as verbal feedback versus verbal feedback alone on the clinical performance of medical students at the Mini Clinical Evaluation Exercise (Mini-CEX) test in an outpatient clinic. Methods This is a quasi-experimental study with pre- and post-test comprising four groups in two terms of medical students’ externship. The students’ performance was assessed through the Mini-Clinical Evaluation Exercise (Mini-CEX) as a clinical performance evaluation tool. Structured written feedbacks were given to two experimental groups by designed feedback cards as well as verbal feedback, while in the two control groups feedback was delivered verbally as a routine approach in clinical education. Results By consecutive sampling method, 62 externship students were enrolled in this study and seven students were excluded from the final analysis due to their absence for three days. According to the ANOVA analysis and Post Hoc Tukey test,  no statistically significant difference was observed among the four groups at the pre-test, whereas a statistically significant difference was observed between the experimental and control groups at the post-test  (F = 4.023, p =0.012). The effect size of the structured written feedbacks on clinical performance was 0.19. Conclusion Structured written feedback by cards could improve the performance of medical students in a statistical sense. Further studies must be conducted in other clinical courses with longer durations. PMID:27382581

  9. Spatially explicit feedbacks between seagrass meadow structure, sediment and light: Habitat suitability for seagrass growth

    NASA Astrophysics Data System (ADS)

    Carr, Joel A.; D'Odorico, Paolo; McGlathery, Karen J.; Wiberg, Patricia L.

    2016-07-01

    In shallow coastal bays where nutrient loading and riverine inputs are low, turbidity, and the consequent light environment are controlled by resuspension of bed sediments due to wind-waves and tidal currents. High sediment resuspension and low light environments can limit benthic primary productivity; however, both currents and waves are affected by the presence of benthic plants such as seagrass. This feedback between the presence of benthic primary producers such as seagrass and the consequent light environment has been predicted to induce bistable dynamics locally. However, these vegetated areas influence a larger area than they footprint, including a barren adjacent downstream area which exhibits reduced shear stresses. Here we explore through modeling how the patchy structure of seagrass meadows on a landscape may affect sediment resuspension and the consequent light environment due to the presence of this sheltered region. Heterogeneous vegetation covers comprising a mosaic of randomly distributed patches were generated to investigate the effect of patch modified hydrodynamics. Actual cover of vegetation on the landscape was used to facilitate comparisons across landscape realizations. Hourly wave and current shear stresses on the landscape along with suspended sediment concentration and light attenuation characteristics were then calculated and spatially averaged to examine how actual cover and mean water depth affect the bulk sediment and light environment. The results indicate that an effective cover, which incorporates the sheltering area, has important controls on the distributions of shear stress, suspended sediment, light environment, and consequent seagrass habitat suitability. Interestingly, an optimal habitat occurs within a depth range where, if actual cover is reduced past some threshold, the bulk light environment would no longer favor seagrass growth.

  10. Spatially explicit feedbacks between seagrass meadow structure, sediment and light: Habitat suitability for seagrass growth

    USGS Publications Warehouse

    Carr, Joel; D'Odorico, Paul; McGlathery, Karen; Wiberg, Patricia L.

    2016-01-01

    In shallow coastal bays where nutrient loading and riverine inputs are low, turbidity, and the consequent light environment are controlled by resuspension of bed sediments due to wind-waves and tidal currents. High sediment resuspension and low light environments can limit benthic primary productivity; however, both currents and waves are affected by the presence of benthic plants such as seagrass. This feedback between the presence of benthic primary producers such as seagrass and the consequent light environment has been predicted to induce bistable dynamics locally. However, these vegetated areas influence a larger area than they footprint, including a barren adjacent downstream area which exhibits reduced shear stresses. Here we explore through modeling how the patchy structure of seagrass meadows on a landscape may affect sediment resuspension and the consequent light environment due to the presence of this sheltered region. Heterogeneous vegetation covers comprising a mosaic of randomly distributed patches were generated to investigate the effect of patch modified hydrodynamics. Actual cover of vegetation on the landscape was used to facilitate comparisons across landscape realizations. Hourly wave and current shear stresses on the landscape along with suspended sediment concentration and light attenuation characteristics were then calculated and spatially averaged to examine how actual cover and mean water depth affect the bulk sediment and light environment. The results indicate that an effective cover, which incorporates the sheltering area, has important controls on the distributions of shear stress, suspended sediment, light environment, and consequent seagrass habitat suitability. Interestingly, an optimal habitat occurs within a depth range where, if actual cover is reduced past some threshold, the bulk light environment would no longer favor seagrass growth.

  11. Mini-max feedback control as a computational theory of sensorimotor control in the presence of structural uncertainty

    PubMed Central

    Ueyama, Yuki

    2014-01-01

    We propose a mini-max feedback control (MMFC) model as a robust approach to human motor control under conditions of uncertain dynamics, such as structural uncertainty. The MMFC model is an expansion of the optimal feedback control (OFC) model. According to this scheme, motor commands are generated to minimize the maximal cost, based on an assumption of worst-case uncertainty, characterized by familiarity with novel dynamics. We simulated linear dynamic systems with different types of force fields–stable and unstable dynamics–and compared the performance of MMFC to that of OFC. MMFC delivered better performance than OFC in terms of stability and the achievement of tasks. Moreover, the gain in positional feedback with the MMFC model in the unstable dynamics was tuned to the direction of instability. It is assumed that the shape modulations of the gain in positional feedback in unstable dynamics played the same role as that played by end-point stiffness observed in human studies. Accordingly, we suggest that MMFC is a plausible model that predicts motor behavior under conditions of uncertain dynamics. PMID:25309415

  12. Integrated Flight/Structural Mode Control for Very Flexible Aircraft Using L1 Adaptive Output Feedback Controller

    NASA Technical Reports Server (NTRS)

    Che, Jiaxing; Cao, Chengyu; Gregory, Irene M.

    2012-01-01

    This paper explores application of adaptive control architecture to a light, high-aspect ratio, flexible aircraft configuration that exhibits strong rigid body/flexible mode coupling. Specifically, an L(sub 1) adaptive output feedback controller is developed for a semi-span wind tunnel model capable of motion. The wind tunnel mount allows the semi-span model to translate vertically and pitch at the wing root, resulting in better simulation of an aircraft s rigid body motion. The control objective is to design a pitch control with altitude hold while suppressing body freedom flutter. The controller is an output feedback nominal controller (LQG) augmented by an L(sub 1) adaptive loop. A modification to the L(sub 1) output feedback is proposed to make it more suitable for flexible structures. The new control law relaxes the required bounds on the unmatched uncertainty and allows dependence on the state as well as time, i.e. a more general unmatched nonlinearity. The paper presents controller development and simulated performance responses. Simulation is conducted by using full state flexible wing models derived from test data at 10 different dynamic pressure conditions. An L(sub 1) adaptive output feedback controller is designed for a single test point and is then applied to all the test cases. The simulation results show that the L(sub 1) augmented controller can stabilize and meet the performance requirements for all 10 test conditions ranging from 30 psf to 130 psf dynamic pressure.

  13. Population genetic structure of mussels from the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Bulnheim, H.-P.; Gosling, E.

    1988-03-01

    In a macrogeographic survey, the population genetic structure of mussels from various regions of the Baltic Sea, a large semi-enclosed brackish-water basin, was examined with reference to Mytilus edulis and M. galloprovincialis samples from the North Sea, Irish coast and southern Portugal. Electrophoretically detectable variation was analysed at 6 polymorphic enzyme loci ( Ap, Est-D, Lap-2, Odh, Pgi and Pgm). Evidence was provided of a remarkably large amount of biochemical genetic differentiation among ecologically and morphologically divergent mussel populations in the Baltic. Patterns of allele frequencies in low-salinity populations from the area of the Baltic Proper were demonstrated to be widely homogeneous but contrast strongly with those of the western Baltic, the latter resembling populations from marine habitats of the North Sea. Associated with a pronounced salinity gradient, the spatial heterogeneity in gene-pool structure is indicated by steep clines of allele frequency changes in the area of the eastern Danish isles. The adaptive significance of the observed allozymic variation is suggested. From genetic distance estimates, the subdivision of population structure is discussed in relation to the significant amount of differentiation detected within Mytilus populations to date and to the evolutionary time required for the divergence of Baltic mussel populations. The allozymic data provide evidence for the genetic distinctiveness of mussels from the low-salinity areas of the Baltic. Their position at the specific or subspecific level of classification requires further consideration.

  14. Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.

    PubMed

    Pérez-Espona, S; Pérez-Barbería, F J; Goodall-Copestake, W P; Jiggins, C D; Gordon, I J; Pemberton, J M

    2009-02-01

    The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.

  15. Comparative population structure of cavity-nesting sea ducks

    USGS Publications Warehouse

    Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

    2014-01-01

    A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

  16. [Analysis on age structure and dynamics of Kindonia uniflora populations].

    PubMed

    Zhang, Wenhui; Li, Jingxia; Li, Hong; Liu, Xiangjun

    2004-04-01

    Kindonia uniflora is a perennial clone herbaceous plant, and also, a native endangered plant in China. This paper studied its age structure, life table and survivorship curve in different habitats in Taibai mountain area. The results indicated that the age structure and dynamics of K. uniflora populations in the Betula utilis forest at altitude 2500-2700 m, in the Abies fargesii forest at altitude 2700-2900 m, and in the Larix chinensis forest at altitude 2900-3100 m had the similar pattern and developing tendency. The number of younger ramets at 1-2 years old or older than 5 years was less, and the number of ramets at 3-5 years old was the highest in the age structures. The negative values of dx (dead number), qx (mortality rate) and Kx (Killing rate) in the life table showed the increasing rate of the population sizes during the age stage. The survivorship curve of K. uniflora populations in different habitats belonged to Deevey C after 3-5 years old. The mortality rate of populations during 5-10 years stage was higher, and was stable after 10 years old. As for the characters of asexual propagation and clone growth, the rhizomes of the populations were in humus of soil, and developed and expanded as guerilla line style. During growth season, only one leaf grew above ground at every inter-node, and the population growth and development were rarely influenced by external factors. The forest communities, such as Betula utilis, Abies fargesii and Larix chinensis forest, in which K. uniflora populations lived, were at middle or higher mountain, where there were rarely disturbance from human being. Therefore, the habitats for K. uniflora populations to live were relatively stable. As the altitude increased, the disturbances from human being became less, the density of K. uniflora populations increased, the life cycle expanded, the peak of population death delayed, and the population living strategy changed to adapt to the habitats. K. uniflora populations preferred to

  17. Population genetic structure of a colonising, triploid weed, Hieracium lepidulum.

    PubMed

    Chapman, H; Robson, B; Pearson, M L

    2004-03-01

    Understanding the breeding system and population genetic structure of invasive weed species is important for biocontrol, and contributes to our understanding of the evolutionary processes associated with invasions. Hieracium lepidulum is an invasive weed in New Zealand, colonising a diverse range of habitats including native Nothofagus forest, pine plantations, scrubland and tussock grassland. It is competing with native subalpine and alpine grassland and herbfield vegetation. H. lepidulum is a triploid, diplosporous apomict, so theoretically all seed is clonal, and there is limited potential for the creation of variation through recombination. We used intersimple sequence repeats (ISSRs) to determine the population genetic structure of New Zealand populations of H. lepidulum. ISSR analysis of five populations from two regions in the South Island demonstrated high intrapopulation genotypic diversity, and high interpopulation genetic structuring; PhiST = 0.54 over all five populations. No private alleles were found in any of the five populations, and allelic differentiation was correlated to geographic distance. Cladistic compatibility analysis indicated that both recombination and mutation were important in the creation of genotypic diversity. Our data will contribute to any biocontrol program developed for H. lepidulum. It will also be a baseline data set for future comparisons of genetic structure during the course of H. lepidulum invasions.

  18. Fine-scale population structure, inbreeding risk and avoidance in a wild insect population.

    PubMed

    Bretman, Amanda; Rodríguez-Muñoz, Rolando; Walling, Craig; Slate, Jon; Tregenza, Tom

    2011-07-01

    The ecological and evolutionary importance of fine-scale genetic structure within populations is increasingly appreciated. However, available data are largely restricted to wild vertebrates and eusocial insects. In addition, there is the expectation that most insects tend to have such large- and high-density populations and are so mobile that they are unlikely to face inbreeding risks through fine-scale population structuring. This has made the growing body of evidence for inbreeding avoidance in insects and its implication in mating systems evolution somewhat enigmatic. We present a 4-year study of a natural population of field crickets. Using detailed video monitoring combined with genotyping, we track the movement of all adults within the population and investigate genetic structure at a fine scale. We find some evidence for relatives being found in closer proximity, both across generations and within a single breeding season. Whilst incestuous matings are not avoided, population inbreeding is low, suggesting that mating is close to random and the limited fine-scale structure does not create significant inbreeding risk. Hence, there is little evidence for selective pressures associated with the evolution of inbreeding avoidance mechanisms in a closely related species.

  19. River mainstem thermal regimes influence population structuring within an Appalachian brook trout population

    USGS Publications Warehouse

    Aunins, Aaron W.; Petty, J. Todd; King, Timothy L.; Schilz, Mariya; Mazik, Patricia M.

    2015-01-01

    Brook trout (Salvelinus fontinalis) often exist as highly differentiated populations, even at small spatial scales, due either to natural or anthropogenic sources of isolation and low rates of dispersal. In this study, we used molecular approaches to describe the unique population structure of brook trout inhabiting the Shavers Fork watershed, located in eastern West Virginia, and contrast it to nearby populations in tributaries of the upper Greenbrier River and North Fork South Branch Potomac Rivers. Bayesian and maximum likelihood clustering methods identified minimal population structuring among 14 collections of brook trout from throughout the mainstem and tributaries of Shavers Fork, highlighting the role of the cold-water mainstem for connectivity and high rates of effective migration among tributaries. In contrast, the Potomac and Greenbrier River collections displayed distinct levels of population differentiation among tributaries, presumably resulting from tributary isolation by warm-water mainstems. Our results highlight the importance of protecting and restoring cold-water mainstem habitats as part of region-wide brook trout conservation efforts. In addition, our results from Shavers Fork provide a contrast to previous genetic studies that characterize Appalachian brook trout as fragmented isolates rather than well-mixed populations. Additional study is needed to determine whether the existence of brook trout as genetically similar populations among tributaries is truly unique and whether connectivity among brook trout populations can potentially be restored within other central Appalachian watersheds.

  20. Evaluating Effectiveness of Modeling Motion System Feedback in the Enhanced Hess Structural Model of the Human Operator

    NASA Technical Reports Server (NTRS)

    Zaychik, Kirill; Cardullo, Frank; George, Gary; Kelly, Lon C.

    2009-01-01

    In order to use the Hess Structural Model to predict the need for certain cueing systems, George and Cardullo significantly expanded it by adding motion feedback to the model and incorporating models of the motion system dynamics, motion cueing algorithm and a vestibular system. This paper proposes a methodology to evaluate effectiveness of these innovations by performing a comparison analysis of the model performance with and without the expanded motion feedback. The proposed methodology is composed of two stages. The first stage involves fine-tuning parameters of the original Hess structural model in order to match the actual control behavior recorded during the experiments at NASA Visual Motion Simulator (VMS) facility. The parameter tuning procedure utilizes a new automated parameter identification technique, which was developed at the Man-Machine Systems Lab at SUNY Binghamton. In the second stage of the proposed methodology, an expanded motion feedback is added to the structural model. The resulting performance of the model is then compared to that of the original one. As proposed by Hess, metrics to evaluate the performance of the models include comparison against the crossover models standards imposed on the crossover frequency and phase margin of the overall man-machine system. Preliminary results indicate the advantage of having the model of the motion system and motion cueing incorporated into the model of the human operator. It is also demonstrated that the crossover frequency and the phase margin of the expanded model are well within the limits imposed by the crossover model.

  1. Universality of fixation probabilities in randomly structured populations.

    PubMed

    Adlam, Ben; Nowak, Martin A

    2014-10-27

    The stage of evolution is the population of reproducing individuals. The structure of the population is known to affect the dynamics and outcome of evolutionary processes, but analytical results for generic random structures have been lacking. The most general result so far, the isothermal theorem, assumes the propensity for change in each position is exactly the same, but realistic biological structures are always subject to variation and noise. We consider a finite population under constant selection whose structure is given by a variety of weighted, directed, random graphs; vertices represent individuals and edges interactions between individuals. By establishing a robustness result for the isothermal theorem and using large deviation estimates to understand the typical structure of random graphs, we prove that for a generalization of the Erdős-Rényi model, the fixation probability of an invading mutant is approximately the same as that of a mutant of equal fitness in a well-mixed population with high probability. Simulations of perturbed lattices, small-world networks, and scale-free networks behave similarly. We conjecture that the fixation probability in a well-mixed population, (1 - r(-1))/(1 - r(-n)), is universal: for many random graph models, the fixation probability approaches the above function uniformly as the graphs become large.

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

    PubMed Central

    2009-01-01

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

  3. Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming

    USGS Publications Warehouse

    Underwood, Zachary E.; Mandeville, Elizabeth G.; Walters, Annika W.

    2016-01-01

    Burbot (Lota lota) occur in the Wind River Basin in central Wyoming, USA, at the southwestern extreme of the species’ native range in North America. The most stable and successful of these populations occur in six glacially carved mountain lakes on three different tributary streams and one large main stem impoundment (Boysen Reservoir) downstream from the tributary populations. Burbot are rarely found in connecting streams and rivers, which are relatively small and high gradient, with a variety of potential barriers to upstream movement of fish. We used high-throughput genomic sequence data for 11,197 SNPs to characterize the genetic diversity, population structure, and connectivity among burbot populations on the Wind River system. Fish from Boysen Reservoir and lower basin tributary populations were genetically differentiated from those in the upper basin tributary populations. In addition, fish within the same tributary streams fell within the same genetic clusters, suggesting there is movement of fish between lakes on the same tributaries but that populations within each tributary system are isolated and genetically distinct from other populations. Observed genetic differentiation corresponded to natural and anthropogenic barriers, highlighting the importance of barriers to fish population connectivity and gene flow in human-altered linked lake-stream habitats.

  4. Feedback & Objectives

    ERIC Educational Resources Information Center

    Butterworth, James R.

    1975-01-01

    Industrial objectives, if they are employee oriented, produce feedback, and the motivation derived from the feedback helps reduce turnover. Feedback is the power to clarify objectives, to stimulate communication, and to motivate people. (Author/MW)

  5. Correlations in the population structure of music, genes and language.

    PubMed

    Brown, Steven; Savage, Patrick E; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A

    2014-01-07

    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers.

  6. Correlations in the population structure of music, genes and language

    PubMed Central

    Brown, Steven; Savage, Patrick E.; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A.

    2014-01-01

    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers. PMID:24225453

  7. Modeling structured population dynamics using data from unmarked individuals

    USGS Publications Warehouse

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  8. Genetic diversity and population structure of cucumber (Cucumis sativus L.).

    PubMed

    Lv, Jing; Qi, Jianjian; Shi, Qiuxiang; Shen, Di; Zhang, Shengping; Shao, Guangjin; Li, Hang; Sun, Zhanyong; Weng, Yiqun; Shang, Yi; Gu, Xingfang; Li, Xixiang; Zhu, Xiaoguo; Zhang, Jinzhe; van Treuren, Robbert; van Dooijeweert, Willem; Zhang, Zhonghua; Huang, Sanwen

    2012-01-01

    Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

  9. Genotypic structure of a Drosophila population for adult locomotor activity

    SciTech Connect

    Grechanyi, G.V.; Korzun, V.M.

    1995-01-01

    Analysis of the variation of adult locomotor activity in four samples taken at different times from a natural population of Drosophila melanogaster showed that the total variation of this trait is relatively stable in time and has a substantial genetic component. Genotypic structure of the population for locomotor activity is characterized by the presence of large groups of genotypes with high and low values of this trait. A possible explanation for the presence of such groups in a population is cyclic density-dependent selection.

  10. Age-structured optimal control in population economics.

    PubMed

    Feichtinger, Gustav; Prskawetz, Alexia; Veliov, Vladimir M

    2004-06-01

    This paper brings both intertemporal and age-dependent features to a theory of population policy at the macro-level. A Lotka-type renewal model of population dynamics is combined with a Solow/Ramsey economy. We consider a social planner who maximizes an aggregate intertemporal utility function which depends on per capita consumption. As control policies we consider migration and saving rate (both age-dependent). By using a new maximum principle for age-structured control systems we derive meaningful results for the optimal migration and saving rate in an aging population. The model used in the numerical calculations is calibrated for Austria.

  11. Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini

    PubMed Central

    BARRETT, LUKE G.; THRALL, PETER H.; BURDON, JEREMY J.; NICOTRA, ADRIENNE B.; LINDE, CELESTE C.

    2009-01-01

    Many pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale, using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini. PMID:18573166

  12. Recombination Hotspots and Population Structure in Plasmodium falciparum

    PubMed Central

    Mu, Jianbing; Duan, Junhui; McGee, Kate M; Joy, Deirdre A; McVean, Gilean A. T

    2005-01-01

    Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously. The parasites are clustered according to continental origin, but alternative groupings were obtained using SNPs at 37 putative transporter genes that are potentially under selection. Geographic isolation and highly variable multiple infection rates are the major factors affecting haplotype structure. Variation in effective recombination rates is high, both among populations and along the chromosome, with recombination hotspots conserved among populations at chromosome ends. This study supports the feasibility of genome-wide association studies in some parasite populations. PMID:16144426

  13. Approximation techniques for parameter estimation and feedback control for distributed models of large flexible structures

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Rosen, I. G.

    1984-01-01

    Approximation ideas are discussed that can be used in parameter estimation and feedback control for Euler-Bernoulli models of elastic systems. Focusing on parameter estimation problems, ways by which one can obtain convergence results for cubic spline based schemes for hybrid models involving an elastic cantilevered beam with tip mass and base acceleration are outlined. Sample numerical findings are also presented.

  14. Variable structure control of linear time invariant fractional order systems using a finite number of state feedback law

    NASA Astrophysics Data System (ADS)

    Balochian, Saeed; Sedigh, Ali Khaki; Zare, Asef

    2011-03-01

    In this paper, an approach based on the variable structure control is proposed for stabilization of linear time invariant fractional order systems (LTI-FOS) using a finite number of available state feedback controls, none of which is capable of stabilizing the LTI-FOS by itself. First, a system with integer order derivatives is defined and its existence is proved, which has stability equivalent properties with respect to the fractional system. This makes it possible to use Lyapunov function and convex analysis in order to define the sliding sector and develop a variable structure control which enables the switching between available control gains and stabilizing the fractional order system.

  15. Population models for passerine birds: structure, parameterization, and analysis

    USGS Publications Warehouse

    Noon, B.R.; Sauer, J.R.; McCullough, D.R.; Barrett, R.H.

    1992-01-01

    Population models have great potential as management tools, as they use infonnation about the life history of a species to summarize estimates of fecundity and survival into a description of population change. Models provide a framework for projecting future populations, determining the effects of management decisions on future population dynamics, evaluating extinction probabilities, and addressing a variety of questions of ecological and evolutionary interest. Even when insufficient information exists to allow complete identification of the model, the modelling procedure is useful because it forces the investigator to consider the life history of the species when determining what parameters should be estimated from field studies and provides a context for evaluating the relative importance of demographic parameters. Models have been little used in the study of the population dynamics of passerine birds because of: (1) widespread misunderstandings of the model structures and parameterizations, (2) a lack of knowledge of life histories of many species, (3) difficulties in obtaining statistically reliable estimates of demographic parameters for most passerine species, and (4) confusion about functional relationships among demographic parameters. As a result, studies of passerine demography are often designed inappropriately and fail to provide essential data. We review appropriate models for passerine bird populations and illustrate their possible uses in evaluating the effects of management or other environmental influences on population dynamics. We identify environmental influences on population dynamics. We identify parameters that must be estimated from field data, briefly review existing statistical methods for obtaining valid estimates, and evaluate the present status of knowledge of these parameters.

  16. Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations.

    PubMed

    Walker, C W; Vilà, C; Landa, A; Lindén, M; Ellegren, H

    2001-01-01

    Wolverine (Gulo gulo) numbers in Scandinavia were significantly reduced during the early part of the century as a result of predator removal programmes and hunting. Protective legislation in both Sweden and Norway in the 1960s and 1970s has now resulted in increased wolverine densities in Scandinavia. We report here the development of 15 polymorphic microsatellite markers in wolverine and their use to examine the population sub-structure and genetic variability in free-ranging Scandinavian wolverine populations as well as in a sample of individuals collected before 1970. Significant subdivision between extant populations was discovered, in particular for the small and isolated population of southern Norway, which represents a recent recolonization. Overall genetic variability was found to be lower than previously reported for other mustelids, with only two to five alleles per locus and observed heterozygosities (H(O)) ranging from 0.269 to 0.376 across the examined populations, being lowest in southern Norway. Analysis of the mitochondrial DNA control region revealed no variation throughout the surveyed populations. As the historical sample did not show higher levels of genetic variability, our results are consistent with a reduction in the genetic variation in Scandinavian wolverines that pre-dates the demographic bottleneck observed during the last century. The observed subdivision between populations calls for management caution when issuing harvest quotas, especially for the geographically isolated south Norwegian population.

  17. Ethnicity and Population Structure in Personal Naming Networks

    PubMed Central

    Mateos, Pablo; Longley, Paul A.; O'Sullivan, David

    2011-01-01

    Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how ‘naming networks’, constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply ‘emerge’ from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new

  18. Structure of the New England herring gull population

    USGS Publications Warehouse

    Kadlec, J.A.; Drury, W.H.

    1968-01-01

    Measurements of the rates of population increase, reproduction, and mortality together with an observed age ratio, were used to analyze the population of the Herring Gull in New England. Data from sporadic censuses prior to this study, aerial censuses by the authors, and National Audubon Society Christmas Bird Count indicated that the New England breeding population has been doubling every 12 to 15 years since the early 1900's. This increase has involved founding new colonies and expanding the breeding range There is evidence that 15 to 30% of the adults do not breed in any given year. Sixty-one productivity measurements on 43 islands from 1963 through 1966, involving almost 13,000 nests, showed that from 0.8 to 1.4 young/breeding pair/year is the usual range of rate of production. The age distribution in the population was determined by classifying Herring Gulls by plumage category on an aerial census of the coast from Tampico, Mexico, to Cape Sable, Nova Scotia. Of the 622,000 gulls observed, 68% were adults, 17% were second- and third-year birds, and 15% were first-year birds. Mortality rates derived from band recovery data were too high to be consistent with the observed rate of population growth, productivity, and age structure. Loss of bands increasing to the rate of about 20%/year 5 years after banding eliminates most of the discrepancy. The age structure and rate of population increase indicate a mortality rate of 4 to 9% for gulls 2 years old or older, compared with the 25 to 30% indicated by band recoveries. The population structure we have developed fits everything we have observed about Herring Gull population dynamics, except mortality based on band recoveries.

  19. Ethnicity and population structure in personal naming networks.

    PubMed

    Mateos, Pablo; Longley, Paul A; O'Sullivan, David

    2011-01-01

    Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how 'naming networks', constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply 'emerge' from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new

  20. The genetic structure of a relict population of wood frogs

    USGS Publications Warehouse

    Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

    2012-01-01

    Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

  1. Genetic structure of the world's polar bear populations

    USGS Publications Warehouse

    Paetkau, David; Amstrup, Steven C.; Born, E.W.; Calvert, W.; Derocher, A.E.; Garner, G.W.; Messier, F.; Stirling, I.; Taylor, M.K.; Wiig, O.; Strobeck, C.

    1999-01-01

    We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

  2. The relationship between Baylisascaris procyonis prevalence and raccoon population structure.

    PubMed

    Page, L Kristen; Gehrt, Stanley D; Cascione, Andrea; Kellner, Kenneth F

    2009-12-01

    Parasite transmission is a dynamic process that can be affected by factors including host and parasite population dynamics. Raccoons ( Procyon lotor ) are the definitive host of Baylisascaris procyonis , an intestinal roundworm. Transmission of this parasite has been linked to raccoon behavior and human land-use patterns; however, we do not know the importance of host population structure. Therefore, the objective of this study was to determine the relationship between raccoon population attributes and prevalence of B. procyonis. We necropsied 307 trapped or road-killed raccoons collected during 2000-2006 from the Chicago area. In addition, we examined, via fecal samples (n  =  433), the patterns of B. procyonis prevalence as they relate to population dynamics among 3 subpopulations within the larger study. Baylisascaris procyonis was seen in 39% of 307 necropsied raccoons. There were differences in prevalence as a function of host age and sex. Baylisascaris procyonis was observed in 18% of 433 fecal samples obtained from live-trapped raccoons, and there were differences according to age, but not by sex. We found that the host populations consistently differed in density across study areas, but were similar regarding sex and age structure. Differences in host density were associated with differences in prevalence, suggesting that possible differences between populations, as well as ecological differences in sites and raccoon behavior, may have influenced parasite prevalence.

  3. Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters.

    PubMed

    Yoon, M; Park, W; Nam, Y K; Kim, D S

    2012-02-01

    Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

  4. Origin, genetic diversity, and population structure of Chinese domestic sheep.

    PubMed

    Chen, Shan-Yuan; Duan, Zi-Yuan; Sha, Tao; Xiangyu, Jinggong; Wu, Shi-Fang; Zhang, Ya-Ping

    2006-07-19

    To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.

  5. Population genetic analysis and sub-structuring in Babesia bovis.

    PubMed

    Simuunza, Martin; Bilgic, Huseyin; Karagenc, Tulin; Syakalima, Michelo; Shiels, Brian; Tait, Andy; Weir, William

    2011-06-01

    The tick-borne protozoan parasite, Babesia bovis is one of the causes of bovine babesiosis, an economically important disease of cattle in tropical and sub-tropical countries. Using the recently published genome sequence of the parasite, we developed a panel of eight mini- and micro-satellite markers and used these to investigate the role of genetic exchange in the population structure and diversity of the parasite using isolates from Zambia and Turkey. This population genetic analysis showed that genetic exchange occurs and that there are high levels of genetic diversity, with geographical sub-structuring quantified using Wright's F Index. Linkage disequilibrium was observed when isolates from both countries were treated as one population, but when isolates from Zambia were analysed separately linkage equilibrium was observed. The Turkish isolates were sub-structured, containing two genetically distinct sub-groups, both of which appeared to be in linkage equilibrium. The results of the Zambian study suggest that a sub-set of the parasite population is responsible for the westward spread of babesiosis into the previously disease-free central region of the country. The Zambian isolates had a significantly higher number of genotypes per sample than those from Turkey and age was found to be a significant predictor of the multiplicity of infection. The high levels of diversity seen in the Zambian and Turkish B. bovis populations have implications in the development of subunit vaccines against the disease and the spread of drug resistance.

  6. Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

    PubMed Central

    Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

    2014-01-01

    Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

  7. Evolutionary snowdrift game incorporating costly punishment in structured populations

    NASA Astrophysics Data System (ADS)

    Chan, Nat W. H.; Xu, C.; Tey, Siew Kian; Yap, Yee Jiun; Hui, P. M.

    2013-01-01

    The role of punishment and the effects of a structured population in promoting cooperation are important issues. Within a recent model of snowdrift game (SG) incorporating a costly punishing strategy (P), we study the effects of a population connected through a square lattice. The punishers, who carry basically a cooperative (C) character, are willing to pay a cost α so as to punish a non-cooperative (D) opponent by β. Depending on α, β, the cost-to-benefit ratio r in SG, and the initial conditions, the system evolves into different phases that could be homogeneous or inhomogeneous. The spatial structure imposes geometrical constraint on how one agent is affected by neighboring agents. Results of extensive numerical simulations, both for the steady state and the dynamics, are presented. Possible phases are identified and discussed, and isolated phases in the r-β space are identified as special local structures of strategies that are stable due to the lattice structure. In contrast to a well-mixed population where punishers are suppressed due to the cost of punishment, the altruistic punishing strategy can flourish and prevail for appropriate values of the parameters, implying an enhancement in cooperation by imposing punishments in a structured population. The system could evolve to a phase corresponding to the coexistence of C, D, and P strategies at some particular payoff parameters, and such a phase is absent in a well-mixed population. The pair approximation, a commonly used analytic approach, is extended from a two-strategy system to a three-strategy system. We show that the pair approximation can, at best, capture the numerical results only qualitatively. Due to the improper way of including spatial correlation imposed by the lattice structure, the approximation does not give the frequencies of C, D, and P accurately and fails to give the homogeneous AllD and AllP phases.

  8. Population structure of barley landrace populations and gene-flow with modern varieties.

    PubMed

    Bellucci, Elisa; Bitocchi, Elena; Rau, Domenico; Nanni, Laura; Ferradini, Nicoletta; Giardini, Alessandro; Rodriguez, Monica; Attene, Giovanna; Papa, Roberto

    2013-01-01

    Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.

  9. Fundamental population-productivity relationships can be modified through density-dependent feedbacks of life-history evolution.

    PubMed

    Kuparinen, Anna; Stenseth, Nils Christian; Hutchings, Jeffrey A

    2014-12-01

    The evolution of life histories over contemporary time scales will almost certainly affect population demography. One important pathway for such eco-evolutionary interactions is the density-dependent regulation of population dynamics. Here, we investigate how fisheries-induced evolution (FIE) might alter density-dependent population-productivity relationships. To this end, we simulate the eco-evolutionary dynamics of an Atlantic cod (Gadus morhua) population under fishing, followed by a period of recovery in the absence of fishing. FIE is associated with increases in juvenile production, the ratio of juveniles to mature population biomass, and the ratio of the mature population biomass relative to the total population biomass. In contrast, net reproductive rate (R 0 ) and per capita population growth rate (r) decline concomitantly with evolution. Our findings suggest that FIE can substantially modify the fundamental population-productivity relationships that underlie density-dependent population regulation and that form the primary population-dynamical basis for fisheries stock-assessment projections. From a conservation and fisheries-rebuilding perspective, we find that FIE reduces R 0 and r, the two fundamental correlates of population recovery ability and inversely extinction probability.

  10. Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.

    PubMed

    Hodoğlugil, Uğur; Mahley, Robert W

    2012-03-01

    Turkey has experienced major population movements. Population structure and genetic relatedness of samples from three regions of Turkey, using over 500,000 SNP genotypes, were compared together with Human Genome Diversity Panel (HGDP) data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analysed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K=3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42-49), 40% European (95% CI, 36-44) and 15% Central Asian (95% CI, 13-16), whereas at K=4 the genetic ancestry of the Turks was 38% European (95% CI, 35-42), 35% Middle Eastern (95% CI, 33-38), 18% South Asian (95% CI, 16-19) and 9% Central Asian (95% CI, 7-11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul and Kayseri) were superimposed, without clear subpopulation structure, suggesting sample homogeneity. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns.

  11. Genetic population structure in the yellow mongoose, Cynictis penicillata.

    PubMed

    Van Vuuren, B J; Robinson, T J

    1997-12-01

    Phylogeographic structure was determined for the yellow mongoose, Cynictis penicillata, using mtDNA RFLPs and control region sequences. The RFLP analysis revealed 13 haplotypes which showed weak geographical patterning consistent with a recent range expansion from a refugial population(s). An analysis of molecular variance (AMOVA) revealed no correspondence between mtDNA phylogeography and subspecies delimitation, nor between matrilines and areas characterized by a high incidence of the viverrid-type rabies, of which the yellow mongoose is the principal vector. The lack of structure was also shown by control region sequences although four of the maternal lineages shared a near-perfect 81 bp repeat. We speculate that regional hot spots of the viverrid rabies biotype reflect population density differences in the yellow mongoose that are not underscored by genetic partitioning, at least at the level of resolution provided by our analyses.

  12. Host Mobility Drives Pathogen Competition in Spatially Structured Populations

    PubMed Central

    Poletto, Chiara; Meloni, Sandro; Colizza, Vittoria; Moreno, Yamir; Vespignani, Alessandro

    2013-01-01

    Interactions among multiple infectious agents are increasingly recognized as a fundamental issue in the understanding of key questions in public health regarding pathogen emergence, maintenance, and evolution. The full description of host-multipathogen systems is, however, challenged by the multiplicity of factors affecting the interaction dynamics and the resulting competition that may occur at different scales, from the within-host scale to the spatial structure and mobility of the host population. Here we study the dynamics of two competing pathogens in a structured host population and assess the impact of the mobility pattern of hosts on the pathogen competition. We model the spatial structure of the host population in terms of a metapopulation network and focus on two strains imported locally in the system and having the same transmission potential but different infectious periods. We find different scenarios leading to competitive success of either one of the strain or to the codominance of both strains in the system. The dominance of the strain characterized by the shorter or longer infectious period depends exclusively on the structure of the population and on the the mobility of hosts across patches. The proposed modeling framework allows the integration of other relevant epidemiological, environmental and demographic factors, opening the path to further mathematical and computational studies of the dynamics of multipathogen systems. PMID:23966843

  13. Population structure and cultural geography of a folktale in Europe.

    PubMed

    Ross, Robert M; Greenhill, Simon J; Atkinson, Quentin D

    2013-04-07

    Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture.

  14. Evolutionary dynamics for persistent cooperation in structured populations

    NASA Astrophysics Data System (ADS)

    Li, Yan; Liu, Xinsheng; Claussen, Jens Christian; Guo, Wanlin

    2015-06-01

    The emergence and maintenance of cooperative behavior is a fascinating topic in evolutionary biology and social science. The public goods game (PGG) is a paradigm for exploring cooperative behavior. In PGG, the total resulting payoff is divided equally among all participants. This feature still leads to the dominance of defection without substantially magnifying the public good by a multiplying factor. Much effort has been made to explain the evolution of cooperative strategies, including a recent model in which only a portion of the total benefit is shared by all the players through introducing a new strategy named persistent cooperation. A persistent cooperator is a contributor who is willing to pay a second cost to retrieve the remaining portion of the payoff contributed by themselves. In a previous study, this model was analyzed in the framework of well-mixed populations. This paper focuses on discussing the persistent cooperation in lattice-structured populations. The evolutionary dynamics of the structured populations consisting of three types of competing players (pure cooperators, defectors, and persistent cooperators) are revealed by theoretical analysis and numerical simulations. In particular, the approximate expressions of fixation probabilities for strategies are derived on one-dimensional lattices. The phase diagrams of stationary states, and the evolution of frequencies and spatial patterns for strategies are illustrated on both one-dimensional and square lattices by simulations. Our results are consistent with the general observation that, at least in most situations, a structured population facilitates the evolution of cooperation. Specifically, here we find that the existence of persistent cooperators greatly suppresses the spreading of defectors under more relaxed conditions in structured populations compared to that obtained in well-mixed populations.

  15. Population Structure Shapes Copy Number Variation in Malaria Parasites

    PubMed Central

    Cheeseman, Ian H.; Miller, Becky; Tan, John C.; Tan, Asako; Nair, Shalini; Nkhoma, Standwell C.; De Donato, Marcos; Rodulfo, Hectorina; Dondorp, Arjen; Branch, Oralee H.; Mesia, Lastenia Ruiz; Newton, Paul; Mayxay, Mayfong; Amambua-Ngwa, Alfred; Conway, David J.; Nosten, François; Ferdig, Michael T.; Anderson, Tim J. C.

    2016-01-01

    If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen. PMID:26613787

  16. Population Structure Shapes Copy Number Variation in Malaria Parasites.

    PubMed

    Cheeseman, Ian H; Miller, Becky; Tan, John C; Tan, Asako; Nair, Shalini; Nkhoma, Standwell C; De Donato, Marcos; Rodulfo, Hectorina; Dondorp, Arjen; Branch, Oralee H; Mesia, Lastenia Ruiz; Newton, Paul; Mayxay, Mayfong; Amambua-Ngwa, Alfred; Conway, David J; Nosten, François; Ferdig, Michael T; Anderson, Tim J C

    2016-03-01

    If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.

  17. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa.

    PubMed

    Khanyile, Khulekani S; Dzomba, Edgar F; Muchadeyi, Farai C

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  18. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    PubMed Central

    Khanyile, Khulekani S.; Dzomba, Edgar F.; Muchadeyi, Farai C.

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  19. Structural basis of biopterin-induced inhibition of GTP cyclohydrolase I by GFRP, its feedback regulatory protein.

    PubMed

    Maita, Nobuo; Hatakeyama, Kazuyuki; Okada, Kengo; Hakoshima, Toshio

    2004-12-03

    GTP cyclohydrolase I (GTPCHI) is the rate-limiting enzyme involved in the biosynthesis of tetrahydrobiopterin, a key cofactor necessary for nitric oxide synthase and for the hydroxylases that are involved in the production of catecholamines and serotonin. In animals, the GTPCHI feedback regulatory protein (GFRP) binds GTPCHI to mediate feed-forward activation of GTPCHI activity in the presence of phenylalanine, whereas it induces feedback inhibition of enzyme activity in the presence of biopterin. Here, we have reported the crystal structure of the biopterin-induced inhibitory complex of GTPCHI and GFRP and compared it with the previously reported phenylalanine-induced stimulatory complex. The structure reveals five biopterin molecules located at each interface between GTPCHI and GFRP. Induced fitting structural changes by the biopterin binding expand large conformational changes in GTPCHI peptide segments forming the active site, resulting in inhibition of the activity. By locating 3,4-dihydroxy-phenylalanine-responsive dystonia mutations in the complex structure, we found mutations that may possibly disturb the GFRP-mediated regulation of GTPCHI.

  20. Expert Group Meeting on Population Growth and Demographic Structure.

    PubMed

    1993-01-01

    As part of the preparation for the forth-coming UN International Conference on Population and Development, an expert group met in Paris, France, in November 1992 to discuss population growth and demographic structure. As part of the demographic background for the meeting provided by the UN Population Division, participants were informed that although the world population growth rate began to decline in the late 1970s, this decline has not yet resulted in declining absolute numbers, and the annual increment to the world population was not expected to decline to the level that existed in 1985 until the period 2020-25. World population increased from 2.5 billion in 1950 to 5.3 billion in 1990. The medium variant population projection of the UN shows world population at 6.3 billion in 2000 and 8.5 billion in 2025 (the high variant shows 9.4 billion in 2025 and the low variant shows 7.6 billion). Population aging is expected to reach unparalleled levels in 2010-20. The meeting then considered the topics of population growth and socioeconomic development, confronting poverty in developing countries, demographic impacts of development patterns, demographic and health transitions, population growth and employment, social change and the elderly in developing countries, and social development and ageing in developed countries, The expert group meeting then prepared 19 recommendations aimed at governments, social institutions, and the international community. The recommendations call for political commitment to human resources development and population and development programs, especially in least developed countries, alleviation of poverty and social inequality, and equality of access to social and health resources that will lead to reduced mortality and fertility. Governments are urged to place a high priority on education and on increasing women's access to education and to remove barriers to economic independence for women. Health-sector priorities should be reassessed

  1. Does Structured Quizzing with Process Specific Feedback Lead to Learning Gains in an Active Learning Geoscience Classroom?

    NASA Astrophysics Data System (ADS)

    Palsole, S.; Serpa, L. F.

    2013-12-01

    There is a great realization that efficient teaching in the geosciences has the potential to have far reaching effects in outreach to decision and policy makers (Herbert, 2006; Manduca & Mogk, 2006). This research in turn informs educators that the geosciences by the virtue of their highly integrative nature play an important role in serving as an entry point into STEM disciplines and helping developing a new cadre of geoscientists, scientists and a general population with an understanding of science. Keeping these goals in mind we set to design introductory geoscience courses for non-majors and majors that move away from the traditional lecture models which don't necessarily contribute well to knowledge building and retention ((Handelsman et al., 2007; Hake, 1997) to a blended active learning classroom where basic concepts and didactic information is acquired online via webquests, lecturettes and virtual field trips and the face to face portions of the class are focused on problem solving exercises. The traditional way to ensure that students are prepared for the in-class activity is to have the students take a quiz online to demonstrate basic competency. In the process of redesign, we decided to leverage the technology to build quizzes that are highly structured and map to a process (formation of divergent boundaries for example) or sets of earth processes that we needed the students to know before in-class activities. The quizzes can be taken multiple times and provide process specific feedback, thus serving as a heuristic to the students to ensure they have acquired the necessary competency. The heuristic quizzes were developed and deployed over a year with the student data driving the redesign process to ensure synchronicity. Preliminary data analysis indicates a positive correlation between higher student scores on in-class application exercises and time spent on the process quizzes. An assessment of learning gains also indicate a higher degree of self

  2. Forecasting spatially structured populations: the role of dispersal and scale.

    PubMed

    Xu, Cailin; Boyce, Mark S; Gadgil, Madhav; Nanjundiah, Vidyanand

    2005-03-21

    We forecasted spatially structured population models with complex dynamics, focusing on the effect of dispersal and spatial scale on the predictive capability of nonlinear forecasting (NLF). Dispersal influences NLF ability by its influence on population dynamics. For simple 2-cell models, when dispersal is small, our ability to predict abundance in subpopulations decreased and then increased with increasing dispersal. Spatial heterogeneity, dispersal manner, and environmental noise did not qualitatively change this result. But results are not clear for complex spatial configurations because of complicated dispersal interactions across subpopulations. Populations undergoing periodic fluctuations could be forecasted perfectly for all deterministic cases that we studied, but less reliably when environmental noise was incorporated. More importantly, for all models that we have examined, NLF was much worse at larger spatial scales as a consequence of the asynchronous dynamics of subpopulations when the dispersal rate was below some critical value. The only difference among models was the critical value of dispersal rate, which varied with growth rate, carrying capacity, mode of dispersal, and spatial configuration. These results were robust even when environmental noise was incorporated. Intermittency, common in the dynamics of spatially structured populations, lowered the predictive capability of NLF. Forecasting population behaviour is of obvious value in resource exploitation and conservation. We suggest that forecasting at local scales holds promise, whereas forecasting abundance at regional scales may yield poor results. Improved understanding of dispersal can enhance the management and conservation of natural resources, and may help us to understand resource-exploitation strategies employed by local indigenous humans.

  3. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  4. Feedbacks Between Wave Energy And Declining Coral Reef Structure: Implications For Coastal Morphodynamics

    NASA Astrophysics Data System (ADS)

    Grady, A. E.; Jenkins, C. J.; Moore, L. J.; Potts, D. C.; Burgess, P. M.; Storlazzi, C. D.; Elias, E.; Reidenbach, M. A.

    2013-12-01

    The incident wave energy dissipated by the structural complexity and bottom roughness of coral reef ecosystems, and the carbonate sediment produced by framework-building corals, provide natural shoreline protection and nourishment, respectively. Globally, coral reef ecosystems are in decline as a result of ocean warming and acidification, which is exacerbated by chronic regional stressors such as pollution and disease. As a consequence of declining reef health, many reef ecosystems are experiencing reduced coral cover and shifts to dominance by macroalgae, resulting in a loss of rugosity and thus hydrodynamic roughness. As coral reef architecture is compromised and carbonate skeletons are eroded, wave energy dissipation and sediment transport patterns--along with the carbonate sediment budget of the coastal environment--may be altered. Using a Delft3D numerical model of the south-central Molokai, Hawaii, fringing reef, we simulate the effects of changing reef states on wave energy and sediment transport. To determine the temporally-varying effects of biotic and abiotic stressors such as storms and bleaching on the reef structure and carbonate production, we couple Delft3D with CarboLOT, a model that simulates growth and competition of carbonate-producing organisms. CarboLOT is driven by the Lotka-Volterra population ecology equations and niche suitability principles, and accesses the CarboKB database for region-specific, carbonate-producing species information on growth rates, reproduction patterns, habitat suitability, as well as organism geometries. Simulations assess how changing reef states--which alter carbonate sediment production and reef morphology and thus hydrodynamic roughness--impact wave attenuation and sediment transport gradients along reef-fronted beaches. Initial results suggest that along fringing reefs having characteristics similar to the Molokai fringing reef, projected sea level rise will likely outpace coral reef accretion, and the increased

  5. Genetic diversity and population structure of Yucca filamentosa (Agavaceae).

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth.

  6. Population structure of the giant garter snake, Thamnophis gigas

    USGS Publications Warehouse

    Paquin, M.M.; Wylie, G.D.; Routman, E.J.

    2006-01-01

    The giant garter snake, Thamnophis gigas, is a threatened species endemic to California's Central Valley. We tested the hypothesis that current watershed boundaries have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the mitochondrial gene indicates there is some genetic structuring of the populations, with high F ST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies at the microsatellite locus NSU3 reveals very low F ST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence data supports conservation practices that identify separate management units for T. gigas. ?? Springer 2006.

  7. A Spatial Framework for Understanding Population Structure and Admixture

    PubMed Central

    Bradburd, Gideon S.; Ralph, Peter L.; Coop, Graham M.

    2016-01-01

    Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix. PMID:26771578

  8. Population structure of loggerhead shrikes in the California Channel Islands.

    PubMed

    Eggert, Lori S; Mundy, Nicholas I; Woodruff, David S

    2004-08-01

    The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.

  9. Evolution in a spatially structured population subject to rare epidemics.

    PubMed

    Socolar, J E; Richards, S; Wilson, W G

    2001-04-01

    We study a model that gives rise to spatially inhomogeneous population densities in a system of host individuals subject to rare, randomly distributed disease events. For stationary hosts that disperse offspring over short distances, evolutionary dynamics can lead to persistent populations with a variety of spatial structures. A mean-field analysis is shown to account for the behavior observed in simulations of a one-dimensional system, where the evolutionarily stable state corresponds to the solution of a straightforward optimization problem. In two dimensions, evolution drives the system to a stable critical state that is less well understood.

  10. Dimensions of global population projections: what do we know about future population trends and structures?

    PubMed

    Lutz, Wolfgang; K C, Samir

    2010-09-27

    The total size of the world population is likely to increase from its current 7 billion to 8-10 billion by 2050. This uncertainty is because of unknown future fertility and mortality trends in different parts of the world. But the young age structure of the population and the fact that in much of Africa and Western Asia, fertility is still very high makes an increase by at least one more billion almost certain. Virtually, all the increase will happen in the developing world. For the second half of the century, population stabilization and the onset of a decline are likely. In addition to the future size of the population, its distribution by age, sex, level of educational attainment and place of residence are of specific importance for studying future food security. The paper provides a detailed discussion of different relevant dimensions in population projections and an evaluation of the methods and assumptions used in current global population projections and in particular those produced by the United Nations and by IIASA.

  11. fastSTRUCTURE: variational inference of population structure in large SNP data sets.

    PubMed

    Raj, Anil; Stephens, Matthew; Pritchard, Jonathan K

    2014-06-01

    Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH-Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford.edu/structure.html.

  12. Demographic analysis from summaries of an age-structured population.

    PubMed

    Link, William A; Royle, J Andrew; Hatfield, Jeff S

    2003-12-01

    Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.

  13. Demographic analysis from summaries of an age-structured population

    USGS Publications Warehouse

    Link, William A.; Royle, J. Andrew; Hatfield, Jeff S.

    2003-01-01

    Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.

  14. Modelling malaria population structure and its implications for control.

    PubMed

    Buckee, Caroline O; Gupta, Sunetra

    2010-01-01

    Mathematical models of malaria transmission have been used to inform the design of malaria control programs since the mid 20th century, and many of these models have provided useful insights into the complexity of the disease. Among developing countries, however and particularly in sub-Saharan Africa, malaria remains a major cause of morbidity and mortality. One of the main difficulties in controlling the most virulent human malaria parasite, Plasmodium falciparum, is its genetic diversity, which confounds attempts to design an effective vaccine. The population structure of P. falciparum remains poorly understood but plays a key role in determining epidemiological patterns of disease and the development of immunity. We discuss the seminal model of malaria transmission developed by Ross and MacDonald, and the modifications that have been made since to include more realism. We show that age profiles of disease and serological data support a theoretical model in which the parasite population is diverse and structured into several antigenic types and highlight the implications of this structure for controlling malaria. Lastly, we discuss the current sequence data on parasite antigen genes that are important for the aquisition of immunity, and the results of a new analysis of P. falciparum population structure at the genomic level.

  15. Visualizing spatial population structure with estimated effective migration surfaces.

    PubMed

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2016-01-01

    Genetic data often exhibit patterns broadly consistent with 'isolation by distance'-a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat, this may occur more quickly in some regions than in others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of 'effective migration' to model the relationship between genetics and geography. In this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across a habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and Arabidopsis thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation.

  16. Visualizing spatial population structure with estimated effective migration surfaces

    PubMed Central

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2015-01-01

    Genetic data often exhibit patterns broadly consistent with “isolation by distance” – a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat this may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of “effective migration” to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across the habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and A. thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation. PMID:26642242

  17. Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand

    PubMed Central

    Mohan, Vathsala; Stevenson, Mark; Marshall, Jonathan; Fearnhead, Paul; Holland, Barbara R; Hotter, Grant; French, Nigel P

    2013-01-01

    Abstract A repeated cross-sectional study was conducted to determine the prevalence of Campylobacter spp. and the population structure of C. jejuni in European starlings and ducks cohabiting multiple public access sites in an urban area of New Zealand. The country's geographical isolation and relatively recent history of introduction of wild bird species, including the European starling and mallard duck, create an ideal setting to explore the impact of geographical separation on the population biology of C. jejuni, as well as potential public health implications. A total of 716 starling and 720 duck fecal samples were collected and screened for C. jejuni over a 12 month period. This study combined molecular genotyping, population genetics and epidemiological modeling and revealed: (i) higher Campylobacter spp. isolation in starlings (46%) compared with ducks (30%), but similar isolation of C. jejuni in ducks (23%) and starlings (21%), (ii) significant associations between the isolation of Campylobacter spp. and host species, sampling location and time of year using logistic regression, (iii) evidence of population differentiation, as indicated by FST, and host-genotype association with clonal complexes CC ST-177 and CC ST-682 associated with starlings, and clonal complexes CC ST-1034, CC ST-692, and CC ST-1332 associated with ducks, and (iv) greater genetic diversity and genotype richness in ducks compared with starlings. These findings provide evidence that host-associated genotypes, such as the starling-associated ST-177 and ST-682, represent lineages that were introduced with the host species in the 19th century. The isolation of sequence types associated with human disease in New Zealand indicate that wild ducks and starlings need to be considered as a potential public health risk, particularly in urban areas. We applied molecular epidemiology and population genetics to obtain insights in to the population structure, host-species relationships, gene flow and

  18. Rivers influence the population genetic structure of bonobos (Pan paniscus).

    PubMed

    Eriksson, J; Hohmann, G; Boesch, C; Vigilant, L

    2004-11-01

    Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.

  19. Different perceptions of social dilemmas: Evolutionary multigames in structured populations

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; Szolnoki, Attila; Perc, Matjaž

    2014-09-01

    Motivated by the fact that the same social dilemma can be perceived differently by different players, we here study evolutionary multigames in structured populations. While the core game is the weak prisoner's dilemma, a fraction of the population adopts either a positive or a negative value of the sucker's payoff, thus playing either the traditional prisoner's dilemma or the snowdrift game. We show that the higher the fraction of the population adopting a different payoff matrix the more the evolution of cooperation is promoted. The microscopic mechanism responsible for this outcome is unique to structured populations, and it is due to the payoff heterogeneity, which spontaneously introduces strong cooperative leaders that give rise to an asymmetric strategy imitation flow in favor of cooperation. We demonstrate that the reported evolutionary outcomes are robust against variations of the interaction network, and they also remain valid if players are allowed to vary which game they play over time. These results corroborate existing evidence in favor of heterogeneity-enhanced network reciprocity, and they reveal how different perceptions of social dilemmas may contribute to their resolution.

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

    PubMed Central

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

    2011-01-01

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

  1. Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density.

    PubMed

    Ehrich, D; Jorde, P E; Krebs, C J; Kenney, A J; Stacy, J E; Stenseth, N C

    2001-02-01

    The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.

  2. Development of paradigms for the dynamics of structured populations

    SciTech Connect

    Not Available

    1994-10-01

    This is a technical progress report on the dynamics of predator-prey systems in a patchy environment. A new phenomenon that might contribute to outbreaks in systems of discrete patches has been determined using a discrete time model with both spatial and age structure. A model for a single species in a patchy environment with migration, local population growth and disasters with in patches has been formulated and a brief description is included.

  3. Population structure and minimum core genome typing of Legionella pneumophila

    PubMed Central

    Qin, Tian; Zhang, Wen; Liu, Wenbin; Zhou, Haijian; Ren, Hongyu; Shao, Zhujun; Lan, Ruiting; Xu, Jianguo

    2016-01-01

    Legionella pneumophila is an important human pathogen causing Legionnaires’ disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous genes were shared by all isolates and were defined as the minimum core genome (MCG) of L. pneumophila. A total of 323,224 single-nucleotide polymorphisms (SNPs) were identified among the 53 strains. After excluding 314,059 SNPs which were likely to be results of recombination, the remaining 9,165 SNPs were referred to as MCG SNPs. Population Structure analysis based on MCG divided the 53 L. pneumophila into nine MCG groups. The within-group distances were much smaller than the between-group distances, indicating considerable divergence between MCG groups. MCG groups were also supplied by phylogenetic analysis and may be considered as robust taxonomic units within L. pneumophila. Among the nine MCG groups, eight showed high intracellular growth ability while one showed low intracellular growth ability. Furthermore, MCG typing also showed high resolution in subtyping ST1 strains. The results obtained in this study provided significant insights into the evolution, population structure and pathogenicity of L. pneumophila. PMID:26888563

  4. A Mechanism for Land-Atmosphere Feedback Involving Planetary Wave Structures

    NASA Technical Reports Server (NTRS)

    Koster, Randal D.; Chang, Yehui; Schubert, Siegfried D.

    2014-01-01

    While the ability of land surface conditions to influence the atmosphere has been demonstrated in various modeling and observational studies, the precise mechanisms by which land-atmosphere feedback occurs are still largely unknown particularly the mechanisms that allow land moisture state in one region to affect atmospheric conditions in another. Such remote impacts are examined here in the context of atmospheric general circulation model (AGCM) simulations, leading to the identification of one potential mechanism: the phase-locking and amplification of a planetary wave through the imposition of a spatial pattern of soil moisture at the land surface. This mechanism, shown here to be relevant in the AGCM, apparently also operates in nature, as suggested by supporting evidence found in reanalysis data.

  5. Slewing maneuvers and vibration control of space structures by feedforward/feedback moment-gyro controls

    NASA Technical Reports Server (NTRS)

    Yang, Li-Farn; Mikulas, Martin M., Jr.; Park, K. C.; Su, Renjeng

    1993-01-01

    This paper presents a moment-gyro control approach to the maneuver and vibration suppression of a flexible truss arm undergoing a constant slewing motion. The overall slewing motion is triggered by a feedforward input, and a companion feedback controller is employed to augment the feedforward input and subsequently to control vibrations. The feedforward input for the given motion requirement is determined from the combined CMG (Control Momentum Gyro) devices and the desired rigid-body motion. The rigid-body dynamic model has enabled us to identify the attendant CMG momentum saturation constraints. The task for vibration control is carried out in two stages; first in the search of a suitable CMG placement along the beam span for various slewing maneuvers, and subsequently in the development of Liapunov-based control algorithms for CMG spin-stabilization. Both analytical and numerical results are presented to show the effectiveness of the present approach.

  6. A field experiment demonstrating plant life-history evolution and its eco-evolutionary feedback to seed predator populations.

    PubMed

    Agrawal, Anurag A; Johnson, Marc T J; Hastings, Amy P; Maron, John L

    2013-05-01

    The extent to which evolutionary change occurs in a predictable manner under field conditions and how evolutionary changes feed back to influence ecological dynamics are fundamental, yet unresolved, questions. To address these issues, we established eight replicate populations of native common evening primrose (Oenothera biennis). Each population was planted with 18 genotypes in identical frequency. By tracking genotype frequencies with microsatellite DNA markers over the subsequent three years (up to three generations, ≈5,000 genotyped plants), we show rapid and consistent evolution of two heritable plant life-history traits (shorter life span and later flowering time). This rapid evolution was only partially the result of differential seed production; genotypic variation in seed germination also contributed to the observed evolutionary response. Since evening primrose genotypes exhibited heritable variation for resistance to insect herbivores, which was related to flowering time, we predicted that evolutionary changes in genotype frequencies would feed back to influence populations of a seed predator moth that specializes on O. biennis. By the conclusion of the experiment, variation in the genotypic composition among our eight replicate field populations was highly predictive of moth abundance. These results demonstrate how rapid evolution in field populations of a native plant can influence ecological interactions.

  7. Population age structure and asset returns: an empirical investigation.

    PubMed

    Poterba, J M

    1998-10-01

    "This paper investigates the association between population age structure, particularly the share of the population in the 'prime saving years' 45-60, and the returns on stocks and bonds. The paper is motivated by the claim that the aging of the 'Baby Boom' cohort in the United States is a key factor in explaining the recent rise in asset values. It also addresses the associated claim that asset prices will decline when this large cohort reaches retirement age and begins to reduce its asset holdings. This paper begins by considering household age-asset accumulation profiles. Data from the Survey of Consumer Finances suggest that while cross-sectional age-wealth profiles peak for households in their early 60s, cohort data on the asset ownership of the same households show a much less pronounced peak.... The paper then considers the historical relationship between demographic structure and real returns on Treasury bills, long-term government bonds, and corporate stock. The results do not suggest any robust relationship between demographic structure and asset returns.... The paper concludes by discussing factors such as international capital flows and forward-looking behavior on the part of market participants that could weaken the relationship between age structure and asset returns in a single nation."

  8. Evolutionary dynamics of collective action in spatially structured populations.

    PubMed

    Peña, Jorge; Nöldeke, Georg; Lehmann, Laurent

    2015-10-07

    Many models proposed to study the evolution of collective action rely on a formalism that represents social interactions as n-player games between individuals adopting discrete actions such as cooperate and defect. Despite the importance of spatial structure in biological collective action, the analysis of n-player games games in spatially structured populations has so far proved elusive. We address this problem by considering mixed strategies and by integrating discrete-action n-player games into the direct fitness approach of social evolution theory. This allows to conveniently identify convergence stable strategies and to capture the effect of population structure by a single structure coefficient, namely, the pairwise (scaled) relatedness among interacting individuals. As an application, we use our mathematical framework to investigate collective action problems associated with the provision of three different kinds of collective goods, paradigmatic of a vast array of helping traits in nature: "public goods" (both providers and shirkers can use the good, e.g., alarm calls), "club goods" (only providers can use the good, e.g., participation in collective hunting), and "charity goods" (only shirkers can use the good, e.g., altruistic sacrifice). We show that relatedness promotes the evolution of collective action in different ways depending on the kind of collective good and its economies of scale. Our findings highlight the importance of explicitly accounting for relatedness, the kind of collective good, and the economies of scale in theoretical and empirical studies of the evolution of collective action.

  9. Patterning and pattern selection in a surface layer: Feedback between point defects population and surface layer temperature variations

    NASA Astrophysics Data System (ADS)

    Kharchenko, Dmitrii O.; Kharchenko, Vasyl O.; Bashtova, Anna I.; Lysenko, Irina O.

    2016-12-01

    We study dynamics of pattern formation in a prototype system of nonequilibrium point defects in thin foils under sustained nonequilibrium conditions. A reaction-diffusion model describing spatio-temporal behaviour of both vacancy population and local temperature of a surface layer is used. It is shown that pattern selection processes caused by coupling between defect population and local temperature of a surface are realized. Associated oscillatory dynamics of main statistical moments of both vacancy concentration field and surface layer temperature is analysed in detail. It is found that during the system evolution spatial distribution of local temperature variations of the surface layer relates to vacancy population distribution. It is shown that the mean size of vacancy clusters (from 30 nm up to 300 nm) evolves in oscillatory manner due to pattern selection processes. Morphology of defect complexes can be controlled by defects generation rate.

  10. An analysis of the basic population structure of Shanghai Municipality.

    PubMed

    Shen, A

    1984-01-01

    This paper analyzes the changes in Shanghai's population structure over the last 30 years in the 4 aspects of age structure, sex composition, urban and rural composition, and labor and employment structure. In 1953 those of the 0 to 6 age group accounted for 21.2% of the total population; in 1957 the group represented a proportion of 24.6%. Since the 1960s, especially after the 1970s, the family planning program gradually took effect, and the birthrate of the entire municipality fell drastically. The number of school-age children in 1979 was 1 1/2 times more than the same age group in 1953; there should be no worry that population control may result in a shortage of manpower to meet the needs of the work force and the armed forces either toward the end of this century or at the beginning of the next. The economy in China is underdeveloped, production and technology remain at a low level, average wages for employees are low, and for a long time the low living standard of the people has shown little sign of improvement. The problem is mainly manifest in the following areas: 1) distribution of the work force in heavy and light industries is not sufficiently rational, 2) the distribution of the work force between captial construction and transport and communications on the 1 hand and the national economy on the other is out of proportion, 3) the distribution of the work force between commerce, service trades, and public utilities on the 1 hand and the national economy on the other is disproportionated, and 4) the distribution of the work force between undertakings of culture, education, scientific research, health, and medical care on the 1 hand and economic construction on the other is improper. How to control population growth and adjust parts of the population structure to suit the national economic development poses a problem that calls for further in-depth study and analysis to resolve it step by step.

  11. Genetic Structure of Loach Population in Yatsu Paddy Field

    NASA Astrophysics Data System (ADS)

    Koizumi, Noriyuki; Takemura, Takeshi; Mori, Atsushi; Okushima, Shuji

    Using repeated sequences of microsatellite DNA, we investigated genetic variation and spatial structure of the loach Misgurnus anguillicaudatus population in drainage canals including a main stream in the Shitada River basin composed of Yatsu paddy fields, Chiba Prefecture. Loach population samples of nine to 48 individuals were collected from 54 sampling sites in eight canals and the main stream, and genotype data in eight microsatellite loci were obtained for each sample in the genetic analysis. The average number of alleles per locus was 3.9 to 9.0, and the average observed and expected heterozygosities were 0.444-0.647 and 0.463-0.628, respectively, across samples. All samples seemed to be random mating, which conformed to the Hardy-Weinberg equilibrium. Values of the fixation index FST, were estimated to range between 0-0.161 among all samples, and a part of these values were significant. The pattern of genetic differentiation between samples with principal component analysis indicated that samples in three distinct canals appeared to differentiate, suggesting that the genetic spatial structure of the loach population in Yatsu paddy fields must be complex.

  12. Behavior and population structure of Anopheles darlingi in Colombia.

    PubMed

    Naranjo-Díaz, Nelson; Conn, Jan E; Correa, Margarita M

    2016-04-01

    Anopheles darlingi is a widely distributed and important malaria vector in Colombia. Biogeographical and ecological heterogeneity across the Colombian distribution led to the hypothesis of behavioral and genetic differentiation among A. darlingi populations. A total of 2017 A. darlingi specimens were collected during 222 h of sampling. This vector was the most abundant anopheline species in most of the localities sampled. Subdivision between samples collected west and east of the Andes was indicated by 1) mitochondrial COI and nuclear CAD sequences from NW-W and CE-S populations (COI ΦST=0.48761-0.81974, CAD FST=0.11319-0.21321), 2) a COI haplotype network, and 3) SAMOVA. Endo- and exophagy were detected in populations west of the Andes, whereas exophagy was evident in PTG, a locality east of the Andes. Isolation by resistance was significant for COI and explained 26% of the genetic differentiation. We suggest that at a macrogeographic scale, the Andes influence the differentiation of A. darlingi in Colombia and may drive divergence, and, at a microgeographic scale, ecological differences have a significant impact on structure. These data could constitute a baseline for the design of effective vector interventions, locality-specific for the east and similar for panmictic populations west of the Andes.

  13. Multi-layered population structure in Island Southeast Asians

    PubMed Central

    Ricaut, Francois-Xavier; Yngvadottir, Bryndis; Harney, Eadaoin; Castillo, Cristina; Hoogervorst, Tom; Antao, Tiago; Kusuma, Pradiptajati; Razafindrazaka, Harilanto; Cardona, Alexia; Pierron, Denis; Letellier, Thierry; Wee, Joseph; Abdullah, Syafiq; Metspalu, Mait; Kivisild, Toomas

    2016-01-01

    The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognized major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5kya we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years. PMID:27302840

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

    PubMed Central

    De la Rúa, Pilar; Galián, José; Serrano, José; Moritz, Robin FA

    2003-01-01

    The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain) was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca) and Pitiusas (Ibiza and Formentera), which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees. PMID:12729553

  15. Multi-layered population structure in Island Southeast Asians.

    PubMed

    Mörseburg, Alexander; Pagani, Luca; Ricaut, Francois-Xavier; Yngvadottir, Bryndis; Harney, Eadaoin; Castillo, Cristina; Hoogervorst, Tom; Antao, Tiago; Kusuma, Pradiptajati; Brucato, Nicolas; Cardona, Alexia; Pierron, Denis; Letellier, Thierry; Wee, Joseph; Abdullah, Syafiq; Metspalu, Mait; Kivisild, Toomas

    2016-11-01

    The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.

  16. Population structure of Serpula lacrymans in Europe with an outlook to the French population.

    PubMed

    Maurice, Sundy; Skrede, Inger; LeFloch, Gaetan; Barbier, Georges; Kauserud, Håvard

    2014-01-01

    In this study the genetic variation and population structure in a French population of the dry rot fungus S. lacrymans was investigated using 14 microsatellites markers and compared to the rest of Europe. In that comparison the French population possessed the same allelic diversity as rest of Europe. A weak geographic structuring of the genetic variation was observed across Europe, where the French isolates to some extent separated from the rest of Europe, indicating that weak barriers to gene flow exists. Eighty percent of the isolates had unique multilocus microsatellite genotypes, which corresponds to high recombination and dispersal by sexual spores. Deviations from Hardy-Weinberg expectations were observed in multiple loci. In most loci there was an excess of heterozygotes, which could be due to either non-random mating, presence of more than two nuclei in the secondary mycelia or another unrecognized process. A total of six vegetative compatibility (VC) groups were present in Europe, out of which four were sampled in France. One VC group was over-represented in France while two others were underrepresented, as compared to the rest of Europe.

  17. A large population parental care game: polymorphisms and feedback between patterns of care and the operational sex ratio.

    PubMed

    Ramsey, David M

    2010-10-21

    This article presents a game theoretic model of parental care which models the feedback between patterns of care and the operational sex ratio. It is assumed here that males can be in one of two states: searching for a mate or breeding (including caring for their offspring). Females can be in one of three states: receptive (searching), non-receptive or breeding. However, these sets of states can be adapted to the physiology of a particular species. The length of time that an individual remains in the breeding state depends on the level of care an individual gives. When in the searching state, individuals find partners at a rate dependent on the proportion of members of the opposite sex searching. These rates are defined to satisfy the Fisher condition that the total number of offspring of males equals the total number of offspring of females. The operational sex ratio is not defined exogenously, but can be derived from the adult sex ratio and the pattern of parental care. Pure strategy profiles and so-called single sex stable polymorphisms, in which behaviour is varied within one sex, are derived analytically. The difference between mixed evolutionarily stable strategies and stable polymorphisms within this framework is highlighted. The effects of various physiological and demographic parameters on patterns of care are considered.

  18. Evolutionary dynamics of group interactions on structured populations: a review

    PubMed Central

    Perc, Matjaž; Gómez-Gardeñes, Jesús; Szolnoki, Attila; Floría, Luis M.; Moreno, Yamir

    2013-01-01

    Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and non-living matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proved valuable for studying pattern formation, equilibrium selection and self-organization in evolutionary games. Here, we review recent advances in the study of evolutionary dynamics of group interactions on top of structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory. PMID:23303223

  19. Characterization of the dominant structural vibration of hearing aid receivers: Towards the moderation of mechanical feedback in hearing aids

    NASA Astrophysics Data System (ADS)

    Varanda, Brenno R.

    Presented are the results from the experimental, analytical, and computational analyses accomplished to characterize the mechanical vibration of hearing aid receivers, a key electro-acoustic component of hearing aids. The function of a receiver in a hearing aid is to provide an amplified sound signal into the ear canal. Unfortunately, as the receiver produces sound, it also undergoes vibration which can be transmitted through the hearing aid package to the microphones, resulting in undesirable feedback oscillations. To gain more knowledge and control on the source of these feedback oscillations, a dynamic rigid body model of the receiver is proposed. The rigid body model captures the essential dynamic features of the receiver. The model is represented by two hinged rigid bodies, under an equal and opposite dynamic moment load, and connected to each other by a torsional spring and damper. The mechanical coupling ratio between the two rigid bodies is proved to be acoustically independent. A method is introduced to estimate the parameters for the proposed model using experimental data. An equivalent finite element analysis model is established and tested against a known and characterized mechanical attachment. The simulated model successfully predicts the structural dynamic response showing excellent agreement between the finite element analysis and measured results.

  20. Diversification and population structure in common beans (Phaseolus vulgaris L.).

    PubMed

    Blair, Matthew W; Soler, Alvaro; Cortés, Andrés J

    2012-01-01

    Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans.

  1. Diversification and Population Structure in Common Beans (Phaseolus vulgaris L.)

    PubMed Central

    Blair, Matthew W.; Soler, Alvaro; Cortés, Andrés J.

    2012-01-01

    Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans

  2. Complex Transition to Cooperative Behavior in a Structured Population Model

    PubMed Central

    Miranda, Luciano; de Souza, Adauto J. F.; Ferreira, Fernando F.; Campos, Paulo R. A.

    2012-01-01

    Cooperation plays an important role in the evolution of species and human societies. The understanding of the emergence and persistence of cooperation in those systems is a fascinating and fundamental question. Many mechanisms were extensively studied and proposed as supporting cooperation. The current work addresses the role of migration for the maintenance of cooperation in structured populations. This problem is investigated in an evolutionary perspective through the prisoner's dilemma game paradigm. It is found that migration and structure play an essential role in the evolution of the cooperative behavior. The possible outcomes of the model are extinction of the entire population, dominance of the cooperative strategy and coexistence between cooperators and defectors. The coexistence phase is obtained in the range of large migration rates. It is also verified the existence of a critical level of structuring beyond that cooperation is always likely. In resume, we conclude that the increase in the number of demes as well as in the migration rate favor the fixation of the cooperative behavior. PMID:22761736

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

    PubMed

    McEvoy, Brian P; Montgomery, Grant W; McRae, Allan F; Ripatti, Samuli; Perola, Markus; Spector, Tim D; Cherkas, Lynn; Ahmadi, Kourosh R; Boomsma, Dorret; Willemsen, Gonneke; Hottenga, Jouke J; Pedersen, Nancy L; Magnusson, Patrik K E; Kyvik, Kirsten Ohm; Christensen, Kaare; Kaprio, Jaakko; Heikkilä, Kauko; Palotie, Aarno; Widen, Elisabeth; Muilu, Juha; Syvänen, Ann-Christine; Liljedahl, Ulrika; Hardiman, Orla; Cronin, Simon; Peltonen, Leena; Martin, Nicholas G; Visscher, Peter M

    2009-05-01

    Population structure can provide novel insight into the human past, and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, United Kingdom, Netherlands, Denmark, Sweden, Finland, Australia, and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and European-American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogeneous region. There is evidence 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 data to explore regional population variation, the events that have crafted it, and their implications in both explaining disease prevalence and mapping these genes by association.

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

    PubMed Central

    McEvoy, Brian P.; Montgomery, Grant W.; McRae, Allan F.; Ripatti, Samuli; Perola, Markus; Spector, Tim D.; Cherkas, Lynn; Ahmadi, Kourosh R.; Boomsma, Dorret; Willemsen, Gonneke; Hottenga, Jouke J.; Pedersen, Nancy L.; Magnusson, Patrik K.E.; Kyvik, Kirsten Ohm; Christensen, Kaare; Kaprio, Jaakko; Heikkilä, Kauko; Palotie, Aarno; Widen, Elisabeth; Muilu, Juha; Syvänen, Ann-Christine; Liljedahl, Ulrika; Hardiman, Orla; Cronin, Simon; Peltonen, Leena; Martin, Nicholas G.; Visscher, Peter M.

    2009-01-01

    Population structure can provide novel insight into the human past, and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, United Kingdom, Netherlands, Denmark, Sweden, Finland, Australia, and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and European-American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogeneous region. There is evidence from FST-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 data to explore regional population variation, the events that have crafted it, and their implications in both explaining disease prevalence and mapping these genes by association. PMID:19265028

  5. Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations.

    PubMed

    Garland, Ellen C; Goldizen, Anne W; Lilley, Matthew S; Rekdahl, Melinda L; Garrigue, Claire; Constantine, Rochelle; Hauser, Nan Daeschler; Poole, M Michael; Robbins, Jooke; Noad, Michael J

    2015-08-01

    For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of information or behavior between conspecifics through social learning) of different versions of this display between distinct but interconnected populations in the western and central South Pacific region presents a unique way to investigate population structure based on the movement dynamics of a song (acoustic) display. Using 11 years of data, we investigated an acoustically based population structure for the region by comparing stereotyped song sequences among populations and years. We used the Levenshtein distance technique to group previously defined populations into (vocally based) clusters based on the overall similarity of their song display in space and time. We identified the following distinct vocal clusters: western cluster, 1 population off eastern Australia; central cluster, populations around New Caledonia, Tonga, and American Samoa; and eastern region, either a single cluster or 2 clusters, one around the Cook Islands and the other off French Polynesia. These results are consistent with the hypothesis that each breeding aggregation represents a distinct population (each occupied a single, terminal node) in a metapopulation, similar to the current understanding of population structure based on genetic and photo-identification studies. However, the central vocal cluster had higher levels of song-sharing among populations than the other clusters, indicating that levels of vocal connectivity varied within the region. Our results demonstrate the utility and value of

  6. Highly stable solution processed metal-halide perovskite lasers on nanoimprinted distributed feedback structures

    NASA Astrophysics Data System (ADS)

    Brenner, Philipp; Stulz, Mareike; Kapp, Dorothee; Abzieher, Tobias; Paetzold, Ulrich W.; Quintilla, Aina; Howard, Ian A.; Kalt, Heinz; Lemmer, Uli

    2016-10-01

    We report on the performance and stability of distributed feedback lasers based on the solution-processed methylammonium lead iodide perovskite (CH3NH3PbI3). The CH3NH3PbI3 layers are processed via solution-casting in ambient atmosphere onto nanoimprinted second order Bragg gratings. This way, we achieve highly polarized surface-emitted lasing at room temperature with a linewidth of less than 0.2 nm and a laser threshold of 120 kW/cm2. The lasing is stable; no change in the laser emission within 15 h of pulsed excitation with a repetition rate of 1 kHz (corresponding to >5 × 107 pulses) is observed, exceeding the stability achieved for solution processed organic semiconductor lasers. Furthermore, adjustment of the grating period allowed the lasing wavelength to be varied over the entire bandwidth of the amplified spontaneous emission (between 781 and 794 nm). The fabrication process of nanoimprinting followed by solution-casting of the gain material demonstrates that stable CH3NH3PbI3 lasers are compatible with scalable production technologies and offers a route towards electrically pumped diode architectures.

  7. [Economic growth and changes in the structure of the population].

    PubMed

    Conroy, M E

    1980-01-01

    A reevaluation of classic works by Simon Kuznets and Wassily Leontief suggests that their conclusions concerning the interrelationships between economic growth and population structure correspond to relatively highly specialized characteristics of present forms of capitalist development or underdevelopment and not necessarily to capitalist development within a new international economic order or to socialist development. Kuznets' work seems to offer conclusive proof of the negative effects of rapid population growth on economic development for 3 reasons: 1) requirements for capital are greater, 2) total production and per capita consumption are greatly reduced with high dependency ratios, and 3) rapid growth in consumption is more difficult when the population is growing more rapidly. However, at least 4 problems are noted when Kuznets' ideas are applied to the 3rd world. Kuznets assumes that growth of physical capital is the only source of growth, so that only increased investment can increase returns. Secondly, assuming the same ratio of capital/output for all cases assumes that no substitution of labor for capital is possible. Third, the assumption that participation rates remain the same regardless of dependency ratios may be incorrect. And finally, the difference in per capita consumption that Kuznets attributes to differences in rates of population growth represents a tiny proportion of the total gap in the standard of living of rich countries with slow population growth and poor countries with rapid growth. Kuznets' argument has considerable validity in Third World countries which relay on traditional patterns of capitalist accumulation, but the problems represent the effects of rapid population growth only under the current modes of capitalist expansion. The negative effect of high fertility on savings has probably been greatly exaggerated, and the problems of providing educational facilities and health care for ever larger numbers of persons have been

  8. Temporal structure of neuronal population oscillations with empirical model decomposition

    NASA Astrophysics Data System (ADS)

    Li, Xiaoli

    2006-08-01

    Frequency analysis of neuronal oscillation is very important for understanding the neural information processing and mechanism of disorder in the brain. This Letter addresses a new method to analyze the neuronal population oscillations with empirical mode decomposition (EMD). Following EMD of neuronal oscillation, a series of intrinsic mode functions (IMFs) are obtained, then Hilbert transform of IMFs can be used to extract the instantaneous time frequency structure of neuronal oscillation. The method is applied to analyze the neuronal oscillation in the hippocampus of epileptic rats in vivo, the results show the neuronal oscillations have different descriptions during the pre-ictal, seizure onset and ictal periods of the epileptic EEG at the different frequency band. This new method is very helpful to provide a view for the temporal structure of neural oscillation.

  9. Genetic diversity and population structure of native maize populations in Latin America and the Caribbean.

    PubMed

    Bedoya, Claudia A; Dreisigacker, Susanne; Hearne, Sarah; Franco, Jorge; Mir, Celine; Prasanna, Boddupalli M; Taba, Suketoshi; Charcosset, Alain; Warburton, Marilyn L

    2017-01-01

    This study describes the genetic diversity and population structure of 194 native maize populations from 23 countries of Latin America and the Caribbean. The germplasm, representing 131 distinct landraces, was genetically characterized as population bulks using 28 SSR markers. Three main groups of maize germplasm were identified. The first, the Mexico and Southern Andes group, highlights the Pre-Columbian and modern exchange of germplasm between North and South America. The second group, Mesoamerica lowland, supports the hypothesis that two separate human migration events could have contributed to Caribbean maize germplasm. The third, the Andean group, displayed early introduction of maize into the Andes, with little mixing since then, other than a regional interchange zone active in the past. Events and activities in the pre- and post-Columbian Americas including the development and expansion of pre-Columbian cultures and the arrival of Europeans to the Americas are discussed in relation to the history of maize migration from its point of domestication in Mesoamerica to South America and the Caribbean through sea and land routes.

  10. Variable structure control of globally feedback-decoupled deformable vehicle maneuvers

    NASA Technical Reports Server (NTRS)

    Dwyer, T. A. W., III; Sira-Ramirez, H.; Monaco, S.; Stornelli, S.

    1987-01-01

    The use of Cayley-Rodrigues attitude parameters as kinematic variables is shown to yield a globally linearized and decoupled model of the equations of motion of a deformable body, where the structural deformation state appears only in the coefficients of the inverse transformation. It is shown how commanded multiaxial attitude maneuvers can be encoded as switching surfaces for a variable-structure control implementation of the corresponding computed slew torques, automatically modulated in respnse only to detected angular rate error signs, for accurate tracking in the presence of separately damped or even uncontrolled (but stable) structural deformations.

  11. Networks and Models with Heterogeneous Population Structure in Epidemiology

    NASA Astrophysics Data System (ADS)

    Kao, R. R.

    Heterogeneous population structure can have a profound effect on infectious disease dynamics, and is particularly important when investigating “tactical” disease control questions. At times, the nature of the network involved in the transmission of the pathogen (bacteria, virus, macro-parasite, etc.) appears to be clear; however, the nature of the network involved is dependent on the scale (e.g. within-host, between-host, or between-population), the nature of the contact, which ranges from the highly specific (e.g. sexual acts or needle sharing at the person-to-person level) to almost completely non-specific (e.g. aerosol transmission, often over long distances as can occur with the highly infectious livestock pathogen foot-and-mouth disease virus—FMDv—at the farm-to-farm level, e.g. Schley et al. in J. R. Soc. Interface 6:455-462, 2008), and the timescale of interest (e.g. at the scale of the individual, the typical infectious period of the host). Theoretical approaches to examining the implications of particular network structures on disease transmission have provided critical insight; however, a greater challenge is the integration of network approaches with data on real population structures. In this chapter, some concepts in disease modelling will be introduced, the relevance of selected network phenomena discussed, and then results from real data and their relationship to network analyses summarised. These include examinations of the patterns of air traffic and its relation to the spread of SARS in 2003 (Colizza et al. in BMC Med., 2007; Hufnagel et al. in Proc. Natl. Acad. Sci. USA 101:15124-15129, 2004), the use of the extensively documented Great Britain livestock movements network (Green et al. in J. Theor. Biol. 239:289-297, 2008; Robinson et al. in J. R. Soc. Interface 4:669-674, 2007; Vernon and Keeling in Proc. R. Soc. Lond. B, Biol. Sci. 276:469-476, 2009) and the growing interest in combining contact structure data with phylogenetics to

  12. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae) Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    PubMed Central

    Pineda-Martos, Rocío; Pujadas-Salvà, Antonio J.; Fernández-Martínez, José M.; Stoyanov, Kiril; Pérez-Vich, Begoña

    2014-01-01

    Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms. PMID:25143963

  13. Corynebacterium diphtheriae: genome diversity, population structure and genotyping perspectives.

    PubMed

    Mokrousov, Igor

    2009-01-01

    The epidemic re-emergence of diphtheria in Russia and the Newly Independent States (NIS) of the former Soviet Union in the 1990s demonstrated the continued threat of this thought to be rare disease. The bacteriophage encoded toxin is a main virulence factor of Corynebacterium diphtheriae, however, an analysis of the first complete genome sequence of C. diphtheriae revealed a recent acquisition of other pathogenicity factors including iron-uptake systems, adhesins and fimbrial proteins as indeed this extracellular pathogen has more possibilities for lateral gene transfer than, e.g., its close relative, mainly intracellular Mycobacterium tuberculosis. C. diphtheriae appears to have a phylogeographical structure mainly represented by area-specific variants whose circulation is under strong influence of human host factors, including health control measures, first of all, vaccination, and social economic conditions. This framework core population structure may be challenged by importation of the endemic and eventually toxigenic strains from new areas thus leading to localized or large epidemics caused directly by imported strains or by bacteriophage-lysogenized indigenous strains converted into toxin production. A feature of C. diphtheriae co-existence with humans is its periodicity: following large epidemic in the 1990s, the present period is marked by increasing heterogeneity of the circulating populations whereas re-emergence of new toxigenic variants along with persistent circulation of invasive non-toxigenic strains appear alarming. To identify and rapidly monitor subtle changes in the genome structure at an infraclonal level during and between epidemics, portable and discriminatory typing methods of C. diphtheriae are still needed. In this view, CRISPRs and minisatellites are promising genomic markers for development of high-resolution typing schemes and databasing of C. diphtheriae.

  14. Effects of spatial structure of population size on the population dynamics of barnacles across their elevational range.

    PubMed

    Fukaya, Keiichi; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

    2014-11-01

    Explanations for why population dynamics vary across the range of a species reflect two contrasting hypotheses: (i) temporal variability of populations is larger in the centre of the range compared to the margins because overcompensatory density dependence destabilizes population dynamics and (ii) population variability is larger near the margins, where populations are more susceptible to environmental fluctuations. In both of these hypotheses, positions within the range are assumed to affect population variability. In contrast, the fact that population variability is often related to mean population size implies that the spatial structure of the population size within the range of a species may also be a useful predictor of the spatial variation in temporal variability of population size over the range of the species. To explore how population temporal variability varies spatially and the underlying processes responsible for the spatial variation, we focused on the intertidal barnacle Chthamalus dalli and examined differences in its population dynamics along the tidal levels it inhabits. Changes in coverage of barnacle populations were monitored for 10.5 years at 25 plots spanning the elevational range of this species. Data were analysed by fitting a population dynamics model to estimate the effects of density-dependent and density-independent processes on population growth. We also examined the temporal mean-variance relationship of population size with parameters estimated from the population dynamics model. We found that the relative variability of populations tended to increase from the centre of the elevational range towards the margins because of an increase in the magnitude of stochastic fluctuations of growth rates. Thus, our results supported hypothesis (2). We also found that spatial variations in temporal population variability were well characterized by Taylor's power law, the relative population variability being inversely related to the mean

  15. Stable isotopes indicate population structuring in the southwest Atlantic population of right whales (Eubalaena australis).

    PubMed

    Vighi, Morgana; Borrell, Asunción; Crespo, Enrique A; Oliveira, Larissa R; Simões-Lopes, Paulo C; Flores, Paulo A C; García, Néstor A; Aguilar, Alex; Aguilar, Alejandro

    2014-01-01

    From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina) and another off central Argentina (Peninsula Valdés). This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n=72) and from contemporary and more recent strandings occurring in central Argentina (n=53). Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas.

  16. Stable Isotopes Indicate Population Structuring in the Southwest Atlantic Population of Right Whales (Eubalaena australis)

    PubMed Central

    Vighi, Morgana; Borrell, Asunción; Crespo, Enrique A.; Oliveira, Larissa R.; Simões-Lopes, Paulo C.; Flores, Paulo A. C.; García, Néstor A.; Aguilar, Alejandro

    2014-01-01

    From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina) and another off central Argentina (Peninsula Valdés). This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n = 72) and from contemporary and more recent strandings occurring in central Argentina (n = 53). Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas. PMID:24598539

  17. Genetic population structure of muskellunge in the Great Lakes

    USGS Publications Warehouse

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

    2013-01-01

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

  18. Local genetic structure in a white-bearded manakin population.

    PubMed

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present.

  19. Latitudinal variation in population structure of wintering Pacific Black Brant

    USGS Publications Warehouse

    Schamber, J.L.; Sedinger, J.S.; Ward, D.H.; Hagmeier, K.R.

    2007-01-01

    Latitudinal variation in population structure during the winter has been reported in many migratory birds, but has been documented in few species of waterfowl. Variation in environmental and social conditions at wintering sites can potentially influence the population dynamics of differential migrants. We examined latitudinal variation in sex and age classes of wintering Pacific Black Brant (Branta bernicla nigricans). Brant are distributed along a wide latitudinal gradient from Alaska to Mexico during the winter. Accordingly, migration distances for brant using different wintering locations are highly variable and winter settlement patterns are likely associated with a spatially variable food resource. We used resightings of brant banded in southwestern Alaska to examine sex and age ratios of birds wintering at Boundary Bay in British Columbia, and at San Quintin Bay, Ojo de Liebre Lagoon, and San Ignacio Lagoon in Baja California from 1998 to 2000. Sex ratios were similar among wintering locations for adults and were consistent with the mating strategy of geese. The distribution of juveniles varied among wintering areas, with greater proportions of juveniles observed at northern (San Quintin Bay and Ojo de Liebre Lagoon) than at southern (San Ignacio Lagoon) locations in Baja California. We suggest that age-related variation in the winter distribution of Pacific Black Brant is mediated by variation in productivity among individuals at different wintering locations and by social interactions among wintering family groups.

  20. Interactive diversity promotes the evolution of cooperation in structured populations

    NASA Astrophysics Data System (ADS)

    Su, Qi; Li, Aming; Zhou, Lei; Wang, Long

    2016-10-01

    Evolutionary games on networks traditionally assume that each individual adopts an identical strategy to interact with all its neighbors in each generation. Considering the prevalent diversity of individual interactions in the real society, here we propose the concept of interactive diversity, which allows individuals to adopt different strategies against different neighbors in each generation. We investigate the evolution of cooperation based on the edge dynamics rather than the traditional nodal dynamics in networked systems. The results show that, without invoking any other mechanisms, interactive diversity drives the frequency of cooperation to a high level for a wide range of parameters in both well-mixed and structured populations. Even in highly connected populations, cooperation still thrives. When interactive diversity and large topological heterogeneity are combined together, however, in the relaxed social dilemma, cooperation level is lower than that with just one of them, implying that the combination of many promotive factors may make a worse outcome. By an analytical approximation, we get the condition under which interactive diversity provides more advantages for cooperation than traditional evolutionary dynamics does. Numerical simulations validating the approximation are also presented. Our work provides a new line to explore the latent relation between the ubiquitous cooperation and individuals’ distinct responses in different interactions. The presented results suggest that interactive diversity should receive more attention in pursuing mechanisms fostering cooperation.

  1. Large scale structure of the globular cluster population in Coma

    NASA Astrophysics Data System (ADS)

    Gagliano, Alexander T.; O'Neill, Conor; Madrid, Juan P.

    2016-01-01

    A search for globular cluster candidates in the Coma Cluster was carried out using Hubble Space Telescope data taken with the Advanced Camera for Surveys. We combine different observing programs including the Coma Treasury Survey in order to obtain the large scale distribution of globular clusters in Coma. Globular cluster candidates were selected through careful morphological inspection and a detailed analysis of their magnitude and colors in the two available wavebands, F475W (Sloan g) and F814W (I). Color Magnitude Diagrams, radial density plots and density maps were then created to characterize the globular cluster population in Coma. Preliminary results show the structure of the intergalactic globular cluster system throughout Coma, among the largest globular clusters catalogues to date. The spatial distribution of globular clusters shows clear overdensities, or bridges, between Coma galaxies. It also becomes evident that galaxies of similar luminosity have vastly different numbers of associated globular clusters.

  2. Disease spread in age structured populations with maternal age effects.

    PubMed

    Clark, Jessica; Garbutt, Jennie S; McNally, Luke; Little, Tom J

    2017-04-01

    Fundamental ecological processes, such as extrinsic mortality, determine population age structure. This influences disease spread when individuals of different ages differ in susceptibility or when maternal age determines offspring susceptibility. We show that Daphnia magna offspring born to young mothers are more susceptible than those born to older mothers, and consider this alongside previous observations that susceptibility declines with age in this system. We used a susceptible-infected compartmental model to investigate how age-specific susceptibility and maternal age effects on offspring susceptibility interact with demographic factors affecting disease spread. Our results show a scenario where an increase in extrinsic mortality drives an increase in transmission potential. Thus, we identify a realistic context in which age effects and maternal effects produce conditions favouring disease transmission.

  3. Population genetic structure and conservation of marbled murrelets (Brachyramphus marmoratus)

    USGS Publications Warehouse

    Friesen, V.L.; Birt, T.P.; Piatt, J.F.; Golightly, R.T.; Newman, S.H.; Hebert, P.N.; Congdon, B.C.; Gissing, G.

    2005-01-01

    Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among 194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of FST or ??ST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California.

  4. Geographic population structure analysis of worldwide human populations infers their biogeographical origins.

    PubMed

    Elhaik, Eran; Tatarinova, Tatiana; Chebotarev, Dmitri; Piras, Ignazio S; Maria Calò, Carla; De Montis, Antonella; Atzori, Manuela; Marini, Monica; Tofanelli, Sergio; Francalacci, Paolo; Pagani, Luca; Tyler-Smith, Chris; Xue, Yali; Cucca, Francesco; Schurr, Theodore G; Gaieski, Jill B; Melendez, Carlalynne; Vilar, Miguel G; Owings, Amanda C; Gómez, Rocío; Fujita, Ricardo; Santos, Fabrício R; Comas, David; Balanovsky, Oleg; Balanovska, Elena; Zalloua, Pierre; Soodyall, Himla; Pitchappan, Ramasamy; Ganeshprasad, Arunkumar; Hammer, Michael; Matisoo-Smith, Lisa; Wells, R Spencer

    2014-04-29

    The search for a method that utilizes biological information to predict humans' place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000-130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS's accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing.

  5. Comparison of various decentralised structural and cavity feedback control strategies for transmitted noise reduction through a double panel structure

    NASA Astrophysics Data System (ADS)

    Ho, Jen-Hsuan; Berkhoff, Arthur

    2014-03-01

    This paper compares various decentralised control strategies, including structural and acoustic actuator-sensor configuration designs, to reduce noise transmission through a double panel structure. The comparison is based on identical control stability indexes. The double panel structure consists of two panels with air in between and offers the advantages of low sound transmission at high frequencies, low heat transmission, and low weight. The double panel structure is widely used, such as in the aerospace and automotive industries. Nevertheless, the resonance of the cavity and the poor sound transmission loss at low frequencies limit the double panel's noise control performance. Applying active structural acoustic control to the panels or active noise control to the cavity has been discussed in many papers. In this paper, the resonances of the panels and the cavity are considered simultaneously to further reduce the transmitted noise through an existing double panel structure. A structural-acoustic coupled model is developed to investigate and compare various structural control and cavity control methods. Numerical analysis and real-time control results show that structural control should be applied to both panels. Three types of cavity control sources are presented and compared. The results indicate that the largest noise reduction is obtained with cavity control by loudspeakers modified to operate as incident pressure sources.

  6. Population structure of the peridomestic mosquito Ochlerotatus notoscriptus in Australia.

    PubMed

    Foley, D H; Russell, R C; Bryan, J H

    2004-06-01

    Ochlerotatus notoscriptus (Skuse) (Diptera: Culicidae) is the predominant peridomestic mosquito in Australia where it is the primary vector of dog heartworm, Dirofilaria immitis (Leidy), and a potentially important vector of arboviruses (Barmah Forest, Ross River) with geographical variation of vector competence. Although widespread, Oc. notoscriptus has low dispersal ability, so it may have isolated subpopulations. The identification of gene flow barriers may assist in understanding arbovirus epidemiology and disease risk, and for developing control strategies for this species. We investigated the population structure of Oc. notoscriptus from 17 sites around Australia, using up to 31 putative allozyme loci, 11 of which were polymorphic. We investigated the effect of larval environment and adult morphology on genetic variation. At least five subpopulations were found, four in New South Wales (NSW) and one unique to Darwin. Perth samples appear to be a product of recent colonization from the Australian east coast. For NSW sites, a Mantel test revealed an isolation by distance effect and spatial autocorrelation analysis revealed an area of effective gene flow of 67 km, which is high given the limited dispersal ability of this species. No consistent difference was observed between 'urban' and 'sylvan' habitats, which suggests frequent movement between these sites. However, a finer-scaled habitat study at Darwin revealed small but significant allele frequency differences, including for Gpi. No fixed allozyme differences were detected for sex, size, integument colour or the colour of species-diagnostic pale scales on the scutum. The domestic habit of Oc. notoscriptus and assisted dispersal have helped to homogenize this species geographically but population structure is still detectable on several levels associated with geographical variation of vector competence.

  7. Decoupling of body-plan diversification and ecological structuring during the Ediacaran–Cambrian transition: evolutionary and geobiological feedbacks

    PubMed Central

    Mángano, M. Gabriela; Buatois, Luis A.

    2014-01-01

    The rapid appearance of bilaterian clades at the beginning of the Phanerozoic is one of the most intriguing topics in macroevolution. However, the complex feedbacks between diversification and ecological interactions are still poorly understood. Here, we show that a systematic and comprehensive analysis of the trace-fossil record of the Ediacaran–Cambrian transition indicates that body-plan diversification and ecological structuring were decoupled. The appearance of a wide repertoire of behavioural strategies and body plans occurred by the Fortunian. However, a major shift in benthic ecological structure, recording the establishment of a suspension-feeder infauna, increased complexity of the trophic web, and coupling of benthos and plankton took place during Cambrian Stage 2. Both phases were accompanied by different styles of ecosystem engineering, but only the second one resulted in the establishment of the Phanerozoic-style ecology. In turn, the suspension-feeding infauna may have been the ecological drivers of a further diversification of deposit-feeding strategies by Cambrian Stage 3, favouring an ecological spillover scenario. Trace-fossil information strongly supports the Cambrian explosion, but allows for a short time of phylogenetic fuse during the terminal Ediacaran–Fortunian. PMID:24523279

  8. Decoupling of body-plan diversification and ecological structuring during the Ediacaran-Cambrian transition: evolutionary and geobiological feedbacks.

    PubMed

    Mángano, M Gabriela; Buatois, Luis A

    2014-04-07

    The rapid appearance of bilaterian clades at the beginning of the Phanerozoic is one of the most intriguing topics in macroevolution. However, the complex feedbacks between diversification and ecological interactions are still poorly understood. Here, we show that a systematic and comprehensive analysis of the trace-fossil record of the Ediacaran-Cambrian transition indicates that body-plan diversification and ecological structuring were decoupled. The appearance of a wide repertoire of behavioural strategies and body plans occurred by the Fortunian. However, a major shift in benthic ecological structure, recording the establishment of a suspension-feeder infauna, increased complexity of the trophic web, and coupling of benthos and plankton took place during Cambrian Stage 2. Both phases were accompanied by different styles of ecosystem engineering, but only the second one resulted in the establishment of the Phanerozoic-style ecology. In turn, the suspension-feeding infauna may have been the ecological drivers of a further diversification of deposit-feeding strategies by Cambrian Stage 3, favouring an ecological spillover scenario. Trace-fossil information strongly supports the Cambrian explosion, but allows for a short time of phylogenetic fuse during the terminal Ediacaran-Fortunian.

  9. The relationship between reproductive success and demographic structure in remnant populations of Primula veris

    NASA Astrophysics Data System (ADS)

    Brys, Rein; Jacquemyn, Hans; Endels, Patrick; Hermy, Martin; De Blust, Geert

    2003-12-01

    Plants often suffer reductions in fecundity due to fragmentation, degradation and destruction of populations and their sites. Whether this decrease in seed production has population-level consequences is generally unknown. Here, we aimed to determine the current status of remnant populations in the perennial herb Primula veris in Belgium. Furthermore, we investigated the effects of reduced population size and morph bias on reproductive success and explored if changes in demographic structure could be associated with population fecundity. We studied 69 populations that differed in population size from three to nearly 1500 flowering plants. Three different population types could be distinguished: (a) "dynamic" populations, characterized by high densities of 1 year old juveniles, (b) "normal" populations with adult age-stages prevailing, but still a considerable number of juveniles, and (c) "regressive" populations, in which only flowering adults dominate and rejuvenation hardly occurs. The three population types differed with respect to population size and morph frequency. Dynamic populations were significantly larger and showed a weaker morph bias compared to the intermediate normal and the small regressive populations. Reproductive success, studied the previous year in 26 populations, decreased significantly with decreasing population size and was significantly associated with the demographic structure of the populations. Coefficients of variation for the proportion of flowers setting fruit, the number of seeds per fruit and the total number of seeds per plant decreased significantly with increasing population size. Hence, the observed variability in seed set may be one of the causal factors affecting the observed types of population demographic structure.

  10. Decomposing variation in population growth into contributions from environment and phenotypes in an age-structured population.

    PubMed

    Pelletier, Fanie; Moyes, Kelly; Clutton-Brock, Tim H; Coulson, Tim

    2012-01-22

    Evaluating the relative importance of ecological drivers responsible for natural population fluctuations in size is challenging. Longitudinal studies where most individuals are monitored from birth to death and where environmental conditions are known provide a valuable resource to characterize complex ecological interactions. We used a recently developed approach to decompose the observed fluctuation in population growth of the red deer population on the Isle of Rum into contributions from climate, density and their interaction and to quantify their relative importance. We also quantified the contribution of individual covariates, including phenotypic and life-history traits, to population growth. Fluctuations in composition in age and sex classes ((st)age structure) of the population contributed substantially to the population dynamics. Density, climate, birth weight and reproductive status contributed less and approximately equally to the population growth. Our results support the contention that fluctuations in the population's (st)age structure have important consequences for population dynamics and underline the importance of including information on population composition to understand the effect of human-driven changes on population performance of long-lived species.

  11. Historical and anthropogenic factors affecting the population genetic structure of Ontario's inland lake populations of Walleye (Sander vitreus).

    PubMed

    Walter, Ryan P; Cena, Christopher J; Morgan, George E; Heath, Daniel D

    2012-01-01

    Populations existing in formerly glaciated areas often display composite historical and contemporary patterns of genetic structure. For Canadian freshwater fishes, population genetic structure is largely reflective of dispersal from glacial refugia and isolation within drainage basins across a range of scales. Enhancement of sport fisheries via hatchery stocking programs and other means has the potential to alter signatures of natural evolutionary processes. Using 11 microsatellite loci genotyped from 2182 individuals, we analyzed the genetic structure of 46 inland lake walleye (Sander vitreus) populations spanning five major drainage basins within the province of Ontario, Canada. Population genetic analyses coupled with genotype assignment allowed us to: 1) characterize broad- and fine-scale genetic structure among Ontario walleye populations; and 2) determine if the observed population divergence is primarily due to natural or historical processes, or recent anthropogenic events. The partitioning of genetic variation revealed higher genetic divergence among lakes than among drainage basins or proposed ancestries-indicative of relatively high isolation among lakes, study-wide. Walleye genotypes were clustered into three major groups, likely reflective of Missourian, Mississippian, and Atlantic glacial refugial ancestry. Despite detectable genetic signatures indicative of anthropogenic influences, province-wide spatial genetic structure remains consistent with the hypothesis of dispersal from distinct glacial refugia and subsequent isolation of lakes within primary drainage basins. Our results provide a novel example of minimal impacts from fishery enhancement to the broad-scale genetic structure of inland fish populations.

  12. Herschel far-infrared observations of the Carina Nebula complex. III. Detailed cloud structure and feedback effects

    NASA Astrophysics Data System (ADS)

    Roccatagliata, V.; Preibisch, T.; Ratzka, T.; Gaczkowski, B.

    2013-06-01

    Context. The star formation process in large clusters/associations can be strongly influenced by the feedback from high-mass stars. Whether the resulting net effect of the feedback is predominantly negative (cloud dispersal) or positive (triggering of star formation due to cloud compression) is still an open question. Aims: The Carina Nebula complex (CNC) represents one of the most massive star-forming regions in our Galaxy. We use our Herschel far-infrared observations to study the properties of the clouds over the entire area of the CNC (with a diameter of ≈3.2°, which corresponds to ≈125 pc at a distance of 2.3 kpc). The good angular resolution (10''-36'') of the Herschel maps corresponds to physical scales of 0.1-0.4 pc, and allows us to analyze the small-scale (i.e., clump-size) structures of the clouds. Methods: The full extent of the CNC was mapped with PACS and SPIRE in the 70, 160, 250, 350, and 500 μm bands. We determined temperatures and column densities at each point in these maps by modeling the observed far-infrared spectral energy distributions. We also derived a map showing the strength of the UV radiation field. We investigated the relation between the cloud properties and the spatial distribution of the high-mass stars and computed total cloud masses for different density thresholds. Results: Our Herschel maps resolve for the first time the small-scale structure of the dense clouds over the entire spatial extent of the CNC. Several particularly interesting regions, including the prominent pillars south of η Car, are analyzed in detail. We compare the cloud masses derived from the Herschel data with previous mass estimates based on sub-mm and molecular line data. Our maps also reveal a peculiar wave-like pattern in the northern part of the Carina Nebula. Finally, we characterize two prominent cloud complexes at the periphery of our Herschel maps, which are probably molecular clouds in the Galactic background. Conclusions: We find that the

  13. Self-optimising control for a class of continuous bioreactor via variable-structure feedback

    NASA Astrophysics Data System (ADS)

    Lara-Cisneros, Gerardo; Alvarez-Ramírez, José; Femat, Ricardo

    2016-04-01

    A self-optimising controller is designed for stabilisation of a class of bioreactor exploiting sliding-mode techniques. The stability analysis for the class of bioreactor, in open-loop configuration, suggests that the optimal behaviour, respect to maximal biomass production, occurs in an unstable region (structurally unstable). In this contribution, a variable-structure controller is designed, exploiting the inhibitory effect of substrate concentration under the biomass growth rate, such that the closed-loop system reaches the optimal manifold where the effect induced by the growth rate gradient is compensated (favouring the maximum growth rate). The self-optimising comprises an uncertainty estimator which computes the unknown terms for increasing the robustness issues of the sliding-mode scheme. Numerical experiments illustrate the performance and execution of the control strategy considering different parameter values for biomass growth rate. The robustness and fragility of the proposed controller are also discussed with respect to the modelling uncertainty and small changes in the controller gains, respectively.

  14. Respiratory sinus arrhythmia feedback in a stressed population exposed to a brief stressor demonstrated by quantitative EEG and sLORETA.

    PubMed

    Sherlin, Leslie; Muench, Fred; Wyckoff, Sarah

    2010-09-01

    Previous investigations of electroencephalograms during relaxation have identified increases in slow wave band power, correlations between increased levels of alpha activity with lower levels of anxiety, and autonomic changes characterized by otherwise documented decreased sympathetic activity. This study was carried out to determine the overall changes in quantitative electroencephalographic activity and the current source as a result of an acute session of respiratory sinus arrhythmia (RSA) biofeedback in a population of subjects experiencing stress. This study's findings provide physiological evidence of RSA feedback effect and suggest that RSA training may decrease arousal by promoting an increase of alpha band frequencies and decrease in beta frequencies overall and in areas critical to the regulation of stress. It was of interest that novices could achieve these objective alterations in EEG activity after minimal training and intervention periods considering that the previous literature on EEG and meditative states involve experienced meditators or participants who had been given extensive training. Additionally, these effects were present immediately following the training suggesting that the intervention may have effects beyond the actual practice.

  15. Numerical simulation of a novel all-optical flip-flop based on a chirped nonlinear distributed feedback semiconductor laser structure using GPGPU computing

    NASA Astrophysics Data System (ADS)

    Zoweil, H.

    2015-05-01

    A novel all-optical flip-flop based on a chirped nonlinear distributed feedback laser structure is proposed. The flip-flop does not require a holding beam. The optical gain is provided by a current injection into an active layer. The nonlinear wave-guiding layer consists of a chirped phase shifted grating accompanied with a negative nonlinear refractive index coefficient that increases in magnitude along the wave-guide. In the 'OFF' state, the chirped grating does not provide the required optical feedback to start lasing. An optical pulse switches the device 'ON' by reducing the chirp due to the negative nonlinear refractive index coefficient. The reduced chirp grating provides enough feedback to sustain a laser mode. The device is switched 'OFF' by cross gain modulation. GPGPU computing allows for long simulation time of multiple SET-RESET operations. The 'ON/OFF' transitions delays are in nanoseconds time scale.

  16. Formation of structures around HII regions: ionization feedback from massive stars

    NASA Astrophysics Data System (ADS)

    Tremblin, P.; Audit, E.; Minier, V.; Schmidt, W.; Schneider, N.

    2015-03-01

    We present a new model for the formation of dense clumps and pillars around HII regions based on shocks curvature at the interface between a HII region and a molecular cloud. UV radiation leads to the formation of an ionization front and of a shock ahead. The gas is compressed between them forming a dense shell at the interface. This shell may be curved due to initial interface or density modulation caused by the turbulence of the molecular cloud. Low curvature leads to instabilities in the shell that form dense clumps while sufficiently curved shells collapse on itself to form pillars. When turbulence is high compared to the ionized-gas pressure, bubbles of cold gas have sufficient kinetic energy to penetrate into the HII region and detach themselves from the parent cloud, forming cometary globules. Using computational simulations, we show that these new models are extremely efficient to form dense clumps and stable and growing elongated structures, pillars, in which star formation might occur (see Tremblin et al. 2012a). The inclusion of turbulence in the model shows its importance in the formation of cometary globules (see Tremblin et al. 2012b). Globally, the density enhancement in the simulations is of one or two orders of magnitude higher than the density enhancement of the classical ``collect and collapse`` scenario. The code used for the simulation is the HERACLES code, that comprises hydrodynamics with various equation of state, radiative transfer, gravity, cooling and heating. Our recent observations with Herschel (see Schneider et al. 2012a) and SOFIA (see Schneider et al. 2012b) and additional Spitzer data archives revealed many more of these structures in regions where OB stars have already formed such as the Rosette Nebula, Cygnus X, M16 and Vela, suggesting that the UV radiation from massive stars plays an important role in their formation. We present a first comparison between the simulations described above and recent observations of these regions.

  17. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

    PubMed Central

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

  18. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    PubMed

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  19. Effects of structural connectivity on fine scale population genetic structure of muskrat, Ondatra zibethicus.

    PubMed

    Laurence, Sophie; Smith, Matthew J; Schulte-Hostedde, Albrecht I

    2013-09-01

    In heterogeneous landscapes, physical barriers and loss of structural connectivity have been shown to reduce gene flow and therefore lead to population structuring. In this study, we assessed the influence of landscape features on population genetic structure and gene flow of a semiaquatic species, the muskrat. A total of 97 muskrats were sampled from three watersheds near Sudbury, Ontario, Canada. We estimated population genetic structure using 11 microsatellite loci and identified a single genetic cluster and no genetic differences were found among the watersheds as a result of high levels of gene flow. At finer scales, we assessed the correlation between individual pairwise genetic distances and Euclidean distance as well as different models of least cost path (LCP). We used a range of cost values for the landscape types in order to build our LCP models. We found a positive relationship between genetic distance and least cost distance when we considered roads as corridors for movements. Open landscapes and urban areas seemed to restrict but not prevent gene flow within the study area. Our study underlines the high-dispersal ability of generalist species in their use of landscape and highlights how landscape features often considered barriers to animal movements are corridors for other species.

  20. Community structure, population structure and topographical specialisation of Gyrodactylus (monogenea) ectoparasites living on sympatric stickleback species.

    PubMed

    Raeymaekers, Joost A M; Huyse, Tine; Maelfait, Hannelore; Hellemans, Bart; Volckaert, Filip A M

    2008-09-01

    In order to disentangle the contribution of host and parasite biology to host specificity, we compared the structure and population dynamics of the Gyrodactylus (von Nordmann, 1832) flatworm community living on sympatric three-spined Gasterosteus aculeatus L. and nine-spined Pungitius pungitius (L.) stickleback. Between April 2002 and March 2003, a small lowland creek was sampled monthly. Species identity of about 75% of the worms per host was determined with a genetic nuclear marker (ITS1). Each stickleback species hosted a characteristic gill- and fin-parasitic Gyrodactylus: G. arcuatus Bychowsky, 1933 and G. gasterostei Gläser, 1974 respectively infecting the three-spined stickleback, with G. rarus Wegener, 1910 and G. pungitii Malmberg, 1964 infecting the nine-spined stickleback. Host size and seasonal dynamics were strong determinants of parasite abundance. A strong interaction between host and parasite species determined infection levels and affected three levels of parasite organisation: community structure, population structure and topographical specialisation. Community and population structure were shaped by asymmetric cross-infections, resulting in a net transmission of the Gyro-dactylus species typical of the nine-spined stickleback towards the three-spined stickleback. Host density was not a major determinant of parasite exchange. Aggregation and topographical specialisation of the Gyrodactylus species of the three-spined stickleback were more pronounced than that of the nine-spined stickleback.

  1. Feedbacks of Composition and Neutral Density Changes on the Structure of the Cusp Density Anomaly

    NASA Astrophysics Data System (ADS)

    Brinkman, D. G.; Walterscheid, R. L.; Clemmons, J. H.

    2015-12-01

    The Earth's magnetospheric cusp provides direct access of energetic particles to the thermosphere. These particles produce ionization and kinetic (particle) heating of the atmosphere. The increased ionization coupled with enhanced electric fields in the cusp produces increased Joule heating and ion drag forcing. These energy inputs cause large wind and temperature changes in the cusp region. Measurements by the CHAMP satellite (460-390- km altitude) have shown strongly enhanced density in the cusp region. The Streak mission (325-123 km), on the other hand, showed a relative depletion. The atmospheric response in the cusp can be sensitive to composition and neutral density changes. In response to heating in the cusp, air of heavier mean molecular weight is brought up from lower altitudes significantly affecting pressure gradients. This opposes the effects of temperature change due to heating and in-turn affects the density and winds produced in the cusp. Also changes in neutral density change the interaction between precipitating particles and the atmosphere and thus change heating rates and ionization in the region affected by cusp precipitation. In this study we assess the sensitivity of the wind and neutral density structure in the cusp region to changes in the mean molecular weight induced by neutral dynamics, and the changes in particle heating rates and ionization which result from changes in neutral density. We use a high resolution two-dimensional time-dependent nonhydrostatic nonlinear dynamical model where inputs can be systematically altered. The resolution of the model allows us to examine the complete range of cusp widths. We compare the current simulations to observations by CHAMP and Streak. Acknowledgements: This research was supported by The Aerospace Corporation's Technical Investment program

  2. Active vibration mitigation of distributed parameter, smart-type structures using Pseudo-Feedback Optimal Control (PFOC)

    NASA Technical Reports Server (NTRS)

    Patten, W. N.; Robertshaw, H. H.; Pierpont, D.; Wynn, R. H.

    1989-01-01

    A new, near-optimal feedback control technique is introduced that is shown to provide excellent vibration attenuation for those distributed parameter systems that are often encountered in the areas of aeroservoelasticity and large space systems. The technique relies on a novel solution methodology for the classical optimal control problem. Specifically, the quadratic regulator control problem for a flexible vibrating structure is first cast in a weak functional form that admits an approximate solution. The necessary conditions (first-order) are then solved via a time finite-element method. The procedure produces a low dimensional, algebraic parameterization of the optimal control problem that provides a rigorous basis for a discrete controller with a first-order like hold output. Simulation has shown that the algorithm can successfully control a wide variety of plant forms including multi-input/multi-output systems and systems exhibiting significant nonlinearities. In order to firmly establish the efficacy of the algorithm, a laboratory control experiment was implemented to provide planar (bending) vibration attenuation of a highly flexible beam (with a first clamped-free mode of approximately 0.5 Hz).

  3. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers

    PubMed Central

    Edea, Zewdu; Dadi, Hailu; Kim, Sang-Wook; Dessie, Tadelle; Lee, Taeheon; Kim, Heebal; Kim, Jong-Joo; Kim, Kwan-Suk

    2013-01-01

    In total, 166 individuals from five indigenous Ethiopian cattle populations – Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) – were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (FST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed. PMID:23518904

  4. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Fee structure for special population... § 50.10 Fee structure for special population censuses. The Bureau of the Census is authorized to conduct special population censuses at the request of and at the expense of the community concerned....

  5. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Fee structure for special population... § 50.10 Fee structure for special population censuses. The Bureau of the Census is authorized to conduct special population censuses at the request of and at the expense of the community concerned....

  6. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Fee structure for special population... § 50.10 Fee structure for special population censuses. The Bureau of the Census is authorized to conduct special population censuses at the request of and at the expense of the community concerned....

  7. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Fee structure for special population... § 50.10 Fee structure for special population censuses. The Bureau of the Census is authorized to conduct special population censuses at the request of and at the expense of the community concerned....

  8. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Fee structure for special population... § 50.10 Fee structure for special population censuses. The Bureau of the Census is authorized to conduct special population censuses at the request of and at the expense of the community concerned....

  9. Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum.

    PubMed Central

    Segovia, L; Piñero, D; Palacios, R; Martínez-Romero, E

    1991-01-01

    The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determined by the electrophoretic mobilities of eight metabolic enzymes. Nonsymbiotic strains were isolated from the rhizosphere of bean plants and characterized by growth on differential media and at different temperatures, intrinsic antibiotic resistance, the lack of homology to a nifH probe, and their inability to form nodules on bean roots. All the isolates clustered with R. leguminosarum bv. phaseoli reference strains and did not encompass any other Rhizobium taxa. Their rRNA operon restriction fragment length polymorphisms and the nucleotide sequence of a fragment of the 16S rRNA gene were also found to be identical to those of R. leguminosarum bv. phaseoli reference strains. When complemented with an R. leguminosarum bv. phaseoli symbiotic plasmid (p42d), the nonsymbiotic isolates were able to fix nitrogen in symbiosis with bean roots at levels similar to those of the parental strain. The symbiotic isolates were found at a relative frequency of 1 in 40 nonsymbiotic R. leguminosarum strains. Images PMID:1707606

  10. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

    PubMed Central

    Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

    2016-01-01

    There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

  11. Genetic structure of the human population in the Po delta

    PubMed Central

    Beretta, M.; Mazzetti, P.; Mamolini, E.; Gavina, R.; Barale, R.; Vullo, C.; Ravani, A.; Franze, A.; Sapigni, T.; Soracco, E.; Davi, D.; Ricci, N.; Cappello, N.; Rendine, S.; Piazza, A.; Barrai, I.

    1989-01-01

    The genetic structure of the population of Ferrara Province in the Po delta in Italy was investigated using χ2 analysis, kinship analysis, analysis of correspondences, and geographical mapping of principal components of gene frequencies, χ2 Analysis tests for Hardy-Weinberg equilibrium and for heterogeneity of gene and phenotype frequencies; kinship analysis tests for association between indicators of genetic and geographic proximity; analysis of correspondences relates localities and genetic systems in an eigenvectorial space; and geographic mapping displays the principal components of gene frequencies in the real space. In 1,364 adults in 26 residential units, seven presumably neutral isoenzyme systems were typed; ACP1 ESD, GLO I, GPT, PGD, PGM1 and PGP. It was found that average kinship for these neutral systems is correlated with geographic distance in this small area, but not as strongly as kinship for beta-thalassemia. A north-south gradient was observed for ESD. Analysis of correspondences indicated GPT, PGM1, and GLO I as the systems contributing most to differentiation within the province. The maps obtained from principal components of gene frequencies were consistent with the migrational history of the area. ImagesFigure 4Figure 5Figure 6Figure 7Figure 8 PMID:2741951

  12. Genetic structure of autochthonous populations of Meso-America: Mexico.

    PubMed

    Lisker, R; Ramírez, E; Babinsky, V

    1996-06-01

    We analyze the possible effect of gene flow on the genetic structure of present-day Mexicans. For this purpose we reviewed previous admixture estimates for various Indian and Mestizo groups. Several facts seem clear: (1) There are no pure Indian groups in Mexico, because all Indian groups show variable degrees of admixture, mostly with whites (range, 0.088 in the Huichol to 0.373 in the Huasteco); (2) the main ancestral contribution to the noncoastal lower middle class Mestizo populations is Indian (above 50%) so that from a genetic standpoint Indians and lower middle class Mestizos are not much different; and (3) black ancestry is quite high on the coasts, ranging from 0.127 to 0.405 on the east coast, and is present in other Mestizos, ranging in large urban centers from 0.027 in Oaxaca to 0.107 in Puebla and in smaller cities from 0.08 in Tlaxcala to 0.181 in Cuanalán.

  13. Geographic population structure analysis of worldwide human populations infers their biogeographical origins

    PubMed Central

    Elhaik, Eran; Tatarinova, Tatiana; Chebotarev, Dmitri; Piras, Ignazio S.; Maria Calò, Carla; De Montis, Antonella; Atzori, Manuela; Marini, Monica; Tofanelli, Sergio; Francalacci, Paolo; Pagani, Luca; Tyler-Smith, Chris; Xue, Yali; Cucca, Francesco; Schurr, Theodore G.; Gaieski, Jill B.; Melendez, Carlalynne; Vilar, Miguel G.; Owings, Amanda C.; Gómez, Rocío; Fujita, Ricardo; Santos, Fabrício R.; Comas, David; Balanovsky, Oleg; Balanovska, Elena; Zalloua, Pierre; Soodyall, Himla; Pitchappan, Ramasamy; GaneshPrasad, ArunKumar; Hammer, Michael; Matisoo-Smith, Lisa; Wells, R. Spencer; Acosta, Oscar; Adhikarla, Syama; Adler, Christina J.; Bertranpetit, Jaume; Clarke, Andrew C.; Cooper, Alan; Der Sarkissian, Clio S. I.; Haak, Wolfgang; Haber, Marc; Jin, Li; Kaplan, Matthew E.; Li, Hui; Li, Shilin; Martínez-Cruz, Begoña; Merchant, Nirav C.; Mitchell, John R.; Parida, Laxmi; Platt, Daniel E.; Quintana-Murci, Lluis; Renfrew, Colin; Lacerda, Daniela R.; Royyuru, Ajay K.; Sandoval, Jose Raul; Santhakumari, Arun Varatharajan; Soria Hernanz, David F.; Swamikrishnan, Pandikumar; Ziegle, Janet S.

    2014-01-01

    The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing. PMID:24781250

  14. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci

    PubMed Central

    2011-01-01

    Background There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region. Result We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. Conclusion We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley. PMID:21542921

  15. EVOLUTION OF BRIGHTEST CLUSTER GALAXY STRUCTURAL PARAMETERS IN THE LAST {approx}6 Gyr: FEEDBACK PROCESSES VERSUS MERGER EVENTS

    SciTech Connect

    Ascaso, B.; Aguerri, J. A. L.; Varela, J.; Cava, A.; Moles, M.

    2011-01-10

    We present results on the evolution of the structural parameters of two samples of brightest cluster galaxies (BCGs) in the last 6 Gyr. The nearby sample of BCGs consists of 69 galaxies from the WINGS survey spanning a redshift range of 0.04 < z < 0.07. The intermediate-redshift (0.3 < z < 0.6) sample is formed by 20 BCGs extracted from the Hubble Space Telescope archive. Both samples have similar spatial resolution and their host clusters have similar X-ray luminosities. We report an increase in the size of the BCGs from intermediate to local redshift. However, we do not detect any variation in the Sersic shape parameter in both samples. These results prove to be robust since the observed tendencies are model independent. We also obtain significant correlations between some of the BCG parameters and the main properties of the host clusters. More luminous, larger, and centrally located BCGs are located in more massive and dominant galaxy clusters. These facts indicate that the host galaxy cluster has played an important role in the formation of their BCGs. We discuss the possible mechanisms that can explain the observed evolution of the structural parameters of the BCGs. We conclude that the main mechanisms that can explain the increase in size and the non-evolution in the Sersic shape parameter of the BCGs in the last 6 Gyr are feedback processes. This result disagrees with semi-analytical simulation results supporting the idea that merging processes are the main mechanism responsible for the evolution of the BCGs up until the present epoch.

  16. Feedbacks between earlywood anatomy and non-structural carbohydrates affect spring phenology and wood production in ring-porous oaks

    NASA Astrophysics Data System (ADS)

    Pérez-de-Lis, Gonzalo; García-González, Ignacio; Rozas, Vicente; Olano, José Miguel

    2016-10-01

    Non-structural carbohydrates (NSC) play a central role in the construction and maintenance of a tree's vascular system, but feedbacks between the NSC status of trees and wood formation are not fully understood. We aimed to evaluate multiple dependencies among wood anatomy, winter NSC, and phenology for coexisting temperate (Quercus robur) and sub-Mediterranean (Q. pyrenaica) oaks along a water-availability gradient in the NW Iberian Peninsula. Sapwood NSC concentrations were quantified at three sites in December 2012 (N = 240). Leaf phenology and wood anatomy were surveyed in 2013. Structural equation modelling was used to analyse the interplay among hydraulic diameter (Dh), winter NSC, budburst date, and earlywood vessel production (EVP), while the effect of Dh and EVP on latewood width was assessed by using a mixed-effects model. NSC and wood production increased under drier conditions for both species. Q. robur showed a narrower Dh and lower soluble sugar (SS) concentration (3.88-5.08 % dry matter) than Q. pyrenaica (4.06-5.57 % dry matter), but Q. robur exhibited larger EVP and wider latewood (1403 µm) than Q. pyrenaica (667 µm). Stem diameter and Dh had a positive effect on SS concentrations, which were related to an earlier leaf flushing in both species. Sapwood sugar content appeared to limit EVP exclusively in Q. pyrenaica. In turn, Dh and EVP were found to be key predictors of latewood growth. Our results confirm that sapwood SS concentrations are involved in modulating growth resumption and xylem production in spring. Q. pyrenaica exhibited a tighter control of carbohydrate allocation to wood formation than Q. robur, which would play a role in protecting against environmental stress in the sub-Mediterranean area.

  17. Geometrical Structures of Chemically Decomposed Thick and Thin Disk Populations

    NASA Astrophysics Data System (ADS)

    Kawata, D.; Brook, C. B.; Rahimi, A.; Gibson, B. K.

    2016-10-01

    We summarize the thick and thin disk formation commonly seen in cosmological N-body simulations. As suggested in Brook et al. (2004), a hierarchical clustering scenario causes multiple minor gas-rich mergers, and leads to the formation of a kinematically hot disk, thick disk population, at a high redshift. Once the mergers become less significant at a later epoch, the thin disk population starts building up. Because in this scenario the thick disk population forms intensively at high redshift through multiple gas-rich mergers, the thick disk population is compact and has systematically higher [α/Fe] abundance than the thin disk population. We discuss that the thick disk population would be affected by the formation of the thin disk and suffer from the radial migration, which helps the thick disk population to be observed in the solar neighborhood. In addition, we show that the current cosmological simulations also naturally predict that the thin disk population is flaring at the outer region. As shown in Rahimi et al. (2014), at high vertical height from the disk plane, the compact thick disk population (low metallicity and high [α/Fe]) is dominant in the inner region and the flaring thin disk population (high metallicity and low [α/Fe]) contributes more in the outer region. This helps to explain the positive radial metallicity gradient and negative radial [α/Fe] gradient observed at high vertical height in the Milky Way stellar disk.

  18. Accurate inference of subtle population structure (and other genetic discontinuities) using principal coordinates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Accurate inference of genetic discontinuities between populations is an essential component of intraspecific biodiversity and evolution studies, as well as associative genetics. The most widely used methods to infer population structure are model based, Bayesian MCMC procedures that minimize Hardy...

  19. Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

    PubMed Central

    Ryberg, Wade A.; Hill, Michael T.; Painter, Charles W.; Fitzgerald, Lee A.

    2013-01-01

    Although defining population structure according to discrete habitat patches is convenient for metapopulation theories, taking this approach may overlook structure within populations continuously distributed across landscapes. For example, landscape features within habitat patches direct the movement of organisms and define the density distribution of individuals, which can generate spatial structure and localized dynamics within populations as well as among them. Here, we use the neighborhood concept, which describes population structure relative to the scale of individual movements, to illustrate how localized dynamics within a population of lizards (Sceloporus arenicolus) arise in response to variation in landscape pattern within a continuous habitat patch. Our results emphasize links between individual movements at small scales and the emergence of spatial structure within populations which resembles metapopulation dynamics at larger scales. We conclude that population dynamics viewed in a landscape context must consider the explicit distribution and movement of individuals within continuous habitat as well as among habitat patches. PMID:23441217

  20. AGN feedback and star formation in ETGs: negative and positive feedback

    NASA Astrophysics Data System (ADS)

    Ciotti, Luca; Ostriker, Jeremiah P.; Novak, Greg; Negri, Andrea; Pellegrini, Silvia; Posacki, Silvia

    2015-08-01

    AGN feedback from supermassive black holes at the center of Early Type Galaxies is commonly invoked as the explanation for the quenching of star formation in these systems, that after this phase are considered “red and dead”. The situation is by far more complicated, due to the significant amount of mass injected in the galaxy by the evolving stellar population over cosmological times. In absence of feedback, this mass would lead to unobserved galactic cooling flows, and to central black holes two orders of magnitude more massive than observed. I will present the results of state-of-the-art hydrodynamical simulations with radiative transport and star formation of the “passive” evolution of ETGs, focusing in particular on highly structured spatial and temporal nature of the intermittent AGN feedback, that is not only negative (shutting down the cooling episodes of the ISM), but also positive, inducing star formation in the inner regions of the host galaxy.

  1. A NEW POPULATION OF HIGH-z, DUSTY Ly{alpha} EMITTERS AND BLOBS DISCOVERED BY WISE: FEEDBACK CAUGHT IN THE ACT?

    SciTech Connect

    Bridge, Carrie R.; Blain, Andrew; Borys, Colin J. K.; Griffith, Roger L.; Tsai, Chao-Wei; Petty, Sara; Farrah, Duncan; Benford, Dominic; Eisenhardt, Peter; Stern, Daniel; Wu Jingwen; Jarrett, Tom; Lonsdale, Carol; Stanford, Spencer A.; Wright, Edward L.

    2013-06-01

    By combining data from the NASA Wide-field Infrared Survey Explorer (WISE) mission with optical spectroscopy from the W. M. Keck telescope, we discover a mid-IR color criterion that yields a 78% success rate in identifying rare, typically radio-quiet, 1.6 {approx}< z {approx}< 4.6 dusty Ly{alpha} emitters (LAEs). Of these, at least 37% have emission extended on scales of 30-100 kpc and are considered Ly{alpha} ''blobs'' (LABs). The objects have a surface density of only {approx}0.1 deg{sup -2}, making them rare enough that they have been largely missed in deep, small area surveys. We measured spectroscopic redshifts for 92 of these galaxies, and find that the LAEs (LABs) have a median redshift of 2.3 (2.5). The WISE photometry coupled with data from Herschel (Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA) reveals that these galaxies are in the Hyper Luminous IR galaxy regime (L{sub IR} {approx}> 10{sup 13}-10{sup 14} L{sub Sun }) and have warm colors. They are typically more luminous and warmer than other dusty, z {approx} 2 populations such as submillimeter-selected galaxies and dust-obscured galaxies. These traits are commonly associated with the dust being illuminated by intense active galactic nucleus activity. We hypothesize that the combination of spatially extended Ly{alpha}, large amounts of warm IR-luminous dust, and rarity (implying a short-lived phase) can be explained if the galaxies are undergoing brief, intense ''feedback'' transforming them from an extreme dusty starburst/QSO into a mature galaxy.

  2. A New Population of High-z, Dusty Lyman-alpha Emitters and Blobs Discovered by WISE: Feedback Caught in the Act?

    NASA Technical Reports Server (NTRS)

    Bridge, Carrie R.; Blain, Andrew; Borys, Colin J. K.; Petty, Sara; Benford, Dominic; Eisenhardt, Peter; Farrah, Duncan; Griffith, Roger, L.; Jarrett, Tom; Lonsdale, Carol; Stanford. Spencer A.; Stern, Daniel; Tsai, Chao-Wei; Wright, Edward L.; Wu, Jingwen

    2013-01-01

    By combining data from the NASA Wide-field Infrared Survey Explorer (WISE) mission with optical spectroscopy from the W. M. Keck telescope, we discover a mid-IR color criterion that yields a 78% success rate in identifying rare, typically radio-quiet, 1.6 approx. < z approx. < 4.6 dusty Ly-alpha emitters (LAEs). Of these, at least 37% have emission extended on scales of 30-100 kpc and are considered Ly-alpha "blobs" (LABs). The objects have a surface density of only approx.. 0.1 deg(exp -2), making them rare enough that they have been largely missed in deep, small area surveys. We measured spectroscopic redshifts for 92 of these galaxies, and find that the LAEs (LABs) have a median redshift of 2.3 (2.5). The WISE photometry coupled with data from Herschel (Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA) reveals that these galaxies are in the Hyper Luminous IR galaxy regime (L(sub IR) approx. > 10(exp 13)-10(exp 14) Solar L) and have warm colors. They are typically more luminous and warmer than other dusty, z approx.. 2 populations such as submillimeter-selected galaxies and dust-obscured galaxies. These traits are commonly associated with the dust being illuminated by intense active galactic nucleus activity. We hypothesize that the combination of spatially extended Ly-alpha, large amounts of warm IR-luminous dust, and rarity (implying a short-lived phase) can be explained if the galaxies are undergoing brief, intense "feedback" transforming them from an extreme dusty starburst/QSO into a mature galaxy.

  3. A New Population of High-z, Dusty Lyα Emitters and Blobs Discovered by WISE: Feedback Caught in the Act?

    NASA Astrophysics Data System (ADS)

    Bridge, Carrie R.; Blain, Andrew; Borys, Colin J. K.; Petty, Sara; Benford, Dominic; Eisenhardt, Peter; Farrah, Duncan; Griffith, Roger L.; Jarrett, Tom; Lonsdale, Carol; Stanford, Spencer A.; Stern, Daniel; Tsai, Chao-Wei; Wright, Edward L.; Wu, Jingwen

    2013-06-01

    By combining data from the NASA Wide-field Infrared Survey Explorer (WISE) mission with optical spectroscopy from the W. M. Keck telescope, we discover a mid-IR color criterion that yields a 78% success rate in identifying rare, typically radio-quiet, 1.6 <~ z <~ 4.6 dusty Lyα emitters (LAEs). Of these, at least 37% have emission extended on scales of 30-100 kpc and are considered Lyα "blobs" (LABs). The objects have a surface density of only ~0.1 deg-2, making them rare enough that they have been largely missed in deep, small area surveys. We measured spectroscopic redshifts for 92 of these galaxies, and find that the LAEs (LABs) have a median redshift of 2.3 (2.5). The WISE photometry coupled with data from Herschel (Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA) reveals that these galaxies are in the Hyper Luminous IR galaxy regime (L IR >~ 1013-1014 L ⊙) and have warm colors. They are typically more luminous and warmer than other dusty, z ~ 2 populations such as submillimeter-selected galaxies and dust-obscured galaxies. These traits are commonly associated with the dust being illuminated by intense active galactic nucleus activity. We hypothesize that the combination of spatially extended Lyα, large amounts of warm IR-luminous dust, and rarity (implying a short-lived phase) can be explained if the galaxies are undergoing brief, intense "feedback" transforming them from an extreme dusty starburst/QSO into a mature galaxy.

  4. [A study on structural responses of Korea population transition].

    PubMed

    Kong, S K; Cho, A J; Kim, E J

    1988-12-01

    The Korean population experienced a drastic demographic transition in this century. The family planning program has dramatically decreased the fertility rate. The total fertility rate, which was 6 in 1960, decreased to 4.3 in 1970, 2.8 in 1980, 2.1 in 1985, and 1.7 in 1988. The government now predicts a stationary population of 52 million in 2020. Population policy must recognize the relationship between population growth and socioeconomic factors. Urban population has increased very rapidly due to socio-political change and industrialization. The urban population comprised 1/5 of the total population in 1960, forms 2/3 of the present population, and will form 4/5 of the population in 2020. Modernization brings the problems associated with education, employment, marriage, housing, family, and ultimately the aging of the population. The 1st step in meeting problems from the demographic transition is organizing the family planning program in an effective way. The very concept family planning should be transferred to family life planning, which includes the family formation period, the family growing period with child education and couple life, and the family reduction period with the older family. The family planning program could retrain its grass roots workers for family health and welfare. The use of effective contraception would preclude the need for induced abortion. The family health program could include diet, nutrition, home environment and sanitation, geriatric diseases, and health services for the aged. Family welfare planning and services are more necessary than ever with the proliferation of the nuclear family and increasing female employment. Population policy must be established on the country level and coordinated with development policy.

  5. Population structure and evolution of pathogenicity of Yersinia pseudotuberculosis.

    PubMed

    Ch'ng, Shear Lane; Octavia, Sophie; Xia, Qiuyu; Duong, An; Tanaka, Mark M; Fukushima, Hiroshi; Lan, Ruiting

    2011-02-01

    Yersinia pseudotuberculosis is an enteric human pathogen but is widespread in the environment. Pathogenicity is determined by a number of virulence factors, including the virulence plasmid pYV, the high-pathogenicity island (HPI), and the Y. pseudotuberculosis-derived mitogen (YPM), a superantigen. The presence of the 3 virulence factors varies among Y. pseudotuberculosis isolates. We developed a multilocus sequence typing (MLST) scheme to address the population structure of Y. pseudotuberculosis and the evolution of its pathogenicity. The seven housekeeping genes selected for MLST were mdh, recA, sucA, fumC, aroC, pgi, and gyrB. An MLST analysis of 83 isolates of Y. pseudotuberculosis, representing 19 different serotypes and six different genetic groups, identified 61 sequence types (STs) and 12 clonal complexes. Out of 26 allelic changes that occurred in the 12 clonal complexes, 13 were mutational events while 13 were recombinational events, indicating that recombination and mutation contributed equally to the diversification of the clonal complexes. The isolates were separated into 2 distinctive clusters, A and B. Cluster A is the major cluster, with 53 STs (including Y. pestis strains), and is distributed worldwide, while cluster B is restricted to the Far East. The YPM gene is widely distributed on the phylogenetic tree, with ypmA in cluster A and ypmB in cluster B. pYV is present in cluster A only but is sporadically absent in some cluster A isolates. In contrast, an HPI is present only in a limited number of lineages and must be gained by lateral transfer. Three STs carry all 3 virulence factors and can be regarded as high-pathogenicity clones. Isolates from the same ST may not carry all 3 virulence factors, indicating frequent gain or loss of these factors. The differences in pathogenicity among Y. pseudotuberculosis strains are likely due to the variable presence and instability of the virulence factors.

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

    PubMed

    Rico, Y; Wagner, H H

    2016-11-01

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

  7. Population structure of Vitis rupestris, an important resource for viticulture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The wild North American grapevine Vitis rupestris Scheele is an important genetic resource for viticulture, but its natural population has been severely depleted. We collected samples from seven V. rupestris populations from the Ozark Plateau in Missouri and Ouachita Mountains in Oklahoma and genoty...

  8. The use of objective structured self-assessment and peer-feedback (OSSP) for learning communication skills: evaluation using a controlled trial.

    PubMed

    Perera, Jennifer; Mohamadou, Galy; Kaur, Satpal

    2010-05-01

    Feedback is essential to guide students towards expected performance goals. The usefulness of teacher feedback on improving communication skills (CS) has been well documented. It has been proposed that self-assessment and peer-feedback has an equally important role to play in enhancing learning. This is the focus of this study. Objectively structured self-assessment and peer feedback (OSSP) was incorporated into small group CS teaching sessions of a group of semester one medical students who were learning CS for the first time, to minimise the influence of previous educational interventions. A control group matched for academic performance, gender and age was used to enable parallel evaluation of the innovation. A reflective log containing closed and open ended questions was used for OSSP. Facilitators and simulated patients provided feedback to students in both groups during CS learning as per routine practice. Student perceptions on OSSP and acceptability as a learning method were explored using a questionnaire. CS were assessed in both groups using objective structured clinical examination (OSCE) as per routine practice and assessors were blinded as to which group the student belonged. Mean total score and scores for specific areas of interview skills were significantly higher in the experimental group. Analysis of the questionnaire data showed that students gained fresh insights into specific areas such as empathy, addressing patients' concerns and interview style during OSSP which clearly corroborated the specific differences in scores. The free text comments were highly encouraging as to acceptability of OSSP, in spite of 67% being never exposed to formal self- and peer-assessment during pre-university studies. OSSP promotes effective CS learning and learner acceptability is high.

  9. Clonal population structures are derived from various population processes in the protistan oyster parasite Perkinsus marinus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Population genetic analysis of genotypes comprised of seven microsatellite loci revealed clonal genetic patterns in each of four populations of the protistan estuarine parasite Perkinsus marinus. Each locus was amplified directly from DNA extracted from infected oysters collected from four geographi...

  10. Variability levels, population size and structure of American and European Drosophila montana populations.

    PubMed

    Vieira, J; Hoikkala, A

    2001-04-01

    The level and patterns of nucleotide diversity have been characterized for two X-linked loci, fused (fu; a region of 2362 bp) and suppressor of sable (su(s); a region of 413 bp), in one European and one American D. montana population. Sequence variation at these loci shows that the two populations are divergent, although they may not be completely isolated. Data on the level of silent site variability at su(s) (1.1% and 0.5% for the European and American populations, respectively) suggest that the effective population sizes of the two populations may be similar. At the fused locus, one European sequence was highly divergent and may have resulted from gene conversion, and was excluded from the analysis. With this sequence removed, the level of silent site variability was significantly lower in the European population (0.28%) than in the American population (2.3%), which suggests a selective sweep at or near fu in the former population.

  11. Population Growth and Demographic Structure. Proceedings of the United Nations Expert Group Meeting on Population Growth and Demographic Structure (Paris, France, November 16-20, 1992).

    ERIC Educational Resources Information Center

    United Nations, New York, NY. Dept. of Economic and Social Affairs.

    This volume contains the report and recommendations of the United Nations-sponsored meeting on population growth and demographic structure which was held in Paris, November 1992. Materials in the volume can serve as useful tools for future research on the relations between population, environment, and development and further the work of the United…

  12. When domestic cat (Felis silvestris catus) population structures interact with their viruses.

    PubMed

    Pontier, Dominique; Fouchet, David; Bahi-Jaber, Narges; Poulet, Hervé; Guiserix, Micheline; Natoli, Eugenia; Sauvage, Frank

    2009-01-01

    Many theoretical studies have proposed different causal mechanisms by which the structure of a host population could have important implications for life history traits of pathogens. However, little information is available from real systems to test these hypotheses. The domestic cat, Felis silvestris catus, whose populations exhibit a great variability in social and spatial structure, represent an ideal case study to assess this question. In the present article, we show how cat population structure may have influenced the evolution of feline viruses and, in return, how these viruses may have modified the genetic structure of cat populations.

  13. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations

    PubMed Central

    Pérez, Jesús M.; Soriguer, Ramón C.; Granados, José E.

    2017-01-01

    Background Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. Methodology/Principal Findings We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Conclusions Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies. PMID:28135293

  14. Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus)

    PubMed Central

    Matsunami, Masatoshi; Igawa, Takeshi; Michimae, Hirofumi; Miura, Toru; Nishimura, Kinya

    2016-01-01

    The Hokkaido salamander (Hynobius retardatus) is endemic to Hokkaido Island, Japan, and shows intriguing flexible phenotypic plasticity and regional morphological diversity. However, to date, allozymes and partial mitochondria DNA sequences have provided only an outline of its demographic histories and the pattern of its genetic diversification. To understand the finer details of the population structure of this species and its evolution since speciation, we genotyped five regional populations by using 12 recently developed microsatellite polymorphic markers. We found a clear population structure with low gene flow among the five populations, but a close genetic relationship between the Teshio and Kitami populations. Our demographic analysis suggested that Teshio and Erimo had the largest effective population sizes among the five populations. These findings regarding the population structure and demography of H. retardatus improve our understanding of the faunal phylogeography on Hokkaido Island and also provide fundamental genetic information that will be useful for future studies. PMID:27257807

  15. Highly Structured Asian Drosophila melanogaster Populations: A New Tool for Hitchhiking Mapping?

    PubMed Central

    Schlötterer, Christian; Neumeier, Hannah; Sousa, Carla; Nolte, Viola

    2006-01-01

    Mark-recapture experiments showed that D. melanogaster has high dispersal capabilities. Consistent with a highly migratory species, only very low levels of differentiation were described for D. melanogaster populations from the same continent. We reinvestigated the population structure in D. melanogaster using 49 polymorphic markers in 23 natural populations. While European and American D. melanogaster populations showed very low differentiation, Asian D. melanogaster populations were highly structured. Despite the high differentiation of Asian flies, we confirm that all non-African populations are derived from a single colonization event. We propose that the availability of D. melanogaster populations with high and low population structure provides a novel tool for the identification of ecologically important adaptations by hitchhiking mapping. PMID:16204221

  16. Population genetic structure of Venezuelan chiropterophilous columnar cacti (Cactaceae).

    PubMed

    Nassar, Jafet M; Hamrick, J L; Fleming, Theodore H

    2003-11-01

    We conducted allozyme surveys of three Venezuelan self-incompatible chiropterophilous columnar cacti: two diploid species, Stenocereus griseus and Cereus repandus, and one tetraploid, Pilosocereus lanuginosus. The three cacti are pollinated by bats, and both bats and birds disperse seeds. Population sampling comprised two spatial scales: all Venezuelan arid zones (macrogeographic) and two arid regions in northwestern Venezuela (regional). Ten to 15 populations and 17-23 loci were analyzed per species. Estimates of genetic diversity were compared with those of other allozyme surveys in the Cactaceae to examine how bat-mediated gene dispersal affects the population genetic attributes of the three cacti. Genetic diversity was high for both diploid (P(s) = 94.1-100, P(p) = 56.7-72.3, H(s) = 0.182-0.242, H(p) = 0.161-0.205) and tetraploid (P(s) = 93.1, P(p) = 76.1, H(s) = 0.274, H(p) = 0.253) species. Within-population heterozygote deficit was detected in the three cacti at macrogeographic (F(IS) = 0.145-0.182) and regional (F(IS) = 0.057-0.174) levels. Low genetic differentiation was detected at both macrogeographic (G(ST) = 0.043-0.126) and regional (G(ST) = 0.009-0.061) levels for the three species, suggesting substantial gene flow among populations. Gene exchange among populations seems to be regulated by distance among populations. Our results support the hypothesis that bat-mediated gene dispersal confers high levels of genetic exchange among populations of the three columnar cacti, a process that enhances levels of genetic diversity within their populations.

  17. Feedback: Now with Physics

    NASA Astrophysics Data System (ADS)

    Hopkins, Philip F.; Quataert, Eliot; Faucher-Giguere, Claude-Andre; Keres, Dusan; Wetzel, Andrew R.; Murray, Norman W.

    2017-01-01

    The most fundamental unsolved problems in galaxy formation revolve around "feedback" from massive stars and black holes. In the last few years, a new generation of theoretical models have emerged which combine new numerical methods and physics in an attempt to realistically model the diverse physics of the interstellar medium, star formation, and feedback from super-massive black holes and massive stars (winds, jets, SNe, and radiation). These mechanisms lead to 'self-regulated' galaxy and star formation, in which global correlations such as the Schmidt-Kennicutt law, the inefficiency of star formation, and the stellar mass function -- emerge naturally. Within galaxies, feedback regulates the structure of the interstellar medium, and many observed properties of the ISM, star formation, and galaxies can be understood as a fundamental consequence of super-sonic turbulence in a rapidly cooling, self-gravitating medium. But feedback also produces galactic super-winds that can dramatically alter the cosmological evolution of galaxies, change the nature of dark matter cores and ‘cusps’, and re-structure the circum-galactic and inter-galactic medium. These winds depend non-linearly on multiple feedback mechanisms in a way that explains why they have been so difficult to model in previous "sub-grid" approaches. This resolves long-standing problems in understanding even apparently "simple" galaxy properties like the mass-metallicity relation. Finally, I'll discuss where feedback fails, and where either additional, exotic physics, or new, previously-dismissed feedback mechanisms, may be needed to explain observations.

  18. Effects of Pleistocene glaciations on population structure of North American chestnut-backed chickadees.

    PubMed

    Burg, Theresa M; Gaston, Anthony J; Winker, Kevin; Friesen, Vicki L

    2006-08-01

    The postglacial recolonization of northern North America was heavily influenced by the Pleistocene glaciation. In the Pacific Northwest, there are two disjunct regions of mesic temperate forest, one coastal and the other interior. The chestnut-backed chickadee is one of the species associated with this distinctive ecosystem. Using seven microsatellite markers we found evidence of population structure among nine populations of chestnut-backed chickadees. High levels of allelic variation were found in each of the populations. Northern British Columbia and central Alaska populations contained a large number of private alleles compared to other populations, including those from unglaciated regions. The disjunct population in the interior was genetically distinct from the coastal population. Genetic and historical records indicate that the interior population originated from postglacial inland dispersal. Population structuring was found within the continuous coastal population, among which the peripheral populations, specifically those on the Queen Charlotte Islands and the central Alaska mainland, were genetically distinct. The pattern of population structure among contemporary chickadee populations is consistent with a pioneer model of recolonization. The persistence of genetic structure in western North American chestnut-backed chickadees may be aided by their sedentary behaviour, linear distribution, and dependence on cedar-hemlock forests.

  19. DEMOGRAPHY AND SPATIAL POPULATION STRUCTURE IN CALIFORNIA TIGER SALAMANDER

    EPA Science Inventory

    Although the causes of many amphibian declines remain mysterious, there is general agreement that human habitat alteration represents the greatest threat to amphibian populations. In January 2000 the US Fish and Wildlife Service proposed listing Santa Barbara County California Ti...

  20. Spatially structured population dynamics in feral oilseed rape.

    PubMed Central

    Crawley, Michael J.; Brown, Susan L.

    2004-01-01

    We studied the population dynamics of feral oilseed rape (Brassica napus) for 10 years (1993-2002) in 3658 adjacent permanent 100 m quadrats in the verges of the M25 motorway around London, UK. The aim was to determine the relative importance of different factors affecting the observed temporal patterns of population dynamics and their spatial correlations. A wide range of population dynamics was observed (downward or upward trends, cycles, local extinctions and recolonizations), but overall the populations were not self-replacing (lambda < 1). Many quadrats remained unoccupied throughout the study period, but a few were occupied at high densities for all 10 years. Most quadrats showed transient oilseed rape populations, lasting 1-4 years. There were strong spatial patterns in mean population density, associated with soil conditions and the successional age of the plant community dominating the verge, and these large-scale spatial patterns were highly consistent from year to year. The importance of seed spilled from trucks in transit to the processing plant at Erith in Kent was confirmed: rape populations were significantly higher on the 'to Erith' verge than the 'from Erith' verge (overall mean 2.83-fold greater stem density). Quadrats in which lambda > 1 were much more frequent in the 'to Erith' verge, indicating that seed immigration can give the spurious impression of self-replacing population dynamics in time-series analysis. There was little evidence of a pervasive Moran effect, and climatic forcing did not produce widespread large-scale synchrony in population dynamics for the motorway as a whole; just 23% of quadrats had significant rank correlations with the mean time-series. There was, however, significant local spatial synchrony of population dynamics, apparently associated with soil disturbance and seed input. This study draws attention to the possibility that different processes may impose population synchrony at different scales. We hypothesize that

  1. Global Population Genetic Structure of Caenorhabditis remanei Reveals Incipient Speciation

    PubMed Central

    Dey, Alivia; Jeon, Yong; Wang, Guo-Xiu; Cutter, Asher D.

    2012-01-01

    Mating system transitions dramatically alter the evolutionary trajectories of genomes that can be revealed by contrasts of species with disparate modes of reproduction. For such transitions in Caenorhabditis nematodes, some major causes of genome variation in selfing species have been discerned. And yet, we have only limited understanding of species-wide population genetic processes for their outcrossing relatives, which represent the reproductive state of the progenitors of selfing species. Multilocus–multipopulation sequence polymorphism data provide a powerful means to uncover the historical demography and evolutionary processes that shape genomes. Here we survey nucleotide polymorphism across the X chromosome for three populations of the outcrossing nematode Caenorhabditis remanei and demonstrate its divergence from a fourth population describing a closely related new species from China, C. sp. 23. We find high genetic variation globally and within each local population sample. Despite geographic barriers and moderate genetic differentiation between Europe and North America, considerable gene flow connects C. remanei populations. We discovered C. sp. 23 while investigating C. remanei, observing strong genetic differentiation characteristic of reproductive isolation that was confirmed by substantial F2 hybrid breakdown in interspecific crosses. That C. sp. 23 represents a distinct biological species provides a cautionary example of how standard practice can fail for mating tests of species identity in this group. This species pair permits full application of divergence population genetic methods to obligately outcrossing species of Caenorhabditis and also presents a new focus for interrogation of the genetics and evolution of speciation with the Caenorhabditis model system. PMID:22649079

  2. Genetic population structure of the blister beetle, Gnathium minimum: core and peripheral populations.

    PubMed

    Marschalek, Daniel A; Berres, Mark E

    2014-01-01

    Populations on the periphery of a species' range tend to contain lower genetic variation and increased genetic differentiation compared to populations at the core of a species range, although some exceptions to this generalization occur. The blister beetle Gnathium minimum (Say) exhibits a wide-ranging distribution in the western United States but has peripheral or disjunct populations in Mexico, Florida, and Wisconsin. We used amplified fragment length polymorphism (AFLP) to compare the genetic variation and magnitude of genetic differentiation of the Wisconsin peripheral population to western core populations (Colorado, Kansas, New Mexico, and Texas). The proportion of polymorphic loci was 53.6 and 54.3, and expected heterozygosity 0.1864 and 0.1933 for the Kansas/Colorado (n = 87) and New Mexico/Texas (n = 35) regions, respectively. Specimens from Wisconsin (n = 121) had a lower proportion of polymorphic loci (38.4) and expected heterozygosity (0.1475). Genetic cluster estimation with GENELAND and F ST values showed greater genetic differentiation among the sampling locations within Wisconsin compared to core regions. Significant isolation-by-distance (IBD) was also observed in Wisconsin but not within the core regions. Lower genetic variation and increased isolation may reduce the Wisconsin population's ability to respond to change, thereby increasing their susceptibility to extinction.

  3. Genetic Population Structure of Macridiscus multifarius (Mollusca: Bivalvia) on the Basis of Mitochondrial Markers: Strong Population Structure in a Species with a Short Planktonic Larval Stage.

    PubMed

    Ye, Ying Ying; Wu, Chang Wen; Li, Ji Ji

    2015-01-01

    The clam Macridiscus multifarius with a planktonic larval stage of about 10 days is an ecologically and economically important species in the coastal regions of China. In this study, 3 mt-DNA markers (COI, 12S rRNA, and ND1) were used to investigate the population structure and demography of wild M. multifarius populations in 3 coastal localities of the East China Sea (ZS and ZP populations) and Beibu Gulf in the South China Sea (BH population). Sequences of 685 bp in COI, 350 bp in 12S rRNA, and 496 bp in ND1 were determined. High level and significant FST values were obtained among the different localities on the basis of either COI (FST = 0.100-0.444, p < 0.05) or 12S rRNA (FST = 0.199-0.742, p < 0.05) gene, indicating a high degree of genetic differentiation among the populations. FST values were significant but weak for the ND1 gene because it is highly conservative. The median-joining network suggested an obvious genetic differentiation between ZS and BH populations, and the finding is consistent with the results of our demographic analyses using the unweighted pair group method with arithmetic mean. Our study unraveled the extant population genetic structure of M. multifarius and explained the strong population structure of a species with a short planktonic larval stage species; this information could be useful for fishery management measures, including artificial breeding and conservation.

  4. Multilocus genotyping reveals high heterogeneity and strong local population structure of the Plasmodium vivax population in the Peruvian Amazon

    PubMed Central

    2010-01-01

    Background Peru is one of the Latin American countries with the highest malaria burden, mainly due to Plasmodium vivax infections. However, little is known about P. vivax transmission dynamics in the Peruvian Amazon, where most malaria cases occur. The genetic diversity and population structure of P. vivax isolates collected in different communities around Iquitos city, the capital of the Peruvian Amazon, was determined. Methods Plasmodium vivax population structure was determined by multilocus genotyping with 16 microsatellites on 159 P. vivax infected blood samples (mono-infections) collected in four sites around Iquitos city. The population characteristics were assessed only in samples with monoclonal infections (n = 94), and the genetic diversity was determined by calculating the expected heterozygosity and allelic richness. Both linkage disequilibrium and the genetic differentiation (θ) were estimated. Results The proportion of polyclonal infections varied substantially by site (11% - 70%), with the expected heterozygosity ranging between 0.44 and 0.69; no haplotypes were shared between the different populations. Linkage disequilibrium was present in all populations (IAS 0.14 - 0.61) but was higher in those with fewer polyclonal infections, suggesting inbreeding and a clonal population structure. Strong population differentiation (θ = 0.45) was found and the Bayesian inference cluster analysis identified six clusters based on distinctive allele frequencies. Conclusion The P. vivax populations circulating in the Peruvian Amazon basin are genetically diverse, strongly differentiated and they have a low effective recombination rate. These results are in line with the low and clustered pattern of malaria transmission observed in the region around Iquitos city. PMID:20525233

  5. Population variation in neuroendocrine activity is associated with behavioral inhibition and hemispheric brain structure in young rhesus monkeys.

    PubMed

    Short, Sarah J; Lubach, Gabriele R; Shirtcliff, Elizabeth A; Styner, Martin A; Gilmore, John H; Coe, Christopher L

    2014-09-01

    Population variation in hypothalamic-pituitary-adrenal (HPA) activity and reactivity was assessed in a healthy sample of 48 juvenile rhesus monkeys. Cluster analysis of the HPA profiles revealed four distinct neuroendocrine phenotypes based on six indices of HPA functioning. Behavioral reactivity was also evaluated in response to novel stimuli, and revealed marked differences between animals in the highest- and lowest-cortisol clusters. Specifically, animals in the high-cortisol cluster showed larger stress-induced cortisol responses and blunted feedback sensitivity to dexamethasone. They were also emotionally reactive, displayed more aggressive behaviors, and were less likely to approach novel objects. In contrast, monkeys in the low-cortisol cluster were more likely to approach and explore novel objects. Representative animals with high or low cortisol profiles were scanned with Magnetic Resonance Imaging to evaluate structural differences in global and regional gray matter (GM) and white matter (WM) volumes. Monkeys with higher cortisol reactivity evinced less hemispheric brain asymmetry, due to decreased GM in the right hemisphere. Stress reactivity was inversely related to global GM and positively related to total cerebrospinal fluid volume. This inverse relationship was also observed in several stress-sensitive regions, including prefrontal and frontal cortices. Our study demonstrates that population variation in pituitary-adrenal activity is related to behavioral disposition and cerebral structure in this nonhuman primate species.

  6. The concurrent evolution of cooperation and the population structures that support it.

    PubMed

    Powers, Simon T; Penn, Alexandra S; Watson, Richard A

    2011-06-01

    The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits that affect their population structure to some degree. These traits, such as a group size preference, affect the relatedness of interacting individuals and hence the opportunity for kin or group selection. We argue that models that do not explicitly consider their evolution cannot provide a satisfactory account of the origin of cooperation, because they cannot explain how the prerequisite population structures arise. Here, we consider the concurrent evolution of genetic traits that affect population structure, with those that affect social behavior. We show that not only does population structure drive social evolution, as in previous models, but that the opportunity for cooperation can in turn drive the creation of population structures that support it. This occurs through the generation of linkage disequilibrium between socio-behavioral and population-structuring traits, such that direct kin selection on social behavior creates indirect selection pressure on population structure. We illustrate our argument with a model of the concurrent evolution of group size preference and social behavior.

  7. Sea otter population structure and ecology in Alaska

    USGS Publications Warehouse

    Bodkin, James L.; Monson, Daniel H.

    2002-01-01

    Sea otters are the only fully marine otter. They share a common ancestry with the Old World land otters, but their route of dispersal to the New World is uncertain. The historic range of the species is along the northern Pacific Ocean rim, between central Baja California and the islands of northern Japan. Because they forage almost exclusively on bottom-dwelling marine invertebrates such as clams, snails, crabs, and sea urchins, they predominantly occur near shore. Their offshore distribution is limited by their diving ability; although they are capable of diving to more than 100 meters deep, most of their feeding takes place between the shoreline and depths of 40 meters. They are social animals, generally resting in protected bays or kelp forests in groups, commonly referred to as rafts. Because they are gregarious, possess a fine fur, and occur primarily near shore, they have been exploited by humans for as long as they have co-occupied coastal marine communities.During the late Pleistocene, glacial advances and retreats in the northern latitudes likely influenced genetic exchange within the sea otter’s northern range. When the glaciers were at their maximum, ice sheets extended over large coastal areas, isolating sea otter populations and causing local extinctions. During periods of glacial retreat, sea otters likely recolonized the newly available habitats, allowing exchange of individuals and gene flow between populations.Beginning in about 1750, sea otter populations underwent dramatic declines as a direct result of commercial harvest for their furs. Explorations by Vitus Bering led to the discovery of abundant sea otter populations in the Aleutian Islands. The early harvest, conducted by Russians with enslaved Aleut hunters, began in the eastern Aleutians. Eventually the harvest became multinational and contributed significantly to the exploration and settlement of the North Pacific coastline by Europeans. There were two distinct periods of harvest

  8. School Formative Feedback Systems

    ERIC Educational Resources Information Center

    Halverson, Richard

    2010-01-01

    Data-driven instructional improvement relies on developing coherent systems that allow school staff to generate, interpret, and act upon quality formative information on students and school programs. This article offers a formative feedback system model that captures how school leaders and teachers structure artifacts and practices to create…

  9. Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain.

    PubMed

    Pérez-Figueroa, A; Fernández, C; Amaro, R; Hermida, M; San Miguel, E

    2015-08-01

    Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N(e)) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N(e) estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N(e) estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30-56 and 47-56 for the Rato and Guisande Rivers, respectively. Estimated census size (N(c)) for the Rato River was 880 individuals. This yielded a N(e)/N(c) estimate of 3-6 % for temporal estimation of N(e), which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.

  10. Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

    NASA Astrophysics Data System (ADS)

    Costantini, Federica; Abbiati, Marco

    2016-03-01

    Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

  11. Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas

    PubMed Central

    Porto-Hannes, Isabel

    2015-01-01

    Patterns of dispersal and connectivity of the Caribbean gorgonian Antillogorgia elisabethae in The Bahamas were assessed in both adults and recently settled recruits from 13 sites using microsatellite loci. Adult populations along the Little Bahama Bank (LBB) exhibited a clear pattern of isolation by distance (IBD) which described 86% of the variance in pairwise genetic distances. Estimates of dispersal based on the IBD model suggested dispersal distances along the LBB on the order of 100 m. Increasing the spatial scale to include sites separated by open ocean generated an apparent IBD signal but the relationship had a greater slope and explained less of the variance. This relationship with distance reflected both stepping stone based IBD and regional differentiation probably created by ocean currents and barriers to dispersal that are correlated with geographic distance. Analysis of recruits from 4 sites on the LBB from up to 6 years did not detect differences between years nor differences with adult populations. The result suggests that neither selection on recruits nor inter-annual variation in dispersal affected adult population structure. Assignment tests of recruits indicated the most likely sources of the recruits were the local or adjacent populations. Most of the patterning in population structure in the northern Bahamas can be explained by geographic distance and oceanographic connectivity. Recognition of these complex patterns is important in developing management plans for A. elisabethae and in understanding the effects of disturbance to adult populations of A. elisabethae and similar species with limited dispersal. PMID:26157606

  12. Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

    PubMed

    Velo-Antón, Guillermo; Godinho, Raquel; Campos, João Carlos; Brito, José Carlos

    2014-01-01

    The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.

  13. Should I Stay or Should I Go? Dispersal and Population Structure in Small, Isolated Desert Populations of West African Crocodiles

    PubMed Central

    Campos, João Carlos; Brito, José Carlos

    2014-01-01

    The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12–0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments. PMID:24740183

  14. Population.

    ERIC Educational Resources Information Center

    King, Pat; Landahl, John

    This pamphlet has been prepared in response to a new problem, a rapidly increasing population, and a new need, population education. It is designed to help teachers provide their students with some basic population concepts with stress placed on the elements of decision making. In the first section of the pamphlet, some of the basic concepts of…

  15. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  16. Inbreeding rate and genetic structure of cat populations in Poland.

    PubMed

    Mucha, S; Wolc, A; Gradowska, A; Szwaczkowski, T

    2011-02-01

    The objective of the study was to analyze effective population size and inbreeding level in populations of cat breeds registered in the Polish Studbook. The Association of Purebred Cat Breeders in Poland provided access to pedigrees of 26725 cats from seven breeds. The most frequent breed was Persian, however increasing tendency in numbers of registered animals from other breeds was recorded in later years. Although the percentage of inbred individuals was increasing over time, mating of close relatives was avoided by most of the breeders, and the average inbreeding coefficient exceeded 5% only for Siberian and Russian breeds. Current analysis suggests that the Polish pedigree cat populations are not threatened by negative effects of inbreeding.

  17. Evolutionary dynamics of social dilemmas in structured heterogeneous populations

    PubMed Central

    Santos, F. C.; Pacheco, J. M.; Lenaerts, Tom

    2006-01-01

    Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations. PMID:16484371

  18. Evolutionary dynamics of social dilemmas in structured heterogeneous populations.

    PubMed

    Santos, F C; Pacheco, J M; Lenaerts, Tom

    2006-02-28

    Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations.

  19. Simulated Population Patterns of Migrating Bacteria in Structured Environments

    NASA Astrophysics Data System (ADS)

    Centler, Florian; Fetzer, Ingo; Thullner, Martin

    2010-05-01

    Many desirable reactive subsurface processes, for example nutrient cycling or the degradation of organic contaminants, are driven by microorganisms populating the soil matrix. Due to the high spatial and temporal complexity of the soil matrix, microbial life is not evenly distributed in the soil matrix but rather concentrated in distinct hot spots. Bacteria are capable of detecting gradients of nutrients or other chemical signals in their environment and direct their movement along such gradients, a process known as chemotaxis. In this theoretical study, we consider two chemotactically mediated movement incentives for bacteria: (i) affinity to nutrients and (ii) affinity to fellow organisms. The first incentive ensures efficient usage of available resources, while the second incentive leads to bacterial accumulation, providing shelter from adverse environments and allowing for synchronized behaviour. Using an individual-based modelling approach we analyse the population patterns that can develop as a consequence of these movement incentives in a hypothetical environment: a linear array of microhabitats in which microorganisms can migrate between adjacent habitats. A preliminary analytical analysis is performed to investigate the steady states of the system and their stability. Each microhabitat is characterized by nutrient level and bacterial occupation level. For an isolated microhabitat, three states are possible: extinction, space limited growth, and nutrient limited growth. These three states can also be observed in the full model of linearly connected microhabitats, leading to uniform population distributions within the array. An analytical analysis reveals that non-uniform spatio-temporal population patterns can develop, if a precondition involving the carrying capacity of the microhabitats, the steady state occupation level, the strength of the bacterial random motility, and the strength of the affinity to fellow organisms is fulfilled. The individual

  20. Stabilizing Spatially-Structured Populations through Adaptive Limiter Control

    PubMed Central

    Sah, Pratha; Dey, Sutirth

    2014-01-01

    Stabilizing the dynamics of complex, non-linear systems is a major concern across several scientific disciplines including ecology and conservation biology. Unfortunately, most methods proposed to reduce the fluctuations in chaotic systems are not applicable to real, biological populations. This is because such methods typically require detailed knowledge of system specific parameters and the ability to manipulate them in real time; conditions often not met by most real populations. Moreover, real populations are often noisy and extinction-prone, which can sometimes render such methods ineffective. Here, we investigate a control strategy, which works by perturbing the population size, and is robust to reasonable amounts of noise and extinction probability. This strategy, called the Adaptive Limiter Control (ALC), has been previously shown to increase constancy and persistence of laboratory populations and metapopulations of Drosophila melanogaster. Here, we present a detailed numerical investigation of the effects of ALC on the fluctuations and persistence of metapopulations. We show that at high migration rates, application of ALC does not require a priori information about the population growth rates. We also show that ALC can stabilize metapopulations even when applied to as low as one-tenth of the total number of subpopulations. Moreover, ALC is effective even when the subpopulations have high extinction rates: conditions under which another control algorithm had previously failed to attain stability. Importantly, ALC not only reduces the fluctuation in metapopulation sizes, but also the global extinction probability. Finally, the method is robust to moderate levels of noise in the dynamics and the carrying capacity of the environment. These results, coupled with our earlier empirical findings, establish ALC to be a strong candidate for stabilizing real biological metapopulations. PMID:25153073

  1. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

    PubMed Central

    Möbius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2015-01-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle’s shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call ‘geometry-enhanced genetic drift’, complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects

  2. Genetic diversity and structure of natural fragmented Chamaecyparis obtusa populations as revealed by microsatellite markers.

    PubMed

    Matsumoto, Asako; Uchida, Kohji; Taguchi, Yuriko; Tani, Naoki; Tsumura, Yoshihiko

    2010-09-01

    The genetic diversity and population structure of hinoki (Chamaecyparis obtusa) in Japan were investigated by examining the distribution of alleles at 13 microsatellite loci in 25 natural populations from Iwaki in northern Japan to Yakushima Island in southern Japan. On average, 26.9 alleles per locus were identified across all populations and 4.0% of the genetic variation was retained among populations (G(ST) = 0.040). According to linkage disequilibrium analysis, estimates of effective population size and detected evidence of bottleneck events, the genetic diversity of some populations may have declined as a result of fragmentation and/or over-exploitation. The central populations located in the Chubu district appear to have relatively large effective population sizes, while marginal populations, such as the Yakushima, Kobayashi and Iwaki populations, have smaller effective population sizes and are isolated from the other populations. Microsatellite analysis revealed the genetic uniqueness of the Yakushima population. Although genetic differentiation between populations was low, we detected a gradual cline in the genetic structure and found that locus Cos2619 may be non-neutral with respect to natural selection.

  3. Population structure of red-cockaded woodpeckers (Picoides borealis) in south Florida: RAPDs revisited

    USGS Publications Warehouse

    Haig, Susan M.; Bowman, R.; Mullins, Thomas D.

    1996-01-01

    Six south Florida populations of the endangered red-cockaded woodpecker (Picoides borealis) were sampled to examine genetic diversity and population structure in the southernmost portion of the species' range relative to 14 previously sampled populations from throughout the species range. Random amplified polymorphic DNA (RAPD) analyses were used to evaluate the populations (n= 161 individuals, 13 primers, one band/primer). Results suggested that south Florida populations have significant among-population genetic differentiation (FST= 0.17, P < 0.000), although gene flow may be adequate to offset drift (Nm= 1.26). Comparison of Florida populations with others sampled indicated differentiation was less in Florida (FST for all populations = 0.21). Cluster analyses of all 20 populations did not reflect complete geographical predictions, although clustering of distant populations resulted in a significant correlation between genetic distance and geographical distance. Overall, results suggest populations in south Florida, similar to the remainder of the species, have low genetic diversity and high population fragmentation. Exact clustering of distant populations supports the ability of RAPDs to differentiate populations accurately. Our results further support past management recommendations that translocations of birds among geographically proximate populations is preferable to movement of birds between distant populations.

  4. Occurrence, sequence polymorphism and population structure of Circulifer tenellus virus 1 in a field population of the beet leafhopper

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The potential of Circulifer tenellus virus 1 (CiTV1) as a surrogate marker to determine population structure of the beet leafhopper (BLH; Circulifer tenellus [Baker]) was assessed. Prevalence, incidence, and nucleotide sequence polymorphism of CiTV1 present in BLH adults collected from the southern...

  5. Genetic structure of introduced populations: 120-year-old DNA footprint of historic introduction in an insular small mammal population

    PubMed Central

    Simpson, Siobhan; Blampied, Nick; Peniche, Gabriela; Dozières, Anne; Blackett, Tiffany; Coleman, Stephen; Cornish, Nina; Groombridge, Jim J

    2013-01-01

    Wildlife populations have been introduced to new areas by people for centuries, but this human-mediated movement can disrupt natural patterns of genetic structure by altering patterns of gene flow. Insular populations are particularly prone to these influences due to limited opportunities for natural dispersal onto islands. Consequently, understanding how genetic patterns develop in island populations is important, particularly given that islands are frequently havens for protected wildlife. We examined the evolutionary origins and extent of genetic structure within the introduced island population of red squirrels (Sciurus vulgaris) on the Channel Island of Jersey using mitochondrial DNA (mtDNA) control region sequence and nuclear microsatellite genotypes. Our findings reveal two different genetic origins and a genetic architecture reflective of the introductions 120 years ago. Genetic structure is marked within the maternally inherited mtDNA, indicating slow dispersal of female squirrels. However, nuclear markers detected only weak genetic structure, indicating substantially greater male dispersal. Data from both mitochondrial and nuclear markers support historic records that squirrels from England were introduced to the west of the island and those from mainland Europe to the east. Although some level of dispersal and introgression across the island between the two introductions is evident, there has not yet been sufficient gene flow to erase this historic genetic “footprint.” We also investigated if inbreeding has contributed to high observed levels of disease, but found no association. Genetic footprints of introductions can persist for considerable periods of time and beyond traditional timeframes of wildlife management. PMID:23532702

  6. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    PubMed

    Gayevskiy, Velimir; Klaere, Steffen; Knight, Sarah; Goddard, Matthew R

    2014-01-01

    Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin) correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  7. Feedback on the Feedback: Sociocultural Interpretation of Saudi ESL Learners' Opinions about Writing Feedback

    ERIC Educational Resources Information Center

    Mustafa, Rami F.

    2012-01-01

    This qualitative study employed informal conversational interviews and semi-structured individual interviews to capture the Saudi students' opinions about the feedback they receive, and about their perceptions on what constitutes helpful feedback. Sociocultural theory was used as the framework of this study. The findings suggest that the Saudi…

  8. Genetic diversity of microsatellite loci in hierarchically structured populations.

    PubMed

    Song, Seongho; Dey, Dipak K; Holsinger, Kent E

    2011-08-01

    Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded. Using these results, we study the behavior of several measures related to Wright's F(ST), including Slatkin's R(ST). Our analytical approximations for F(ST) and R(ST) show that familiar relationships between N(e)m and F(ST) or R(ST) hold when the migration and mutation rates are small. Using the exact expressions for F(ST) and R(ST), our numerical results show that, when the migration and mutation rates are large, these relationships no longer hold. Our numerical results also show that the diversity measures most closely related to F(ST) depend on mutation rates, mutational models (stepwise versus two-phase), migration rates, and population sizes. Surprisingly, R(ST) is relatively insensitive to the mutation rates and mutational models. The differing behaviors of R(ST) and F(ST) suggest that properties of the among-population distribution of allele frequencies may allow the roles of mutation and migration in producing patterns of diversity to be distinguished, a topic of continuing investigation.

  9. Demography and genetic structure of a recovering grizzly bear population

    USGS Publications Warehouse

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  10. Global climate feedbacks

    SciTech Connect

    Manowitz, B.

    1990-10-01

    The important physical, chemical, and biological events that affect global climate change occur on a mesoscale -- requiring high spatial resolution for their analysis. The Department of Energy has formulated two major initiatives under the US Global Change Program: ARM (Atmospheric Radiation Measurements), and CHAMMP (Computer Hardware Advanced Mathematics and Model Physics). ARM is designed to use ground and air-craft based observations to document profiles of atmospheric composition, clouds, and radiative fluxes. With research and models of important physical processes, ARM will delineate the relationships between trace gases, aerosol and cloud structure, and radiative transfer in the atmosphere, and will improve the parameterization of global circulation models. The present GCMs do not model important feedbacks, including those from clouds, oceans, and land processes. The purpose of this workshop is to identify such potential feedbacks, to evaluate the uncertainties in the feedback processes (and, if possible, to parameterize the feedback processes so that they can be treated in a GCM), and to recommend research programs that will reduce the uncertainties in important feedback processes. Individual reports are processed separately for the data bases.

  11. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    PubMed

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  12. The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis.

    PubMed

    Rodríguez-Ramilo, Silvia T; Wang, Jinliang

    2012-09-01

    The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Under this assumption, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.

  13. Simulation study on control of spill structure of slow extracted beam from a medical synchrotron with feed-forward and feedback using a fast quadruple magnet and RF-knockout system

    NASA Astrophysics Data System (ADS)

    Muraoka, Ryo; Nakanishi, Tetsuya

    2017-02-01

    A feedback control of the spill structure for the slow beam extraction from the medical synchrotron using a fast quadruple and radio frequency (RF)-knockout (QAR method) is studied to obtain the designed spill structure. In addition the feed-forward control is used so that the feedback control is performed effectively. In this extraction method, the spill of several ms are extracted continuously with an interval time of less than 1 ms. Beam simulation showed that a flat spill structure was effectively obtained with feed-forward and feedback control system as well as a step-wise structure which is useful for the shortening of an irradiation time in a spot scanning operation. The effect of current ripples from main quadruple magnet's power supplies could be also reduced with the feedback control application.

  14. Population genetic structure of Anopheles gambiae mosquitoes on Lake Victoria islands, west Kenya

    PubMed Central

    Chen, Hong; Minakawa, Noboru; Beier, John; Yan, Guiyun

    2004-01-01

    Background Understanding the genetic structure of island Anopheles gambiae populations is important for the current tactics in mosquito control and for the proposed strategy using genetically-modified mosquitoes (GMM). Genetically-isolated mosquito populations on islands are a potential site for testing GMM. The objective of this study was to determine the genetic structure of A. gambiae populations on the islands in Lake Victoria, western Kenya. Methods The genetic diversity and the population genetic structures of 13 A. gambiae populations from five islands on Lake Victoria and six villages from the surrounding mainland area in the Suba District were examined using six microsatellite markers. The distance range of sampling sites varied between 2.5 and 35.1 km. Results A similar level of genetic diversity between island mosquito populations and adjacent mainland populations was found. The average number of alleles per locus was 7.3 for the island populations and 6.8 for the mainland populations. The average observed heterozygosity was 0.32 and 0.28 for the island and mainland populations, respectively. A low but statistically significant genetic structure was detected among the island populations (FST = 0.019) and between the island and mainland populations (FST = 0.003). A total of 12 private alleles were found, and nine of them were from the island populations. Conclusion A level of genetic differentiation between the island and mainland populations was found. Large extent of gene flow between the island and mainland mosquito populations may result from wind- or human-assisted dispersal. Should the islands on Lake Victoria be used as a trial site for the release program of GMM, mosquito dispersal between the islands and between the island and the mainland should be vigorously monitored. PMID:15581429

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

    PubMed

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

    2008-10-01

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

  16. Ecology and Population Structure of Vibrionaceae in the Coastal Ocean

    DTIC Science & Technology

    2010-02-01

    determines the allele frequency within the patch. Gut microbiota are a unique assembly of 21 populations (Eckburg et al., 2005; Gao et al., 2007; Pei et al...et al., 2006). Microbiota of Animals Bacteria are attached to nearly all animal surfaces that are exposed to the environment and play important roles...in the health of the organism. Bacteria are particularly abundant in the gut , where nutrients are concentrated and conditions are fairly stable

  17. Blue whale population structure along the eastern South Pacific Ocean: evidence of more than one population.

    PubMed

    Torres-Florez, J P; Hucke-Gaete, R; LeDuc, R; Lang, A; Taylor, B; Pimper, L E; Bedriñana-Romano, L; Rosenbaum, H C; Figueroa, C C

    2014-12-01

    Blue whales (Balaenoptera musculus) were among the most intensively exploited species of whales in the world. As a consequence of this intense exploitation, blue whale sightings off the coast of Chile were uncommon by the end of the 20th century. In 2004, a feeding and nursing ground was reported in southern Chile (SCh). With the aim to investigate the genetic identity and relationship of these Chilean blue whales to those in other Southern Hemisphere areas, 60 biopsy samples were collected from blue whales in SCh between 2003 and 2009. These samples were genotyped at seven microsatellite loci and the mitochondrial control region was sequenced, allowing us to identify 52 individuals. To investigate the genetic identity of this suspected remnant population, we compared these 52 individuals to blue whales from Antarctica (ANT, n = 96), Northern Chile (NCh, n = 19) and the eastern tropical Pacific (ETP, n = 31). No significant differentiation in haplotype frequencies (mtDNA) or among genotypes (nDNA) was found between SCh, NCh and ETP, while significant differences were found between those three areas and Antarctica for both the mitochondrial and microsatellite analyses. Our results suggest at least two breeding population units or subspecies exist, which is also supported by other lines of evidence such as morphometrics and acoustics. The lack of differences detected between SCh/NCh/ETP areas supports the hypothesis that eastern South Pacific blue whales are using the ETP area as a possible breeding area. Considering the small population sizes previously reported for the SCh area, additional conservation measures and monitoring of this population should be developed and prioritized.

  18. Size-specific sensitivity: Applying a new structured population model

    SciTech Connect

    Easterling, M.R.; Ellner, S.P.; Dixon, P.M.

    2000-03-01

    Matrix population models require the population to be divided into discrete stage classes. In many cases, especially when classes are defined by a continuous variable, such as length or mass, there are no natural breakpoints, and the division is artificial. The authors introduce the integral projection model, which eliminates the need for division into discrete classes, without requiring any additional biological assumptions. Like a traditional matrix model, the integral projection model provides estimates of the asymptotic growth rate, stable size distribution, reproductive values, and sensitivities of the growth rate to changes in vital rates. However, where the matrix model represents the size distributions, reproductive value, and sensitivities as step functions (constant within a stage class), the integral projection model yields smooth curves for each of these as a function of individual size. The authors describe a method for fitting the model to data, and they apply this method to data on an endangered plant species, northern monkshood (Aconitum noveboracense), with individuals classified by stem diameter. The matrix and integral models yield similar estimates of the asymptotic growth rate, but the reproductive values and sensitivities in the matrix model are sensitive to the choice of stage classes. The integral projection model avoids this problem and yields size-specific sensitivities that are not affected by stage duration. These general properties of the integral projection model will make it advantageous for other populations where there is no natural division of individuals into stage classes.

  19. The influence of multiple dispersal mechanisms and landscape structure on population clustering and connectivity in fragmented artesian spring snail populations.

    PubMed

    Worthington Wilmer, J; Elkin, C; Wilcox, C; Murray, L; Niejalke, D; Possingham, H

    2008-08-01

    Many organisms occupy heterogeneous landscapes that contain both barriers to movement as well as corridors that facilitate dispersal. The extent to which such features determine population connectivity will depend on the mechanisms utilized by organisms to disperse. Here we examined the interaction between landscape structure and dispersal in the endemic aquatic snail, Fonscochlea accepta, in the fragmented artesian spring ecosystem of arid central Australia. We used frequentist and Bayesian analyses of microsatellite data to identify population structure and immigration for 1130 snails sampled from 50 springs across an entire spring complex. We introduce a modified isolation-by-distance analysis to test hypotheses about how populations are clustered and to distinguish the most likely dispersal pathways within and between those clusters. Highly significant differences in F(ST) values and significant isolation-by-distance patterns were detected among springs across the entire complex, while Bayesian assignment tests revealed the presence of two hierarchical levels of spring clustering. Clusters were defined by the spatial aggregation of springs, dynamic aquatic habitat connections between springs and the ecology of the snails. Bayesian immigrant identification and our modified isolation-by-distance analysis revealed that dispersal occurs at two geographical scales via two very different mechanisms. Short range dispersal (usually or= 3 km) is likely facilitated by an animal vector (phoresy). These results underline the importance of both dispersal mode and landscape structure in influencing connectivity rates and patterns among populations.

  20. Recent physical connections may explain weak genetic structure in western Alaskan chum salmon (Oncorhynchus keta) populations

    PubMed Central

    Garvin, Michael R; Kondzela, Christine M; Martin, Patrick C; Finney, Bruce; Guyon, Jeffrey; Templin, William D; DeCovich, Nick; Gilk-Baumer, Sara; Gharrett, Anthony J

    2013-01-01

    Low genetic divergence at neutral loci among populations is often the result of high levels of contemporary gene flow. Western Alaskan summer-run chum salmon (Oncorhynchus keta) populations demonstrate weak genetic structure, but invoking contemporary gene flow as the basis for the low divergence is problematic because salmon home to their natal streams and some of the populations are thousands of kilometers apart. We used genotypes from microsatellite and single nucleotide polymorphism loci to investigate alternative explanations for the current genetic structure of chum salmon populations from western Alaska. We also estimated current levels of gene flow among Kuskokwim River populations. Our results suggest that weak genetic structure is best explained by physical connections that occurred after the Holocene Thermal Maximum among the Yukon, Kuskokwim, and Nushagak drainages that allowed gene flow to occur among now distant populations. PMID:23919176

  1. Recent physical connections may explain weak genetic structure in western Alaskan chum salmon (Oncorhynchus keta) populations.

    PubMed

    Garvin, Michael R; Kondzela, Christine M; Martin, Patrick C; Finney, Bruce; Guyon, Jeffrey; Templin, William D; Decovich, Nick; Gilk-Baumer, Sara; Gharrett, Anthony J

    2013-07-01

    Low genetic divergence at neutral loci among populations is often the result of high levels of contemporary gene flow. Western Alaskan summer-run chum salmon (Oncorhynchus keta) populations demonstrate weak genetic structure, but invoking contemporary gene flow as the basis for the low divergence is problematic because salmon home to their natal streams and some of the populations are thousands of kilometers apart. We used genotypes from microsatellite and single nucleotide polymorphism loci to investigate alternative explanations for the current genetic structure of chum salmon populations from western Alaska. We also estimated current levels of gene flow among Kuskokwim River populations. Our results suggest that weak genetic structure is best explained by physical connections that occurred after the Holocene Thermal Maximum among the Yukon, Kuskokwim, and Nushagak drainages that allowed gene flow to occur among now distant populations.

  2. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    PubMed

    Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

    2013-01-01

    While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

  3. Population structure of Aggarwals of north India as revealed by molecular markers.

    PubMed

    Gupta, Vipin; Khadgawat, Rajesh; Ng, Hon Keung Tony; Kumar, Satish; Rao, Vadlamudi Raghavendra; Sachdeva, Mohinder Pal

    2010-12-01

    Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.

  4. Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

    USGS Publications Warehouse

    Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

    2012-01-01

    Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

  5. Evidence of habitat structuring Aedes albopictus populations in Réunion Island.

    PubMed

    Delatte, Hélène; Toty, Céline; Boyer, Sébastien; Bouetard, Anthony; Bastien, Fanny; Fontenille, Didier

    2013-01-01

    Arbovirus vector dynamics and spread are influenced by climatic, environmental and geographic factors. Major Chikungunya and Dengue fever outbreaks occurring the last 10 years have coincided with the expansion of the mosquito vector Aedes albopictus to nearly all the continents. We characterized the ecological (larval development sites, population dynamics, insemination and daily survival rates) and genetic (diversity, gene flow, population structure) features of two Aedes albopictus populations from distinct environments (rural and urban) on Réunion Island, in the South-West Indian Ocean. Microsatellite analysis suggests population sub-structuring Ae. albopictus populations. Two genetic clusters were identified that were significantly linked to natural versus urban habitats with a mixed population in both areas. Ae. albopictus individuals prefer urban areas for mating and immature development, where hosts and containers that serve as larval development sites are readily available and support high population densities, whereas natural environments appear to serve as reservoirs for the mosquito.

  6. Evidence of Habitat Structuring Aedes albopictus Populations in Réunion Island

    PubMed Central

    Delatte, Hélène; Toty, Céline; Boyer, Sébastien; Bouetard, Anthony; Bastien, Fanny; Fontenille, Didier

    2013-01-01

    Arbovirus vector dynamics and spread are influenced by climatic, environmental and geographic factors. Major Chikungunya and Dengue fever outbreaks occurring the last 10 years have coincided with the expansion of the mosquito vector Aedes albopictus to nearly all the continents. We characterized the ecological (larval development sites, population dynamics, insemination and daily survival rates) and genetic (diversity, gene flow, population structure) features of two Aedes albopictus populations from distinct environments (rural and urban) on Réunion Island, in the South-West Indian Ocean. Microsatellite analysis suggests population sub-structuring Ae. albopictus populations. Two genetic clusters were identified that were significantly linked to natural versus urban habitats with a mixed population in both areas. Ae. albopictus individuals prefer urban areas for mating and immature development, where hosts and containers that serve as larval development sites are readily available and support high population densities, whereas natural environments appear to serve as reservoirs for the mosquito. PMID:23556012

  7. AGN feedback in the Perseus cluster

    NASA Astrophysics Data System (ADS)

    Gendron-Marsolais, Marie-Lou; Hlavacek-Larrondo, Julie; Clarke, Tracy E.; Intema, Huib; Fabian, Andrew C.; Taylor, Gregory B.; Blundell, Katherine

    2016-04-01

    Deep Chandra images of the Perseus cluster of galaxies have revealed a succession of cavities created by the jets of the central supermassive black hole, pushing away the X-ray emitting gas and leaving bubbles filled with radio emission. Perseus is one of the rare examples showing buoyantly rising lobes from past radio outbursts, characterized by a steep spectral index and known as ghost cavities. All of these structures trace the complete history of mechanical AGN feedback over the past 500 Myrs. I will present results on new, ultra deep 230-470 MHz JVLA data. This low-frequency view of the Perseus cluster will probe the old radio-emitting electron population and will allow us to build the most detailed map of AGN feedback in a cluster thus far.

  8. Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis.

    PubMed

    Novick, Rachel Roth; Dick, Christopher W; Lemes, Maristerra R; Navarro, Carlos; Caccone, Adalgisa; Bermingham, Eldredge

    2003-11-01

    While microsatellites have been used to examine genetic structure in local populations of Neotropical trees, genetic studies based on such high-resolution markers have not been carried out for Mesoamerica as a whole. Here we assess the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries. Measures of genetic differentiation (FST and RST) indicated significant differences between most populations. Unrooted dendrograms based on genetic distances between populations provide evidence of strong phylogeographic structure in Mesoamerican mahogany. The two populations on the Pacific coasts of Costa Rica and Panama were genetically distant from all the others, and from one another. The remaining populations formed two clusters, one comprised of the northern populations of Mexico, Belize and Guatemala and the other containing the southern Atlantic populations of Nicaragua and Costa Rica. Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation.

  9. Genetic Diversity and Population Structure in Polygonum cespitosum: Insights to an Ongoing Plant Invasion

    PubMed Central

    Matesanz, Silvia; Theiss, Kathryn E.; Holsinger, Kent E.; Sultan, Sonia E.

    2014-01-01

    Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America), via the analyses of 516 individuals, and asked the following questions: 1) Do populations have differing levels of within-population genetic diversity? 2) Do populations form distinct genetic clusters? 3) Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering) and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources) in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further contribute to the

  10. Agroecosystems shape population genetic structure of the greenhouse whitefly in Northern and Southern Europe

    PubMed Central

    2014-01-01

    Background To predict further invasions of pests it is important to understand what factors contribute to the genetic structure of their populations. Cosmopolitan pest species are ideal for studying how different agroecosystems affect population genetic structure within a species at different climatic extremes. We undertook the first population genetic study of the greenhouse whitefly (Trialeurodes vaporariorum), a cosmopolitan invasive herbivore, and examined the genetic structure of this species in Northern and Southern Europe. In Finland, cold temperatures limit whiteflies to greenhouses and prevent them from overwintering in nature, and in Greece, milder temperatures allow whiteflies to inhabit both fields and greenhouses year round, providing a greater potential for connectivity among populations. Using nine microsatellite markers, we genotyped 1274 T. vaporariorum females collected from 18 greenhouses in Finland and eight greenhouses as well as eight fields in Greece. Results Populations from Finland were less diverse than those from Greece, suggesting that Greek populations are larger and subjected to fewer bottlenecks. Moreover, there was significant population genetic structure in both countries that was explained by different factors. Habitat (field vs. greenhouse) together with longitude explained genetic structure in Greece, whereas in Finland, genetic structure was explained by host plant species. Furthermore, there was no temporal genetic structure among populations in Finland, suggesting that year-round populations are able to persist in greenhouses. Conclusions Taken together our results show that greenhouse agroecosystems can limit gene flow among populations in both climate zones. Fragmented populations in greenhouses could allow for efficient pest management. However, pest persistence in both climate zones, coupled with increasing opportunities for naturalization in temperate latitudes due to climate change, highlight challenges for the

  11. Population.

    ERIC Educational Resources Information Center

    International Planned Parenthood Federation, London (England).

    In an effort to help meet the growing interest and concern about the problems created by the rapid growth of population, The International Planned Parenthood Federation has prepared this booklet with the aim of assisting the study of the history and future trends of population growth and its impact on individual and family welfare, national,…

  12. Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species

    PubMed Central

    2010-01-01

    Background The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US) and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated). Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern consistent with plant

  13. Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

    PubMed

    Lesser, M R; Parchman, T L; Jackson, S T

    2013-05-01

    Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.

  14. Temporal analysis of genetic structure to assess population dynamics of reintroduced swift foxes.

    PubMed

    Cullingham, Catherine I; Moehrenschlager, Axel

    2013-12-01

    Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos.

  15. The fine scale genetic structure of the British population

    PubMed Central

    Davison, Dan; Boumertit, Abdelhamid; Day, Tammy; Hutnik, Katarzyna; Royrvik, Ellen C; Cunliffe, Barry; Lawson, Daniel J; Falush, Daniel; Freeman, Colin; Pirinen, Matti; Myers, Simon; Robinson, Mark; Donnelly, Peter; Bodmer, Walter

    2015-01-01

    Summary Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide SNP data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom (UK). This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to SE England from Anglo-Saxon migrations to be under half, identify the regions not carrying genetic material from these migrations, suggest significant pre-Roman but post-Mesolithic movement into SE England from the Continent, and show that in non-Saxon parts of the UK there exist genetically differentiated subgroups rather than a general “Celtic” population. PMID:25788095

  16. Clonal population structure of Colombian sylvatic Trypanosoma cruzi.

    PubMed

    Márquez, E; Arcos-Burgos, M; Triana, O; Moreno, J; Jaramillo, N

    1998-12-01

    Isoenzyme variability and evidence of genetic exchange were evaluated in 75 wild stocks of Trypanosoma cruzi obtained from different hosts from 5 geographical regions within the endemic area in Colombia. Cluster analysis of genetic variability was attempted. Thirty-three multilocus enzyme genotypes (clonets) were identified from 75 stocks, 27 of which clustered with zymodeme Z1 and 6 with zymodeme Z3. Two stocks isolated from human infections showed the potential risk to rural communities in Colombia. The stocks exhibited departures from Hardy-Weinberg expectations, including both fixed heterozygote and fixed homozygote demes, where both segregation and recombination were absent. To inspect for population subdivision that might falsely imply clonality in these stocks, Wright's F statistics were calculated. Theta values (Fst) were significantly different from 0 when 33 clonets, 27 Z1-like clonets, and 5 geographical subpopulations were compared; thus, a significant amount of divergence has occurred between and within them. In addition, linkage disequilibrium was detected for most possible pairwise comparisons of loci. In conclusion, the above results all support a scenario of long-term clonal evolution in Colombian sylvatic T. cruzi populations.

  17. Geographically structured populations of Cryptococcus neoformans Variety grubii in Asia correlate with HIV status and show a clonal population structure.

    PubMed

    Khayhan, Kantarawee; Hagen, Ferry; Pan, Weihua; Simwami, Sitali; Fisher, Matthew C; Wahyuningsih, Retno; Chakrabarti, Arunaloke; Chowdhary, Anuradha; Ikeda, Reiko; Taj-Aldeen, Saad J; Khan, Ziauddin; Ip, Margaret; Imran, Darma; Sjam, Ridhawati; Sriburee, Pojana; Liao, Wanqing; Chaicumpar, Kunyaluk; Vuddhakul, Varaporn; Meyer, Wieland; Trilles, Luciana; van Iersel, Leo J J; Meis, Jacques F; Klaassen, Corné H W; Boekhout, Teun

    2013-01-01

    Cryptococcosis is an important fungal disease in Asia with an estimated 140,000 new infections annually the majority of which occurs in patients suffering from HIV/AIDS. Cryptococcus neoformans variety grubii (serotype A) is the major causative agent of this disease. In the present study, multilocus sequence typing (MLST) using the ISHAM MLST consensus scheme for the C. neoformans/C. gattii species complex was used to analyse nucleotide polymorphisms among 476 isolates of this pathogen obtained from 8 Asian countries. Population genetic analysis showed that the Asian C. neoformans var. grubii population shows limited genetic diversity and demonstrates a largely clonal mode of reproduction when compared with the global MLST dataset. HIV-status, sequence types and geography were found to be confounded. However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates. Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia.

  18. Gene flow and population structure of a solitary top carnivore in a human-dominated landscape.

    PubMed

    McManus, Jeannine S; Dalton, Desiré L; Kotzé, Antoinette; Smuts, Bool; Dickman, Amy; Marshal, Jason P; Keith, Mark

    2015-01-01

    While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free-roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human-carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human-caused extinctions.

  19. Gene flow and population structure of a solitary top carnivore in a human-dominated landscape

    PubMed Central

    McManus, Jeannine S; Dalton, Desiré L; Kotzé, Antoinette; Smuts, Bool; Dickman, Amy; Marshal, Jason P; Keith, Mark

    2015-01-01

    While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free-roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human–carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human-caused extinctions. PMID:25691961

  20. Population dynamics of bowfin in a south Georgia reservoir: latitudinal comparisons of population structure, growth, and mortality

    USGS Publications Warehouse

    Porter, Nicholas J.; Bonvechio, Timothy F.; McCormick, Joshua L.; Quist, Michael

    2014-01-01

    The objectives of this study were to evaluate the population dynamics of bowfin (Amia calva) in Lake Lindsay Grace, Georgia, and to compare those dynamics to other bowfin populations. Relative abundance of bowfin sampled in 2010 in Lake Lindsay Grace was low and variable (mean±SD; 2.7±4.7 fish per hour of electrofishing). Total length (TL) of bowfin collected in Lake Lindsay Grace varied from 233–683 mm. Age of bowfin in Lake Lindsay Grace varied from 0–5 yr. Total annual mortality (A) was estimated at 68%. Both sexes appeared to be fully mature by age 2 with gonadosomatic index values above 8 for females and close to 1 for males. The majority of females were older, longer, and heavier than males. Bowfin in Lake Lindsay Grace had fast growth up to age 4 and higher total annual mortality than the other populations examined in this study. A chi-square test indicated that size structure of bowfin from Lake Lindsay Grace was different than those of a Louisiana population and two bowfin populations from the upper Mississippi River. To further assess bowfin size structure, we proposed standard length (i.e., TL) categories: stock (200 mm, 8 inches), quality (350 mm, 14 inches), preferred (460 mm, 18 inches), memorable (560 mm, 22, inches), and trophy (710 mm, 28 inches). Because our knowledge of bowfin ecology is limited, additional understanding of bowfin population dynamics provides important insight that can be used in management of bowfin across their distribution.

  1. Phylogeography of the Endangered Otago Skink, Oligosoma otagense: Population Structure, Hybridisation and Genetic Diversity in Captive Populations

    PubMed Central

    Chapple, David G.; Birkett, Alisha; Miller, Kimberly A.; Daugherty, Charles H.; Gleeson, Dianne M.

    2012-01-01

    Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key

  2. Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations.

    PubMed

    Chapple, David G; Birkett, Alisha; Miller, Kimberly A; Daugherty, Charles H; Gleeson, Dianne M

    2012-01-01

    Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key

  3. [On the competition among discrete-structured populations: a matrix model for population dynamics of woodreed and birch growing together].

    PubMed

    Ulanova, N G; Belova, I N; Logofet, D O

    2008-01-01

    Presented is a synthesis of field, theoretical and modelling studies on joint dynamics of two species--common birch (Betula pendula Roth) and wood small reed (Calamagrostis epigeios (L.) Roth)--overgrowing a spruce forest clear-cut. A nonlinear matrix model for population dynamics of two species, which both possess non-trivial population structures and compete for a resource in common was developed as an expansion of the linear models for single-species, age-stage-structured population dynamics. Constant values of the age-stage-specific survival and reproduction rates have been modified with some decreasing functions of the (competitive group) abundances in the competitor species or/and the species itself. Special aggregation of the age-stage structure for each of the competitor species has reduced the dimension of the nonlinear matrix operator down to the level that admits accurate calibration of the model parameters on the observation data, as well as the search for an equilibrium and its stability analysis. When calibrated, the nonlinear model exhibits convergence to the steady equilibrium--a state of the phytocoenosis that is interpreted as young, closed-canopy, birch forest with suppressed woodreed population. The model illustrates the observed course of forest renewal: the appearance of birch germs and the growth of birch population overpass the woodreed competitive resistance and result in formation of young birch forest, where the birch exerts a strong suppressive impact on both the woodreed growth and the own young growth. Remarked is a potential of the model as an object of more general mathematical study and a tool to predict the course of forest renewal.

  4. Evidence for population bottlenecks and subtle genetic structure in the yellow rail

    USGS Publications Warehouse

    Popper, Kenneth J.; Miller, Leonard F.; Green, Michael; Haig, Susan M.; Mullins, Thomas D.

    2012-01-01

    The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. We used mitochondrial DNA sequences (mtDNA) and six microsatellite loci to characterize the Yellow Rail's genetic structure and diversity patterns in six areas. Our mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail's main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. At this time, we are unable to determine if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail's entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed.

  5. Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

    USGS Publications Warehouse

    Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Schaeffer, Jeff; Roseman, Edward F.; Harford, William J.; Johnson, James E.; Fietsch, Cherie-Lee

    2012-01-01

    Genetic analysis of spawning lake whitefish (Coregonus clupeaformis) from six sites in the main basin of Lake Huron was conducted to determine population structure. Samples from fisheryindependent assessment surveys in the northwest main basin were analyzed to determine the relative contributions of lake whitefish genetic populations. Genetic population structure was identified using data from seven microsatellite DNA loci. One population was identified at Manitoulin Island, one to two were observed in the east-central main basin (Fishing Island and Douglas Point), and one to two populations were found in the northwest (Thunder Bay and Duncan Bay). The genetic identity of collections from Duncan Bay and Thunder Bay was not consistent among methods used to analyze population structure. Low genetic distances suggested that they comprised one population, but genic differences indicated that they may constitute separate populations. Simulated data indicated that the genetic origins of samples from a mixed-fishery could be accurately identified, but accuracy could be improved by incorporating additional microsatellite loci. Mixture analysis and individual assignment tests performed on mixed-stock samples collected from the western main basin suggested that genetic populations from the east-central main basin contributed less than those from the western main basin and that the proportional contribution of each baseline population was similar in each assessment sample. Analysis of additional microsatellite DNA loci may be useful to help improve the precision of the estimates, thus increasing our ability to manage and protect this valuable resource.

  6. Range-wide population genetic structure of the Caribbean sea fan coral, Gorgonia ventalina.

    PubMed

    Andras, Jason P; Rypien, Krystal L; Harvell, Catherine D

    2013-01-01

    The population structure of benthic marine organisms is of central relevance to the conservation and management of these often threatened species, as well as to the accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow for strong general inferences. Here, we describe the range-wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically modelled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometres, estimated dispersal was low, and populations were differentiated across distances <2 km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks found in other taxa (e.g. an east/west divide near Puerto Rico), and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally.

  7. Population structure of root nodulating Rhizobium leguminosarum in Vicia cracca populations at local to regional geographic scales.

    PubMed

    Van Cauwenberghe, Jannick; Verstraete, Brecht; Lemaire, Benny; Lievens, Bart; Michiels, Jan; Honnay, Olivier

    2014-12-01

    The genetic diversity and population structure of about 350 Rhizobium leguminosarum biovar viciae isolates from Vicia cracca were analysed. A hierarchical sampling design was used covering three regions, one region in Belgium and two in France, in which multiple local V. cracca populations were sampled. Rhizobium isolates were genotyped using RAPD and by sequencing two chromosomal housekeeping genes (glnII and recA) and one plasmid-borne gene (nodC). Twenty-six nodC types and sixty-seven chromosomal types were identified, many of which appeared to be regional or local endemics. We found strong genetic differentiation both among V. cracca populations that are separated by only a few kilometres, and among regions that are 50 to 350km apart. Despite significant plasmid exchange, chromosomal and nod types were similarly structured among host populations and regions. We found two lineages of which one prevailed in the Belgian region while the other dominated the French regions. Although a significant correlation between genetic differentiation and geographic distance was found, it is deemed more likely that the observed biogeographic patterns are rather due to coevolutionary interactions and environmental pressures. Furthermore, the impact of recombination on the chromosomal differentiation was found to be considerable.

  8. A Global Perspective on the Population Structure and Reproductive System of Phyllosticta citricarpa.

    PubMed

    Carstens, Elma; Linde, Celeste; Slabbert, Ruhan; Miles, Andrew; Donovan, Nerida; Li, Hong-Ye; Zhang, Ke; Dewdney, Megan M; Rollins, Jeffrey A; Glienke, Chirlei; Schutte, Gerhardus Christian; Fourie, Paul; McLeod, Adele

    2017-01-30

    The citrus pathogen Phyllosticta citricarpa was first described 117 years ago in Australia, and subsequently from the summer rainfall citrus-growing regions in China, Africa, South America and recently the United States of America (USA). Limited information is available on the pathogen's population structure, mode of reproduction and introduction pathways, which were investigated by genotyping 383 isolates representing 12 populations from South Africa, USA, Australia, China and Brazil. Populations were genotyped using seven published and eight newly developed polymorphic simple sequence repeat (SSR) markers. The Chinese and Australian populations had the highest genetic diversities, whereas populations from Brazil, USA and South Africa exhibited characteristics of founder populations. The USA population was clonal. Based on principal coordinate and minimum spanning network analyses the Chinese populations were distinct from the other populations. Population differentiation and clustering analyses revealed high connectivity and possibly linked introduction pathways between South Africa, Australia and Brazil. With the exception of the clonal USA populations that only contained one mating type, all the other populations contained both mating types in a ratio that did not deviate significantly from 1:1. Whilst most populations exhibited sexual reproduction, linkage disequilibrium analyses indicated that asexual reproduction is important in the pathogen's life cycle.

  9. Genetic structure in insular and mainland populations of house sparrows (Passer domesticus) and their hemosporidian parasites

    PubMed Central

    Bichet, Coraline; Moodley, Yoshan; Penn, Dustin J; Sorci, Gabriele; Garnier, Stéphane

    2015-01-01

    Small and isolated populations usually exhibit low levels of genetic variability, and thus, they are expected to have a lower capacity to adapt to changes in environmental conditions, such as exposure to pathogens and parasites. Comparing the genetic variability of selectively neutral versus functional loci allows one to assess the evolutionary history of populations and their future evolutionary potential. The genes of the major histocompatibility complex (MHC) control immune recognition of parasites, and their unusually high diversity is genes which is likely driven by parasite-mediated balancing selection. Here, we examined diversity and differentiation of neutral microsatellite loci and functional MHC class I genes in house sparrows (Passer domesticus), living in six insular and six mainland populations, and we aimed to determine whether their diversity or differentiation correlates with the diversity and the prevalence of infection of hemosporidian parasites. We found that island bird populations tended to have lower neutral genetic variability, whereas MHC variability gene was similar between island and mainland populations. Similarly, island populations tended to show greater genetic differentiation than mainland populations, especially at microsatellite markers. The maintenance of MHC genetic diversity and its less marked structure in the island populations could be attributed to balancing-selection. The greater MHC differentiation among populations was negatively correlated with similarity in blood parasites (prevalence and diversity of parasite strains) between populations. Even at low prevalence and small geographical scale, haemosporidian parasites might contribute to structure the variability of immune genes among populations of hosts. PMID:25937907

  10. Genetic population structure of US atlantic coastal striped bass (Morone saxatilis).

    PubMed

    Gauthier, David T; Audemard, Corinne A; Carlsson, Jeanette E L; Darden, Tanya L; Denson, Michael R; Reece, Kimberly S; Carlsson, Jens

    2013-01-01

    Genetic population structure of anadromous striped bass along the US Atlantic coast was analyzed using 14 neutral nuclear DNA microsatellites. Young-of-the-year and adult striped bass (n = 1114) were sampled from Hudson River, Delaware River, Chesapeake Bay, North Carolina, and South Carolina. Analyses indicated clear population structure with significant genetic differentiation between all regions. Global multilocus F ST was estimated at 0.028 (P < 0.001). Population structure followed an isolation-by-distance model and temporal sampling indicated a stable population structure more than 2 years at all locations. Significant structure was absent within Hudson River, whereas weak but significant genetic differences were observed between northern and southern samples in Chesapeake Bay. The largest and smallest effective striped bass population sizes were found in Chesapeake Bay and South Carolina, respectively. Coalescence analysis indicated that the highest historical gene flow has been between Chesapeake Bay and Hudson River populations, and that exchange has not been unidirectional. Bayesian analysis of contemporary migration indicated that Chesapeake Bay serves as a major source of migrants for Atlantic coastal regions from Albemarle Sound northward. In addition to examining population genetic structure, the data acquired during this project were capable of serving as a baseline for assigning fish with unknown origin to source region.

  11. First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes ( Canis latrans)

    PubMed Central

    Monzón, Javier

    2014-01-01

    Previous genetic studies of eastern coyotes ( Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species. PMID:25075291

  12. mStruct: inference of population structure in light of both genetic admixing and allele mutations.

    PubMed

    Shringarpure, Suyash; Xing, Eric P

    2009-06-01

    Traditional methods for analyzing population structure, such as the Structure program, ignore the influence of the effect of allele mutations between the ancestral and current alleles of genetic markers, which can dramatically influence the accuracy of the structural estimation of current populations. Studying these effects can also reveal additional information about population evolution such as the divergence time and migration history of admixed populations. We propose mStruct, an admixture of population-specific mixtures of inheritance models that addresses the task of structure inference and mutation estimation jointly through a hierarchical Bayesian framework, and a variational algorithm for inference. We validated our method on synthetic data and used it to analyze the Human Genome Diversity Project-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) cell line panel of microsatellites and HGDP single-nucleotide polymorphism (SNP) data. A comparison of the structural maps of world populations estimated by mStruct and Structure is presented, and we also report potentially interesting mutation patterns in world populations estimated by mStruct.

  13. First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes ( Canis latrans).

    PubMed

    Monzón, Javier

    2014-01-01

    Previous genetic studies of eastern coyotes ( Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

  14. Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

    PubMed

    Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

    2016-04-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  15. Simulating population recovery of an aquatic isopod: Effects of timing of stress and landscape structure.

    PubMed

    Galic, Nika; Baveco, Hans; Hengeveld, Geerten M; Thorbek, Pernille; Bruns, Eric; van den Brink, Paul J

    2012-04-01

    In agroecosystems, organisms may regularly be exposed to anthropogenic stressors, e.g. pesticides. Species' sensitivity to stress depends on toxicity, life-history, and landscape structure. We developed an individual-based model of an isopod, Asellus aquaticus, to explore how timing of stress events affects population dynamics in a seasonal environment. Furthermore, we tested the relevance of habitat connectivity and spatial distribution of stress for the recovery of a local and total population. The simulation results indicated that population recovery is mainly driven by reproductive periods. Furthermore, high habitat connectivity led to faster recovery both for local and total populations. However, effects of landscape structure disappeared for homogeneously stressed populations, where local survivors increased recovery rate. Finally, local populations recovered faster, implying that assessing recovery in the field needs careful consideration of spatial scale for sampling. We emphasize the need for a coherent definition of recovery for more relevant ecosystem risk assessment and management.

  16. The role of population inertia in predicting the outcome of stage-structured biological invasions.

    PubMed

    Guiver, Chris; Dreiwi, Hanan; Filannino, Donna-Maria; Hodgson, Dave; Lloyd, Stephanie; Townley, Stuart

    2015-07-01

    Deterministic dynamic models for coupled resident and invader populations are considered with the purpose of finding quantities that are effective at predicting when the invasive population will become established asymptotically. A key feature of the models considered is the stage-structure, meaning that the populations are described by vectors of discrete developmental stage- or age-classes. The vector structure permits exotic transient behaviour-phenomena not encountered in scalar models. Analysis using a linear Lyapunov function demonstrates that for the class of population models considered, a large so-called population inertia is indicative of successful invasion. Population inertia is an indicator of transient growth or decline. Furthermore, for the class of models considered, we find that the so-called invasion exponent, an existing index used in models for invasion, is not always a reliable comparative indicator of successful invasion. We highlight these findings through numerical examples and a biological interpretation of why this might be the case is discussed.

  17. Visualizing Transient Low-Populated Structures of RNA

    PubMed Central

    Dethoff, Elizabeth A.; Petzold, Katja; Chugh, Jeetender; Casiano-Negroni, Anette; Al-Hashimi, Hashim M.

    2012-01-01

    The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized to date involve long-lived species that can be captured by structure characterization techniques. Here, we report the Nuclear Magnetic Resonance visualization of RNA transitions towards invisible ‘excited states’ (ES), which exist in too little abundance (2–13%) and for too short periods of time (45–250 μs) to allow structural characterization by conventional techniques. Transitions towards ESs result in localized rearrangements in base-pairing that alter building block elements of RNA architecture, including helix-junction-helix motifs and apical loops. The ES can inhibit function by sequestering residues involved in recognition and signaling or promote ATP-independent strand exchange. Thus, RNAs do not adopt a single conformation, but rather exist in rapid equilibrium with alternative ESs, which can be stabilized by cellular cues to affect functional outcomes. PMID:23041928

  18. Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation

    SciTech Connect

    Wubben, T.; Mesecar, A.D.

    2014-10-02

    Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 {angstrom} resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observed in the MtPPAT-CoA complex.

  19. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    USGS Publications Warehouse

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

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

    PubMed

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

    2015-01-01

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

  1. Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

    USGS Publications Warehouse

    Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

    2004-01-01

    Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

  2. SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies.

    PubMed

    Bouaziz, Matthieu; Paccard, Caroline; Guedj, Mickael; Ambroise, Christophe

    2012-01-01

    Inferring the structure of populations has many applications for genetic research. In addition to providing information for evolutionary studies, it can be used to account for the bias induced by population stratification in association studies. To this end, many algorithms have been proposed to cluster individuals into genetically homogeneous sub-populations. The parametric algorithms, such as Structure, are very popular but their underlying complexity and their high computational cost led to the development of faster parametric alternatives such as Admixture. Alternatives to these methods are the non-parametric approaches. Among this category, AWclust has proven efficient but fails to properly identify population structure for complex datasets. We present in this article a new clustering algorithm called Spectral Hierarchical clustering for the Inference of Population Structure (SHIPS), based on a divisive hierarchical clustering strategy, allowing a progressive investigation of population structure. This method takes genetic data as input to cluster individuals into homogeneous sub-populations and with the use of the gap statistic estimates the optimal number of such sub-populations. SHIPS was applied to a set of simulated discrete and admixed datasets and to real SNP datasets, that are data from the HapMap and Pan-Asian SNP consortium. The programs Structure, Admixture, AWclust and PCAclust were also investigated in a comparison study. SHIPS and the parametric approach Structure were the most accurate when applied to simulated datasets both in terms of individual assignments and estimation of the correct number of clusters. The analysis of the results on the real datasets highlighted that the clusterings of SHIPS were the more consistent with the population labels or those produced by the Admixture program. The performances of SHIPS when applied to SNP data, along with its relatively low computational cost and its ease of use make this method a promising

  3. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

    PubMed Central

    Larson, Wesley A; Seeb, Lisa W; Everett, Meredith V; Waples, Ryan K; Templin, William D; Seeb, James E

    2014-01-01

    Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure. PMID:24665338

  4. Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

    PubMed

    Vickruck, J L; Richards, M H

    2017-02-18

    While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance.

  5. Temperature-driven regime shifts in the dynamics of size-structured populations.

    PubMed

    Ohlberger, Jan; Edeline, Eric; Vøllestad, Leif Asbjørn; Stenseth, Nils C; Claessen, David

    2011-02-01

    Global warming impacts virtually all biota and ecosystems. Many of these impacts are mediated through direct effects of temperature on individual vital rates. Yet how this translates from the individual to the population level is still poorly understood, hampering the assessment of global warming impacts on population structure and dynamics. Here, we study the effects of temperature on intraspecific competition and cannibalism and the population dynamical consequences in a size-structured fish population. We use a physiologically structured consumer-resource model in which we explicitly model the temperature dependencies of the consumer vital rates and the resource population growth rate. Our model predicts that increased temperature decreases resource density despite higher resource growth rates, reflecting stronger intraspecific competition among consumers. At a critical temperature, the consumer population dynamics destabilize and shift from a stable equilibrium to competition-driven generation cycles that are dominated by recruits. As a consequence, maximum age decreases and the proportion of younger and smaller-sized fish increases. These model predictions support the hypothesis of decreasing mean body sizes due to increased temperatures. We conclude that in size-structured fish populations, global warming may increase competition, favor smaller size classes, and induce regime shifts that destabilize population and community dynamics.

  6. Population structure and molecular characterization of Nigerian field genebank collections of cacao, Theobroma cacao L

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Over the last 130 years since cacao introduction into Nigeria, genetic variability in cacao cultivated which has increased as a result of further introduction and breeding activities, remain largely unknown. To determine the genetic diversity and population structure of cacao populations, 13 cacao ...

  7. Population structure and genetic diversity of Fusicladium effusum in the USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Scab (Fusicladium effusum) is the most destructive disease of pecan in the Southeast US. Infection is thought to occur solely through asexually produced conidia. To explore the population structure and genetic diversity of F. effusum, populations were hierarchically sampled from 11 orchards in Alaba...

  8. A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collectio...

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

    EPA Science Inventory

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

  10. Virulence structure of the eastern U.S. wheat powdery mildew population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Little is known about the population structure of wheat powdery mildew in the eastern 2 U.S., and the most recent report on virulence in this pathogen population involved isolates 3 collected in 1993-94. In the present study, wheat leaves naturally infected with powdery mildew 4 were collected from ...

  11. Population structure of Annona crassiflora: an endemic plant species of the Brazilian Cerrado.

    PubMed

    Gwinner, R; Setotaw, T A; Rodrigues, F A; França, D V C; da Silveira, F A; Pio, L A S; Pasqual, M

    2016-12-23

    Habitat fragmentation has numerous consequences, particularly to endemic species, and has a negative impact on the genetic diversity of neglected species, leading to genetic drift. Annona crassiflora Mart. is a species that is endemic to Brazil, and its incidence in the Cerrado biome has decreased. The identification and characterization of its remaining diversity is necessary for its conservation. Our aim was to study the population structure of A. crassiflora populations from different Cerrado regions in Minas Gerais State, Brazil (Corinto, Curvelo, Carmo da Mata, Boa Esperança, and Paraguaçu) using inter-simple sequence repeat (ISSR) markers and DNA content. Nuclear DNA content was estimated by flow cytometry using 10 individuals from each population. ISSR markers were used for genotyping accessions in order to study their genetic diversity and population structures. We found considerable genetic variation among populations, with the highest variability observed in the Curvelo population. There was a significant positive correlation between DNA content and latitude (r = 0.46, P = 0. 0003). A Bayesian-based cluster analysis grouped the populations into three clusters, which followed their geographical origins. There was some level of genetic diversity and differentiation among the populations, suggesting the need for a conservation plan for this species. The ISSR markers and DNA content analysis were effective in studying the genetic diversity and population structure of A. crassiflora.

  12. Population structure in contemporary Sweden--a Y-chromosomal and mitochondrial DNA analysis.

    PubMed

    Lappalainen, T; Hannelius, U; Salmela, E; von Döbeln, U; Lindgren, C M; Huoponen, K; Savontaus, M-L; Kere, J; Lahermo, P

    2009-01-01

    A population sample representing the current Swedish population was analysed for maternally and paternally inherited markers with the aim of characterizing genetic variation and population structure. The sample set of 820 females and 883 males were extracted and amplified from Guthrie cards of all the children born in Sweden during one week in 2003. 14 Y-chromosomal and 34 mitochondrial DNA SNPs were genotyped. The haplogroup frequencies of the counties closest to Finland, Norway, Denmark and the Saami region in the north exhibited similarities to the neighbouring populations, resulting from the formation of the Swedish nation during the past millennium. Moreover, the recent immigration waves of the 20th century are visible in haplogroup frequencies, and have led to increased diversity and divergence of the major cities. Signs of genetic drift can be detected in several counties in northern as well as in southern Sweden. With the exception of the most drifted subpopulations, the population structure in Sweden appears mostly clinal. In conclusion, our study yielded valuable information of the structure of the Swedish population, and demonstrated the usefulness of biobanks as a source of population genetic research. Our sampling strategy, nonselective on the current population rather than stratified according to ancestry, is informative for capturing the contemporary variation in the increasingly panmictic populations of the world.

  13. Duelling timescales of host mixing and disease spread determine invasion of disease in structured populations

    USGS Publications Warehouse

    Cross, P.C.; Lloyd-Smith, J. O.; Johnson, P.L.F.; Getz, W.M.

    2005-01-01

    The epidemic potential of a disease is traditionally assessed using the basic reproductive number, R0. However, in populations with social or spatial structure a chronic disease is more likely to invade than an acute disease with the same R0, because it persists longer within each group and allows for more host movement between groups. Acute diseases ‘perceive’ a more structured host population, and it is more important to consider host population structure in analyses of these diseases. The probability of a pandemic does not arise independently from characteristics of either the host or disease, but rather from the interaction of host movement and disease recovery timescales. The R* statistic, a group-level equivalent of R0, is a better indicator of disease invasion in structured populations than the individual-level R0.

  14. Variogram Analysis of the Spatial Genetic Structure of Continuous Populations Using Multilocus Microsatellite Data

    PubMed Central

    Wagner, Helene H.; Holderegger, Rolf; Werth, Silke; Gugerli, Felix; Hoebee, Susan E.; Scheidegger, Christoph

    2005-01-01

    A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation. PMID:15654102

  15. Asymmetric competition causes multimodal size distributions in spatially structured populations.

    PubMed

    Velázquez, Jorge; Allen, Robert B; Coomes, David A; Eichhorn, Markus P

    2016-01-27

    Plant sizes within populations often exhibit multimodal distributions, even when all individuals are the same age and have experienced identical conditions. To establish the causes of this, we created an individual-based model simulating the growth of trees in a spatially explicit framework, which was parametrized using data from a long-term study of forest stands in New Zealand. First, we demonstrate that asymmetric resource competition is a necessary condition for the formation of multimodal size distributions within cohorts. By contrast, the legacy of small-scale clustering during recruitment is transient and quickly overwhelmed by density-dependent mortality. Complex multi-layered size distributions are generated when established individuals are restricted in the spatial domain within which they can capture resources. The number of modes reveals the effective number of direct competitors, while the separation and spread of modes are influenced by distances among established individuals. Asymmetric competition within local neighbourhoods can therefore generate a range of complex size distributions within even-aged cohorts.

  16. Asymmetric competition causes multimodal size distributions in spatially structured populations

    PubMed Central

    Velázquez, Jorge; Allen, Robert B.; Coomes, David A.; Eichhorn, Markus P.

    2016-01-01

    Plant sizes within populations often exhibit multimodal distributions, even when all individuals are the same age and have experienced identical conditions. To establish the causes of this, we created an individual-based model simulating the growth of trees in a spatially explicit framework, which was parametrized using data from a long-term study of forest stands in New Zealand. First, we demonstrate that asymmetric resource competition is a necessary condition for the formation of multimodal size distributions within cohorts. By contrast, the legacy of small-scale clustering during recruitment is transient and quickly overwhelmed by density-dependent mortality. Complex multi-layered size distributions are generated when established individuals are restricted in the spatial domain within which they can capture resources. The number of modes reveals the effective number of direct competitors, while the separation and spread of modes are influenced by distances among established individuals. Asymmetric competition within local neighbourhoods can therefore generate a range of complex size distributions within even-aged cohorts. PMID:26817778

  17. Harvesting in a resource dependent age structured Leslie type population model.

    PubMed

    Dilão, Rui; Domingos, Tiago; Shahverdiev, Elman M

    2004-06-01

    We analyse the effect of harvesting in a resource dependent age structured population model, deriving the conditions for the existence of a stable steady state as a function of fertility coefficients, harvesting mortality and carrying capacity of the resources. Under the effect of proportional harvest, we give a sufficient condition for a population to extinguish, and we show that the magnitude of proportional harvest depends on the resources available to the population. We show that the harvesting yield can be periodic, quasi-periodic or chaotic, depending on the dynamics of the harvested population. For populations with large fertility numbers, small harvesting mortality leads to abrupt extinction, but larger harvesting mortality leads to controlled population numbers by avoiding over consumption of resources. Harvesting can be a strategy in order to stabilise periodic or quasi-periodic oscillations in the number of individuals of a population.

  18. Genetic Markers and Quantitative Genetic Variation in Medicago Truncatula (Leguminosae): A Comparative Analysis of Population Structure

    PubMed Central

    Bonnin, I.; Prosperi, J. M.; Olivieri, I.

    1996-01-01

    Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations. PMID:8844165

  19. Genetic structure of colline and montane populations of an endangered plant species

    PubMed Central

    Maurice, Tiphaine; Matthies, Diethart; Muller, Serge; Colling, Guy

    2016-01-01

    Due to land-use intensification, lowland and colline populations of many plants of nutrient-poor grasslands have been strongly fragmented in the last decades, with potentially negative consequences for their genetic diversity and persistence. Populations in mountains might represent a genetic reservoir for grassland plants, because they have been less affected by land-use changes. We studied the genetic structure and diversity of colline and montane Vosges populations of the threatened perennial plant Arnica montana in western central Europe using AFLP markers. Our results indicate that in contrast to our expectation even strongly fragmented colline populations of A. montana have conserved a considerable amount of genetic diversity. However, mean seed mass increased with the proportion of polymorphic loci, suggesting inbreeding effects in low diversity populations. At a similar small geographical scale, there was a clear IBD pattern for the montane Vosges but not for the colline populations. However, there was a strong IBD-pattern for the colline populations at a large geographical scale suggesting that this pattern is a legacy of historical gene flow, as most of the colline populations are today strongly isolated from each other. Genetic differentiation between colline and montane Vosges populations was strong. Moreover, results of a genome scan study indicated differences in loci under selection, suggesting that plants from montane Vosges populations might be maladapted to conditions at colline sites. Our results suggest caution in using material from montane populations of rare plants for the reinforcement of small genetically depauperate lowland populations. PMID:27519913

  20. Population structure in the endangered Mauna Loa silversword, Argyroxiphium kauense (Asteraceae), and its bearing on reintroduction.

    PubMed

    Friar, E A; Boose, D L; LaDoux, T; Roalson, E H; Robichaux, R H

    2001-07-01

    Reintroduction of populations of endangered species is a challenging task, involving a number of environmental, demographic and genetic factors. Genetic parameters of interest include historical patterns of genetic structure and gene flow. Care must be taken during reintroduction to balance the contrasting risks of inbreeding and outbreeding depression. The Mauna Loa silversword, Argyroxiphium kauense, has experienced a severe decline in population size and distribution in the recent past. Currently, three populations with a total of fewer than 1000 individuals remain. We measured genetic variation within and among the remnant populations using seven microsatellite loci. We found significant genetic variation remaining within all populations, probably related to the recent nature of the population impact, the longevity of the plants, and their apparent self-incompatibility. We also found significant genetic differentiation among the populations, reinforcing previous observations of ecological and morphological differentiation. With respect to reintroduction, the results suggest that, in the absence of additional data to the contrary, inbreeding depression may not be a substantial risk as long as propagules for the founding of new populations are adequately sampled from within each source population before additional inbreeding takes place. The results further suggest that if mixing of propagules from different source populations is not required to increase within-population genetic variation in the reintroduced populations, it may best be avoided.

  1. Genetic structure of colline and montane populations of an endangered plant species.

    PubMed

    Maurice, Tiphaine; Matthies, Diethart; Muller, Serge; Colling, Guy

    2016-08-12

    Due to land-use intensification, lowland and colline populations of many plants of nutrient-poor grasslands have been strongly fragmented in the last decades, with potentially negative consequences for their genetic diversity and persistence. Populations in mountains might represent a genetic reservoir for grassland plants, because they have been less affected by land-use changes. We studied the genetic structure and diversity of colline and montane Vosges populations of the threatened perennial plant Arnica montana in western central Europe using AFLP markers. Our results indicate that in contrast to our expectation even strongly fragmented colline populations of A. montana have conserved a considerable amount of genetic diversity. However, mean seed mass increased with the proportion of polymorphic loci, suggesting inbreeding effects in low diversity populations. At a similar small geographical scale there was a clear IBD pattern for the montane Vosges but not for the colline populations. However, there was a strong IBD-pattern for the colline populations at a large geographical scale suggesting that this pattern is a legacy of historical gene flow, as most of the colline populations are today strongly isolated from each other. Genetic differentiation between colline and montane Vosges populations was strong. Moreover, results of a genome scan study indicated differences in loci under selection, suggesting that plants from montane Vosges populations might be maladapted to conditions at colline sites. Our results suggest caution in using material from montane populations of rare plants for the reinforcement of small genetically depauperate lowland populations.

  2. Spatial genetic structure in continuous and fragmented populations of Pinus pinaster Aiton.

    PubMed

    De-Lucas, A I; González-Martínez, S C; Vendramin, G G; Hidalgo, E; Heuertz, M

    2009-11-01

    Habitat fragmentation, i.e., the reduction of populations into small isolated remnants, is expected to increase spatial genetic structure (SGS) in plant populations through nonrandom mating, lower population densities and potential aggregation of reproductive individuals. We investigated the effects of population size reduction and genetic isolation on SGS in maritime pine (Pinus pinaster Aiton) using a combined experimental and simulation approach. Maritime pine is a wind-pollinated conifer which has a scattered distribution in the Iberian Peninsula as a result of forest fires and habitat fragmentation. Five highly polymorphic nuclear microsatellites were genotyped in a total of 394 individuals from two population pairs from the Iberian Peninsula, formed by one continuous and one fragmented population each. In agreement with predictions, SGS was significant and stronger in fragments (Sp = 0.020 and Sp = 0.026) than in continuous populations, where significant SGS was detected for one population only (Sp = 0.010). Simulations suggested that under fat-tailed dispersal, small population size is a stronger determinant of SGS than genetic isolation, while under normal dispersal, genetic isolation has a stronger effect. SGS was always stronger in real populations than in simulations, except if unrealistically narrow dispersal and/or high variance of reproductive success were modelled (even when accounting for potential overestimation of SGS in real populations as a result of short-distance sampling). This suggests that factors such as nonrandom mating or selection not considered in the simulations were additionally operating on SGS in Iberian maritime pine populations.

  3. Stability and optimization in structured population models on graphs.

    PubMed

    Colombo, Rinaldo M; Garavello, Mauro

    2015-04-01

    We prove existence and uniqueness of solutions, continuous dependence from the initial datum and stability with respect to the boundary condition in a class of initial--boundary value problems for systems of balance laws. The particular choice of the boundary condition allows to comprehend models with very different structures. In particular, we consider a juvenile-adult model, the problem of the optimal mating ratio and a model for the optimal management of biological resources. The stability result obtained allows to tackle various optimal management/control problems, providing sufficient conditions for the existence of optimal choices/controls.

  4. [Age structure and growth pattern of Polytrichum juniperum populations in a mire of Changbai Mountains].

    PubMed

    Bu, Zhaojun; Yan, Yunfei; Dai, Dan; Wang, Xianwei

    2005-01-01

    In this paper, the age structure and growth pattern of two Polytrichum juniperum populations with and without sporophytes in Hani mire of Changbai Mountains were studied by 'innate annual marker' method. The ramets of both populations were composed of 6 age classes, and their quantity and biomass showed a declining age structure, which was more obvious in the sporophyte produced population. No significant difference of biomass was found (P > 0.05) between the two populations. The dry material accumulation of the ramets in both populations increased with aging, and showed similar patterns of linear function. The ramets mean height of sporophyte-produced population was 6.17% shorter (P < 0.05) than the another, because sporophyte production limited the height growth. The ramets mean height also increased with aging, and showed similar patterns of linear function. In non-sporophyte produced population, the variation coefficient of ramets height was only 2.44%, which indicated the significance of similar height for ramets survival. In sporophyte produced population, the variation coefficient of ramets height was 25.07%, while that of ramets biomass was 8.25%, suggesting the significance of similar biomass to the reproduction of population. The biomass of ramets had a significantly positive correlation with height in both populations (P < 0.001), and no allometric growth was showed.

  5. Population Structure Analysis of Bull Genomes of European and Western Ancestry

    PubMed Central

    Chung, Neo Christopher; Szyda, Joanna; Frąszczak, Magdalena; Fries, Hans Rudolf; SandøLund, Mogens; Guldbrandtsen, Bernt; Boichard, Didier; Stothard, Paul; Veerkamp, Roel; Goddard, Michael; Van Tassell, Curtis P.; Hayes, Ben

    2017-01-01

    Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6 harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull genomes can support genetic management strategies that capture structural complexity and promote sustainable genetic breadth. PMID:28084449

  6. Fine-scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populations.

    PubMed

    Zamudio, Kelly R; Wieczorek, Ania M

    2007-01-01

    We examined fine-scale genetic variation among breeding aggregations of the spotted salamander (Ambystoma maculatum) to quantify dispersal, interpopulation connectivity and population genetic structure. Spotted salamanders rely on temporary ponds or wetlands for aggregate breeding. Adequate breeding sites are relatively isolated from one another and field studies suggest considerable adult site fidelity; therefore, we expected to find population structure and differentiation at small spatial scales. We used microsatellites to estimate population structure and dispersal among 29 breeding aggregations in Tompkins County, New York, USA, an area encompassing 1272 km(2). Bayesian and frequency-based analyses revealed fine-scale genetic structure with two genetically defined demes: the North deme included seven breeding ponds, and the South deme included 13 ponds. Nine ponds showed evidence of admixture between these two genetic pools. Bayesian assignment tests for detection of interpopulation dispersal indicate that immigration among ponds is common within demes, and that certain populations serve as sources of immigrants to neighbouring ponds. Likewise, spatial genetic correlation analyses showed that populations < or = 4.8 km distant from each other show significant genetic correlation that is not evident at higher scales. Within-population levels of relatedness are consistently larger than expected if mating were completely random across ponds, and in the case of a few ponds, within-population processes such as inbreeding or reproductive skew contribute significantly to differentiation from neighbouring ponds. Our data underscore the importance of these within-population processes as a source of genetic diversity across the landscape, despite considerable population connectivity. Our data further suggest that spotted salamander breeding groups behave as metapopulations, with population clusters as functional units, but sufficient migration among demes to allow for

  7. Demographic connectivity for ursid populations at wildlife crossing structures in Banff National Park.

    PubMed

    Sawaya, Michael A; Clevenger, Anthony P; Kalinowski, Steven T

    2013-08-01

    Wildlife crossing structures are one solution to mitigating the fragmentation of wildlife populations caused by roads, but their effectiveness in providing connectivity has only been superficially evaluated. Hundreds of grizzly (Ursus arctos) and black bear (Ursus americanus) passages through under and overpasses have been recorded in Banff National Park, Alberta, Canada. However, the ability of crossing structures to allow individual and population-level movements across road networks remains unknown. In April 2006, we initiated a 3-year investigation into whether crossing structures provide demographic connectivity for grizzly and black bears in Banff National Park. We collected hair with multiple noninvasive methods to obtain genetic samples from grizzly and black bears around the Bow Valley. Our objectives were to determine the number of male and female grizzly and black bears that use crossing structures; examine spatial and temporal patterns of crossings; and estimate the proportions of grizzly and black bear populations in the Bow Valley that use crossing structures. Fifteen grizzly (7 female, 8 male) and 17 black bears (8 female, 9 male) used wildlife crossing structures. The number of individuals detected at wildlife crossing structures was highly correlated with the number of passages in space and time. Grizzly bears used open crossing structures (e.g., overpasses) more often than constricted crossings (e.g., culverts). Peak use of crossing structures for both bear species occurred in July, when high rates of foraging activity coincide with mating season. We compared the number of bears that used crossings with estimates of population abundance from a related study and determined that substantial percentages of grizzly (15.0% in 2006, 19.8% in 2008) and black bear (17.6% in 2006, 11.0% in 2008) populations used crossing structures. On the basis of our results, we concluded wildlife crossing structures provide demographic connectivity for bear populations

  8. Genetic diversity and population structure of cottons (Gossypium spp.) of the New World assessed by SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A global analysis of cotton (Gossypium spp.) genetic diversity is the first step to understand its geographical distribution, dissemination, genetic relatedness, and population structure. To assess the genetic diversity and population structure in Gossypium species, 111 cotton accessions representin...

  9. Dynamics of climate-based malaria transmission model with age-structured human population

    NASA Astrophysics Data System (ADS)

    Addawe, Joel; Pajimola, Aprimelle Kris

    2016-10-01

    In this paper, we proposed to study the dynamics of malaria transmission with periodic birth rate of the vector and an age-structure for the human population. The human population is divided into two compartments: pre-school (0-5 years) and the rest of the human population. We showed the existence of a disease-free equilibrium point. Using published epidemiological parameters, we use numerical simulations to show potential effect of climate change in the dynamics of age-structured malaria transmission. Numerical simulations suggest that there exists an asymptotically attractive solution that is positive and periodic.

  10. A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data.

    PubMed

    Flores, Kevin B

    2013-07-01

    We formulated a structured population model with distributed parameters to identify mechanisms that contribute to gene expression noise in time-dependent flow cytometry data. The model was validated using cell population-level gene expression data from two experiments with synthetically engineered eukaryotic cells. Our model captures the qualitative noise features of both experiments and accurately fit the data from the first experiment. Our results suggest that cellular switching between high and low expression states and transcriptional re-initiation are important factors needed to accurately describe gene expression noise with a structured population model.

  11. Genetic Diversity and Structure of Brazilian Populations of Diatraea saccharalis (Lepidoptera: Crambidae): Implications for Pest Management.

    PubMed

    Silva-Brandão, Karina L; Santos, Thiago V; Cônsoli, Fernando L; Omoto, Celso

    2015-02-01

    The sugarcane borer, Diatraea saccharalis (F.), is the main pest of sugarcane in Brazil. Genetic variability and gene flow among 13 Brazilian populations of the species were evaluated based on mitochondrial DNA sequences to estimate the exchange of genetic information within and among populations. We found high genetic structure among sampled localities (ΦST=0.50923), and pairwise genetic distances were significantly correlated to geographic distances. Demographic analysis and genealogical network of mitochondrial sequences indicate population growth and admixture of D. saccharalis populations, events likely related to the sequential expansion of the corn and sugarcane crops in Brazil. The implications of these findings for pest management are discussed.

  12. An agent-based computational model for tuberculosis spreading on age-structured populations

    NASA Astrophysics Data System (ADS)

    Graciani Rodrigues, C. C.; Espíndola, Aquino L.; Penna, T. J. P.

    2015-06-01

    In this work we present an agent-based computational model to study the spreading of the tuberculosis (TB) disease on age-structured populations. The model proposed is a merge of two previous models: an agent-based computational model for the spreading of tuberculosis and a bit-string model for biological aging. The combination of TB with the population aging, reproduces the coexistence of health states, as seen in real populations. In addition, the universal exponential behavior of mortalities curves is still preserved. Finally, the population distribution as function of age shows the prevalence of TB mostly in elders, for high efficacy treatments.

  13. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia.

    PubMed

    Menegon, Michela; Durand, Patrick; Menard, Didier; Legrand, Eric; Picot, Stéphane; Nour, Bakri; Davidyants, Vladimir; Santi, Flavia; Severini, Carlo

    2014-10-01

    Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed.

  14. Genetic structure of Sesamia nonagrioides (Lefebvre) populations in the Mediterranean area.

    PubMed

    de la Poza, Marta; Farinós, Gema P; Beroiz, Beatriz; Ortego, Félix; Hernández-Crespo, Pedro; Castañera, Pedro

    2008-10-01

    The Mediterranean corn borer, Sesamia nonagrioides (Lefebvre) (Lepidoptera: Noctuidae), is a major pest of maize in the Mediterranean area. Transgenic Bt maize expressing the Cry1Ab toxin from the bacterium Bacillus thuringiensis can effectively control this pest. The characterization of S. nonagrioides population structure, at a large geographical scale, would provide some insight in decision making for resistance management. The genetic relationships among nine populations from Spain, one from France, one from Italy, three from Greece, and one from Turkey were assessed using Random Amplyfied Polymorphic DNA (RAPD) markers. Populations from France and Spain formed a cluster independent from a cluster of populations collected in Italy, Turkey, and Greece in a unweighted pair-group method with arithmetic average dendrogram constructed from Nei's genetic distances. Average genetic differentiation among samples was significant for all geographical groupings analyzed (F (ST) = 0.160 +/- 0.014 for Spanish populations; 0.133 +/- 0.022 for Spanish and French populations; and 0.095 +/- 0.010 for Greek, Italian, and Turkish populations). Genetic differentiation was also significant for all paired comparisons of populations, including two Spanish populations separated by only 15 km with no apparent geographical barriers. No pattern of isolation by distance was observed among Mediterranean corn borer populations collected in Spain and France. These results suggest a limited genetic exchange between relatively distant S. nonagrioides populations in Europe, which might contribute to decreased rate of spread of resistance alleles once resistance has developed at a certain site.

  15. Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

    PubMed

    Cooper, Dawn; Cory, Jenny S; Myers, Judith H

    2003-04-01

    The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

  16. Comparison of Genetic Structure of Epixylic Liverwort Crossocalyx hellerianus between Central European and Fennoscandian Populations

    PubMed Central

    Holá, Eva; Košnar, Jiří; Kučera, Jan

    2015-01-01

    Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei’s gene diversity in large populations reached high values and ranged between 4.41–4.97, 3.13–4.45, and 0.94–0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00–4.42, 1.00–2.73, and 0.00–0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at

  17. Comparison of Genetic Structure of Epixylic Liverwort Crossocalyx hellerianus between Central European and Fennoscandian Populations.

    PubMed

    Holá, Eva; Košnar, Jiří; Kučera, Jan

    2015-01-01

    Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei's gene diversity in large populations reached high values and ranged between 4.41-4.97, 3.13-4.45, and 0.94-0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00-4.42, 1.00-2.73, and 0.00-0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at longer distances

  18. Long-term changes in the fine-scale population structure of coho salmon populations (Oncorhynchus kisutch) subject to extensive supportive breeding.

    PubMed

    Eldridge, W H; Myers, J M; Naish, K A

    2009-10-01

    The long-term viability of a metapopulation depends partly on the gene flow among sub-populations. Management approaches such as translocations and supportive breeding between closely related populations may affect gene flow and overall structure, and therefore viability. Here, we examined temporal changes in the fine-scale population structure of coho salmon (Oncorhynchus kisutch) by comparing archived (1938) and modern (2001-2005) populations in six rivers within a single conservation unit (Puget Sound, Washington) sampled before and after an extended period of between-river transfers and releases of millions of cultured salmon. Genotype frequencies at eight microsatellite loci showed that current populations descended from historical Puget Sound populations, but populations in different rivers that exchanged fish for hatchery propagation share more of their ancestry recently than they did historically. Historically, populations in different rivers were isolated by geographic distance, but that relationship is no longer significant. Allelic richness among all populations declined significantly, suggesting that genetic drift has increased because of a population bottleneck. Populations in different rivers and within the same river have become more diverged, providing further evidence for a widespread bottleneck. Previously, we observed that genetic distance significantly decreased with the number of fish exchanged; however, some populations apparently resisted introgression. Altered gene flow and lost diversity may affect the complexity, and therefore resiliency of sub-populations within a conservation unit. Plans for artificial culture need to maintain existing genetic diversity and avoid disrupting the fine-scale structure by using local populations for parents whenever possible.

  19. Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

    PubMed Central

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-01-01

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia. PMID:21483678

  20. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    PubMed

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-04-05

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  1. Genetic structure of cougar populations across the Wyoming basin: Metapopulation or megapopulation

    USGS Publications Warehouse

    Anderson, C.R.; Lindzey, F.G.; McDonald, D.B.

    2004-01-01

    We examined the genetic structure of 5 Wyoming cougar (Puma concolor) populations surrounding the Wyoming Basin, as well as a population from southwestern Colorado. When using 9 microsatellite DNA loci, observed heterozygosity was similar among populations (HO = 0.49-0.59) and intermediate to that of other large carnivores. Estimates of genetic structure (FST = 0.028, RST = 0.029) and number of migrants per generation (Nm) suggested high gene flow. Nm was lowest between distant populations and highest among adjacent populations. Examination of these data, plus Mantel test results of genetic versus geographic distance (P ??? 0.01), suggested both isolation by distance and an effect of habitat matrix. Bayesian assignment to population based on individual genotypes showed that cougars in this region were best described as a single panmictic population. Total effective population size for cougars in this region ranged from 1,797 to 4,532 depending on mutation model and analytical method used. Based on measures of gene flow, extinction risk in the near future appears low. We found no support for the existence of metapopulation structure among cougars in this region.

  2. Invasion threshold in structured populations with recurrent mobility patterns

    PubMed Central

    Balcan, Duygu; Vespignani, Alessandro

    2011-01-01

    In this paper we develop a framework to analyze the behavior of contagion and spreading processes in complex subpopulation networks where individuals have memory of their subpopulation of origin. We introduce a metapopulation model in which subpopulations are connected through heterogeneous fluxes of individuals. The mobility process among communities takes into account the memory of residence of individuals and is incorporated with the classical susceptible-infectious-recovered epidemic model within each subpopulation. In order to gain analytical insight into the behavior of the system we use degree-block variables describing the heterogeneity of the subpopulation network and a time-scale separation technique for the dynamics of individuals. By considering the stochastic nature of the epidemic process we obtain the explicit expression of the global epidemic invasion threshold, below which the disease dies out before reaching a macroscopic fraction of the subpopulations. This threshold is not present in continuous deterministic diffusion models and explicitly depends on the disease parameters, the mobility rates, and the properties of the coupling matrices describing the mobility across subpopulations. The results presented here take a step further in offering insight into the fundamental mechanisms controlling the spreading of infectious diseases and other contagion processes across spatially-structured communities. PMID:22019505

  3. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    PubMed

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.

  4. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  5. Feedback: Breakfast of Champions.

    ERIC Educational Resources Information Center

    Justman, Jeffrey J.

    Feedback is an important skill that people need to learn in life. Feedback is crucial in a public speaking class to improve speaking skills. Providing and receiving feedback is what champions feed on to be successful, thus feedback is called the "Breakfast of Champions." Feedback builds speakers' confidence. Providing in-depth feedback…

  6. Population structure of Tor tor inferred from mitochondrial gene cytochrome b.

    PubMed

    Pasi, Komal Shyamakant; Lakra, W S; Bhatt, J P; Goswami, M; Malakar, A Kr

    2013-06-01

    Tor tor, commonly called as Tor mahseer, is a high-valued food and game fish endemic to trans-Himalayan region. Mitochondrial cytochrome b (cyt b) gene region of 967 bp was used to estimate the population structure of T. tor. Three populations of T. tor were collected from Narmada (Hosangabad), Ken (Madla), and Parbati river (Sheopur) in Madhya Pradesh, India. The sequence analysis revealed that the nucleotide diversity (π) was low, ranging from 0.000 to 0.0150. Haplotype diversity (h) ranged from 0.000 to 1.000. The analysis of molecular variance analysis indicated significant genetic divergence among the three populations of T. tor. Neighboring-joining tree also showed that all individuals from three populations clustered into three distinct clades. The data generated by cyt b marker revealed interesting insight about population structure of T. tor, which would serve as baseline data for conservation and management of mahseer fishery.

  7. Population structure of the gomphothere Stegomastodon waringi (Mammalia: Proboscidea: Gomphotheriidae) from the Pleistocene of Brazil.