The Equilibrium Allele Frequency Distribution for a Population with Reproductive Skew

PubMed Central

Der, Ricky; Plotkin, Joshua B.

2014-01-01

We study the population genetics of two neutral alleles under reversible mutation in a model that features a skewed offspring distribution, called the Λ-Fleming–Viot process. We describe the shape of the equilibrium allele frequency distribution as a function of the model parameters. We show that the mutation rates can be uniquely identified from this equilibrium distribution, but the form of the offspring distribution cannot itself always be so identified. We introduce an estimator for the mutation rate that is consistent, independent of the form of reproductive skew. We also introduce a two-allele infinite-sites version of the Λ-Fleming–Viot process, and we use it to study how reproductive skew influences standing genetic diversity in a population. We derive asymptotic formulas for the expected number of segregating sites as a function of sample size and offspring distribution. We find that the Wright–Fisher model minimizes the equilibrium genetic diversity, for a given mutation rate and variance effective population size, compared to all other Λ-processes. PMID:24473932

Predicting the variation in Echinogammarus marinus at its southernmost limits under global warming scenarios: can the sex-ratio make a difference?

PubMed

Guerra, Alexandra; Leite, Nuno; Marques, João Carlos; Ford, Alex T; Martins, Irene

2014-01-01

Understanding the environmental parameters that constrain the distribution of a species at its latitudinal extremes is critical for predicting how ecosystems react to climate change. Our first aim was to predict the variation in the amphipod populations of Echinogammarus marinus from the southernmost limit of its distribution under global warming scenarios. Our second aim was to test whether sex-ratio fluctuations - a mechanism frequently displayed by amphipods - respond to the variations in populations under altered climate conditions. To achieve these aims, scenarios were run with a validated model of E. marinus populations. Simulations were divided into: phase I - simulation of the effect of climate change on amphipod populations, and phase II - simulation of the effect of climate change on populations with male and female proportions. In both phases, temperature (T), salinity (S) and temperature and salinity (T-S) were tested. Results showed that E. marinus populations are highly sensitive to increases in temperature (>2 °C), which has adverse effects on amphipod recruitment and growth. Results from the climate change scenarios coupled with the sex-ratio fluctuations depended largely on the degree of female bias within population. Temperature increase of 2 °C had less impact on female-biased populations, particularly when conjugated with increases in salinity. Male-biased populations were highly sensitive to any variation in temperature and/or salinity; these populations exhibited a long-term decline in density. Simulations in which temperature increased more than 4 °C led to a continuous decline in the E. marinus population. According to this work, E. marinus populations at their southernmost limit are vulnerable to global warming. We anticipate that in Europe, temperature increases of 2 °C will incite a withdrawal of the population of 5°N from the amphipod species located at southernmost geographical borders. This effect is discussed in relation to the distribution of E. marinus along the Atlantic coast. © 2013 Elsevier B.V. All rights reserved.

Lognormal Distribution of Cellular Uptake of Radioactivity: Statistical Analysis of α-Particle Track Autoradiography

PubMed Central

Neti, Prasad V.S.V.; Howell, Roger W.

2010-01-01

Recently, the distribution of radioactivity among a population of cells labeled with 210Po was shown to be well described by a log-normal (LN) distribution function (J Nucl Med. 2006;47:1049–1058) with the aid of autoradiography. To ascertain the influence of Poisson statistics on the interpretation of the autoradiographic data, the present work reports on a detailed statistical analysis of these earlier data. Methods The measured distributions of α-particle tracks per cell were subjected to statistical tests with Poisson, LN, and Poisson-lognormal (P-LN) models. Results The LN distribution function best describes the distribution of radioactivity among cell populations exposed to 0.52 and 3.8 kBq/mL of 210Po-citrate. When cells were exposed to 67 kBq/mL, the P-LN distribution function gave a better fit; however, the underlying activity distribution remained log-normal. Conclusion The present analysis generally provides further support for the use of LN distributions to describe the cellular uptake of radioactivity. Care should be exercised when analyzing autoradiographic data on activity distributions to ensure that Poisson processes do not distort the underlying LN distribution. PMID:18483086

Log Normal Distribution of Cellular Uptake of Radioactivity: Statistical Analysis of Alpha Particle Track Autoradiography

PubMed Central

Neti, Prasad V.S.V.; Howell, Roger W.

2008-01-01

Recently, the distribution of radioactivity among a population of cells labeled with 210Po was shown to be well described by a log normal distribution function (J Nucl Med 47, 6 (2006) 1049-1058) with the aid of an autoradiographic approach. To ascertain the influence of Poisson statistics on the interpretation of the autoradiographic data, the present work reports on a detailed statistical analyses of these data. Methods The measured distributions of alpha particle tracks per cell were subjected to statistical tests with Poisson (P), log normal (LN), and Poisson – log normal (P – LN) models. Results The LN distribution function best describes the distribution of radioactivity among cell populations exposed to 0.52 and 3.8 kBq/mL 210Po-citrate. When cells were exposed to 67 kBq/mL, the P – LN distribution function gave a better fit, however, the underlying activity distribution remained log normal. Conclusions The present analysis generally provides further support for the use of LN distributions to describe the cellular uptake of radioactivity. Care should be exercised when analyzing autoradiographic data on activity distributions to ensure that Poisson processes do not distort the underlying LN distribution. PMID:16741316

Measuring the Sensitivity of Single-locus “Neutrality Tests” Using a Direct Perturbation Approach

PubMed Central

Garrigan, Daniel; Lewontin, Richard; Wakeley, John

2010-01-01

A large number of statistical tests have been proposed to detect natural selection based on a sample of variation at a single genetic locus. These tests measure the deviation of the allelic frequency distribution observed within populations from the distribution expected under a set of assumptions that includes both neutral evolution and equilibrium population demography. The present study considers a new way to assess the statistical properties of these tests of selection, by their behavior in response to direct perturbations of the steady-state allelic frequency distribution, unconstrained by any particular nonequilibrium demographic scenario. Results from Monte Carlo computer simulations indicate that most tests of selection are more sensitive to perturbations of the allele frequency distribution that increase the variance in allele frequencies than to perturbations that decrease the variance. Simulations also demonstrate that it requires, on average, 4N generations (N is the diploid effective population size) for tests of selection to relax to their theoretical, steady-state distributions following different perturbations of the allele frequency distribution to its extremes. This relatively long relaxation time highlights the fact that these tests are not robust to violations of the other assumptions of the null model besides neutrality. Lastly, genetic variation arising under an example of a regularly cycling demographic scenario is simulated. Tests of selection performed on this last set of simulated data confirm the confounding nature of these tests for the inference of natural selection, under a demographic scenario that likely holds for many species. The utility of using empirical, genomic distributions of test statistics, instead of the theoretical steady-state distribution, is discussed as an alternative for improving the statistical inference of natural selection. PMID:19744997

Projection of invertebrate populations in the headwater streams of a temperate catchment under a changing climate.

PubMed

Nukazawa, Kei; Arai, Ryosuke; Kazama, So; Takemon, Yasuhiro

2018-06-14

Climate change places considerable stress on riverine ecosystems by altering flow regimes and increasing water temperature. This study evaluated how water temperature increases under climate change scenarios will affect stream invertebrates in pristine headwater streams. The studied headwater-stream sites were distributed within a temperate catchment of Japan and had similar hydraulic-geographical conditions, but were subject to varying temperature conditions due to altitudinal differences (100 to 850 m). We adopted eight general circulation models (GCMs) to project air temperature under conservative (RCP2.6), intermediate (RCP4.5), and extreme climate scenarios (RCP8.5) during the near (2031-2050) and far (2081-2100) future. Using the water temperature of headwater streams computed by a distributed hydrological-thermal model as a predictor variable, we projected the population density of stream invertebrates in the future scenarios based on generalized linear models. The mean decrease in the temporally averaged population density of Plecoptera was 61.3% among the GCMs, even under RCP2.6 in the near future, whereas density deteriorated even further (90.7%) under RCP8.5 in the far future. Trichoptera density was also projected to greatly deteriorate under RCP8.5 in the far future. We defined taxa that exhibited temperature-sensitive declines under climate change as cold stenotherms and found that most Plecoptera taxa were cold stenotherms in comparison to other orders. Specifically, the taxonomic families that only distribute in Palearctic realm (e.g., Megarcys ochracea and Scopura longa) were selectively assigned, suggesting that Plecoptera family with its restricted distribution in the Palearctic might be a sensitive indicator of climate change. Plecoptera and Trichoptera populations in the headwaters are expected/anticipated to decrease over the considerable geographical range of the catchment, even under the RCP2.6 in the near future. Given headwater invertebrates play important roles in streams, such as contributing to watershed productivity, our results provide useful information for managing streams at the catchment-level. Copyright © 2018 Elsevier B.V. All rights reserved.

Moment and maximum likelihood estimators for Weibull distributions under length- and area-biased sampling

Treesearch

Jeffrey H. Gove

2003-01-01

Many of the most popular sampling schemes used in forestry are probability proportional to size methods. These methods are also referred to as size biased because sampling is actually from a weighted form of the underlying population distribution. Length- and area-biased sampling are special cases of size-biased sampling where the probability weighting comes from a...

Parameter estimation techniques based on optimizing goodness-of-fit statistics for structural reliability

NASA Technical Reports Server (NTRS)

Starlinger, Alois; Duffy, Stephen F.; Palko, Joseph L.

1993-01-01

New methods are presented that utilize the optimization of goodness-of-fit statistics in order to estimate Weibull parameters from failure data. It is assumed that the underlying population is characterized by a three-parameter Weibull distribution. Goodness-of-fit tests are based on the empirical distribution function (EDF). The EDF is a step function, calculated using failure data, and represents an approximation of the cumulative distribution function for the underlying population. Statistics (such as the Kolmogorov-Smirnov statistic and the Anderson-Darling statistic) measure the discrepancy between the EDF and the cumulative distribution function (CDF). These statistics are minimized with respect to the three Weibull parameters. Due to nonlinearities encountered in the minimization process, Powell's numerical optimization procedure is applied to obtain the optimum value of the EDF. Numerical examples show the applicability of these new estimation methods. The results are compared to the estimates obtained with Cooper's nonlinear regression algorithm.

Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation.

PubMed

Boitard, Simon; Loisel, Patrice

2007-05-01

The probability distribution of haplotype frequencies in a population, and the way it is influenced by genetical forces such as recombination, selection, random drift ...is a question of fundamental interest in population genetics. For large populations, the distribution of haplotype frequencies for two linked loci under the classical Wright-Fisher model is almost impossible to compute because of numerical reasons. However the Wright-Fisher process can in such cases be approximated by a diffusion process and the transition density can then be deduced from the Kolmogorov equations. As no exact solution has been found for these equations, we developed a numerical method based on finite differences to solve them. It applies to transient states and models including selection or mutations. We show by several tests that this method is accurate for computing the conditional joint density of haplotype frequencies given that no haplotype has been lost. We also prove that it is far less time consuming than other methods such as Monte Carlo simulations.

The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes.

PubMed

Hayden, Eric J; Bratulic, Sinisa; Koenig, Iwo; Ferrada, Evandro; Wagner, Andreas

2014-02-01

The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a population's response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged.

THE ROLE OF INDIVIDUAL VARIABILITY IN POPULATION DYNAMICS UNDER CHANGING ENVIRONMENTAL CONDITIONS

EPA Science Inventory

Environmental variability can influence species distributions through changes in
survival, fecundity, behavior, and metabolic activities. As worldwide coastal populations rise, the associated deforestation and development can increase both quantities and variability in runoff...

Empirical Distributions of F ST from Large-Scale Human Polymorphism Data

PubMed Central

Elhaik, Eran

2012-01-01

Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright’s F ST that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F ST may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F ST analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F ST distribution closely follows an exponential distribution. Third, although the overall F ST distribution is similarly shaped (inverse J), F ST distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F ST of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F ST distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection. PMID:23185452

Empirical distributions of F(ST) from large-scale human polymorphism data.

PubMed

Elhaik, Eran

2012-01-01

Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright's F(ST) that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F(ST) may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F(ST) analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F(ST) distribution closely follows an exponential distribution. Third, although the overall F(ST) distribution is similarly shaped (inverse J), F(ST) distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F(ST) of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F(ST) distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection.

Applying GIS and fine-resolution digital terrain models to assess three-dimensional population distribution under traffic impacts.

PubMed

Wu, Chih-Da; Lung, Shih-Chun Candice

2012-01-01

Pollution exhibits significant variations horizontally and vertically within cities; therefore, the size and three-dimensional (3D) spatial distribution of population are significant determinants of urban health. This paper presents a novel methodology, 3D digital geography (3DIG) methodology, for investigating 3D spatial distributions of population in close proximity to traffic, thus the potential highly exposed population under traffic impacts. 3DIG applies geographic information system and fine-resolution (5 m) digital terrain models to obtain the number of building floors in residential zones of the Taipei metropolis; the vertical distribution of population at different floors was estimated based on demographic data in each census tract. In addition, population within 5, 10, 20, 50, and 100 m from the roadways was estimated. Field validation indicated that model results were reliable and accurate; the final population estimation differs only by 0.88% from the demographic database. The results showed that among the total 6.5 million Taipei residents, 0.8 (12.3%), 1.5 (22.9%), 2.3 (34.9), and 2.7 (41.1%) million residents live on the first or second floor within 5, 10, 20, and 50 m, respectively, of municipal roads. There are 22 census tracts with more than half of their residents living on the first or second floor within 5 m of municipal roads. In addition, half of the towns in Taipei city and county with >13.9% and 12.1% of residents live on the first and second floors within 5 m of municipal roads, respectively. These findings highlight the huge number of Taipei residents in close proximity to traffic and have significant implications for exposure assessment and environmental epidemiological studies. This study demonstrates that 3DIG is a versatile methodology for various research and policy planning in which 3D spatial population distribution is the central focus.

On joint subtree distributions under two evolutionary models.

PubMed

Wu, Taoyang; Choi, Kwok Pui

2016-04-01

In population and evolutionary biology, hypotheses about micro-evolutionary and macro-evolutionary processes are commonly tested by comparing the shape indices of empirical evolutionary trees with those predicted by neutral models. A key ingredient in this approach is the ability to compute and quantify distributions of various tree shape indices under random models of interest. As a step to meet this challenge, in this paper we investigate the joint distribution of cherries and pitchforks (that is, subtrees with two and three leaves) under two widely used null models: the Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model. Based on two novel recursive formulae, we propose a dynamic approach to numerically compute the exact joint distribution (and hence the marginal distributions) for trees of any size. We also obtained insights into the statistical properties of trees generated under these two models, including a constant correlation between the cherry and the pitchfork distributions under the YHK model, and the log-concavity and unimodality of the cherry distributions under both models. In addition, we show that there exists a unique change point for the cherry distributions between these two models. Copyright © 2015 Elsevier Inc. All rights reserved.

On the proportional abundance of species: Integrating population genetics and community ecology.

PubMed

Marquet, Pablo A; Espinoza, Guillermo; Abades, Sebastian R; Ganz, Angela; Rebolledo, Rolando

2017-12-01

The frequency of genes in interconnected populations and of species in interconnected communities are affected by similar processes, such as birth, death and immigration. The equilibrium distribution of gene frequencies in structured populations is known since the 1930s, under Wright's metapopulation model known as the island model. The equivalent distribution for the species frequency (i.e. the species proportional abundance distribution (SPAD)), at the metacommunity level, however, is unknown. In this contribution, we develop a stochastic model to analytically account for this distribution (SPAD). We show that the same as for genes SPAD follows a beta distribution, which provides a good description of empirical data and applies across a continuum of scales. This stochastic model, based upon a diffusion approximation, provides an alternative to neutral models for the species abundance distribution (SAD), which focus on number of individuals instead of proportions, and demonstrate that the relative frequency of genes in local populations and of species within communities follow the same probability law. We hope our contribution will help stimulate the mathematical and conceptual integration of theories in genetics and ecology.

Computer program determines exact two-sided tolerance limits for normal distributions

NASA Technical Reports Server (NTRS)

Friedman, H. A.; Webb, S. R.

1968-01-01

Computer program determines by numerical integration the exact statistical two-sided tolerance limits, when the proportion between the limits is at least a specified number. The program is limited to situations in which the underlying probability distribution for the population sampled is the normal distribution with unknown mean and variance.

Why sampling scheme matters: the effect of sampling scheme on landscape genetic results

Treesearch

Michael K. Schwartz; Kevin S. McKelvey

2008-01-01

There has been a recent trend in genetic studies of wild populations where researchers have changed their sampling schemes from sampling pre-defined populations to sampling individuals uniformly across landscapes. This reflects the fact that many species under study are continuously distributed rather than clumped into obvious "populations". Once individual...

Genetic variation and evolution of Polaskia chichipe (Cactaceae) under domestication in the Tehuacán Valley, central Mexico.

PubMed

Otero-Arnaiz, Adriana; Casas, Alejandro; Hamrick, James L; Cruse-Sanders, Jennifer

2005-05-01

Polaskia chichipe is a columnar cactus under artificial selection in central Mexico because of its edible fruits. Our study explored the effect of human manipulation on levels and distribution of genetic variation in wild, silviculturally managed and cultivated sympatric populations. Total genetic variation, estimated in nine populations with five microsatellite loci, was H(T) = 0.658 +/- 0.026 SE, which was mainly distributed within populations (H(S) = 0.646) with low differentiation among them (F(ST) = 0.015). Fixation index (F(IS)) in all populations was positive, indicating a deficit of heterozygous individuals with respect to Hardy-Weinberg expectations. When populations were pooled by management type, the highest expected heterozygosity (H(E) = 0.631 +/- 0.031 SE) and the lowest fixation index (F(IS) = 0.07) were observed in wild populations, followed by cultivated populations (H(E) = 0.56 +/- 0.03 SE, F(IS) = 0.14), whereas the lowest variation was found in silviculturally managed populations (H(E) = 0.51 +/- 0.05 SE, F(IS) = 0.17). Low differentiation among populations under different management types (F(ST) 0.005, P < 0.04) was observed. A pattern of migration among neighbouring populations, suggested from isolation by distance (r2 = 0.314, P < 0.01), may have contributed to homogenizing populations and counteracting the effects of artificial selection. P. chichipe, used and managed for at least 700 generations, shows morphological differentiation, changes in breeding system and seed germination patterns associated with human management, with only slight genetic differences detected by neutral markers.

Synthetic Survey of the Kepler Field

NASA Astrophysics Data System (ADS)

Wells, Mark; Prša, Andrej

2018-01-01

In the era of large scale surveys, including LSST and Gaia, binary population studies will flourish due to the large influx of data. In addition to probing binary populations as a function of galactic latitude, under-sampled groups such as low mass binaries will be observed at an unprecedented rate. To prepare for these missions, binary population simulations need to be carried out at high fidelity. These simulations will enable the creation of simulated data and, through comparison with real data, will allow the underlying binary parameter distributions to be explored. In order for the simulations to be considered robust, they should reproduce observed distributions accurately. To this end we have developed a simulator which takes input models and creates a synthetic population of eclipsing binaries. Starting from a galactic single star model, implemented using Galaxia, a code by Sharma et al. (2011), and applying observed multiplicity, mass-ratio, period, and eccentricity distributions, as reported by Raghavan et al. (2010), Duchêne & Kraus (2013), and Moe & Di Stefano (2017), we are able to generate synthetic binary surveys that correspond to any survey cadences. In order to calibrate our input models we compare the results of our synthesized eclipsing binary survey to the Kepler Eclipsing Binary catalog.

Pleiotropic Effects of Immune Responses Explain Variation in the Prevalence of Fibroproliferative Diseases

PubMed Central

Russell, Shirley B.; Smith, Joan C.; Huang, Minjun; Trupin, Joel S.; Williams, Scott M.

2015-01-01

Many diseases are differentially distributed among human populations. Differential selection on genetic variants in ancestral environments that coincidentally predispose to disease can be an underlying cause of these unequal prevalence patterns. Selected genes may be pleiotropic, affecting multiple phenotypes and resulting in more than one disease or trait. Patterns of pleiotropy may be helpful in understanding the underlying causes of an array of conditions in a population. For example, several fibroproliferative diseases are more prevalent and severe in populations of sub-Saharan ancestry. We propose that this disparity is due to selection for an enhanced Th2 response that confers resistance to helminthic infections, and concurrently increases susceptibility to fibrosis due to the profibrotic action of Th2 cytokines. Many studies on selection of Th2-related genes for host resistance to helminths have been reported, but the pleiotropic impact of this selection on the distribution of fibrotic disorders has not been explicitly investigated. We discuss the disproportionate occurrence of fibroproliferative diseases in individuals of African ancestry and provide evidence that adaptation of the immune system has shaped the genetic structure of these human populations in ways that alter the distribution of multiple fibroproliferative diseases. PMID:26540410

Losing your edge: climate change and the conservation value of range-edge populations.

PubMed

Rehm, Evan M; Olivas, Paulo; Stroud, James; Feeley, Kenneth J

2015-10-01

Populations occurring at species' range edges can be locally adapted to unique environmental conditions. From a species' perspective, range-edge environments generally have higher severity and frequency of extreme climatic events relative to the range core. Under future climates, extreme climatic events are predicted to become increasingly important in defining species' distributions. Therefore, range-edge genotypes that are better adapted to extreme climates relative to core populations may be essential to species' persistence during periods of rapid climate change. We use relatively simple conceptual models to highlight the importance of locally adapted range-edge populations (leading and trailing edges) for determining the ability of species to persist under future climates. Using trees as an example, we show how locally adapted populations at species' range edges may expand under future climate change and become more common relative to range-core populations. We also highlight how large-scale habitat destruction occurring in some geographic areas where many species range edge converge, such as biome boundaries and ecotones (e.g., the arc of deforestation along the rainforest-cerrado ecotone in the southern Amazonia), can have major implications for global biodiversity. As climate changes, range-edge populations will play key roles in helping species to maintain or expand their geographic distributions. The loss of these locally adapted range-edge populations through anthropogenic disturbance is therefore hypothesized to reduce the ability of species to persist in the face of rapid future climate change.

Appalachia -- A Reference Book. First Edition.

ERIC Educational Resources Information Center

Linkous, Jonathan; And Others

With a total area of 197,116 square miles, the Appalachian Region has an uneven distribution of population, income, wealth, and natural resources. The Region's 19 million people live in 397 counties and 5 independent cities in Virginia, which range in population size from 2.6 thousand to 1.5 million. Under 50% of the population live in…

The relationship between climate change and the endangered rainforest shrub Triunia robusta (Proteaceae) endemic to southeast Queensland, Australia

NASA Astrophysics Data System (ADS)

Shimizu-Kimura, Yoko; Accad, Arnon; Shapcott, Alison

2017-04-01

Threatened species in rainforests may be vulnerable to climate change, because of their potentially narrow thermal tolerances, small population sizes and restricted distributions. This study modelled climate induced changes on the habitat distribution of the endangered rainforest plant Triunia robusta, endemic to southeast Queensland, Australia. Species distribution models were developed for eastern Australia at 250 m grids and southeast Queensland at 25 m grids using ground-truthed presence records and environmental predictor data. The species’ habitat distribution under the current climate was modelled, and the future potential habitat distributions were projected for the epochs 2030, 2050 and 2070. The eastern Australia model identified several spatially disjunct, broad habitat areas of coastal eastern Australia consistent with the current distribution of rainforests, and projected a southward and upslope contraction driven mainly by average temperatures exceeding current range limits. The southeast Queensland models suggest a dramatic upslope contraction toward locations where the majority of known populations are found. Populations located in the Sunshine Coast hinterland, consistent with past rainforest refugia, are likely to persist long-term. Upgrading the level of protection for less formal nature reserves containing viable populations is a high priority to better protect refugial T. robusta populations with respect to climate change.

The relationship between climate change and the endangered rainforest shrub Triunia robusta (Proteaceae) endemic to southeast Queensland, Australia

PubMed Central

Shimizu-Kimura, Yoko; Accad, Arnon; Shapcott, Alison

2017-01-01

Threatened species in rainforests may be vulnerable to climate change, because of their potentially narrow thermal tolerances, small population sizes and restricted distributions. This study modelled climate induced changes on the habitat distribution of the endangered rainforest plant Triunia robusta, endemic to southeast Queensland, Australia. Species distribution models were developed for eastern Australia at 250 m grids and southeast Queensland at 25 m grids using ground-truthed presence records and environmental predictor data. The species’ habitat distribution under the current climate was modelled, and the future potential habitat distributions were projected for the epochs 2030, 2050 and 2070. The eastern Australia model identified several spatially disjunct, broad habitat areas of coastal eastern Australia consistent with the current distribution of rainforests, and projected a southward and upslope contraction driven mainly by average temperatures exceeding current range limits. The southeast Queensland models suggest a dramatic upslope contraction toward locations where the majority of known populations are found. Populations located in the Sunshine Coast hinterland, consistent with past rainforest refugia, are likely to persist long-term. Upgrading the level of protection for less formal nature reserves containing viable populations is a high priority to better protect refugial T. robusta populations with respect to climate change. PMID:28422136

How much inequality in income is fair? A microeconomic game theoretic perspective

NASA Astrophysics Data System (ADS)

Venkatasubramanian, Venkat; Luo, Yu; Sethuraman, Jay

2015-10-01

The increasing inequality in income and wealth in recent years, and the associated excessive pay packages of CEOs in the US and elsewhere, is of growing concern among policy makers as well as the common person. However, there seems to be no satisfactory answer, in conventional economic theories and models, to the fundamental questions of what kind of income distribution we ought to see, at least under ideal conditions, in a free market environment, and whether this distribution is fair. We propose a novel microeconomic game theoretic framework that addresses these questions and proves that the lognormal distribution is the fairest inequality of pay in an organization comprising of homogeneous agents, under ideal free market conditions at equilibrium. We also show that for a population of two different classes of agents, the equilibrium distribution is a combination of two different lognormal distributions where one of them, corresponding to the top ˜3-5% of the population, can be misidentified as a Pareto distribution. We compare our predictions with empirical data on global income inequality trends provided by Piketty and others. Our analysis suggests that the Scandinavian countries, and to a lesser extent Switzerland, Netherlands and Australia, have managed to get close to the ideal distribution for the bottom ˜99% of the population, while the US and UK remain less fair at the other extreme. Other European countries such as France and Germany, and Japan and Canada, are in the middle. Our theory also shows the deep and direct connection between potential game theory and statistical mechanics through entropy, which we identify as a measure of fairness in a distribution. This leads us to propose the fair market hypothesis, that the self-organizing dynamics of the ideal free market, i.e., Adam Smith's "invisible hand", not only promotes efficiency but also maximizes fairness under the given constraints.

Uncertainty Quantification Techniques for Population Density Estimates Derived from Sparse Open Source Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, Robert N; White, Devin A; Urban, Marie L

2013-01-01

The Population Density Tables (PDT) project at the Oak Ridge National Laboratory (www.ornl.gov) is developing population density estimates for specific human activities under normal patterns of life based largely on information available in open source. Currently, activity based density estimates are based on simple summary data statistics such as range and mean. Researchers are interested in improving activity estimation and uncertainty quantification by adopting a Bayesian framework that considers both data and sociocultural knowledge. Under a Bayesian approach knowledge about population density may be encoded through the process of expert elicitation. Due to the scale of the PDT effort whichmore » considers over 250 countries, spans 40 human activity categories, and includes numerous contributors, an elicitation tool is required that can be operationalized within an enterprise data collection and reporting system. Such a method would ideally require that the contributor have minimal statistical knowledge, require minimal input by a statistician or facilitator, consider human difficulties in expressing qualitative knowledge in a quantitative setting, and provide methods by which the contributor can appraise whether their understanding and associated uncertainty was well captured. This paper introduces an algorithm that transforms answers to simple, non-statistical questions into a bivariate Gaussian distribution as the prior for the Beta distribution. Based on geometric properties of the Beta distribution parameter feasibility space and the bivariate Gaussian distribution, an automated method for encoding is developed that responds to these challenging enterprise requirements. Though created within the context of population density, this approach may be applicable to a wide array of problem domains requiring informative priors for the Beta distribution.« less

Volcanisme, activité anthropique et circulation des masses océaniques : leur influence respective sur la distribution des populations d'ostracodes dans la baie de Kagoshima (île de Kyushu, Japon)Impact of volcanism, human activities, and water mass circulation on the distribution of ostracod populations in Kagoshima Bay (Kyushu Island, southern Japan)

NASA Astrophysics Data System (ADS)

Bodergat, Anne-Marie; Oki, Kimihiko; Ishizaki, Kunihiro; Rio, Michel

2002-11-01

The distribution of ostracod populations in Kagoshima Bay (Japan) is analysed with reference to different environmental parameters. The bay is an area of volcanic activity of Sakurajima volcano under the influence of the Kuroshio Current. Most of the Head environment is occupied by an acidic water mass. Numbers of individual and species decrease from the Mouth of the bay towards the Basin and Head environments. In this latter, acidic water mass has a drastic effect on ostracod populations, whereas volcanic ashes and domestic inputs are not hostile. Ostracod distribution is influenced by the quality and structure of water masses. To cite this article: A.-M. Bodergat et al., C. R. Geoscience 334 (2002) 1053-1059.

Quantitative Genetic Architecture at Latitudinal Range Boundaries: Reduced Variation but Higher Trait Independence.

PubMed

Paccard, Antoine; Van Buskirk, Josh; Willi, Yvonne

2016-05-01

Species distribution limits are hypothesized to be caused by small population size and limited genetic variation in ecologically relevant traits, but earlier studies have not evaluated genetic variation in multivariate phenotypes. We asked whether populations at the latitudinal edges of the distribution have altered quantitative genetic architecture of ecologically relevant traits compared with midlatitude populations. We calculated measures of evolutionary potential in nine Arabidopsis lyrata populations spanning the latitudinal range of the species in eastern and midwestern North America. Environments at the latitudinal extremes have reduced water availability, and therefore plants were assessed under wet and dry treatments. We estimated genetic variance-covariance (G-) matrices for 10 traits related to size, development, and water balance. Populations at southern and northern distribution edges had reduced levels of genetic variation across traits, but their G-matrices were more spherical; G-matrix orientation was unrelated to latitude. As a consequence, the predicted short-term response to selection was at least as strong in edge populations as in central populations. These results are consistent with genetic drift eroding variation and reducing the effectiveness of correlational selection at distribution margins. We conclude that genetic variation of isolated traits poorly predicts the capacity to evolve in response to multivariate selection and that the response to selection may frequently be greater than expected at species distribution margins because of genetic drift.

Han's model parameters for microalgae grown under intermittent illumination: Determined using particle swarm optimization.

PubMed

Pozzobon, Victor; Perre, Patrick

2018-01-21

This work provides a model and the associated set of parameters allowing for microalgae population growth computation under intermittent lightning. Han's model is coupled with a simple microalgae growth model to yield a relationship between illumination and population growth. The model parameters were obtained by fitting a dataset available in literature using Particle Swarm Optimization method. In their work, authors grew microalgae in excess of nutrients under flashing conditions. Light/dark cycles used for these experimentations are quite close to those found in photobioreactor, i.e. ranging from several seconds to one minute. In this work, in addition to producing the set of parameters, Particle Swarm Optimization robustness was assessed. To do so, two different swarm initialization techniques were used, i.e. uniform and random distribution throughout the search-space. Both yielded the same results. In addition, swarm distribution analysis reveals that the swarm converges to a unique minimum. Thus, the produced set of parameters can be trustfully used to link light intensity to population growth rate. Furthermore, the set is capable to describe photodamages effects on population growth. Hence, accounting for light overexposure effect on algal growth. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ecology of Meimuna mongolica (Hemiptera: Cicadidae) Nymphs: Instars, Morphological Variation, Vertical Distribution and Population Density, Host-Plant Selection, and Emergence Phenology

PubMed Central

Li, Qinglong; Yang, Mingsheng; Liu, Yunxiang; Wei, Cong

2015-01-01

The cicada Meimuna mongolica (Distant) (Hemiptera: Cicadidae) is one of the most important pests of economic forest in Guanzhong Plain of Shaanxi Province, China. Information about ecological characteristics and some sustainable control measures of this species is urgently required for its control. In this study, nymphal instars, morphological variation, vertical distribution, and population density in soil, and emergence phenology of nymphs of M. mongolica on three main host plants (Pinus tabuliformis Carr., Populus tomentosa Carr., and Pyrus xerophila Yü) were studied, based on combined morphological and molecular identification, investigation of the first-instar nymphs hatched from eggs and others excavated from soil, and investigation of exuviae in the adult emergence period. Five nymphal instars of M. mongolica were redetermined according to the distribution plots of the head capsule widths of the nymphs. Nymphs of third and fourth instars showed morphological variation, which is closely related to host-plant association. The mean densities of nymphs in soil under the three host plants were significantly different, indicating a distinct host preference. The nymphs could extend their distribution from the 0–10 cm soil layer to the 51–60 cm soil layer underground but not beyond 60 cm soil layer under all the three host plants. The 21–30 cm soil layer under all the three host plants has the highest nymphal population density. The sex ratio of the entire population was nearly 50:50, but males dominated in the early half of the duration of the emergence. These ecological characteristics of M. mongolica could provide important information for sustainable control measures.

Measurements of the populations of metastable and resonance levels in the plasma of an RF capacitive discharge in argon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vasilieva, A. N.; Voloshin, D. G.; Kovalev, A. S., E-mail: kovalev@dnph.phys.msu.su

2015-05-15

The behavior of the populations of two metastable and two lower resonance levels of argon atoms in the plasma of an RF capacitive discharge was studied. The populations were measured by two methods: the method of emission self-absorption and the method based on measurements of the intensity ratios of spectral lines. It is shown that the populations of resonance levels increase with increasing power deposited in the discharge, whereas the populations of metastable levels is independent of the RF power. The distribution of the populations over energy levels is not equilibrium under these conditions. The population kinetics of argon atomicmore » levels in the discharge plasma is simulated numerically. The distribution function of plasma electrons recovered from the measured populations of atomic levels and numerical simulations is found to be non-Maxwellian.« less

Characteristic fragment size distributions in dynamic fragmentation

NASA Astrophysics Data System (ADS)

Zhou, Fenghua; Molinari, Jean-François; Ramesh, K. T.

2006-06-01

The one-dimensional fragmentation of a dynamically expanding ring (Mott's problem) is studied numerically to obtain the fragment signatures under different strain rates. An empirical formula is proposed to calculate an average fragment size. Rayleigh distribution is found to describe the statistical properties of the fragment populations.

A size-structured model of bacterial growth and reproduction.

PubMed

Ellermeyer, S F; Pilyugin, S S

2012-01-01

We consider a size-structured bacterial population model in which the rate of cell growth is both size- and time-dependent and the average per capita reproduction rate is specified as a model parameter. It is shown that the model admits classical solutions. The population-level and distribution-level behaviours of these solutions are then determined in terms of the model parameters. The distribution-level behaviour is found to be different from that found in similar models of bacterial population dynamics. Rather than convergence to a stable size distribution, we find that size distributions repeat in cycles. This phenomenon is observed in similar models only under special assumptions on the functional form of the size-dependent growth rate factor. Our main results are illustrated with examples, and we also provide an introductory study of the bacterial growth in a chemostat within the framework of our model.

Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change.

PubMed

Maguire, Kaitlin C; Shinneman, Douglas J; Potter, Kevin M; Hipkins, Valerie D

2018-03-14

Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results demonstrate the utility in modeling intraspecific response to changing climate and they inform management and conservation strategies, by identifying haplotypes and geographic areas that may be most at risk, or most secure, under projected climate change.

Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change

USGS Publications Warehouse

Maguire, Kaitlin C.; Shinneman, Douglas; Potter, Kevin M.; Hipkins, Valerie D.

2018-01-01

Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results demonstrate the utility in modeling intraspecific response to changing climate and they inform management and conservation strategies, by identifying haplotypes and geographic areas that may be most at risk, or most secure, under projected climate change.

The effects of nongenetic memory on population level sensitivity to stress

NASA Astrophysics Data System (ADS)

Adams, Rhys; Nevozhay, Dmitry; van Itallie, Elizabeth; Bennett, Matthew; Balazsi, Gabor

2011-03-01

While gene expression is often thought of as a unidirectional determinant of cellular fitness, recent studies have shown how growth retardation due to protein expression can affect gene expression levels in single cells. We developed two yeast strains carrying a drug resistance protein under the control of different synthetic gene constructs, one of which was monostable, while the other was bistable. The gene expression of these cell populations was tuned using a molecular inducer so that their respective means and noises were identical, while their nongenetic memory properties were different. We tested the sensitivity of these two cell population distributions to the antibiotic zeocin. We found that the gene expression distributions of bistable cell populations were sensitive to stressful environments, while the gene expression distribution of monostable cells were nearly unchanged by stress. We conclude that cell populations with high nongenetic memory are more adaptable to their environment. This work was funded by the National Institutes of Health through the NIH Director's New Innovator Award Program, 1-DP2- OD006481-01.

Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds.

PubMed

Ndihokubwayo, Noel; Nguyen, Viet-Thang; Cheng, Dandan

2016-01-01

Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north-eastern and south-western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations.

Statistical characteristics of dynamics for population migration driven by the economic interests

NASA Astrophysics Data System (ADS)

Huo, Jie; Wang, Xu-Ming; Zhao, Ning; Hao, Rui

2016-06-01

Population migration typically occurs under some constraints, which can deeply affect the structure of a society and some other related aspects. Therefore, it is critical to investigate the characteristics of population migration. Data from the China Statistical Yearbook indicate that the regional gross domestic product per capita relates to the population size via a linear or power-law relation. In addition, the distribution of population migration sizes or relative migration strength introduced here is dominated by a shifted power-law relation. To reveal the mechanism that creates the aforementioned distributions, a dynamic model is proposed based on the population migration rule that migration is facilitated by higher financial gains and abated by fewer employment opportunities at the destination, considering the migration cost as a function of the migration distance. The calculated results indicate that the distribution of the relative migration strength is governed by a shifted power-law relation, and that the distribution of migration distances is dominated by a truncated power-law relation. These results suggest the use of a power-law to fit a distribution may be not always suitable. Additionally, from the modeling framework, one can infer that it is the randomness and determinacy that jointly create the scaling characteristics of the distributions. The calculation also demonstrates that the network formed by active nodes, representing the immigration and emigration regions, usually evolves from an ordered state with a non-uniform structure to a disordered state with a uniform structure, which is evidenced by the increasing structural entropy.

Individual heterogeneity and identifiability in capture-recapture models

USGS Publications Warehouse

Link, W.A.

2004-01-01

Individual heterogeneity in detection probabilities is a far more serious problem for capture-recapture modeling than has previously been recognized. In this note, I illustrate that population size is not an identifiable parameter under the general closed population mark-recapture model Mh. The problem of identifiability is obvious if the population includes individuals with pi = 0, but persists even when it is assumed that individual detection probabilities are bounded away from zero. Identifiability may be attained within parametric families of distributions for pi, but not among parametric families of distributions. Consequently, in the presence of individual heterogeneity in detection probability, capture-recapture analysis is strongly model dependent.

Bridging the Timescales of Single-Cell and Population Dynamics

NASA Astrophysics Data System (ADS)

Jafarpour, Farshid; Wright, Charles S.; Gudjonson, Herman; Riebling, Jedidiah; Dawson, Emma; Lo, Klevin; Fiebig, Aretha; Crosson, Sean; Dinner, Aaron R.; Iyer-Biswas, Srividya

2018-04-01

How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a data-validated theoretical framework that accounts for observables at both single-cell and population scales. We derive exact analytical complete time-dependent solutions to cell-age distributions and population growth rates as functionals of the underlying interdivision time distributions, for symmetric and asymmetric cell division. These results provide insights into the surprising implications of stochastic single-cell dynamics for population growth. Using our results for asymmetric division, we deduce the time to transition from the reproductively quiescent (swarmer) to the replication-competent (stalked) stage of the Caulobacter crescentus life cycle. Remarkably, population numbers can spontaneously oscillate with time. We elucidate the physics leading to these population oscillations. For C. crescentus cells, we show that a simple measurement of the population growth rate, for a given growth condition, is sufficient to characterize the condition-specific cellular unit of time and, thus, yields the mean (single-cell) growth and division timescales, fluctuations in cell division times, the cell-age distribution, and the quiescence timescale.

Framework for assessing impacts of pile-driving noise from offshore wind farm construction on a harbour seal population

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Paul M., E-mail: lighthouse@abdn.ac.uk; Hastie, Gordon D., E-mail: gdh10@st-andrews.ac.uk; Nedwell, Jeremy, E-mail: Jeremy.Nedwell@subacoustech.com

2013-11-15

Offshore wind farm developments may impact protected marine mammal populations, requiring appropriate assessment under the EU Habitats Directive. We describe a framework developed to assess population level impacts of disturbance from piling noise on a protected harbour seal population in the vicinity of proposed wind farm developments in NE Scotland. Spatial patterns of seal distribution and received noise levels are integrated with available data on the potential impacts of noise to predict how many individuals are displaced or experience auditory injury. Expert judgement is used to link these impacts to changes in vital rates and applied to population models thatmore » compare population changes under baseline and construction scenarios over a 25 year period. We use published data and hypothetical piling scenarios to illustrate how the assessment framework has been used to support environmental assessments, explore the sensitivity of the framework to key assumptions, and discuss its potential application to other populations of marine mammals. -- Highlights: • We develop a framework to support Appropriate Assessment for harbour seal populations. • We assessed potential impacts of wind farm construction noise. • Data on distribution of seals and noise were used to predict effects on individuals. • Expert judgement linked these impacts to vital rates to model population change. • We explore the sensitivity of the framework to key assumptions and uncertainties.« less

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

PubMed

Allman, Elizabeth S; Degnan, James H; Rhodes, John A

2011-06-01

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

The evolution of human mobility based on the public goods game

NASA Astrophysics Data System (ADS)

Yan, Shiqing

2017-07-01

We explore the evolution of human mobility behavior based on public goods game. By using mean field method, the population distribution in different regions is theoretical calculated. Numerical simulation results show that the correlation between the region's degree and its final population is not significant under a larger human migration rate. Human mobility could effectively promote cooperative behavior and the population balance of different regions. Therefore, encouraging individuals to migrate may increase the total benefits of the whole society. Moreover, increasing the cooperation cost could reduce the number of cooperators, and that would happen to the correlation between the region's degree and its final population. The results indicate the total population could not dramatically rise with the region's degree under an unfair society.

Spatio-temporal dynamics of a fish predator: Density-dependent and hydrographic effects on Baltic Sea cod population

PubMed Central

Bartolino, Valerio; Tian, Huidong; Bergström, Ulf; Jounela, Pekka; Aro, Eero; Dieterich, Christian; Meier, H. E. Markus; Cardinale, Massimiliano; Bland, Barbara

2017-01-01

Understanding the mechanisms of spatial population dynamics is crucial for the successful management of exploited species and ecosystems. However, the underlying mechanisms of spatial distribution are generally complex due to the concurrent forcing of both density-dependent species interactions and density-independent environmental factors. Despite the high economic value and central ecological importance of cod in the Baltic Sea, the drivers of its spatio-temporal population dynamics have not been analytically investigated so far. In this paper, we used an extensive trawl survey dataset in combination with environmental data to investigate the spatial dynamics of the distribution of the Eastern Baltic cod during the past three decades using Generalized Additive Models. The results showed that adult cod distribution was mainly affected by cod population size, and to a minor degree by small-scale hydrological factors and the extent of suitable reproductive areas. As population size decreases, the cod population concentrates to the southern part of the Baltic Sea, where the preferred more marine environment conditions are encountered. Using the fitted models, we predicted the Baltic cod distribution back to the 1970s and a temporal index of cod spatial occupation was developed. Our study will contribute to the management and conservation of this important resource and of the ecosystem where it occurs, by showing the forces shaping its spatial distribution and therefore the potential response of the population to future exploitation and environmental changes. PMID:28207804

Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa.

PubMed

Lyam, Paul Terwase; Duque-Lazo, Joaquín; Durka, Walter; Hauenschild, Frank; Schnitzler, Jan; Michalak, Ingo; Ogundipe, Oluwatoyin Temitayo; Muellner-Riehl, Alexandra Nora

2018-01-01

Climate change is predicted to impact species' genetic diversity and distribution. We used Senegalia senegal (L.) Britton, an economically important species distributed in the Sudano-Sahelian savannah belt of West Africa, to investigate the impact of climate change on intraspecific genetic diversity and distribution. We used ten nuclear and two plastid microsatellite markers to assess genetic variation, population structure and differentiation across thirteen sites in West Africa. We projected suitable range, and potential impact of climate change on genetic diversity using a maximum entropy approach, under four different climate change scenarios. We found higher genetic and haplotype diversity at both nuclear and plastid markers than previously reported. Genetic differentiation was strong for chloroplast and moderate for the nuclear genome. Both genomes indicated three spatially structured genetic groups. The distribution of Senegalia senegal is strongly correlated with extractable nitrogen, coarse fragments, soil organic carbon stock, precipitation of warmest and coldest quarter and mean temperature of driest quarter. We predicted 40.96 to 6.34 per cent of the current distribution to favourably support the species' ecological requirements under future climate scenarios. Our results suggest that climate change is going to affect the population genetic structure of Senegalia senegal, and that patterns of genetic diversity are going to influence the species' adaptive response to climate change. Our study contributes to the growing evidence predicting the loss of economically relevant plants in West Africa in the next decades due to climate change.

Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa

PubMed Central

Duque-Lazo, Joaquín; Durka, Walter; Hauenschild, Frank; Schnitzler, Jan; Michalak, Ingo; Ogundipe, Oluwatoyin Temitayo; Muellner-Riehl, Alexandra Nora

2018-01-01

Climate change is predicted to impact species’ genetic diversity and distribution. We used Senegalia senegal (L.) Britton, an economically important species distributed in the Sudano-Sahelian savannah belt of West Africa, to investigate the impact of climate change on intraspecific genetic diversity and distribution. We used ten nuclear and two plastid microsatellite markers to assess genetic variation, population structure and differentiation across thirteen sites in West Africa. We projected suitable range, and potential impact of climate change on genetic diversity using a maximum entropy approach, under four different climate change scenarios. We found higher genetic and haplotype diversity at both nuclear and plastid markers than previously reported. Genetic differentiation was strong for chloroplast and moderate for the nuclear genome. Both genomes indicated three spatially structured genetic groups. The distribution of Senegalia senegal is strongly correlated with extractable nitrogen, coarse fragments, soil organic carbon stock, precipitation of warmest and coldest quarter and mean temperature of driest quarter. We predicted 40.96 to 6.34 per cent of the current distribution to favourably support the species’ ecological requirements under future climate scenarios. Our results suggest that climate change is going to affect the population genetic structure of Senegalia senegal, and that patterns of genetic diversity are going to influence the species’ adaptive response to climate change. Our study contributes to the growing evidence predicting the loss of economically relevant plants in West Africa in the next decades due to climate change. PMID:29659603

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

USGS Publications Warehouse

Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

Use of Genetic Data to Infer Population-Specific Ecological and Phenotypic Traits from Mixed Aggregations

PubMed Central

Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions. PMID:24905464

The interaction between the spatial distribution of resource patches and population density: consequences for intraspecific growth and morphology.

PubMed

Jacobson, Bailey; Grant, James W A; Peres-Neto, Pedro R

2015-07-01

How individuals within a population distribute themselves across resource patches of varying quality has been an important focus of ecological theory. The ideal free distribution predicts equal fitness amongst individuals in a 1 : 1 ratio with resources, whereas resource defence theory predicts different degrees of monopolization (fitness variance) as a function of temporal and spatial resource clumping and population density. One overlooked landscape characteristic is the spatial distribution of resource patches, altering the equitability of resource accessibility and thereby the effective number of competitors. While much work has investigated the influence of morphology on competitive ability for different resource types, less is known regarding the phenotypic characteristics conferring relative ability for a single resource type, particularly when exploitative competition predominates. Here we used young-of-the-year rainbow trout (Oncorhynchus mykiss) to test whether and how the spatial distribution of resource patches and population density interact to influence the level and variance of individual growth, as well as if functional morphology relates to competitive ability. Feeding trials were conducted within stream channels under three spatial distributions of nine resource patches (distributed, semi-clumped and clumped) at two density levels (9 and 27 individuals). Average trial growth was greater in high-density treatments with no effect of resource distribution. Within-trial growth variance had opposite patterns across resource distributions. Here, variance decreased at low-population, but increased at high-population densities as patches became increasingly clumped as the result of changes in the levels of interference vs. exploitative competition. Within-trial growth was related to both pre- and post-trial morphology where competitive individuals were those with traits associated with swimming capacity and efficiency: larger heads/bodies/caudal fins and less angled pectoral fins. The different degrees of within-population growth variance at the same density level found here, as a function of spatial resource distribution, provide an explanation for the inconsistencies in within-site growth variance and population regulation often noted with regard to density dependence in natural landscapes. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Spatio-temporal distribution of dengue fever under scenarios of climate change in the southern Taiwan

NASA Astrophysics Data System (ADS)

Lee, Chieh-Han; Yu, Hwa-Lung

2014-05-01

Dengue fever has been recognized as the most important widespread vector-borne infectious disease in recent decades. Over 40% of the world's population is risk from dengue and about 50-100 million people are infected world wide annually. Previous studies have found that dengue fever is highly correlated with climate covariates. Thus, the potential effects of global climate change on dengue fever are crucial to epidemic concern, in particular, the transmission of the disease. This present study investigated the nonlinearity of time-delayed impact of climate on spatio-temporal variations of dengue fever in the southern Taiwan during 1998 to 2011. A distributed lag nonlinear model (DLNM) is used to assess the nonlinear lagged effects of meteorology. The statistically significant meteorological factors are considered, including weekly minimum temperature and maximum 24-hour rainfall. The relative risk and the distribution of dengue fever then predict under various climate change scenarios. The result shows that the relative risk is similar for different scenarios. In addition, the impact of rainfall on the incidence risk is higher than temperature. Moreover, the incidence risk is associated to spatially population distribution. The results can be served as practical reference for environmental regulators for the epidemic prevention under climate change scenarios.

Social Determinants of Population Health: A Systems Sciences Approach

PubMed Central

Fink, David S.; Keyes, Katherine M.; Cerdá, Magdalena

2016-01-01

Population distributions of health emerge from the complex interplay of health-related factors at multiple levels, from the biological to the societal level. Individuals are aggregated within social networks, affected by their locations, and influenced differently across time. From aggregations of individuals, group properties can emerge, including some exposures that are ubiquitous within populations but variant across populations. By combining a focus on social determinants of health with a conceptual framework for understanding how genetics, biology, behavior, psychology, society, and environment interact, a systems science approach can inform our understanding of the underlying causes of the unequal distribution of health across generations and populations, and can help us identify promising approaches to reduce such inequalities. In this paper, we discuss how systems science approaches have already made several substantive and methodological contributions to the study of population health from a social epidemiology perspective. PMID:27642548

Predicting the genetic consequences of future climate change: The power of coupling spatial demography, the coalescent, and historical landscape changes.

PubMed

Brown, Jason L; Weber, Jennifer J; Alvarado-Serrano, Diego F; Hickerson, Michael J; Franks, Steven J; Carnaval, Ana C

2016-01-01

Climate change is a widely accepted threat to biodiversity. Species distribution models (SDMs) are used to forecast whether and how species distributions may track these changes. Yet, SDMs generally fail to account for genetic and demographic processes, limiting population-level inferences. We still do not understand how predicted environmental shifts will impact the spatial distribution of genetic diversity within taxa. We propose a novel method that predicts spatially explicit genetic and demographic landscapes of populations under future climatic conditions. We use carefully parameterized SDMs as estimates of the spatial distribution of suitable habitats and landscape dispersal permeability under present-day, past, and future conditions. We use empirical genetic data and approximate Bayesian computation to estimate unknown demographic parameters. Finally, we employ these parameters to simulate realistic and complex models of responses to future environmental shifts. We contrast parameterized models under current and future landscapes to quantify the expected magnitude of change. We implement this framework on neutral genetic data available from Penstemon deustus. Our results predict that future climate change will result in geographically widespread declines in genetic diversity in this species. The extent of reduction will heavily depend on the continuity of population networks and deme sizes. To our knowledge, this is the first study to provide spatially explicit predictions of within-species genetic diversity using climatic, demographic, and genetic data. Our approach accounts for climatic, geographic, and biological complexity. This framework is promising for understanding evolutionary consequences of climate change, and guiding conservation planning. © 2016 Botanical Society of America.

Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

PubMed Central

He, Zhangyi; Beaumont, Mark; Yu, Feng

2017-01-01

We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium. PMID:28500051

The impact of global warming on the range distribution of different climatic groups of Aspidoscelis costata costata.

PubMed

Güizado-Rodríguez, Martha Anahí; Ballesteros-Barrera, Claudia; Casas-Andreu, Gustavo; Barradas-Miranda, Victor Luis; Téllez-Valdés, Oswaldo; Salgado-Ugarte, Isaías Hazarmabeth

2012-12-01

The ectothermic nature of reptiles makes them especially sensitive to global warming. Although climate change and its implications are a frequent topic of detailed studies, most of these studies are carried out without making a distinction between populations. Here we present the first study of an Aspidoscelis species that evaluates the effects of global warming on its distribution using ecological niche modeling. The aims of our study were (1) to understand whether predicted warmer climatic conditions affect the geographic potential distribution of different climatic groups of Aspidoscelis costata costata and (2) to identify potential altitudinal changes of these groups under global warming. We used the maximum entropy species distribution model (MaxEnt) to project the potential distributions expected for the years 2020, 2050, and 2080 under a single simulated climatic scenario. Our analysis suggests that some climatic groups of Aspidoscelis costata costata will exhibit reductions and in others expansions in their distribution, with potential upward shifts toward higher elevation in response to climate warming. Different climatic groups were revealed in our analysis that subsequently showed heterogeneous responses to climatic change illustrating the complex nature of species geographic responses to environmental change and the importance of modeling climatic or geographic groups and/or populations instead of the entire species' range treated as a homogeneous entity.

Topographic, latitudinal and climatic distribution of Pinus coulteri: geographic range limits are not at the edge of the climate envelope

USGS Publications Warehouse

Chardon, Nathalie I.; Cornwell, William K.; Flint, Lorraine E.; Flint, Alan L.; Ackerly, David D.

2015-01-01

With changing climate, many species are projected to move poleward or to higher elevations to track suitable climates. The prediction that species will move poleward assumes that geographically marginal populations are at the edge of the species' climatic range. We studied Pinus coulteri from the center to the northern (poleward) edge of its range, and examined three scenarios regarding the relationship between the geographic and climatic margins of a species' range. We used herbarium and iNaturalist.org records to identify P. coulteri sites, generated a species distribution model based on temperature, precipitation, climatic water deficit, and actual evapotranspiration, and projected suitability under future climate scenarios. In fourteen populations from the central to northern portions of the range, we conducted field studies and recorded elevation, slope and aspect (to estimate solar insolation) to examine relationships between local and regional distributions. We found that northern populations of P. coulteri do not occupy the cold or wet edge of the species' climatic range; mid-latitude, high elevation populations occupy the cold margin. Aspect and insolation of P. coulteri populations changed significantly across latitudes and elevations. Unexpectedly, northern, low-elevation stands occupy north-facing aspects and receive low insolation, while central, high-elevation stands grow on more south-facing aspects that receive higher insolation. Modeled future climate suitability is projected to be highest in the central, high elevation portion of the species range, and in low-lying coastal regions under some scenarios, with declining suitability in northern areas under most future scenarios. For P. coulteri, the lack of high elevation habitat combined with a major dispersal barrier may limit northward movement in response to a warming climate. Our analyses demonstrate the importance of distinguishing geographically vs. climatically marginal populations, and the importance of quantitative analysis of the realized climate space to understand species range limits.

A model study of assisted adiabatic transfer of population in the presence of collisional dephasing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Masuda, Shumpei, E-mail: shumpei.masuda@aalto.fi; Rice, Stuart A., E-mail: s-rice@uchicago.edu

2015-06-28

Previous studies have demonstrated that when experimental conditions generate non-adiabatic dynamics that prevents highly efficient population transfer between states of an isolated system by stimulated Raman adiabatic passage (STIRAP), the addition of an auxiliary counter-diabatic field (CDF) can restore most or all of that efficiency. This paper examines whether that strategy is also successful in a non-isolated system in which the energies of the states fluctuate, e.g., when a solute is subject to collisions with solvent. We study population transfer in two model systems: (i) the three-state system used by Demirplak and Rice [J. Chem. Phys. 116, 8028 (2002)] andmore » (ii) a four-state system, derived from the simulation studies of Demirplak and Rice [J. Chem. Phys. 125, 194517 (2006)], that mimics HCl in liquid Ar. Simulation studies of the vibrational manifold of HCl in dense fluid Ar show that the collision induced vibrational energy level fluctuations have asymmetric distributions. Representations of these asymmetric energy level fluctuation distributions are used in both models (i) and (ii). We identify three sources of degradation of the efficiency of STIRAP generated selective population transfer in model (ii): too small pulse areas of the laser fields, unwanted interference arising from use of strong fields, and the vibrational detuning. For both models (i) and (ii), our examination of the efficiency of STIRAP + CDF population transfer under the influence of the asymmetric distribution of the vibrational energy fluctuations shows that there is a range of field strengths and pulse durations under which STIRAP + CDF control of population transfer has greater efficiency than does STIRAP generated population transfer.« less

Biotic and abiotic influences on abundance and distribution of nonnative Chinook salmon and native ESA-listed steelhead in the Wind River, Washington

USGS Publications Warehouse

Jezorek, Ian G.; Connolly, Patrick J.

2015-01-01

Biotic and abiotic factors influence fish populations and distributions. Concerns have been raised about the influence of hatchery fish on wild populations. Carson National Fish Hatchery produces spring Chinook salmon Oncorhynchus tshawytscha in the Wind River, Washington, and some spawn in the river. Managers were concerned that Chinook salmon could negatively affect wild steelhead O. mykiss and that a self-sustaining population of Chinook salmon may develop. Our objectives were to assess: 1) the distribution and populations of juvenile spring Chinook salmon and juvenile steelhead in the upper Wind River; 2) the influence of stream flow and of each population on the other; and 3) if Chinook salmon populations were self-sustaining. We snorkeled to determine distribution and abundance. Flow in the fall influenced upstream distribution and abundance of juvenile Chinook salmon. Juvenile Chinook salmon densities were consistently low (range 0.0 to 5.7 fish 100 m-2) and not influenced by number of spawners, winter flow magnitude, or steelhead abundance. Juvenile steelhead were distributed through the study section each year. Age-0 and age-1 steelhead densities (age-0 range: 0.04 to 37.0 fish 100 m-2; age-1 range: 0.02 to 6.21 fish 100 m-2) were consistently higher than for juvenile Chinook salmon. Steelhead spawner abundance positively influenced juvenile steelhead abundance. During this study, Chinook salmon in the Wind River appear to have had little effect on steelhead. Low juvenile Chinook salmon abundance and a lack of a spawner-to-juvenile relationship suggest Chinook salmon are not self-sustaining and potential for such a population is low under current conditions.

The Not So Simple Globular Cluster ω Cen. I. Spatial Distribution of the Multiple Stellar Populations

NASA Astrophysics Data System (ADS)

Calamida, A.; Strampelli, G.; Rest, A.; Bono, G.; Ferraro, I.; Saha, A.; Iannicola, G.; Scolnic, D.; James, D.; Smith, C.; Zenteno, A.

2017-04-01

We present a multi-band photometric catalog of ≈1.7 million cluster members for a field of view of ≈2° × 2° across ω Cen. Photometry is based on images collected with the Dark Energy Camera on the 4 m Blanco telescope and the Advanced Camera for Surveys on the Hubble Space Telescope. The unprecedented photometric accuracy and field coverage allowed us, for the first time, to investigate the spatial distribution of ω Cen multiple populations from the core to the tidal radius, confirming its very complex structure. We found that the frequency of blue main-sequence stars is increasing compared to red main-sequence stars starting from a distance of ≈25‧ from the cluster center. Blue main-sequence stars also show a clumpy spatial distribution, with an excess in the northeast quadrant of the cluster pointing toward the direction of the Galactic center. Stars belonging to the reddest and faintest red-giant branch also show a more extended spatial distribution in the outskirts of ω Cen, a region never explored before. Both these stellar sub-populations, according to spectroscopic measurements, are more metal-rich compared to the cluster main stellar population. These findings, once confirmed, make ω Cen the only stellar system currently known where metal-rich stars have a more extended spatial distribution compared to metal-poor stars. Kinematic and chemical abundance measurements are now needed for stars in the external regions of ω Cen to better characterize the properties of these sub-populations. Based on observations made with the Dark Energy Camera (DECam) on the 4 m Blanco telescope (NOAO) under programs 2014A-0327, 2015A-0151, 2016A-0189, PIs: A. Calamida, A. Rest, and on observations made with the NASA/ESA Hubble Space Telescope, obtained by the Space Telescope Science Institute. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

Random versus maximum entropy models of neural population activity

NASA Astrophysics Data System (ADS)

Ferrari, Ulisse; Obuchi, Tomoyuki; Mora, Thierry

2017-04-01

The principle of maximum entropy provides a useful method for inferring statistical mechanics models from observations in correlated systems, and is widely used in a variety of fields where accurate data are available. While the assumptions underlying maximum entropy are intuitive and appealing, its adequacy for describing complex empirical data has been little studied in comparison to alternative approaches. Here, data from the collective spiking activity of retinal neurons is reanalyzed. The accuracy of the maximum entropy distribution constrained by mean firing rates and pairwise correlations is compared to a random ensemble of distributions constrained by the same observables. For most of the tested networks, maximum entropy approximates the true distribution better than the typical or mean distribution from that ensemble. This advantage improves with population size, with groups as small as eight being almost always better described by maximum entropy. Failure of maximum entropy to outperform random models is found to be associated with strong correlations in the population.

Rare events in stochastic populations under bursty reproduction

NASA Astrophysics Data System (ADS)

Be'er, Shay; Assaf, Michael

2016-11-01

Recently, a first step was made by the authors towards a systematic investigation of the effect of reaction-step-size noise—uncertainty in the step size of the reaction—on the dynamics of stochastic populations. This was done by investigating the effect of bursty influx on the switching dynamics of stochastic populations. Here we extend this formalism to account for bursty reproduction processes, and improve the accuracy of the formalism to include subleading-order corrections. Bursty reproduction appears in various contexts, where notable examples include bursty viral production from infected cells, and reproduction of mammals involving varying number of offspring. The main question we quantitatively address is how bursty reproduction affects the overall fate of the population. We consider two complementary scenarios: population extinction and population survival; in the former a population gets extinct after maintaining a long-lived metastable state, whereas in the latter a population proliferates despite undergoing a deterministic drift towards extinction. In both models reproduction occurs in bursts, sampled from an arbitrary distribution. Using the WKB approach, we show in the extinction problem that bursty reproduction broadens the quasi-stationary distribution of population sizes in the metastable state, which results in a drastic reduction of the mean time to extinction compared to the non-bursty case. In the survival problem, it is shown that bursty reproduction drastically increases the survival probability of the population. Close to the bifurcation limit our analytical results simplify considerably and are shown to depend solely on the mean and variance of the burst-size distribution. Our formalism is demonstrated on several realistic distributions which all compare well with numerical Monte-Carlo simulations.

Congruence between distribution modelling and phylogeographical analyses reveals Quaternary survival of a toadflax species (Linaria elegans) in oceanic climate areas of a mountain ring range.

PubMed

Fernández-Mazuecos, Mario; Vargas, Pablo

2013-06-01

· The role of Quaternary climatic shifts in shaping the distribution of Linaria elegans, an Iberian annual plant, was investigated using species distribution modelling and molecular phylogeographical analyses. Three hypotheses are proposed to explain the Quaternary history of its mountain ring range. · The distribution of L. elegans was modelled using the maximum entropy method and projected to the last interglacial and to the last glacial maximum (LGM) using two different paleoclimatic models: the Community Climate System Model (CCSM) and the Model for Interdisciplinary Research on Climate (MIROC). Two nuclear and three plastid DNA regions were sequenced for 24 populations (119 individuals sampled). Bayesian phylogenetic, phylogeographical, dating and coalescent-based population genetic analyses were conducted. · Molecular analyses indicated the existence of northern and southern glacial refugia and supported two routes of post-glacial recolonization. These results were consistent with the LGM distribution as inferred under the CCSM paleoclimatic model (but not under the MIROC model). Isolation between two major refugia was dated back to the Riss or Mindel glaciations, > 100 kyr before present (bp). · The Atlantic distribution of inferred refugia suggests that the oceanic (buffered)-continental (harsh) gradient may have played a key and previously unrecognized role in determining Quaternary distribution shifts of Mediterranean plants. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

PubMed Central

Good, Benjamin H.; Rouzine, Igor M.; Balick, Daniel J.; Hallatschek, Oskar; Desai, Michael M.

2012-01-01

When large asexual populations adapt, competition between simultaneously segregating mutations slows the rate of adaptation and restricts the set of mutations that eventually fix. This phenomenon of interference arises from competition between mutations of different strengths as well as competition between mutations that arise on different fitness backgrounds. Previous work has explored each of these effects in isolation, but the way they combine to influence the dynamics of adaptation remains largely unknown. Here, we describe a theoretical model to treat both aspects of interference in large populations. We calculate the rate of adaptation and the distribution of fixed mutational effects accumulated by the population. We focus particular attention on the case when the effects of beneficial mutations are exponentially distributed, as well as on a more general class of exponential-like distributions. In both cases, we show that the rate of adaptation and the influence of genetic background on the fixation of new mutants is equivalent to an effective model with a single selection coefficient and rescaled mutation rate, and we explicitly calculate these effective parameters. We find that the effective selection coefficient exactly coincides with the most common fixed mutational effect. This equivalence leads to an intuitive picture of the relative importance of different types of interference effects, which can shift dramatically as a function of the population size, mutation rate, and the underlying distribution of fitness effects. PMID:22371564

Impact of climate change on global malaria distribution.

PubMed

Caminade, Cyril; Kovats, Sari; Rocklov, Joacim; Tompkins, Adrian M; Morse, Andrew P; Colón-González, Felipe J; Stenlund, Hans; Martens, Pim; Lloyd, Simon J

2014-03-04

Malaria is an important disease that has a global distribution and significant health burden. The spatial limits of its distribution and seasonal activity are sensitive to climate factors, as well as the local capacity to control the disease. Malaria is also one of the few health outcomes that has been modeled by more than one research group and can therefore facilitate the first model intercomparison for health impacts under a future with climate change. We used bias-corrected temperature and rainfall simulations from the Coupled Model Intercomparison Project Phase 5 climate models to compare the metrics of five statistical and dynamical malaria impact models for three future time periods (2030s, 2050s, and 2080s). We evaluated three malaria outcome metrics at global and regional levels: climate suitability, additional population at risk and additional person-months at risk across the model outputs. The malaria projections were based on five different global climate models, each run under four emission scenarios (Representative Concentration Pathways, RCPs) and a single population projection. We also investigated the modeling uncertainty associated with future projections of populations at risk for malaria owing to climate change. Our findings show an overall global net increase in climate suitability and a net increase in the population at risk, but with large uncertainties. The model outputs indicate a net increase in the annual person-months at risk when comparing from RCP2.6 to RCP8.5 from the 2050s to the 2080s. The malaria outcome metrics were highly sensitive to the choice of malaria impact model, especially over the epidemic fringes of the malaria distribution.

Impact of climate change on global malaria distribution

PubMed Central

Caminade, Cyril; Kovats, Sari; Rocklov, Joacim; Tompkins, Adrian M.; Morse, Andrew P.; Colón-González, Felipe J.; Stenlund, Hans; Martens, Pim; Lloyd, Simon J.

2014-01-01

Malaria is an important disease that has a global distribution and significant health burden. The spatial limits of its distribution and seasonal activity are sensitive to climate factors, as well as the local capacity to control the disease. Malaria is also one of the few health outcomes that has been modeled by more than one research group and can therefore facilitate the first model intercomparison for health impacts under a future with climate change. We used bias-corrected temperature and rainfall simulations from the Coupled Model Intercomparison Project Phase 5 climate models to compare the metrics of five statistical and dynamical malaria impact models for three future time periods (2030s, 2050s, and 2080s). We evaluated three malaria outcome metrics at global and regional levels: climate suitability, additional population at risk and additional person-months at risk across the model outputs. The malaria projections were based on five different global climate models, each run under four emission scenarios (Representative Concentration Pathways, RCPs) and a single population projection. We also investigated the modeling uncertainty associated with future projections of populations at risk for malaria owing to climate change. Our findings show an overall global net increase in climate suitability and a net increase in the population at risk, but with large uncertainties. The model outputs indicate a net increase in the annual person-months at risk when comparing from RCP2.6 to RCP8.5 from the 2050s to the 2080s. The malaria outcome metrics were highly sensitive to the choice of malaria impact model, especially over the epidemic fringes of the malaria distribution. PMID:24596427

Competitive or weak cooperative stochastic Lotka-Volterra systems conditioned on non-extinction.

PubMed

Cattiaux, Patrick; Méléard, Sylvie

2010-06-01

We are interested in the long time behavior of a two-type density-dependent biological population conditioned on non-extinction, in both cases of competition or weak cooperation between the two species. This population is described by a stochastic Lotka-Volterra system, obtained as limit of renormalized interacting birth and death processes. The weak cooperation assumption allows the system not to blow up. We study the existence and uniqueness of a quasi-stationary distribution, that is convergence to equilibrium conditioned on non-extinction. To this aim we generalize in two-dimensions spectral tools developed for one-dimensional generalized Feller diffusion processes. The existence proof of a quasi-stationary distribution is reduced to the one for a d-dimensional Kolmogorov diffusion process under a symmetry assumption. The symmetry we need is satisfied under a local balance condition relying the ecological rates. A novelty is the outlined relation between the uniqueness of the quasi-stationary distribution and the ultracontractivity of the killed semi-group. By a comparison between the killing rates for the populations of each type and the one of the global population, we show that the quasi-stationary distribution can be either supported by individuals of one (the strongest one) type or supported by individuals of the two types. We thus highlight two different long time behaviors depending on the parameters of the model: either the model exhibits an intermediary time scale for which only one type (the dominant trait) is surviving, or there is a positive probability to have coexistence of the two species.

Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.

PubMed

Jueterbock, A; Franssen, S U; Bergmann, N; Gu, J; Coyer, J A; Reusch, T B H; Bornberg-Bauer, E; Olsen, J L

2016-11-01

Populations distributed across a broad thermal cline are instrumental in addressing adaptation to increasing temperatures under global warming. Using a space-for-time substitution design, we tested for parallel adaptation to warm temperatures along two independent thermal clines in Zostera marina, the most widely distributed seagrass in the temperate Northern Hemisphere. A North-South pair of populations was sampled along the European and North American coasts and exposed to a simulated heatwave in a common-garden mesocosm. Transcriptomic responses under control, heat stress and recovery were recorded in 99 RNAseq libraries with ~13 000 uniquely annotated, expressed genes. We corrected for phylogenetic differentiation among populations to discriminate neutral from adaptive differentiation. The two southern populations recovered faster from heat stress and showed parallel transcriptomic differentiation, as compared with northern populations. Among 2389 differentially expressed genes, 21 exceeded neutral expectations and were likely involved in parallel adaptation to warm temperatures. However, the strongest differentiation following phylogenetic correction was between the three Atlantic populations and the Mediterranean population with 128 of 4711 differentially expressed genes exceeding neutral expectations. Although adaptation to warm temperatures is expected to reduce sensitivity to heatwaves, the continued resistance of seagrass to further anthropogenic stresses may be impaired by heat-induced downregulation of genes related to photosynthesis, pathogen defence and stress tolerance. © 2016 John Wiley & Sons Ltd.

Comparison of Exposure Controls, Item Pool Characteristics, and Population Distributions for CAT Using the Partial Credit Model

ERIC Educational Resources Information Center

Lee, HwaYoung; Dodd, Barbara G.

2012-01-01

This study investigated item exposure control procedures under various combinations of item pool characteristics and ability distributions in computerized adaptive testing based on the partial credit model. Three variables were manipulated: item pool characteristics (120 items for each of easy, medium, and hard item pools), two ability…

Appalachia--A Reference Book. Second Edition.

ERIC Educational Resources Information Center

Pickard, Jerome P.; And Others

With a total area of 197,116 square miles, the Appalachian Region has an uneven distribution of population, income, wealth and natural resources. The Region's 19.3 million people live in 397 counties and 5 independent cities in Virginia. Under 50% of the population live in metropolitan counties while only 25% live in rural counties. In 1975 the…

A mistletoe tale: postglacial invasion of Psittacanthus schiedeanus (Loranthaceae) to Mesoamerican cloud forests revealed by molecular data and species distribution modeling.

PubMed

Ornelas, Juan Francisco; Gándara, Etelvina; Vásquez-Aguilar, Antonio Acini; Ramírez-Barahona, Santiago; Ortiz-Rodriguez, Andrés Ernesto; González, Clementina; Mejía Saules, María Teresa; Ruiz-Sanchez, Eduardo

2016-04-12

Ecological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities. Our analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate Bayesian Computation (ABC) analyses strongly supported a scenario of simultaneous divergence among the three groups isolated recently. Our results provide support for the predominant role of isolation and environmental factors in driving genetic differentiation of Mesoamerican parrot-flower mistletoes. The ABC results are consistent with a scenario of post-glacial mistletoe invasion, independent of host identity, and that habitat types recently isolated P. schiedeanus populations, accumulating slight phenotypic differences among genetic groups due to recent migration across habitats. Under this scenario, climatic fluctuations throughout the Pleistocene would have altered the distribution of suitable habitat for mistletoes throughout Mesoamerica leading to variation in population continuity and isolation. Our findings add to an understanding of the role of recent isolation and colonization in shaping cloud forest communities in the region.

Geomasking sensitive health data and privacy protection: an evaluation using an E911 database.

PubMed

Allshouse, William B; Fitch, Molly K; Hampton, Kristen H; Gesink, Dionne C; Doherty, Irene A; Leone, Peter A; Serre, Marc L; Miller, William C

2010-10-01

Geomasking is used to provide privacy protection for individual address information while maintaining spatial resolution for mapping purposes. Donut geomasking and other random perturbation geomasking algorithms rely on the assumption of a homogeneously distributed population to calculate displacement distances, leading to possible under-protection of individuals when this condition is not met. Using household data from 2007, we evaluated the performance of donut geomasking in Orange County, North Carolina. We calculated the estimated k-anonymity for every household based on the assumption of uniform household distribution. We then determined the actual k-anonymity by revealing household locations contained in the county E911 database. Census block groups in mixed-use areas with high population distribution heterogeneity were the most likely to have privacy protection below selected criteria. For heterogeneous populations, we suggest tripling the minimum displacement area in the donut to protect privacy with a less than 1% error rate.

Geomasking sensitive health data and privacy protection: an evaluation using an E911 database

PubMed Central

Allshouse, William B; Fitch, Molly K; Hampton, Kristen H; Gesink, Dionne C; Doherty, Irene A; Leone, Peter A; Serre, Marc L; Miller, William C

2010-01-01

Geomasking is used to provide privacy protection for individual address information while maintaining spatial resolution for mapping purposes. Donut geomasking and other random perturbation geomasking algorithms rely on the assumption of a homogeneously distributed population to calculate displacement distances, leading to possible under-protection of individuals when this condition is not met. Using household data from 2007, we evaluated the performance of donut geomasking in Orange County, North Carolina. We calculated the estimated k-anonymity for every household based on the assumption of uniform household distribution. We then determined the actual k-anonymity by revealing household locations contained in the county E911 database. Census block groups in mixed-use areas with high population distribution heterogeneity were the most likely to have privacy protection below selected criteria. For heterogeneous populations, we suggest tripling the minimum displacement area in the donut to protect privacy with a less than 1% error rate. PMID:20953360

Stationary Size Distributions of Growing Cells with Binary and Multiple Cell Division

NASA Astrophysics Data System (ADS)

Rading, M. M.; Engel, T. A.; Lipowsky, R.; Valleriani, A.

2011-10-01

Populations of unicellular organisms that grow under constant environmental conditions are considered theoretically. The size distribution of these cells is calculated analytically, both for the usual process of binary division, in which one mother cell produces always two daughter cells, and for the more complex process of multiple division, in which one mother cell can produce 2 n daughter cells with n=1,2,3,… . The latter mode of division is inspired by the unicellular algae Chlamydomonas reinhardtii. The uniform response of the whole population to different environmental conditions is encoded in the individual rates of growth and division of the cells. The analytical treatment of the problem is based on size-dependent rules for cell growth and stochastic transition processes for cell division. The comparison between binary and multiple division shows that these different division processes lead to qualitatively different results for the size distribution and the population growth rates.

77 FR 55456 - Marine Mammals; File No. 17410

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-10

... proposed research are to obtain information on population status and distribution, stock structure, age... occur world-wide. No live animal takes are being requested under this permit. The requested duration of...

Predicting extinction risks under climate change: coupling stochastic population models with dynamic bioclimatic habitat models.

PubMed

Keith, David A; Akçakaya, H Resit; Thuiller, Wilfried; Midgley, Guy F; Pearson, Richard G; Phillips, Steven J; Regan, Helen M; Araújo, Miguel B; Rebelo, Tony G

2008-10-23

Species responses to climate change may be influenced by changes in available habitat, as well as population processes, species interactions and interactions between demographic and landscape dynamics. Current methods for assessing these responses fail to provide an integrated view of these influences because they deal with habitat change or population dynamics, but rarely both. In this study, we linked a time series of habitat suitability models with spatially explicit stochastic population models to explore factors that influence the viability of plant species populations under stable and changing climate scenarios in South African fynbos, a global biodiversity hot spot. Results indicate that complex interactions between life history, disturbance regime and distribution pattern mediate species extinction risks under climate change. Our novel mechanistic approach allows more complete and direct appraisal of future biotic responses than do static bioclimatic habitat modelling approaches, and will ultimately support development of more effective conservation strategies to mitigate biodiversity losses due to climate change.

Population dynamical behavior of Lotka-Volterra system under regime switching

NASA Astrophysics Data System (ADS)

Li, Xiaoyue; Jiang, Daqing; Mao, Xuerong

2009-10-01

In this paper, we investigate a Lotka-Volterra system under regime switching where B(t) is a standard Brownian motion. The aim here is to find out what happens under regime switching. We first obtain the sufficient conditions for the existence of global positive solutions, stochastic permanence and extinction. We find out that both stochastic permanence and extinction have close relationships with the stationary probability distribution of the Markov chain. The limit of the average in time of the sample path of the solution is then estimated by two constants related to the stationary distribution and the coefficients. Finally, the main results are illustrated by several examples.

Minimum relative entropy distributions with a large mean are Gaussian

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2016-12-01

Entropy optimization principles are versatile tools with wide-ranging applications from statistical physics to engineering to ecology. Here we consider the following constrained problem: Given a prior probability distribution q , find the posterior distribution p minimizing the relative entropy (also known as the Kullback-Leibler divergence) with respect to q under the constraint that mean (p ) is fixed and large. We show that solutions to this problem are approximately Gaussian. We discuss two applications of this result. In the context of dissipative dynamics, the equilibrium distribution of a Brownian particle confined in a strong external field is independent of the shape of the confining potential. We also derive an H -type theorem for evolutionary dynamics: The entropy of the (standardized) distribution of fitness of a population evolving under natural selection is eventually increasing in time.

Population Dynamics of Genetic Regulatory Networks

NASA Astrophysics Data System (ADS)

Braun, Erez

2005-03-01

Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

Does beekeeping reduce genetic variability in Melipona scutellaris (Apidae, Meliponini)?

PubMed

Carvalho-Zilse, G A; Costa-Pinto, M F F; Nunes-Silva, C G; Kerr, W E

2009-06-30

Many factors have contributed to reductions in wild populations of stingless bees, such as: deforestation, displacement and destruction of nests by honey gatherers, as well as use of insecticides and other agrochemicals. All of these can potentially affect the populational structure of native species. We analyzed genetic variability and populational structure of Melipona scutellaris, based on five microsatellite loci, using heterologous primers of M. bicolor. Samples were taken from 43 meliponaries distributed among 30 sites of four northeastern states of Brazil (Pernambuco, Alagoas, Sergipe, and Bahia). Thirty-one alleles were found to be well distributed among the populations, with sizes ranging from 85 to 146 bp. In general, there was a variable distribution and frequency of alleles among populations, with either exclusive and/or fixed alleles at some sites. The population of Pernambuco was the most polymorphic, followed by Bahia, Alagoas and Sergipe. The heterozygosity was Ho = 0.36 on average, much lower than what has been reported for M. bicolor (Ho = 0.65). Most populations were not under Hardy-Weinberg equilibrium. We found a higher variation within rather than among populations, indicating no genetic structuring in those bees maintained in meliponaries. This apparent homogenization may be due to intense beekeeping activity, including exchange of genetic material among beekeepers. Based on our findings, we recommend more studies of meliponaries and of wild populations in order to help orient management and conservation of these native pollinators.

A Soil Service Index: Potential Soil Services to Society under Scenarios of Human Land Use and Population Growth

NASA Astrophysics Data System (ADS)

Hugelius, G.; Ahlström, A.; Loisel, J.; Harden, J. W.

2017-12-01

Soils provide numerous and indispensable services to ecological systems and human societies. As human populations and human land use changes, the capacity of soils to maintain these services may also change. To investigate this we provide the first global scale study based on the soil service index (SSI; see presentations by Harden et al. and Loisel et al. in this session for more details). In this index multiple soil services are numerically or quantitatively assessed, normalized to a unit-less scale for purposes of intercomparability. Soil services assessed under the SSI include organic matter and/or organic carbon storage; plant productivity; CO2 or GHG exchange with the atmosphere; water storage capacity; and nutrient storage and/or availability. The SSI may be applied at any scale. Here we present a first global application of the SSI and provide broad-scale analyses of soil service spatial distributions. We assess how the SSI will change under projected changes in human societies populations and human land use (following representative concentration pathway scenarios). Present and future potential utilization and vulnerability of soil resources are analyzed in the context of human population distributions and its projected changes. The SSI is designed to be broadly useful across scientific, governance and resource management organizations. To exemplify this, the parameterization of this is global soil service estimate is based on only open source input data.

The Evolution of Galaxies Through the Spatial Distribution of Their Globular Clusters: the Brightest Galaxies in Fornax

NASA Astrophysics Data System (ADS)

Zegeye, David W.

2018-01-01

We present a study of the evolution of the 10 brightest galaxies in the Fornax Cluster, as reconstructed through their Globular Cluster (GC) populations. GCs can be characterized by their projected two-dimensional (2D) spatial distribution. Over- or under-densities in the GC distribution, can be linked to events in the host galaxy assembly history, and used to constrain the properties of their progenitors. With HST/ACS imaging, we identified significant structures in the GC distribution of the 10 galaxies investigated, with some of the galaxies possessing structures with >10-sigma significance. GC over-densities have been found within the galaxies, with significant differences between the red and blue GC population. For elongated galaxies, structures are preferentially to be aligned along the major axis. Fornax Cluster galaxies appear to be more dynamically relaxed than the Virgo Cluster galaxies previously investigated with the same methodology by D'Abrusco et al. (2016). However, from these observations, the evident imprints left in the spatial distribution of GCs in these galaxies suggest a similarly intense history of interactions.The SAO REU program is funded by the National Science Foundation REU and Department of Defense ASSURE programs under NSF Grant AST-1659473, and by the Smithsonian Institution.

Poster - Thur Eve - 55: Monte Carlo simulations of variations in planned dose distributions in a prostate patient population.

PubMed

Balderson, M J; Brown, D W; Quirk, S; Ghasroddashti, E; Kirkby, C

2012-07-01

Clinical outcome studies with clear and objective endpoints are necessary to make informed radiotherapy treatment decisions. Commonly, clinical outcomes are established after lengthy and costly clinical trials are performed and the data are analyzed and published. One the challenges with obtaining meaningful data from clinical trials is that by the time the information gets to the medical profession the results may be less clinically relevant than when the trial began, An alternative approach is to estimate clinical outcomes through patient population modeling. We are developing a mathematical tool that uses Monte Carlo techniques to simulate variations in planned and delivered dose distributions of prostate patients receiving radiotherapy. Ultimately, our simulation will calculate a distribution of Tumor Control Probabilities (TCPs) for a population of patients treated under a given protocol. Such distributions can serve as a metric for comparing different treatment modalities, planning and setup approaches, and machine parameter settings or tolerances with respect to outcomes on broad patient populations. It may also help researchers understand differences one might expect to find before actually doing the clinical trial. As a first step and for the focus of this abstract we wanted to see if we could answer the question: "Can a population of dose distributions of prostate patients be accurately modeled by a set of randomly generated Gaussian functions?" Our results have demonstrated that using a set of randomly generated Gaussian functions can simulate a distribution of prostate patients. © 2012 American Association of Physicists in Medicine.

Geographic Information System Software to Remodel Population Data Using Dasymetric Mapping Methods

USGS Publications Warehouse

Sleeter, Rachel; Gould, Michael

2007-01-01

The U.S. Census Bureau provides decadal demographic data collected at the household level and aggregated to larger enumeration units for anonymity purposes. Although this system is appropriate for the dissemination of large amounts of national demographic data, often the boundaries of the enumeration units do not reflect the distribution of the underlying statistical phenomena. Conventional mapping methods such as choropleth mapping, are primarily employed due to their ease of use. However, the analytical drawbacks of choropleth methods are well known ranging from (1) the artificial transition of population at the boundaries of mapping units to (2) the assumption that the phenomena is evenly distributed across the enumeration unit (when in actuality there can be significant variation). Many methods to map population distribution have been practiced in geographic information systems (GIS) and remote sensing fields. Many cartographers prefer dasymetric mapping to map population because of its ability to more accurately distribute data over geographic space. Similar to ?choropleth maps?, a dasymetric map utilizes standardized data (for example, census data). However, rather than using arbitrary enumeration zones to symbolize population distribution, a dasymetric approach introduces ancillary information to redistribute the standardized data into zones relative to land use and land cover (LULC), taking into consideration actual changing densities within the boundaries of the enumeration unit. Thus, new zones are created that correlate to the function of the map, capturing spatial variations in population density. The transfer of data from census enumeration units to ancillary-driven homogenous zones is performed by a process called areal interpolation.

Cryptic sexual populations account for genetic diversity and ecological success in a widely distributed, asexual fungus-growing ant.

PubMed

Rabeling, Christian; Gonzales, Omar; Schultz, Ted R; Bacci, Maurício; Garcia, Marcos V B; Verhaagh, Manfred; Ishak, Heather D; Mueller, Ulrich G

2011-07-26

Sex and recombination are central processes in life generating genetic diversity. Organisms that rely on asexual propagation risk extinction due to the loss of genetic diversity and the inability to adapt to changing environmental conditions. The fungus-growing ant species Mycocepurus smithii was thought to be obligately asexual because only parthenogenetic populations have been collected from widely separated geographic localities. Nonetheless, M. smithii is ecologically successful, with the most extensive distribution and the highest population densities of any fungus-growing ant. Here we report that M. smithii actually consists of a mosaic of asexual and sexual populations that are nonrandomly distributed geographically. The sexual populations cluster along the Rio Amazonas and the Rio Negro and appear to be the source of independently evolved and widely distributed asexual lineages, or clones. Either apomixis or automixis with central fusion and low recombination rates is inferred to be the cytogenetic mechanism underlying parthenogenesis in M. smithii. Males appear to be entirely absent from asexual populations, but their existence in sexual populations is indicated by the presence of sperm in the reproductive tracts of queens. A phylogenetic analysis of the genus suggests that M. smithii is monophyletic, rendering a hybrid origin of asexuality unlikely. Instead, a mitochondrial phylogeny of sexual and asexual populations suggests multiple independent origins of asexual reproduction, and a divergence-dating analysis indicates that M. smithii evolved 0.5-1.65 million years ago. Understanding the evolutionary origin and maintenance of asexual reproduction in this species contributes to a general understanding of the adaptive significance of sex.

A general modeling framework for describing spatially structured population dynamics

USGS Publications Warehouse

Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

2017-01-01

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles

Making sense of snapshot data: ergodic principle for clonal cell populations

PubMed Central

2017-01-01

Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. PMID:29187636

Making sense of snapshot data: ergodic principle for clonal cell populations.

PubMed

Thomas, Philipp

2017-11-01

Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. © 2017 The Author(s).

Geographical distribution of Musa gracilis Holttum in Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Norfazlina, B.; Wickneswari, R.; Choong, C. Y.

2016-11-01

Musa gracilis (Musaceae) is placed under section Callimusa and was considered endemic to Peninsular Malaysia. The objective of this study was to evaluate the current occurrence of Musa gracilis in Peninsular Malaysia. The coordinates of each population was recorded using the Global Positioning System (GPS) and mapped to show the geographical distribution of Musa gracilis. This study revealed that Musa gracilis exhibits specific pattern of distribution, which exists only in a lowland areas on the eastern and southern part of Peninsular Malaysia.

Distribution of lod scores in oligogenic linkage analysis.

PubMed

Williams, J T; North, K E; Martin, L J; Comuzzie, A G; Göring, H H; Blangero, J

2001-01-01

In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

Reliability and validity analysis of modified Nursing Stress Scale for Indian population.

PubMed

Pathak, Vasundhara; Chakraborty, Tania; Mukhopadhyay, Suman

2013-01-01

The original Nursing Stress Scale (NSS) was structurally modified according to results of factorial analysis and a new scale was named as modified nursing stress scale (MNSS). This is the first study to modify and validate NSS for Indian nursing population. Factorial analysis showed different factor loading for two subscales and items were shifted according to their loading to provide a more meaningful structure. After relocation of Items 13, 14, and 15 into first factor, this factor was renamed as "emotional and painful conditions of patients" to provide a more appropriate name to the first factor. Items 24, 25, 26, 27, 28, and 29 were found to be distributed under two different factors; one of these two was renamed as "unpredictable changes" and another retained its original name (i.e., workload). This distribution was also supported by rational analysis. All other items were distributed under factors as in the original scale. Rest of the validity assessment was done with the modified scale. Thus, with minor changes in structure, the scale was found to have better content validity.

Investigation of runaway electron dissipation in DIII-D using a gamma ray imager

NASA Astrophysics Data System (ADS)

Lvovskiy, A.; Paz-Soldan, C.; Eidietis, N.; Pace, D.; Taussig, D.

2017-10-01

We report the findings of a novel gamma ray imager (GRI) to study runaway electron (RE) dissipation in the quiescent regime on the DIII-D tokamak. The GRI measures the bremsstrahlung emission by RE providing information on RE energy spectrum and distribution across a poloidal cross-section. It consists of a lead pinhole camera illuminating a matrix of BGO detectors placed in the DIII-D mid-plane. The number of detectors was recently doubled to provide better spatial resolution and additional detector shielding was implemented to reduce un-collimated gamma flux and increase single-to-noise ratio. Under varying loop voltage, toroidal magnetic field and plasma density, a non-monotonic RE distribution function has been revealed as a result of the interplay between electric field, synchrotron radiation and collisional damping. A fraction of the high-energy RE population grows forming a bump at the RE distribution function while synchrotron radiation decreases. A possible destabilizing effect of Parail-Pogutse instability on the RE population will be also discussed. Work supported by the US DOE under DE-FC02-04ER54698.

Tracking the evolutionary history of Cortinarius species in section Calochroi, with transoceanic disjunct distributions.

PubMed

Garnica, Sigisfredo; Spahn, Philipp; Oertel, Bernhard; Ammirati, Joseph; Oberwinkler, Franz

2011-07-19

Cortinarius species in section Calochroi display local, clinal and circumboreal patterns of distribution across the Northern Hemisphere where these ectomycorrhizal fungi occur with host trees throughout their geographical range within a continent, or have disjunct intercontinental distributions, the origins of which are not understood. We inferred evolutionary histories of four species, 1) C. arcuatorum, 2) C. aureofulvus, 3) C. elegantior and 4) C. napus, from populations distributed throughout the Old World, and portions of the New World (Central- and North America) based on genetic variation of 154 haplotype internal transcribed spacer (ITS) sequences from 83 population samples. By describing the population structure of these species across their geographical distribution, we attempt to identify their historical migration and patterns of diversification. Models of population structure from nested clade, demographic and coalescent-based analyses revealed genetically differentiated and geographically structured haplotypes in C. arcuatorum and C. elegantior, while C. aureofulvus showed considerably less population structure and C. napus lacked sufficient genetic differentiation to resolve any population structure. Disjunct populations within C. arcuatorum, C. aureofulvus and C. elegantior show little or no morphological differentiation, whereas in C. napus there is a high level of homoplasy and phenotypic plasticity for veil and lamellae colour. The ITS sequences of the type specimens of C. albobrunnoides and C. albobrunnoides var. violaceovelatus were identical to one another and are treated as one species with a wider range of geographic distribution under C. napus. Our results indicate that each of the Calochroi species has undergone a relatively independent evolutionary history, hypothesised as follows: 1) a widely distributed ancestral population of C. arcuatorum diverged into distinctive sympatric populations in the New World; 2) two divergent lineages in C. elegantior gave rise to the New World and Old World haplotypes, respectively; and 3) the low levels of genetic divergence within C. aureofulvus and C. napus may be the result of more recent demographic population expansions. The scenario of migration via the Bering Land Bridge provides the most probable explanation for contemporaneous disjunct geographic distributions of these species, but it does not offer an explanation for the low degree of genetic divergence between populations of C. aureofulvus and C. napus. Our findings are mostly consistent with the designation of New World allopatric populations as separate species from the European counterpart species C. arcuatorum and C. elegantior. We propose the synonymy of C. albobrunnoides, C. albobrunnoides var. violaceovelatus and C. subpurpureophyllus var. sulphureovelatus with C. napus. The results also reinforce previous observations that linked C. arcuatorum and C. aureofulvus displaying distributions in parts of North America and Europe. Interpretations of the population structure of these fungi suggest that host tree history has heavily influenced their modern distributions; however, the complex issues related to co-migration of these fungi with their tree hosts remain unclear at this time.

Birds of a feather

USGS Publications Warehouse

Knick, Steven T.; Gondhaleker, Carmen

2014-01-01

Greater sage-grouse (Centrocercus urophasiunus, hereafter sage-grouse) are broadly distributed, occupy a diversity of sagebrush habitats, and face multiple threats. As a result of these threats, sage-grouse populations are declining and are now absent from almost one-half of their estimated range prior to Euro-American settlement. The risks to sage-grouse are significant enough to merit candidate status for this species for listing under the U.S. Endangered Species Act (Federal Register Notice, March 5, 2010). According to this decision by the U.S. Fish and Wildlife Service in 2010, population and habitat fragmentation coupled with lack of regulatory mechanisms warranted listing, although implementation of actions has been precluded by other priorities. Candidate status for listing under the Endangered Species Act and possible regulatory action in the near future provide strong motivation to better understand the dynamics of sage-grouse populations and their habitat requirements. The general approach currently taken by managers focuses on maintaining or enhancing sage-grouse populations across their distribution in regions containing the highest densities of breeding birds and their important seasonal habitats, also known as priority areas for conservation (PACs). The rationale behind this approach is that it permits limited resources to be applied in regions that have the greatest potential to benefit the largest proportion of sage-grouse. Development and other forms of land use can then proceed under standard regulations in areas outside PACs. Implementation of this approach requires detailed information about habitat, connections among sage-grouse populations, and approaches to restore and maintain sagebrush. These are important topics of study by the U.S. Geological Survey (USGS) and its research partners.

Extended Shared Socioeconomic Pathways for Coastal Impact Assessment: Spatial Coastal Population Scenarios

NASA Astrophysics Data System (ADS)

Merkens, Jan-Ludolf; Reimann, Lena; Hinkel, Jochen; Vafeidis, Athanasios T.

2016-04-01

This work extends the Shared Socioeconomic Pathways (SSPs) by developing spatial projections of global coastal population distribution for the five basic SSPs. Based on a series of coastal migration drivers, which were identified from existing literature, we develop coastal narratives for the five basic SSPs (SSP1-5). These narratives account for differences in coastal versus inland population development in urban and rural areas. To spatially distribute population we use the International Institute for Applied Systems Analysis (IIASA) national population and urbanisation projections and employ country-specific growth rates which differ for coastal and inland as well as for urban and rural regions. These rates are derived from spatial analysis of historical population data. We then adjust these rates for each SSP based on the coastal narratives. The resulting global population grids depict the projected distribution of coastal population for each SSP, until the end of the 21st century, at a spatial resolution of 30 arc seconds. These grids exhibit a three- to four-fold increase in coastal population compared to the basic SSPs. Across all SSPs, except for SSP3, coastal population peaks by the middle of the 21st century and declines afterwards. In SSP3 the coastal population grows continuously until 2100. Compared to the base year 2000 the coastal population increases considerably in all SSPs. The extended SSPs are intended to be utilised in Impact, Adaptation and Vulnerability (IAV) assessments as they allow for improved analysis of exposure to sea-level rise and coastal flooding under different physical and socioeconomic scenarios.

A Third Moment Adjusted Test Statistic for Small Sample Factor Analysis.

PubMed

Lin, Johnny; Bentler, Peter M

2012-01-01

Goodness of fit testing in factor analysis is based on the assumption that the test statistic is asymptotically chi-square; but this property may not hold in small samples even when the factors and errors are normally distributed in the population. Robust methods such as Browne's asymptotically distribution-free method and Satorra Bentler's mean scaling statistic were developed under the presumption of non-normality in the factors and errors. This paper finds new application to the case where factors and errors are normally distributed in the population but the skewness of the obtained test statistic is still high due to sampling error in the observed indicators. An extension of Satorra Bentler's statistic is proposed that not only scales the mean but also adjusts the degrees of freedom based on the skewness of the obtained test statistic in order to improve its robustness under small samples. A simple simulation study shows that this third moment adjusted statistic asymptotically performs on par with previously proposed methods, and at a very small sample size offers superior Type I error rates under a properly specified model. Data from Mardia, Kent and Bibby's study of students tested for their ability in five content areas that were either open or closed book were used to illustrate the real-world performance of this statistic.

Integrating physiology, population dynamics and climate to make multi-scale predictions for the spread of an invasive insect: the Argentine ant at Haleakala National Park, Hawaii

USGS Publications Warehouse

Hartley, Stephen; Krushelnycky, Paul D.; Lester, Philip J.

2010-01-01

Mechanistic models for predicting species’ distribution patterns present particular advantages and challenges relative to models developed from statistical correlations between distribution and climate. They can be especially useful for predicting the range of invasive species whose distribution has not yet reached equilibrium. Here, we illustrate how a physiological model of development for the invasive Argentine ant can be connected to differences in micro-site suitability, population dynamics and climatic gradients; processes operating at quite different spatial scales. Our study is located in the subalpine shrubland of Haleakala National Park, Hawaii, where the spread of Argentine ants Linepithema humile has been documented for the past twenty-five years. We report four main results. First, at a microsite level, the accumulation of degree-days recorded in potential ant nest sites under bare ground or rocks was significantly greater than under a groundcover of grassy vegetation. Second, annual degree-days measured where population boundaries have not expanded (456-521 degree-days), were just above the developmental requirements identified from earlier laboratory studies (445 degree-days above 15.98C). Third, rates of population expansion showed a strong linear relationship with annual degree-days. Finally, an empirical relationship between soil degree-days and climate variables mapped at a broader scale predicts the potential for future range expansion of Argentine ants at Haleakala, particularly to the west of the lower colony and the east of the upper colony. Variation in the availability of suitable microsites, driven by changes in vegetation cover and ultimately climate, provide a hierarchical understanding of the distribution of Argentine ants close to their cold-wet limit of climatic tolerances. We conclude that the integration of physiology, population dynamics and climate mapping holds much promise for making more robust predictions about the potential spread of invasive species.

The Ethnic Composition of Rural Youth in the United States: General Characteristics and Regional Comparisons. Information Report No. 73-3.

ERIC Educational Resources Information Center

Jimenez, Luis A.

Population characteristics of rural youth (persons under 25 years of age) living in the rural areas of the four national regions of North Central, Northeast, West, and South are presented. Emphasis is placed on describing the racial and ethnic variations shown by the target population; focus is on the regional distribution of ethnic minority…

77 FR 28902 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-16

... the census surveys is to evaluate the status of the Ross Sea population because a) annual chick counts at Coulman Island, the largest emperor colony in the world, have declined by 50% in 2010 and 2011, b... raise questions as to a possible decline in the Ross Sea population and/or a shift in the distribution...

"Stop, You're Killing us!" An Alternative Take on Populism and Public Health Comment on "The Rise of Post-truth Populism in Pluralist Liberal Democracies: Challenges for Health Policy".

PubMed

Schrecker, Ted

2017-04-26

Ewen Speed and Russell Mannion correctly identify several contours of the challenges for health policy in what it is useful to think of as a post-democratic era. I argue that the problem for public health is not populism per se, but rather the distinctive populism of the right coupled with the failure of the left to develop compelling counternarratives. Further, defences of 'science' must be tempered by recognition of the unavoidably political dimensions of the (mis)use of scientific findings in public policy. © 2017 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The population ecology of despotism. Concessions and migration between central and peripheral habitats.

PubMed

Bell, Adrian Viliami; Winterhalder, Bruce

2014-03-01

Since despotism is a common evolutionary development in human history, we seek to understand the conditions under which it can originate, persist, and affect population trajectories. We describe a general system of population ecology equations representing the Ideal Free and Despotic Distributions for one and two habitats, one of which contains a despotic class that controls the distribution of resources. Using analytical and numerical solutions we derive the optimal concession strategy by despots with and without subordinate migration to an alternative habitat. We show that low concessions exponentially increase the time it takes for the despotic habitat to fill, and we discuss the trade-offs despots and subordinates confront at various levels of exploitation. Contrary to previous hypotheses, higher levels of despotism do not necessarily cause faster migration to alternative habitats. We further show how, during colonization, divergent population trajectories may arise if despotic systems experience Allee-type economies of scale.

Robustness of S1 statistic with Hodges-Lehmann for skewed distributions

NASA Astrophysics Data System (ADS)

Ahad, Nor Aishah; Yahaya, Sharipah Soaad Syed; Yin, Lee Ping

2016-10-01

Analysis of variance (ANOVA) is a common use parametric method to test the differences in means for more than two groups when the populations are normally distributed. ANOVA is highly inefficient under the influence of non- normal and heteroscedastic settings. When the assumptions are violated, researchers are looking for alternative such as Kruskal-Wallis under nonparametric or robust method. This study focused on flexible method, S1 statistic for comparing groups using median as the location estimator. S1 statistic was modified by substituting the median with Hodges-Lehmann and the default scale estimator with the variance of Hodges-Lehmann and MADn to produce two different test statistics for comparing groups. Bootstrap method was used for testing the hypotheses since the sampling distributions of these modified S1 statistics are unknown. The performance of the proposed statistic in terms of Type I error was measured and compared against the original S1 statistic, ANOVA and Kruskal-Wallis. The propose procedures show improvement compared to the original statistic especially under extremely skewed distribution.

Environmental factors affecting survival of immature Ixodes scapularis and implications for geographical distribution of lyme disease: The climate/behavior hypothesis

USGS Publications Warehouse

Ginsberg, Howard; Albert, Marisa; Acevedo, Lixis; Dyer, Megan C.; Arsnoe, Isis M.; Tsao, Jean I.; Mather, Thomas N.; LeBrun, Roger A.

2017-01-01

Recent reports suggest that host-seeking nymphs in southern populations of Ixodes scapularis remain below the leaf litter surface, while northern nymphs seek hosts on leaves and twigs above the litter surface. This behavioral difference potentially results in decreased tick contact with humans in the south, and fewer cases of Lyme disease. We studied whether north-south differences in tick survival patterns might contribute to this phenomenon. Four month old larvae resulting from a cross between Wisconsin males and South Carolina females died faster under southern than under northern conditions in the lab, as has previously been reported for ticks from both northern and southern populations. However, newly-emerged larvae from Rhode Island parents did not differ consistently in mortality under northern and southern conditions, possibly because of their younger age. Survival is lower, and so the north-south survival difference might be greater in older ticks. Larval survival was positively related to larval size (as measured by scutal area), while survival was positively related to larval fat content in some, but not all, trials. The difference in larval survival under northern vs. southern conditions might simply result from faster metabolism under warmer southern conditions leading to shorter life spans. However, ticks consistently died faster under southern than under northern conditions in the laboratory when relative humidity was low (75%), but not under moderate (85%) or high (95%) RH. Therefore, mortality due to desiccation stress is greater under southern than under northern conditions. We hypothesize that mortality resulting from the greater desiccation stress under southern conditions acts as a selective pressure resulting in the evolution of host-seeking behavior in which immatures remain below the leaf litter surface in southern I. scapularis populations, so as to avoid the desiccating conditions at the surface. If this hypothesis is correct, it has implications for the effect of climate change on the future distribution of Lyme disease.

Estimating the ratios of the stationary distribution values for Markov chains modeling evolutionary algorithms.

PubMed

Mitavskiy, Boris; Cannings, Chris

2009-01-01

The evolutionary algorithm stochastic process is well-known to be Markovian. These have been under investigation in much of the theoretical evolutionary computing research. When the mutation rate is positive, the Markov chain modeling of an evolutionary algorithm is irreducible and, therefore, has a unique stationary distribution. Rather little is known about the stationary distribution. In fact, the only quantitative facts established so far tell us that the stationary distributions of Markov chains modeling evolutionary algorithms concentrate on uniform populations (i.e., those populations consisting of a repeated copy of the same individual). At the same time, knowing the stationary distribution may provide some information about the expected time it takes for the algorithm to reach a certain solution, assessment of the biases due to recombination and selection, and is of importance in population genetics to assess what is called a "genetic load" (see the introduction for more details). In the recent joint works of the first author, some bounds have been established on the rates at which the stationary distribution concentrates on the uniform populations. The primary tool used in these papers is the "quotient construction" method. It turns out that the quotient construction method can be exploited to derive much more informative bounds on ratios of the stationary distribution values of various subsets of the state space. In fact, some of the bounds obtained in the current work are expressed in terms of the parameters involved in all the three main stages of an evolutionary algorithm: namely, selection, recombination, and mutation.

Ecological and evolutionary dynamics of interconnectedness and modularity

PubMed Central

Nordbotten, Jan M.; Levin, Simon A.; Szathmáry, Eörs; Stenseth, Nils C.

2018-01-01

In this contribution, we develop a theoretical framework for linking microprocesses (i.e., population dynamics and evolution through natural selection) with macrophenomena (such as interconnectedness and modularity within an ecological system). This is achieved by developing a measure of interconnectedness for population distributions defined on a trait space (generalizing the notion of modularity on graphs), in combination with an evolution equation for the population distribution. With this contribution, we provide a platform for understanding under what environmental, ecological, and evolutionary conditions ecosystems evolve toward being more or less modular. A major contribution of this work is that we are able to decompose the overall driver of changes at the macro level (such as interconnectedness) into three components: (i) ecologically driven change, (ii) evolutionarily driven change, and (iii) environmentally driven change. PMID:29311333

Distributions of microbial activities in deep subseafloor sediments

NASA Technical Reports Server (NTRS)

D'Hondt, Steven; Jorgensen, Bo Barker; Miller, D. Jay; Batzke, Anja; Blake, Ruth; Cragg, Barry A.; Cypionka, Heribert; Dickens, Gerald R.; Ferdelman, Timothy; Hinrichs, Kai-Uwe;

Structured Modeling and Analysis of Stochastic Epidemics with Immigration and Demographic Effects

PubMed Central

Baumann, Hendrik; Sandmann, Werner

2016-01-01

Stochastic epidemics with open populations of variable population sizes are considered where due to immigration and demographic effects the epidemic does not eventually die out forever. The underlying stochastic processes are ergodic multi-dimensional continuous-time Markov chains that possess unique equilibrium probability distributions. Modeling these epidemics as level-dependent quasi-birth-and-death processes enables efficient computations of the equilibrium distributions by matrix-analytic methods. Numerical examples for specific parameter sets are provided, which demonstrates that this approach is particularly well-suited for studying the impact of varying rates for immigration, births, deaths, infection, recovery from infection, and loss of immunity. PMID:27010993

Structured Modeling and Analysis of Stochastic Epidemics with Immigration and Demographic Effects.

PubMed

Baumann, Hendrik; Sandmann, Werner

2016-01-01

Stochastic epidemics with open populations of variable population sizes are considered where due to immigration and demographic effects the epidemic does not eventually die out forever. The underlying stochastic processes are ergodic multi-dimensional continuous-time Markov chains that possess unique equilibrium probability distributions. Modeling these epidemics as level-dependent quasi-birth-and-death processes enables efficient computations of the equilibrium distributions by matrix-analytic methods. Numerical examples for specific parameter sets are provided, which demonstrates that this approach is particularly well-suited for studying the impact of varying rates for immigration, births, deaths, infection, recovery from infection, and loss of immunity.

Exploiting the Adaptation Dynamics to Predict the Distribution of Beneficial Fitness Effects

PubMed Central

2016-01-01

Adaptation of asexual populations is driven by beneficial mutations and therefore the dynamics of this process, besides other factors, depends on the distribution of beneficial fitness effects. It is known that on uncorrelated fitness landscapes, this distribution can only be of three types: truncated, exponential and power law. We performed extensive stochastic simulations to study the adaptation dynamics on rugged fitness landscapes, and identified two quantities that can be used to distinguish the underlying distribution of beneficial fitness effects. The first quantity studied here is the fitness difference between successive mutations that spread in the population, which is found to decrease in the case of truncated distributions, remains nearly a constant for exponentially decaying distributions and increases when the fitness distribution decays as a power law. The second quantity of interest, namely, the rate of change of fitness with time also shows quantitatively different behaviour for different beneficial fitness distributions. The patterns displayed by the two aforementioned quantities are found to hold good for both low and high mutation rates. We discuss how these patterns can be exploited to determine the distribution of beneficial fitness effects in microbial experiments. PMID:26990188

The timing of life history events in the presence of soft disturbances.

PubMed

Bertacchi, Daniela; Zucca, Fabio; Ambrosini, Roberto

2016-01-21

We study a model for the evolutionarily stable strategy (ESS) used by biological populations for choosing the time of life-history events, such as arrival from migration and breeding. In our model we account for both intra-species competition (early individuals have a competitive advantage) and a disturbance which strikes at a random time, killing a fraction 1-p of the population. Disturbances include spells of bad weather, such as freezing or heavily raining days. It has been shown by Iwasa and Levin (1995) that when the disturbance is so strong that it kills any individual present when it strikes (hard disturbance, p=0), then the ESS is a mixed strategy (individuals choose their arrival date in an interval of possible dates, according to a certain probability distribution). In this case, individuals wait for a certain time and afterwards start arriving (or breeding) every day. In this paper we explore a biologically more realistic situation whereby the disturbance kills only a fraction of the individuals (soft disturbance, p>0). We also remove some technical assumptions which Iwasa and Levin made on the distribution of the disturbance. We prove that the ESS is still a mixed choice of times, however with respect to the case of hard disturbance, a new phenomenon arises: whenever the disturbance is soft, if the competition is sufficiently strong, the waiting time disappears and a fraction of the population arrives at the earliest day possible, while the rest will arrive throughout the whole period during which the disturbance may occur. This means that under strong competition, the payoff of early arrival balances the increased risk of being killed by the disturbance. We study the behaviour of the ESS and of the average fitness of the population, depending on the parameters involved. We also investigate how the population may be affected by climate change: namely the occurrence of more extreme weather events, which may kill a larger fraction of the population, and time shifts of the distribution of the disturbance. We show how the ESS and the average fitness change under the new climate and discuss which is the impact of the new climate on a population that still follows the old strategy. In particular, we show that, at least under some conditions, extreme weather events imply a temporary decrease of the average fitness of the population due to an increased mortality. In addition, if the population adapts to the new climate, the population may have a larger fitness. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Leverage Effect on Wealth Distribution in a Controllable Laboratory Stock Market

PubMed Central

Zhu, Chenge; Yang, Guang; An, Kenan; Huang, Jiping

2014-01-01

Wealth distribution has always been an important issue in our economic and social life, since it affects the harmony and stabilization of the society. Under the background of widely used financial tools to raise leverage these years, we studied the leverage effect on wealth distribution of a population in a controllable laboratory market in which we have conducted several human experiments, and drawn the conclusion that higher leverage leads to a higher Gini coefficient in the market. A higher Gini coefficient means the wealth distribution among a population becomes more unequal. This is a result of the ascending risk with growing leverage level in the market plus the diversified trading abilities and risk preference of the participants. This work sheds light on the effects of leverage and its related regulations, especially its impact on wealth distribution. It also shows the capability of the method of controllable laboratory markets which could be helpful in several fields of study such as economics, econophysics and sociology. PMID:24968222

The leverage effect on wealth distribution in a controllable laboratory stock market.

PubMed

Zhu, Chenge; Yang, Guang; An, Kenan; Huang, Jiping

2014-01-01

Wealth distribution has always been an important issue in our economic and social life, since it affects the harmony and stabilization of the society. Under the background of widely used financial tools to raise leverage these years, we studied the leverage effect on wealth distribution of a population in a controllable laboratory market in which we have conducted several human experiments, and drawn the conclusion that higher leverage leads to a higher Gini coefficient in the market. A higher Gini coefficient means the wealth distribution among a population becomes more unequal. This is a result of the ascending risk with growing leverage level in the market plus the diversified trading abilities and risk preference of the participants. This work sheds light on the effects of leverage and its related regulations, especially its impact on wealth distribution. It also shows the capability of the method of controllable laboratory markets which could be helpful in several fields of study such as economics, econophysics and sociology.

This Is My (Post) Truth, Tell Me Yours Comment on "The Rise of Post-truth Populism in Pluralist Liberal Democracies: Challenges for Health Policy".

PubMed

Powell, Martin

2017-05-15

This is a commentary on the article 'The rise of post-truth populism in pluralist liberal democracies: challenges for health policy.' It critically examines two of its key concepts: populism and 'post truth.' This commentary argues that there are different types of populism, with unclear links to impacts, and that in some ways, 'post-truth' has resonances with arguments advanced in the period at the beginning of the British National Health Service (NHS). In short, 'post-truth' populism' may be 'déjà vu all over again,' and there are multiple (post) truths: this is my (post) truth, tell me yours. © 2017 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Spatial modeling of the geographic distribution of wildlife populations: A case study in the lower Mississippi River region

USGS Publications Warehouse

Ji, W.; Jeske, C.

2000-01-01

A geographic information system (GIS)-based spatial modeling approach was developed to study environmental and land use impacts on the geographic distribution of wintering northern pintails (Arias acuta) in the Lower Mississippi River region. Pintails were fitted with backpack radio transmitter packages at Catahoula Lake, LA, in October 1992-1994 and located weekly through the following March. Pintail survey data were converted into a digital database in ARC/INFO GIS format and integrated with environmental GIS data through a customized modeling interface. The study verified the relationship between pintail distributions and major environmental factors and developed a conceptual relation model. Visualization-based spatial simulations were used to display the movement patterns of specific population groups under spatial and temporal constraints. The spatial modeling helped understand the seasonal movement patterns of pintails in relation to their habitat usage in Arkansas and southwestern Louisiana for wintering and interchange situations among population groups wintering in Texas and southeastern Louisiana. (C) 2000 Elsevier Science B.V.

Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Island Model.

PubMed

Chao, Anne; Jost, Lou; Hsieh, T C; Ma, K H; Sherwin, William B; Rollins, Lee Ann

2015-01-01

Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Mathematical Modeling of Extinction of Inhomogeneous Populations

PubMed Central

Karev, G.P.; Kareva, I.

2016-01-01

Mathematical models of population extinction have a variety of applications in such areas as ecology, paleontology and conservation biology. Here we propose and investigate two types of sub-exponential models of population extinction. Unlike the more traditional exponential models, the life duration of sub-exponential models is finite. In the first model, the population is assumed to be composed clones that are independent from each other. In the second model, we assume that the size of the population as a whole decreases according to the sub-exponential equation. We then investigate the “unobserved heterogeneity”, i.e. the underlying inhomogeneous population model, and calculate the distribution of frequencies of clones for both models. We show that the dynamics of frequencies in the first model is governed by the principle of minimum of Tsallis information loss. In the second model, the notion of “internal population time” is proposed; with respect to the internal time, the dynamics of frequencies is governed by the principle of minimum of Shannon information loss. The results of this analysis show that the principle of minimum of information loss is the underlying law for the evolution of a broad class of models of population extinction. Finally, we propose a possible application of this modeling framework to mechanisms underlying time perception. PMID:27090117

Influence of Pleistocene glacial/interglacial cycles on the genetic structure of the mistletoe cactus Rhipsalis baccifera (Cactaceae) in Mesoamerica.

PubMed

Ornelas, Juan Francisco; Rodríguez-Gómez, Flor

2015-01-01

Phylogeographical work on cloud forest-adapted species provides inconsistent evidence on cloud forest dynamics during glacial cycles. A study of Rhipsalis baccifera (Cactaceae), a bird-dispersed epiphytic mistletoe cactus, was conducted to investigate genetic variation at sequence data from nuclear [internal transcribed spacer (ITS), 677 bp] and chloroplast (rpl32-trnL, 1092bp) DNA for 154 individuals across the species range in Mesoamerica to determine if such patterns are consistent with the expansion/contraction model of cloud forest during glacial cycles. We conducted population and spatial genetic analyses as well as gene flow and divergence time estimates between 24 populations comprising the distribution of R. baccifera in Mexico and Guatemala to gain insight of the evolutionary history of these populations, and a complementary species distribution modeling approach to frame information derived from the genetic analyses into an explicit paleoecological context. The results revealed a phylogeographical break at the Isthmus of Tehuantepec, and high levels of genetic diversity among populations and cloud forest areas. Despite the genetic differentiation of some R. baccifera populations, the widespread ITS ribotypes suggest effective nuclear gene flow via pollen and population differentiation shown by the rpl32-trnL suggests more restricted seed flow. Predictions of species distribution models under past last glacial maximum (LGM) climatic conditions and a significant signal of demographic expansion suggest that R. baccifera populations experienced a range expansion tracking the conditions of the cloud forest distribution and shifted to the lowlands with population connectivity during the LGM. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Coupled CFD-PBE Predictions of Renal Stone Size Distributions in the Nephron in Microgravity

NASA Technical Reports Server (NTRS)

Kassemi, Mohammad; Griffin, Elise; Thompson, David

2016-01-01

In this paper, a deterministic model is developed to assess the risk of critical renal stone formation for astronauts during space travel. A Population Balance Equation (PBE) model is used to compute the size distribution of a population of nucleating, growing and agglomerating renal calculi as they are transported through different sections of the nephron. The PBE model is coupled to a Computational Fluid Dynamics (CFD) model that solves for steady state flow of urine and transport of renal calculi along with the concentrations of ionic species, calcium and oxalate, in the nephron using an Eulerian two-phase mathematical framework. Parametric simulation are performed to study stone size enhancement and steady state volume fraction distributions in the four main sections of the nephron under weightlessness conditions. Contribution of agglomeration to the stone size distribution and effect of wall friction on the stone volume fraction distributions are carefully examined. Case studies using measured astronaut urinary calcium and oxalate concentrations in microgravity as input indicate that under nominal conditions the largest stone sizes developed in Space will be still considerably below the critical range for problematic stone development. However, results also indicate that the highest stone volume fraction occurs next to the tubule and duct walls. This suggests that there is an increased potential for wall adhesion with the possibility of evolution towards critical stone sizes.

Spatial Pattern and Population Structure of Artemisia ordosica Shrub in a Desert Grassland under Enclosure, Northwest China.

PubMed

Liu, Jiankang; Zhang, Kebin

2018-05-09

Enclosure is an effective practice for restoring and rehabilitating the degraded grassland ecosystem caused by overgrazing. Shrub species, which are dominant in most desert grasslands in arid and semiarid regions, have some beneficial ecological functions for grassland restoration. However, how the population structure and spatial pattern of the Artemisia ordosica shrub changes in a grassland ecosystem under enclosed practice is not well understood. This study, conducted in the Mu Us desert in northwest China, was designed to measure the A. ordosica population according to the chronosequence of enclosure (enclosure periods ranged from 5 years, 10 years, 15 years, and 25 years), contrasting this with an adjacent continuously grazed grassland. The results showed that the enclosed grasslands had a higher number of individuals of different age classes (seedling, adult, aging, and dead group) and greater population coverage, but shrubs had significant lower ( p < 0.05) crown diameter and height in comparison with those in continuously grazed grassland. Further, enclosed grasslands had a significantly higher ( p < 0.05) Shannon-Wiener index (H) and Evenness index (E), but a significantly lower ( p < 0.05) Richness index (R) than continuously grazed grassland. The crown of A. ordosica showed a significant linear positive correlation with height in all plots across succession, indicating that it was feasible to analyze the age structure by crown. The crown-class distribution structure of the A. ordosica population approximated a Gaussian distribution model in all survey plots. Within the population, seedling and adult groups exhibited aggregated spatial distribution at small scales, while aging and dead A. ordosica groups showed random distribution at almost all scales in different plots. The seedling A. ordosica group showed a positive correlation with adults at small scales in all plots except in 10 years of enclosure. However, it showed independent correlation with aging and dead groups at almost all scales. In long-term enclosed plots, the mortality rate of the A. ordosica population increased, therefore assistance management practices, such as fertilization, mowing, interval grazing, and seasonal grazing, must be employed to maintain population stability after long-term enclosure. This study can improve understanding and clarify the effects of enclosures in the desert grasslands of northwest China.

Obesity in Scotland: a persistent inequality.

PubMed

Tod, Elaine; Bromley, Catherine; Millard, Andrew D; Boyd, Allan; Mackie, Phil; McCartney, Gerry

2017-07-27

Obesity is a health problem in its own right and a risk factor for other conditions such as cardiovascular disease. The prevalence of overweight and obesity increased in Scotland between 1995 and 2008 with socio-economic inequalities persisting in adults over time and increasing in children. This paper explores changes in the underlying distribution of body mass index (BMI) which is less well understood. Using data from the Scottish Health Survey (SHeS) between 1995 and 2014 for adults aged 18-64 years, we calculated population distributions for BMI for the population overall, and for age, sex and deprivation strata. We used SHeS data for children aged 2-15 years between 1998 and 2014, in addition to data from the Child Health Systems Programme (CHSP) collected from primary one (P1) children in participating local authorities, to describe the overall trends and to compare trends in inequalities by deprivation strata. Amongst adults, the BMI distribution shifted upwards, with a large proportion of the population gaining a small amount of weight between 1995 and 2008 before subsequently stabilising across the distribution. In men the prevalence of obesity showed a linear deprivation gradient in 1995 but over time obesity declined in the least deprived quintile while the remaining four quintiles converged (and stabilised). In contrast, a persistent and generally linear gradient is evident among women for most of the 1995-2014 period. For those aged 2-15 years, obesity increased between 1998 and 2014 for the most deprived 40% of children contrasted with stable trends for the least deprived. The surveillance data for P1 children in Scotland showed a persistent inequality between 2005/06 and 2014/15 though it was less clear if this is widening. The BMI distribution for adults increased between 1995 and 2008 with a large proportion of the population gaining a small amount of weight before stabilising across the distribution. Inequalities in obesity persist for adults (with different underlying patterns evident for men and women), and may be widening for children. Actions to reduce the obesogenic environment, including structural changes not dependent on individual agency, are urgently needed if the long-term health, social and inequality consequences of obesity are to be reduced.

Indonesia [Population education in countries of the region].

PubMed

Hardjosawarmono, S

1982-06-01

Indonesia currently faces 5 population problems: 1) large total population, estimated by 1980 census data at 147,383,075; 2) rapid population growth, increasing at the rate of 2.8 million annually by 1980; 3) a young population distribution, with 44% of the population under age 15; 4) uneven population distribution; and 5) rapid urbanization. The National Family Planning Coordinating Board (NFPCB), established in 1970 to plan and control family planning and population education, has set the goal of reducing the 1971 fertility rate by 50% by 1990. Population education is aimed at achieving voluntary acceptance of the small family idea. This is to be attained through awareness of the factors causing rapid population growth and the close interaction between such growth and development programs to enhance the standard of living. The population education program, which is administered by the Department of Education and Culture in cooperation with the NFPCB, underwent an orientation stage in 1970-72 and a pilot project stage in 1973-75. In the latter stage, teaching materials were developed and tested in 30 junior high schools. During the institutionalization stage, 1976-79, the program was systematically integrated into the educational system. Population topics are integrated with relevant subject areas from the 4th grade of elementary school to the 3rd grade of senior high school. A cell system is used to train teachers, who in turn train teachers in their respective schools. Population education has also been introduced into Indonesia's subsidiary schools under religious and Armed Forces jurisdiction. Current population education activities include the training of an additional 50,000 teachers and provision of teaching kits, slide projectors, and textbooks to all of the 160 nonformal learning centers. In addition, a number of government agencies, including the Ministries of Sports and Culture, Education, Health, Transmigration, Information, Religious Affairs, Home Affairs, and Defense, are involved in education programs aimed at those ages 10-45 who are outside of the educational system.

An assessment of the portability of ancestry informative markers between human populations

PubMed Central

Myles, Sean; Stoneking, Mark; Timpson, Nic

2009-01-01

Background Recent work has shown that population stratification can have confounding effects on genetic association studies and statistical methods have been developed to correct for these effects. Subsets of markers that are highly-differentiated between populations, ancestry-informative markers (AIMs), have been used to correct for population stratification. Often AIMs are discovered in one set of populations and then employed in a different set of populations. The underlying assumption in these cases is that the population under study has the same substructure as the population in which the AIMs were discovered. The present study assesses this assumption and evaluates the portability between worldwide populations of 10 SNPs found to be highly-differentiated within Britain (BritAIMs). Methods We genotyped 10 BritAIMs in ~1000 individuals from 53 populations worldwide. We assessed the degree to which these 10 BritAIMs capture population stratification in other groups of populations by use of the Fst statistic. We used Fst values from 2750 random markers typed in the same set of individuals as an empirical distribution to which the Fst values of the 10 BritAIMs were compared. Results Allele frequency differences between continental groups for the BritAIMs are not unusually high. This is also the case for comparisons within continental groups distantly related to Britain. However, two BritAIMs show high Fst between European populations and two BritAIMs show high Fst between populations from the Middle East. Overall the median Fst across all BritAIMs is not unusually high compared to the empirical distribution. Conclusion We find that BritAIMs are generally not useful to distinguish between continental groups or within continental groups distantly related to Britain. Moreover, our analyses suggest that the portability of AIMs across geographical scales (e.g. between Europe and Britain) can be limited and should therefore be taken into consideration in the design and interpretation of genetic association studies. PMID:19619313

Development a computer codes to couple PWR-GALE output and PC-CREAM input

NASA Astrophysics Data System (ADS)

Kuntjoro, S.; Budi Setiawan, M.; Nursinta Adi, W.; Deswandri; Sunaryo, G. R.

2018-02-01

Radionuclide dispersion analysis is part of an important reactor safety analysis. From the analysis it can be obtained the amount of doses received by radiation workers and communities around nuclear reactor. The radionuclide dispersion analysis under normal operating conditions is carried out using the PC-CREAM code, and it requires input data such as source term and population distribution. Input data is derived from the output of another program that is PWR-GALE and written Population Distribution data in certain format. Compiling inputs for PC-CREAM programs manually requires high accuracy, as it involves large amounts of data in certain formats and often errors in compiling inputs manually. To minimize errors in input generation, than it is make coupling program for PWR-GALE and PC-CREAM programs and a program for writing population distribution according to the PC-CREAM input format. This work was conducted to create the coupling programming between PWR-GALE output and PC-CREAM input and programming to written population data in the required formats. Programming is done by using Python programming language which has advantages of multiplatform, object-oriented and interactive. The result of this work is software for coupling data of source term and written population distribution data. So that input to PC-CREAM program can be done easily and avoid formatting errors. Programming sourceterm coupling program PWR-GALE and PC-CREAM is completed, so that the creation of PC-CREAM inputs in souceterm and distribution data can be done easily and according to the desired format.

Meeting the ONCHIT population health mandate: a proposed model for security in selective transportable distributed environments.

PubMed

Lorence, Daniel; Chin, John; Richards, Michael

2010-08-01

Goal Two of the US ONCHIT Plan focuses on enabling the use of electronic health information for critical health improvement activities that promote the health of targeted communities, and the US population as a whole. Because of the focus on communities and populations, the activities under this second goal differ fundamentally from those of the first goal, which focus on the care of individuals. Proposed here is a model for health information management in such population-based environments, which allows selective access and use of information, and maintains transportability while ensuring security and confidentiality.

Conformation Types of Ubiquitin [M+8H]8+ Ions from Water:Methanol Solutions: Evidence for the N and A States in Aqueous Solution

PubMed Central

Shi, Huilin; Pierson, Nicholas A.; Valentine, Stephen J.; Clemmer, David E.

2012-01-01

Ion mobility and mass spectrometry measurements are used to examine the gas-phase populations of [M+8H]8+ ubiquitin ions formed upon electrospraying 20 different solutions: from 100:0 to 5:95 water:methanol that are maintained at pH = 2.0. Over this range of solution conditions, mobility distributions for the +8 charge state show substantial variations. Here we develop a model that treats the combined measurements as one data set. By varying the relative abundances of a discrete set of conformation types, it is possible to represent distributions obtained from any solution. For solutions that favor the well-known A-state ubiquitin, it is possible to represent the gas-phase distributions with seven conformation types. Aqueous conditions that favor the native structure require four more structural types to represent the distribution. This analysis provides the first direct evidence for trace amounts of the A state under native conditions. The method of analysis presented here should help illuminate how solution populations evolve into new gas-phase structures as solvent is removed. Evidence for trace quantities of previously unknown states under native solution conditions may provide insight about the relationship of dynamics to protein function as well as misfolding and aggregation phenomena. PMID:22315998

The characteristic pitch angle distributions of 1 eV to 600 keV protons near the equator based on Van Allen Probes observations

NASA Astrophysics Data System (ADS)

Yue, C.; Bortnik, J.; Thorne, R. M.; Ma, Q.; An, X.; Chappell, C. R.; Gerrard, A. J.; Lanzerotti, L. J.; Shi, Q.

2017-12-01

Understanding the source and loss processes of various plasma populations is greatly aided by having accurate knowledge of their pitch angle distributions (PADs). Here, we statistically analyze 1 eV to 600 keV hydrogen (H+) PADs near the geomagnetic equator in the inner magnetosphere based on Van Allen Probes measurements, to comprehensively investigate how the H+ PADs vary with different energies, magnetic local times (MLTs), L-shells, and geomagnetic conditions. Our survey clearly indicates four distinct populations with different PADs: (1) a pancake distribution of the plasmaspheric H+ at low L-shells except for dawn sector; (2) a bi-directional field-aligned distribution of the warm plasma cloak; (3) pancake or isotropic distributions of ring current H+; (4) radiation belt particles show pancake, butterfly and isotropic distributions depending on their energy, MLT and L-shell. Meanwhile, the pancake distribution of ring current H+ moves to lower energies as L-shell increases which is primarily caused by adiabatic transport. Furthermore, energetic H+ (> 10 keV) PADs become more isotropic following the substorm injections, indicating wave-particle interactions. The radiation belt H+ butterfly distributions are identified in a narrow energy range of 100 < E < 400 keV at large L (L > 5), which are less significant during quiet times and extend from dusk to dawn sector through midnight during substorms. The different PADs near the equator provide clues of the underlying physical processes that produce the dynamics of these different populations.

Thermal onset of cellular and endocrine stress responses correspond to ecological limits in brook trout, an iconic cold-water fish

USGS Publications Warehouse

Chadwick, Joseph G; Nislow, Kieth H; McCormick, Stephen

2015-01-01

Climate change is predicted to change the distribution and abundance of species, yet underlying physiological mechanisms are complex and methods for detecting populations at risk from rising temperature are poorly developed. There is increasing interest in using physiological mediators of the stress response as indicators of individual and population-level response to environmental stressors. Here, we use laboratory experiments to show that the temperature thresholds in brook trout (Salvelinus fontinalis) for increased gill heat shock protein-70 (20.7°C) and plasma glucose (21.2°C) are similar to their proposed thermal ecological limit of 21.0°C. Field assays demonstrated increased plasma glucose, cortisol and heat shock protein-70 concentrations at field sites where mean daily temperature exceeded 21.0°C. Furthermore, population densities of brook trout were lowest at field sites where temperatures were warm enough to induce a stress response, and a co-occurring species with a higher thermal tolerance showed no evidence of physiological stress at a warm site. The congruence of stress responses and proposed thermal limits supports the use of these thresholds in models of changes in trout distribution under climate change scenarios and suggests that the induction of the stress response by elevated temperature may play a key role in driving the distribution of species.

Spatial patterns of a tropical tree species growing under an eucalyptus plantation in South-East Brazil.

PubMed

Higuchi, P; Silva, A C; Louzada, J N C; Machado, E L M

2010-05-01

The objectives of this study were to evaluate the influence of propagules source and the implication of tree size class on the spatial pattern of Xylopia brasiliensis Spreng. individuals growing under the canopy of an experimental plantation of eucalyptus. To this end, all individuals of Xylopia brasiliensis with diameter at soil height (dsh) > 1 cm were mapped in the understory of a 3.16 ha Eucalyptus spp. and Corymbia spp. plantation, located in the municipality of Lavras, SE Brazil. The largest nearby mature tree of X. brasiliensis was considered as the propagules source. Linear regressions were used to assess the influence of the distance of propagules source on the population parameters (density, basal area and height). The spatial pattern of trees was assessed through the Ripley K function. The overall pattern showed that the propagules source distance had strong influence over spatial distribution of trees, mainly the small ones, indicating that the closer the distance from the propagules source, the higher the tree density and the lower the mean tree height. The population showed different spatial distribution patterns according to the spatial scale and diameter class considered. While small trees tended to be aggregated up to around 80 m, the largest individuals were randomly distributed in the area. A plausible explanation for observed patterns might be limited seed rain and intra-population competition.

The intrinsic growth rate as a predictor of population viability under climate warming.

PubMed

Amarasekare, Priyanga; Coutinho, Renato M

2013-11-01

1. Lately, there has been interest in using the intrinsic growth rate (rm) to predict the effects of climate warming on ectotherm population viability. However, because rm is calculated using the Euler-Lotka equation, its reliability in predicting population persistence depends on whether ectotherm populations can achieve a stable age/stage distribution in thermally variable environments. Here, we investigate this issue using a mathematical framework that incorporates mechanistic descriptions of temperature effects on vital rates into a stage-structured population model that realistically captures the temperature-induced variability in developmental delays that characterize ectotherm life cycles. 2. We find that populations experiencing seasonal temperature variation converge to a stage distribution whose intra-annual pattern remains invariant across years. As a result, the mean annual per capita growth rate also remains constant between years. The key insight is the mechanism that allows populations converge to a stationary stage distribution. Temperature effects on the biochemical processes (e.g. enzyme kinetics, hormonal regulation) that underlie life-history traits (reproduction, development and mortality) exhibit well-defined thermodynamical properties (e.g. changes in entropy and enthalpy) that lead to predictable outcomes (e.g. reduction in reaction rates or hormonal action at temperature extremes). As a result, life-history traits exhibit a systematic and predictable response to seasonal temperature variation. This in turn leads to temporally predictable temperature responses of the stage distribution and the per capita growth rate. 3. When climate warming causes an increase in the mean annual temperature and/or the amplitude of seasonal fluctuations, the population model predicts the mean annual per capita growth rate to decline to zero within 100 years when warming is slow relative to the developmental period of the organism (0.03-0.05°C per year) and to become negative, causing population extinction, well before 100 years when warming is fast (e.g. 0.1°C per year). The Euler-Lotka equation predicts a slower decrease in rm when warming is slow and a longer persistence time when warming is fast, with the deviation between the two metrics increasing with increasing developmental period. These results suggest that predictions of ectotherm population viability based on rm may be valid only for species with short developmental delays, and even then, only over short time-scales and under slow warming regimes. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Integrating bioclimate with population models to improve forecasts of species extinctions under climate change.

PubMed

Brook, Barry W; Akçakaya, H Resit; Keith, David A; Mace, Georgina M; Pearson, Richard G; Araújo, Miguel B

2009-12-23

Climate change is already affecting species worldwide, yet existing methods of risk assessment have not considered interactions between demography and climate and their simultaneous effect on habitat distribution and population viability. To address this issue, an international workshop was held at the University of Adelaide in Australia, 25-29 May 2009, bringing leading species distribution and population modellers together with plant ecologists. Building on two previous workshops in the UK and Spain, the participants aimed to develop methodological standards and case studies for integrating bioclimatic and metapopulation models, to provide more realistic forecasts of population change, habitat fragmentation and extinction risk under climate change. The discussions and case studies focused on several challenges, including spatial and temporal scale contingencies, choice of predictive climate, land use, soil type and topographic variables, procedures for ensemble forecasting of both global climate and bioclimate models and developing demographic structures that are realistic and species-specific and yet allow generalizations of traits that make species vulnerable to climate change. The goal is to provide general guidelines for assessing the Red-List status of large numbers of species potentially at risk, owing to the interactions of climate change with other threats such as habitat destruction, overexploitation and invasive species.

The distribution of genetic variance across phenotypic space and the response to selection.

PubMed

Blows, Mark W; McGuigan, Katrina

2015-05-01

The role of adaptation in biological invasions will depend on the availability of genetic variation for traits under selection in the new environment. Although genetic variation is present for most traits in most populations, selection is expected to act on combinations of traits, not individual traits in isolation. The distribution of genetic variance across trait combinations can be characterized by the empirical spectral distribution of the genetic variance-covariance (G) matrix. Empirical spectral distributions of G from a range of trait types and taxa all exhibit a characteristic shape; some trait combinations have large levels of genetic variance, while others have very little genetic variance. In this study, we review what is known about the empirical spectral distribution of G and show how it predicts the response to selection across phenotypic space. In particular, trait combinations that form a nearly null genetic subspace with little genetic variance respond only inconsistently to selection. We go on to set out a framework for understanding how the empirical spectral distribution of G may differ from the random expectations that have been developed under random matrix theory (RMT). Using a data set containing a large number of gene expression traits, we illustrate how hypotheses concerning the distribution of multivariate genetic variance can be tested using RMT methods. We suggest that the relative alignment between novel selection pressures during invasion and the nearly null genetic subspace is likely to be an important component of the success or failure of invasion, and for the likelihood of rapid adaptation in small populations in general. © 2014 John Wiley & Sons Ltd.

MOLECULAR DIVERSITY OF DRINKING WATER MICROBIAL COMMUNITIES: A PHYLOGENETIC APPROACH

EPA Science Inventory

Culture-based methods are traditionally used to determine microbiological quality of drinking water even though these methods are highly selective and tend to underestimate the densities and diversity bacterial populations inhabiting distribution systems. In order to better under...

Shaping Policy Change in Population Health: Policy Entrepreneurs, Ideas, and Institutions.

PubMed

Béland, Daniel; Katapally, Tarun R

2018-01-14

Political realities and institutional structures are often ignored when gathering evidence to influence population health policies. If these policies are to be successful, social science literature on policy change should be integrated into the population health approach. In this contribution, drawing on the work of John W. Kingdon and related scholarship, we set out to examine how key components of the policy change literature could contribute towards the effective development of population health policies. Shaping policy change would require a realignment of the existing school of thought, where the contribution of population health seems to end at knowledge translation. Through our critical analysis of selected literature, we extend recommendations to advance a burgeoning discussion in adopting new approaches to successfully implement evidence-informed population health policies. © 2018 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Spatial genetic structure of the cyprinid fish Onychostoma lepturum on Hainan Island.

PubMed

Zhou, Tian-Qi; Lin, Hung-Du; Hsu, Kui-Ching; Kuo, Po-Hsun; Wang, Wei-Kuang; Tang, Wen-Qiao; Liu, Dong; Yang, Jin-Quan

2017-11-01

Population genetic structure of Onychostoma lepturum on Hainan Island was investigated based on mitochondrial CR + cyt b region in 63 specimens collected from four populations. Population analyses indicated significant genetic structure (F ST  = 0.749) and displayed a significant relationship between phylogeny and geography (N ST  = 0.750 and G ST  = 0.140). Thirty-one mtDNA haplotypes were classified into four lineages, and these lineages had an almost allopatric distribution. The results of a statistical dispersal-vicariance analysis suggest that the ancestral populations were distributed widely on Hainan Island, and the rising of the central mountainous area of Hainan Island, the Wuzhi and Yinggeling Mountain Range, separated these four drainages into independent lineages. According to a spatial analysis of molecular variance analysis, we divided these populations into three units: ND, CH and WQ + LS, running into Qiongzhou Strait, the Gulf of Tokin and the South China Sea, respectively. According to our study, the exposure of straits and shelf under water retreat gave chances for population dispersion during the glaciations.

Genetic diversity and divergence at the Arbutus unedo L. (Ericaceae) westernmost distribution limit.

PubMed

Ribeiro, Maria Margarida; Piotti, Andrea; Ricardo, Alexandra; Gaspar, Daniel; Costa, Rita; Parducci, Laura; Vendramin, Giovanni Giuseppe

2017-01-01

Mediterranean forests are fragile ecosystems vulnerable to recent global warming and reduction of precipitation, and a long-term negative effect is expected on vegetation with increasing drought and in areas burnt by fires. We investigated the spatial distribution of genetic variation of Arbutus unedo in the western Iberia Peninsula, using plastid markers with conservation and provenance regions design purposes. This species is currently undergoing an intense domestication process in the region, and, like other species, is increasingly under the threat from climate change, habitat fragmentation and wildfires. We sampled 451 trees from 15 natural populations from different ecological conditions spanning the whole species' distribution range in the region. We applied Bayesian analysis and identified four clusters (north, centre, south, and a single-population cluster). Hierarchical AMOVA showed higher differentiation among clusters than among populations within clusters. The relatively low within-clusters differentiation can be explained by a common postglacial history of nearby populations. The genetic structure found, supported by the few available palaeobotanical records, cannot exclude the hypothesis of two independent A. unedo refugia in western Iberia Peninsula during the Last Glacial Maximum. Based on the results we recommend a conservation strategy by selecting populations for conservation based on their allelic richness and diversity and careful seed transfer consistent with current species' genetic structure.

Genetic diversity and divergence at the Arbutus unedo L. (Ericaceae) westernmost distribution limit

PubMed Central

Ribeiro, Maria Margarida; Piotti, Andrea; Ricardo, Alexandra; Gaspar, Daniel; Costa, Rita; Parducci, Laura; Vendramin, Giovanni Giuseppe

2017-01-01

Mediterranean forests are fragile ecosystems vulnerable to recent global warming and reduction of precipitation, and a long-term negative effect is expected on vegetation with increasing drought and in areas burnt by fires. We investigated the spatial distribution of genetic variation of Arbutus unedo in the western Iberia Peninsula, using plastid markers with conservation and provenance regions design purposes. This species is currently undergoing an intense domestication process in the region, and, like other species, is increasingly under the threat from climate change, habitat fragmentation and wildfires. We sampled 451 trees from 15 natural populations from different ecological conditions spanning the whole species’ distribution range in the region. We applied Bayesian analysis and identified four clusters (north, centre, south, and a single-population cluster). Hierarchical AMOVA showed higher differentiation among clusters than among populations within clusters. The relatively low within-clusters differentiation can be explained by a common postglacial history of nearby populations. The genetic structure found, supported by the few available palaeobotanical records, cannot exclude the hypothesis of two independent A. unedo refugia in western Iberia Peninsula during the Last Glacial Maximum. Based on the results we recommend a conservation strategy by selecting populations for conservation based on their allelic richness and diversity and careful seed transfer consistent with current species’ genetic structure. PMID:28384294

Ecological and evolutionary dynamics of interconnectedness and modularity.

PubMed

Nordbotten, Jan M; Levin, Simon A; Szathmáry, Eörs; Stenseth, Nils C

2018-01-23

In this contribution, we develop a theoretical framework for linking microprocesses (i.e., population dynamics and evolution through natural selection) with macrophenomena (such as interconnectedness and modularity within an ecological system). This is achieved by developing a measure of interconnectedness for population distributions defined on a trait space (generalizing the notion of modularity on graphs), in combination with an evolution equation for the population distribution. With this contribution, we provide a platform for understanding under what environmental, ecological, and evolutionary conditions ecosystems evolve toward being more or less modular. A major contribution of this work is that we are able to decompose the overall driver of changes at the macro level (such as interconnectedness) into three components: ( i ) ecologically driven change, ( ii ) evolutionarily driven change, and ( iii ) environmentally driven change. Copyright © 2018 the Author(s). Published by PNAS.

Quantifying Adventitious Error in a Covariance Structure as a Random Effect

PubMed Central

Wu, Hao; Browne, Michael W.

2017-01-01

We present an approach to quantifying errors in covariance structures in which adventitious error, identified as the process underlying the discrepancy between the population and the structured model, is explicitly modeled as a random effect with a distribution, and the dispersion parameter of this distribution to be estimated gives a measure of misspecification. Analytical properties of the resultant procedure are investigated and the measure of misspecification is found to be related to the RMSEA. An algorithm is developed for numerical implementation of the procedure. The consistency and asymptotic sampling distributions of the estimators are established under a new asymptotic paradigm and an assumption weaker than the standard Pitman drift assumption. Simulations validate the asymptotic sampling distributions and demonstrate the importance of accounting for the variations in the parameter estimates due to adventitious error. Two examples are also given as illustrations. PMID:25813463

Historical range, current distribution, and conservation status of the Swift Fox, Vulpes velox, in North America

USGS Publications Warehouse

Sovada, Marsha A.; Woodward, Robert O.; Igl, Lawrence D.

2009-01-01

The Swift Fox (Vulpes velox) was once common in the shortgrass and mixed-grass prairies of the Great Plains of North America. The species' abundance declined and its distribution retracted following European settlement of the plains. By the late 1800s, the species had been largely extirpated from the northern portion of its historical range, and its populations were acutely depleted elsewhere. Swift Fox populations have naturally recovered somewhat since the 1950s, but overall abundance and distribution remain below historical levels. In a 1995 assessment of the species' status under the US Endangered Species Act, the US Fish and Wildlife Service concluded that a designation of threatened or endangered was warranted, but the species was "precluded from listing by higher listing priorities." A major revelation of the 1995 assessment was the recognition that information useful for determining population status was limited. Fundamental information was missing, including an accurate estimate of the species' distribution before European settlement and an estimate of the species' current distribution and trends. The objectives of this paper are to fill those gaps in knowledge. Historical records were compiled and, in combination with knowledge of the habitat requirements of the species, the historical range of the Swift Fox is estimated to be approximately 1.5 million km2. Using data collected between 2001 and 2006, the species' current distribution is estimated to be about 44% of its historical range in the United States and 3% in Canada. Under current land use, approximately 39% of the species' historical range contains grassland habitats with very good potential for Swift Fox occupation and another 10% supports grasslands with characteristics that are less preferred (e.g., a sparse shrub component or taller stature) but still suitable. Additionally, land use on at least 25% of the historical range supports dryland farming, which can be suitable for Swift Fox occupation. In the United States, approximately 52% of highest quality habitats currently available are occupied by Swift Foxes.

A simple approximation of moments of the quasi-equilibrium distribution of an extended stochastic theta-logistic model with non-integer powers.

PubMed

Bhowmick, Amiya Ranjan; Bandyopadhyay, Subhadip; Rana, Sourav; Bhattacharya, Sabyasachi

2016-01-01

The stochastic versions of the logistic and extended logistic growth models are applied successfully to explain many real-life population dynamics and share a central body of literature in stochastic modeling of ecological systems. To understand the randomness in the population dynamics of the underlying processes completely, it is important to have a clear idea about the quasi-equilibrium distribution and its moments. Bartlett et al. (1960) took a pioneering attempt for estimating the moments of the quasi-equilibrium distribution of the stochastic logistic model. Matis and Kiffe (1996) obtain a set of more accurate and elegant approximations for the mean, variance and skewness of the quasi-equilibrium distribution of the same model using cumulant truncation method. The method is extended for stochastic power law logistic family by the same and several other authors (Nasell, 2003; Singh and Hespanha, 2007). Cumulant truncation and some alternative methods e.g. saddle point approximation, derivative matching approach can be applied if the powers involved in the extended logistic set up are integers, although plenty of evidence is available for non-integer powers in many practical situations (Sibly et al., 2005). In this paper, we develop a set of new approximations for mean, variance and skewness of the quasi-equilibrium distribution under more general family of growth curves, which is applicable for both integer and non-integer powers. The deterministic counterpart of this family of models captures both monotonic and non-monotonic behavior of the per capita growth rate, of which theta-logistic is a special case. The approximations accurately estimate the first three order moments of the quasi-equilibrium distribution. The proposed method is illustrated with simulated data and real data from global population dynamics database. Copyright © 2015 Elsevier Inc. All rights reserved.

Poor sexual reproduction on the distribution limit of the rare tree Sorbus torminalis

NASA Astrophysics Data System (ADS)

Rasmussen, Kristine Kjørup; Kollmann, Johannes

2004-05-01

Plants growing in small fragmented populations under stressful environmental conditions may have reduced sexual reproduction. This can cause low gene flow between populations and eventually extinction. Here we report on a pollination experiment with Sorbus torminalis, a rare fleshy-fruited tree with a submediterranean distribution in Europe. At the northern limit of its range in SE-Denmark two relatively small and isolated populations were studied for effects of seven pollination treatments on fruit production and on the timing of fruit abortion. There was evidence that lack of pollination and spontaneous self-pollination caused particularly high fruit abortion, which indicates that apomixis is unlikely and spontaneous self-pollination not efficient. Fruit abortion was delayed after hand pollination, which suggests limitation by pollen quantity. Self-pollination caused earlier abortion than experimental cross-pollination within or between populations indicating inbreeding depression. There was no evidence for outbreeding depression as measured by fruit abortion. We conclude that generative reproduction of S. torminalis is reduced on its northern distribution limit and that it might be negatively affected by pollen limitation and inbreeding effects, which have not been compensated for by increased self-compatibility or apomixis.

A Theoretical Approach to Analyze the Parametric Influence on Spatial Patterns of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) Populations.

PubMed

Garcia, A G; Godoy, W A C

2017-06-01

Studies of the influence of biological parameters on the spatial distribution of lepidopteran insects can provide useful information for managing agricultural pests, since the larvae of many species cause serious impacts on crops. Computational models to simulate the spatial dynamics of insect populations are increasingly used, because of their efficiency in representing insect movement. In this study, we used a cellular automata model to explore different patterns of population distribution of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), when the values of two biological parameters that are able to influence the spatial pattern (larval viability and adult longevity) are varied. We mapped the spatial patterns observed as the parameters varied. Additionally, by using population data for S. frugiperda obtained in different hosts under laboratory conditions, we were able to describe the expected spatial patterns occurring in corn, cotton, millet, and soybean crops based on the parameters varied. The results are discussed from the perspective of insect ecology and pest management. We concluded that computational approaches can be important tools to study the relationship between the biological parameters and spatial distributions of lepidopteran insect pests.

Psychiatric Resident and Attending Diagnostic and Prescribing Practices

ERIC Educational Resources Information Center

Tripp, Adam C.; Schwartz, Thomas L.

2008-01-01

Objective: This study investigates whether two patient population groups, under resident or attending treatment, are equivalent or different in the distribution of patient characteristics, diagnoses, or pharmacotherapy. Methods: Demographic data, psychiatric diagnoses, and pharmacotherapy data were collected for 100 random patient charts of…

Evidence for a freezing tolerance-growth rate trade-off in the live oaks (Quercus series Virentes) across the tropical-temperate divide.

PubMed

Koehler, Kari; Center, Alyson; Cavender-Bares, Jeannine

2012-02-01

• It has long been hypothesized that species are limited to the north by minimum temperature and to the south by competition, resulting in a trade-off between freezing tolerance and growth rate. We investigated the extent to which the climatic origins of populations from four live oak species (Quercus series Virentes) were associated with freezing tolerance and growth rate, and whether species fitted a model of locally adapted populations, each with narrow climatic tolerances, or of broadly adapted populations with wide climatic tolerances. • Acorns from populations of four species across a tropical-temperate gradient were grown under common tropical and temperate conditions. Growth rate, seed mass, and leaf and stem freezing traits were compared with source minimum temperatures. • Maximum growth rates under tropical conditions were negatively correlated with freezing tolerance under temperate conditions. The minimum source temperature predicted the freezing tolerance of populations under temperate conditions. The tropical species Q. oleoides was differentiated from the three temperate species, and variation among species was greater than among populations. • The trade-off between freezing tolerance and growth rate supports the range limit hypothesis. Limited variation within species indicates that the distributions of species may be driven more strongly by broad climatic factors than by highly local conditions. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Simulated fissioning of uranium and testing of the fission-track dating method

USGS Publications Warehouse

McGee, V.E.; Johnson, N.M.; Naeser, C.W.

1985-01-01

A computer program (FTD-SIM) faithfully simulates the fissioning of 238U with time and 235U with neutron dose. The simulation is based on first principles of physics where the fissioning of 238U with the flux of time is described by Ns = ??f 238Ut and the fissioning of 235U with the fluence of neutrons is described by Ni = ??235U??. The Poisson law is used to set the stochastic variation of fissioning within the uranium population. The life history of a given crystal can thus be traced under an infinite variety of age and irradiation conditions. A single dating attempt or up to 500 dating attempts on a given crystal population can be simulated by specifying the age of the crystal population, the size and variation in the areas to be counted, the amount and distribution of uranium, the neutron dose to be used and its variation, and the desired ratio of 238U to 235U. A variety of probability distributions can be applied to uranium and counting-area. The Price and Walker age equation is used to estimate age. The output of FTD-SIM includes the tabulated results of each individual dating attempt (sample) on demand and/or the summary statistics and histograms for multiple dating attempts (samples) including the sampling age. An analysis of the results from FTD-SIM shows that: (1) The external detector method is intrinsically more precise than the population method. (2) For the external detector method a correlation between spontaneous track count, Ns, and induced track count, Ni, results when the population of grains has a stochastic uranium content and/or when the counting areas between grains are stochastic. For the population method no correlation can exist. (3) In the external detector method the sampling distribution of age is independent of the number of grains counted. In the population method the sampling distribution of age is highly dependent on the number of grains counted. (4) Grains with zero-track counts, either in Ns or Ni, are in integral part of fissioning theory and under certain circumstances must be included in any estimate of age. (5) In estimating standard error of age the standard error of Ns and Ni and ?? must be accurately estimated and propagated through the age equation. Several statistical models are presently available to do so. ?? 1985.

Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera.

PubMed

Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Bosserelle, Cyprien; Zenger, Kyall R

2017-01-10

Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted. The unique life history characteristics of many marine invertebrates such as high dispersal rates, stochastic survival and variable recruitment are also likely to influence how populations are organised. To examine the microevolutionary forces influencing population structure, connectivity and adaptive variation in a highly-dispersive bivalve, populations of the black-lip pearl oyster Pinctada margaritifera were examined across its ~18,000 km Indo-Pacific distribution. Analyses utilising 9,624 genome-wide SNPs and 580 oysters, discovered differing patterns of significant and substantial broad-scale genetic structure between the Indian and Pacific Ocean basins. Indian Ocean populations were markedly divergent (F st  = 0.2534-0.4177, p < 0.001), compared to Pacific Ocean oysters, where basin-wide gene flow was much higher (F st  = 0.0007-0.1090, p < 0.001). Partitioning of genetic diversity (hierarchical AMOVA) attributed 18.1% of variance between ocean basins, whereas greater proportions were resolved within samples and populations (45.8% and 35.7% respectively). Visualisation of population structure at selectively neutral loci resolved three and five discrete genetic clusters for the Indian and Pacific Oceans respectively. Evaluation of genetic structure at adaptive loci for Pacific populations (89 SNPs under directional selection; F st  = 0.1012-0.4371, FDR = 0.05), revealed five clusters identical to those detected at neutral SNPs, suggesting environmental heterogeneity within the Pacific. Patterns of structure and connectivity were supported by Mantel tests of isolation by distance (IBD) and independent hydrodynamic particle dispersal simulations. It is evident that genetic structure and connectivity across the natural range of P. margaritifera is highly complex, and produced by the interaction of ocean currents, IBD and seascape features at a broad scale, together with habitat geomorphology and local adaptation at regional levels. Overall population organisation is far more elaborate than generalised CPH predictions, however valuable insights for regional fishery management, and a greater understanding of range-wide genetic structure in a highly-dispersive marine invertebrate have been gained.

An Investigation of the Pareto Distribution as a Model for High Grazing Angle Clutter

DTIC Science & Technology

2011-03-01

radar detection schemes under controlled conditions. Complicated clutter models result in mathematical difficulties in the determination of optimal and...a population [7]. It has been used in the modelling of actuarial data; an example is in excess of loss quotations in insurance [8]. Its usefulness as...UNCLASSIFIED modified Bessel functions, making it difficult to employ in radar detection schemes. The Pareto Distribution is amenable to mathematical

A Third Moment Adjusted Test Statistic for Small Sample Factor Analysis

PubMed Central

Lin, Johnny; Bentler, Peter M.

2012-01-01

Goodness of fit testing in factor analysis is based on the assumption that the test statistic is asymptotically chi-square; but this property may not hold in small samples even when the factors and errors are normally distributed in the population. Robust methods such as Browne’s asymptotically distribution-free method and Satorra Bentler’s mean scaling statistic were developed under the presumption of non-normality in the factors and errors. This paper finds new application to the case where factors and errors are normally distributed in the population but the skewness of the obtained test statistic is still high due to sampling error in the observed indicators. An extension of Satorra Bentler’s statistic is proposed that not only scales the mean but also adjusts the degrees of freedom based on the skewness of the obtained test statistic in order to improve its robustness under small samples. A simple simulation study shows that this third moment adjusted statistic asymptotically performs on par with previously proposed methods, and at a very small sample size offers superior Type I error rates under a properly specified model. Data from Mardia, Kent and Bibby’s study of students tested for their ability in five content areas that were either open or closed book were used to illustrate the real-world performance of this statistic. PMID:23144511

Declining Prevalence of Disease Vectors Under Climate Change

NASA Astrophysics Data System (ADS)

Escobar, Luis E.; Romero-Alvarez, Daniel; Leon, Renato; Lepe-Lopez, Manuel A.; Craft, Meggan E.; Borbor-Cordova, Mercy J.; Svenning, Jens-Christian

2016-12-01

More than half of the world population is at risk of vector-borne diseases including dengue fever, chikungunya, zika, yellow fever, leishmaniasis, chagas disease, and malaria, with highest incidences in tropical regions. In Ecuador, vector-borne diseases are present from coastal and Amazonian regions to the Andes Mountains; however, a detailed characterization of the distribution of their vectors has never been carried out. We estimate the distribution of 14 vectors of the above vector-borne diseases under present-day and future climates. Our results consistently suggest that climate warming is likely threatening some vector species with extinction, locally or completely. These results suggest that climate change could reduce the burden of specific vector species. Other vector species are likely to shift and constrain their geographic range to the highlands in Ecuador potentially affecting novel areas and populations. These forecasts show the need for development of early prevention strategies for vector species currently absent in areas projected as suitable under future climate conditions. Informed interventions could reduce the risk of human exposure to vector species with distributional shifts, in response to current and future climate changes. Based on the mixed effects of future climate on human exposure to disease vectors, we argue that research on vector-borne diseases should be cross-scale and include climatic, demographic, and landscape factors, as well as forces facilitating disease transmission at fine scales.

Demography of the Early Neolithic Population in Central Balkans: Population Dynamics Reconstruction Using Summed Radiocarbon Probability Distributions

PubMed Central

2016-01-01

The Central Balkans region is of great importance for understanding the spread of the Neolithic in Europe but the Early Neolithic population dynamics of the region is unknown. In this study we apply the method of summed calibrated probability distributions to a set of published radiocarbon dates from the Republic of Serbia in order to reconstruct population dynamics in the Early Neolithic in this part of the Central Balkans. The results indicate that there was a significant population growth after ~6200 calBC, when the Neolithic was introduced into the region, followed by a bust at the end of the Early Neolithic phase (~5400 calBC). These results are broadly consistent with the predictions of the Neolithic Demographic Transition theory and the patterns of population booms and busts detected in other regions of Europe. These results suggest that the cultural process that underlies the patterns observed in Central and Western Europe was also in operation in the Central Balkan Neolithic and that the population increase component of this process can be considered as an important factor for the spread of the Neolithic as envisioned in the demic diffusion hypothesis. PMID:27508413

Geographic and ecologic distributions of the Anopheles gambiae complex predicted using a genetic algorithm.

PubMed

Levine, Rebecca S; Peterson, A Townsend; Benedict, Mark Q

2004-02-01

The distribution of the Anopheles gambiae complex of malaria vectors in Africa is uncertain due to under-sampling of vast regions. We use ecologic niche modeling to predict the potential distribution of three members of the complex (A. gambiae, A. arabiensis, and A. quadriannulatus) and demonstrate the statistical significance of the models. Predictions correspond well to previous estimates, but provide detail regarding spatial discontinuities in the distribution of A. gambiae s.s. that are consistent with population genetic studies. Our predictions also identify large areas of Africa where the presence of A. arabiensis is predicted, but few specimens have been obtained, suggesting under-sampling of the species. Finally, we project models developed from African distribution data for the late 1900s into the past and to South America to determine retrospectively whether the deadly 1929 introduction of A. gambiae sensu lato into Brazil was more likely that of A. gambiae sensu stricto or A. arabiensis.

Local adaptation and evolutionary potential along a temperature gradient in the fungal pathogen Rhynchosporium commune

PubMed Central

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2013-01-01

To predict the response of plant pathogens to climate warming, data are needed on current thermal adaptation, the pathogen's evolutionary potential, and the link between them. We conducted a common garden experiment using isolates of the fungal pathogen Rhynchosporium commune from nine barley populations representing climatically diverse locations. Clonal replicates of 126 genetically distinct isolates were assessed for their growth rate at 12°C, 18°C, and 22°C. Populations originating from climates with higher monthly temperature variation had higher growth rate at all three temperatures compared with populations from climates with less temperature fluctuation. Population differentiation in growth rate (QST) was significantly higher at 22°C than population differentiation for neutral microsatellite loci (GST), consistent with local adaptation for growth at higher temperatures. At 18°C, we found evidence for stabilizing selection for growth rate as QST was significantly lower than GST. Heritability of growth rate under the three temperatures was substantial in all populations (0.58–0.76). Genetic variation was lower in populations with higher growth rate at the three temperatures and evolvability increased under heat stress in seven of nine populations. Our findings imply that the distribution of this pathogen is unlikely to be genetically limited under climate warming, due to its high genetic variation and plasticity for thermal tolerance. PMID:23745143

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

PubMed

Lacerda, Miguel; Seoighe, Cathal

2014-11-01

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

Predicting potential distribution of poorly known species with small database: the case of four-horned antelope Tetracerus quadricornis on the Indian subcontinent.

PubMed

Pokharel, Krishna Prasad; Ludwig, Tobias; Storch, Ilse

2016-04-01

Information gaps on the distribution of data deficient and rare species such as four-horned antelope (FHA) in Nepal may impair their conservation. We aimed to empirically predict the distribution of FHA in Nepal with the help of data from the Indian subcontinent. Additionally, we wanted to identify core areas and gaps within the reported range limits and to assess the degree of isolation of known Nepalese populations from the main distribution areas in India. The tropical part of the Indian subcontinent (65°-90° eastern longitude, 5°-30° northern latitude), that is, the areas south of the Himalayan Mountains. Using MaxEnt and accounting for sampling bias, we developed predictive distribution models from environmental and topographical variables, and known presence locations of the study species in India and Nepal. We address and discuss the use of target group vs. random background. The prediction map reveals a disjunct distribution of FHA with core areas in the tropical parts of central to southern-western India. At the scale of the Indian subcontinent, suitable FHA habitat area in Nepal was small. The Indo-Gangetic Plain isolates Nepalese from the Indian FHA populations, but the distribution area extends further south than proposed by the current IUCN map. A low to intermediate temperature seasonality as well as low precipitation during the dry and warm season contributed most to the prediction of FHA distribution. The predicted distribution maps confirm other FHA range maps but also indicate that suitable areas exist south of the known range. Results further highlight that small populations in the Nepalese Terai Arc are isolated from the Indian core distribution and therefore might be under high extinction risk.

New Evidence on the Persistence of Health Spending

PubMed Central

Hirth, Richard A.; Gibson, Teresa B.; Levy, Helen G.; Smith, Jeffrey A.; Calónico, Sebastian; Das, Anup

2015-01-01

Surprisingly little is known about long-term spending patterns in the under-65 population. Such information could inform efforts to improve coverage and control costs. Using the MarketScan claims database, we characterize the persistence of healthcare spending in the privately-insured, under-65 population. Over a six-year period, 69.8% of enrollees never had annual spending in the top 10% of the distribution and the bottom 50% of spenders accounted for less than 10% of spending. Those in the top 10% in 2003 were almost as likely (34.4%) to be in the top 10% five years later as one year later (43.4%). Many comorbid conditions retained much of their predictive power even five years later. The persistence at both ends of the spending distribution indicates the potential for adverse selection and cream-skimming and supports the use of disease-management, particularly for those with the conditions that remained strong predictors of high spending throughout the follow-up period. PMID:25701579

New evidence on the persistence of health spending.

PubMed

Hirth, Richard A; Gibson, Teresa B; Levy, Helen G; Smith, Jeffrey A; Calónico, Sebastian; Das, Anup

2015-06-01

Surprisingly little is known about long-term spending patterns in the under-65 population. Such information could inform efforts to improve coverage and control costs. Using the MarketScan claims database, we characterize the persistence of health care spending in the privately insured, under-65 population. Over a 6-year period, 69.8% of enrollees never had annual spending in the top 10% of the distribution and the bottom 50% of spenders accounted for less than 10% of spending. Those in the top 10% in 2003 were almost as likely (34.4%) to be in the top 10% five years later as one year later (43.4%). Many comorbid conditions retained much of their predictive power even 5 years later. The persistence at both ends of the spending distribution indicates the potential for adverse selection and cream skimming and supports the use of disease management, particularly for those with the conditions that remained strong predictors of high spending throughout the follow-up period. © The Author(s) 2015.

On sample size of the kruskal-wallis test with application to a mouse peritoneal cavity study.

PubMed

Fan, Chunpeng; Zhang, Donghui; Zhang, Cun-Hui

2011-03-01

As the nonparametric generalization of the one-way analysis of variance model, the Kruskal-Wallis test applies when the goal is to test the difference between multiple samples and the underlying population distributions are nonnormal or unknown. Although the Kruskal-Wallis test has been widely used for data analysis, power and sample size methods for this test have been investigated to a much lesser extent. This article proposes new power and sample size calculation methods for the Kruskal-Wallis test based on the pilot study in either a completely nonparametric model or a semiparametric location model. No assumption is made on the shape of the underlying population distributions. Simulation results show that, in terms of sample size calculation for the Kruskal-Wallis test, the proposed methods are more reliable and preferable to some more traditional methods. A mouse peritoneal cavity study is used to demonstrate the application of the methods. © 2010, The International Biometric Society.

The Far Right Challenge Comment on "The Rise of Post-truth Populism in Pluralist Liberal Democracies: Challenges for Health Policy".

PubMed

Halikiopoulou, Daphne

2017-07-11

Speed and Mannion make a good case that the rise of populism poses significant challenges for health policy. This commentary suggests that the link between populism and health policy should be further nuanced in four ways. First, a deconstruction of the term populism itself and a focus on the far right dimension of populist politics; second, a focus on the supply side and more specifically the question of nationalism and the 'national preference'; third, the dynamics of party competition during economic crisis; and fourth the question of policy, and more specifically the extent to which certain labour market policies are able to mediate demand for the far right. © 2018 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Evolution of plant–pollinator mutualisms in response to climate change

PubMed Central

Gilman, R Tucker; Fabina, Nicholas S; Abbott, Karen C; Rafferty, Nicole E

2012-01-01

Climate change has the potential to desynchronize the phenologies of interdependent species, with potentially catastrophic effects on mutualist populations. Phenologies can evolve, but the role of evolution in the response of mutualisms to climate change is poorly understood. We developed a model that explicitly considers both the evolution and the population dynamics of a plant–pollinator mutualism under climate change. How the populations evolve, and thus whether the populations and the mutualism persist, depends not only on the rate of climate change but also on the densities and phenologies of other species in the community. Abundant alternative mutualist partners with broad temporal distributions can make a mutualism more robust to climate change, while abundant alternative partners with narrow temporal distributions can make a mutualism less robust. How community composition and the rate of climate change affect the persistence of mutualisms is mediated by two-species Allee thresholds. Understanding these thresholds will help researchers to identify those mutualisms at highest risk owing to climate change. PMID:25568025

Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)

PubMed Central

Ma, Xin; Kelley, Joanna L.; Eilertson, Kirsten; Musharoff, Shaila; Degenhardt, Jeremiah D.; Martins, André L.; Vinar, Tomas; Kosiol, Carolin; Siepel, Adam; Gutenkunst, Ryan N.; Bustamante, Carlos D.

2013-01-01

To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (∼3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations. PMID:24194868

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).

PubMed

Ma, Xin; Kelley, Joanna L; Eilertson, Kirsten; Musharoff, Shaila; Degenhardt, Jeremiah D; Martins, André L; Vinar, Tomas; Kosiol, Carolin; Siepel, Adam; Gutenkunst, Ryan N; Bustamante, Carlos D

2013-01-01

To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.

[The use of RAPD and ITE molecular markers to study genetical structure of the Crimean population of Triticum boeoticum Boiss].

PubMed

Mallabaeva, D Sh; Ignatov, A N; Sheĭko, I A; Isikov, V P; Geliuta, V P; Boĭko, N G; Seriapin, A A; Dorokhov, D B

2007-01-01

Wild wheat Triticum boeoticum Boiss. is the rare species are included in the Red Book of Ukraine. This species are reducing the magnitude of population and the area of distribution under anthropogenic activity. We studied genetic structure of two populations of T. boeoticum, located on Sapun Mountain and in Baidar Valley in Crimea. According RAPD and ITE molecular analysis we have estimated that the population of T. boeoticum on Sapun Mountain is genetically more impoverished than a population from the Baidar Valley. For preservation of maximal natural genetic polymorphism of the rare species it is recommended to direct efforts to preservations of a population of T. boeoticum from the Baidar Valley.

The Characteristic Pitch Angle Distributions of 1 eV to 600 keV Protons Near the Equator Based On Van Allen Probes Observations

DOE PAGES

Yue, Chao; Bortnik, Jacob; Thorne, Richard M.; ...

2017-08-31

Understanding the source and loss processes of various plasma populations is greatly aided by having accurate knowledge of their pitch angle distributions (PADs). Here we statistically analyze ~1 eV to 600 keV hydrogen (H+) PADs near the geomagnetic equator in the inner magnetosphere based on Van Allen Probes measurements, to comprehensively investigate how the H+ PADs vary with different energies, magnetic local times (MLTs), L shells, and geomagnetic conditions. Our survey clearly indicates four distinct populations with different PADs: a pancake distribution of the plasmaspheric H+ at low L shells except for dawn sector; a bidirectional field-aligned distribution of themore » warm plasma cloak; pancake or isotropic distributions of ring current H+; radiation belt particles show pancake, butterfly, and isotropic distributions depending on their energy, MLT, and L shell. Meanwhile, the pancake distribution of ring current H+ moves to lower energies as shell increases, which is primarily caused by adiabatic transport. Furthermore, energetic H+ (>10 keV) PADs become more isotropic following the substorm injections, indicating wave-particle interactions. The radiation belt H+ butterfly distributions are identified in a narrow energy range of 100 < E < 400 keV at large L ( L > 5), which are less significant during quiet times and extend from dusk to dawn sector through midnight during substorms. In conclusion, the different PADs near the equator provide clues of the underlying physical processes that produce the dynamics of these different populations.« less

The Characteristic Pitch Angle Distributions of 1 eV to 600 keV Protons Near the Equator Based On Van Allen Probes Observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yue, Chao; Bortnik, Jacob; Thorne, Richard M.

Understanding the source and loss processes of various plasma populations is greatly aided by having accurate knowledge of their pitch angle distributions (PADs). Here we statistically analyze ~1 eV to 600 keV hydrogen (H+) PADs near the geomagnetic equator in the inner magnetosphere based on Van Allen Probes measurements, to comprehensively investigate how the H+ PADs vary with different energies, magnetic local times (MLTs), L shells, and geomagnetic conditions. Our survey clearly indicates four distinct populations with different PADs: a pancake distribution of the plasmaspheric H+ at low L shells except for dawn sector; a bidirectional field-aligned distribution of themore » warm plasma cloak; pancake or isotropic distributions of ring current H+; radiation belt particles show pancake, butterfly, and isotropic distributions depending on their energy, MLT, and L shell. Meanwhile, the pancake distribution of ring current H+ moves to lower energies as shell increases, which is primarily caused by adiabatic transport. Furthermore, energetic H+ (>10 keV) PADs become more isotropic following the substorm injections, indicating wave-particle interactions. The radiation belt H+ butterfly distributions are identified in a narrow energy range of 100 < E < 400 keV at large L ( L > 5), which are less significant during quiet times and extend from dusk to dawn sector through midnight during substorms. In conclusion, the different PADs near the equator provide clues of the underlying physical processes that produce the dynamics of these different populations.« less

Relative importance of population size, fishing pressure and temperature on the spatial distribution of nine Northwest Atlantic groundfish stocks.

PubMed

Adams, Charles F; Alade, Larry A; Legault, Christopher M; O'Brien, Loretta; Palmer, Michael C; Sosebee, Katherine A; Traver, Michele L

2018-01-01

The spatial distribution of nine Northwest Atlantic groundfish stocks was documented using spatial indicators based on Northeast Fisheries Science Center spring and fall bottom trawl survey data, 1963-2016. We then evaluated the relative importance of population size, fishing pressure and bottom temperature on spatial distribution with an information theoretic approach. Northward movement in the spring was generally consistent with prior analyses, whereas changes in depth distribution and area occupancy were not. Only two stocks exhibited the same changes in spatiotemporal distribution in the fall as compared with the spring. Fishing pressure was the most important predictor of the center of gravity (i.e., bivariate mean location of the population) for the majority of stocks in the spring, whereas in the fall this was restricted to the east-west component. Fishing pressure was also the most important predictor of the dispersion around the center of gravity in both spring and fall. In contrast, biomass was the most important predictor of area occupancy for the majority of stocks in both seasons. The relative importance of bottom temperature was ranked highest in the fewest number of cases. This study shows that fishing pressure, in addition to the previously established role of climate, influences the spatial distribution of groundfish in the Northwest Atlantic. More broadly, this study is one of a small but growing body of literature to demonstrate that fishing pressure has an effect on the spatial distribution of marine resources. Future work must consider both fishing pressure and climate when examining mechanisms underlying fish distribution shifts.

Relative importance of population size, fishing pressure and temperature on the spatial distribution of nine Northwest Atlantic groundfish stocks

PubMed Central

Alade, Larry A.; Legault, Christopher M.; O’Brien, Loretta; Palmer, Michael C.; Sosebee, Katherine A.; Traver, Michele L.

2018-01-01

The spatial distribution of nine Northwest Atlantic groundfish stocks was documented using spatial indicators based on Northeast Fisheries Science Center spring and fall bottom trawl survey data, 1963–2016. We then evaluated the relative importance of population size, fishing pressure and bottom temperature on spatial distribution with an information theoretic approach. Northward movement in the spring was generally consistent with prior analyses, whereas changes in depth distribution and area occupancy were not. Only two stocks exhibited the same changes in spatiotemporal distribution in the fall as compared with the spring. Fishing pressure was the most important predictor of the center of gravity (i.e., bivariate mean location of the population) for the majority of stocks in the spring, whereas in the fall this was restricted to the east-west component. Fishing pressure was also the most important predictor of the dispersion around the center of gravity in both spring and fall. In contrast, biomass was the most important predictor of area occupancy for the majority of stocks in both seasons. The relative importance of bottom temperature was ranked highest in the fewest number of cases. This study shows that fishing pressure, in addition to the previously established role of climate, influences the spatial distribution of groundfish in the Northwest Atlantic. More broadly, this study is one of a small but growing body of literature to demonstrate that fishing pressure has an effect on the spatial distribution of marine resources. Future work must consider both fishing pressure and climate when examining mechanisms underlying fish distribution shifts. PMID:29698454

Reductions in labour capacity from heat stress under climate warming

NASA Astrophysics Data System (ADS)

Dunne, John P.; Stouffer, Ronald J.; John, Jasmin G.

2013-06-01

A fundamental aspect of greenhouse-gas-induced warming is a global-scale increase in absolute humidity. Under continued warming, this response has been shown to pose increasingly severe limitations on human activity in tropical and mid-latitudes during peak months of heat stress. One heat-stress metric with broad occupational health applications is wet-bulb globe temperature. We combine wet-bulb globe temperatures from global climate historical reanalysis and Earth System Model (ESM2M) projections with industrial and military guidelines for an acclimated individual's occupational capacity to safely perform sustained labour under environmental heat stress (labour capacity)--here defined as a global population-weighted metric temporally fixed at the 2010 distribution. We estimate that environmental heat stress has reduced labour capacity to 90% in peak months over the past few decades. ESM2M projects labour capacity reduction to 80% in peak months by 2050. Under the highest scenario considered (Representative Concentration Pathway 8.5), ESM2M projects labour capacity reduction to less than 40% by 2200 in peak months, with most tropical and mid-latitudes experiencing extreme climatological heat stress. Uncertainties and caveats associated with these projections include climate sensitivity, climate warming patterns, CO2 emissions, future population distributions, and technological and societal change.

Metabolism drives distribution and abundance in extremophile fish

PubMed Central

McHugh, Peter A.; Glover, Chris N.; McIntosh, Angus R.

2017-01-01

Differences in population density between species of varying size are frequently attributed to metabolic rates which are assumed to scale with body size with a slope of 0.75. This assumption is often criticised on the grounds that 0.75 scaling of metabolic rate with body size is not universal and can vary significantly depending on species and life-history. However, few studies have investigated how interspecific variation in metabolic scaling relationships affects population density in different sized species. Here we predict inter-specific differences in metabolism from niche requirements, thereby allowing metabolic predictions of species distribution and abundance at fine spatial scales. Due to the differences in energetic efficiency required along harsh-benign gradients, an extremophile fish (brown mudfish, Neochanna apoda) living in harsh environments had slower metabolism, and thus higher population densities, compared to a fish species (banded kōkopu, Galaxias fasciatus) in physiologically more benign habitats. Interspecific differences in the intercepts for the relationship between body and density disappeared when species mass-specific metabolic rates, rather than body sizes, were used to predict density, implying population energy use was equivalent between mudfish and kōkopu. Nevertheless, despite significant interspecific differences in the slope of the metabolic scaling relationships, mudfish and kōkopu had a common slope for the relationship between body size and population density. These results support underlying logic of energetic equivalence between different size species implicit in metabolic theory. However, the precise slope of metabolic scaling relationships, which is the subject of much debate, may not be a reliable indicator of population density as expected under metabolic theory. PMID:29176819

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks.

PubMed

Billiard, Sylvain; Ferrière, Régis; Méléard, Sylvie; Tran, Viet Chi

2015-11-01

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

Populism, Exclusion, Post-truth. Some Conceptual Caveats Comment on "The Rise of Post-truth Populism in Pluralist Liberal Democracies: Challenges for Health Policy".

PubMed

De Cleen, Benjamin

2017-07-15

In their editorial, Speed and Mannion identify two main challenges "the rise of post-truth populism" poses for health policy: the populist threat to inclusive healthcare policies, and the populist threat to well-designed health policies that draw on professional expertise and research evidence. This short comment suggests some conceptual clarifications that might help in thinking through more profoundly these two important issues. It argues that we should approach right-wing populism as a combination of a populist down/up (people/elite) axis with an exclusionary nationalist in/out (member/non-member) axis. And it raises some questions regarding the equation between populism, demagogy and the rejection of expertise and scientific knowledge. © 2018 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The Rise of Post-truth Populism in Pluralist Liberal Democracies: Challenges for Health Policy.

PubMed

Speed, Ewen; Mannion, Russell

2017-02-12

Recent years have witnessed the rise of populism and populist leaders, movements and policies in many pluralist liberal democracies, with Brexit and the election of Trump the two most recent high profile examples of this backlash against established political elites and the institutions that support them. This new populism is underpinned by a post-truth politics which is using social media as a mouthpiece for 'fake news' and 'alternative facts' with the intention of inciting fear and hatred of 'the other' and thereby helping to justify discriminatory health policies for marginalised groups. In this article, we explore what is meant by populism and highlight some of the challenges for health and health policy posed by the new wave of post-truth populism. © 2017 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Entrapped by the uneven central and Middle Eastern terrains: Genetic status of populations of Hirudo orientalis (Annelida, Clitellata, Hirudinida) with a phylogenetic review of the genus Hirudo.

PubMed

Darabi-Darestani, Kaveh; Sari, Alireza; Sarafrazi, Alimorad; Utevsky, Serge

2018-04-01

Phylogenetic relationships between species of the genus Hirudo plus genetic variation in the entire distribution range of Hirudo orientalis were investigated based on mitochondrial (COI and 12S rDNA) and nuclear (ITS1+5.8S+ITS2) genome regions. The sister relationship of Hirudo orientalis and H. medicinalis was revealed with a high posterior probability. A broad and patchy distribution with minor genetic differences was observed in populations of H. orientalis along the central and Middle Eastern parts of Asia. The known distribution range occurred in topographically heterogeneous landscapes around the Caspian Sea. The demographic analysis suggests the selection of the COI locus under unfavourable respiratory conditions, but population size expansion cannot be fully rejected. The genetic variation trend indicated northward dispersal. Higher haplotype diversity in the South Caspian region potentially suggests the area as a historical refugium for the species. The vast dispersal is assumed to occur after the Pleistocene glaciations via vertebrate hosts. Copyright © 2017 Elsevier Inc. All rights reserved.

Projected distributions and diversity of flightless ground beetles within the Australian Wet Tropics and their environmental correlates.

PubMed

Staunton, Kyran M; Robson, Simon K A; Burwell, Chris J; Reside, April E; Williams, Stephen E

2014-01-01

With the impending threat of climate change, greater understanding of patterns of species distributions and richness and the environmental factors driving them are required for effective conservation efforts. Species distribution models enable us to not only estimate geographic extents of species and subsequent patterns of species richness, but also generate hypotheses regarding environmental factors determining these spatial patterns. Projected changes in climate can then be used to predict future patterns of species distributions and richness. We created distribution models for most of the flightless ground beetles (Carabidae) within the Wet Tropics World Heritage Area of Australia, a major component of regionally endemic invertebrates. Forty-three species were modelled and the environmental correlates of these distributions and resultant patterns of species richness were examined. Flightless ground beetles generally inhabit upland areas characterised by stable, cool and wet environmental conditions. These distribution and richness patterns are best explained using the time-stability hypothesis as this group's primary habitat, upland rainforest, is considered to be the most stable regional habitat. Projected changes in distributions indicate that as upward shifts in distributions occur, species currently confined to lower and drier mountain ranges will be more vulnerable to climate change impacts than those restricted to the highest and wettest mountains. Distribution models under projected future climate change suggest that there will be reductions in range size, population size and species richness under all emission scenarios. Eighty-eight per cent of species modelled are predicted to decline in population size by over 80%, for the most severe emission scenario by the year 2080. These results suggest that flightless ground beetles are among the most vulnerable taxa to climate change impacts so far investigated in the Wet Tropics World Heritage Area. These findings have dramatic implications for all other flightless insect taxa and the future biodiversity of this region.

Projected Distributions and Diversity of Flightless Ground Beetles within the Australian Wet Tropics and Their Environmental Correlates

PubMed Central

Staunton, Kyran M.; Robson, Simon K. A.; Burwell, Chris J.; Reside, April E.; Williams, Stephen E.

2014-01-01

With the impending threat of climate change, greater understanding of patterns of species distributions and richness and the environmental factors driving them are required for effective conservation efforts. Species distribution models enable us to not only estimate geographic extents of species and subsequent patterns of species richness, but also generate hypotheses regarding environmental factors determining these spatial patterns. Projected changes in climate can then be used to predict future patterns of species distributions and richness. We created distribution models for most of the flightless ground beetles (Carabidae) within the Wet Tropics World Heritage Area of Australia, a major component of regionally endemic invertebrates. Forty-three species were modelled and the environmental correlates of these distributions and resultant patterns of species richness were examined. Flightless ground beetles generally inhabit upland areas characterised by stable, cool and wet environmental conditions. These distribution and richness patterns are best explained using the time-stability hypothesis as this group’s primary habitat, upland rainforest, is considered to be the most stable regional habitat. Projected changes in distributions indicate that as upward shifts in distributions occur, species currently confined to lower and drier mountain ranges will be more vulnerable to climate change impacts than those restricted to the highest and wettest mountains. Distribution models under projected future climate change suggest that there will be reductions in range size, population size and species richness under all emission scenarios. Eighty-eight per cent of species modelled are predicted to decline in population size by over 80%, for the most severe emission scenario by the year 2080. These results suggest that flightless ground beetles are among the most vulnerable taxa to climate change impacts so far investigated in the Wet Tropics World Heritage Area. These findings have dramatic implications for all other flightless insect taxa and the future biodiversity of this region. PMID:24586362

Costs of the multimicronutrient supplementation program in Chiclayo, Peru.

PubMed

Lechtig, Aarón; Gross, Rainer; Paulini, Javier; de Romaã, Daniel López

2006-01-01

There is little information on the cost parameters of weekly multimicronutrient supplementation programs. To assess the cost parameters and cost-effectiveness of a weekly multimicronutrient supplementation program in an urban population of Peru. Data from the Integrated Food Security Program (Programa Integrado de Seguridad Alimentaria [PISA]), which distributed capsules and foodlets to women and adolescent girls and to children under five, were extrapolated to a population of 100,000 inhabitants. The annual cost per community member was US$1.51. The cost-effectiveness ratio was US$0.12 per 1% of prevented anemia per community member. These costs are in the upper margin of iron supplementation alone. They will decrease notably when weekly multimicronutrient supplementation programs are integrated into health packages and participation by women increases. Focusing on micronutrient deficiencies would prevent these problems, and food-distribution programs would be effectively targeted to food-deficient populations.

Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

PubMed Central

Dey, Snigdhadip; Joshi, Amitabh

2013-01-01

Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546

What is too much variation? The null hypothesis in small-area analysis.

PubMed Central

Diehr, P; Cain, K; Connell, F; Volinn, E

1990-01-01

A small-area analysis (SAA) in health services research often calculates surgery rates for several small areas, compares the largest rate to the smallest, notes that the difference is large, and attempts to explain this discrepancy as a function of service availability, physician practice styles, or other factors. SAAs are often difficult to interpret because there is little theoretical basis for determining how much variation would be expected under the null hypothesis that all of the small areas have similar underlying surgery rates and that the observed variation is due to chance. We developed a computer program to simulate the distribution of several commonly used descriptive statistics under the null hypothesis, and used it to examine the variability in rates among the counties of the state of Washington. The expected variability when the null hypothesis is true is surprisingly large, and becomes worse for procedures with low incidence, for smaller populations, when there is variability among the populations of the counties, and when readmissions are possible. The characteristics of four descriptive statistics were studied and compared. None was uniformly good, but the chi-square statistic had better performance than the others. When we reanalyzed five journal articles that presented sufficient data, the results were usually statistically significant. Since SAA research today is tending to deal with low-incidence events, smaller populations, and measures where readmissions are possible, more research is needed on the distribution of small-area statistics under the null hypothesis. New standards are proposed for the presentation of SAA results. PMID:2312306

What is too much variation? The null hypothesis in small-area analysis.

PubMed

Diehr, P; Cain, K; Connell, F; Volinn, E

1990-02-01

A small-area analysis (SAA) in health services research often calculates surgery rates for several small areas, compares the largest rate to the smallest, notes that the difference is large, and attempts to explain this discrepancy as a function of service availability, physician practice styles, or other factors. SAAs are often difficult to interpret because there is little theoretical basis for determining how much variation would be expected under the null hypothesis that all of the small areas have similar underlying surgery rates and that the observed variation is due to chance. We developed a computer program to simulate the distribution of several commonly used descriptive statistics under the null hypothesis, and used it to examine the variability in rates among the counties of the state of Washington. The expected variability when the null hypothesis is true is surprisingly large, and becomes worse for procedures with low incidence, for smaller populations, when there is variability among the populations of the counties, and when readmissions are possible. The characteristics of four descriptive statistics were studied and compared. None was uniformly good, but the chi-square statistic had better performance than the others. When we reanalyzed five journal articles that presented sufficient data, the results were usually statistically significant. Since SAA research today is tending to deal with low-incidence events, smaller populations, and measures where readmissions are possible, more research is needed on the distribution of small-area statistics under the null hypothesis. New standards are proposed for the presentation of SAA results.

Molecular insights into seed dispersal mutualisms driving plant population recruitment

NASA Astrophysics Data System (ADS)

García, Cristina; Grivet, Delphine

2011-11-01

Most plant species require mutualistic interactions with animals to fulfil their demographic cycle. In this regard frugivory (i.e., the intake of fruits by animals) enhances natural regeneration by mobilizing a large amount of seeds from source trees to deposition sites across the landscape. By doing so, frugivores move propagules, and the genotypes they harbour creating the spatial, ecological, and genetic environment under which subsequent recruitment proceeds. Recruitment patterns can be envisioned as the result of two density- and distance-dependent processes: seed dispersal and seed/seedling survival (the Janzen-Connell model). Population genetic studies add another layer of complexity for understanding the fate of dispersed propagules: the genetic relatedness among neighbouring seeds within a seed clump, a major outcome of frugivore activity, modifies their chances of germinating and surviving. Yet, we virtually ignore how the spatial distribution of maternal progenies and recruitment patterns relate with each other in frugivore-generated seed rains. Here we focus on the critical role of frugivore-mediated seed dispersal in shaping the spatial distribution of maternal progenies in the seed rain. We first examine which genetic mechanisms underlying recruitment are influenced by the spatial distribution of maternal progenies. Next, we examine those studies depicting the spatial distribution of maternal progenies in a frugivore-generated seed rain. In doing so, we briefly review the most suitable analytical approaches applied to track the contribution of fruiting trees to the seed rain based on molecular data. Then we look more specifically at the role of distinct frugivore guilds in determining maternal genetic correlations and their expected consequences for recruitment patterns. Finally we posit some general conclusions and suggest future research directions that would provide a more comprehensive understanding of the ecological and evolutionary consequences of dispersal mutualisms in plant populations.

Projected continent-wide declines of the emperor penguin under climate change

NASA Astrophysics Data System (ADS)

Jenouvrier, Stéphanie; Holland, Marika; Stroeve, Julienne; Serreze, Mark; Barbraud, Christophe; Weimerskirch, Henri; Caswell, Hal

2014-08-01

Climate change has been projected to affect species distribution and future trends of local populations, but projections of global population trends are rare. We analyse global population trends of the emperor penguin (Aptenodytes forsteri), an iconic Antarctic top predator, under the influence of sea ice conditions projected by coupled climate models assessed in the Intergovernmental Panel on Climate Change (IPCC) effort. We project the dynamics of all 45 known emperor penguin colonies by forcing a sea-ice-dependent demographic model with local, colony-specific, sea ice conditions projected through to the end of the twenty-first century. Dynamics differ among colonies, but by 2100 all populations are projected to be declining. At least two-thirds are projected to have declined by >50% from their current size. The global population is projected to have declined by at least 19%. Because criteria to classify species by their extinction risk are based on the global population dynamics, global analyses are critical for conservation. We discuss uncertainties arising in such global projections and the problems of defining conservation criteria for species endangered by future climate change.

The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change.

PubMed

Valladares, Fernando; Matesanz, Silvia; Guilhaumon, François; Araújo, Miguel B; Balaguer, Luis; Benito-Garzón, Marta; Cornwell, Will; Gianoli, Ernesto; van Kleunen, Mark; Naya, Daniel E; Nicotra, Adrienne B; Poorter, Hendrik; Zavala, Miguel A

2014-11-01

Species are the unit of analysis in many global change and conservation biology studies; however, species are not uniform entities but are composed of different, sometimes locally adapted, populations differing in plasticity. We examined how intraspecific variation in thermal niches and phenotypic plasticity will affect species distributions in a warming climate. We first developed a conceptual model linking plasticity and niche breadth, providing five alternative intraspecific scenarios that are consistent with existing literature. Secondly, we used ecological niche-modeling techniques to quantify the impact of each intraspecific scenario on the distribution of a virtual species across a geographically realistic setting. Finally, we performed an analogous modeling exercise using real data on the climatic niches of different tree provenances. We show that when population differentiation is accounted for and dispersal is restricted, forecasts of species range shifts under climate change are even more pessimistic than those using the conventional assumption of homogeneously high plasticity across a species' range. Suitable population-level data are not available for most species so identifying general patterns of population differentiation could fill this gap. However, the literature review revealed contrasting patterns among species, urging greater levels of integration among empirical, modeling and theoretical research on intraspecific phenotypic variation. © 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

Impact of Arsenic Treatment Systems on Distribution System Water

EPA Science Inventory

Under the USEPA Arsenic Demonstration Program, 50 arsenic removal treatment systems were installed and their performance evaluated over a period of one to three years. The program was limited to small systems whose population served were less than 10,000. Ten of the systems were ...

[A general review of the discussion at the Beijing International Symposium on Population and Development].

PubMed

Ren, Y

1985-03-29

A general review of papers and discussions at the Beijing International Symposium on Population and Development held December 10-14, 1984 is presented. Discussions on population and development included China's population change 1949-1982, impacts of economic change on Tianjin's population, the population factor in economic development policy-making, Japanese population and development, recent population development in Hungary, population and economy, comprehensive long-term population development in Russia, fertility rate change factors in China, Shanghai's population change, and population and economic development in Mian County, Shaanxi Province. Fertility rate changes were discussed, including multinational borderline value assumptions, recent trends in life span fertility rate in China, fertility rate in Jiangsu Province, fertility rate change in Zhejiang Province, and sterilization in Yangjiaping, Thailand. Population and employment discussions included the economic impact of world population change, the 1984 International Population Conference, changes in economically productive population and employment strategy, employed/unemployed populations in Guangdong Province, and the economic composition of China's population. Urbanization discussions covered population and development methodological problems, population growth and economic development in the Pacific region, surplus rural population transfer and economic development in China, urbanization analysis, trends and urban population distribution problems, and Laioning Province population development. Issues in migration, population distribution, and regional population included migration and development of the Great Northwest, internal migration to Beijing, Chinese population growth and economic development by major region, and current population changes of Chinese Tibetans. Under social problems of population, discussions included women's status, development and population change, Shanghai's aging trend, analysis of the aged population, analysis of educational quality in Anhui Province, and the retirement system in Chinese villages.

Query Health: standards-based, cross-platform population health surveillance.

PubMed

Klann, Jeffrey G; Buck, Michael D; Brown, Jeffrey; Hadley, Marc; Elmore, Richard; Weber, Griffin M; Murphy, Shawn N

2014-01-01

Understanding population-level health trends is essential to effectively monitor and improve public health. The Office of the National Coordinator for Health Information Technology (ONC) Query Health initiative is a collaboration to develop a national architecture for distributed, population-level health queries across diverse clinical systems with disparate data models. Here we review Query Health activities, including a standards-based methodology, an open-source reference implementation, and three pilot projects. Query Health defined a standards-based approach for distributed population health queries, using an ontology based on the Quality Data Model and Consolidated Clinical Document Architecture, Health Quality Measures Format (HQMF) as the query language, the Query Envelope as the secure transport layer, and the Quality Reporting Document Architecture as the result language. We implemented this approach using Informatics for Integrating Biology and the Bedside (i2b2) and hQuery for data analytics and PopMedNet for access control, secure query distribution, and response. We deployed the reference implementation at three pilot sites: two public health departments (New York City and Massachusetts) and one pilot designed to support Food and Drug Administration post-market safety surveillance activities. The pilots were successful, although improved cross-platform data normalization is needed. This initiative resulted in a standards-based methodology for population health queries, a reference implementation, and revision of the HQMF standard. It also informed future directions regarding interoperability and data access for ONC's Data Access Framework initiative. Query Health was a test of the learning health system that supplied a functional methodology and reference implementation for distributed population health queries that has been validated at three sites. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Recent and historical distributions of Canada lynx in Maine and the Northeast

USGS Publications Warehouse

Hoving, C.L.; Joseph, R.A.; Krohn, W.B.

2003-01-01

The contiguous United States population of Canada lynx (Lynx canadensis Kerr) is listed as threatened under the federal Endangered Species Act. However, the historic distribution of lynx in the Northeast is poorly understood. We used museum records, bibliographic records, and interviews to reconstruct the past distribution of lynx in Maine, which is at the current southern limit of the species' distribution in the eastern United States. We found a total of 118 records, representing at least 509 lynx in Maine. Lynx were observed throughout Maine, 1833-1912, with the exception of coastal areas. After 1913, lynx were most common in the forests of western and northern Maine, and absent to rare along the coast, but had not returned to southern Maine by 1999. Thirty-nine kittens representing at least 21 litters were distributed throughout northern and western Maine, 1864-1999. Populations apparently fluctuated, and in some years 200-300 lynx were harvested in Maine. Prior to the 1900s, lynx were much more widely distributed in the Northeast, ranging from Pennsylvania north into Quebec. Because Canada lynx have had a long presence in northern New England, and at times were relatively common, this species merits serious consideration in conservation planning in this region.

Preparedness for pandemics: does variation among states affect the nation as a whole?

PubMed

Potter, Margaret A; Brown, Shawn T; Lee, Bruce Y; Grefenstette, John; Keane, Christopher R; Lin, Chyongchiou J; Quinn, Sandra C; Stebbins, Samuel; Sweeney, Patricia M; Burke, Donald S

2012-01-01

Since states' public health systems differ as to pandemic preparedness, this study explored whether such heterogeneity among states could affect the nation's overall influenza rate. The Centers for Disease Control and Prevention produced a uniform set of scores on a 100-point scale from its 2008 national evaluation of state preparedness to distribute materiel from the Strategic National Stockpile (SNS). This study used these SNS scores to represent each state's relative preparedness to distribute influenza vaccine in a timely manner and assumed that "optimal" vaccine distribution would reach at least 35% of the state's population within 4 weeks. The scores were used to determine the timing of vaccine distribution for each state: each 10-point decrement of score below 90 added an additional delay increment to the distribution time. A large-scale agent-based computational model simulated an influenza pandemic in the US population. In this synthetic population each individual or agent had an assigned household, age, workplace or school destination, daily commute, and domestic intercity air travel patterns. Simulations compared influenza case rates both nationally and at the state level under 3 scenarios: no vaccine distribution (baseline), optimal vaccine distribution in all states, and vaccine distribution time modified according to state-specific SNS score. Between optimal and SNS-modified scenarios, attack rates rose not only in low-scoring states but also in high-scoring states, demonstrating an interstate spread of infections. Influenza rates were sensitive to variation of the SNS-modified scenario (delay increments of 1 day versus 5 days), but the interstate effect remained. The effectiveness of a response activity such as vaccine distribution could benefit from national standards and preparedness funding allocated in part to minimize interstate disparities.

Simulating the Distribution of Individual Livestock Farms and Their Populations in the United States: An Example Using Domestic Swine (Sus scrofa domesticus) Farms

PubMed Central

Garza, Sarah J.; Miller, Ryan S.

2015-01-01

Livestock distribution in the United States (U.S.) can only be mapped at a county-level or worse resolution. We developed a spatial microsimulation model called the Farm Location and Agricultural Production Simulator (FLAPS) that simulated the distribution and populations of individual livestock farms throughout the conterminous U.S. Using domestic pigs (Sus scrofa domesticus) as an example species, we customized iterative proportional-fitting algorithms for the hierarchical structure of the U.S. Census of Agriculture and imputed unpublished state- or county-level livestock population totals that were redacted to ensure confidentiality. We used a weighted sampling design to collect data on the presence and absence of farms and used them to develop a national-scale distribution model that predicted the distribution of individual farms at a 100 m resolution. We implemented microsimulation algorithms that simulated the populations and locations of individual farms using output from our imputed Census of Agriculture dataset and distribution model. Approximately 19% of county-level pig population totals were unpublished in the 2012 Census of Agriculture and needed to be imputed. Using aerial photography, we confirmed the presence or absence of livestock farms at 10,238 locations and found livestock farms were correlated with open areas, cropland, and roads, and also areas with cooler temperatures and gentler topography. The distribution of swine farms was highly variable, but cross-validation of our distribution model produced an area under the receiver-operating characteristics curve value of 0.78, which indicated good predictive performance. Verification analyses showed FLAPS accurately imputed and simulated Census of Agriculture data based on absolute percent difference values of < 0.01% at the state-to-national scale, 3.26% for the county-to-state scale, and 0.03% for the individual farm-to-county scale. Our output data have many applications for risk management of agricultural systems including epidemiological studies, food safety, biosecurity issues, emergency-response planning, and conflicts between livestock and other natural resources. PMID:26571497

Simulating the Distribution of Individual Livestock Farms and Their Populations in the United States: An Example Using Domestic Swine (Sus scrofa domesticus) Farms.

PubMed

Burdett, Christopher L; Kraus, Brian R; Garza, Sarah J; Miller, Ryan S; Bjork, Kathe E

2015-01-01

Livestock distribution in the United States (U.S.) can only be mapped at a county-level or worse resolution. We developed a spatial microsimulation model called the Farm Location and Agricultural Production Simulator (FLAPS) that simulated the distribution and populations of individual livestock farms throughout the conterminous U.S. Using domestic pigs (Sus scrofa domesticus) as an example species, we customized iterative proportional-fitting algorithms for the hierarchical structure of the U.S. Census of Agriculture and imputed unpublished state- or county-level livestock population totals that were redacted to ensure confidentiality. We used a weighted sampling design to collect data on the presence and absence of farms and used them to develop a national-scale distribution model that predicted the distribution of individual farms at a 100 m resolution. We implemented microsimulation algorithms that simulated the populations and locations of individual farms using output from our imputed Census of Agriculture dataset and distribution model. Approximately 19% of county-level pig population totals were unpublished in the 2012 Census of Agriculture and needed to be imputed. Using aerial photography, we confirmed the presence or absence of livestock farms at 10,238 locations and found livestock farms were correlated with open areas, cropland, and roads, and also areas with cooler temperatures and gentler topography. The distribution of swine farms was highly variable, but cross-validation of our distribution model produced an area under the receiver-operating characteristics curve value of 0.78, which indicated good predictive performance. Verification analyses showed FLAPS accurately imputed and simulated Census of Agriculture data based on absolute percent difference values of < 0.01% at the state-to-national scale, 3.26% for the county-to-state scale, and 0.03% for the individual farm-to-county scale. Our output data have many applications for risk management of agricultural systems including epidemiological studies, food safety, biosecurity issues, emergency-response planning, and conflicts between livestock and other natural resources.

Modeling responses of large-river fish populations to global climate change through downscaling and incorporation of predictive uncertainty

USGS Publications Warehouse

Wildhaber, Mark L.; Wikle, Christopher K.; Anderson, Christopher J.; Franz, Kristie J.; Moran, Edward H.; Dey, Rima; Mader, Helmut; Kraml, Julia

2012-01-01

Climate change operates over a broad range of spatial and temporal scales. Understanding its effects on ecosystems requires multi-scale models. For understanding effects on fish populations of riverine ecosystems, climate predicted by coarse-resolution Global Climate Models must be downscaled to Regional Climate Models to watersheds to river hydrology to population response. An additional challenge is quantifying sources of uncertainty given the highly nonlinear nature of interactions between climate variables and community level processes. We present a modeling approach for understanding and accomodating uncertainty by applying multi-scale climate models and a hierarchical Bayesian modeling framework to Midwest fish population dynamics and by linking models for system components together by formal rules of probability. The proposed hierarchical modeling approach will account for sources of uncertainty in forecasts of community or population response. The goal is to evaluate the potential distributional changes in an ecological system, given distributional changes implied by a series of linked climate and system models under various emissions/use scenarios. This understanding will aid evaluation of management options for coping with global climate change. In our initial analyses, we found that predicted pallid sturgeon population responses were dependent on the climate scenario considered.

Generalised joint hypermobility and neurodevelopmental traits in a non-clinical adult population

PubMed Central

Glans, Martin; Humble, Mats B.

2017-01-01

Background Generalised joint hypermobility (GJH) is reportedly overrepresented among clinical cases of attention deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD) and developmental coordination disorder (DCD). It is unknown if these associations are dimensional and, therefore, also relevant among non-clinical populations. Aims To investigate if GJH correlates with sub-syndromal neurodevelopmental symptoms in a normal population. Method Hakim-Grahame’s 5-part questionnaire (5PQ) on GJH, neuropsychiatric screening scales measuring ADHD and ASD traits, and a DCD-related question concerning clumsiness were distributed to a non-clinical, adult, Swedish population (n=1039). Results In total, 887 individuals met our entry criteria. We found no associations between GJH and sub-syndromal symptoms of ADHD, ASD or DCD. Conclusions Although GJH is overrepresented in clinical cases with neurodevelopmental disorders, such an association seems absent in a normal population. Thus, if GJH serves as a biomarker cutting across diagnostic boundaries, this association is presumably limited to clinical populations. Declaration of interest None. Copyright and usage © The Royal College of Psychiatrists 2017. This is an open access article distributed under the terms of the Creative Commons Non-Commercial, No Derivatives (CC BY-NC-ND) license. PMID:28959454

The usefulness of "corrected" body mass index vs. self-reported body mass index: comparing the population distributions, sensitivity, specificity, and predictive utility of three correction equations using Canadian population-based data.

PubMed

Dutton, Daniel J; McLaren, Lindsay

2014-05-06

National data on body mass index (BMI), computed from self-reported height and weight, is readily available for many populations including the Canadian population. Because self-reported weight is found to be systematically under-reported, it has been proposed that the bias in self-reported BMI can be corrected using equations derived from data sets which include both self-reported and measured height and weight. Such correction equations have been developed and adopted. We aim to evaluate the usefulness (i.e., distributional similarity; sensitivity and specificity; and predictive utility vis-à-vis disease outcomes) of existing and new correction equations in population-based research. The Canadian Community Health Surveys from 2005 and 2008 include both measured and self-reported values of height and weight, which allows for construction and evaluation of correction equations. We focused on adults age 18-65, and compared three correction equations (two correcting weight only, and one correcting BMI) against self-reported and measured BMI. We first compared population distributions of BMI. Second, we compared the sensitivity and specificity of self-reported BMI and corrected BMI against measured BMI. Third, we compared the self-reported and corrected BMI in terms of association with health outcomes using logistic regression. All corrections outperformed self-report when estimating the full BMI distribution; the weight-only correction outperformed the BMI-only correction for females in the 23-28 kg/m2 BMI range. In terms of sensitivity/specificity, when estimating obesity prevalence, corrected values of BMI (from any equation) were superior to self-report. In terms of modelling BMI-disease outcome associations, findings were mixed, with no correction proving consistently superior to self-report. If researchers are interested in modelling the full population distribution of BMI, or estimating the prevalence of obesity in a population, then a correction of any kind included in this study is recommended. If the researcher is interested in using BMI as a predictor variable for modelling disease, then both self-reported and corrected BMI result in biased estimates of association.

Lowland tapir (Tapirus terrestris) distribution, activity patterns and relative abundance in the Greater Madidi-Tambopata Landscape.

PubMed

Wallace, Robert; Ayala, Guido; Viscarra, Maria

2012-12-01

Lowland tapir distribution is described in northwestern Bolivia and southeastern Peru within the Greater Madidi-Tambopata Landscape, a priority Tapir Conservation Unit, using 1255 distribution points derived from camera trapping efforts, field research and interviews with park guards from 5 national protected areas and hunters from 19 local communities. A total of 392 independent camera trapping events from 14 camera trap surveys at 11 sites demonstrated the nocturnal and crepuscular activity patterns (86%) of the lowland tapir and provide 3 indices of relative abundance for spatial and temporal comparison. Capture rates for lowland tapirs were not significantly different between camera trapping stations placed on river beaches versus those placed in the forest. Lowland tapir capture rates were significantly higher in the national protected areas of the region versus indigenous territories and unprotected portions of the landscape. Capture rates through time suggested that lowland tapir populations are recovering within the Tuichi Valley, an area currently dedicated towards ecotourism activities, following the creation (1995) and subsequent implementation (1997) of the Madidi National Park in Bolivia. Based on our distributional data and published conservative estimates of population density, we calculated that this transboundary landscape holds an overall lowland tapir population of between 14 540 and 36 351 individuals, of which at least 24.3% are under protection from national and municipal parks. As such, the Greater Madidi-Tambopata Landscape should be considered a lowland tapir population stronghold and priority conservation efforts are discussed in order to maintain this population. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terai, Tsuyoshi; Takahashi, Jun; Itoh, Yoichi, E-mail: tsuyoshi.terai@nao.ac.jp

Main-belt asteroids have been continuously colliding with one another since they were formed. Their size distribution is primarily determined by the size dependence of asteroid strength against catastrophic impacts. The strength scaling law as a function of body size could depend on collision velocity, but the relationship remains unknown, especially under hypervelocity collisions comparable to 10 km s{sup –1}. We present a wide-field imaging survey at an ecliptic latitude of about 25° for investigating the size distribution of small main-belt asteroids that have highly inclined orbits. The analysis technique allowing for efficient asteroid detections and high-accuracy photometric measurements provides sufficientmore » sample data to estimate the size distribution of sub-kilometer asteroids with inclinations larger than 14°. The best-fit power-law slopes of the cumulative size distribution are 1.25 ± 0.03 in the diameter range of 0.6-1.0 km and 1.84 ± 0.27 in 1.0-3.0 km. We provide a simple size distribution model that takes into consideration the oscillations of the power-law slope due to the transition from the gravity-scaled regime to the strength-scaled regime. We find that the high-inclination population has a shallow slope of the primary components of the size distribution compared to the low-inclination populations. The asteroid population exposed to hypervelocity impacts undergoes collisional processes where large bodies have a higher disruptive strength and longer lifespan relative to tiny bodies than the ecliptic asteroids.« less

Obesity as malnutrition: the role of capitalism in the obesity global epidemic.

PubMed

Wells, Jonathan C K

2012-01-01

The global obesity epidemic remains poorly understood, partly because it has emerged alongside persisting under-nutrition in many populations. At an abstract level, obesity develops from exposure to the "obesogenic niche," comprising diverse factors predisposing to weight gain. This article first explores how susceptibility to the obesogenic niche is influenced by developmental and life-history experience. Human growth is sensitive to early-life ecological conditions, under the transducing effect of maternal phenotype. Such plasticity is associated with subsequent variability in body composition and metabolism, impacting susceptibility to the obesogenic niche, albeit with heterogeneity across populations. Both nutritional constraint and nutritional excess during early life are associated with variability in relevant molecular pathways. The article then considers the fundamental contribution of capitalist economics to population under-nutrition and over-nutrition. Historically, capitalism contributed to the under-nutrition of many populations through demand for cheap labor. As the limiting factor for economic growth switched to consumption, capitalism has increasingly driven consumer behavior inducing widespread over-nutrition. In populations undergoing nutritional transition, many individuals encounter both under- and over-nutrition within the life course, elevating both susceptibility and exposure to the obesogenic niche. The interactions between global economic forces and nutritional shifts are distributed across generations, and are strongly transduced by maternal effects. The structural connections between undernourished and overnourished worldwide and between under- and over-nutrition within individual life-courses highlight the central role of capitalist economics in the global obesity epidemic. Prevention policies targeting individual behavior have proved ineffective and economic policies are arguably the optimal target for intervention. Copyright © 2012 Wiley Periodicals, Inc.

Spatial Distribution of Cyanobacteria in Modern Stromatolites

NASA Technical Reports Server (NTRS)

Prufert-Bebout, Lee; Dacles-Mariani, Jennifer; Herbert, Alice; DeVincenzi, Donald (Technical Monitor)

2001-01-01

Living stromatolites consist of complex microbial communities with distinct distribution patterns for different microbial groups. The cyanobacterial populations of Highborne Cay Bahamas exemplify this phenomenon. Field observations reveal distinct distribution patterns for several of these cyanobacterial species. To date 10 different cyanobacterial cultures, including both filamentous and endolithic species, have been isolated from these stromatolites. We will present data on the growth and motility characteristics as well as on the nutritional requirements of these isolates. These data will then be correlated with the field observed distributions for these species. Lastly laboratory simulations of stromatolites grown under various conditions of irradiance, flow and cyanobacterial community composition will be presented. These experiments allow us to evaluate our predictions regarding controls on cyanobacterial distribution.

Reliability of Different Mark-Recapture Methods for Population Size Estimation Tested against Reference Population Sizes Constructed from Field Data

PubMed Central

Grimm, Annegret; Gruber, Bernd; Henle, Klaus

2014-01-01

Reliable estimates of population size are fundamental in many ecological studies and biodiversity conservation. Selecting appropriate methods to estimate abundance is often very difficult, especially if data are scarce. Most studies concerning the reliability of different estimators used simulation data based on assumptions about capture variability that do not necessarily reflect conditions in natural populations. Here, we used data from an intensively studied closed population of the arboreal gecko Gehyra variegata to construct reference population sizes for assessing twelve different population size estimators in terms of bias, precision, accuracy, and their 95%-confidence intervals. Two of the reference populations reflect natural biological entities, whereas the other reference populations reflect artificial subsets of the population. Since individual heterogeneity was assumed, we tested modifications of the Lincoln-Petersen estimator, a set of models in programs MARK and CARE-2, and a truncated geometric distribution. Ranking of methods was similar across criteria. Models accounting for individual heterogeneity performed best in all assessment criteria. For populations from heterogeneous habitats without obvious covariates explaining individual heterogeneity, we recommend using the moment estimator or the interpolated jackknife estimator (both implemented in CAPTURE/MARK). If data for capture frequencies are substantial, we recommend the sample coverage or the estimating equation (both models implemented in CARE-2). Depending on the distribution of catchabilities, our proposed multiple Lincoln-Petersen and a truncated geometric distribution obtained comparably good results. The former usually resulted in a minimum population size and the latter can be recommended when there is a long tail of low capture probabilities. Models with covariates and mixture models performed poorly. Our approach identified suitable methods and extended options to evaluate the performance of mark-recapture population size estimators under field conditions, which is essential for selecting an appropriate method and obtaining reliable results in ecology and conservation biology, and thus for sound management. PMID:24896260

Confronting species distribution model predictions with species functional traits.

PubMed

Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

2016-02-01

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

Role of genetics in adapting forests under climate change: lessons learned from common garden experiments in central Europe

NASA Astrophysics Data System (ADS)

Chakraborty, Debojyoti; Schueler, Silvio

2017-04-01

Adaptive management aiming at reducing vulnerability and enhancing the resilience of forested ecosystems is a key to preserving the potential of forests to provide multiple ecosystem services under climate change. Planting alternative or non native tree species adapted to future conditions and also utilizing the genetic variation within tree species has also been suggested as an important adaptive management strategy under climate change. Therefore, knowledge on suitable provenances/populations is a key issue. Provenance trial experiments, where several populations of a species are planted in a particular climate or throughout an appropriate climatic gradient offers a great opportunity to understand adaptive genetic variation within a tree species. These trials were primarily established, for identifying populations with desired growth and fitness characteristics. Due to the increasing interest in climate change, such trials were revisited to understand the relation between growth performance and climate and to recommend suitable populations for future conditions. Here we present the lessons learned from provenance trials of Norway spruce and Douglas -fir in central Europe. With data from provenance trials planted across a wide range of environmental conditions in central Europe we developed multivariate models, Universal Response Functions (URFs). The URFs predict growth performance as a function of climate of planting locations (i.e. environmental factors) and provenance/ population origin (i.e. genetic factors). The flexibility of the URFs as a decision making tool is remarkable. The model can be used as to identify suitable planting material for a give site, and vice versa and also as a species distribution model (SDM) with integrated genetic variation. Under current and climate change scenarios, the URFs were applied to predict populations with higher growth performance in central Europe and also as species distribution models for Douglas-fir (Pseudotsuga menziesii [Mirbel] Franco) and Norway spruce (Picea abies (L.) Karst). For both Douglas-fir and Norway spruce wide variation in growth performance were detected. Populations of Douglas-fir identified by the URFs to be optimum for central Europe current climate and climate change scenarios originate from western Cascades and coastal areas of British Columbia, Washington and Oregon. The current seed stands of Douglas-fir in North America, providing planting materials for Central Europe under the legal framework of the Organization for Economic Cooperation and Development (OECD) were found to be suitable for under future conditions. In case of Norway spruce provenances originating from warm and drier regions of south east Europe were found to be suitable for central Europe under future conditions. Even though calibrated with data from Central Europe, when applied as SDMs, the URFs predicted the observed occurrence of Douglas-fir in its native range in North America with reasonable accuracy compared to contemporary SDMs developed in North America. For both Douglas-fir and Norway spruce significant variation in habitat suitability was found depending on the planted population or seed source indicating the role of intraspecific variation in buffering effects of climate change.

THE SCHOOL SITE--ITS SELECTION, ANALYSIS, DEVELOPMENT AND MAINTENANCE.

ERIC Educational Resources Information Center

BRUNING, WALTER F.

SCHOOL ADMINISTRATORS AND COMMUNITY PLANNERS CAN AID THE SCHOOL SITE SELECTION PROCESS BY WORKING TOGETHER ON A COMMUNITY MASTER PLAN. MANY COMMUNITIES HAVE DEVELOPED SUCH A PLAN UNDER THE STATE AND FEDERALLY AIDED 701 PROGRAM. SOUND SITE SELECTION PRINCIPLES REQUIRE CONSIDERATION OF OTHER FACTORS THAN STUDENT POPULATION DISTRIBUTION. IDEALLY…

Colorado River cutthroat trout: a technical conservation assessment

Treesearch

Michael K. Young

2008-01-01

The Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus) was once distributed throughout the colder waters of the Colorado River basin above the Grand Canyon. About 8 percent of its historical range is occupied by unhybridized or ecologically significant populations. It has been petitioned for listing under the Endangered Species Act...

The impact of eliminating age inequalities in stage at diagnosis on breast cancer survival for older women.

PubMed

Rutherford, M J; Abel, G A; Greenberg, D C; Lambert, P C; Lyratzopoulos, G

2015-03-31

Older women with breast cancer have poorer relative survival outcomes, but whether achieving earlier stage at diagnosis would translate to substantial reductions in mortality is uncertain. We analysed data on East of England women with breast cancer (2006-2010) aged 70+ years. We estimated survival for different stage-deprivation-age group strata using both the observed and a hypothetical stage distribution (assuming that all women aged 75+ years acquired the stage distribution of those aged 70-74 years). We subsequently estimated deaths that could be postponed beyond 5 years from diagnosis if women aged 75+ years had the hypothetical stage distribution. We projected findings to the English population using appropriate age and socioeconomic group weights. For a typically sized annual cohort in the East of England, 27 deaths in women with breast cancer aged 75+ years can be postponed within 5 years from diagnosis if their stage distribution matched that of the women aged 70-74 years (4.8% of all 566 deaths within 5 years post diagnosis in this population). Under assumptions, we estimate that the respective number for England would be 280 deaths (5.0% of all deaths within 5 years post diagnosis in this population). The findings support ongoing development of targeted campaigns aimed at encouraging prompt presentation in older women.

The impact of individual-level heterogeneity on estimated infectious disease burden: a simulation study.

PubMed

McDonald, Scott A; Devleesschauwer, Brecht; Wallinga, Jacco

2016-12-08

Disease burden is not evenly distributed within a population; this uneven distribution can be due to individual heterogeneity in progression rates between disease stages. Composite measures of disease burden that are based on disease progression models, such as the disability-adjusted life year (DALY), are widely used to quantify the current and future burden of infectious diseases. Our goal was to investigate to what extent ignoring the presence of heterogeneity could bias DALY computation. Simulations using individual-based models for hypothetical infectious diseases with short and long natural histories were run assuming either "population-averaged" progression probabilities between disease stages, or progression probabilities that were influenced by an a priori defined individual-level frailty (i.e., heterogeneity in disease risk) distribution, and DALYs were calculated. Under the assumption of heterogeneity in transition rates and increasing frailty with age, the short natural history disease model predicted 14% fewer DALYs compared with the homogenous population assumption. Simulations of a long natural history disease indicated that assuming homogeneity in transition rates when heterogeneity was present could overestimate total DALYs, in the present case by 4% (95% quantile interval: 1-8%). The consequences of ignoring population heterogeneity should be considered when defining transition parameters for natural history models and when interpreting the resulting disease burden estimates.

Phylogeography of declining relict and lowland leopard frogs in the desert Southwest of North America

USGS Publications Warehouse

Olah-Hemmings, V.; Jaeger, J.R.; Sredl, M.J.; Schlaepfer, Martin A.; Jennings, R.D.; Drost, C.A.; Bradford, D.F.; Riddle, B.R.

2010-01-01

We investigated the phylogeography of the closely related relict leopard frog Rana onca (=Lithobates onca) and lowland leopard frog Rana yavapaiensis (=Lithobates yavapaiensis) – two declining anurans from the warm-desert regions of south-western North America. We used sequence data from mitochondrial DNA (mtDNA) to assess 276 individuals representing 30 sites from across current distributions. Our analysis supports a previously determined phylogenetic break between these taxa, and we found no admixing of R. onca and R. yavapaiensis haplotypes within our extensive sampling of sites. Our phylogeographic assessment, however, further divided R. yavapaiensis into two distinct mtDNA lineages, one representing populations across Arizona and northern Mexico and the other a newly discovered population within the western Grand Canyon, Arizona. Estimates of sequence evolution indicate a possible Early Pleistocene divergence of R. onca and R. yavapaiensis, followed by a Middle Pleistocene separation of the western Grand Canyon population of R. yavapaiensis from the main R. yavapaiensis clade. Phylogeographic and demographic analyses indicate population or range expansion for R. yavapaiensis within its core distribution that appears to predate the latest glacial maximum. Species distribution models under current and latest glacial climatic conditions suggest that R. onca and R. yavapaiensis may not have greatly shifted ranges.

Combined effects between temporal heterogeneity of water supply, nutrient level, and population density on biomass of four broadly distributed herbaceous species.

PubMed

Hagiwara, Yousuke; Kachi, Naoki; Suzuki, Jun-Ichirou

2012-01-01

Temporal heterogeneity of water supply affects grassland community productivity and it can interact with nutrient level and intraspecific competition. To understand community responses, the responses of individual species to water heterogeneity must be evaluated while considering the interactions of this heterogeneity with nutrient levels and population density. We compared responses of four herbaceous species grown in monocultures to various combinations of water heterogeneity, nutrient level, and population density: two grasses (Cynodon dactylon and Lolium perenne), a forb (Artemisia princeps), and a legume (Trifolium repens). Treatment effects on shoot and root biomass were analyzed. In all four species, shoot biomass was larger under homogeneous than under heterogeneous water supply. Shoot responses of L. perenne tended to be greater at high nutrient levels. Although root biomass was also larger under homogeneous water supply, effects of water heterogeneity on root biomass were not significant in the grasses. Trifolium repens showed marked root responses, particularly at high population density. Although greater shoot and root growth under homogeneous water supply appears to be a general trend among herbaceous species, our results suggested differences among species could be found in the degree of response to water heterogeneity and its interactions with nutrient level and intraspecific competition.

Spatially-Explicit Simulation Modeling of Ecological Response to Climate Change: Methodological Considerations in Predicting Shifting Population Dynamics of Infectious Disease Vectors.

PubMed

Dhingra, Radhika; Jimenez, Violeta; Chang, Howard H; Gambhir, Manoj; Fu, Joshua S; Liu, Yang; Remais, Justin V

2013-09-01

Poikilothermic disease vectors can respond to altered climates through spatial changes in both population size and phenology. Quantitative descriptors to characterize, analyze and visualize these dynamic responses are lacking, particularly across large spatial domains. In order to demonstrate the value of a spatially explicit, dynamic modeling approach, we assessed spatial changes in the population dynamics of Ixodes scapularis , the Lyme disease vector, using a temperature-forced population model simulated across a grid of 4 × 4 km cells covering the eastern United States, using both modeled (Weather Research and Forecasting (WRF) 3.2.1) baseline/current (2001-2004) and projected (Representative Concentration Pathway (RCP) 4.5 and RCP 8.5; 2057-2059) climate data. Ten dynamic population features (DPFs) were derived from simulated populations and analyzed spatially to characterize the regional population response to current and future climate across the domain. Each DPF under the current climate was assessed for its ability to discriminate observed Lyme disease risk and known vector presence/absence, using data from the US Centers for Disease Control and Prevention. Peak vector population and month of peak vector population were the DPFs that performed best as predictors of current Lyme disease risk. When examined under baseline and projected climate scenarios, the spatial and temporal distributions of DPFs shift and the seasonal cycle of key questing life stages is compressed under some scenarios. Our results demonstrate the utility of spatial characterization, analysis and visualization of dynamic population responses-including altered phenology-of disease vectors to altered climate.

Spatially-Explicit Simulation Modeling of Ecological Response to Climate Change: Methodological Considerations in Predicting Shifting Population Dynamics of Infectious Disease Vectors

PubMed Central

Dhingra, Radhika; Jimenez, Violeta; Chang, Howard H.; Gambhir, Manoj; Fu, Joshua S.; Liu, Yang; Remais, Justin V.

2014-01-01

Poikilothermic disease vectors can respond to altered climates through spatial changes in both population size and phenology. Quantitative descriptors to characterize, analyze and visualize these dynamic responses are lacking, particularly across large spatial domains. In order to demonstrate the value of a spatially explicit, dynamic modeling approach, we assessed spatial changes in the population dynamics of Ixodes scapularis, the Lyme disease vector, using a temperature-forced population model simulated across a grid of 4 × 4 km cells covering the eastern United States, using both modeled (Weather Research and Forecasting (WRF) 3.2.1) baseline/current (2001–2004) and projected (Representative Concentration Pathway (RCP) 4.5 and RCP 8.5; 2057–2059) climate data. Ten dynamic population features (DPFs) were derived from simulated populations and analyzed spatially to characterize the regional population response to current and future climate across the domain. Each DPF under the current climate was assessed for its ability to discriminate observed Lyme disease risk and known vector presence/absence, using data from the US Centers for Disease Control and Prevention. Peak vector population and month of peak vector population were the DPFs that performed best as predictors of current Lyme disease risk. When examined under baseline and projected climate scenarios, the spatial and temporal distributions of DPFs shift and the seasonal cycle of key questing life stages is compressed under some scenarios. Our results demonstrate the utility of spatial characterization, analysis and visualization of dynamic population responses—including altered phenology—of disease vectors to altered climate. PMID:24772388

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.

PubMed

Matuszewski, Sebastian; Hildebrandt, Marcel E; Achaz, Guillaume; Jensen, Jeffrey D

2018-01-01

Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale-analogous to the Kingman coalescent-we find that the ancestral process can be rescaled to its time-homogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion. Copyright © 2018 by the Genetics Society of America.

The use of Bacillus thuringiensis kurstaki for managing gypsy moth populations under the Slow the Spread Program, 1996-2010, relative to the distributional range of threatened and endangered species

Treesearch

Laura M. Blackburn; Donna S. Leonard; Patrick C. Tobin

2011-01-01

The Slow the Spread Program operates along the expanding population front of the gypsy moth, from Minnesota to North Carolina. The primary objective of the program is to eliminate newly-founded colonies that form ahead of the leading edge to reduce the gypsy moth's rate of spread and delay the costs associated with infestation and outbreaks. Although the majority...

Efficient simulation and likelihood methods for non-neutral multi-allele models.

PubMed

Joyce, Paul; Genz, Alan; Buzbas, Erkan Ozge

2012-06-01

Throughout the 1980s, Simon Tavaré made numerous significant contributions to population genetics theory. As genetic data, in particular DNA sequence, became more readily available, a need to connect population-genetic models to data became the central issue. The seminal work of Griffiths and Tavaré (1994a , 1994b , 1994c) was among the first to develop a likelihood method to estimate the population-genetic parameters using full DNA sequences. Now, we are in the genomics era where methods need to scale-up to handle massive data sets, and Tavaré has led the way to new approaches. However, performing statistical inference under non-neutral models has proved elusive. In tribute to Simon Tavaré, we present an article in spirit of his work that provides a computationally tractable method for simulating and analyzing data under a class of non-neutral population-genetic models. Computational methods for approximating likelihood functions and generating samples under a class of allele-frequency based non-neutral parent-independent mutation models were proposed by Donnelly, Nordborg, and Joyce (DNJ) (Donnelly et al., 2001). DNJ (2001) simulated samples of allele frequencies from non-neutral models using neutral models as auxiliary distribution in a rejection algorithm. However, patterns of allele frequencies produced by neutral models are dissimilar to patterns of allele frequencies produced by non-neutral models, making the rejection method inefficient. For example, in some cases the methods in DNJ (2001) require 10(9) rejections before a sample from the non-neutral model is accepted. Our method simulates samples directly from the distribution of non-neutral models, making simulation methods a practical tool to study the behavior of the likelihood and to perform inference on the strength of selection.

Inferring responses to climate dynamics from historical demography in neotropical forest lizards

PubMed Central

Xue, Alexander T.; Brown, Jason L.; Alvarado-Serrano, Diego F.; Rodrigues, Miguel T.; Hickerson, Michael J.; Carnaval, Ana C.

2016-01-01

We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future. PMID:27432951

Inferring responses to climate dynamics from historical demography in neotropical forest lizards.

PubMed

Prates, Ivan; Xue, Alexander T; Brown, Jason L; Alvarado-Serrano, Diego F; Rodrigues, Miguel T; Hickerson, Michael J; Carnaval, Ana C

2016-07-19

We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.

Is a data set distributed as a power law? A test, with application to gamma-ray burst brightnesses

NASA Technical Reports Server (NTRS)

Wijers, Ralph A. M. J.; Lubin, Lori M.

1994-01-01

We present a method to determine whether an observed sample of data is drawn from a parent distribution that is pure power law. The method starts from a class of statistics which have zero expectation value under the null hypothesis, H(sub 0), that the distribution is a pure power law: F(x) varies as x(exp -alpha). We study one simple member of the class, named the `bending statistic' B, in detail. It is most effective for detection a type of deviation from a power law where the power-law slope varies slowly and monotonically as a function of x. Our estimator of B has a distribution under H(sub 0) that depends only on the size of the sample, not on the parameters of the parent population, and is approximated well by a normal distribution even for modest sample sizes. The bending statistic can therefore be used to test a set of numbers is drawn from any power-law parent population. Since many measurable quantities in astrophysics have distriibutions that are approximately power laws, and since deviations from the ideal power law often provide interesting information about the object of study (e.g., a `bend' or `break' in a luminosity function, a line in an X- or gamma-ray spectrum), we believe that a test of this type will be useful in many different contexts. In the present paper, we apply our test to various subsamples of gamma-ray burst brightness from the first-year Burst and Transient Source Experiment (BATSE) catalog and show that we can only marginally detect the expected steepening of the log (N (greater than C(sub max))) - log (C(sub max)) distribution.

Process-based modeling of species' responses to climate change - a proof of concept using western North American trees

NASA Astrophysics Data System (ADS)

Evans, M. E.; Merow, C.; Record, S.; Menlove, J.; Gray, A.; Cundiff, J.; McMahon, S.; Enquist, B. J.

2013-12-01

Current attempts to forecast how species' distributions will change in response to climate change suffer under a fundamental trade-off: between modeling many species superficially vs. few species in detail (between correlative vs. mechanistic models). The goals of this talk are two-fold: first, we present a Bayesian multilevel modeling framework, dynamic range modeling (DRM), for building process-based forecasts of many species' distributions at a time, designed to address the trade-off between detail and number of distribution forecasts. In contrast to 'species distribution modeling' or 'niche modeling', which uses only species' occurrence data and environmental data, DRMs draw upon demographic data, abundance data, trait data, occurrence data, and GIS layers of climate in a single framework to account for two processes known to influence range dynamics - demography and dispersal. The vision is to use extensive databases on plant demography, distributions, and traits - in the Botanical Information and Ecology Network, the Forest Inventory and Analysis database (FIA), and the International Tree Ring Data Bank - to develop DRMs for North American trees. Second, we present preliminary results from building the core submodel of a DRM - an integral projection model (IPM) - for a sample of dominant tree species in western North America. IPMs are used to infer demographic niches - i.e., the set of environmental conditions under which population growth rate is positive - and project population dynamics through time. Based on >550,000 data points derived from FIA for nine tree species in western North America, we show IPM-based models of their current and future distributions, and discuss how IPMs can be used to forecast future forest productivity, mortality patterns, and inform efforts at assisted migration.

Native fishes in the Truckee River: Are in-stream structures and patterns of population genetic structure related?

PubMed

Peacock, Mary M; Gustin, Mae S; Kirchoff, Veronica S; Robinson, Morgan L; Hekkala, Evon; Pizzarro-Barraza, Claudia; Loux, Tim

2016-09-01

In-stream structures are recognized as significant impediments to movement for freshwater fishes. Apex predators such as salmonids have been the focus of much research on the impacts of such barriers to population dynamics and population viability however much less research has focused on native fishes, where in-stream structures may have a greater impact on long term population viability of these smaller, less mobile species. Patterns of genetic structure on a riverscape can provide information on which structures represent real barriers to movement for fish species and under what specific flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Microsatellite loci were used to estimate total allelic diversity, effective population size and assess genetic population structure. Although there is spatial overlap among species within the river there are clear differences in species distributions within the watershed. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Our results suggest that restricted movement of fish species, as a result of in-stream barriers, can be mitigated by flow management. However, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate stream fishes into small subpopulations susceptible to both demographic losses and losses of genetic variation. Copyright © 2016 Elsevier B.V. All rights reserved.

Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations

PubMed Central

Vina, Marcelo A. Fernandez; Hollenbach, Jill A.; Lyke, Kirsten E.; Sztein, Marcelo B.; Maiers, Martin; Klitz, William; Cano, Pedro; Mack, Steven; Single, Richard; Brautbar, Chaim; Israel, Shosahna; Raimondi, Eduardo; Khoriaty, Evelyne; Inati, Adlette; Andreani, Marco; Testi, Manuela; Moraes, Maria Elisa; Thomson, Glenys; Stastny, Peter; Cao, Kai

2012-01-01

The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans. PMID:22312049

Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates.

PubMed

García-Verdugo, C; Sajeva, M; La Mantia, T; Harrouni, C; Msanda, F; Caujapé-Castells, J

2015-02-01

Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations. © 2015 John Wiley & Sons Ltd.

Evolutionary Dynamics and Diversity in Microbial Populations

NASA Astrophysics Data System (ADS)

Thompson, Joel; Fisher, Daniel

2013-03-01

Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

Interpreting the concordance statistic of a logistic regression model: relation to the variance and odds ratio of a continuous explanatory variable.

PubMed

Austin, Peter C; Steyerberg, Ewout W

2012-06-20

When outcomes are binary, the c-statistic (equivalent to the area under the Receiver Operating Characteristic curve) is a standard measure of the predictive accuracy of a logistic regression model. An analytical expression was derived under the assumption that a continuous explanatory variable follows a normal distribution in those with and without the condition. We then conducted an extensive set of Monte Carlo simulations to examine whether the expressions derived under the assumption of binormality allowed for accurate prediction of the empirical c-statistic when the explanatory variable followed a normal distribution in the combined sample of those with and without the condition. We also examine the accuracy of the predicted c-statistic when the explanatory variable followed a gamma, log-normal or uniform distribution in combined sample of those with and without the condition. Under the assumption of binormality with equality of variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the product of the standard deviation of the normal components (reflecting more heterogeneity) and the log-odds ratio (reflecting larger effects). Under the assumption of binormality with unequal variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the standardized difference of the explanatory variable in those with and without the condition. In our Monte Carlo simulations, we found that these expressions allowed for reasonably accurate prediction of the empirical c-statistic when the distribution of the explanatory variable was normal, gamma, log-normal, and uniform in the entire sample of those with and without the condition. The discriminative ability of a continuous explanatory variable cannot be judged by its odds ratio alone, but always needs to be considered in relation to the heterogeneity of the population.

Effects of habitat fragmentation on passerine birds breeding in Intermountain shrubsteppe

USGS Publications Warehouse

Knick, S.T.; Rotenberry, J.T.

2002-01-01

Habitat fragmentation and loss strongly influence the distribution and abundance of passerine birds breeding in Intermountain shrubsteppe. Wildfires, human activities, and change in vegetation communities often are synergistic in these systems and can result in radical conversion from shrubland to grasslands dominated by exotic annuals at large temporal and spatial scales from which recovery to native conditions is unlikely. As a result, populations of 5 of the 12 species in our review of Intermountain shrubsteppe birds are undergoing significant declines; 5 species are listed as at-risk or as candidates for protection in at least one state. The process by which fragmentation affects bird distributions in these habitats remains unknown because most research has emphasized the detection of population trends and patterns of habitat associations at relatively large spatial scales. Our research indicates that the distribution of shrubland-obligate species, such as Brewer's Sparrows (Spizella breweri), Sage Sparrows (Amphispiza belli), and Sage Thrashers (Oreoscoptes montanus), was highly sensitive to fragmentation of shrublands at spatial scales larger than individual home ranges. In contrast, the underlying mechanisms for both habitat change and bird population dynamics may operate independently of habitat boundaries. We propose alternative, but not necessarily exclusive, mechanisms to explain the relationship between habitat fragmentation and bird distribution and abundance. Fragmentation might influence productivity through differences in breeding density, nesting success, or predation. However, local and landscape variables were not significant determinants either of success, number fledged, or probability of predation or parasitism (although our tests had relatively low statistical power). Alternatively, relative absence of natal philopatry and redistribution by individuals among habitats following fledging or post-migration could account for the pattern of distribution and abundance. Thus, boundary dynamics may be important in determining the distribution of shrubland-obligate species but insignificant relative to the mechanisms causing the pattern of habitat and bird distribution. Because of the dichotomy in responses, Intermountain shrubsteppe systems present a unique challenge in understanding how landscape composition, configuration, and change influence bird population dynamics.

Adam Smith on population.

PubMed

Spengler, J J

1970-11-01

Abstract Adam Smith dealt with questions of population mainly in his Wealth of Nations. His discussion falls roughly under five heads and reflects in considerable measure his image of the English economy. (1) A country's population capacity, given the average level of consumption, was conditioned by the stock of land, the skill with which it was cultivated, and the degree to which division of labour could be increased and thereby augment output for domestic use and sale in external markets. (2) Growth of population was essentially in response to growth of the demand for labour and served to increase division of labour. (3) The social mechanisms underlying elevation of the scale of living are touched upon, and in an optimistic spirit. (4) The distribution of a country's population responded to its progress in opulence, with the rate of this progress conditioned by the degree to which inappropriate (e.g. mercantilist) policies were avoided. (5) Smith dealt briefly with such matters as colonies, education, size of economy, environmental influences, and public policy, all of which he recognized as significant for the quantity and quality of a country's numbers.

[Geographic distribution of supportive care for disabled young people].

PubMed

Bourgarel, Sophie; Piteau-Delord, Monique

2013-01-01

To analyse the logic for the distribution of home care services for disabled children (SESSAD) in a context of under-equipment. Questionnaire-based survey of 75 units (82% of the region's SESSAD units) concerning patient transport. Equipment and transport mapping. Support units for disabled children are often set up in the housing facilities that contributed to their creation. These sites are sometimes situated a long way from densely populated regions, thereby generating unnecessary travel times and expenses. Chronic under-equipment makes these sites viable, as the various units are always full, despite their distance from the children for whom they provide support. Mapping illustrates the extensive recruitment zones overlapping several units managing similar patients. The major revision of accreditation of these units, planned for 2017, could lead to redefinition of geographical zones of accreditations. New unit opening procedures based on ARS calls for tenders may help to improve the geographical distribution of this supportive care.

Butterfly Species Richness and Diversity in the Trishna Wildlife Sanctuary in South Asia

PubMed Central

Majumder, Joydeb; Lodh, Rahul; Agarwala, B. K.

2013-01-01

Several wildlife sanctuaries in the world are home to the surviving populations of many endemic species. Trishna wildlife sanctuary in northeast India is protected by law, and is home to the last surviving populations of Asian bison (Bos gorus Smith), spectacle monkey (Trachypithecus phayrie Blyth), capped langur (Trachypithecus pileatus Blyth), slow loris (Nycticebus coucang Boddaert), wild cat (Felis chaus Schreber), and wild boars (Sus scrofa L.), among many other animals and plants. The sanctuary was explored for species richness and diversity of butterflies. A six-month-long study revealed the occurrence of 59 butterfly species that included 21 unique species and 9 species listed in the threatened category. The mixed moist deciduous mature forest of the sanctuary harbored greater species richness and species diversity (39 species under 31 genera) than other parts of the sanctuary, which is comprised of regenerated secondary mixed deciduous forest (37 species under 32 genera), degraded forests (32 species under 28 genera), and open grassland with patches of plantations and artificial lakes (24 species under 17 genera). The majority of these species showed a distribution range throughout the Indo-Malayan region and Australasia tropics, and eight species were distributed in the eastern parts of South Asia, including one species, Labadea martha (F.), which is distributed in the eastern Himalayas alone. Estimator Chao 2 provided the best-predicted value of species richness. The steep slope of the species accumulation curve suggested the occurrence of a large number of rare species, and a prolonged gentle slope suggested a higher species richness at a higher sample abundance. The species composition of vegetation-rich habitats showed high similarity in comparison to vegetation-poor habitats. PMID:24219624

Butterfly species richness and diversity in the Trishna Wildlife Sanctuary in South Asia.

PubMed

Majumder, Joydeb; Lodh, Rahul; Agarwala, B K

2013-01-01

Several wildlife sanctuaries in the world are home to the surviving populations of many endemic species. Trishna wildlife sanctuary in northeast India is protected by law, and is home to the last surviving populations of Asian bison (Bos gorus Smith), spectacle monkey (Trachypithecus phayrie Blyth), capped langur (Trachypithecus pileatus Blyth), slow loris (Nycticebus coucang Boddaert), wild cat (Felis chaus Schreber), and wild boars (Sus scrofa L.), among many other animals and plants. The sanctuary was explored for species richness and diversity of butterflies. A six-month-long study revealed the occurrence of 59 butterfly species that included 21 unique species and 9 species listed in the threatened category. The mixed moist deciduous mature forest of the sanctuary harbored greater species richness and species diversity (39 species under 31 genera) than other parts of the sanctuary, which is comprised of regenerated secondary mixed deciduous forest (37 species under 32 genera), degraded forests (32 species under 28 genera), and open grassland with patches of plantations and artificial lakes (24 species under 17 genera). The majority of these species showed a distribution range throughout the Indo-Malayan region and Australasia tropics, and eight species were distributed in the eastern parts of South Asia, including one species, Labadea martha (F.), which is distributed in the eastern Himalayas alone. Estimator Chao 2 provided the best-predicted value of species richness. The steep slope of the species accumulation curve suggested the occurrence of a large number of rare species, and a prolonged gentle slope suggested a higher species richness at a higher sample abundance. The species composition of vegetation-rich habitats showed high similarity in comparison to vegetation-poor habitats.

Population declines lead to replicate patterns of internal range structure at the tips of the distribution of the California red-legged frog (Rana draytonii)

USGS Publications Warehouse

Richmond, Jonathan Q.; Backlin, Adam R.; Tatarian, Patricia J.; Solvesky, Ben G.; Fisher, Robert N.

2014-01-01

Demographic declines and increased isolation of peripheral populations of the threatened California red-legged frog (Rana draytonii) have led to the formation of internal range boundaries at opposite ends of the species’ distribution. While the population genetics of the southern internal boundary has been studied in some detail, similar information is lacking for the northern part of the range. In this study, we used microsatellite and mtDNA data to examine the genetic structuring and diversity of some of the last remaining R. draytonii populations in the northern Sierra Nevada, which collectively form the northern external range boundary. We compared these data to coastal populations in the San Francisco Bay Area, where the species is notably more abundant and still exists throughout much of its historic range. We show that ‘external’ Sierra Nevada populations have lower genetic diversity and are more differentiated from one another than their ‘internal’ Bay Area counterparts. This same pattern was mirrored across the distribution in California, where Sierra Nevada and Bay Area populations had lower allelic variability compared to those previously studied in coastal southern California. This genetic signature of northward range expansion was mirrored in the phylogeography of mtDNA haplotypes; northern Sierra Nevada haplotypes showed greater similarity to haplotypes from the south Coast Ranges than to the more geographically proximate populations in the Bay Area. These data cast new light on the geographic origins of Sierra Nevada R. draytonii populations and highlight the importance of distinguishing the genetic effects of contemporary demographic declines from underlying signatures of historic range expansion when addressing the most immediate threats to population persistence. Because there is no evidence of contemporary gene flow between any of the Sierra Nevada R. draytonii populations, we suggest that management activities should focus on maintaining and creating additional ponds to support breeding within typical dispersal distances of occupied habitat.

Parabolic replicator dynamics and the principle of minimum Tsallis information gain

PubMed Central

2013-01-01

Background Non-linear, parabolic (sub-exponential) and hyperbolic (super-exponential) models of prebiological evolution of molecular replicators have been proposed and extensively studied. The parabolic models appear to be the most realistic approximations of real-life replicator systems due primarily to product inhibition. Unlike the more traditional exponential models, the distribution of individual frequencies in an evolving parabolic population is not described by the Maximum Entropy (MaxEnt) Principle in its traditional form, whereby the distribution with the maximum Shannon entropy is chosen among all the distributions that are possible under the given constraints. We sought to identify a more general form of the MaxEnt principle that would be applicable to parabolic growth. Results We consider a model of a population that reproduces according to the parabolic growth law and show that the frequencies of individuals in the population minimize the Tsallis relative entropy (non-additive information gain) at each time moment. Next, we consider a model of a parabolically growing population that maintains a constant total size and provide an “implicit” solution for this system. We show that in this case, the frequencies of the individuals in the population also minimize the Tsallis information gain at each moment of the ‘internal time” of the population. Conclusions The results of this analysis show that the general MaxEnt principle is the underlying law for the evolution of a broad class of replicator systems including not only exponential but also parabolic and hyperbolic systems. The choice of the appropriate entropy (information) function depends on the growth dynamics of a particular class of systems. The Tsallis entropy is non-additive for independent subsystems, i.e. the information on the subsystems is insufficient to describe the system as a whole. In the context of prebiotic evolution, this “non-reductionist” nature of parabolic replicator systems might reflect the importance of group selection and competition between ensembles of cooperating replicators. Reviewers This article was reviewed by Viswanadham Sridhara (nominated by Claus Wilke), Puushottam Dixit (nominated by Sergei Maslov), and Nick Grishin. For the complete reviews, see the Reviewers’ Reports section. PMID:23937956

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

PubMed

Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

2015-09-15

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Genetic structure characterization of Chileans reflects historical immigration patterns.

PubMed

Eyheramendy, Susana; Martinez, Felipe I; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M

2015-03-17

Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

Genetic structure characterization of Chileans reflects historical immigration patterns

PubMed Central

Eyheramendy, Susana; Martinez, Felipe I.; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M.

2015-01-01

Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. PMID:25778948

Success of Senegal's first nationwide distribution of long-lasting insecticide-treated nets to children under five - contribution toward universal coverage

PubMed Central

2011-01-01

Background In 2009, the first national long-lasting insecticide-treated net (LLIN) distribution campaign in Senegal resulted in the distribution of 2.2 million LLINs in two phases to children aged 6-59 months. Door-to-door teams visited all households to administer vitamin A and mebendazole, and to give a coupon to redeem later for an LLIN. Methods A nationwide community-based two-stage cluster survey was conducted, with clusters selected within regions by probability proportional to size sampling, followed by GPS-assisted mapping, simple random selection of households in each cluster, and administration of a questionnaire using personal digital assistants (PDAs). The questionnaire followed the Malaria Indicator Survey format, with rosters of household members and bed nets, and questions on campaign participation. Results There were 3,280 households in 112 clusters representing 33,993 people. Most (92.1%) guardians of eligible children had heard about the campaign, the primary sources being health workers (33.7%), neighbours (26.2%), and radio (22.0%). Of eligible children, 82.4% received mebendazole, 83.8% received vitamin A, and 75.4% received LLINs. Almost all (91.4%) LLINs received during the campaign remained in the household; of those not remaining, 74.4% had been given away and none were reported sold. At least one insecticide-treated net (ITN) was present in 82.3% of all households, 89.2% of households with a child < 5 years and 57.5% of households without a child < 5 years. Just over half (52.4%) of ITNs had been received during the campaign. Considering possible indicators of universal coverage, 39.8% of households owned at least one ITN per two people, 21.6% owned at least one ITN per sleeping space and 34.7% of the general population slept under an ITN the night before the survey. In addition, 45.6% of children < 5 years, and 49.2% of pregnant women had slept under an ITN. Conclusions The nationwide integrated LLIN distribution campaign allowed household ITN ownership of one or more ITNs to surpass the RBM target of 80% set for 2010, though additional distribution strategies are needed to reach populations missed by the targeted campaign and to reach the universal coverage targets of one ITN per sleeping space and 80% of the population using an ITN. PMID:21489278

Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health.

PubMed

Rasmussen, Karen; Thyrring, Jakob; Muscarella, Robert; Borchsenius, Finn

2017-01-01

Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species ( Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in 'high allergy risk' (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27-100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.

Allowable levels of take for the trade in Nearctic songbirds.

PubMed

Johnson, Fred A; Walters, Matthew A H; Boomer, G Scott

2012-06-01

The take of Nearctic songbirds for the caged-bird trade is an important cultural and economic activity in Mexico, but its sustainability has been questioned. We relied on the theta-logistic population model to explore options for setting allowable levels of take for 11 species of passerines that were subject to legal take in Mexico in 2010. Because estimates of population size necessary for making-periodic adjustments to levels of take are not routinely available, we examined the conditions under which a constant level of take might contribute to population depletion (i.e., a population below its level of maximum net productivity). The chance of depleting a population is highest when levels of take are based on population sizes that happen to be much lower or higher than the level of maximum net productivity, when environmental variation is relatively high and serially correlated, and when the interval between estimation of population size is relatively long (> or = 5 years). To estimate demographic rates of songbirds involved in the Mexican trade we relied on published information and allometric relationships to develop probability distributions for key rates, and then sampled from those distributions to characterize the uncertainty in potential levels of take. Estimates of the intrinsic rate of growth (r) were highly variable, but median estimates were consistent with those expected for relatively short-lived, highly fecund species. Allowing for the possibility of nonlinear density dependence generally resulted in allowable levels of take that were lower than would have been the case under an assumption of linearity. Levels of take authorized by the Mexican government in 2010 for the 11 species we examined were small in comparison to relatively conservative allowable levels of take (i.e., those intended to achieve 50% of maximum sustainable yield). However, the actual levels of take in Mexico are unknown and almost certainly exceed the authorized take. Also, the take of Nearctic songbirds in other Latin American and Caribbean countries ultimately must be considered in assessing population-level impacts.

Allowable levels of take for the trade in Nearctic songbirds

USGS Publications Warehouse

Johnson, Fred A.; Walters, Matthew A.H.; Boomer, G. Scott

2012-01-01

The take of Nearctic songbirds for the caged-bird trade is an important cultural and economic activity in Mexico, but its sustainability has been questioned. We relied on the theta-logistic population model to explore options for setting allowable levels of take for 11 species of passerines that were subject to legal take in Mexico in 2010. Because estimates of population size necessary for making periodic adjustments to levels of take are not routinely available, we examined the conditions under which a constant level of take might contribute to population depletion (i.e., a population below its level of maximum net productivity). The chance of depleting a population is highest when levels of take are based on population sizes that happen to be much lower or higher than the level of maximum net productivity, when environmental variation is relatively high and serially correlated, and when the interval between estimation of population size is relatively long (≥5 years). To estimate demographic rates of songbirds involved in the Mexican trade we relied on published information and allometric relationships to develop probability distributions for key rates, and then sampled from those distributions to characterize the uncertainty in potential levels of take. Estimates of the intrinsic rate of growth (r) were highly variable, but median estimates were consistent with those expected for relatively short-lived, highly fecund species. Allowing for the possibility of nonlinear density dependence generally resulted in allowable levels of take that were lower than would have been the case under an assumption of linearity. Levels of take authorized by the Mexican government in 2010 for the 11 species we examined were small in comparison to relatively conservative allowable levels of take (i.e., those intended to achieve 50% of maximum sustainable yield). However, the actual levels of take in Mexico are unknown and almost certainly exceed the authorized take. Also, the take of Nearctic songbirds in other Latin American and Caribbean countries ultimately must be considered in assessing population-level impacts.

Socio economic position in TB prevalence and access to services: results from a population prevalence survey and a facility-based survey in Bangladesh.

PubMed

Hossain, Shahed; Quaiyum, Mohammad Abdul; Zaman, Khalequ; Banu, Sayera; Husain, Mohammad Ashaque; Islam, Mohammad Akramul; Cooreman, Erwin; Borgdorff, Martien; Lönnroth, Knut; Salim, Abdul Hamid; van Leth, Frank

2012-01-01

In Bangladesh DOTS has been provided free of charge since 1993, yet information on access to TB services by different population group is not well documented. The objective of this study was to assess and compare the socio economic position (SEP) of actively detected cases from the community and the cases being routinely detected under National Tuberculosis Control Programme (NTP) in Bangladesh. SEP was assessed by validated asset item for each of the 21,427 households included in the national tuberculosis prevalence survey 2007-2009. A principal component analysis generated household scores and categorized in quartiles. The distribution of 33 actively identified cases was compared with the 240 NTP cases over the identical SEP quartiles to evaluate access to TB services by different groups of the population. The population prevalence of tuberculosis was 5 times higher in the lowest quartiles of population (95.4, 95% CI: 48.0-189.7) to highest quartile population (19.5, 95% CI: 6.9-55.0). Among the 33 cases detected during survey, 25 (75.8%) were from lower two quartiles, and the rest 8 (24.3%) were from upper two quartiles. Among TB cases detected passively under NTP, more than half of them 137 (57.1%) were from uppermost two quartiles, 98 (41%) from the second quartile, and 5 (2%) in the lowest quartile of the population. This distribution is not affected when adjusted for other factors or interactions among them. The findings indicate that despite availability free of charge, DOTS is not equally accessed by the poorer sections of the population. However, these figures should be interpreted with caution since there is a need for additional studies that assess in-depth poverty indicators and its determinants in relation to access of the TB services provided in Bangladesh.

Genetic diversity and geographic differentiation in the threatened species Dysosma pleiantha in China as revealed by ISSR analysis.

PubMed

Zong, Min; Liu, Hai-Long; Qiu, Ying-Xiong; Yang, Shu-Zhen; Zhao, Ming-Shui; Fu, Cheng-Xin

2008-04-01

Dysosma pleiantha, an important threatened medicinal plant species, is restricted in distribution to southeastern China. The species is capable of reproducing both sexually and asexually. In this study, inter-simple sequence repeat marker data were obtained and analyzed with respect to genetic variation and genetic structure. The extent of clonality, together with the clonal and sexual reproductive strategies, varied among sites, and the populations under harsh ecological conditions tended to have large clones with relatively low clonal diversity caused by vegetative reproduction. The ramets sharing the same genotype show a clumped distribution. Across all populations surveyed, average within-population diversity was remarkably low (e.g., 0.111 for Nei's gene diversity), with populations from the nature reserves maintaining relatively high amounts of genetic diversity. Among all populations, high genetic differentiation (AMOVA: Phi(ST) = 0.500; Nei's genetic diversity: G (ST) = 0.465, Bayesian analysis: Phi(B) = 0.436) was detected, together with an isolation-by-distance pattern. Low seedling recruitment due to inbreeding, restricted gene flow, and genetic drift are proposed as determinant factors responsible for the low genetic diversity and high genetic differentiation observed.

Environmental metabolomics reveal geographic variation in aerobic metabolism and metabolic substrates in Mongolian gerbils (Meriones unguiculatus).

PubMed

Shi, Yao-Long; Chi, Qing-Sheng; Liu, Wei; Fu, He-Ping; Wang, De-Hua

2015-06-01

Mongolian gerbils (Meriones unguiculatus) have a large-scale distribution in northern China. Geographic physiological variations which related to energy and water metabolism are critical to animals' local adaptation and distribution. However, the underlying biochemical mechanism of such variation and its role in adaptation remains largely unknown. We used GC-MS metabolomics approach to investigate the biochemical adaptation of Mongolian gerbils from xeric (desert), transition (desert steppe) and mesic (typical steppe) environments. Gerbils in desert population had lower resting metabolic rate (RMR) and total evaporative water loss (TEWL) than mesic population. Serum metabolomics revealed that concentrations of five tricarboxylic acid cycle intermediates (citrate, cis-aconitate, α-ketoglutarate, fumarate and malate) were lower in desert population than mesic population. Gastrocnemius metabolomics and citrate synthase activity analysis showed a lower concentration of citrate and lower citrate synthase activity in desert population. These findings suggest that desert dwelling gerbils decrease RMR and TEWL via down-regulation of aerobic respiration. Gastrocnemius metabolomics also revealed that there were higher concentrations of glucose and glycolytic intermediates, but lower concentrations of lipids, amino acids and urea in desert population than mesic population. This geographic variation in metabolic substrates may enhance metabolic water production per oxygen molecule for desert population while constraining aerobic respiration to reduce RMR and TEWL. Copyright © 2015 Elsevier Inc. All rights reserved.

Phonon Mapping in Flowing Equilibrium

NASA Astrophysics Data System (ADS)

Ruff, J. P. C.

2015-03-01

When a material conducts heat, a modification of the phonon population occurs. The equilibrium Bose-Einstein distribution is perturbed towards flowing-equilibrium, for which the distribution function is not analytically known. Here I argue that the altered phonon population can be efficiently mapped over broad regions of reciprocal space, via diffuse x-ray scattering or time-of-flight neutron scattering, while a thermal gradient is applied across a single crystal sample. When compared to traditional transport measurements, this technique offers a superior, information-rich new perspective on lattice thermal conductivity, wherein the band and momentum dependences of the phonon thermal current are directly resolved. The proposed method is benchmarked using x-ray thermal diffuse scattering measurements of single crystal diamond under transport conditions. CHESS is supported by the NSF & NIH/NIGMS via NSF Award DMR-1332208.

A population model for a long-lived, resprouting chaparral shrub: Adenostoma fasciculatum

USGS Publications Warehouse

Stohlgren, Thomas J.; Rundel, Philip W.

1986-01-01

Extensive stands of Adenostoma fasciculatum H.&A. (chamise) in the chaparral of California are periodically rejuvenated by fire. A population model based on size-specific demographic characteristics (thinning and fire-caused mortality) was developed to generate probable age distributions within size classes and survivorship curves for typical stands. The model was modified to assess the long term effects of different mortality rates on age distributions. Under observed mean mortality rates (28.7%), model output suggests some shrubs can survive more than 23 fires. A 10% increase in mortality rate by size class slightly shortened the survivorship curve, while a 10% decrease in mortality rate by size class greatly elongated the curve. This approach may be applicable to other long-lived plant species with complex life histories.

77 FR 12246 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-29

... under USFWS's now-discontinued program, are considered non-essential experimental populations. The black... daylight hours. Additional methodological detail is available in VanBlaricom, 1993 and VanBlaricom et al..., 1987). The non-breeding distribution extends from Baja California north to Alaska for males, and...

Serious games for elderly continuous monitoring.

PubMed

Lemus-Zúñiga, Lenin-G; Navarro-Pardo, Esperanza; Moret-Tatay, Carmen; Pocinho, Ricardo

2015-01-01

Information technology (IT) and serious games allow older population to remain independent for longer. Hence, when designing technology for this population, developmental changes, such as attention and/or perception, should be considered. For instance, a crucial developmental change has been related to cognitive speed in terms of reaction time (RT). However, this variable presents a skewed distribution that difficult data analysis. An alternative strategy is to characterize the data to an ex-Gaussian function. Furthermore, this procedure provides different parameters that have been related to underlying cognitive processes in the literature. Another issue to be considered is the optimal data recording, storing and processing. For that purpose mobile devices (smart phones and tablets) are a good option for targeting serious games where valuable information can be stored (time spent in the application, reaction time, frequency of use, and a long etcetera). The data stored inside the smartphones and tablets can be sent to a central computer (cloud storage) in order to store the data collected to not only fill the distribution of reaction times to mathematical functions, but also to estimate parameters which may reflect cognitive processes underlying language, aging, and decisional process.

Simultaneous population pharmacokinetic modelling of plasma and intracellular PBMC miltefosine concentrations in New World cutaneous leishmaniasis and exploration of exposure-response relationships.

PubMed

Kip, Anke E; Castro, María Del Mar; Gomez, Maria Adelaida; Cossio, Alexandra; Schellens, Jan H M; Beijnen, Jos H; Saravia, Nancy Gore; Dorlo, Thomas P C

2018-05-10

Leishmania parasites reside within macrophages and the direct target of antileishmanial drugs is therefore intracellular. We aimed to characterize the intracellular PBMC miltefosine kinetics by developing a population pharmacokinetic (PK) model simultaneously describing plasma and intracellular PBMC pharmacokinetics. Furthermore, we explored exposure-response relationships and simulated alternative dosing regimens. A population PK model was developed with NONMEM, based on 339 plasma and 194 PBMC miltefosine concentrations from Colombian cutaneous leishmaniasis patients [29 children (2-12 years old) and 22 adults] receiving 1.8-2.5 mg/kg/day miltefosine for 28 days. A three-compartment model with miltefosine distribution into an intracellular PBMC effect compartment best fitted the data. Intracellular PBMC distribution was described with an intracellular-to-plasma concentration ratio of 2.17 [relative standard error (RSE) 4.9%] and intracellular distribution rate constant of 1.23 day-1 (RSE 14%). In exploring exposure-response relationships, both plasma and intracellular model-based exposure estimates significantly influenced probability of cure. A proposed PK target for the area under the plasma concentration-time curve (day 0-28) of >535 mg·day/L corresponded to >95% probability of cure. In linear dosing simulations, 18.3% of children compared with 2.8% of adults failed to reach 535 mg·day/L. In children, this decreased to 1.8% after allometric dosing simulation. The developed population PK model described the rate and extent of miltefosine distribution from plasma into PBMCs. Miltefosine exposure was significantly related to probability of cure in this cutaneous leishmaniasis patient population. We propose an exploratory PK target, which should be validated in a larger cohort study.

Statistical genetics and evolution of quantitative traits

NASA Astrophysics Data System (ADS)

Neher, Richard A.; Shraiman, Boris I.

2011-10-01

The distribution and heritability of many traits depends on numerous loci in the genome. In general, the astronomical number of possible genotypes makes the system with large numbers of loci difficult to describe. Multilocus evolution, however, greatly simplifies in the limit of weak selection and frequent recombination. In this limit, populations rapidly reach quasilinkage equilibrium (QLE) in which the dynamics of the full genotype distribution, including correlations between alleles at different loci, can be parametrized by the allele frequencies. This review provides a simplified exposition of the concept and mathematics of QLE which is central to the statistical description of genotypes in sexual populations. Key results of quantitative genetics such as the generalized Fisher’s “fundamental theorem,” along with Wright’s adaptive landscape, are shown to emerge within QLE from the dynamics of the genotype distribution. This is followed by a discussion under what circumstances QLE is applicable, and what the breakdown of QLE implies for the population structure and the dynamics of selection. Understanding the fundamental aspects of multilocus evolution obtained through simplified models may be helpful in providing conceptual and computational tools to address the challenges arising in the studies of complex quantitative phenotypes of practical interest.

Direct measurement of the concentration of metastable ions produced from neutral gas particles using laser-induced fluorescence

NASA Astrophysics Data System (ADS)

Chu, Feng; Skiff, Fred; Berumen, Jorge; Mattingly, Sean; Hood, Ryan

2017-10-01

Extensive information can be obtained on wave-particle interactions and wave fields by direct measurement of perturbed ion distribution functions using laser-induced fluorescence (LIF). For practical purposes, LIF is frequently performed on metastables that are produced from neutral gas particles and existing ions in other electronic states. We numerically simulate the ion velocity distribution measurement and wave-detection process using a Lagrangian model for the LIF signal. The results show that under circumstances where the metastable ion population is coming directly from the ionization of neutrals (as opposed to the excitation of ground-state ions), the velocity distribution will only faithfully represent processes which act on the ion dynamics in a time shorter than the metastable lifetime. Therefore, it is important to know the ratio of metastable population coming from neutrals to that from existing ions to correct the LIF measurements of plasma ion temperature and electrostatic waves. In this paper, we experimentally investigate the ratio of these two populations by externally launching an ion acoustic wave and comparing the wave amplitudes that are measured with LIF and a Langmuir probe using a lock-in amplifier. DE-FG02-99ER54543.

Genetic diversity of lactase persistence in East African populations.

PubMed

Hassan, Hisham Y; van Erp, Anke; Jaeger, Martin; Tahir, Hanan; Oosting, Marije; Joosten, Leo A B; Netea, Mihai G

2016-01-04

The expression of lactase which digests lactose from milk in humans is generally lost after weaning, but selected mutations influencing the promoter of the lactase gene have spread into the human populations. This is considered a classical example of gene-culture co-evolution, and several studies suggested that the lactase gene has been under strong directional evolutionary selective pressure in the past 5000 to 10,000 years. In the present study we investigated the distribution of three gene variants leading to lactase persistence in 12 different East African populations as well as one European population. Our results show that with the exception of Copts and Nilotic populations who are fully lactose non-persistent, the majority of populations of East Africa show at least partly lactose persistence, with both ethnic and socio-economic aspects playing an important role in the distribution of genetic variants. In this study, the variants C/G-13907 and T/G-13915, which are the major variants among the nomadic Arabs in the Arabia and Beja of East Africa, showed remarkable frequencies in Sudanese populations, especially those of pastoralists, in line with the historical links and bidirectional migration of nomadic populations between Arabia and East Africa. The C/T-13910 variant, generally associated with European populations is uniquely present among the Fulani. These data indicate that a combination of socio-economic, ethnic and evolutionary factors converged to shape the genetic structure of lactase persistence in East African populations.

Field-based random sampling without a sampling frame: control selection for a case-control study in rural Africa.

PubMed

Crampin, A C; Mwinuka, V; Malema, S S; Glynn, J R; Fine, P E

2001-01-01

Selection bias, particularly of controls, is common in case-control studies and may materially affect the results. Methods of control selection should be tailored both for the risk factors and disease under investigation and for the population being studied. We present here a control selection method devised for a case-control study of tuberculosis in rural Africa (Karonga, northern Malawi) that selects an age/sex frequency-matched random sample of the population, with a geographical distribution in proportion to the population density. We also present an audit of the selection process, and discuss the potential of this method in other settings.

Finite-size effects and switching times for Moran process with mutation.

PubMed

DeVille, Lee; Galiardi, Meghan

2017-04-01

We consider the Moran process with two populations competing under an iterated Prisoner's Dilemma in the presence of mutation, and concentrate on the case where there are multiple evolutionarily stable strategies. We perform a complete bifurcation analysis of the deterministic system which arises in the infinite population size. We also study the Master equation and obtain asymptotics for the invariant distribution and metastable switching times for the stochastic process in the case of large but finite population. We also show that the stochastic system has asymmetries in the form of a skew for parameter values where the deterministic limit is symmetric.

Ectoparasites of murids in peninsular Malaysia and their associated diseases.

PubMed

Mohd Zain, Siti Nursheena; Amdan, Syed Arnez Syed Khalil; Braima, Kamil A; Abdul-Aziz, Noraishah M; Wilson, John-James; Sithambaran, Paramesvaran; Jeffery, John

2015-04-29

A considerable number of rat-borne ectoparasite studies have been conducted since the early 1930s in the Malayan Peninsula (now known as peninsular Malaysia). The majority of studies were field surveys and collections of specimens across the region, and were conducted primarily to catalogue the ectoparasite host distribution and discover novel species. This has generated a signification amount of information, particularly on the diversity and host distribution; other aspects such as morphology, host distribution and medical significance have also been investigated. Amongst the four main groups (mites, fleas, ticks, lice), rat-borne mites have received the most attention with a particular emphasis on chiggers, due to their medical importance. More recent studies have examined the distribution of ectoparasites in rats from different habitat type simplicating a high prevalence of zoonotic species infesting rat populations. Despite being capable of transmitting dangerous pathogens to human, the health risks of rat-borne ectoparasites appear to be small with no serious outbreaks of diseases recorded. Although an extensive number of works have been published, there remain gaps in knowledge that need to be addressed, such as, the distribution of under studied ectoparasite groups (listrophorids and myobiids), determining factors influencing infestation, and understanding changes to the population distribution over time.

Human X-chromosome inactivation pattern distributions fit a model of genetically influenced choice better than models of completely random choice

PubMed Central

Renault, Nisa K E; Pritchett, Sonja M; Howell, Robin E; Greer, Wenda L; Sapienza, Carmen; Ørstavik, Karen Helene; Hamilton, David C

2013-01-01

In eutherian mammals, one X-chromosome in every XX somatic cell is transcriptionally silenced through the process of X-chromosome inactivation (XCI). Females are thus functional mosaics, where some cells express genes from the paternal X, and the others from the maternal X. The relative abundance of the two cell populations (X-inactivation pattern, XIP) can have significant medical implications for some females. In mice, the ‘choice' of which X to inactivate, maternal or paternal, in each cell of the early embryo is genetically influenced. In humans, the timing of XCI choice and whether choice occurs completely randomly or under a genetic influence is debated. Here, we explore these questions by analysing the distribution of XIPs in large populations of normal females. Models were generated to predict XIP distributions resulting from completely random or genetically influenced choice. Each model describes the discrete primary distribution at the onset of XCI, and the continuous secondary distribution accounting for changes to the XIP as a result of development and ageing. Statistical methods are used to compare models with empirical data from Danish and Utah populations. A rigorous data treatment strategy maximises information content and allows for unbiased use of unphased XIP data. The Anderson–Darling goodness-of-fit statistics and likelihood ratio tests indicate that a model of genetically influenced XCI choice better fits the empirical data than models of completely random choice. PMID:23652377

Implications of recurrent disturbance for genetic diversity.

PubMed

Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

2016-02-01

Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

A Longitudinal Analysis of Mosquito Net Ownership and Use in an Indigenous Batwa Population after a Targeted Distribution.

PubMed

Clark, Sierra; Berrang-Ford, Lea; Lwasa, Shuaib; Namanya, Didacus; Twesigomwe, Sabastian; Kulkarni, Manisha

2016-01-01

Major efforts for malaria prevention programs have gone into scaling up ownership and use of insecticidal mosquito nets, particularly in sub-Saharan Africa where the malaria burden is high. Socioeconomic inequities in access to long lasting insecticidal nets (LLINs) are reduced with free distributions of nets. However, the relationship between social factors and retention of nets after a free distribution has been less studied, particularly using a longitudinal approach. Our research aimed to estimate the ownership and use of LLINs, and examine the determinants of LLIN retention, within an Indigenous Batwa population after a free LLIN distribution. Two LLINs were given free of charge to each Batwa household in Kanungu District, Uganda in November 2012. Surveyors collected data on LLIN ownership and use through six cross-sectional surveys pre- and post-distribution. Household retention, within household access, and individual use of LLINs were assessed over an 18-month period. Socioeconomic determinants of household retention of LLINs post-distribution were modelled longitudinally using logistic regression with random effects. Direct house-to-house distribution of free LLINs did not result in sustainable increases in the ownership and use of LLINs. Three months post-distribution, only 73% of households owned at least one LLIN and this period also saw the greatest reduction in ownership compared to other study periods. Eighteen-months post distribution, only a third of households still owned a LLIN. Self-reported age-specific use of LLINs was generally higher for children under five, declined for children aged 6-12, and was highest for older adults aged over 35. In the model, household wealth was a significant predictor of LLIN retention, controlling for time and other variables. This research highlights on-going socioeconomic inequities in access to malaria prevention measures among the Batwa in southwestern Uganda, even after free distribution of LLINs, and provides critical information to inform local malaria programs on possible intervention entry-points to increase access and use among this marginalized population.

Coalescence of repelling colloidal droplets: a route to monodisperse populations.

PubMed

Roger, Kevin; Botet, Robert; Cabane, Bernard

2013-05-14

Populations of droplets or particles dispersed in a liquid may evolve through Brownian collisions, aggregation, and coalescence. We have found a set of conditions under which these populations evolve spontaneously toward a narrow size distribution. The experimental system consists of poly(methyl methacrylate) (PMMA) nanodroplets dispersed in a solvent (acetone) + nonsolvent (water) mixture. These droplets carry electrical charges, located on the ionic end groups of the macromolecules. We used time-resolved small angle X-ray scattering to determine their size distribution. We find that the droplets grow through coalescence events: the average radius (R) increases logarithmically with elapsed time while the relative width σR/(R) of the distribution decreases as the inverse square root of (R). We interpret this evolution as resulting from coalescence events that are hindered by ionic repulsions between droplets. We generalize this evolution through a simulation of the Smoluchowski kinetic equation, with a kernel that takes into account the interactions between droplets. In the case of vanishing or attractive interactions, all droplet encounters lead to coalescence. The corresponding kernel leads to the well-known "self-preserving" particle distribution of the coalescence process, where σR/(R) increases to a plateau value. However, for droplets that interact through long-range ionic repulsions, "large + small" droplet encounters are more successful at coalescence than "large + large" encounters. We show that the corresponding kernel leads to a particular scaling of the droplet-size distribution-known as the "second-scaling law" in the theory of critical phenomena, where σR/(R) decreases as 1/√(R) and becomes independent of the initial distribution. We argue that this scaling explains the narrow size distributions of colloidal dispersions that have been synthesized through aggregation processes.

Detecting hierarchical levels of connectivity in a population of Acacia tortilis at the northern edge of the species' global distribution: Combining classical population genetics and network analyses.

PubMed

Rodger, Yael S; Greenbaum, Gili; Silver, Micha; Bar-David, Shirli; Winters, Gidon

2018-01-01

Genetic diversity and structure of populations at the edge of the species' spatial distribution are important for potential adaptation to environmental changes and consequently, for the long-term survival of the species. Here, we combined classical population genetic methods with newly developed network analyses to gain complementary insights into the genetic structure and diversity of Acacia tortilis, a keystone desert tree, at the northern edge of its global distribution, where the population is under threat from climatic, ecological, and anthropogenic changes. We sampled A. tortilis from 14 sites along the Dead Sea region and the Arava Valley in Israel and in Jordan. In addition, we obtained samples from Egypt and Sudan, the hypothesized origin of the species. Samples from all sites were genotyped using six polymorphic microsatellite loci.Our results indicate a significant genetic structure in A. tortilis along the Arava Valley. This was detected at different hierarchical levels-from the basic unit of the subpopulation, corresponding to groups of trees within ephemeral rivers (wadis), to groups of subpopulations (communities) that are genetically more connected relative to others. The latter structure mostly corresponds to the partition of the major drainage basins in the area. Network analyses, combined with classical methods, allowed for the identification of key A. tortilis subpopulations in this region, characterized by their relatively high level of genetic diversity and centrality in maintaining gene flow in the population. Characterizing such key subpopulations may enable conservation managers to focus their efforts on certain subpopulations that might be particularly important for the population's long-term persistence, thus contributing to species conservation within its peripheral range.

Approximate Bayesian estimation of extinction rate in the Finnish Daphnia magna metapopulation.

PubMed

Robinson, John D; Hall, David W; Wares, John P

2013-05-01

Approximate Bayesian computation (ABC) is useful for parameterizing complex models in population genetics. In this study, ABC was applied to simultaneously estimate parameter values for a model of metapopulation coalescence and test two alternatives to a strict metapopulation model in the well-studied network of Daphnia magna populations in Finland. The models shared four free parameters: the subpopulation genetic diversity (θS), the rate of gene flow among patches (4Nm), the founding population size (N0) and the metapopulation extinction rate (e) but differed in the distribution of extinction rates across habitat patches in the system. The three models had either a constant extinction rate in all populations (strict metapopulation), one population that was protected from local extinction (i.e. a persistent source), or habitat-specific extinction rates drawn from a distribution with specified mean and variance. Our model selection analysis favoured the model including a persistent source population over the two alternative models. Of the closest 750,000 data sets in Euclidean space, 78% were simulated under the persistent source model (estimated posterior probability = 0.769). This fraction increased to more than 85% when only the closest 150,000 data sets were considered (estimated posterior probability = 0.774). Approximate Bayesian computation was then used to estimate parameter values that might produce the observed set of summary statistics. Our analysis provided posterior distributions for e that included the point estimate obtained from previous data from the Finnish D. magna metapopulation. Our results support the use of ABC and population genetic data for testing the strict metapopulation model and parameterizing complex models of demography. © 2013 Blackwell Publishing Ltd.

Efficiency or equity? Simulating the impact of high-risk and population intervention strategies for the prevention of disease.

PubMed

Platt, Jonathan M; Keyes, Katherine M; Galea, Sandro

2017-12-01

Maximizing both efficiency and equity are core considerations for population health. These considerations can result in tension in population health science as we seek to improve overall population health while achieving equitable health distributions within populations. Limited work has explored empirically the consequences of different population health intervention strategies on the burden of disease and on within- and between-group differences in disease. To address this gap, we compared the impact of four simulated interventions using data from the National Health and Nutrition Examination Survey. In particular, we focus on assessing how population and high-risk primary prevention and population and high-risk secondary interventions efforts to reduce smoking behavior influence systolic blood pressure (SBP) and hypertension, and how such strategies influence inequalities in SBP by income. The greatest reductions in SBP mean and standard deviation resulted from the population secondary prevention. High-risk primary and secondary prevention and population secondary prevention programs all yielded substantial reductions in hypertension prevalence. The effect of population primary prevention did little to decrease population SBP mean and standard deviation, as well as hypertension prevalence. Both high-risk strategies had a larger impact in the low-income population, leading to the greatest narrowing the income-related gap in disease. The population prevention strategies had a larger impact in the high-income population. Population health approaches must consider the potential impact on both the whole population and also on those with different levels of risk for disease within a population, including those in under-represented or under-served groups.

Estimating population abundance and mapping distribution of wintering sea ducks in coastal waters of the mid-Atlantic

USGS Publications Warehouse

Koneff, M.D.; Royle, J. Andrew; Forsell, D.J.; Wortham, J.S.; Boomer, G.S.; Perry, M.C.

2005-01-01

Survey design for wintering scoters (Melanitta sp.) and other sea ducks that occur in offshore waters is challenging because these species have large ranges, are subject to distributional shifts among years and within a season, and can occur in aggregations. Interest in winter sea duck population abundance surveys has grown in recent years. This interest stems from concern over the population status of some sea ducks, limitations of extant breeding waterfowl survey programs in North America and logistical challenges and costs of conducting surveys in northern breeding regions, high winter area philopatry in some species and potential conservation implications, and increasing concern over offshore development and other threats to sea duck wintering habitats. The efficiency and practicality of statistically-rigorous monitoring strategies for mobile, aggregated wintering sea duck populations have not been sufficiently investigated. This study evaluated a 2-phase adaptive stratified strip transect sampling plan to estimate wintering population size of scoters, long-tailed ducks (Clangua hyemalis), and other sea ducks and provide information on distribution. The sampling plan results in an optimal allocation of a fixed sampling effort among offshore strata in the U.S. mid-Atlantic coast region. Phase I transect selection probabilities were based on historic distribution and abundance data, while Phase 2 selection probabilities were based on observations made during Phase 1 flights. Distance sampling methods were used to estimate detection rates. Environmental variables thought to affect detection rates were recorded during the survey and post-stratification and covariate modeling were investigated to reduce the effect of heterogeneity on detection estimation. We assessed cost-precision tradeoffs under a number of fixed-cost sampling scenarios using Monte Carlo simulation. We discuss advantages and limitations of this sampling design for estimating wintering sea duck abundance and mapping distribution and suggest improvements for future surveys.

An Analysis of Thaumarchaeota Populations from the Northern Gulf of Mexico

PubMed Central

Tolar, Bradley B.; King, Gary M.; Hollibaugh, James T.

2013-01-01

We sampled Thaumarchaeota populations in the northern Gulf of Mexico, including shelf waters under the Mississippi River outflow plume that are subject to recurrent hypoxia. Data from this study allowed us to: (1) test the hypothesis that Thaumarchaeota would be abundant in this region; (2) assess phylogenetic composition of these populations for comparison with other regions; (3) compare the efficacy of quantitative PCR (qPCR) based on primers for 16S rRNA genes (rrs) with primers for genes in the ammonia oxidation (amoA) and carbon fixation (accA, hcd) pathways; (4) compare distributions obtained by qPCR with the relative abundance of Thaumarchaeota rrs in pyrosequenced libraries; (5) compare Thaumarchaeota distributions with environmental variables to help us elucidate the factors responsible for the distributions; (6) compare the distribution of Thaumarchaeota with Nitrite-Oxidizing Bacteria (NOB) to gain insight into the coupling between ammonia and nitrite oxidation. We found up to 108 copies L−1 of Thaumarchaeota rrs in our samples (up to 40% of prokaryotes) by qPCR, with maximum abundance in slope waters at 200–800 m. Thaumarchaeota rrs were also abundant in pyrosequenced libraries and their relative abundance correlated well with values determined by qPCR (r2 = 0.82). Thaumarchaeota populations were strongly stratified by depth. Canonical correspondence analysis using a suite of environmental variables explained 92% of the variance in qPCR-estimated gene abundances. Thaumarchaeota rrs abundance was correlated with salinity and depth, while accA abundance correlated with fluorescence and pH. Correlations of Archaeal amoA abundance with environmental variables were primer-dependent, suggesting differential responses of sub-populations to environmental variables. Bacterial amoA was at the limit of qPCR detection in most samples. NOB and Euryarchaeota rrs were found in the pyrosequenced libraries; NOB distribution was correlated with that of Thaumarchaeota (r2 = 0.49). PMID:23577005

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.

Shifts in the climate space of temperate cyprinid fishes due to climate change are coupled with altered body sizes and growth rates.

PubMed

Ruiz-Navarro, Ana; Gillingham, Phillipa K; Britton, J Robert

2016-09-01

Predictions of species responses to climate change often focus on distribution shifts, although responses can also include shifts in body sizes and population demographics. Here, shifts in the distributional ranges ('climate space'), body sizes (as maximum theoretical body sizes, L∞) and growth rates (as rate at which L∞ is reached, K) were predicted for five fishes of the Cyprinidae family in a temperate region over eight climate change projections. Great Britain was the model area, and the model species were Rutilus rutilus, Leuciscus leuciscus, Squalius cephalus, Gobio gobio and Abramis brama. Ensemble models predicted that the species' climate spaces would shift in all modelled projections, with the most drastic changes occurring under high emissions; all range centroids shifted in a north-westerly direction. Predicted climate space expanded for R. rutilus and A. brama, contracted for S. cephalus, and for L. leuciscus and G. gobio, expanded under low-emission scenarios but contracted under high emissions, suggesting the presence of some climate-distribution thresholds. For R. rutilus, A. brama, S. cephalus and G. gobio, shifts in their climate space were coupled with predicted shifts to significantly smaller maximum body sizes and/or faster growth rates, aligning strongly to aspects of temperature-body size theory. These predicted shifts in L∞ and K had considerable consequences for size-at-age per species, suggesting substantial alterations in population age structures and abundances. Thus, when predicting climate change outcomes for species, outputs that couple shifts in climate space with altered body sizes and growth rates provide considerable insights into the population and community consequences, especially for species that cannot easily track their thermal niches. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Population Distribution Analyses Reveal a Hierarchy of Molecular Players Underlying Parallel Endocytic Pathways

PubMed Central

Gupta, Gagan D.; Howes, Mark T.; Chandran, Ruma; Das, Anupam; Menon, Sindhu; Parton, Robert G.; Sowdhamini, R.; Thattai, Mukund; Mayor, Satyajit

2014-01-01

Single-cell-resolved measurements reveal heterogeneous distributions of clathrin-dependent (CD) and -independent (CLIC/GEEC: CG) endocytic activity in Drosophila cell populations. dsRNA-mediated knockdown of core versus peripheral endocytic machinery induces strong changes in the mean, or subtle changes in the shapes of these distributions, respectively. By quantifying these subtle shape changes for 27 single-cell features which report on endocytic activity and cell morphology, we organize 1072 Drosophila genes into a tree-like hierarchy. We find that tree nodes contain gene sets enriched in functional classes and protein complexes, providing a portrait of core and peripheral control of CD and CG endocytosis. For 470 genes we obtain additional features from separate assays and classify them into early- or late-acting genes of the endocytic pathways. Detailed analyses of specific genes at intermediate levels of the tree suggest that Vacuolar ATPase and lysosomal genes involved in vacuolar biogenesis play an evolutionarily conserved role in CG endocytosis. PMID:24971745

Sintering of polydisperse viscous droplets

NASA Astrophysics Data System (ADS)

Wadsworth, Fabian B.; Vasseur, Jérémie; Llewellin, Edward W.; Dingwell, Donald B.

2017-03-01

Sintering—or coalescence—of compacts of viscous droplets is driven by the interfacial tension between the droplets and the interstitial gas phase. The process, which occurs in a range of industrial and natural settings, such as the manufacture of ceramics and the welding of volcanic ash, causes the compact to densify, to become stronger, and to become less permeable. We investigate the role of droplet polydispersivity in sintering dynamics by conducting experiments in which populations of glass spheres with different size distributions are heated to temperatures above the glass transition interval. We quantify the progress of sintering by tracking changes in porosity with time. The sintering dynamics is modeled by treating the system as a random distribution of interstitial gas bubbles shrinking under the action of interfacial tension only. We identify the scaling between the polydispersivity of the initial droplets and the dynamics of bulk densification. The framework that we develop allows the sintering dynamics of arbitrary polydisperse populations of droplets to be predicted if the initial droplet (or particle) size distribution is known.

MOECSW trains master trainers and supervisors.

PubMed

1995-01-01

The Ministry of Education, Culture and Social Welfare (MOECSW), as part of the Population Education Programs (formal and informal), undertook a series of training programs to upgrade the knowledge and skills of master trainers, supervisors, and resource persons. As part of the Population Education in the Formal School Sector Project (NEP/93/P01), under the Curriculum Development Centre five training courses were organized to train 220 master trainers. Under the "Three Steps Training Strategy," these 220 master trainers would teach 825 secondary school headmasters who would reach 2025 secondary school teachers. The training courses were held in Dhangadi, April 23-27, 1995; in Pokhara, April 2-7; and in Biratnagar, February 20-24. The areas covered included: 1) the pedagogical aspect of population education (content, scope, objectives, nature, teaching methodologies); 2) demography and population dynamics (composition, distribution and density, sources of population data, demographic transition, consequences and determinants of population growth); 3) family life and adolescence and human sexuality education, including acquired immunodeficiency syndrome (AIDS) education; 4) maternal and child health, and family planning; 5) environment; and 6) population policy and programs. As part of the Population Education Programme (NEP/93/P08), a Master Trainers Training Workshop was held in Makwanpur, March 26-28, 1995. These master trainers would train trainers who would train the facilitators and teachers at learning centers for adult learners under the literacy and post literacy programs. This course focused on the approaches and strategies for integrating population education in development programs, and non-formal education, adult literacy, post literacy, and out-of-school children programs. Dr. D. de Rebello and Mr. S. Hutabarat, CST Advisors on Population Education, organized the training courses and served as resource persons.

Coccidian infection may explain the differences in the life history of octopus host populations.

PubMed

Storero, Lorena P; Narvarte, Maite A

2013-11-01

The prevalence of coccidian parasites in three Octopus tehuelchus populations from San Matías Gulf (Patagonia, Argentina) is compared. The prevalence was similar between sexes, but varied between seasons (being highest during cold months) and sites. Islote Lobos had the highest prevalence (42.7-100%) followed by San Antonio Bay (0-66%) and El Fuerte (0-24.5%). Octopuses under 27 mm of dorsal mantle length showed a low prevalence (less than 50%), which increased with size. We hypothesize that the high prevalence of parasites, which affect the three populations differentially, could account for the observed variability in life-span and growth, size-frequency distributions, reproduction and densities of O. tehuelchus populations. Copyright © 2013 Elsevier Inc. All rights reserved.

From blackbirds to black holes: Investigating capture-recapture methods for time domain astronomy

NASA Astrophysics Data System (ADS)

Laycock, Silas G. T.

2017-07-01

In time domain astronomy, recurrent transients present a special problem: how to infer total populations from limited observations. Monitoring observations may give a biassed view of the underlying population due to limitations on observing time, visibility and instrumental sensitivity. A similar problem exists in the life sciences, where animal populations (such as migratory birds) or disease prevalence, must be estimated from sparse and incomplete data. The class of methods termed Capture-Recapture is used to reconstruct population estimates from time-series records of encounters with the study population. This paper investigates the performance of Capture-Recapture methods in astronomy via a series of numerical simulations. The Blackbirds code simulates monitoring of populations of transients, in this case accreting binary stars (neutron star or black hole accreting from a stellar companion) under a range of observing strategies. We first generate realistic light-curves for populations of binaries with contrasting orbital period distributions. These models are then randomly sampled at observing cadences typical of existing and planned monitoring surveys. The classical capture-recapture methods, Lincoln-Peterson, Schnabel estimators, related techniques, and newer methods implemented in the Rcapture package are compared. A general exponential model based on the radioactive decay law is introduced which is demonstrated to recover (at 95% confidence) the underlying population abundance and duty cycle, in a fraction of the observing visits (10-50%) required to discover all the sources in the simulation. Capture-Recapture is a promising addition to the toolbox of time domain astronomy, and methods implemented in R by the biostats community can be readily called from within python.

Predicting malaria vector distribution under climate change scenarios in China: Challenges for malaria elimination

NASA Astrophysics Data System (ADS)

Ren, Zhoupeng; Wang, Duoquan; Ma, Aimin; Hwang, Jimee; Bennett, Adam; Sturrock, Hugh J. W.; Fan, Junfu; Zhang, Wenjie; Yang, Dian; Feng, Xinyu; Xia, Zhigui; Zhou, Xiao-Nong; Wang, Jinfeng

2016-02-01

Projecting the distribution of malaria vectors under climate change is essential for planning integrated vector control activities for sustaining elimination and preventing reintroduction of malaria. In China, however, little knowledge exists on the possible effects of climate change on malaria vectors. Here we assess the potential impact of climate change on four dominant malaria vectors (An. dirus, An. minimus, An. lesteri and An. sinensis) using species distribution models for two future decades: the 2030 s and the 2050 s. Simulation-based estimates suggest that the environmentally suitable area (ESA) for An. dirus and An. minimus would increase by an average of 49% and 16%, respectively, under all three scenarios for the 2030 s, but decrease by 11% and 16%, respectively in the 2050 s. By contrast, an increase of 36% and 11%, respectively, in ESA of An. lesteri and An. sinensis, was estimated under medium stabilizing (RCP4.5) and very heavy (RCP8.5) emission scenarios. in the 2050 s. In total, we predict a substantial net increase in the population exposed to the four dominant malaria vectors in the decades of the 2030 s and 2050 s, considering land use changes and urbanization simultaneously. Strategies to achieve and sustain malaria elimination in China will need to account for these potential changes in vector distributions and receptivity.

Predicting malaria vector distribution under climate change scenarios in China: Challenges for malaria elimination.

PubMed

Ren, Zhoupeng; Wang, Duoquan; Ma, Aimin; Hwang, Jimee; Bennett, Adam; Sturrock, Hugh J W; Fan, Junfu; Zhang, Wenjie; Yang, Dian; Feng, Xinyu; Xia, Zhigui; Zhou, Xiao-Nong; Wang, Jinfeng

2016-02-12

Projecting the distribution of malaria vectors under climate change is essential for planning integrated vector control activities for sustaining elimination and preventing reintroduction of malaria. In China, however, little knowledge exists on the possible effects of climate change on malaria vectors. Here we assess the potential impact of climate change on four dominant malaria vectors (An. dirus, An. minimus, An. lesteri and An. sinensis) using species distribution models for two future decades: the 2030 s and the 2050 s. Simulation-based estimates suggest that the environmentally suitable area (ESA) for An. dirus and An. minimus would increase by an average of 49% and 16%, respectively, under all three scenarios for the 2030 s, but decrease by 11% and 16%, respectively in the 2050 s. By contrast, an increase of 36% and 11%, respectively, in ESA of An. lesteri and An. sinensis, was estimated under medium stabilizing (RCP4.5) and very heavy (RCP8.5) emission scenarios. in the 2050 s. In total, we predict a substantial net increase in the population exposed to the four dominant malaria vectors in the decades of the 2030 s and 2050 s, considering land use changes and urbanization simultaneously. Strategies to achieve and sustain malaria elimination in China will need to account for these potential changes in vector distributions and receptivity.

Predicting malaria vector distribution under climate change scenarios in China: Challenges for malaria elimination

PubMed Central

Ren, Zhoupeng; Wang, Duoquan; Ma, Aimin; Hwang, Jimee; Bennett, Adam; Sturrock, Hugh J. W.; Fan, Junfu; Zhang, Wenjie; Yang, Dian; Feng, Xinyu; Xia, Zhigui; Zhou, Xiao-Nong; Wang, Jinfeng

2016-01-01

Projecting the distribution of malaria vectors under climate change is essential for planning integrated vector control activities for sustaining elimination and preventing reintroduction of malaria. In China, however, little knowledge exists on the possible effects of climate change on malaria vectors. Here we assess the potential impact of climate change on four dominant malaria vectors (An. dirus, An. minimus, An. lesteri and An. sinensis) using species distribution models for two future decades: the 2030 s and the 2050 s. Simulation-based estimates suggest that the environmentally suitable area (ESA) for An. dirus and An. minimus would increase by an average of 49% and 16%, respectively, under all three scenarios for the 2030 s, but decrease by 11% and 16%, respectively in the 2050 s. By contrast, an increase of 36% and 11%, respectively, in ESA of An. lesteri and An. sinensis, was estimated under medium stabilizing (RCP4.5) and very heavy (RCP8.5) emission scenarios. in the 2050 s. In total, we predict a substantial net increase in the population exposed to the four dominant malaria vectors in the decades of the 2030 s and 2050 s, considering land use changes and urbanization simultaneously. Strategies to achieve and sustain malaria elimination in China will need to account for these potential changes in vector distributions and receptivity. PMID:26868185

The usefulness of “corrected” body mass index vs. self-reported body mass index: comparing the population distributions, sensitivity, specificity, and predictive utility of three correction equations using Canadian population-based data

PubMed Central

2014-01-01

Background National data on body mass index (BMI), computed from self-reported height and weight, is readily available for many populations including the Canadian population. Because self-reported weight is found to be systematically under-reported, it has been proposed that the bias in self-reported BMI can be corrected using equations derived from data sets which include both self-reported and measured height and weight. Such correction equations have been developed and adopted. We aim to evaluate the usefulness (i.e., distributional similarity; sensitivity and specificity; and predictive utility vis-à-vis disease outcomes) of existing and new correction equations in population-based research. Methods The Canadian Community Health Surveys from 2005 and 2008 include both measured and self-reported values of height and weight, which allows for construction and evaluation of correction equations. We focused on adults age 18–65, and compared three correction equations (two correcting weight only, and one correcting BMI) against self-reported and measured BMI. We first compared population distributions of BMI. Second, we compared the sensitivity and specificity of self-reported BMI and corrected BMI against measured BMI. Third, we compared the self-reported and corrected BMI in terms of association with health outcomes using logistic regression. Results All corrections outperformed self-report when estimating the full BMI distribution; the weight-only correction outperformed the BMI-only correction for females in the 23–28 kg/m2 BMI range. In terms of sensitivity/specificity, when estimating obesity prevalence, corrected values of BMI (from any equation) were superior to self-report. In terms of modelling BMI-disease outcome associations, findings were mixed, with no correction proving consistently superior to self-report. Conclusions If researchers are interested in modelling the full population distribution of BMI, or estimating the prevalence of obesity in a population, then a correction of any kind included in this study is recommended. If the researcher is interested in using BMI as a predictor variable for modelling disease, then both self-reported and corrected BMI result in biased estimates of association. PMID:24885210

From K giants to G dwarfs: stellar lifetime effects on metallicity distributions derived from red giants

NASA Astrophysics Data System (ADS)

Manning, Ellen M.; Cole, Andrew A.

2017-11-01

We examine the biases inherent to chemical abundance distributions when targets are selected from the red giant branch (RGB), using simulated giant branches created from isochrones. We find that even when stars are chosen from the entire colour range of RGB stars and over a broad range of magnitudes, the relative numbers of stars of different ages and metallicities, integrated over all stellar types, are not accurately represented in the giant branch sample. The result is that metallicity distribution functions derived from RGB star samples require a correction before they can be fitted by chemical evolution models. We derive simple correction factors for over- and under-represented populations for the limiting cases of single-age populations with a broad range of metallicities and of continuous star formation at constant metallicity; an important general conclusion is that intermediate-age populations (≈1-4 Gyr) are over-represented in RGB samples. We apply our models to the case of the Large Magellanic Cloud bar and show that the observed metallicity distribution underestimates the true number of metal-poor stars by more than 25 per cent; as a result, the inferred importance of gas flows in chemical evolution models could potentially be overestimated. The age- and metallicity-dependences of RGB lifetimes require careful modelling if they are not to lead to spurious conclusions about the chemical enrichment history of galaxies.

Cell phone-generated radio frequency electromagnetic field effects on the locomotor behaviors of the fishes Poecilia reticulata and Danio rerio.

PubMed

Lee, David; Lee, Joshua; Lee, Imshik

2015-01-01

The locomotor behavior of small fish was characterized under a cell phone-generated radio frequency electromagnetic field (RF EMF). The trajectory of movement of 10 pairs of guppy (Poecilia reticulate) and 15 pairs of Zebrafish (Danio rerio) in a fish tank was recorded and tracked under the presence of a cell phone-generated RF EMF. The measures were based on spatial and temporal distributions. A time-series trajectory was utilized to emphasize the dynamic nature of locomotor behavior. Fish movement was recorded in real-time. Their spatial, velocity, turning angle and sinuosity distribution were analyzed in terms of F(v,x), P[n(x,t)], P(v), F (θ) and F(s), respectively. In addition, potential temperature elevation caused by a cellular phone was also examined. We demonstrated that a cellular phone-induced temperature elevation was not relevant, and that our measurements reflected RF EMF-induced effects on the locomotor behavior of Poecilia reticulata and Danio rerio. Fish locomotion was observed under normal conditions, in the visual presence of a cell phone, after feeding, and under starvation. Fish locomotor behavior was random both in normal conditions and in the presence of an off-signaled cell phone. However, there were significant changes in the locomotion of the fish after feeding under the RF EMF. The locomotion of the fed fish was affected in terms of changes in population and velocity distributions under the presence of the RF EMF emitted by the cell phone. There was, however, no significant difference in angular distribution.

A changing climate: impacts on human exposures to O3 using ...

EPA Pesticide Factsheets

Predicting the impacts of changing climate on human exposure to air pollution requires future scenarios that account for changes in ambient pollutant concentrations, population sizes and distributions, and housing stocks. An integrated methodology to model changes in human exposures due to these impacts was developed by linking climate, air quality, land-use, and human exposure models. This methodology was then applied to characterize changes in predicted human exposures to O3 under multiple future scenarios. Regional climate projections for the U.S. were developed by downscaling global circulation model (GCM) scenarios for three of the Intergovernmental Panel on Climate Change’s (IPCC’s) Representative Concentration Pathways (RCPs) using the Weather Research and Forecasting (WRF) model. The regional climate results were in turn used to generate air quality (concentration) projections using the Community Multiscale Air Quality (CMAQ) model. For each of the climate change scenarios, future U.S. census-tract level population distributions from the Integrated Climate and Land Use Scenarios (ICLUS) model for four future scenarios based on the IPCC’s Special Report on Emissions Scenarios (SRES) storylines were used. These climate, air quality, and population projections were used as inputs to EPA’s Air Pollutants Exposure (APEX) model for 12 U.S. cities. Probability density functions show changes in the population distribution of 8 h maximum daily O3 exposur

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system

PubMed Central

Ling, Fangqiong; Hwang, Chiachi; LeChevallier, Mark W; Andersen, Gary L; Liu, Wen-Tso

2016-01-01

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a ‘core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems. PMID:26251872

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system.

PubMed

Ling, Fangqiong; Hwang, Chiachi; LeChevallier, Mark W; Andersen, Gary L; Liu, Wen-Tso

2016-03-01

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a 'core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems.

Spatial quantification of the world population potentially exposed to Zika virus.

PubMed

Alaniz, Alberto J; Bacigalupo, Antonella; Cattan, Pedro E

2017-06-01

Zika virus is an emerging Flaviviridae virus, which has spread rapidly in the last few years. It has raised concern because it has been associated with fetus microcephaly when pregnant women are infected. The main vector is the mosquito Aedes aegypti , distributed in tropical areas. Niche modelling techniques were used to estimate the potential distribution area of A. aegypti. This was overlapped with human population density, determining areas of potential transmission risk worldwide. Afterwards, we quantified the population at risk according to risk level. The vector transmission risk is distributed mainly in Asia and Oceania on the shores of the Indian Ocean. In America, the risk concentrates in the Atlantic coast of South America and in the Caribbean Sea shores in Central and North America. In Africa, the major risk is concentrated in the Pacific and Atlantic coasts of Central and South Africa. The world population under high and very high risk levels includes 2.261 billion people. These results illustrate Zika virus risk at the global level and provide maps to target the prevention and control measures especially in areas with higher risk, in countries with less sanitation and poorer resources. Many countries without previous vector reports could become active transmission zones in the future, so vector surveillance should be implemented or reinforced in these areas. © The Author 2017; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

A new methodological approach to adjust alcohol exposure distributions to improve the estimation of alcohol-attributable fractions.

PubMed

Parish, William J; Aldridge, Arnie; Allaire, Benjamin; Ekwueme, Donatus U; Poehler, Diana; Guy, Gery P; Thomas, Cheryll C; Trogdon, Justin G

2017-11-01

To assess the burden of excessive alcohol use, researchers estimate alcohol-attributable fractions (AAFs) routinely. However, under-reporting in survey data can bias these estimates. We present an approach that adjusts for under-reporting in the estimation of AAFs, particularly within subgroups. This framework is a refinement of a previous method conducted by Rehm et al. We use a measurement error model to derive the 'true' alcohol distribution from a 'reported' alcohol distribution. The 'true' distribution leverages per-capita sales data to identify the distribution average and then identifies the shape of the distribution with self-reported survey data. Data are from the National Alcohol Survey (NAS), the National Household Survey on Drug Abuse (NHSDA) and the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC). We compared our approach with previous approaches by estimating the AAF of female breast cancer cases. Compared with Rehm et al.'s approach, our refinement performs similarly under a gamma assumption. For example, among females aged 18-25 years, the two approaches produce estimates from NHSDA that are within a percentage point. However, relaxing the gamma assumption generally produces more conservative evidence. For example, among females aged 18-25 years, estimates from NHSDA based on the best-fitting distribution are only 19.33% of breast cancer cases, which is a much smaller proportion than the gamma-based estimates of approximately 28%. A refinement of Rehm et al.'s approach to adjusting for underreporting in the estimation of alcohol-attributable fractions provides more flexibility. This flexibility can avoid biases associated with failing to account for the underlying differences in alcohol consumption patterns across different study populations. Comparisons of our refinement with Rehm et al.'s approach show that results are similar when a gamma distribution is assumed. However, results are appreciably lower when the best-fitting distribution is chosen versus gamma-based results. © 2017 Society for the Study of Addiction.

Genetic wealth, population health: Major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta).

PubMed

Grogan, Kathleen E; Sauther, Michelle L; Cuozzo, Frank P; Drea, Christine M

2017-10-01

Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur ( Lemur catta ) as a model, we compared two populations under long-term study: a relatively "open," wild population ( n  = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003-2013) and a "closed," captive population ( n  = 121) derived from the Duke Lemur Center (DLC, 1980-2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.

The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.

PubMed

Pedersen, Casper-Emil T; Lohmueller, Kirk E; Grarup, Niels; Bjerregaard, Peter; Hansen, Torben; Siegismund, Hans R; Moltke, Ida; Albrechtsen, Anders

2017-02-01

The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit we show that the Inuit have undergone a severe ∼20,000-year-long bottleneck. This has led to a markedly more extreme distribution of allele frequencies than seen for any other human population tested to date, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation. When comparing proxies for genetic load that assume an additive effect of deleterious alleles, the Inuit show, at most, a slight increase in load compared to European, East Asian, and African populations. Specifically, we observe <4% increase in the number of derived deleterious alleles in the Inuit. In contrast, proxies for genetic load under a recessive model suggest that the Inuit have a significantly higher load (20% increase or more) compared to other less bottlenecked human populations. Forward simulations under realistic models of demography support our empirical findings, showing up to a 6% increase in the genetic load for the Inuit population across all models of dominance. Further, the Inuit population carries fewer deleterious variants than other human populations, but those that are present tend to be at higher frequency than in other populations. Overall, our results show how recent demographic history has affected patterns of deleterious variants in human populations. Copyright © 2017 by the Genetics Society of America.

Insecticide resistance in the dengue vector Aedes aegypti from Martinique: distribution, mechanisms and relations with environmental factors.

PubMed

Marcombe, Sébastien; Mathieu, Romain Blanc; Pocquet, Nicolas; Riaz, Muhammad-Asam; Poupardin, Rodolphe; Sélior, Serge; Darriet, Frédéric; Reynaud, Stéphane; Yébakima, André; Corbel, Vincent; David, Jean-Philippe; Chandre, Fabrice

2012-01-01

Dengue is an important mosquito borne viral disease in Martinique Island (French West Indies). The viruses responsible for dengue are transmitted by Aedes aegypti, an indoor day-biting mosquito. The most effective proven method for disease prevention has been by vector control by various chemical or biological means. Unfortunately insecticide resistance has already been observed on the Island and recently showed to significantly reduce the efficacy of vector control interventions. In this study, we investigated the distribution of resistance and the underlying mechanisms in nine Ae. aegypti populations. Statistical multifactorial approach was used to investigate the correlations between insecticide resistance levels, associated mechanisms and environmental factors characterizing the mosquito populations. Bioassays revealed high levels of resistance to temephos and deltamethrin and susceptibility to Bti in the 9 populations tested. Biochemical assays showed elevated detoxification enzyme activities of monooxygenases, carboxylesterases and glutathione S-tranferases in most of the populations. Molecular screening for common insecticide target-site mutations, revealed the presence of the "knock-down resistance" V1016I Kdr mutation at high frequency (>87%). Real time quantitative RT-PCR showed the potential involvement of several candidate detoxification genes in insecticide resistance. Principal Component Analysis (PCA) performed with variables characterizing Ae. aegypti from Martinique permitted to underline potential links existing between resistance distribution and other variables such as agriculture practices, vector control interventions and urbanization. Insecticide resistance is widespread but not homogeneously distributed across Martinique. The influence of environmental and operational factors on the evolution of the resistance and mechanisms are discussed.

Insecticide Resistance in the Dengue Vector Aedes aegypti from Martinique: Distribution, Mechanisms and Relations with Environmental Factors

PubMed Central

Marcombe, Sébastien; Mathieu, Romain Blanc; Pocquet, Nicolas; Riaz, Muhammad-Asam; Poupardin, Rodolphe; Sélior, Serge; Darriet, Frédéric; Reynaud, Stéphane; Yébakima, André; Corbel, Vincent; David, Jean-Philippe; Chandre, Fabrice

2012-01-01

Dengue is an important mosquito borne viral disease in Martinique Island (French West Indies). The viruses responsible for dengue are transmitted by Aedes aegypti, an indoor day-biting mosquito. The most effective proven method for disease prevention has been by vector control by various chemical or biological means. Unfortunately insecticide resistance has already been observed on the Island and recently showed to significantly reduce the efficacy of vector control interventions. In this study, we investigated the distribution of resistance and the underlying mechanisms in nine Ae. aegypti populations. Statistical multifactorial approach was used to investigate the correlations between insecticide resistance levels, associated mechanisms and environmental factors characterizing the mosquito populations. Bioassays revealed high levels of resistance to temephos and deltamethrin and susceptibility to Bti in the 9 populations tested. Biochemical assays showed elevated detoxification enzyme activities of monooxygenases, carboxylesterases and glutathione S-tranferases in most of the populations. Molecular screening for common insecticide target-site mutations, revealed the presence of the “knock-down resistance” V1016I Kdr mutation at high frequency (>87%). Real time quantitative RT-PCR showed the potential involvement of several candidate detoxification genes in insecticide resistance. Principal Component Analysis (PCA) performed with variables characterizing Ae. aegypti from Martinique permitted to underline potential links existing between resistance distribution and other variables such as agriculture practices, vector control interventions and urbanization. Insecticide resistance is widespread but not homogeneously distributed across Martinique. The influence of environmental and operational factors on the evolution of the resistance and mechanisms are discussed. PMID:22363529

Optimal sampling design for estimating spatial distribution and abundance of a freshwater mussel population

USGS Publications Warehouse

Pooler, P.S.; Smith, D.R.

2005-01-01

We compared the ability of simple random sampling (SRS) and a variety of systematic sampling (SYS) designs to estimate abundance, quantify spatial clustering, and predict spatial distribution of freshwater mussels. Sampling simulations were conducted using data obtained from a census of freshwater mussels in a 40 X 33 m section of the Cacapon River near Capon Bridge, West Virginia, and from a simulated spatially random population generated to have the same abundance as the real population. Sampling units that were 0.25 m 2 gave more accurate and precise abundance estimates and generally better spatial predictions than 1-m2 sampling units. Systematic sampling with ???2 random starts was more efficient than SRS. Estimates of abundance based on SYS were more accurate when the distance between sampling units across the stream was less than or equal to the distance between sampling units along the stream. Three measures for quantifying spatial clustering were examined: Hopkins Statistic, the Clumping Index, and Morisita's Index. Morisita's Index was the most reliable, and the Hopkins Statistic was prone to false rejection of complete spatial randomness. SYS designs with units spaced equally across and up stream provided the most accurate predictions when estimating the spatial distribution by kriging. Our research indicates that SYS designs with sampling units equally spaced both across and along the stream would be appropriate for sampling freshwater mussels even if no information about the true underlying spatial distribution of the population were available to guide the design choice. ?? 2005 by The North American Benthological Society.

Genetically informed ecological niche models improve climate change predictions.

PubMed

Ikeda, Dana H; Max, Tamara L; Allan, Gerard J; Lau, Matthew K; Shuster, Stephen M; Whitham, Thomas G

2017-01-01

We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, local adaptation. Local adaptation is common in species that span a range of environmental gradients (e.g., soils and climate). Moreover, common garden studies have demonstrated a covariance between neutral markers and functional traits associated with a species' ability to adapt to environmental change. We therefore predicted that genetically distinct populations would respond differently to climate change, resulting in predicted distributions with little overlap. To test whether genetic information improves our ability to predict a species' niche space, we created genetically informed ecological niche models (gENMs) using Populus fremontii (Salicaceae), a widespread tree species in which prior common garden experiments demonstrate strong evidence for local adaptation. Four major findings emerged: (i) gENMs predicted population occurrences with up to 12-fold greater accuracy than models without genetic information; (ii) tests of niche similarity revealed that three ecotypes, identified on the basis of neutral genetic markers and locally adapted populations, are associated with differences in climate; (iii) our forecasts indicate that ongoing climate change will likely shift these ecotypes further apart in geographic space, resulting in greater niche divergence; (iv) ecotypes that currently exhibit the largest geographic distribution and niche breadth appear to be buffered the most from climate change. As diverse agents of selection shape genetic variability and structure within species, we argue that gENMs will lead to more accurate predictions of species distributions under climate change. © 2016 John Wiley & Sons Ltd.

Maintenance of algal endosymbionts in Paramecium bursaria: a simple model based on population dynamics.

PubMed

Iwai, Sosuke; Fujiwara, Kenji; Tamura, Takuro

2016-09-01

Algal endosymbiosis is widely distributed in eukaryotes including many protists and metazoans, and plays important roles in aquatic ecosystems, combining phagotrophy and phototrophy. To maintain a stable symbiotic relationship, endosymbiont population size in the host must be properly regulated and maintained at a constant level; however, the mechanisms underlying the maintenance of algal endosymbionts are still largely unknown. Here we investigate the population dynamics of the unicellular ciliate Paramecium bursaria and its Chlorella-like algal endosymbiont under various experimental conditions in a simple culture system. Our results suggest that endosymbiont population size in P. bursaria was not regulated by active processes such as cell division coupling between the two organisms, or partitioning of the endosymbionts at host cell division. Regardless, endosymbiont population size was eventually adjusted to a nearly constant level once cells were grown with light and nutrients. To explain this apparent regulation of population size, we propose a simple mechanism based on the different growth properties (specifically the nutrient requirements) of the two organisms, and based from this develop a mathematical model to describe the population dynamics of host and endosymbiont. The proposed mechanism and model may provide a basis for understanding the maintenance of algal endosymbionts. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Climate change influences on the potential geographic distribution of the disease vector tick Ixodes ricinus

PubMed Central

Peterson, A. Townsend; Samy, Abdallah M.

2017-01-01

Background Ixodes ricinus is a species of hard tick that transmits several important diseases in Europe and North Africa, including Lyme borreliosis and tick-borne encephalitis. Climate change is affecting the geographic distributions and abundances of arthropod vectors, which in turn influence the geographic distribution and epidemiology of associated vector-borne diseases. To date, few studies have investigated effects of climate change on the spatial distribution of I. ricinus at continental extents. Here, we assessed the potential distribution of I. ricinus under current and future climate conditions to understand how climate change will influence the geographic distribution of this important tick vector in coming decades. Method We used ecological niche modeling to estimate the geographic distribution of I. ricinus with respect to current climate, and then assessed its future potential distribution under different climate change scenarios. This approach integrates occurrence records of I. ricinus with six relevant environmental variables over a continental extent that includes Europe, North Africa, and the Middle East. Future projections were based on climate data from 17 general circulation models (GCMs) under 2 representative concentration pathway emissions scenarios (RCPs), for the years 2050 and 2070. Result The present and future potential distributions of I. ricinus showed broad overlap across most of western and central Europe, and in more narrow zones in eastern and northern Europe, and North Africa. Potential expansions were observed in northern and eastern Europe. These results indicate that I. ricinus populations could emerge in areas in which they are currently lacking, posing increased risks to human health in those areas. However, the future of I. ricinus ticks in some important regions such the Mediterranean was unclear owing to high uncertainty in model predictions. PMID:29206879

Climate change influences on the potential geographic distribution of the disease vector tick Ixodes ricinus.

PubMed

Alkishe, Abdelghafar A; Peterson, A Townsend; Samy, Abdallah M

2017-01-01

Ixodes ricinus is a species of hard tick that transmits several important diseases in Europe and North Africa, including Lyme borreliosis and tick-borne encephalitis. Climate change is affecting the geographic distributions and abundances of arthropod vectors, which in turn influence the geographic distribution and epidemiology of associated vector-borne diseases. To date, few studies have investigated effects of climate change on the spatial distribution of I. ricinus at continental extents. Here, we assessed the potential distribution of I. ricinus under current and future climate conditions to understand how climate change will influence the geographic distribution of this important tick vector in coming decades. We used ecological niche modeling to estimate the geographic distribution of I. ricinus with respect to current climate, and then assessed its future potential distribution under different climate change scenarios. This approach integrates occurrence records of I. ricinus with six relevant environmental variables over a continental extent that includes Europe, North Africa, and the Middle East. Future projections were based on climate data from 17 general circulation models (GCMs) under 2 representative concentration pathway emissions scenarios (RCPs), for the years 2050 and 2070. The present and future potential distributions of I. ricinus showed broad overlap across most of western and central Europe, and in more narrow zones in eastern and northern Europe, and North Africa. Potential expansions were observed in northern and eastern Europe. These results indicate that I. ricinus populations could emerge in areas in which they are currently lacking, posing increased risks to human health in those areas. However, the future of I. ricinus ticks in some important regions such the Mediterranean was unclear owing to high uncertainty in model predictions.

A centroid model of species distribution with applications to the Carolina wren Thryothorus ludovicianus and house finch Haemorhous mexicanus in the United States

USGS Publications Warehouse

Huang, Qiongyu; Sauer, John R.; Swatantran, Anu; Dubayah, Ralph

2016-01-01

Drastic shifts in species distributions are a cause of concern for ecologists. Such shifts pose great threat to biodiversity especially under unprecedented anthropogenic and natural disturbances. Many studies have documented recent shifts in species distributions. However, most of these studies are limited to regional scales, and do not consider the abundance structure within species ranges. Developing methods to detect systematic changes in species distributions over their full ranges is critical for understanding the impact of changing environments and for successful conservation planning. Here, we demonstrate a centroid model for range-wide analysis of distribution shifts using the North American Breeding Bird Survey. The centroid model is based on a hierarchical Bayesian framework which models population change within physiographic strata while accounting for several factors affecting species detectability. Yearly abundance-weighted range centroids are estimated. As case studies, we derive annual centroids for the Carolina wren and house finch in their ranges in the U.S. We further evaluate the first-difference correlation between species’ centroid movement and changes in winter severity, total population abundance. We also examined associations of change in centroids from sub-ranges. Change in full-range centroid movements of Carolina wren significantly correlate with snow cover days (r = −0.58). For both species, the full-range centroid shifts also have strong correlation with total abundance (r = 0.65, and 0.51 respectively). The movements of the full-range centroids of the two species are correlated strongly (up to r = 0.76) with that of the sub-ranges with more drastic population changes. Our study demonstrates the usefulness of centroids for analyzing distribution changes in a two-dimensional spatial context. Particularly it highlights applications that associate the centroid with factors such as environmental stressors, population characteristics, and progression of invasive species. Routine monitoring of changes in centroid will provide useful insights into long-term avian responses to environmental changes.

PHENOTYPIC DIFFERENTIATION AT SOUTHERN LIMIT BORDERS: THE CASE STUDY OF TWO FUCOID MACROALGAL SPECIES WITH DIFFERENT LIFE-HISTORY TRAITS1.

PubMed

Araújo, Rita; Serrão, Ester A; Sousa-Pinto, Isabel; Åberg, Per

2011-06-01

Marginal populations are often geographically isolated, smaller, and more fragmented than central populations and may frequently have to face suboptimal local environmental conditions. Persistence of these populations frequently involves the development of adaptive traits at phenotypic and genetic levels. We compared population structure and demographic variables in two fucoid macroalgal species contrasting in patterns of genetic diversity and phenotypic plasticity at their southern distribution limit with a more central location. Models were Ascophyllum nodosum (L.) Le Jol. (whose extreme longevity and generation overlap may buffer genetic loss by drift) and Fucus serratus L. (with low genetic diversity at southern margins). At edge locations, both species exhibited trends in life-history traits compatible with population persistence but by using different mechanisms. Marginal populations of A. nodosum had higher reproductive output in spite of similar mortality rates at all life stages, making edge populations denser and with smaller individuals. In F. serratus, rather than demographic changes, marginal populations differed in habitat, occurring restricted to a narrower vertical habitat range. We conclude that persistence of both A. nodosum and F. serratus at the southern-edge locations depends on different strategies. Marginal population persistence in A. nodosum relies on a differentiation in life-history traits, whereas F. serratus, putatively poorer in evolvability potential, is restricted to a narrower vertical range at border locations. These results contribute to the general understanding of mechanisms that lead to population persistence at distributional limits and to predict population resilience under a scenario of environmental change. © 2011 Phycological Society of America.

Simple Indices Provide Insight to Climate Attributes Delineating the Geographic Range of Aedes albopictus (Diptera: Culicidae) Prior to Worldwide Invasion.

PubMed

Mogi, Motoyoshi; Armbruster, Peter; Tuno, Nobuko; Campos, Raúl; Eritja, Roger

2015-07-01

Aedes albopictus (Skuse) has expanded its distribution worldwide during the past decades. Despite attempts to explain and predict its geographic occurrence, analyses of the distribution of Ae. albopictus in the context of broad climatic regions (biomes) has not been performed. We analyzed climate conditions at its distribution sites in the range before the worldwide invasions (from the easternmost Hawaii through westernmost Madagascar) by using thermal and aridity-humidity indices descriptive of major biomes. A significant advantage of this approach is that it uses simple indices clearly related to the population dynamics of Ae. albopictus. Although Ae. albopictus has been regarded as a forest species preferring humid climate, in areas with significant human habitation, the distribution sites extended from the perhumid, rain forest zone to the semiarid, steppe zone. This pattern was common from the tropics through the temperate zone. Across the distribution range, there was no seasonal discordance between temperature and precipitation; at sites where winter prevents Ae. albopictus reproduction (monthly means<10°C), precipitation was concentrated in warm months (>10°C) under the Asian summer monsoon. Absence of the species in northern and eastern coastal Australia and eastern coastal Africa was not attributable solely to climate conditions. However, Asia west of the summer monsoon range was climatically unsuitable because of low precipitation throughout the year or in warm months favorable to reproduction (concentration of precipitation in winter). We hypothesized that Ae. albopictus originated in continental Asia under the monsoon climate with distinct dry seasons and hot, wet summer, enabling rapid population growth. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Predicting impacts of climate change on habitat connectivity of Kalopanax septemlobus in South Korea

NASA Astrophysics Data System (ADS)

Kang, Wanmo; Minor, Emily S.; Lee, Dowon; Park, Chan-Ryul

2016-02-01

Understanding the drivers of habitat distribution patterns and assessing habitat connectivity are crucial for conservation in the face of climate change. In this study, we examined a sparsely distributed tree species, Kalopanax septemlobus (Araliaceae), which has been heavily disturbed by human use in temperate forests of South Korea. We used maximum entropy distribution modeling (MaxEnt) to identify the climatic and topographic factors driving the distribution of the species. Then, we constructed habitat models under current and projected climate conditions for the year 2050 and evaluated changes in the extent and connectivity of the K. septemlobus habitat. Annual mean temperature and terrain slope were the two most important predictors of species distribution. Our models predicted the range shift of K. septemlobus toward higher elevations under medium-low and high emissions scenarios for 2050, with dramatic reductions in suitable habitat (51% and 85%, respectively). In addition, connectivity analysis indicated that climate change is expected to reduce future levels of habitat connectivity. Even under the Representative Construction Pathway (RCP) 4.5 medium-low warming scenario, the projected climate conditions will decrease habitat connectivity by 78%. Overall, suitable habitats for K. septemlobus populations will likely become more isolated depending on the severity of global warming. The approach presented here can be used to efficiently assess species and habitat vulnerability to climate change.

The Lesser of Two Weevils: Molecular-Genetics of Pest Palm Weevil Populations Confirm Rhynchophorus vulneratus (Panzer 1798) as a Valid Species Distinct from R. ferrugineus (Olivier 1790), and Reveal the Global Extent of Both

PubMed Central

Rugman-Jones, Paul F.; Hoddle, Christina D.; Hoddle, Mark S.; Stouthamer, Richard

2013-01-01

The red palm weevil (RPW) is a major pest of palms. It is native to southeast Asia and Melanesia, but in recent decades has vastly expanded its range as the result of multiple accidental anthropogenic introductions into the Middle East, Mediterranean Basin, Caribbean, and U.S.A. Currently regarded as a single species, Rhynchophorus ferrugineus (Olivier), RPW displays remarkable color variation across its range, and consequently has a taxonomic history littered with new species descriptions and synonymization. We compared DNA sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene from RPW populations throughout the native and invaded ranges, to investigate the specific status and invasion history of this serious economic pest, and to identify possible common routes of entry. Analyses of COI haplotype data provide conclusive support, corroborated by sequences of additional nuclear gene regions, for the existence of at least two predominantly allopatric species. The true R. ferrugineus is native only to the northern and western parts of continental southeast Asia, Sri Lanka and the Philippines, and is responsible for almost all invasive populations worldwide. In contrast, the second species, which is currently synonymized under R. ferrugineus and should be resurrected under the name R. vulneratus (Panzer), has a more southern distribution across Indonesia, and is responsible for only one invasive population; that in California, U.S.A. The distribution of COI haplotypes is used to discuss the possible existence of further cryptic species, sources and routes of entry of different invasive populations, and the implications of our findings for current control methods. PMID:24143263

A Comparison of Limited-Information and Full-Information Methods in M"plus" for Estimating Item Response Theory Parameters for Nonnormal Populations

ERIC Educational Resources Information Center

DeMars, Christine E.

2012-01-01

In structural equation modeling software, either limited-information (bivariate proportions) or full-information item parameter estimation routines could be used for the 2-parameter item response theory (IRT) model. Limited-information methods assume the continuous variable underlying an item response is normally distributed. For skewed and…

Evolution of stochastic demography with life history tradeoffs in density-dependent age-structured populations.

PubMed

Lande, Russell; Engen, Steinar; Sæther, Bernt-Erik

2017-10-31

We analyze the stochastic demography and evolution of a density-dependent age- (or stage-) structured population in a fluctuating environment. A positive linear combination of age classes (e.g., weighted by body mass) is assumed to act as the single variable of population size, [Formula: see text], exerting density dependence on age-specific vital rates through an increasing function of population size. The environment fluctuates in a stationary distribution with no autocorrelation. We show by analysis and simulation of age structure, under assumptions often met by vertebrate populations, that the stochastic dynamics of population size can be accurately approximated by a univariate model governed by three key demographic parameters: the intrinsic rate of increase and carrying capacity in the average environment, [Formula: see text] and [Formula: see text], and the environmental variance in population growth rate, [Formula: see text] Allowing these parameters to be genetically variable and to evolve, but assuming that a fourth parameter, [Formula: see text], measuring the nonlinearity of density dependence, remains constant, the expected evolution maximizes [Formula: see text] This shows that the magnitude of environmental stochasticity governs the classical trade-off between selection for higher [Formula: see text] versus higher [Formula: see text] However, selection also acts to decrease [Formula: see text], so the simple life-history trade-off between [Formula: see text]- and [Formula: see text]-selection may be obscured by additional trade-offs between them and [Formula: see text] Under the classical logistic model of population growth with linear density dependence ([Formula: see text]), life-history evolution in a fluctuating environment tends to maximize the average population size. Published under the PNAS license.

Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient.

PubMed

Acuña-Rodríguez, Ian S; Torres-Díaz, Cristian; Hereme, Rasme; Molina-Montenegro, Marco A

2017-01-01

The increase in temperature as consequence of the recent global warming has been reported to generate new ice-free areas in the Antarctic continent, facilitating the colonization and spread of plant populations. Consequently, Antarctic vascular plants have been observed extending their southern distribution. But as the environmental conditions toward southern localities become progressively more departed from the species' physiological optimum, the ecophysiological responses and survival to the expected global warming could be reduced. However, if processes of local adaptation are the main cause of the observed southern expansion, those populations could appear constrained to respond positively to the expected global warming. Using individuals from the southern tip of South America, the South Shetland Islands and the Antarctic Peninsula, we assess with a long term experiment (three years) under controlled conditions if the responsiveness of Colobanthus quitensis populations to the expected global warming, is related with their different foliar traits and photoprotective mechanisms along the latitudinal gradient. In addition, we tested if the release of the stress condition by the global warming in these cold environments increases the ecophysiological performance. For this, we describe the latitudinal pattern of net photosynthetic capacity, biomass accumulation, and number of flowers under current and future temperatures respective to each site of origin after three growing seasons. Overall, was found a clinal trend was found in the foliar traits and photoprotective mechanisms in the evaluated C. quitensis populations. On the other hand, an asymmetric response to warming was observed for southern populations in all ecophysiological traits evaluated, suggesting that low temperature is limiting the performance of C. quitensis populations. Our results suggest that under a global warming scenario, plant populations that inhabiting cold zones at high latitudes could increase in their ecophysiological performance, enhancing the size of populations or their spread.

Projected Irrigation Requirement Under Climate Change in Korean Peninsula by Apply Global Hydrologic Model to Local Scale.

NASA Astrophysics Data System (ADS)

Yang, B.; Lee, D. K.

2016-12-01

Understanding spatial distribution of irrigation requirement is critically important for agricultural water management. However, many studies considering future agricultural water management in Korea assessed irrigation requirement on watershed or administrative district scale, but have not accounted the spatial distribution. Lumped hydrologic model has typically used in Korea for simulating watershed scale irrigation requirement, while distribution hydrologic model can simulate the spatial distribution grid by grid. To overcome this shortcoming, here we applied a grid base global hydrologic model (H08) into local scale to estimate spatial distribution under future irrigation requirement of Korean Peninsula. Korea is one of the world's most densely populated countries, with also high produce and demand of rice which requires higher soil moisture than other crops. Although, most of the precipitation concentrate in particular season and disagree with crop growth season. This precipitation character makes management of agricultural water which is approximately 60% of total water usage critical issue in Korea. Furthermore, under future climate change, the precipitation predicted to be more concentrated and necessary need change of future water management plan. In order to apply global hydrological model into local scale, we selected appropriate major crops under social and local climate condition in Korea to estimate cropping area and yield, and revised the cropping area map more accurately. As a result, future irrigation requirement estimation varies under each projection, however, slightly decreased in most case. The simulation reveals, evapotranspiration increase slightly while effective precipitation also increase to balance the irrigation requirement. This finding suggest practical guideline to decision makers for further agricultural water management plan including future development of water supply plan to resolve water scarcity.

Laser fluorescence fluctuation excesses in molecular immunology experiments

NASA Astrophysics Data System (ADS)

Galich, N. E.; Filatov, M. V.

2007-04-01

A novel approach to statistical analysis of flow cytometry fluorescence data have been developed and applied for population analysis of blood neutrophils stained with hydroethidine during respiratory burst reaction. The staining based on intracellular oxidation hydroethidine to ethidium bromide, which intercalate into cell DNA. Fluorescence of the resultant product serves as a measure of the neutrophil ability to generate superoxide radicals after induction respiratory burst reaction by phorbol myristate acetate (PMA). It was demonstrated that polymorphonuclear leukocytes of persons with inflammatory diseases showed a considerably changed response. Cytofluorometric histograms obtained have unique information about condition of neutrophil population what might to allow a determination of the pathology processes type connecting with such inflammation. A novel approach to histogram analysis is based on analysis of high-momentum dynamic of distribution. The features of fluctuation excesses of distribution have unique information about disease under consideration.

A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence

PubMed Central

Spain, S L; Pedroso, I; Kadeva, N; Miller, M B; Iacono, W G; McGue, M; Stergiakouli, E; Smith, G D; Putallaz, M; Lubinski, D; Meaburn, E L; Plomin, R; Simpson, M A

2016-01-01

Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case–control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence. PMID:26239293

A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence.

PubMed

Spain, S L; Pedroso, I; Kadeva, N; Miller, M B; Iacono, W G; McGue, M; Stergiakouli, E; Davey Smith, G; Putallaz, M; Lubinski, D; Meaburn, E L; Plomin, R; Simpson, M A

2016-08-01

Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.

Culture modifies expectations of kinship and sex-biased dispersal patterns: a case study of patrilineality and patrilocality in tribal Yemen.

PubMed

Raaum, Ryan L; Al-Meeri, Ali; Mulligan, Connie J

2013-04-01

Studies of the impact of post-marital residence patterns on the distribution of genetic variation within populations have returned conflicting results. These studies have generally examined genetic diversity within and between groups with different post-marriage residence patterns. Here, we directly examine Y chromosome microsatellite variation in individuals carrying a chromosome in the same Y haplogroup. We analyze Y chromosome data from two samples of Yemeni males: a sample representing the entire country and a sample from a large highland village. Our results support a normative patrilocality in highland Yemeni tribal populations, but also suggest that patrilocality is violated often enough to break down the expected correlation of genetic and geographic distance. We propose that a great deal of variation in male dispersal distance distributions is subsumed under the "patrilocal" label and that few human societies are likely to realize the idealized male dispersal distribution expected under strict patrilocality. In addition, we found almost no specific correspondence between social kinship and genetic patriline at the level of the clan (large, extended patrilineal kinship group) within a large, highland Yemeni village. We discuss ethnographic accounts that offer several cultural practices that explain exceptions to patrilocality and means by which social kinship and genetic patriline may become disentangled. Copyright © 2013 Wiley Periodicals, Inc.

Vertical Distribution of Pasteuria penetrans Parasitizing Meloidogyne incognita on Pittosporum tobira in Florida.

PubMed

Baidoo, Richard; Mengistu, Tesfamariam Mekete; Brito, Janete A; McSorley, Robert; Stamps, Robert H; Crow, William T

2017-09-01

Pasteuria penetrans is considered as the primary agent responsible for soil suppressiveness to root-knot nematodes widely distributed in many agricultural fields. A preliminary survey on a Pittosporum tobira field where the grower had experienced a continuous decline in productivity caused by Meloidogyne incognita showed that the nematode was infected with Pasteuria penetrans . For effective control of the nematode, the bacterium and the host must coexist in the same root zone. The vertical distribution of Pasteuria penetrans and its relationship with the nematode host in the soil was investigated to identify (i) the vertical distribution of P. penetrans endospores in an irrigated P. tobira field and (ii) the relationship among P. penetrans endospore density, M. incognita J2 population density, and host plant root distribution over time. Soil bioassays revealed that endospore density was greater in the upper 18 cm of the top soil compared with the underlying depths. A correlation analysis showed that the endospore density was positively related to the J2 population density and host plant root distribution. Thus, the vertical distribution of P. penetrans was largely dependent on its nematode host which in turn was determined by the distribution of the host plant roots. The Pasteuria was predominant mostly in the upper layers of the soil where their nematode host and the plant host roots are abundant, a factor which may be a critical consideration when using P. penetrans as a nematode biological control agent.

Vertical Distribution of Pasteuria penetrans Parasitizing Meloidogyne incognita on Pittosporum tobira in Florida

PubMed Central

Baidoo, Richard; Mengistu, Tesfamariam Mekete; Brito, Janete A.; McSorley, Robert; Stamps, Robert H.; Crow, William T.

2017-01-01

Pasteuria penetrans is considered as the primary agent responsible for soil suppressiveness to root-knot nematodes widely distributed in many agricultural fields. A preliminary survey on a Pittosporum tobira field where the grower had experienced a continuous decline in productivity caused by Meloidogyne incognita showed that the nematode was infected with Pasteuria penetrans. For effective control of the nematode, the bacterium and the host must coexist in the same root zone. The vertical distribution of Pasteuria penetrans and its relationship with the nematode host in the soil was investigated to identify (i) the vertical distribution of P. penetrans endospores in an irrigated P. tobira field and (ii) the relationship among P. penetrans endospore density, M. incognita J2 population density, and host plant root distribution over time. Soil bioassays revealed that endospore density was greater in the upper 18 cm of the top soil compared with the underlying depths. A correlation analysis showed that the endospore density was positively related to the J2 population density and host plant root distribution. Thus, the vertical distribution of P. penetrans was largely dependent on its nematode host which in turn was determined by the distribution of the host plant roots. The Pasteuria was predominant mostly in the upper layers of the soil where their nematode host and the plant host roots are abundant, a factor which may be a critical consideration when using P. penetrans as a nematode biological control agent. PMID:29062154

Gridded population projections for the coastal zone under the Shared Socioeconomic Pathways

NASA Astrophysics Data System (ADS)

Merkens, Jan-Ludolf; Reimann, Lena; Hinkel, Jochen; Vafeidis, Athanasios T.

2016-10-01

Existing quantifications of the Shared Socioeconomic Pathways (SSP) used for climate impact assessment do not account for subnational population dynamics such as coastward-migration that can be critical for coastal impact assessment. This paper extends the SSPs by developing spatial projections of global coastal population distribution for the five basic SSPs. Based on a series of coastal migration drivers we develop coastal narratives for each SSP. These narratives account for differences in coastal and inland population developments in urban and rural areas. To spatially distribute population, we use the International Institute for Applied Systems Analysis (IIASA) national population and urbanisation projections and employ country-specific growth rates, which differ for coastal and inland as well as for urban and rural regions, to project coastal population for each SSP. These rates are derived from spatial analysis of historical population data and adjusted for each SSP based on the coastal narratives. Our results show that, compared to the year 2000 (638 million), the population living in the Low Elevated Coastal Zone (LECZ) increases by 58% to 71% until 2050 and exceeds one billion in all SSPs. By the end of the 21st century, global coastal population declines to 830-907 million in all SSPs except for SSP3, where coastal population growth continues and reaches 1.184 billion. Overall, the population living in the LECZ is higher by 85 to 239 million compared to the original IIASA projections. Asia expects the highest absolute growth (238-303 million), Africa the highest relative growth (153% to 218%). Our results highlight regions where high coastal population growth is expected and will therefore face an increased exposure to coastal flooding.

Incorporating population-level variation in thermal performance into predictions of geographic range shifts.

PubMed

Angert, Amy L; Sheth, Seema N; Paul, John R

2011-11-01

Determining how species' geographic ranges are governed by current climates and how they will respond to rapid climatic change poses a major biological challenge. Geographic ranges are often spatially fragmented and composed of genetically differentiated populations that are locally adapted to different thermal regimes. Tradeoffs between different aspects of thermal performance, such as between tolerance to high temperature and tolerance to low temperature or between maximal performance and breadth of performance, suggest that the performance of a given population will be a subset of that of the species. Therefore, species-level projections of distribution might overestimate the species' ability to persist at any given location. However, current approaches to modeling distributions often do not consider variation among populations. Here, we estimated genetically-based differences in thermal performance curves for growth among 12 populations of the scarlet monkeyflower, Mimulus cardinalis, a perennial herb of western North America. We inferred the maximum relative growth rate (RGR(max)), temperature optimum (T(opt)), and temperature breadth (T(breadth)) for each population. We used these data to test for tradeoffs in thermal performance, generate mechanistic population-level projections of distribution under current and future climates, and examine how variation in aspects of thermal performance influences forecasts of range shifts. Populations differed significantly in RGR(max) and had variable, but overlapping, estimates of T(opt) and T(breadth). T(opt) declined with latitude and increased with temperature of origin, consistent with tradeoffs between performances at low temperatures versus those at high temperatures. Further, T(breadth) was negatively related to RGR(max), as expected for a specialist-generalist tradeoff. Parameters of the thermal performance curve influenced properties of projected distributions. For both current and future climates, T(opt) was negatively related to latitudinal position, while T(breadth) was positively related to projected range size. The magnitude and direction of range shifts also varied with T(opt) and T(breadth), but sometimes in unexpected ways. For example, the fraction of habitat remaining suitable increased with T(opt) but decreased with T(breadth). Northern limits of all populations were projected to shift north, but the magnitude of shift decreased with T(opt) and increased with T(breadth). Median latitude was projected to shift north for populations with high T(breadth) and low T(opt), but south for populations with low T(breadth) and high T(opt). Distributions inferred by integrating population-level projections did not differ from a species-level projection that ignored variation among populations. However, the species-level approach masked the potential array of divergent responses by populations that might lead to genotypic sorting within the species' range. Thermal performance tradeoffs among populations within the species' range had important, but sometimes counterintuitive, effects on projected responses to climatic change. © The Author 2011. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved.

Finding differentially expressed genes in high dimensional data: Rank based test statistic via a distance measure.

PubMed

Mathur, Sunil; Sadana, Ajit

2015-12-01

We present a rank-based test statistic for the identification of differentially expressed genes using a distance measure. The proposed test statistic is highly robust against extreme values and does not assume the distribution of parent population. Simulation studies show that the proposed test is more powerful than some of the commonly used methods, such as paired t-test, Wilcoxon signed rank test, and significance analysis of microarray (SAM) under certain non-normal distributions. The asymptotic distribution of the test statistic, and the p-value function are discussed. The application of proposed method is shown using a real-life data set. © The Author(s) 2011.

Stochastic growth of cloud droplets by collisions during settling

NASA Astrophysics Data System (ADS)

Madival, Deepak G.

2018-04-01

In the last stage of droplet growth in clouds which leads to drizzle formation, larger droplets begin to settle under gravity and collide and coalesce with smaller droplets in their path. In this article, we shall deal with the simplified problem of a large drop settling amidst a population of identical smaller droplets. We present an expression for the probability that a given large drop suffers a given number of collisions, for a general statistically homogeneous distribution of droplets. We hope that our approach will serve as a valuable tool in dealing with droplet distribution in real clouds, which has been found to deviate from the idealized Poisson distribution due to mechanisms such as inertial clustering.

A Comparison of Agent-Based Models and the Parametric G-Formula for Causal Inference.

PubMed

Murray, Eleanor J; Robins, James M; Seage, George R; Freedberg, Kenneth A; Hernán, Miguel A

2017-07-15

Decision-making requires choosing from treatments on the basis of correctly estimated outcome distributions under each treatment. In the absence of randomized trials, 2 possible approaches are the parametric g-formula and agent-based models (ABMs). The g-formula has been used exclusively to estimate effects in the population from which data were collected, whereas ABMs are commonly used to estimate effects in multiple populations, necessitating stronger assumptions. Here, we describe potential biases that arise when ABM assumptions do not hold. To do so, we estimated 12-month mortality risk in simulated populations differing in prevalence of an unknown common cause of mortality and a time-varying confounder. The ABM and g-formula correctly estimated mortality and causal effects when all inputs were from the target population. However, whenever any inputs came from another population, the ABM gave biased estimates of mortality-and often of causal effects even when the true effect was null. In the absence of unmeasured confounding and model misspecification, both methods produce valid causal inferences for a given population when all inputs are from that population. However, ABMs may result in bias when extrapolated to populations that differ on the distribution of unmeasured outcome determinants, even when the causal network linking variables is identical. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Coevolutionary dynamics in large, but finite populations

NASA Astrophysics Data System (ADS)

Traulsen, Arne; Claussen, Jens Christian; Hauert, Christoph

2006-07-01

Coevolving and competing species or game-theoretic strategies exhibit rich and complex dynamics for which a general theoretical framework based on finite populations is still lacking. Recently, an explicit mean-field description in the form of a Fokker-Planck equation was derived for frequency-dependent selection with two strategies in finite populations based on microscopic processes [A. Traulsen, J. C. Claussen, and C. Hauert, Phys. Rev. Lett. 95, 238701 (2005)]. Here we generalize this approach in a twofold way: First, we extend the framework to an arbitrary number of strategies and second, we allow for mutations in the evolutionary process. The deterministic limit of infinite population size of the frequency-dependent Moran process yields the adjusted replicator-mutator equation, which describes the combined effect of selection and mutation. For finite populations, we provide an extension taking random drift into account. In the limit of neutral selection, i.e., whenever the process is determined by random drift and mutations, the stationary strategy distribution is derived. This distribution forms the background for the coevolutionary process. In particular, a critical mutation rate uc is obtained separating two scenarios: above uc the population predominantly consists of a mixture of strategies whereas below uc the population tends to be in homogeneous states. For one of the fundamental problems in evolutionary biology, the evolution of cooperation under Darwinian selection, we demonstrate that the analytical framework provides excellent approximations to individual based simulations even for rather small population sizes. This approach complements simulation results and provides a deeper, systematic understanding of coevolutionary dynamics.

Mitochondrial genetic variations in natural house fly (Musca domestica L.) populations from the western and southern parts of Turkey.

PubMed

Doğaç, Ersin

2016-09-01

The house fly Musca domestica Linnaeus (Diptera) is one of the most studied species that is globally distributed and well known to everyone. In order to ensure baseline knowledge for the genetic resources of the species, genetic variation in M. domestica populations from western and southern parts of Turkey was investigated using nucleotide sequence analysis of 348 base pairs (bp) in the mitochondrial cytochrome oxidase subunit I gene (COI). Samples of 192 individuals were collected from 16 localities of Turkey. There were 10 variable sites defining two haplotypes of COI in this species. There was no difference in geographical distribution frequency between the two regions of Turkey. Overall, haplotype diversity (h) was low, ranging from 0 to 0.5606 with the average overall value of 0.178 ± 0.04 and nucleotide diversity (π), ranged from 0 to 0.0056 with the overall mean of 0.0016. Analysis of molecular variance (AMOVA) indicated that genetic differentiation within individuals and populations was low and significant (p < 0.05). Except Afyon population, conventional population statistic FST showed no significant genetic structure along the range of M. domestica populations. Sixteen populations clustered under six haplotypes and two of them are unique to Turkey. Haplotype networks suggested that house fly populations in Turkey are grouped with the Palearctic region, which is the most probable place for the origin of this species.

Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health

PubMed Central

Muscarella, Robert; Borchsenius, Finn

2017-01-01

Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species (Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in ‘high allergy risk’ (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27–100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe. PMID:28321366

Divergent selection along climatic gradients in a rare central European endemic species, Saxifraga sponhemica

PubMed Central

Walisch, Tania J.; Colling, Guy; Bodenseh, Melanie; Matthies, Diethart

2015-01-01

Background and Aims The effects of habitat fragmentation on quantitative genetic variation in plant populations are still poorly known. Saxifraga sponhemica is a rare endemic of Central Europe with a disjunct distribution, and a stable and specialized habitat of treeless screes and cliffs. This study therefore used S. sponhemica as a model species to compare quantitative and molecular variation in order to explore (1) the relative importance of drift and selection in shaping the distribution of quantitative genetic variation along climatic gradients; (2) the relationship between plant fitness, quantitative genetic variation, molecular genetic variation and population size; and (3) the relationship between the differentiation of a trait among populations and its evolvability. Methods Genetic variation within and among 22 populations from the whole distribution area of S. sponhemica was studied using RAPD (random amplified polymorphic DNA) markers, and climatic variables were obtained for each site. Seeds were collected from each population and germinated, and seedlings were transplanted into a common garden for determination of variation in plant traits. Key Results In contrast to previous results from rare plant species, strong evidence was found for divergent selection. Most population trait means of S. sponhemica were significantly related to climate gradients, indicating adaptation. Quantitative genetic differentiation increased with geographical distance, even when neutral molecular divergence was controlled for, and QST exceeded FST for some traits. The evolvability of traits was negatively correlated with the degree of differentiation among populations (QST), i.e. traits under strong selection showed little genetic variation within populations. The evolutionary potential of a population was not related to its size, the performance of the population or its neutral genetic diversity. However, performance in the common garden was lower for plants from populations with reduced molecular genetic variation, suggesting inbreeding depression due to genetic erosion. Conclusions The findings suggest that studies of molecular and quantitative genetic variation may provide complementary insights important for the conservation of rare species. The strong differentiation of quantitative traits among populations shows that selection can be an important force for structuring variation in evolutionarily important traits even for rare endemic species restricted to very specific habitats. PMID:25862244

Estimation of selection intensity under overdominance by Bayesian methods.

PubMed

Buzbas, Erkan Ozge; Joyce, Paul; Abdo, Zaid

2009-01-01

A balanced pattern in the allele frequencies of polymorphic loci is a potential sign of selection, particularly of overdominance. Although this type of selection is of some interest in population genetics, there exists no likelihood based approaches specifically tailored to make inference on selection intensity. To fill this gap, we present Bayesian methods to estimate selection intensity under k-allele models with overdominance. Our model allows for an arbitrary number of loci and alleles within a locus. The neutral and selected variability within each locus are modeled with corresponding k-allele models. To estimate the posterior distribution of the mean selection intensity in a multilocus region, a hierarchical setup between loci is used. The methods are demonstrated with data at the Human Leukocyte Antigen loci from world-wide populations.

The effects of spatial population dataset choice on estimates of population at risk of disease

PubMed Central

2011-01-01

Background The spatial modeling of infectious disease distributions and dynamics is increasingly being undertaken for health services planning and disease control monitoring, implementation, and evaluation. Where risks are heterogeneous in space or dependent on person-to-person transmission, spatial data on human population distributions are required to estimate infectious disease risks, burdens, and dynamics. Several different modeled human population distribution datasets are available and widely used, but the disparities among them and the implications for enumerating disease burdens and populations at risk have not been considered systematically. Here, we quantify some of these effects using global estimates of populations at risk (PAR) of P. falciparum malaria as an example. Methods The recent construction of a global map of P. falciparum malaria endemicity enabled the testing of different gridded population datasets for providing estimates of PAR by endemicity class. The estimated population numbers within each class were calculated for each country using four different global gridded human population datasets: GRUMP (~1 km spatial resolution), LandScan (~1 km), UNEP Global Population Databases (~5 km), and GPW3 (~5 km). More detailed assessments of PAR variation and accuracy were conducted for three African countries where census data were available at a higher administrative-unit level than used by any of the four gridded population datasets. Results The estimates of PAR based on the datasets varied by more than 10 million people for some countries, even accounting for the fact that estimates of population totals made by different agencies are used to correct national totals in these datasets and can vary by more than 5% for many low-income countries. In many cases, these variations in PAR estimates comprised more than 10% of the total national population. The detailed country-level assessments suggested that none of the datasets was consistently more accurate than the others in estimating PAR. The sizes of such differences among modeled human populations were related to variations in the methods, input resolution, and date of the census data underlying each dataset. Data quality varied from country to country within the spatial population datasets. Conclusions Detailed, highly spatially resolved human population data are an essential resource for planning health service delivery for disease control, for the spatial modeling of epidemics, and for decision-making processes related to public health. However, our results highlight that for the low-income regions of the world where disease burden is greatest, existing datasets display substantial variations in estimated population distributions, resulting in uncertainty in disease assessments that utilize them. Increased efforts are required to gather contemporary and spatially detailed demographic data to reduce this uncertainty, particularly in Africa, and to develop population distribution modeling methods that match the rigor, sophistication, and ability to handle uncertainty of contemporary disease mapping and spread modeling. In the meantime, studies that utilize a particular spatial population dataset need to acknowledge the uncertainties inherent within them and consider how the methods and data that comprise each will affect conclusions. PMID:21299885

An Empirical Analysis of the Impact of Recruitment Patterns on RDS Estimates among a Socially Ordered Population of Female Sex Workers in China

PubMed Central

Yamanis, Thespina J.; Merli, M. Giovanna; Neely, William Whipple; Tian, Felicia Feng; Moody, James; Tu, Xiaowen; Gao, Ersheng

2013-01-01

Respondent-driven sampling (RDS) is a method for recruiting “hidden” populations through a network-based, chain and peer referral process. RDS recruits hidden populations more effectively than other sampling methods and promises to generate unbiased estimates of their characteristics. RDS’s faithful representation of hidden populations relies on the validity of core assumptions regarding the unobserved referral process. With empirical recruitment data from an RDS study of female sex workers (FSWs) in Shanghai, we assess the RDS assumption that participants recruit nonpreferentially from among their network alters. We also present a bootstrap method for constructing the confidence intervals around RDS estimates. This approach uniquely incorporates real-world features of the population under study (e.g., the sample’s observed branching structure). We then extend this approach to approximate the distribution of RDS estimates under various peer recruitment scenarios consistent with the data as a means to quantify the impact of recruitment bias and of rejection bias on the RDS estimates. We find that the hierarchical social organization of FSWs leads to recruitment biases by constraining RDS recruitment across social classes and introducing bias in the RDS estimates. PMID:24288418

Harvesting, predation and competition effects on a red coral population

NASA Astrophysics Data System (ADS)

Abbiati, M.; Buffoni, G.; Caforio, G.; Di Cola, G.; Santangelo, G.

A Corallium rubrum population, dwelling in the Ligurian Sea, has been under observation since 1987. Biometric descriptors of colonies (base diameter, weight, number of polyps, number of growth rings) have been recorded and correlated. The population size structure was obtained by distributing the colonies into diameter classes, each size class representing the average annual increment of diameter growth. The population was divided into ten classes, including a recruitment class. This size structure showed a fairly regular trend in the first four classes. The irregularity of survival in the older classes agreed with field observations on harvesting and predation. Demographic parameters such as survival, growth plasticity and natality coefficients were estimated from the experimental data. On this basis a discrete nonlinear model was implemented. The model is based on a kind of density-dependent Leslie matrix, where the feedback term only occurs in survival of the first class; the recruitment function is assumed to be dependent on the total biomass and related to inhibiting effects due to competitive interactions. Stability analysis was applied to steady-state solutions. Numerical simulations of population evolution were carried out under different conditions. The dynamics of settlement and the effects of disturbances such as harvesting, predation and environmental variability were studied.

Exact Markov chains versus diffusion theory for haploid random mating.

PubMed

Tyvand, Peder A; Thorvaldsen, Steinar

2010-05-01

Exact discrete Markov chains are applied to the Wright-Fisher model and the Moran model of haploid random mating. Selection and mutations are neglected. At each discrete value of time t there is a given number n of diploid monoecious organisms. The evolution of the population distribution is given in diffusion variables, to compare the two models of random mating with their common diffusion limit. Only the Moran model converges uniformly to the diffusion limit near the boundary. The Wright-Fisher model allows the population size to change with the generations. Diffusion theory tends to under-predict the loss of genetic information when a population enters a bottleneck. 2010 Elsevier Inc. All rights reserved.

Social-group identity and population substructure in admixed populations in New Mexico and Latin America.

PubMed

Healy, Meghan E; Hill, Deirdre; Berwick, Marianne; Edgar, Heather; Gross, Jessica; Hunley, Keith

2017-01-01

We examined the relationship between continental-level genetic ancestry and racial and ethnic identity in an admixed population in New Mexico with the goal of increasing our understanding of how racial and ethnic identity influence genetic substructure in admixed populations. Our sample consists of 98 New Mexicans who self-identified as Hispanic or Latino (NM-HL) and who further categorized themselves by race and ethnic subgroup membership. The genetic data consist of 270 newly-published autosomal microsatellites from the NM-HL sample and previously published data from 57 globally distributed populations, including 13 admixed samples from Central and South America. For these data, we 1) summarized the major axes of genetic variation using principal component analyses, 2) performed tests of Hardy Weinberg equilibrium, 3) compared empirical genetic ancestry distributions to those predicted under a model of admixture that lacked substructure, 4) tested the hypotheses that individuals in each sample had 100%, 0%, and the sample-mean percentage of African, European, and Native American ancestry. We found that most NM-HL identify themselves and their parents as belonging to one of two groups, conforming to a region-specific narrative that distinguishes recent immigrants from Mexico from individuals whose families have resided in New Mexico for generations and who emphasize their Spanish heritage. The "Spanish" group had significantly lower Native American ancestry and higher European ancestry than the "Mexican" group. Positive FIS values, PCA plots, and heterogeneous ancestry distributions suggest that most Central and South America admixed samples also contain substructure, and that this substructure may be related to variation in social identity. Genetic substructure appears to be common in admixed populations in the Americas and may confound attempts to identify disease-causing genes and to understand the social causes of variation in health outcomes and social inequality.

Evaluation of the 2011 long-lasting, insecticide-treated net distribution for universal coverage in Togo.

PubMed

Stevens, Elizabeth R; Aldridge, Abigail; Degbey, Yawo; Pignandi, Akou; Dorkenoo, Monique A; Hugelen-Padin, Justin

2013-05-16

Malaria remains a substantial public health problem in Togo. An integrated child health campaign was conducted in Togo in October 2011. This campaign included a component of free distribution of 2,799,800 long-lasting, insecticide-treated nets (LLINs) to households throughout Togo. This distribution marked the first effort in Togo at universal LLIN coverage and was not targeted specifically to children under five years and pregnant women, but to all household members. This study reports the results of the LLIN distribution campaign in terms of bed net possession and utilization. A representative household survey was implemented during the rainy season nine months after the LLIN distribution component of the campaign. Some 6,015 households selected through two stages of probability proportion to size stratified random sampling were interviewed using a brief questionnaire that included a demographic section with questions on the number of household members and sleeping spaces, and a campaign participation section with questions used to evaluate non-LLIN aspects of the campaign. A net roster listed all nets and their characteristics, and a household roster listed all members and visitors with information about bed net use. The questions addressed different aspects of bed net and LLIN possession and utilization. Crude weighted frequencies, percentages, and t- tests of association were calculated using the Stata 12.0 Survey features. Possession of at least one bed net and/or LLIN increased from 41.3% to 96.7% (P <0.001). Household possession of at least one campaign LLIN was 93.3%. Report LLIN among pregnant women was 77.5% and 79.3% for children under five. For the general population LLIN use was 68.3%. Due to the gap in LLIN possession and use and the significant number of individuals reporting a lack of nets as a reason for non-use, additional national LLIN distribution campaigns with a stronger educational component need to be implemented in order increase the use of available LLINs and to reach and maintain universal coverage of LLINs in Togo. The LLIN distribution campaign focusing on universal coverage of the general population in Togo was more successful at increasing LLIN possession and use of children under five years and pregnant women than other campaigns focusing only on these target groups.

How will climate change affect the potential distribution of Eurasian Tree Sparrows Passer montanus in North America?

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine; Young, Nick; Newman, Greg; Stohlgren, Thomas

2011-01-01

Habitat suitability models have been used to predict the present and future potential distribution of a variety of species. Eurasian tree sparrows Passer montanus, native to Eurasia, have established populations in other parts of the world. In North America, their current distribution is limited to a relatively small region around its original introduction to St. Louis, Missouri. We combined data from the Global Biodiversity Information Facility with current and future climate data to create habitat suitability models using Maxent for this species. Under projected climate change scenarios, our models show that the distribution and range of the Eurasian tree sparrow could increase as far as the Pacific Northwest and Newfoundland. This is potentially important information for prioritizing the management and control of this non-native species.

Mate-finding as an overlooked critical determinant of dispersal variation in sexually-reproducing animals.

PubMed

Gilroy, James J; Lockwood, Julie L

2012-01-01

Dispersal is a critically important process in ecology, but robust predictive models of animal dispersal remain elusive. We identify a potentially ubiquitous component of variation in animal dispersal that has been largely overlooked until now: the influence of mate encounters on settlement probability. We use an individual-based model to simulate dispersal in sexually-reproducing organisms that follow a simple set of movement rules based on conspecific encounters, within an environment lacking spatial habitat heterogeneity. We show that dispersal distances vary dramatically with fluctuations in population density in such a model, even in the absence of variation in dispersive traits between individuals. In a simple random-walk model with promiscuous mating, dispersal distributions become increasingly 'fat-tailed' at low population densities due to the increasing scarcity of mates. Similar variation arises in models incorporating territoriality. In a model with polygynous mating, we show that patterns of sex-biased dispersal can even be reversed across a gradient of population density, despite underlying dispersal mechanisms remaining unchanged. We show that some widespread dispersal patterns found in nature (e.g. fat tailed distributions) can arise as a result of demographic variability in the absence of heterogeneity in dispersive traits across the population. This implies that models in which individual dispersal distances are considered to be fixed traits might be unrealistic, as dispersal distances vary widely under a single dispersal mechanism when settlement is influenced by mate encounters. Mechanistic models offer a promising means of advancing our understanding of dispersal in sexually-reproducing organisms.

Time Evolving Fission Chain Theory and Fast Neutron and Gamma-Ray Counting Distributions

DOE PAGES

Kim, K. S.; Nakae, L. F.; Prasad, M. K.; ...

2015-11-01

Here, we solve a simple theoretical model of time evolving fission chains due to Feynman that generalizes and asymptotically approaches the point model theory. The point model theory has been used to analyze thermal neutron counting data. This extension of the theory underlies fast counting data for both neutrons and gamma rays from metal systems. Fast neutron and gamma-ray counting is now possible using liquid scintillator arrays with nanosecond time resolution. For individual fission chains, the differential equations describing three correlated probability distributions are solved: the time-dependent internal neutron population, accumulation of fissions in time, and accumulation of leaked neutronsmore » in time. Explicit analytic formulas are given for correlated moments of the time evolving chain populations. The equations for random time gate fast neutron and gamma-ray counting distributions, due to randomly initiated chains, are presented. Correlated moment equations are given for both random time gate and triggered time gate counting. There are explicit formulas for all correlated moments are given up to triple order, for all combinations of correlated fast neutrons and gamma rays. The nonlinear differential equations for probabilities for time dependent fission chain populations have a remarkably simple Monte Carlo realization. A Monte Carlo code was developed for this theory and is shown to statistically realize the solutions to the fission chain theory probability distributions. Combined with random initiation of chains and detection of external quanta, the Monte Carlo code generates time tagged data for neutron and gamma-ray counting and from these data the counting distributions.« less

A landscape perspective of the stream corridor invasion and habitat characteristics of an exotic (Dioscorea oppositifolia) in a pristine watershed in Illinois

USGS Publications Warehouse

Thomas, J.R.; Middleton, B.; Gibson, D.J.

2006-01-01

The spatial distribution of exotics across riparian landscapes is not uniform, and research elaborating the environmental constraints and dispersal behavior that underlie these patterns of distribution is warranted. This study examined the spatial distribution, growth patterns, and habitat constraints of populations of the invasive Dioscorea oppositifolia in a forested stream corridor of a tributary of Drury Creek in Giant City State Park, IL. The distribution of D. oppositifolia was determined at the watershed scale mainly by floodplain structure and connectivity. Populations of D. oppositifolia were confined to the floodplain, with overbank flooding from the stream. Dioscorea oppositifolia probably originates in disturbed areas upstream of natural corridors, and subsequently, the species disperses downstream into pristine canyons or ravines via bulbils dispersing in the water. In Giant City State Park, populations of D. oppositifolia were distributed on the floodplain across broad gradients of soil texture, light, slope, and potential radiation. The study also examined the longevity of bulbils in various micro-environments to illuminate strategies for the management of the species in invaded watersheds. After 1 year, the highest percentages of bulbils were viable under leaves, and much lower percentages were viable over leaves, in soil, and in the creek (76.0??6.8, 21.2??9.6, 21.6??3.6, and 5.2??5.2%), respectively. This study suggests that management procedures that reduce leaf litter on the forest floor (e.g., prescribed burning) could reduce the number of bulbils of D. oppositifolia stored in the watershed. ?? Springer 2006.

Population density equations for stochastic processes with memory kernels

NASA Astrophysics Data System (ADS)

Lai, Yi Ming; de Kamps, Marc

2017-06-01

We present a method for solving population density equations (PDEs)-a mean-field technique describing homogeneous populations of uncoupled neurons—where the populations can be subject to non-Markov noise for arbitrary distributions of jump sizes. The method combines recent developments in two different disciplines that traditionally have had limited interaction: computational neuroscience and the theory of random networks. The method uses a geometric binning scheme, based on the method of characteristics, to capture the deterministic neurodynamics of the population, separating the deterministic and stochastic process cleanly. We can independently vary the choice of the deterministic model and the model for the stochastic process, leading to a highly modular numerical solution strategy. We demonstrate this by replacing the master equation implicit in many formulations of the PDE formalism by a generalization called the generalized Montroll-Weiss equation—a recent result from random network theory—describing a random walker subject to transitions realized by a non-Markovian process. We demonstrate the method for leaky- and quadratic-integrate and fire neurons subject to spike trains with Poisson and gamma-distributed interspike intervals. We are able to model jump responses for both models accurately to both excitatory and inhibitory input under the assumption that all inputs are generated by one renewal process.

Effects of resource-dependent cannibalism on population size distribution and individual life history in a case-bearing caddisfly

PubMed Central

Okuda, Noboru

2018-01-01

Resource availability often determines the intensity of cannibalism, which has a considerable effect on population size distribution and individual life history. Larvae of the caddisfly Psilotreta kisoensis build portable cases from sedimentary sands and often display cannibalism. For this species, the availability of preferable case material is a critical factor that affects larval fitness, and material is locally variable depending on the underlying geology. In this study, we investigated how sand quality as a case material determines cannibalism frequency among larvae and, in turn, how the differential cannibalism frequency affects the body-size distribution and voltinism. Rearing experiments within a cohort revealed that a bimodal size distribution developed regardless of material quality. However, as the preferable material became abundant, the proportion of larger to smaller individuals increased. Consecutive experiments suggested that smaller larvae were more frequently cannibalized by larger ones and excluded from the population when preferable smooth material was abundant. This frequent cannibalism resulted in a bimodal size distribution with a significantly higher proportion of larger compared to smaller individuals. The size-dependent cannibalism was significantly suppressed when the larvae were raised in an environment with a scarcity of the preferable case material. This is probably because larvae cannot enjoy the benefit of rapid growth by cannibalism due to the difficulties in enlarging their case. At low cannibalism the growth of smaller individuals was stunted, and this was probably due to risk of cannibalism by larger individuals. This growth reduction in small individuals led to a bimodal size-distribution but with a lower proportion of larger to smaller individuals compared to at high cannibalism. A field study in two streams showed a similar size distribution of larvae as was found in the rearing experiment. The bimodal ratio has consequences for life history, since a size-bimodal population causes a cohort splitting: only larvae that were fully grown at 1 year had a univoltine life cycle, whereas larvae with a stunted growth continued their larval life for another year (semivoltine). This study suggests that availability of preferable case building material is an important factor that affects cannibalism, which in turn affects larval population size structure and cohort splitting. PMID:29466375

Effects of resource-dependent cannibalism on population size distribution and individual life history in a case-bearing caddisfly.

PubMed

Okano, Jun-Ichi; Okuda, Noboru

2018-01-01

Resource availability often determines the intensity of cannibalism, which has a considerable effect on population size distribution and individual life history. Larvae of the caddisfly Psilotreta kisoensis build portable cases from sedimentary sands and often display cannibalism. For this species, the availability of preferable case material is a critical factor that affects larval fitness, and material is locally variable depending on the underlying geology. In this study, we investigated how sand quality as a case material determines cannibalism frequency among larvae and, in turn, how the differential cannibalism frequency affects the body-size distribution and voltinism. Rearing experiments within a cohort revealed that a bimodal size distribution developed regardless of material quality. However, as the preferable material became abundant, the proportion of larger to smaller individuals increased. Consecutive experiments suggested that smaller larvae were more frequently cannibalized by larger ones and excluded from the population when preferable smooth material was abundant. This frequent cannibalism resulted in a bimodal size distribution with a significantly higher proportion of larger compared to smaller individuals. The size-dependent cannibalism was significantly suppressed when the larvae were raised in an environment with a scarcity of the preferable case material. This is probably because larvae cannot enjoy the benefit of rapid growth by cannibalism due to the difficulties in enlarging their case. At low cannibalism the growth of smaller individuals was stunted, and this was probably due to risk of cannibalism by larger individuals. This growth reduction in small individuals led to a bimodal size-distribution but with a lower proportion of larger to smaller individuals compared to at high cannibalism. A field study in two streams showed a similar size distribution of larvae as was found in the rearing experiment. The bimodal ratio has consequences for life history, since a size-bimodal population causes a cohort splitting: only larvae that were fully grown at 1 year had a univoltine life cycle, whereas larvae with a stunted growth continued their larval life for another year (semivoltine). This study suggests that availability of preferable case building material is an important factor that affects cannibalism, which in turn affects larval population size structure and cohort splitting.

Morphology and distribution of seamounts surrounding Easter Island

USGS Publications Warehouse

Rappaport, Y.; Naar, D.F.; Barton, C.C.; Liu, Z.-J.; Hey, R.N.

1997-01-01

We investigate the morphology and distribution of a seamount population on a section of seafloor influenced by both superfast seafloor spreading and hotspot volcanism. The population under investigation is part of a broad chain of seamounts extending eastward from the East Pacific Rise, near Easter Island. In order to define the morphological variability of the seamounts, basal shape, cross-sectional area, volume, flatness, and flank slope are plotted against height for 383 seamounts with heights greater than 200 m, based on bathymetry data collected by GLORI-B and SeaBeam 2000, during three cruises onboard the R/V Melville in the spring of 1993. Nearly complete swath mapping coverage of the seamounts is available for the analysis of size and shape distribution. We quantitatively describe the seamount population of this active region, in which seamounts cover ???27% of the seafloor, and account for ???4.2% of the total crustal volume. Over 50% of the total volume (61,000 km3) of seamounts used in this study is made up by the 14 largest seamounts, and the remaining volume is made up by the 369 smaller seamounts (>200 m in height). Our analysis indicates there are at least two seamount populations in the Easter Island-Salas y Gomez Island (25??-29??S, 113??-104??W) study area. One population of seamounts is composed of short seamounts (1200 m), shield-like, pointy cones (flatness ???1200 m) originate exclusively from a hotspot source, but only a portion of the smaller volcanoes (

Long-term variability of the siphonophores Muggiaea atlantica and M. kochi in the Western English Channel

NASA Astrophysics Data System (ADS)

Blackett, Michael; Licandro, Priscilla; Coombs, Steve H.; Lucas, Cathy H.

2014-11-01

We investigated long-term variability of the calycophoran siphonophores Muggiaea atlantica and Muggiaea kochi in the Western English Channel (WEC) between 1930 and 2011. Our aims were to describe long-term changes in abundance and temporal distribution in relation to local environmental dynamics. In order to better understand mechanisms that regulate the species' populations, we identified periods that were characteristic of in situ population growth and the environmental optima associated with these events. Our results show that between 1930 and the 1960s both M. atlantica and M. kochi were transient components of the WEC ecosystem. In the late 1960s M. atlantica, successfully established a resident population in the WEC, while the occurrence of M. kochi became increasingly sporadic. Once established as a resident species, the seasonal abundance and distribution of M. atlantica increased. Analysis of environmental conditions associated with in situ population growth revealed that temperature and prey were key determinants of the seasonal distribution and abundance of M. atlantica. Salinity was shown to have an indirect effect, likely representing a proxy for water circulation in the WEC. Anomalies in the seasonal cycle of salinity, indicating deviation from the usual circulation pattern in the WEC, were negatively associated with in situ growth, suggesting dispersal of the locally developing M. atlantica population. However, our findings identified complexity in the relationship between characteristics of the environment and M. atlantica variability. The transition from a period of transiency (1930-1968) to residency (1969-2011) was tentatively attributed to structural changes in the WEC ecosystem that occurred under the forcing of wider-scale hydroclimatic changes.

The cyclophosphamide equivalent dose as an approach for quantifying alkylating agent exposure: a report from the Childhood Cancer Survivor Study.

PubMed

Green, Daniel M; Nolan, Vikki G; Goodman, Pamela J; Whitton, John A; Srivastava, DeoKumar; Leisenring, Wendy M; Neglia, Joseph P; Sklar, Charles A; Kaste, Sue C; Hudson, Melissa M; Diller, Lisa R; Stovall, Marilyn; Donaldson, Sarah S; Robison, Leslie L

2014-01-01

Estimation of the risk of adverse long-term outcomes such as second malignant neoplasms and infertility often requires reproducible quantification of exposures. The method for quantification should be easily utilized and valid across different study populations. The widely used Alkylating Agent Dose (AAD) score is derived from the drug dose distribution of the study population and thus cannot be used for comparisons across populations as each will have a unique distribution of drug doses. We compared the performance of the Cyclophosphamide Equivalent Dose (CED), a unit for quantifying alkylating agent exposure independent of study population, to the AAD. Comparisons included associations from three Childhood Cancer Survivor Study (CCSS) outcome analyses, receiver operator characteristic (ROC) curves and goodness of fit based on the Akaike's Information Criterion (AIC). The CED and AAD performed essentially identically in analyses of risk for pregnancy among the partners of male CCSS participants, risk for adverse dental outcomes among all CCSS participants and risk for premature menopause among female CCSS participants, based on similar associations, lack of statistically significant differences between the areas under the ROC curves and similar model fit values for the AIC between models including the two measures of exposure. The CED is easily calculated, facilitating its use for patient counseling. It is independent of the drug dose distribution of a particular patient population, a characteristic that will allow direct comparisons of outcomes among epidemiological cohorts. We recommend the use of the CED in future research assessing cumulative alkylating agent exposure. © 2013 Wiley Periodicals, Inc.

Limits to gene flow in a cosmopolitan marine planktonic diatom.

PubMed

Casteleyn, Griet; Leliaert, Frederik; Backeljau, Thierry; Debeer, Ann-Eline; Kotaki, Yuichi; Rhodes, Lesley; Lundholm, Nina; Sabbe, Koen; Vyverman, Wim

2010-07-20

The role of geographic isolation in marine microbial speciation is hotly debated because of the high dispersal potential and large population sizes of planktonic microorganisms and the apparent lack of strong dispersal barriers in the open sea. Here, we show that gene flow between distant populations of the globally distributed, bloom-forming diatom species Pseudo-nitzschia pungens (clade I) is limited and follows a strong isolation by distance pattern. Furthermore, phylogenetic analysis implies that under appropriate geographic and environmental circumstances, like the pronounced climatic changes in the Pleistocene, population structuring may lead to speciation and hence may play an important role in diversification of marine planktonic microorganisms. A better understanding of the factors that control population structuring is thus essential to reveal the role of allopatric speciation in marine microorganisms.

Investigating the case of human nose shape and climate adaptation

PubMed Central

Zaidi, Arslan A.; Claes, Peter; McEcoy, Brian; Shriver, Mark D.

2017-01-01

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection. PMID:28301464

Quantification of HTLV-1 Clonality and TCR Diversity

PubMed Central

Laydon, Daniel J.; Melamed, Anat; Sim, Aaron; Gillet, Nicolas A.; Sim, Kathleen; Darko, Sam; Kroll, J. Simon; Douek, Daniel C.; Price, David A.; Bangham, Charles R. M.; Asquith, Becca

2014-01-01

Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological “species” in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations. PMID:24945836

Using Species Distribution Model to Estimate the Wintering Population Size of the Endangered Scaly-Sided Merganser in China

PubMed Central

Zeng, Qing; Zhang, Yamian; Sun, Gongqi; Duo, Hairui; Wen, Li; Lei, Guangchun

2015-01-01

Scaly-sided Merganser is a globally endangered species restricted to eastern Asia. Estimating its population is difficult and considerable gap exists between populations at its breeding grounds and wintering sites. In this study, we built a species distribution model (SDM) using Maxent with presence-only data to predict the potential wintering habitat for Scaly-sided Merganser in China. Area under the receiver operating characteristic curve (AUC) method suggests high predictive power of the model (training and testing AUC were 0.97 and 0.96 respectively). The most significant environmental variables included annual mean temperature, mean temperature of coldest quarter, minimum temperature of coldest month and precipitation of driest quarter. Suitable conditions for Scaly-sided Merganser are predicted in the middle and lower reaches of the Yangtze River, especially in Jiangxi, Hunan and Hubei Provinces. The predicted suitable habitat embraces 6,984 km of river. Based on survey results from three consecutive winters (2010–2012) and previous studies, we estimated that the entire wintering population of Scaly-sided Merganser in China to be 3,561 ± 478 individuals, which is consistent with estimate in its breeding ground. PMID:25646969

Towards a Global Water Scarcity Risk Assessment Framework: Incorporation of Probability Distributions and Hydro-Climatic Variability

NASA Technical Reports Server (NTRS)

Veldkamp, T. I. E.; Wada, Y.; Aerts, J. C. J. H.; Ward, P. J.

2016-01-01

Changing hydro-climatic and socioeconomic conditions increasingly put pressure on fresh water resources and are expected to aggravate water scarcity conditions towards the future. Despite numerous calls for risk-based water scarcity assessments, a global-scale framework that includes UNISDR's definition of risk does not yet exist. This study provides a first step towards such a risk based assessment, applying a Gamma distribution to estimate water scarcity conditions at the global scale under historic and future conditions, using multiple climate change and population growth scenarios. Our study highlights that water scarcity risk, expressed in terms of expected annual exposed population, increases given all future scenarios, up to greater than 56.2% of the global population in 2080. Looking at the drivers of risk, we find that population growth outweigh the impacts of climate change at global and regional scales. Using a risk-based method to assess water scarcity, we show the results to be less sensitive than traditional water scarcity assessments to the use of fixed threshold to represent different levels of water scarcity. This becomes especially important when moving from global to local scales, whereby deviations increase up to 50% of estimated risk levels.

Investigating the case of human nose shape and climate adaptation.

PubMed

Zaidi, Arslan A; Mattern, Brooke C; Claes, Peter; McEvoy, Brian; Hughes, Cris; Shriver, Mark D

2017-03-01

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst-Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.

Genetic connectivity and self-replenishment of inshore and offshore populations of the endemic anemonefish, Amphiprion latezonatus

NASA Astrophysics Data System (ADS)

Steinberg, Rosemary; van der Meer, Martin; Walker, Emily; Berumen, Michael L.; Hobbs, Jean-Paul A.; van Herwerden, Lynne

2016-09-01

Globally, marine species are under increasing pressure from human activities, including ocean warming, acidification, pollution, and overfishing. Species most vulnerable to these pressures tend to be ecological specialists that have low abundance and small distribution ranges (endemics). Marine endemics often exist as meta-populations distributed among few isolated locations. Determining genetic connectivity among these locations is essential to understanding the recovery potential of endemics after local extinction events. This study examined connectivity in the endemic anemonefish, Amphiprion latezonatus, a habitat specialist with low abundance at most locations. Evolutionary and contemporary migration, genetic diversity, and self-replenishment among the four main locations (Sunshine Coast, North Solitary Island, Lord Howe Island, and Norfolk Island) that comprise the entire A. latezonatus geographic range were assessed using mtDNA and microsatellite markers. Though historical gene flow inferred from mtDNA appeared high, population genetic differentiation was evident and contemporary gene flow inferred from microsatellites was limited, alongside very high (≥89 %) self-replenishment at all locations. Together, these data suggest prolonged recovery times following severe population decline (or extirpation) and indicate a need to protect this species at all locations, particularly Norfolk Island and Sunshine Coast where marine protected areas are lacking.

Did Large-Scale Vaccination Drive Changes in the Circulating Rotavirus Population in Belgium?

PubMed Central

Pitzer, Virginia E.; Bilcke, Joke; Heylen, Elisabeth; Crawford, Forrest W.; Callens, Michael; De Smet, Frank; Van Ranst, Marc; Zeller, Mark; Matthijnssens, Jelle

2015-01-01

Vaccination can place selective pressures on viral populations, leading to changes in the distribution of strains as viruses evolve to escape immunity from the vaccine. Vaccine-driven strain replacement is a major concern after nationwide rotavirus vaccine introductions. However, the distribution of the predominant rotavirus genotypes varies from year to year in the absence of vaccination, making it difficult to determine what changes can be attributed to the vaccines. To gain insight in the underlying dynamics driving changes in the rotavirus population, we fitted a hierarchy of mathematical models to national and local genotype-specific hospitalization data from Belgium, where large-scale vaccination was introduced in 2006. We estimated that natural- and vaccine-derived immunity was strongest against completely homotypic strains and weakest against fully heterotypic strains, with an intermediate immunity amongst partially heterotypic strains. The predominance of G2P[4] infections in Belgium after vaccine introduction can be explained by a combination of natural genotype fluctuations and weaker natural and vaccine-induced immunity against infection with strains heterotypic to the vaccine, in the absence of significant variation in strain-specific vaccine effectiveness against disease. However, the incidence of rotavirus gastroenteritis is predicted to remain low despite vaccine-driven changes in the distribution of genotypes. PMID:26687288

Lot quality assurance sampling (LQAS) for monitoring a leprosy elimination program.

PubMed

Gupte, M D; Narasimhamurthy, B

1999-06-01

In a statistical sense, prevalences of leprosy in different geographical areas can be called very low or rare. Conventional survey methods to monitor leprosy control programs, therefore, need large sample sizes, are expensive, and are time-consuming. Further, with the lowering of prevalence to the near-desired target level, 1 case per 10,000 population at national or subnational levels, the program administrator's concern will be shifted to smaller areas, e.g., districts, for assessment and, if needed, for necessary interventions. In this paper, Lot Quality Assurance Sampling (LQAS), a quality control tool in industry, is proposed to identify districts/regions having a prevalence of leprosy at or above a certain target level, e.g., 1 in 10,000. This technique can also be considered for identifying districts/regions at or below the target level of 1 per 10,000, i.e., areas where the elimination level is attained. For simulating various situations and strategies, a hypothetical computerized population of 10 million persons was created. This population mimics the actual population in terms of the empirical information on rural/urban distributions and the distribution of households by size for the state of Tamil Nadu, India. Various levels with respect to leprosy prevalence are created using this population. The distribution of the number of cases in the population was expected to follow the Poisson process, and this was also confirmed by examination. Sample sizes and corresponding critical values were computed using Poisson approximation. Initially, villages/towns are selected from the population and from each selected village/town households are selected using systematic sampling. Households instead of individuals are used as sampling units. This sampling procedure was simulated 1000 times in the computer from the base population. The results in four different prevalence situations meet the required limits of Type I error of 5% and 90% Power. It is concluded that after validation under field conditions, this method can be considered for a rapid assessment of the leprosy situation.

Phylogenetic Distribution of Leaf Spectra and Optically Derived Functional Traits in the American Oaks

NASA Astrophysics Data System (ADS)

Cavender-Bares, J.; Meireles, J. E.; Couture, J. J.; Kaproth, M.; Townsend, P. A.

2015-12-01

Detecting functional traits of species, genotypes and phylogenetic lineages is critical in monitoring functional biodiversity remotely. We examined the phylogenetic distribution of leaf spectra across the American Oaks for 35 species under greenhouse conditions as well as genetic variation in leaf spectra across Central American populations of a single species grown in common gardens in Honduras. We found significant phylogenetic signal in the leaf spectra (Blomberg's K > 1.0), indicating similarity in spectra among close relatives. Across species, full range leaf spectra were used in a Partial Least Squares Discriminant Analysis (PLS-DA) that allowed species calibration (kappa statistic = 0.55). Validation of the model used to detect species (kappa statistic = 0.4) indicated reasonably good detection of individual species within the same the genus. Among four populations from Belize, Costa Rica, Honduras, and Mexico within a single species (Quercus oleoides), leaf spectra were also able to differentiate populations. Ordination of population-level data using dissimilarities of predicted foliar traits, including leaf mass per area (LMA), lignin content, fiber content, chlorophyll a+b, and C:N ratio in genotypes in either watered or unwatered conditions showed significant differentiation among populations and treatments. These results provide promise for remote detection and differentiation of plant functional traits among plant phylogenetic lineages and genotypes, even among closely related populations and species.

Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides.

PubMed

Ramírez-Valiente, José A; Deacon, Nicholas J; Etterson, Julie; Center, Alyson; Sparks, Jed P; Sparks, Kimberlee L; Longwell, Timothy; Pilz, George; Cavender-Bares, Jeannine

2018-05-01

The impacts of drought are expanding worldwide as a consequence of climate change. However, there is still little knowledge of how species respond to long-term selection in seasonally dry ecosystems. In this study, we used Q ST -F ST comparisons to investigate (i) the role of natural selection on population genetic differentiation for a set of functional traits related to drought resistance in the seasonally dry tropical oak Quercus oleoides and (ii) the influence of water availability at the site of population origin and in experimental treatments on patterns of trait divergence. We conducted a thorough phenotypic characterization of 1912 seedlings from ten populations growing in field and greenhouse common gardens under replicated watering treatments. We also genotyped 218 individuals from the same set of populations using eleven nuclear microsatellites. Q ST distributions for leaf lamina area, specific leaf area, leaf thickness and stomatal pore index were higher than F ST distribution. Results were consistent across growth environments. Genetic differentiation among populations for these functional traits was associated with the index of moisture at the origin of the populations. Together, our results suggest that drought is an important selective agent for Q. oleoides and that differences in length and severity of the dry season have driven the evolution of genetic differences in functional traits. © 2018 John Wiley & Sons Ltd.

Population structure and demographic history of a tropical lowland rainforest tree species Shorea parvifolia (Dipterocarpaceae) from Southeastern Asia.

PubMed

Iwanaga, Hiroko; Teshima, Kosuke M; Khatab, Ismael A; Inomata, Nobuyuki; Finkeldey, Reiner; Siregar, Iskandar Z; Siregar, Ulfah J; Szmidt, Alfred E

2012-07-01

Distribution of tropical rainforests in Southeastern Asia has changed over geo-logical time scale, due to movement of tectonic plates and/or global climatic changes. Shorea parvifolia is one of the most common tropical lowland rainforest tree species in Southeastern Asia. To infer population structure and demographic history of S. parvifolia, as indicators of temporal changes in the distribution and extent of tropical rainforest in this region, we studied levels and patterns of nucleotide polymorphism in the following five nuclear gene regions: GapC, GBSSI, PgiC, SBE2, and SODH. Seven populations from peninsular Malaysia, Sumatra, and eastern Borneo were included in the analyses. STRUCTURE analysis revealed that the investigated populations are divided into two groups: Sumatra-Malay and Borneo. Furthermore, each group contained one admixed population. Under isolation with migration model, divergence of the two groups was estimated to occur between late Pliocene (2.6 MYA) and middle Pleistocene (0.7 MYA). The log-likelihood ratio tests of several demographic models strongly supported model with population expansion and low level of migration after divergence of the Sumatra-Malay and Borneo groups. The inferred demographic history of S. parvifolia suggested the presence of a scarcely forested land bridge on the Sunda Shelf during glacial periods in the Pleistocene and predominance of tropical lowland rainforest at least in Sumatra and eastern Borneo.

Assessment of radiation doses from residential smoke detectors that contain americium-241

NASA Astrophysics Data System (ADS)

Odonnell, F. R.; Etnier, E. L.; Holton, G. A.; Travis, C. C.

1981-10-01

External dose equivalents and internal dose commitments were estimated for individuals and populations from annual distribution, use, and disposal of 10 million ionization chamber smoke detectors that contain 110 kBq americium-241 each. Under exposure scenarios developed for normal distribution, use, and disposal using the best available information, annual external dose equivalents to average individuals were estimated to range from 4 fSv to 20 nSv for total body and from 7 fSv to 40 nSv for bone. Internal dose commitments to individuals under post disposal scenarios were estimated to range from 0.006 to 80 micro-Sv (0.0006 to 8 mrem) to total body and from 0.06 to 800 micro-Sv to bone. The total collective dose (the sum of external dose equivalents and 50-year internal dose commitments) for all individuals involved with distribution, use, or disposal of 10 million smoke detectors was estimated to be about 0.38 person-Sv (38 person-rem) to total body and 00 ft squared.

The Principles of Buoyancy in Marine Fish Eggs and Their Vertical Distributions across the World Oceans.

PubMed

Sundby, Svein; Kristiansen, Trond

2015-01-01

Buoyancy acting on plankton, i.e. the difference in specific gravity between plankton and the ambient water, is a function of salinity and temperature. From specific gravity measurements of marine fish eggs salinity appears to be the only determinant of the buoyancy indicating that the thermal expansions of the fish egg and the ambient seawater are equal. We analyze the mechanisms behind thermal expansion in fish eggs in order to determine to what extent it can be justified to neglect the effects of temperature on buoyancy. Our results confirm the earlier assumptions that salinity is the basic determinant on buoyancy in marine fish eggs that, in turn, influence the vertical distributions and, consequently, the dispersal of fish eggs from the spawning areas. Fish populations have adapted accordingly by producing egg specific gravities that tune the egg buoyancy to create specific vertical distributions for each local population. A wide variety of buoyancy adaptations are found among fish populations. The ambient physical conditions at the spawning sites form a basic constraint for adaptation. In coastal regions where salinity increases with depth, and where the major fraction of the fish stocks spawns, pelagic and mesopelagic egg distributions dominate. However, in the larger part of worlds' oceans salinity decreases with depth resulting in different egg distributions. Here, the principles of vertical distributions of fish eggs in the world oceans are presented in an overarching framework presenting the basic differences between regions, mainly coastal, where salinity increases with depth and the major part of the world oceans where salinity decreases with depth. We show that under these latter conditions, steady-state vertical distribution of mesopelagic fish eggs cannot exist as it does in most coastal regions. In fact, a critical spawning depth must exist where spawning below this depth threshold results in eggs sinking out of the water column and become lost for recruitment to the population. An example of adaptation to such conditions is Cape hake spawning above the critical layer in the Northern Benguela upwelling ecosystem. The eggs rise slowly in the onshore subsurface current below the Ekman layer, hence being advected inshore where the hatched larvae concentrate with optimal feeding conditions.

Selective toxin effects on faster and slower growing individuals in the formation of hormesis at the population level - A case study with Lactuca sativa and PCIB.

PubMed

Belz, Regina G; Sinkkonen, Aki

2016-10-01

Natural plant populations have large phenotypic plasticity that enhances acclimation to local stress factors such as toxin exposures. While consequences of high toxin exposures are well addressed, effects of low-dose toxin exposures on plant populations are seldom investigated. In particular, the importance of 'selective low-dose toxicity' and hormesis, i.e. stimulatory effects, has not been studied simultaneously. Since selective toxicity can change the size distribution of populations, we assumed that hormesis alters the size distribution at the population level, and investigated whether and how these two low-dose phenomena coexist. The study was conducted with Lactuca sativa L. exposed to the auxin-inhibitor 2-(p-chlorophenoxy)-2-methylpropionic acid (PCIB) in vitro. In two separate experiments, L. sativa was exposed to 12 PCIB doses in 24 replicates (50 plants/replicate). Shoot/root growth responses at the population level were compared to the fast-growing (≥90% percentile) and the slow-growing subpopulations (≤10% percentile) by Mann-Whitney U testing and dose-response modelling. In the formation of pronounced PCIB hormesis at the population level, low-dose effects proved selective, but widely stimulatory which seems to counteract low-dose selective toxicity. The selectivity of hormesis was dose- and growth rate-dependent. Stimulation occurred at lower concentrations and stimulation percentage was higher among slow-growing individuals, but partly or entirely masked at the population level by moderate or negligible stimulation among the faster growing individuals. We conclude that the hormetic effect up to the maximum stimulation may be primarily facilitated by an increase in size of the most slow-growing individuals, while thereafter it seems that mainly the fast-growing individuals contributed to the observed hormesis at the population level. As size distribution within a population is related to survival, our study hints that selective effects on slow- and fast-growing individuals may change population dynamics, providing that similar effects can be repeated under field conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Interpreting the concordance statistic of a logistic regression model: relation to the variance and odds ratio of a continuous explanatory variable

PubMed Central

2012-01-01

Background When outcomes are binary, the c-statistic (equivalent to the area under the Receiver Operating Characteristic curve) is a standard measure of the predictive accuracy of a logistic regression model. Methods An analytical expression was derived under the assumption that a continuous explanatory variable follows a normal distribution in those with and without the condition. We then conducted an extensive set of Monte Carlo simulations to examine whether the expressions derived under the assumption of binormality allowed for accurate prediction of the empirical c-statistic when the explanatory variable followed a normal distribution in the combined sample of those with and without the condition. We also examine the accuracy of the predicted c-statistic when the explanatory variable followed a gamma, log-normal or uniform distribution in combined sample of those with and without the condition. Results Under the assumption of binormality with equality of variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the product of the standard deviation of the normal components (reflecting more heterogeneity) and the log-odds ratio (reflecting larger effects). Under the assumption of binormality with unequal variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the standardized difference of the explanatory variable in those with and without the condition. In our Monte Carlo simulations, we found that these expressions allowed for reasonably accurate prediction of the empirical c-statistic when the distribution of the explanatory variable was normal, gamma, log-normal, and uniform in the entire sample of those with and without the condition. Conclusions The discriminative ability of a continuous explanatory variable cannot be judged by its odds ratio alone, but always needs to be considered in relation to the heterogeneity of the population. PMID:22716998

Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties

PubMed Central

Rostoks, Nils; Ramsay, Luke; MacKenzie, Katrin; Cardle, Linda; Bhat, Prasanna R.; Roose, Mikeal L.; Svensson, Jan T.; Stein, Nils; Varshney, Rajeev K.; Marshall, David F.; Graner, Andreas; Close, Timothy J.; Waugh, Robbie

2006-01-01

Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD, and consequently, a very large number of markers are required for effective whole-genome association genetic scans. In contrast, several of the world's major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudooutbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1,524 genomewide SNPs we demonstrate that, after accounting for population substructure, the level of LD exhibited in elite northwest European barley, a typical inbred cereal crop, can be effectively exploited to map traits by using whole-genome association scans with several hundred to thousands of biallelic SNPs. PMID:17085595

Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification.

PubMed

Zhang, Z; Guillaume, F; Sartelet, A; Charlier, C; Georges, M; Farnir, F; Druet, T

2012-10-01

In many situations, genome-wide association studies are performed in populations presenting stratification. Mixed models including a kinship matrix accounting for genetic relatedness among individuals have been shown to correct for population and/or family structure. Here we extend this methodology to generalized linear mixed models which properly model data under various distributions. In addition we perform association with ancestral haplotypes inferred using a hidden Markov model. The method was shown to properly account for stratification under various simulated scenari presenting population and/or family structure. Use of ancestral haplotypes resulted in higher power than SNPs on simulated datasets. Application to real data demonstrates the usefulness of the developed model. Full analysis of a dataset with 4600 individuals and 500 000 SNPs was performed in 2 h 36 min and required 2.28 Gb of RAM. The software GLASCOW can be freely downloaded from www.giga.ulg.ac.be/jcms/prod_381171/software. francois.guillaume@jouy.inra.fr Supplementary data are available at Bioinformatics online.

Quantifying the entropic cost of cellular growth control

NASA Astrophysics Data System (ADS)

De Martino, Daniele; Capuani, Fabrizio; De Martino, Andrea

2017-07-01

Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.

The mathematical formula of the intravaginal ejaculation latency time (IELT) distribution of lifelong premature ejaculation differs from the IELT distribution formula of men in the general male population

PubMed Central

Janssen, Paddy K.C.

2016-01-01

Purpose To find the most accurate mathematical description of the intravaginal ejaculation latency time (IELT) distribution in the general male population. Materials and Methods We compared the fitness of various well-known mathematical distributions with the IELT distribution of two previously published stopwatch studies of the Caucasian general male population and a stopwatch study of Dutch Caucasian men with lifelong premature ejaculation (PE). The accuracy of fitness is expressed by the Goodness of Fit (GOF). The smaller the GOF, the more accurate is the fitness. Results The 3 IELT distributions are gamma distributions, but the IELT distribution of lifelong PE is another gamma distribution than the IELT distribution of men in the general male population. The Lognormal distribution of the gamma distributions most accurately fits the IELT distribution of 965 men in the general population, with a GOF of 0.057. The Gumbel Max distribution most accurately fits the IELT distribution of 110 men with lifelong PE with a GOF of 0.179. There are more men with lifelong PE ejaculating within 30 and 60 seconds than can be extrapolated from the probability density curve of the Lognormal IELT distribution of men in the general population. Conclusions Men with lifelong PE have a distinct IELT distribution, e.g., a Gumbel Max IELT distribution, that can only be retrieved from the general male population Lognormal IELT distribution when thousands of men would participate in a IELT stopwatch study. The mathematical formula of the Lognormal IELT distribution is useful for epidemiological research of the IELT. PMID:26981594

Comparative phylogeography of a coevolved community: concerted population expansions in Joshua trees and four yucca moths

USGS Publications Warehouse

Smith, Christopher Irwin; Tank, Shantel; Godsoe, William; Levenick, Jim; Strand, Eva; Esque, Todd C.; Pellmyr, Olle

2011-01-01

Comparative phylogeographic studies have had mixed success in identifying common phylogeographic patterns among co-distributed organisms. Whereas some have found broadly similar patterns across a diverse array of taxa, others have found that the histories of different species are more idiosyncratic than congruent. The variation in the results of comparative phylogeographic studies could indicate that the extent to which sympatrically-distributed organisms share common biogeographic histories varies depending on the strength and specificity of ecological interactions between them. To test this hypothesis, we examined demographic and phylogeographic patterns in a highly specialized, coevolved community – Joshua trees (Yucca brevifolia) and their associated yucca moths. This tightly-integrated, mutually interdependent community is known to have experienced significant range changes at the end of the last glacial period, so there is a strong a priori expectation that these organisms will show common signatures of demographic and distributional changes over time. Using a database of >5000 GPS records for Joshua trees, and multi-locus DNA sequence data from the Joshua tree and four species of yucca moth, we combined paleaodistribution modeling with coalescent-based analyses of demographic and phylgeographic history. We extensively evaluated the power of our methods to infer past population size and distributional changes by evaluating the effect of different inference procedures on our results, comparing our palaeodistribution models to Pleistocene-aged packrat midden records, and simulating DNA sequence data under a variety of alternative demographic histories. Together the results indicate that these organisms have shared a common history of population expansion, and that these expansions were broadly coincident in time. However, contrary to our expectations, none of our analyses indicated significant range or population size reductions at the end of the last glacial period, and the inferred demographic changes substantially predate Holocene climate changes.

Comparative phylogeography of a coevolved community: Concerted population expansions in Joshua trees and four Yucca moths

USGS Publications Warehouse

Smith, C.I.; Tank, S.; Godsoe, W.; Levenick, J.; Strand, Espen; Esque, T.; Pellmyr, O.

2011-01-01

Comparative phylogeographic studies have had mixed success in identifying common phylogeographic patterns among co-distributed organisms. Whereas some have found broadly similar patterns across a diverse array of taxa, others have found that the histories of different species are more idiosyncratic than congruent. The variation in the results of comparative phylogeographic studies could indicate that the extent to which sympatrically-distributed organisms share common biogeographic histories varies depending on the strength and specificity of ecological interactions between them. To test this hypothesis, we examined demographic and phylogeographic patterns in a highly specialized, coevolved community - Joshua trees (Yucca brevifolia) and their associated yucca moths. This tightly-integrated, mutually interdependent community is known to have experienced significant range changes at the end of the last glacial period, so there is a strong a priori expectation that these organisms will show common signatures of demographic and distributional changes over time. Using a database of >5000 GPS records for Joshua trees, and multi-locus DNA sequence data from the Joshua tree and four species of yucca moth, we combined paleaodistribution modeling with coalescent-based analyses of demographic and phylgeographic history. We extensively evaluated the power of our methods to infer past population size and distributional changes by evaluating the effect of different inference procedures on our results, comparing our palaeodistribution models to Pleistocene-aged packrat midden records, and simulating DNA sequence data under a variety of alternative demographic histories. Together the results indicate that these organisms have shared a common history of population expansion, and that these expansions were broadly coincident in time. However, contrary to our expectations, none of our analyses indicated significant range or population size reductions at the end of the last glacial period, and the inferred demographic changes substantially predate Holocene climate changes.

Variation in the sizes of eggs and oncospheres and the numbers and distributions of testes in the tapeworm, Hymenolepis diminuta.

PubMed

Pappas, P W; Leiby, D A

1986-06-01

Four "strains" of Hymenolepis diminuta were examined for morphological variation. These included the ARME "strain" (currently maintained at the University of Keele, U.K.), the OSU "strain" (currently maintained at The Ohio State University) and the TOR (or UT) "strain" (currently maintained at the University of Toronto), all of which were derived from the parental RICE "strain," and the ANU "strain" (currently maintained at the Australian National University). Additionally, 2 separate "clonal" populations (populations derived from single cysticercoids) from both the OSU and ANU "strains" were examined. All "strains" and "clones" were maintained under identical conditions using Tenebrio molitor and male Sprague-Dawley rats as the intermediate and definitive hosts, respectively. The lengths and widths of eggs and larvae (oncospheres) passed in the hosts' feces, and the numbers and distributions of testes in proglottids were quantified and the data analyzed. Although analyses of the lengths and widths of eggs and larvae demonstrated significant differences among some "strains" and "clones," a discriminate analysis of the data indicated these parameters to be of questionable taxonomic significance. The eggs of all "strains" and "clones" consisted of 2 distinct populations differing in density and size but not infectivity; the relative proportions of eggs in the 2 populations were not determined. Considering all possible numbers and distributions of testes, 17 variations were seen in the strobilae of tapeworms. Analyses of the data demonstrated that the "strains" and "clones" could be differentiated clearly using only the frequencies of the 1p2a (1 poral and 2 aporal testes) or 1p3a distribution, or the frequencies of proglottids containing 3 or 4 testes; all other variations failed to clearly differentiate or group the various "strains" and "clones."(ABSTRACT TRUNCATED AT 250 WORDS)

Contrasting responses to a climate regime change by sympatric, ice-dependent predators.

PubMed

Younger, Jane L; van den Hoff, John; Wienecke, Barbara; Hindell, Mark; Miller, Karen J

2016-03-15

Models that predict changes in the abundance and distribution of fauna under future climate change scenarios often assume that ecological niche and habitat availability are the major determinants of species' responses to climate change. However, individual species may have very different capacities to adapt to environmental change, as determined by intrinsic factors such as their dispersal ability, genetic diversity, generation time and rate of evolution. These intrinsic factors are usually excluded from forecasts of species' abundance and distribution changes. We aimed to determine the importance of these factors by comparing the impact of the most recent climate regime change, the late Pleistocene glacial-interglacial transition, on two sympatric, ice-dependent meso-predators, the emperor penguin (Aptenodytes forsteri) and Weddell seal (Leptonychotes weddellii). We reconstructed the population trend of emperor penguins and Weddell seals in East Antarctica over the past 75,000 years using mitochondrial DNA sequences and an extended Bayesian skyline plot method. We also assessed patterns of contemporary population structure and genetic diversity. Despite their overlapping distributions and shared dependence on sea ice, our genetic data revealed very different responses to climate warming between these species. The emperor penguin population grew rapidly following the glacial-interglacial transition, but the size of the Weddell seal population did not change. The expansion of emperor penguin numbers during the warm Holocene may have been facilitated by their higher dispersal ability and gene flow among colonies, and fine-scale differences in preferred foraging locations. The vastly different climate change responses of two sympatric ice-dependent predators suggests that differing adaptive capacities and/or fine-scale niche differences can play a major role in species' climate change responses, and that adaptive capacity should be considered alongside niche and distribution in future species forecasts.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, K. S.; Nakae, L. F.; Prasad, M. K.

Here, we solve a simple theoretical model of time evolving fission chains due to Feynman that generalizes and asymptotically approaches the point model theory. The point model theory has been used to analyze thermal neutron counting data. This extension of the theory underlies fast counting data for both neutrons and gamma rays from metal systems. Fast neutron and gamma-ray counting is now possible using liquid scintillator arrays with nanosecond time resolution. For individual fission chains, the differential equations describing three correlated probability distributions are solved: the time-dependent internal neutron population, accumulation of fissions in time, and accumulation of leaked neutronsmore » in time. Explicit analytic formulas are given for correlated moments of the time evolving chain populations. The equations for random time gate fast neutron and gamma-ray counting distributions, due to randomly initiated chains, are presented. Correlated moment equations are given for both random time gate and triggered time gate counting. There are explicit formulas for all correlated moments are given up to triple order, for all combinations of correlated fast neutrons and gamma rays. The nonlinear differential equations for probabilities for time dependent fission chain populations have a remarkably simple Monte Carlo realization. A Monte Carlo code was developed for this theory and is shown to statistically realize the solutions to the fission chain theory probability distributions. Combined with random initiation of chains and detection of external quanta, the Monte Carlo code generates time tagged data for neutron and gamma-ray counting and from these data the counting distributions.« less

Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia.

PubMed

Thomas, Evert; Tovar, Eduardo; Villafañe, Carolina; Bocanegra, José Leonardo; Moreno, Rodrigo

2017-12-01

Crop wild relatives (CWRs) of rice hold important traits that can contribute to enhancing the ability of cultivated rice (Oryza sativa and O. glaberrima) to produce higher yields, cope with the effects of climate change, and resist attacks of pests and diseases, among others. However, the genetic resources of these species remain dramatically understudied, putting at risk their future availability from in situ and ex situ sources. Here we assess the distribution of genetic diversity of the four rice CWRs known to occur in Colombia (O. glumaepatula, O. alta, O. grandiglumis, and O. latifolia). Furthermore, we estimated the degree of overlap between areas with suitable habitat for cultivated and wild rice, both under current and predicted future climate conditions to assess the potential spatiotemporal scale of potential gene flow from GM rice to its CWRs. Our findings suggest that part of the observed genetic diversity and structure, at least of the most exhaustively sampled species, may be explained by their glacial and post-glacial range dynamics. Furthermore, in assessing the expected impact of climate change and the potential spatiotemporal scale of gene flow between populations of CWRs and GM rice we find significant overlap between present and future suitable areas for cultivated rice and its four CWRs. Climate change is expected to have relatively limited negative effects on the rice CWRs, with three species showing opportunities to expand their distribution ranges in the future. Given (i) the sparse presence of CWR populations in protected areas (ii) the strong suitability overlap between cultivated rice and its four CWRs; and (iii) the complexity of managing and regulating areas to prevent alien gene flow, the first priority should be to establish representative ex situ collections for all CWR species, which currently do not exist. In the absence of studies under field conditions on the scale and extent of gene flow between cultivated rice and its Colombian CWRs, effective in situ conservation might best be achieved through tailor-made management plans and exclusion of GM rice cultivation in areas holding the most genetically diverse CWR populations. This may be combined with assisted migration of populations to suitable areas where rice is unlikely to be cultivated under current and future climate conditions.

Population genetic implications from sequence variation in four Y chromosome genes.

PubMed

Shen, P; Wang, F; Underhill, P A; Franco, C; Yang, W H; Roxas, A; Sung, R; Lin, A A; Hyman, R W; Vollrath, D; Davis, R W; Cavalli-Sforza, L L; Oefner, P J

2000-06-20

Some insight into human evolution has been gained from the sequencing of four Y chromosome genes. Primary genomic sequencing determined gene SMCY to be composed of 27 exons that comprise 4,620 bp of coding sequence. The unfinished sequencing of the 5' portion of gene UTY1 was completed by primer walking, and a total of 20 exons were found. By using denaturing HPLC, these two genes, as well as DBY and DFFRY, were screened for polymorphic sites in 53-72 representatives of the five continents. A total of 98 variants were found, yielding nucleotide diversity estimates of 2.45 x 10(-5), 5. 07 x 10(-5), and 8.54 x 10(-5) for the coding regions of SMCY, DFFRY, and UTY1, respectively, with no variant having been observed in DBY. In agreement with most autosomal genes, diversity estimates for the noncoding regions were about 2- to 3-fold higher and ranged from 9. 16 x 10(-5) to 14.2 x 10(-5) for the four genes. Analysis of the frequencies of derived alleles for all four genes showed that they more closely fit the expectation of a Luria-Delbrück distribution than a distribution expected under a constant population size model, providing evidence for exponential population growth. Pairwise nucleotide mismatch distributions date the occurrence of population expansion to approximately 28,000 years ago. This estimate is in accord with the spread of Aurignacian technology and the disappearance of the Neanderthals.

Impact of correlation of predictors on discrimination of risk models in development and external populations.

PubMed

Kundu, Suman; Mazumdar, Madhu; Ferket, Bart

2017-04-19

The area under the ROC curve (AUC) of risk models is known to be influenced by differences in case-mix and effect size of predictors. The impact of heterogeneity in correlation among predictors has however been under investigated. We sought to evaluate how correlation among predictors affects the AUC in development and external populations. We simulated hypothetical populations using two different methods based on means, standard deviations, and correlation of two continuous predictors. In the first approach, the distribution and correlation of predictors were assumed for the total population. In the second approach, these parameters were modeled conditional on disease status. In both approaches, multivariable logistic regression models were fitted to predict disease risk in individuals. Each risk model developed in a population was validated in the remaining populations to investigate external validity. For both approaches, we observed that the magnitude of the AUC in the development and external populations depends on the correlation among predictors. Lower AUCs were estimated in scenarios of both strong positive and negative correlation, depending on the direction of predictor effects and the simulation method. However, when adjusted effect sizes of predictors were specified in the opposite directions, increasingly negative correlation consistently improved the AUC. AUCs in external validation populations were higher or lower than in the derivation cohort, even in the presence of similar predictor effects. Discrimination of risk prediction models should be assessed in various external populations with different correlation structures to make better inferences about model generalizability.

Addressing potential local adaptation in species distribution models: implications for conservation under climate change

USGS Publications Warehouse

Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason D. K.; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C.; Hellmann, Jessica J.

2016-01-01

Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

Ecological Speciation in Nolina parviflora (Asparagaceae): Lacking Spatial Connectivity along of the Trans-Mexican Volcanic Belt

PubMed Central

Ruiz-Sanchez, Eduardo; Specht, Chelsea D.

2014-01-01

The hypothesis of ecological speciation states that as populations diverge in different niches, reproductive isolation evolves as a by-product of adaptation to these different environments. In this context, we used Nolina parviflora as a model to test if this species evolved via ecological speciation and to explore current and historical gene flow among its populations. Nolina parviflora is a montane species endemic to Mexico with its geographical distribution restricted largely to the Trans-Mexican Volcanic Belt. This mountain range is one of the most complex geological regions in Mexico, having undergone volcanism from the mid-Miocene to the present. Ecologically, the Trans-Mexican Volcanic Belt possesses different types of vegetation, including tropical dry forest; oak, pine, pine-oak, and pine-juniper forests; and xerophytic scrub - all of which maintain populations of N. parviflora. Using species distribution models, climatic analyses, spatial connectivity and morphological comparisons, we found significant differences in climatic and morphological variables between populations of N. parviflora in two distinct Trans-Mexican Volcanic Belt regions (east vs. west). This could mean that the geographically isolated populations diverged from one another via niche divergence, indicating ecological speciation. Spatial connectivity analysis revealed no connectivity between these regions under the present or last glacial maximum climate models, indicating a lack of gene flow between the populations of the two regions. The results imply that these populations may encompass more than a single species. PMID:24905911

Ecological speciation in Nolina parviflora (Asparagaceae): lacking spatial connectivity along of the Trans-Mexican Volcanic Belt.

PubMed

Ruiz-Sanchez, Eduardo; Specht, Chelsea D

2014-01-01

The hypothesis of ecological speciation states that as populations diverge in different niches, reproductive isolation evolves as a by-product of adaptation to these different environments. In this context, we used Nolina parviflora as a model to test if this species evolved via ecological speciation and to explore current and historical gene flow among its populations. Nolina parviflora is a montane species endemic to Mexico with its geographical distribution restricted largely to the Trans-Mexican Volcanic Belt. This mountain range is one of the most complex geological regions in Mexico, having undergone volcanism from the mid-Miocene to the present. Ecologically, the Trans-Mexican Volcanic Belt possesses different types of vegetation, including tropical dry forest; oak, pine, pine-oak, and pine-juniper forests; and xerophytic scrub--all of which maintain populations of N. parviflora. Using species distribution models, climatic analyses, spatial connectivity and morphological comparisons, we found significant differences in climatic and morphological variables between populations of N. parviflora in two distinct Trans-Mexican Volcanic Belt regions (east vs. west). This could mean that the geographically isolated populations diverged from one another via niche divergence, indicating ecological speciation. Spatial connectivity analysis revealed no connectivity between these regions under the present or last glacial maximum climate models, indicating a lack of gene flow between the populations of the two regions. The results imply that these populations may encompass more than a single species.

Climate Modelling Shows Increased Risk to Eucalyptus sideroxylon on the Eastern Coast of Australia Compared to Eucalyptus albens

PubMed Central

Shabani, Farzin; Ahmadi, Mohsen

2017-01-01

Aim: To identify the extent and direction of range shift of Eucalyptus sideroxylon and E. albens in Australia by 2050 through an ensemble forecast of four species distribution models (SDMs). Each was generated using four global climate models (GCMs), under two representative concentration pathways (RCPs). Location: Australia. Methods: We used four SDMs of (i) generalized linear model, (ii) MaxEnt, (iii) random forest, and (iv) boosted regression tree to construct SDMs for species E. sideroxylon and E. albens under four GCMs including (a) MRI-CGCM3, (b) MIROC5, (c) HadGEM2-AO and (d) CCSM4, under two RCPs of 4.5 and 6.0. Here, the true skill statistic (TSS) index was used to assess the accuracy of each SDM. Results: Results showed that E. albens and E. sideroxylon will lose large areas of their current suitable range by 2050 and E. sideroxylon is projected to gain in eastern and southeastern Australia. Some areas were also projected to remain suitable for each species between now and 2050. Our modelling showed that E. sideroxylon will lose suitable habitat on the western side and will not gain any on the eastern side because this region is one the most heavily populated areas in the country, and the populated areas are moving westward. The predicted decrease in E. sideroxylon’s distribution suggests that land managers should monitor its population closely, and evaluate whether it meets criteria for a protected legal status. Main conclusions: Both Eucalyptus sideroxylon and E. albens will be negatively affected by climate change and it is projected that E. sideroxylon will be at greater risk of losing habitat than E. albens. PMID:29186755

Getting under the hood: how and for whom does increasing course structure work?

PubMed

Eddy, Sarah L; Hogan, Kelly A

2014-01-01

At the college level, the effectiveness of active-learning interventions is typically measured at the broadest scales: the achievement or retention of all students in a course. Coarse-grained measures like these cannot inform instructors about an intervention's relative effectiveness for the different student populations in their classrooms or about the proximate factors responsible for the observed changes in student achievement. In this study, we disaggregate student data by racial/ethnic groups and first-generation status to identify whether a particular intervention-increased course structure-works better for particular populations of students. We also explore possible factors that may mediate the observed changes in student achievement. We found that a "moderate-structure" intervention increased course performance for all student populations, but worked disproportionately well for black students-halving the black-white achievement gap-and first-generation students-closing the achievement gap with continuing-generation students. We also found that students consistently reported completing the assigned readings more frequently, spending more time studying for class, and feeling an increased sense of community in the moderate-structure course. These changes imply that increased course structure improves student achievement at least partially through increasing student use of distributed learning and creating a more interdependent classroom community. © 2014 S. L. Eddy and K. A. Hogan. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Can genetically modified Escherichia coli with neutral buoyancy induced by gas vesicles be used as an alternative method to clinorotation for microgravity studies?

PubMed

Benoit, Michael; Klaus, David

2005-01-01

Space flight has been shown to affect various bacterial growth parameters. It is proposed that weightlessness allows the cells to remain evenly distributed, consequently altering the chemical makeup of their surrounding fluid, and hence indirectly affecting their physiological behaviour. In support of this argument, ground-based studies using clinostats to partially simulate the quiescent environment attained in microgravity have generally been successful in producing bacterial growth characteristics that mimic responses reported under actual space conditions. A novel approach for evaluating the effects of reduced cell sedimentation is presented here through use of Escherichia coli cultures genetically modified to be neutrally buoyant. Since clinorotation would not (or would only minimally) affect cell distribution of this already near-colloidal cell system, it was hypothesized that the effects on final population density would be eliminated relative to a static control. Gas-vesicle-producing E. coli cultures were grown under clinostat and static conditions and the culture densities at 60 h were compared. As a control, E. coli that do not produce gas vesicles, but were otherwise identical to the experimental strain, were also grown under clinostat and static conditions. As hypothesized, no significant difference was observed in cell populations at 60 h between the clinorotated and static gas-vesicle-producing E. coli cultures, while the cells that did not produce gas vesicles showed a mean increase in population density of 10.5 % (P = 0.001). These results further suggest that the lack of cumulative cell sedimentation is the dominant effect of space flight on non-stirred, in vitro E. coli cultures.

Effect of global climate on termites population. Effect of termites population on global climate

NASA Astrophysics Data System (ADS)

Sapunov, Valentin

2010-05-01

The global climate is under control of factors having both earth and space origin. Global warming took place from XVII century till 1997. Then global cold snap began. This dynamics had effect on global distribution of some animals including termites. Direct human effect on climate is not significant. At the same time man plays role of trigger switching on significant biosphere processes controlling climate. The transformation of marginal lands, development of industry and building, stimulated increase of termite niche and population. Termite role in green house gases production increases too. It may have regular effect on world climate. The dry wood is substrate for metabolism of termites living under symbiosis with bacteria Hypermastigina (Flagellata). The use of dry wood by humanity increased from 18 *108 ton in XVIII to 9*109 to the middle of XX century. Then use of wood decreased because of a new technology development. Hence termite population is controlled by microevolution depending on dry wood and climate dynamics. Producing by them green house gases had reciprocal effect on world climate. It is possible to describe and predict dynamic of termite population using methods of mathematical ecology and analogs with other well studied insects (Colorado potatoes beetle, Chrisomelid beetle Zygogramma and so on). Reclamation of new ecological niche for such insects as termites needs 70 - 75 years. That is delay of population dynamics in relation to dynamics of dry wood production. General principles of population growth were described by G.Gause (1934) and some authors of the end of XX century. This works and analogs with other insects suggest model of termite distribution during XXI century. The extremum of population and its green house gases production would be gotten during 8 - 10 years. Then the number of specimens and sum biological mass would be stabilized and decreased. Termite gas production is not priority for climate regulation, but it has importance as fine regulator of global temperature and climate stability. Key words: termites, green house gases, mathematical modeling. Union symposia Biogeoscience BG2.1

Loss of migration and urbanization in birds: a case study of the blackbird (Turdus merula).

PubMed

Møller, Anders Pape; Jokimäki, Jukka; Skorka, Piotr; Tryjanowski, Piotr

2014-07-01

Many organisms have invaded urban habitats, although the underlying factors initially promoting urbanization remain poorly understood. Partial migration may facilitate urbanization because such populations benefit from surplus food in urban environments during winter, and hence enjoy reduced fitness costs of migratory deaths. We tested this hypothesis in the European blackbird Turdus merula, which has been urbanized since the 19th century, by compiling information on timing of urbanization, migratory status, and population density for 99 cities across the continent. Timing of urbanization was spatially auto-correlated at scales up to 600 km. Analyses of timing of urbanization revealed that urbanization occurred earlier in partially migratory and resident populations than in migratory populations of blackbirds. Independently, this effect was most pronounced in the range of the distribution that currently has the highest population density, suggesting that urbanization facilitated population growth. These findings are consistent with the hypothesis that timing of urbanization is facilitated by partial migration, resulting in subsequent residency and population growth.

New distribution record for the rare limpet Acroloxus coloradensis (Henderson) (Gastropoda: Acroloxidae) from Montana

USGS Publications Warehouse

Hossack, Blake R.; Robert L. Newell,

2013-01-01

The Rocky Mountain Capshell, Acroloxus coloradensis (Henderson, 1930), the only North American member of the basommatophoran family Acroloxidae, is broadly distributed across southern Canada and south into the Rocky Mountains in the USA (Turgeon et al., 1998; Lee and Ackerman, 2000). Despite its wide geographic range, A. coloradensis has been documented from < 30 locations, mostly in British Columbia, Alberta, Ontario, and Quebec (Lee and Ackerman, 2000; Anderson, 2005). Relict populations of A. coloradensis in the USA have been documented from only 6 sites in Colorado and 2 sites in Glacier National Park (Glacier NP), Montana (Anderson, 2005; Ellis et al., 2004). In Glacier NP, A. coloradensis was first reported from Lost Lake (Figure 1; Russell and Brunson, 1967). A second population in the park was discovered in Trout Lake in 2001 (Ellis et al., 2004). In both lakes, A. coloradensis was found primarily under rocks and other cover objects.

Exploring the effect of power law social popularity on language evolution.

PubMed

Gong, Tao; Shuai, Lan

2014-01-01

We evaluate the effect of a power-law-distributed social popularity on the origin and change of language, based on three artificial life models meticulously tracing the evolution of linguistic conventions including lexical items, categories, and simple syntax. A cross-model analysis reveals an optimal social popularity, in which the λ value of the power law distribution is around 1.0. Under this scaling, linguistic conventions can efficiently emerge and widely diffuse among individuals, thus maintaining a useful level of mutual understandability even in a big population. From an evolutionary perspective, we regard this social optimality as a tradeoff among social scaling, mutual understandability, and population growth. Empirical evidence confirms that such optimal power laws exist in many large-scale social systems that are constructed primarily via language-related interactions. This study contributes to the empirical explorations and theoretical discussions of the evolutionary relations between ubiquitous power laws in social systems and relevant individual behaviors.

Lithotype characterizations by Nuclear Magnetic Resonance (NMR): A case study on limestone and associated rocks from the eastern Dahomey Basin, Nigeria

NASA Astrophysics Data System (ADS)

Olatinsu, O. B.; Olorode, D. O.; Clennell, B.; Esteban, L.; Josh, M.

2017-05-01

Three representative rock types (limestone, sandstone, and shale) and glauconite samples collected from Ewekoro Quarry, eastern Dahomey Basin in Nigeria were characterized using low field 2 MHz and 20 MHz Nuclear Magnetic Resonance (NMR) techniques. NMR T2 relaxation time decay measurement was conducted on disc samples under partial water-saturation and full water-saturation conditions using CPMG spin-echo routine. The T2 relaxation decay was converted into T2 distribution in the time domain to assess and evaluate the pore size distribution of the samples. Good agreement exists between water content from T2 NMR distributions and water imbibition porosity (WIP) technique. Results show that the most useful characteristics to discriminate the different facies come from full saturation NMR 2 MHz pore size distribution (PSD). Shale facies depict a quasi-unimodal distribution with greater than 90% contribution from clay bound water component (T2s) coupled to capillary bound water component (T2i) centred on 2 ms. The other facies with well connected pore structure show either bimodal or trimodal T2 distribution composed of the similar clay bound water component centred on 0.3 ms and quasi-capillary bound water component centred on 10 ms. But their difference depends on the movable water T2 component (T2l) that does not exist in the glauconite facies (bimodal distribution) while it exists in both the sandstone and limestone facies. The basic difference between the limestone and sandstone facies is related to the longer T2 coupling: T2i and T2l populations are coupled in sandstone generating a single population which convolves both populations (bimodal distribution). Limestone with a trimodal distribution attests to the fact that carbonate rocks have more complex pore system than siliclastic rocks. The degree of pore connectivity is highest in sandstone, followed by limestone and least in glauconite. Therefore a basic/quick NMR log run on samples along a geological formation can provide precise lithofacies characterization with quantitative information on pore size, structure and distributions.

A Longitudinal Analysis of Mosquito Net Ownership and Use in an Indigenous Batwa Population after a Targeted Distribution

PubMed Central

Clark, Sierra; Berrang-Ford, Lea; Lwasa, Shuaib; Namanya, Didacus; Twesigomwe, Sabastian; Kulkarni, Manisha

2016-01-01

Major efforts for malaria prevention programs have gone into scaling up ownership and use of insecticidal mosquito nets, particularly in sub-Saharan Africa where the malaria burden is high. Socioeconomic inequities in access to long lasting insecticidal nets (LLINs) are reduced with free distributions of nets. However, the relationship between social factors and retention of nets after a free distribution has been less studied, particularly using a longitudinal approach. Our research aimed to estimate the ownership and use of LLINs, and examine the determinants of LLIN retention, within an Indigenous Batwa population after a free LLIN distribution. Two LLINs were given free of charge to each Batwa household in Kanungu District, Uganda in November 2012. Surveyors collected data on LLIN ownership and use through six cross-sectional surveys pre- and post-distribution. Household retention, within household access, and individual use of LLINs were assessed over an 18-month period. Socioeconomic determinants of household retention of LLINs post-distribution were modelled longitudinally using logistic regression with random effects. Direct house-to-house distribution of free LLINs did not result in sustainable increases in the ownership and use of LLINs. Three months post-distribution, only 73% of households owned at least one LLIN and this period also saw the greatest reduction in ownership compared to other study periods. Eighteen-months post distribution, only a third of households still owned a LLIN. Self-reported age-specific use of LLINs was generally higher for children under five, declined for children aged 6–12, and was highest for older adults aged over 35. In the model, household wealth was a significant predictor of LLIN retention, controlling for time and other variables. This research highlights on-going socioeconomic inequities in access to malaria prevention measures among the Batwa in southwestern Uganda, even after free distribution of LLINs, and provides critical information to inform local malaria programs on possible intervention entry-points to increase access and use among this marginalized population. PMID:27145034

Climate-change impacts on understorey bamboo species and giant pandas in China's Qinling Mountains

NASA Astrophysics Data System (ADS)

Tuanmu, Mao-Ning; Viña, Andrés; Winkler, Julie A.; Li, Yu; Xu, Weihua; Ouyang, Zhiyun; Liu, Jianguo

2013-03-01

Climate change is threatening global ecosystems through its impact on the survival of individual species and their ecological functions. Despite the important role of understorey plants in forest ecosystems, climate impact assessments on understorey plants and their role in supporting wildlife habitat are scarce in the literature. Here we assess climate-change impacts on understorey bamboo species with an emphasis on their ecological function as a food resource for endangered giant pandas (Ailuropoda melanoleuca). An ensemble of bamboo distribution projections associated with multiple climate-change projections and bamboo dispersal scenarios indicates a substantial reduction in the distributional ranges of three dominant bamboo species in the Qinling Mountains, China during the twenty-first century. As these three species comprise almost the entire diet of the panda population in the region, the projected changes in bamboo distribution suggest a potential shortage of food for this population, unless alternative food sources become available. Although the projections were developed under unavoidable simplifying assumptions and uncertainties, they indicate potential challenges for panda conservation and underscore the importance of incorporating interspecific interactions into climate-change impact assessments and associated conservation planning.

Estimating the Attack Ratio of Dengue Epidemics under Time-varying Force of Infection using Aggregated Notification Data

NASA Astrophysics Data System (ADS)

Coelho, Flavio Codeço; Carvalho, Luiz Max De

2015-12-01

Quantifying the attack ratio of disease is key to epidemiological inference and public health planning. For multi-serotype pathogens, however, different levels of serotype-specific immunity make it difficult to assess the population at risk. In this paper we propose a Bayesian method for estimation of the attack ratio of an epidemic and the initial fraction of susceptibles using aggregated incidence data. We derive the probability distribution of the effective reproductive number, Rt, and use MCMC to obtain posterior distributions of the parameters of a single-strain SIR transmission model with time-varying force of infection. Our method is showcased in a data set consisting of 18 years of dengue incidence in the city of Rio de Janeiro, Brazil. We demonstrate that it is possible to learn about the initial fraction of susceptibles and the attack ratio even in the absence of serotype specific data. On the other hand, the information provided by this approach is limited, stressing the need for detailed serological surveys to characterise the distribution of serotype-specific immunity in the population.

A general class of multinomial mixture models for anuran calling survey data

USGS Publications Warehouse

Royle, J. Andrew; Link, W.A.

2005-01-01

We propose a general framework for modeling anuran abundance using data collected from commonly used calling surveys. The data generated from calling surveys are indices of calling intensity (vocalization of males) that do not have a precise link to actual population size and are sensitive to factors that influence anuran behavior. We formulate a model for calling-index data in terms of the maximum potential calling index that could be observed at a site (the 'latent abundance class'), given its underlying breeding population, and we focus attention on estimating the distribution of this latent abundance class. A critical consideration in estimating the latent structure is imperfect detection, which causes the observed abundance index to be less than or equal to the latent abundance class. We specify a multinomial sampling model for the observed abundance index that is conditional on the latent abundance class. Estimation of the latent abundance class distribution is based on the marginal likelihood of the index data, having integrated over the latent class distribution. We apply the proposed modeling framework to data collected as part of the North American Amphibian Monitoring Program (NAAMP).

Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus.

PubMed

Dixit, Jyotsana; Arunyawat, Uraiwan; Huong, Ngo Thi; Das, Aparup

2014-11-01

Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B. © 2014 John Wiley & Sons Ltd.

Seroprevalence of Toxocara canis infection in tropical Venezuela.

PubMed

Lynch, N R; Eddy, K; Hodgen, A N; Lopez, R I; Turner, K J

1988-01-01

An enzyme-linked immunosorbent assay (ELISA) was used to determine the seroprevalence of Toxocara canis infection in different socio-economic groups of the tropical population of Venezuela. The lack of definitive independent diagnostic criteria for toxocariasis required the establishment of operational upper limits of normality for Toxocara ELISA values, based upon their log-normalized distribution in a presumptive "non-toxocariasis" sub-population. Only 1.8% of urban subjects of medium-high socio-economic level were considered to be clearly positive in Toxocara ELISA, compared to 20.0% of urban slum dwellers, 25.6% rural subsistence farmers and 34.9% Amazon Indians. As the test was performed using excretory-secretory antigen, and under conditions of competitive inhibition by soluble extracts of non-homologous parasites, co-infection by common intestinal helminths, protozoa or other organisms did not give rise to false positive results. However, strong cross-reactivity with Onchocerca volvulus may have influenced the prevalence figure obtained for the Amazon Indians. These results indicate that T. canis is yet another parasite that is widely distributed in economically underprivileged tropical populations.

Potential Information Loss Due to Categorization of Minimum Inhibitory Concentration Frequency Distributions.

PubMed

Mazloom, Reza; Jaberi-Douraki, Majid; Comer, Jeffrey R; Volkova, Victoriya

2018-01-01

A bacterial isolate's susceptibility to antimicrobial is expressed as the lowest drug concentration inhibiting its visible growth, termed minimum inhibitory concentration (MIC). The susceptibilities of isolates from a host population at a particular time vary, with isolates with specific MICs present at different frequencies. Currently, for either clinical or monitoring purposes, an isolate is most often categorized as Susceptible, Intermediate, or Resistant to the antimicrobial by comparing its MIC to a breakpoint value. Such data categorizations are known in statistics to cause information loss compared to analyzing the underlying frequency distributions. The U.S. National Antimicrobial Resistance Monitoring System (NARMS) includes foodborne bacteria at the food animal processing and retail product points. The breakpoints used to interpret the MIC values for foodborne bacteria are those relevant to clinical treatments by the antimicrobials in humans in whom the isolates were to cause infection. However, conceptually different objectives arise when inference is sought concerning changes in susceptibility/resistance across isolates of a bacterial species in host populations among different sampling points or times. For the NARMS 1996-2013 data for animal processing and retail, we determined the fraction of comparisons of susceptibility/resistance to 44 antimicrobial drugs of twelve classes of a bacterial species in a given animal host or product population where there was a significant change in the MIC frequency distributions between consecutive years or the two sampling points, while the categorization-based analyses concluded no change. The categorization-based analyses missed significant changes in 54% of the year-to-year comparisons and in 71% of the slaughter-to-retail within-year comparisons. Hence, analyses using the breakpoint-based categorizations of the MIC data may miss significant developments in the resistance distributions between the sampling points or times. Methods considering the MIC frequency distributions in their entirety may be superior for epidemiological analyses of resistance dynamics in populations.

A Computational Framework for Analyzing Stochasticity in Gene Expression

PubMed Central

Sherman, Marc S.; Cohen, Barak A.

2014-01-01

Stochastic fluctuations in gene expression give rise to distributions of protein levels across cell populations. Despite a mounting number of theoretical models explaining stochasticity in protein expression, we lack a robust, efficient, assumption-free approach for inferring the molecular mechanisms that underlie the shape of protein distributions. Here we propose a method for inferring sets of biochemical rate constants that govern chromatin modification, transcription, translation, and RNA and protein degradation from stochasticity in protein expression. We asked whether the rates of these underlying processes can be estimated accurately from protein expression distributions, in the absence of any limiting assumptions. To do this, we (1) derived analytical solutions for the first four moments of the protein distribution, (2) found that these four moments completely capture the shape of protein distributions, and (3) developed an efficient algorithm for inferring gene expression rate constants from the moments of protein distributions. Using this algorithm we find that most protein distributions are consistent with a large number of different biochemical rate constant sets. Despite this degeneracy, the solution space of rate constants almost always informs on underlying mechanism. For example, we distinguish between regimes where transcriptional bursting occurs from regimes reflecting constitutive transcript production. Our method agrees with the current standard approach, and in the restrictive regime where the standard method operates, also identifies rate constants not previously obtainable. Even without making any assumptions we obtain estimates of individual biochemical rate constants, or meaningful ratios of rate constants, in 91% of tested cases. In some cases our method identified all of the underlying rate constants. The framework developed here will be a powerful tool for deducing the contributions of particular molecular mechanisms to specific patterns of gene expression. PMID:24811315

Optimal H1N1 vaccination strategies based on self-interest versus group interest.

PubMed

Shim, Eunha; Meyers, Lauren Ancel; Galvani, Alison P

2011-02-25

Influenza vaccination is vital for reducing H1N1 infection-mediated morbidity and mortality. To reduce transmission and achieve herd immunity during the initial 2009-2010 pandemic season, the US Centers for Disease Control and Prevention (CDC) recommended that initial priority for H1N1 vaccines be given to individuals under age 25, as these individuals are more likely to spread influenza than older adults. However, due to significant delay in vaccine delivery for the H1N1 influenza pandemic, a large fraction of population was exposed to the H1N1 virus and thereby obtained immunity prior to the wide availability of vaccines. This exposure affects the spread of the disease and needs to be considered when prioritizing vaccine distribution. To determine optimal H1N1 vaccine distributions based on individual self-interest versus population interest, we constructed a game theoretical age-structured model of influenza transmission and considered the impact of delayed vaccination. Our results indicate that if individuals decide to vaccinate according to self-interest, the resulting optimal vaccination strategy would prioritize adults of age 25 to 49 followed by either preschool-age children before the pandemic peak or older adults (age 50-64) at the pandemic peak. In contrast, the vaccine allocation strategy that is optimal for the population as a whole would prioritize individuals of ages 5 to 64 to curb a growing pandemic regardless of the timing of the vaccination program. Our results indicate that for a delayed vaccine distribution, the priorities that are optimal at a population level do not align with those that are optimal according to individual self-interest. Moreover, the discordance between the optimal vaccine distributions based on individual self-interest and those based on population interest is even more pronounced when vaccine availability is delayed. To determine optimal vaccine allocation for pandemic influenza, public health agencies need to consider both the changes in infection risks among age groups and expected patterns of adherence.

Language deficits, localization, and grammar: evidence for a distributive model of language breakdown in aphasic patients and neurologically intact individuals.

PubMed

Dick, F; Bates, E; Wulfeck, B; Utman, J A; Dronkers, N; Gernsbacher, M A

2001-10-01

Selective deficits in aphasic patients' grammatical production and comprehension are often cited as evidence that syntactic processing is modular and localizable in discrete areas of the brain (e.g., Y. Grodzinsky, 2000). The authors review a large body of experimental evidence suggesting that morpho-syntactic deficits can be observed in a number of aphasic and neurologically intact populations. They present new data showing that receptive agrammatism is found not only over a range of aphasic groups, but is also observed in neurologically intact individuals processing under stressful conditions. The authors suggest that these data are most compatible with a domain-general account of language, one that emphasizes the interaction of linguistic distributions with the properties of an associative processor working under normal or suboptimal conditions.

Brown planthopper Nilaparvata lugens was concentrated at the rear of the typhoon Soudelor in Eastern China in August 2015.

PubMed

Ma, Jian; Wang, Ye-Chen; Hu, Yan-Yue; Lu, Ming-Hong; Wan, Gui-Jun; Chen, Fa-Jun; Liu, Wan-Cai; Zhai, Bao-Ping; Hu, Gao

2017-03-28

Sometimes, extreme weather is vital for the population survival of migratory insects by causing sudden population collapse or outbreak. Several studies have shown that rice planthopper migration was significantly influenced by typhoons in eastern Asia. Most typhoons occur in the summer, especially in August. In August, brown planthopper Nilaparvata lugens (Stål) migrates northward or southward depending on wind direction, and thus typhoons can potentially influence its migration process and population distribution. However, this has not yet been studied. This paper reported a case study on the effects of Typhoon Soudelor on the summer migration of N. lugens in eastern China in 2015. The migration pathways of N. lugens were reconstructed for the period under the influence of a typhoon by calculating the trajectories and migration events in eight counties of the Yangtze River Valley region with ancillary information. Trajectory modelling showed that most migrants took short distance migrations (less than 200 km) under the influence of the Typhoon Soudelor. Numerous N. lugens migrants were concentrated and deposited at the rear of the typhoon during the last 5 days of Typhoon Soudelor on August 9-13 due to horizontal convergence, and this led to an outbreak population. These results indicated that the N. lugens population was redistributed by the typhoon in the summer and that the population dynamics at the rear of a typhoon should be kept under close surveillance. This study provided insight into migratory organisms adapting to atmospheric features. © 2017 Institute of Zoology, Chinese Academy of Sciences.

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

PubMed

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2014-01-01

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

A hierarchical integrated population model for greater sage-grouse (Centrocercus urophasianus) in the Bi-State Distinct Population Segment, California and Nevada

USGS Publications Warehouse

Coates, Peter S.; Halstead, Brian J.; Blomberg, Erik J.; Brussee, Brianne; Howe, Kristy B.; Wiechman, Lief; Tebbenkamp, Joel; Reese, Kerry P.; Gardner, Scott C.; Casazza, Michael L.

2014-01-01

Greater sage-grouse (Centrocercus urophasianus, hereafter referred to as “sage-grouse”) are endemic to sagebrush (Artemisia spp.) ecosystems throughout Western North America. Populations of sage-grouse have declined in distribution and abundance across the range of the species (Schroeder and others, 2004; Knick and Connelly, 2011), largely as a result of human disruption of sagebrush communities (Knick and Connelly, 2011). The Bi-State Distinct Population Segment (DPS) represents sage-grouse populations that are geographically isolated and genetically distinct (Benedict and others, 2003; Oyler-McCance and others, 2005) and that are present at the extreme southwestern distribution of the sage-grouse range (Schroeder and others, 2004), straddling the border of California and Nevada. Subpopulations of sage-grouse in the DPS may be at increased risk of extirpation because of a substantial loss of sagebrush habitat and lack of connectivity (Oyler-McCance and others, 2005). Sage-grouse in the Bi-State DPS represent small, localized breeding populations distributed across 18,325 km2. The U.S. Fish and Wildlife Service currently (2014) is evaluating the Bi-State DPS as threatened or endangered under the Endangered Species Act of 1973, independent of other sage-grouse populations. This DPS was designated as a higher priority for listing than sage-grouse in other parts of the species’ range (U.S. Department of the Interior, 2010). Range-wide population analyses for sage-grouse have included portions of the Bi-State DPS (Sage and Columbian Sharp-tailed Grouse Technical Committee 2008; Garton and others, 2011). Although these analyses are informative, the underlying data only represent a portion of the DPS and are comprised of lek count observations only. A thorough examination of population dynamics and persistence that includes multiple subpopulations and represents the majority of the DPS is largely lacking. Furthermore, fundamental information on population growth rate (i.e., finite rate of change, λ) and specific demographic parameters that explain sources of variation in λ within different subpopulations would be valuable for making conservation and management decisions for this DPS. During 2003–12, agencies and universities collaborated to conduct extensive monitoring of sage-grouse populations within the Bi-State DPS. Data regarding lek attendance, movement, and survival of sage-grouse across multiple life stages were documented. Specifically, sage-grouse from nearly all subpopulations were marked and tracked across multiple seasons using radio-telemetry techniques. A hierarchical integrated population modeling (IPM) approach was used to derive demographic parameters for the Bi-State DPS using the large amount of data collected over a 10-year period. This modeling approach allows integration of multiple data sources to inform population growth rates and population vital rates for the Bi-State DPS overall, as well as for individual subpopulations. These models are more informative than other models because they integrate inputs of demographic data (for example, survival and fecundity rates) and survey data (for example, lek observations). The findings here will help characterize population growth rates within the Bi-State DPS.

Population pharmacokinetics of blonanserin in Chinese healthy volunteers and the effect of the food intake.

PubMed

Wen, Yu-Guan; Shang, De-Wei; Xie, He-Zhi; Wang, Xi-Pei; Ni, Xiao-Jia; Zhang, Ming; Lu, Wei; Qiu, Chang; Liu, Xia; Li, Fang-Fang; Li, Xuan; Luo, Fu-Tian

2013-03-01

The aim of the study was to better understand blonanserin population pharmacokinetic (PK) characteristics in Chinese healthy subjects. Data from two studies with 50 subjects were analyzed to investigate the population PK characteristics of blonanserin at single dose (4, 8, and 12 mg) under fasting, multidose (4 mg bid or 8 mg qd for 7 days) and under food intake condition (single dose, 8 mg). Blonanserin plasma concentrations were detected using the high performance liquid chromatography tandem mass spectrometry (LC/MS/MS). A nonlinear mixed-effects model was developed to describe the blonanserin concentration-time profiles. A two compartment model with first-order absorption was built to describe the time-course of blonanserin. The population-predicted system apparent clearance (CL/F), volume of apparent distribution in center (V(1)/F), and the first-order absorption rate constant (Ka) of blonanserin under fasting was 1230 L/h, 9500 L, and 3.02 h(-1), respectively. Food intake decreased Ka of blonanserin to 0.78 h(-1). The relative bioavailability between fasting and food intake estimated by the final model was 55%. No clinically significant safety issues were identified. This is the first study assessing the PK profile of blonanserin with population PKs method. The results can be used for simulation in further clinical trial and optimize individual dosage regimens using a Bayesian methodology in patients. Copyright © 2013 John Wiley & Sons, Ltd.

[Community outbreak of hepatitis A in a marginal population. Vaccination for its control and acceptance of the measure].

PubMed

Arce Arnáez, Araceli; Cabello Ballesteros, Luisa; Iñigo Martínez, Jesús

2007-03-01

To study a community outbreak of hepatitis A in a marginal population and the public health response in order to bring it under control. Descriptive study of the outbreak that occurred in February-June, 2004. An epidemiological survey was conducted to detect prior cases and active vigilance was set up. Case and susceptibility definitions were established. A gypsy population in Madrid, Spain. They had basic provision of sewerage, water supply and waste disposal. A population of 550 in census; estimated population, 800. 70% were under 40 and 55% were illiterate. Control measures were: a) health education activities to strengthen habits of hygiene, and b) immunisation of susceptible individuals. A total of 646 people were vaccinated, with the active help of staff from the Institute of Rehousing and Integration into Society. The outbreak affected 26 people, with an average age of 8 (95% CI, 6.2-9.8), similar distribution by sex and 3.3% attack rate. Fourteen cases were students at state schools, not all in the same classes. There were 7 pairs of siblings among the cases. The diagnosis was conformed by serology in 17 cases. Five needed hospital admission. The epidemic curve suggested person-person transmission. All those affected were under 20 years old. Vaccination was seen to be effective in controlling the outbreak. Interventions were assisted by intermediaries in order to respect the gypsies' cultural context and were well accepted.

Population genetics of Plasmodium falciparum and Plasmodium vivax and asymptomatic malaria in Temotu Province, Solomon Islands

PubMed Central

2013-01-01

Background Temotu Province, Solomon Islands is progressing toward malaria elimination. A baseline survey conducted in 2008 showed that most Plasmodium infections in the province were of low parasite density and asymptomatic infections. To better understand mechanisms underlying these malaria transmission characteristics genetic diversity and relationships among Plasmodium falciparum and Plasmodium vivax populations in the province were examined. Methods Forty-five P. falciparum and 67 P. vivax samples collected in the 2008 baseline survey were successfully genotyped using eight P. falciparum and seven P. vivax microsatellite markers. Genetic diversity, relationships and distribution of both P. falciparum and P. vivax populations were analysed. Results Plasmodium falciparum population exhibited low diversity with 19 haplotypes identified and had closely related clusters indicating clonal expansion. Interestingly, a dominant haplotype was significantly associated with fever and high parasite density. In contrast, the P. vivax population was highly diverse with 58 haplotypes identified that were not closely related. Parasite populations between different islands in the province showed low genetic differentiation. Conclusion The low diversity and clonal population of P. falciparum population may partially account for clinical immunity developed against illness. However, it is possible that importation of a new P. falciparum strain was the major cause of illness. High diversity in P. vivax population and low relatedness between strains suggested clinical immunity to P. vivax may be maintained by different mechanisms. The genetic diversity, population structure and distribution of strains indicate that transmission of P. falciparum was low, but that of P. vivax was still high in 2008. These data will be useful for assessing changes in malaria transmission resulting from interventions. PMID:24261646

Universal characteristics of fractal fluctuations in prime number distribution

NASA Astrophysics Data System (ADS)

Selvam, A. M.

2014-11-01

The frequency of occurrence of prime numbers at unit number spacing intervals exhibits self-similar fractal fluctuations concomitant with inverse power law form for power spectrum generic to dynamical systems in nature such as fluid flows, stock market fluctuations and population dynamics. The physics of long-range correlations exhibited by fractals is not yet identified. A recently developed general systems theory visualizes the eddy continuum underlying fractals to result from the growth of large eddies as the integrated mean of enclosed small scale eddies, thereby generating a hierarchy of eddy circulations or an inter-connected network with associated long-range correlations. The model predictions are as follows: (1) The probability distribution and power spectrum of fractals follow the same inverse power law which is a function of the golden mean. The predicted inverse power law distribution is very close to the statistical normal distribution for fluctuations within two standard deviations from the mean of the distribution. (2) Fractals signify quantum-like chaos since variance spectrum represents probability density distribution, a characteristic of quantum systems such as electron or photon. (3) Fractal fluctuations of frequency distribution of prime numbers signify spontaneous organization of underlying continuum number field into the ordered pattern of the quasiperiodic Penrose tiling pattern. The model predictions are in agreement with the probability distributions and power spectra for different sets of frequency of occurrence of prime numbers at unit number interval for successive 1000 numbers. Prime numbers in the first 10 million numbers were used for the study.

Neo-liberal economic practices and population health: a cross-national analysis, 1980-2004.

PubMed

Tracy, Melissa; Kruk, Margaret E; Harper, Christine; Galea, Sandro

2010-04-01

Although there has been substantial debate and research concerning the economic impact of neo-liberal practices, there is a paucity of research about the potential relation between neo-liberal economic practices and population health. We assessed the extent to which neo-liberal policies and practices are associated with population health at the national level. We collected data on 119 countries between 1980 and 2004. We measured neo-liberalism using the Fraser Institute's Economic Freedom of the World (EFW) Index, which gives an overall score as well as a score for each of five different aspects of neo-liberal economic practices: (1) size of government, (2) legal structure and security of property rights, (3) access to sound money, (4) freedom to exchange with foreigners and (5) regulation of credit, labor and business. Our measure of population health was under-five mortality. We controlled for potential mediators (income distribution, social capital and openness of political institutions) and confounders (female literacy, total population, rural population, fertility, gross domestic product per capita and time period). In longitudinal multivariable analyses, we found that the EFW index did not have an effect on child mortality but that two of its components: improved security of property rights and access to sound money were associated with lower under-five mortality (p = 0.017 and p = 0.024, respectively). When stratifying the countries by level of income, less regulation of credit, labor and business was associated with lower under-five mortality in high-income countries (p = 0.001). None of the EFW components were significantly associated with under-five mortality in low-income countries. This analysis suggests that the concept of 'neo-liberalism' is not a monolithic entity in its relation to health and that some 'neo-liberal' policies are consistent with improved population health. Further work is needed to corroborate or refute these findings.

Simulation of concentration distribution of urban particles under wind

NASA Astrophysics Data System (ADS)

Chen, Yanghou; Yang, Hangsheng

2018-02-01

The concentration of particulate matter in the air is too high, which seriously affects people’s health. The concentration of particles in densely populated towns is also high. Understanding the distribution of particles in the air helps to remove them passively. The concentration distribution of particles in urban streets is simulated by using the FLUENT software. The simulation analysis based on Discrete Phase Modelling (DPM) of FLUENT. Simulation results show that the distribution of the particles is caused by different layout of buildings. And it is pointed out that in the windward area of the building and the leeward sides of the high-rise building are the areas with high concentration of particles. Understanding the concentration of particles in different areas is also helpful for people to avoid and reduce the concentration of particles in high concentration areas.

Large-scale implementation of disease control programmes: a cost-effectiveness analysis of long-lasting insecticide-treated bed net distribution channels in a malaria-endemic area of western Kenya-a study protocol.

PubMed

Gama, Elvis; Were, Vincent; Ouma, Peter; Desai, Meghna; Niessen, Louis; Buff, Ann M; Kariuki, Simon

2016-11-21

Historically, Kenya has used various distribution models for long-lasting insecticide-treated bed nets (LLINs) with variable results in population coverage. The models presently vary widely in scale, target population and strategy. There is limited information to determine the best combination of distribution models, which will lead to sustained high coverage and are operationally efficient and cost-effective. Standardised cost information is needed in combination with programme effectiveness estimates to judge the efficiency of LLIN distribution models and options for improvement in implementing malaria control programmes. The study aims to address the information gap, estimating distribution cost and the effectiveness of different LLIN distribution models, and comparing them in an economic evaluation. Evaluation of cost and coverage will be determined for 5 different distribution models in Busia County, an area of perennial malaria transmission in western Kenya. Cost data will be collected retrospectively from health facilities, the Ministry of Health, donors and distributors. Programme-effectiveness data, defined as the number of people with access to an LLIN per 1000 population, will be collected through triangulation of data from a nationally representative, cross-sectional malaria survey, a cross-sectional survey administered to a subsample of beneficiaries in Busia County and LLIN distributors' records. Descriptive statistics and regression analysis will be used for the evaluation. A cost-effectiveness analysis will be performed from a health-systems perspective, and cost-effectiveness ratios will be calculated using bootstrapping techniques. The study has been evaluated and approved by Kenya Medical Research Institute, Scientific and Ethical Review Unit (SERU number 2997). All participants will provide written informed consent. The findings of this economic evaluation will be disseminated through peer-reviewed publications. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Consequences of the genetic threshold model for observing partial migration under climate change scenarios.

PubMed

Cobben, Marleen M P; van Noordwijk, Arie J

2017-10-01

Migration is a widespread phenomenon across the animal kingdom as a response to seasonality in environmental conditions. Partially migratory populations are populations that consist of both migratory and residential individuals. Such populations are very common, yet their stability has long been debated. The inheritance of migratory activity is currently best described by the threshold model of quantitative genetics. The inclusion of such a genetic threshold model for migratory behavior leads to a stable zone in time and space of partially migratory populations under a wide range of demographic parameter values, when assuming stable environmental conditions and unlimited genetic diversity. Migratory species are expected to be particularly sensitive to global warming, as arrival at the breeding grounds might be increasingly mistimed as a result of the uncoupling of long-used cues and actual environmental conditions, with decreasing reproduction as a consequence. Here, we investigate the consequences for migratory behavior and the stability of partially migratory populations under five climate change scenarios and the assumption of a genetic threshold value for migratory behavior in an individual-based model. The results show a spatially and temporally stable zone of partially migratory populations after different lengths of time in all scenarios. In the scenarios in which the species expands its range from a particular set of starting populations, the genetic diversity and location at initialization determine the species' colonization speed across the zone of partial migration and therefore across the entire landscape. Abruptly changing environmental conditions after model initialization never caused a qualitative change in phenotype distributions, or complete extinction. This suggests that climate change-induced shifts in species' ranges as well as changes in survival probabilities and reproductive success can be met with flexibility in migratory behavior at the species level, which will reduce the risk of extinction.

A theory of bimodal acceleration of pick up ions by compression solar wind turbulence under pressure balance

DOE PAGES

Zhang, Ming; Schlickeiser, Reinhard

2012-08-22

Recently, it was demonstrated that stochastic acceleration of particles going through a series of compressive plasma waves can be efficient and fast. It could be too fast so that the pressure built up by the accelerated particles may in turn modify the amplitude of waves to prevent the particles from having an exploding pressure. We call this condition pressure balance. In this paper, we take into account the fact that active acceleration of particles only occupies a limited volume of space due to a possible intermittent nature of plasma waves or turbulence. We also develop a bimodal acceleration theory thatmore » treats the populations of particles in the active and inactive acceleration regions separately and allows the two populations to exchange particles efficiently. We show that the system automatically produces a solution of v -5 steady state distribution for the accelerated particles, under the requirement of the pressure balance condition. It is found that the v -5 distribution is more robust and easier to achieve with a small volume of intense particle acceleration. These properties explain why the v -5 distribution is commonly observed in space. We apply our model to pickup ion propagation and acceleration throughout the entire heliosphere. These results can reproduce various observations in some great detail. We also found that this mechanism could be responsible for producing anomalous cosmic rays deep in the heliosheath.« less

A test for selection employing quantitative trait locus and mutation accumulation data.

PubMed

Rice, Daniel P; Townsend, Jeffrey P

2012-04-01

Evolutionary biologists attribute much of the phenotypic diversity observed in nature to the action of natural selection. However, for many phenotypic traits, especially quantitative phenotypic traits, it has been challenging to test for the historical action of selection. An important challenge for biologists studying quantitative traits, therefore, is to distinguish between traits that have evolved under the influence of strong selection and those that have evolved neutrally. Most existing tests for selection employ molecular data, but selection also leaves a mark on the genetic architecture underlying a trait. In particular, the distribution of quantitative trait locus (QTL) effect sizes and the distribution of mutational effects together provide information regarding the history of selection. Despite the increasing availability of QTL and mutation accumulation data, such data have not yet been effectively exploited for this purpose. We present a model of the evolution of QTL and employ it to formulate a test for historical selection. To provide a baseline for neutral evolution of the trait, we estimate the distribution of mutational effects from mutation accumulation experiments. We then apply a maximum-likelihood-based method of inference to estimate the range of selection strengths under which such a distribution of mutations could generate the observed QTL. Our test thus represents the first integration of population genetic theory and QTL data to measure the historical influence of selection.

Statistical analysis of latent generalized correlation matrix estimation in transelliptical distribution.

PubMed

Han, Fang; Liu, Han

2017-02-01

Correlation matrix plays a key role in many multivariate methods (e.g., graphical model estimation and factor analysis). The current state-of-the-art in estimating large correlation matrices focuses on the use of Pearson's sample correlation matrix. Although Pearson's sample correlation matrix enjoys various good properties under Gaussian models, its not an effective estimator when facing heavy-tail distributions with possible outliers. As a robust alternative, Han and Liu (2013b) advocated the use of a transformed version of the Kendall's tau sample correlation matrix in estimating high dimensional latent generalized correlation matrix under the transelliptical distribution family (or elliptical copula). The transelliptical family assumes that after unspecified marginal monotone transformations, the data follow an elliptical distribution. In this paper, we study the theoretical properties of the Kendall's tau sample correlation matrix and its transformed version proposed in Han and Liu (2013b) for estimating the population Kendall's tau correlation matrix and the latent Pearson's correlation matrix under both spectral and restricted spectral norms. With regard to the spectral norm, we highlight the role of "effective rank" in quantifying the rate of convergence. With regard to the restricted spectral norm, we for the first time present a "sign subgaussian condition" which is sufficient to guarantee that the rank-based correlation matrix estimator attains the optimal rate of convergence. In both cases, we do not need any moment condition.

Population genetic structure of endangered Mongolian racerunner (Eremias argus) from the Korean Peninsula.

PubMed

Park, Han-Chan; Suk, Ho Young; Jeong, Eu-Jin; Park, Dae-Sik; Lee, Hang; Min, Mi-Sook

2014-11-01

The Mongolian racerunner (Eremias argus) is a small lacertid lizard species, and its distribution range encompasses the Korean Peninsula, Mongolia, China and Russia. Eremias argus is widespread, but populations on the Korean Peninsula are small and declining, provoking concerns that genetic diversity is being lost. This species is currently listed under the Protection of Wild Fauna and Flora Act in South Korea. In this study, nine novel microsatellites for E. argus were developed with a biotin-enrichment method and used to understand its population genetic structure and delineate conservation units on the Korean Peninsula. Overall, low intrapopulation genetic diversity was observed (mean number of alleles per locus = 2.463; mean H E = 0.398) from 10 populations investigated (n = 110). Two populations (among five with n≥ 10) showed an excess of heterozygosity expected under HWE relative to that expected at mutation-drift equilibrium, indicating severe reduction in population sizes. With only a few exceptions, the overall genetic differentiation among populations was substantial with the high levels of pairwise-F ST (0.006-0.746) and -R ST (0.034-0.940) values. The results of Bayesian STRUCTURE analysis showed that E. argus populations on the Korean Peninsula were most likely partitioned into three genetic clusters. Taken all together, such low levels of gene flow and strong genetic structuring have critical implications for the conservation of this endangered species and its management.

Nash Equilibria in Noncooperative Predator-Prey Games

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramos, Angel Manuel; Roubicek, Tomas

2007-09-15

A noncooperative game governed by a distributed-parameter predator-prey system is considered, assuming that two players control initial conditions for predator and prey, respectively. Existence of a Nash equilibrium is shown under the condition that the desired population profiles and the environmental carrying capacity for the prey are sufficiently small. A conceptual approximation algorithm is proposed and analyzed. Finally, numerical simulations are performed, too.

Landscape-and regional-scale shifts in forest composition under climate change in the Central Hardwood Region of the United States

Treesearch

Wen J. Wang; Hong S. He; Frank R. Thompson; Jacob S. Fraser; William D. Dijak

2016-01-01

Tree species distribution and abundance are affected by forces operating at multiple scales. Niche and biophysical process models have been commonly used to predict climate change effects at regional scales, however, these models have limited capability to include site-scale population dynamics and landscape- scale disturbance and dispersal. We applied a landscape...

Inducible variation in anaerobic energy metabolism reflects hypoxia tolerance across the intertidal and subtidal distribution of the Pacific oyster (Crassostrea gigas).

PubMed

Meng, Jie; Wang, Ting; Li, Li; Zhang, Guofan

2018-07-01

Pacific oyster (Crassostrea gigas) distribute a steep gradient of environmental stress between intertidal and subtidal habits and provide insight into population-scale patterns and underlying processes of variation in physiological tolerance. In this study, 1-year-old-F 1 oysters, collected from subtidal and intertidal habitats, were obtained after common garden experiment. Genetic differentiation and physiological responses under air exposure were examined to determine whether they had evolved into local adapted subpopulations. Mortality rate, anaerobic glycolysis metabolism, and energy status indicated that oyster had initiated metabolism depression and anaerobic glycolysis metabolism in both intertidal and subtidal oysters under air exposure. However, the subtidal oysters displayed the larger energy metabolism depressions and the earlier anaerobic glycolysis responses. This may indicate that subtidal oysters were more sensitives to hypoxia stress, which may lead the higher mortality rate under long term of air exposure. Based on a common garden experimental design, we propose that this diversification may have a genetic background. Overall, the clear differences between intertidal and subtidal oysters under air exposure have provided an important reference for their aquaculture and transportation used in commercial production. Copyright © 2018. Published by Elsevier Ltd.

The Effects of Grain Size and Temperature Distributions on the Formation of Interstellar Ice Mantles

NASA Astrophysics Data System (ADS)

Pauly, Tyler; Garrod, Robin T.

2016-02-01

Computational models of interstellar gas-grain chemistry have historically adopted a single dust-grain size of 0.1 micron, assumed to be representative of the size distribution present in the interstellar medium. Here, we investigate the effects of a broad grain-size distribution on the chemistry of dust-grain surfaces and the subsequent build-up of molecular ices on the grains, using a three-phase gas-grain chemical model of a quiescent dark cloud. We include an explicit treatment of the grain temperatures, governed both by the visual extinction of the cloud and the size of each individual grain-size population. We find that the temperature difference plays a significant role in determining the total bulk ice composition across the grain-size distribution, while the effects of geometrical differences between size populations appear marginal. We also consider collapse from a diffuse to a dark cloud, allowing dust temperatures to fall. Under the initial diffuse conditions, small grains are too warm to promote grain-mantle build-up, with most ices forming on the mid-sized grains. As collapse proceeds, the more abundant, smallest grains cool and become the dominant ice carriers; the large population of small grains means that this ice is distributed across many grains, with perhaps no more than 40 monolayers of ice each (versus several hundred assuming a single grain size). This effect may be important for the subsequent processing and desorption of the ice during the hot-core phase of star formation, exposing a significant proportion of the ice to the gas phase, increasing the importance of ice-surface chemistry and surface-gas interactions.

Logistical constraints lead to an intermediate optimum in outbreak response vaccination

PubMed Central

Shea, Katriona; Ferrari, Matthew

2018-01-01

Dynamic models in disease ecology have historically evaluated vaccination strategies under the assumption that they are implemented homogeneously in space and time. However, this approach fails to formally account for operational and logistical constraints inherent in the distribution of vaccination to the population at risk. Thus, feedback between the dynamic processes of vaccine distribution and transmission might be overlooked. Here, we present a spatially explicit, stochastic Susceptible-Infected-Recovered-Vaccinated model that highlights the density-dependence and spatial constraints of various diffusive strategies of vaccination during an outbreak. The model integrates an agent-based process of disease spread with a partial differential process of vaccination deployment. We characterize the vaccination response in terms of a diffusion rate that describes the distribution of vaccination to the population at risk from a central location. This generates an explicit trade-off between slow diffusion, which concentrates effort near the central location, and fast diffusion, which spreads a fixed vaccination effort thinly over a large area. We use stochastic simulation to identify the optimum vaccination diffusion rate as a function of population density, interaction scale, transmissibility, and vaccine intensity. Our results show that, conditional on a timely response, the optimal strategy for minimizing outbreak size is to distribute vaccination resource at an intermediate rate: fast enough to outpace the epidemic, but slow enough to achieve local herd immunity. If the response is delayed, however, the optimal strategy for minimizing outbreak size changes to a rapidly diffusive distribution of vaccination effort. The latter may also result in significantly larger outbreaks, thus suggesting a benefit of allocating resources to timely outbreak detection and response. PMID:29791432

A new model of the lunar ejecta cloud

NASA Astrophysics Data System (ADS)

Christou, A. A.

2014-04-01

Every airless body in the solar system is surrounded by a cloud of ejecta produced by the impact of interplanetary meteoroids on its surface [1]. Such "dust exospheres" have been observed around the Galilean satellites of Jupiter [2, 3]. The prospect of long-term robotic and human operations on the Moon by the US and other countries has rekindled interest on the subject [4]. This interest has culminated with the recent investigation of the Moon's dust exosphere by the LADEE spacecraft [5]. Here a model is presented of a ballistic, collisionless, steady state population of ejecta launched vertically at randomly distributed times and velocities. Assuming a uniform distribution of launch times I derive closed form solutions for the probability density functions (pdfs) of the height distribution of particles and the distribution of their speeds in a rest frame both at the surface and at altitude. The treatment is then extended to particle motion with respect to a moving platform such as an orbiting spacecraft. These expressions are compared with numerical simulations under lunar surface gravity where the underlying ejection speed distribution is (a) uniform (b) a power law. I discuss the predictions of the model, its limitations, and how it can be validated against near-surface and orbital measurements.

Spatial Variation and Survival of Salmonella enterica Subspecies in a Population of Australian Sleepy Lizards (Tiliqua rugosa).

PubMed

Parsons, Sandra K; Bull, C Michael; Gordon, David M

2015-09-01

The life cycles of many enteric bacterial species require a transition between two very distinct environments. Their primary habitat is the gastrointestinal tract of the host, while their secondary habitat, during transmission from one host to another, consists of environments external to the host, such as soil, water, and sediments. Consequently, both host and environmental factors shape the genetic structure of enteric bacterial populations. This study examined the distribution of four Salmonella enterica subspecies in a population of sleepy lizards, Tiliqua rugosa, in a semiarid region of South Australia. The lizards living within the 1,920-m by 720-m study site were radio tracked, and their enteric bacteria were sampled at regular intervals throughout their active seasons in the years 2001, 2002, and 2006. Four of the six subspecies of S. enterica were present in this population and were nonrandomly distributed among the lizards. In particular, S. enterica subsp. diarizonae was restricted to lizards living in the most shaded parts of the study site with an overstorey of Casuarina trees. Experiments undertaken to investigate the survival of S. enterica cells under seminatural conditions revealed that cell survival decreased with increased exposure to elevated temperatures and UV light. Among the three S. enterica subspecies tested, S. enterica subsp. diarizonae consistently had an average expected life span that was shorter than that observed for the other two subspecies. There was no indication in the data that there was any competitive dominance hierarchy among the S. enterica subspecies within individual hosts. Thus, the nonrandom distribution of S. enterica subspecies in this population of lizards appears to be driven by their different survival characteristics in the external environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Spatial Variation and Survival of Salmonella enterica Subspecies in a Population of Australian Sleepy Lizards (Tiliqua rugosa)

PubMed Central

Parsons, Sandra K.; Bull, C. Michael

2015-01-01

The life cycles of many enteric bacterial species require a transition between two very distinct environments. Their primary habitat is the gastrointestinal tract of the host, while their secondary habitat, during transmission from one host to another, consists of environments external to the host, such as soil, water, and sediments. Consequently, both host and environmental factors shape the genetic structure of enteric bacterial populations. This study examined the distribution of four Salmonella enterica subspecies in a population of sleepy lizards, Tiliqua rugosa, in a semiarid region of South Australia. The lizards living within the 1,920-m by 720-m study site were radio tracked, and their enteric bacteria were sampled at regular intervals throughout their active seasons in the years 2001, 2002, and 2006. Four of the six subspecies of S. enterica were present in this population and were nonrandomly distributed among the lizards. In particular, S. enterica subsp. diarizonae was restricted to lizards living in the most shaded parts of the study site with an overstorey of Casuarina trees. Experiments undertaken to investigate the survival of S. enterica cells under seminatural conditions revealed that cell survival decreased with increased exposure to elevated temperatures and UV light. Among the three S. enterica subspecies tested, S. enterica subsp. diarizonae consistently had an average expected life span that was shorter than that observed for the other two subspecies. There was no indication in the data that there was any competitive dominance hierarchy among the S. enterica subspecies within individual hosts. Thus, the nonrandom distribution of S. enterica subspecies in this population of lizards appears to be driven by their different survival characteristics in the external environment. PMID:26092451

Dental and phylogeographic patterns of variation in gorillas.

PubMed

Pilbrow, Varsha

2010-07-01

Gorilla patterns of variation have great relevance for studies of human evolution. In this study, molar morphometrics were used to evaluate patterns of geographic variation in gorillas. Dental specimens of 323 adult individuals, drawn from the current distribution of gorillas in equatorial Africa were divided into 14 populations. Discriminant analyses and Mahalanobis distances were used to study population structure. Results reveal that: 1) the West and East African gorillas form distinct clusters, 2) the Cross River gorillas are well separated from the rest of the western populations, 3) gorillas from the Virunga mountains and the Bwindi Forest can be differentiated from the lowland gorillas of Utu and Mwenga-Fizi, 4) the Tshiaberimu gorillas are distinct from other eastern gorillas, and the Kahuzi-Biega gorillas are affiliated with them. These findings provide support for a species distinction between Gorilla gorilla and Gorilla beringei, with subspecies G. g. diehli, G. g. gorilla, G. b. graueri, G. b. beringei, and possibly, G. b. rex-pygmaeorum. Clear correspondence between dental and other patterns of taxonomic diversity demonstrates that dental data reveal underlying genetic patterns of differentiation. Dental distances increased predictably with altitude but not with geographic distances, indicating that altitudinal segregation explains gorilla patterns of population divergence better than isolation-by-distance. The phylogeographic pattern of gorilla dental metric variation supports the idea that Plio-Pleistocene climatic fluctuations and local mountain building activity in Africa affected gorilla phylogeography. I propose that West Africa comprised the historic center of gorilla distribution and experienced drift-gene flow equilibrium, whereas Nigeria and East Africa were at the periphery, where climatic instability and altitudinal variation promoted drift and genetic differentiation. This understanding of gorilla population structure has implications for gorilla conservation, and for understanding the distribution of sympatric chimpanzees and Plio-Pleistocene hominins.

Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment

PubMed Central

Xu, Jian; Li, Jiong-Tang; Jiang, Yanliang; Peng, Wenzhu; Yao, Zongli; Chen, Baohua; Jiang, Likun; Feng, Jingyan; Ji, Peifeng; Liu, Guiming; Liu, Zhanjiang; Tai, Ruyu; Dong, Chuanju; Sun, Xiaoqing; Zhao, Zi-Xia; Zhang, Yan; Wang, Jian; Li, Shangqi; Zhao, Yunfeng; Yang, Jiuhui; Sun, Xiaowen; Xu, Peng

2017-01-01

The Amur ide (Leuciscus waleckii) is a cyprinid fish that is widely distributed in Northeast Asia. The Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50 mmol/L (pH 9.6), thus providing an exceptional model with which to characterize the mechanisms of genomic evolution underlying adaptation to extreme environments. Here, we developed the reference genome assembly for L. waleckii from Lake Dali Nur. Intriguingly, we identified unusual expanded long terminal repeats (LTRs) with higher nucleotide substitution rates than in many other teleosts, suggesting their more recent insertion into the L. waleckii genome. We also identified expansions in genes encoding egg coat proteins and natriuretic peptide receptors, possibly underlying the adaptation to extreme environmental stress. We further sequenced the genomes of 10 additional individuals from freshwater and 18 from Lake Dali Nur populations, and we detected a total of 7.6 million SNPs from both populations. In a genome scan and comparison of these two populations, we identified a set of genomic regions under selective sweeps that harbor genes involved in ion homoeostasis, acid-base regulation, unfolded protein response, reactive oxygen species elimination, and urea excretion. Our findings provide comprehensive insight into the genomic mechanisms of teleost fish that underlie their adaptation to extreme alkaline environments. PMID:28007977

The concerted movement of the switch region of Troponin I in cardiac muscle thin filaments as tracked by conventional and pulsed (DEER) EPR.

PubMed

Potluri, Phani R; Chamoun, Jean; Cooke, James A; Badr, Myriam; Guse, Joanna A; Rayes, Roni; Cordina, Nicole M; McCamey, Dane; Fajer, Piotr G; Brown, Louise J

2017-12-01

The absence of a crystal structure of the calcium free state of the cardiac isoform of the troponin complex has hindered our understanding of how the simple binding of Ca 2+ triggers conformational changes in troponin which are then propagated to enable muscle contraction. Here we have used continuous wave (CW) and Double Electron-Electron Resonance (DEER) pulsed EPR spectroscopy to measure distances between TnI and TnC to track the movement of the functionally important regulatory 'switch' region of cardiac Tn. Spin labels were placed on the switch region of Troponin I and distances measured to Troponin C. Under conditions of high Ca 2+ , the interspin distances for one set (TnI151/TnC84) were 'short' (9-10Å) with narrow distance distribution widths (3-8Å) indicating the close interaction of the switch region with the N-lobe of TnC. Additional spin populations representative of longer interspin distances were detected by DEER. These longer distance populations, which were ∼16-19Å longer than the short distance populations, possessed notably broader distance distribution widths (14-29Å). Upon Ca 2+ removal, the interspin population shifted toward the longer distances, indicating the release of the switch region from TnC and an overall increase in disorder for this region. Together, our results suggest that under conditions of low Ca 2+ , the close proximity of the TnI switch region to TnC in the cardiac isoform is necessary for promoting the interaction between the regulatory switch helix with the N-lobe of cardiac Troponin C, which, unlike the skeletal isoform, is largely in a closed conformation. Copyright © 2017 Elsevier Inc. All rights reserved.

First regional CSM program planned.

PubMed

1982-09-01

6 countries in the English-speaking Caribbean (Antigua, Barbados, Dominica, St. Kitts/Nevis, St. Lucia, and St. Vincent) are scheduled to form the 1st regional contraceptive social marketing program. The program will be under the auspices of the Barbados Family Planning Association. By combining resources, contraceptive social marketing should be able to effectively augment family planning activities in smaller countries where individual programs wuld be too costly. The regional program will also determine whether program elements from 1 country in a region are relevant in other countries. The Caribbean region as a whole has experienced a general decline in both crude birth rates and fertility rates during the past 15 years; however, adolescent fertility rates remain high and an average of 46% of the populations of Caribbean countries are under 15 years of age. Although heavy emigration has traditionally curbed population increases, new restrictive immigration laws are expected. Further increases in the working age population will contribute to already high unemployment rates and hinder economic development. The 6 countries selected for the social marketing program are receptive to innovative family planning approaches and have the basic marketing infrastructure required. Community-based distribution programs already in operation in these countries distribute condoms, oral contraceptives, and barrier methods. The success of these programs has plateaued, and there is a need for delivery systems capable of reaching broader segments of the population. The social marketing program will be phased in to ensure local acceptance among national leaders and consumers. The regional program hopes to borrow elements from Jamaica's contraceptive social marketing program to avoid the costs involved in starting a program from scratch. A major innovation will be the use of mass media advertising for contraceptives.

The effects of selection and genetic drift on the genomic distribution of sexually antagonistic alleles.

PubMed

Mullon, Charles; Pomiankowski, Andrew; Reuter, Max

2012-12-01

Sexual antagonism (SA) occurs when an allele that is beneficial to one sex, is detrimental to the other. This conflict can result in balancing, directional, or disruptive selection acting on SA alleles. A body of theory predicts the conditions under which sexually antagonistic mutants will invade and be maintained in stable polymorphism under balancing selection. There remains, however, considerable debate over the distribution of SA genetic variation across autosomes and sex chromosomes, with contradictory evidence coming from data and theory. In this article, we investigate how the interplay between selection and genetic drift will affect the genomic distribution of sexually antagonistic alleles. The effective population sizes can differ between the autosomes and the sex chromosomes due to a number of ecological factors and, consequently, the distribution of SA genetic variation in genomes. In general, we predict the interplay of SA selection and genetic drift should lead to the accumulation of SA alleles on the X in male heterogametic (XY) species and, on the autosomes in female heterogametic (ZW) species, especially when sexual competition is strong among males. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates.

PubMed

Vogl, Claus; Clemente, Florian

2012-05-01

We analyze a decoupled Moran model with haploid population size N, a biallelic locus under mutation and drift with scaled forward and backward mutation rates θ(1)=μ(1)N and θ(0)=μ(0)N, and directional selection with scaled strength γ=sN. With small scaled mutation rates θ(0) and θ(1), which is appropriate for single nucleotide polymorphism data in highly recombining regions, we derive a simple approximate equilibrium distribution for polymorphic alleles with a constant of proportionality. We also put forth an even simpler model, where all mutations originate from monomorphic states. Using this model we derive the sojourn times, conditional on the ancestral and fixed allele, and under equilibrium the distributions of fixed and polymorphic alleles and fixation rates. Furthermore, we also derive the distribution of small samples in the diffusion limit and provide convenient recurrence relations for calculating this distribution. This enables us to give formulas analogous to the Ewens-Watterson estimator of θ for biased mutation rates and selection. We apply this theory to a polymorphism dataset of fourfold degenerate sites in Drosophila melanogaster. Copyright © 2012 Elsevier Inc. All rights reserved.

Influence of environmental heterogeneity on the distribution and persistence of a subterranean rodent in a highly unstable landscape.

PubMed

Gómez Fernández, María Jimena; Boston, Emma S M; Gaggiotti, Oscar E; Kittlein, Marcelo J; Mirol, Patricia M

2016-12-01

In this study we combine information from landscape characteristics, demographic inference and species distribution modelling to identify environmental factors that shape the genetic distribution of the fossorial rodent Ctenomys. We sequenced the mtDNA control region and amplified 12 microsatellites from 27 populations distributed across the Iberá wetland ecosystem. Hierarchical Bayesian modelling was used to construct phylogenies and estimate divergence times. We developed species distribution models to determine what climatic variables and soil parameters predicted species presence by comparing the current to the historic and predicted future distribution of the species. Finally, we explore the impact of environmental variables on the genetic structure of Ctenomys based on current and past species distributions. The variables that consistently correlated with the predicted distribution of the species and explained the observed genetic differentiation among populations included the distribution of well-drained sandy soils and temperature seasonality. A core region of stable suitable habitat was identified from the Last Interglacial, which is projected to remain stable into the future. This region is also the most genetically diverse and is currently under strong anthropogenic pressure. Results reveal complex demographic dynamics, which have been in constant change in both time and space, and are likely linked to the evolution of the Paraná River. We suggest that any alteration of soil properties (climatic or anthropic) may significantly impact the availability of suitable habitat and consequently the ability of individuals to disperse. The protection of this core stable habitat is of prime importance given the increasing levels of human disturbance across this wetland system and the threat of climate change.

Establishing a Wild, Ex Situ Population of a Critically Endangered Shade-Tolerant Rainforest Conifer: A Translocation Experiment

PubMed Central

Zimmer, Heidi C.; Offord, Catherine A.; Auld, Tony D.; Baker, Patrick J.

2016-01-01

Translocation can reduce extinction risk by increasing population size and geographic range, and is increasingly being used in the management of rare and threatened plant species. A critical determinant of successful plant establishment is light environment. Wollemia nobilis (Wollemi pine) is a critically endangered conifer, with a wild population of 83 mature trees and a highly restricted distribution of less than 10 km2. We used under-planting to establish a population of W. nobilis in a new rainforest site. Because its optimal establishment conditions were unknown, we conducted an experimental translocation, planting in a range of different light conditions from deeply shaded to high light gaps. Two years after the experimental translocation, 85% of plants had survived. There were two distinct responses: very high survival (94%) but very low growth, and lower survival (69%) and higher growth, associated with initial plant condition. Overall survival of translocated W. nobilis was strongly increased in planting sites with higher light, in contrast to previous studies demonstrating long-term survival of wild W. nobilis juveniles in deep shade. Translocation by under-planting may be useful in establishing new populations of shade-tolerant plant species, not least by utilizing the range of light conditions that occur in forest understories. PMID:27403527

Establishing a Wild, Ex Situ Population of a Critically Endangered Shade-Tolerant Rainforest Conifer: A Translocation Experiment.

PubMed

Zimmer, Heidi C; Offord, Catherine A; Auld, Tony D; Baker, Patrick J

2016-01-01

Translocation can reduce extinction risk by increasing population size and geographic range, and is increasingly being used in the management of rare and threatened plant species. A critical determinant of successful plant establishment is light environment. Wollemia nobilis (Wollemi pine) is a critically endangered conifer, with a wild population of 83 mature trees and a highly restricted distribution of less than 10 km2. We used under-planting to establish a population of W. nobilis in a new rainforest site. Because its optimal establishment conditions were unknown, we conducted an experimental translocation, planting in a range of different light conditions from deeply shaded to high light gaps. Two years after the experimental translocation, 85% of plants had survived. There were two distinct responses: very high survival (94%) but very low growth, and lower survival (69%) and higher growth, associated with initial plant condition. Overall survival of translocated W. nobilis was strongly increased in planting sites with higher light, in contrast to previous studies demonstrating long-term survival of wild W. nobilis juveniles in deep shade. Translocation by under-planting may be useful in establishing new populations of shade-tolerant plant species, not least by utilizing the range of light conditions that occur in forest understories.

Geographic Distribution of Trauma Centers and Injury Related Mortality in the United States

PubMed Central

Brown, Joshua B.; Rosengart, Matthew R.; Billiar, Timothy R.; Peitzman, Andrew B.; Sperry, Jason L.

2015-01-01

Background Regionalized trauma care improves outcomes; however access to care is not uniform across the US. The objective was to evaluate whether geographic distribution of trauma centers correlates with injury mortality across state trauma systems. Methods Level I/II trauma centers in the contiguous US were mapped. State-level age-adjusted injury fatality rates/100,000people were obtained and evaluated for spatial autocorrelation. Nearest neighbor ratios (NNR) were generated for each state. A NNR<1 indicates clustering, while NNR>1 indicates dispersion. NNR were tested for difference from random geographic distribution. Fatality rates and NNR were examined for correlation. Fatality rates were compared between states with trauma center clustering versus dispersion. Trauma center distribution and population density were evaluated. Spatial-lag regression determined the association between fatality rate and NNR, controlling for state-level demographics, population density, injury severity, trauma system resources, and socioeconomic factors. Results Fatality rates were spatially autocorrelated (Moran's I=0.35, p<0.01). Nine states had a clustered pattern (median NNR 0.55, IQR 0.48–0.60), 22 had a dispersed pattern (median NNR 2.00, IQR 1.68–3.99), and 10 had a random pattern (median NNR 0.90, IQR 0.85–1.00) of trauma center distribution. Fatality rate and NNR were correlated (ρ=0.34, p=0.03). Clustered states had a lower median injury fatality rate compared to dispersed states (56.9 [IQR 46.5–58.9] versus 64.9 [IQR 52.5–77.1], p=0.04). Dispersed compared to clustered states had more counties without a trauma center that had higher population density than counties with a trauma center (5.7% versus 1.2%, p<0.01). Spatial-lag regression demonstrated fatality rates increased 0.02/100,000persons for each unit increase in NNR (p<0.01). Conclusions Geographic distribution of trauma centers correlates with injury mortality, with more clustered state trauma centers associated with lower fatality rates. This may be a result of access relative to population density. These results may have implications for trauma system planning and requires further study to investigate underlying mechanisms PMID:26517780

Colonization of a territory by a stochastic population under a strong Allee effect and a low immigration pressure

NASA Astrophysics Data System (ADS)

Be'er, Shay; Assaf, Michael; Meerson, Baruch

2015-06-01

We study the dynamics of colonization of a territory by a stochastic population at low immigration pressure. We assume a sufficiently strong Allee effect that introduces, in deterministic theory, a large critical population size for colonization. At low immigration rates, the average precolonization population size is small, thus invalidating the WKB approximation to the master equation. We circumvent this difficulty by deriving an exact zero-flux solution of the master equation and matching it with an approximate nonzero-flux solution of the pertinent Fokker-Planck equation in a small region around the critical population size. This procedure provides an accurate evaluation of the quasistationary probability distribution of population sizes in the precolonization state and of the mean time to colonization, for a wide range of immigration rates. At sufficiently high immigration rates our results agree with WKB results obtained previously. At low immigration rates the results can be very different.

Colonization of a territory by a stochastic population under a strong Allee effect and a low immigration pressure.

PubMed

Be'er, Shay; Assaf, Michael; Meerson, Baruch

2015-06-01

We study the dynamics of colonization of a territory by a stochastic population at low immigration pressure. We assume a sufficiently strong Allee effect that introduces, in deterministic theory, a large critical population size for colonization. At low immigration rates, the average precolonization population size is small, thus invalidating the WKB approximation to the master equation. We circumvent this difficulty by deriving an exact zero-flux solution of the master equation and matching it with an approximate nonzero-flux solution of the pertinent Fokker-Planck equation in a small region around the critical population size. This procedure provides an accurate evaluation of the quasistationary probability distribution of population sizes in the precolonization state and of the mean time to colonization, for a wide range of immigration rates. At sufficiently high immigration rates our results agree with WKB results obtained previously. At low immigration rates the results can be very different.

Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus.

PubMed

Manni, Mosè; Gomulski, Ludvik M; Aketarawong, Nidchaya; Tait, Gabriella; Scolari, Francesca; Somboon, Pradya; Guglielmino, Carmela R; Malacrida, Anna R; Gasperi, Giuliano

2015-03-28

The dramatic worldwide expansion of Aedes albopictus (the Asian tiger mosquito) and its vector competence for numerous arboviruses represent a growing threat to public health security. Molecular markers are crucially needed for tracking the rapid spread of this mosquito and to obtain a deeper knowledge of population structure. This is a fundamental requirement for the development of strict monitoring protocols and for the improvement of sustainable control measures. Wild population samples from putative source areas and from newly colonised regions were analysed for variability at the ribosomal DNA internal transcribed spacer 2 (ITS2). Moreover, a new set of 23 microsatellite markers (SSR) was developed. Sixteen of these SSRs were tested in an ancestral (Thailand) and two adventive Italian populations. Seventy-six ITS2 sequences representing 52 unique haplotypes were identified, and AMOVA indicated that most of their variation occurred within individuals (74.36%), while only about 8% was detected among populations. Spatial analyses of molecular variance revealed that haplotype genetic similarity was not related to the geographic proximity of populations and the haplotype phylogeny clearly indicated that highly related sequences were distributed across populations from different geographical regions. The SSR markers displayed a high level of polymorphism both in the ancestral and in adventive populations, and F ST estimates suggested the absence of great differentiation. The ancestral nature of the Thai population was corroborated by its higher level of variability. The two types of genetic markers here implemented revealed the distribution of genetic diversity within and between populations and provide clues on the dispersion dynamics of this species. It appears that the diffusion of this mosquito does not conform to a progressive expansion from the native Asian source area, but to a relatively recent and chaotic propagule distribution mediated by human activities. Under this scenario, multiple introductions and admixture events probably play an important role in maintaining the genetic diversity and in avoiding bottleneck effects. The polymorphic SSR markers here implemented will provide an important tool for reconstructing the routes of invasion followed by this mosquito.

Using multitype branching processes to quantify statistics of disease outbreaks in zoonotic epidemics

NASA Astrophysics Data System (ADS)

Singh, Sarabjeet; Schneider, David J.; Myers, Christopher R.

2014-03-01

Branching processes have served as a model for chemical reactions, biological growth processes, and contagion (of disease, information, or fads). Through this connection, these seemingly different physical processes share some common universalities that can be elucidated by analyzing the underlying branching process. In this work we focus on coupled branching processes as a model of infectious diseases spreading from one population to another. An exceedingly important example of such coupled outbreaks are zoonotic infections that spill over from animal populations to humans. We derive several statistical quantities characterizing the first spillover event from animals to humans, including the probability of spillover, the first passage time distribution for human infection, and disease prevalence in the animal population at spillover. Large stochastic fluctuations in those quantities can make inference of the state of the system at the time of spillover difficult. Focusing on outbreaks in the human population, we then characterize the critical threshold for a large outbreak, the distribution of outbreak sizes, and associated scaling laws. These all show a strong dependence on the basic reproduction number in the animal population and indicate the existence of a novel multicritical point with altered scaling behavior. The coupling of animal and human infection dynamics has crucial implications, most importantly allowing for the possibility of large human outbreaks even when human-to-human transmission is subcritical.

Population pharmacokinetic (PK) analysis of laromustine, an emerging alkylating agent, in cancer patients.

PubMed

Nassar, Ala F; Wisnewski, Adam V; King, Ivan

2017-05-01

1. Alkylating agents are capable of introducing an alkyl group into nucleophilic sites on DNA or RNA through covalent bond. Laromustine is an active member of a relatively new class of sulfonylhydrazine prodrugs under development as antineoplastic alkylating agents, and displays significant single-agent activity. 2. This is the first report of the population pharmacokinetic analysis of laromustine, 106 patients, 66 with hematologic malignancies and 40 with solid tumors, participated in five clinical trials worldwide. Of these, 104 patients were included in the final NONMEM analysis. 3. The population estimates for total clearance (CL) and volume of distribution of the central compartment (V 1 ) were 96.3 L/h and 45.9 L, associated with high inter-patient variability of 52.9% and 79.8% and inter-occasion variability of 26.7% and 49.3%, respectively. The population estimates for Q and V 2 were 73.2 L/h and 29.9 L, and inter-patient variability in V 2 was 63.1%, respectively. 4. The estimate of V ss (75.8 L) exceeds total body water, indicating that laromustine is distributed to tissues. The half-life is short, less than 1 h, reflecting rapid clearance. Population PK analysis showed laromustine pharmacokinetics to be independent of dose and organ function with no effect on subsequent dosing cycles.

Dispersal leads to spatial autocorrelation in species distributions: A simulation model

USGS Publications Warehouse

Bahn, V.; Krohn, W.B.; O'Connor, R.J.

2008-01-01

Compared to population growth regulated by local conditions, dispersal has been underappreciated as a central process shaping the spatial distribution of populations. This paper asks: (a) which conditions increase the importance of dispersers relative to local recruits in determining population sizes? and (b) how does dispersal influence the spatial distribution patterns of abundances among connected populations? We approached these questions with a simulation model of populations on a coupled lattice with cells of continuously varying habitat quality expressed as carrying capacities. Each cell contained a population with the basic dynamics of density-regulated growth, and was connected to other populations by immigration and emigration. The degree to which dispersal influenced the distribution of population sizes depended most strongly on the absolute amount of dispersal, and then on the potential population growth rate. Dispersal decaying in intensity with distance left close neighbours more alike in population size than distant populations, leading to an increase in spatial autocorrelation. The spatial distribution of species with low potential growth rates is more dependent on dispersal than that of species with high growth rates; therefore, distribution modelling for species with low growth rates requires particular attention to autocorrelation, and conservation management of these species requires attention to factors curtailing dispersal, such as fragmentation and dispersal barriers. ?? 2007 Elsevier B.V. All rights reserved.

Distance from sub-Saharan Africa predicts mutational load in diverse human genomes.

PubMed

Henn, Brenna M; Botigué, Laura R; Peischl, Stephan; Dupanloup, Isabelle; Lipatov, Mikhail; Maples, Brian K; Martin, Alicia R; Musharoff, Shaila; Cann, Howard; Snyder, Michael P; Excoffier, Laurent; Kidd, Jeffrey M; Bustamante, Carlos D

2016-01-26

The Out-of-Africa (OOA) dispersal ∼ 50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

Unravelling the genetic differentiation among varieties of the Neotropical savanna tree Hancornia speciosa Gomes.

PubMed

Collevatti, Rosane G; Rodrigues, Eduardo E; Vitorino, Luciana C; Lima-Ribeiro, Matheus S; Chaves, Lázaro J; Telles, Mariana P C

2018-04-20

Spatial distribution of species genetic diversity is often driven by geographical distance (isolation by distance) or environmental conditions (isolation by environment), especially under climate change scenarios such as Quaternary glaciations. Here, we used coalescent analyses coupled with ecological niche modelling (ENM), spatially explicit quantile regression analyses and the multiple matrix regression with randomization (MMRR) approach to unravel the patterns of genetic differentiation in the widely distributed Neotropical savanna tree, Hancornia speciosa (Apocynaceae). Due to its high morphological differentiation, the species was originally classified into six botanical varieties by Monachino, and has recently been recognized as only two varieties by Flora do Brasil 2020. Thus, H. speciosa is a good biological model for learning about evolution of phenotypic plasticity under genetic and ecological effects, and predicting their responses to changing environmental conditions. We sampled 28 populations (777 individuals) of Monachino's four varieties of H. speciosa and used seven microsatellite loci to genotype them. Bayesian clustering showed five distinct genetic groups (K = 5) with high admixture among Monachino's varieties, mainly among populations in the central area of the species geographical range. Genetic differentiation among Monachino's varieties was lower than the genetic differentiation among populations within varieties, with higher within-population inbreeding. A high historical connectivity among populations of the central Cerrado shown by coalescent analyses may explain the high admixture among varieties. In addition, areas of higher climatic suitability also presented higher genetic diversity in such a way that the wide historical refugium across central Brazil might have promoted the long-term connectivity among populations. Yet, FST was significantly related to geographic distances, but not to environmental distances, and coalescent analyses and ENM predicted a demographical scenario of quasi-stability through time. Our findings show that demographical history and isolation by distance, but not isolation by environment, drove genetic differentiation of populations. Finally, the genetic clusters do not support the two recently recognized botanical varieties of H. speciosa, but partially support Monachino's classification at least for the four sampled varieties, similar to morphological variation.

Population signatures of large-scale, long-term disjunction and small-scale, short-term habitat fragmentation in an Afromontane forest bird

PubMed Central

Habel, J C; Mulwa, R K; Gassert, F; Rödder, D; Ulrich, W; Borghesio, L; Husemann, M; Lens, L

2014-01-01

The Eastern Afromontane cloud forests occur as geographically distinct mountain exclaves. The conditions of these forests range from large to small and from fairly intact to strongly degraded. For this study, we sampled individuals of the forest bird species, the Montane White-eye Zosterops poliogaster from 16 sites and four mountain archipelagos. We analysed 12 polymorphic microsatellites and three phenotypic traits, and calculated Species Distribution Models (SDMs) to project past distributions and predict potential future range shifts under a scenario of climate warming. We found well-supported genetic and morphologic clusters corresponding to the mountain ranges where populations were sampled, with 43% of all alleles being restricted to single mountains. Our data suggest that large-scale and long-term geographic isolation on mountain islands caused genetically and morphologically distinct population clusters in Z. poliogaster. However, major genetic and biometric splits were not correlated to the geographic distances among populations. This heterogeneous pattern can be explained by past climatic shifts, as highlighted by our SDM projections. Anthropogenically fragmented populations showed lower genetic diversity and a lower mean body mass, possibly in response to suboptimal habitat conditions. On the basis of these findings and the results from our SDM analysis we predict further loss of genotypic and phenotypic uniqueness in the wake of climate change, due to the contraction of the species' climatic niche and subsequent decline in population size. PMID:24713824

Population signatures of large-scale, long-term disjunction and small-scale, short-term habitat fragmentation in an Afromontane forest bird.

PubMed

Habel, J C; Mulwa, R K; Gassert, F; Rödder, D; Ulrich, W; Borghesio, L; Husemann, M; Lens, L

2014-09-01

The Eastern Afromontane cloud forests occur as geographically distinct mountain exclaves. The conditions of these forests range from large to small and from fairly intact to strongly degraded. For this study, we sampled individuals of the forest bird species, the Montane White-eye Zosterops poliogaster from 16 sites and four mountain archipelagos. We analysed 12 polymorphic microsatellites and three phenotypic traits, and calculated Species Distribution Models (SDMs) to project past distributions and predict potential future range shifts under a scenario of climate warming. We found well-supported genetic and morphologic clusters corresponding to the mountain ranges where populations were sampled, with 43% of all alleles being restricted to single mountains. Our data suggest that large-scale and long-term geographic isolation on mountain islands caused genetically and morphologically distinct population clusters in Z. poliogaster. However, major genetic and biometric splits were not correlated to the geographic distances among populations. This heterogeneous pattern can be explained by past climatic shifts, as highlighted by our SDM projections. Anthropogenically fragmented populations showed lower genetic diversity and a lower mean body mass, possibly in response to suboptimal habitat conditions. On the basis of these findings and the results from our SDM analysis we predict further loss of genotypic and phenotypic uniqueness in the wake of climate change, due to the contraction of the species' climatic niche and subsequent decline in population size.

The impact of new transportation modes on population distribution in Jing-Jin-Ji region of China

PubMed Central

Wang, Lizhe; Chen, Lajiao

2018-01-01

This paper conducts a novel study in China’s Jing-Jin-Ji region to investigate the determinants of population distribution and short-term migration based on a comprehensive dataset including traditional census data, earth observation data, and emerging Internet data. Our results show that due to the high level of urbanization in this region, natural conditions are no longer the strongest determinants of population distribution. New transportation modes, such as high-speed rail, have arisen as a significant determinant of population distribution and short-term migration, particularly in large cities. Socio-economic factors such as GDP, investment, urbanization level, and technology, which are traditionally assumed to govern population distribution and short-term migration, have less influence although education still remains an important factor affecting population distribution. These findings will contribute valuable information to regional planning decision-making in the Jing-Jin-Ji region. PMID:29360105

Appendix B: Fisher, lynx, wolverine summary of distribution information

Treesearch

Mary Maj

1994-01-01

We present maps depicting distributions of fisher, lynx, and wolverine in the western United States since 1961. Comparison of past and current distributions of species can shed light on population persistence, periods of population isolation, meta-population structure, and important connecting landscapes. Information on the distribution of the American marten is not...

Genetic variation for pseudo-self-compatibility in self-incompatible populations of Leavenworthia alabamica (Brassicaceae).

PubMed

Baldwin, Sarah J; Schoen, Daniel J

2017-01-01

Self-incompatibility (SI) promotes outcrossing, but transitions to self-compatibility (SC) are frequent. Population genetic theory describing the breakdown of SI to SC suggests that, under most conditions, populations should be composed of either SI or SC individuals. Under a narrow range of conditions, theory suggests that SI may persist alongside reduced expression of SI (pseudo-SI, PSI) in mixed-mating populations. We studied genetic variation for PSI segregating in four SI populations of Leavenworthia alabamica by measurement of the heritability of pollen tube number after self-pollination. We tested for the role of the S-locus in this variation by sequencing seven S-alleles from plants with high pseudo-SC (PSC) and testing for the co-segregation of these alleles with PSC. We found a continuous distribution of PSC in all populations and 90% of plants exhibited PSC. The heritability ranged from 0.39 to 0.57. All seven S-alleles from plants with high PSC exhibited trans-specific polymorphism, and no stop codons were observed within the c. 600-bp region sequenced. One of these S-alleles was directly associated with the inheritance of PSC. We conclude that heritable variation in PSC is largely a result of genetic variation in the signaling cascade downstream of the S-locus reaction, together with the presence of one leaky S-allele. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Predicting the geographical distribution of two invasive termite species from occurrence data.

PubMed

Tonini, Francesco; Divino, Fabio; Lasinio, Giovanna Jona; Hochmair, Hartwig H; Scheffrahn, Rudolf H

2014-10-01

Predicting the potential habitat of species under both current and future climate change scenarios is crucial for monitoring invasive species and understanding a species' response to different environmental conditions. Frequently, the only data available on a species is the location of its occurrence (presence-only data). Using occurrence records only, two models were used to predict the geographical distribution of two destructive invasive termite species, Coptotermes gestroi (Wasmann) and Coptotermes formosanus Shiraki. The first model uses a Bayesian linear logistic regression approach adjusted for presence-only data while the second one is the widely used maximum entropy approach (Maxent). Results show that the predicted distributions of both C. gestroi and C. formosanus are strongly linked to urban development. The impact of future scenarios such as climate warming and population growth on the biotic distribution of both termite species was also assessed. Future climate warming seems to affect their projected probability of presence to a lesser extent than population growth. The Bayesian logistic approach outperformed Maxent consistently in all models according to evaluation criteria such as model sensitivity and ecological realism. The importance of further studies for an explicit treatment of residual spatial autocorrelation and a more comprehensive comparison between both statistical approaches is suggested.

Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient

PubMed Central

Acuña-Rodríguez, Ian S.; Torres-Díaz, Cristian; Hereme, Rasme

2017-01-01

The increase in temperature as consequence of the recent global warming has been reported to generate new ice-free areas in the Antarctic continent, facilitating the colonization and spread of plant populations. Consequently, Antarctic vascular plants have been observed extending their southern distribution. But as the environmental conditions toward southern localities become progressively more departed from the species’ physiological optimum, the ecophysiological responses and survival to the expected global warming could be reduced. However, if processes of local adaptation are the main cause of the observed southern expansion, those populations could appear constrained to respond positively to the expected global warming. Using individuals from the southern tip of South America, the South Shetland Islands and the Antarctic Peninsula, we assess with a long term experiment (three years) under controlled conditions if the responsiveness of Colobanthus quitensis populations to the expected global warming, is related with their different foliar traits and photoprotective mechanisms along the latitudinal gradient. In addition, we tested if the release of the stress condition by the global warming in these cold environments increases the ecophysiological performance. For this, we describe the latitudinal pattern of net photosynthetic capacity, biomass accumulation, and number of flowers under current and future temperatures respective to each site of origin after three growing seasons. Overall, was found a clinal trend was found in the foliar traits and photoprotective mechanisms in the evaluated C. quitensis populations. On the other hand, an asymmetric response to warming was observed for southern populations in all ecophysiological traits evaluated, suggesting that low temperature is limiting the performance of C. quitensis populations. Our results suggest that under a global warming scenario, plant populations that inhabiting cold zones at high latitudes could increase in their ecophysiological performance, enhancing the size of populations or their spread. PMID:28948096

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Multiple Comorbidities and Interest in Research Participation Among Clients of a Nonprofit Food Distribution Site.

PubMed

Higashi, Robin T; Craddock Lee, Simon J; Leonard, Tammy; Cuate, Erica L; Cole, Jay; Pruitt, Sandi L

2015-10-01

Persons accessing food from nonprofit distribution sites face numerous challenges and typically have significant unmet health needs. However, given limited and intermittent healthcare system engagement, this vulnerable population is underrepresented in clinical research. We sought to better understand the health needs of a nonclinical population to inform future research and interventions. Focus groups were conducted in English (n = 4) and Spanish (n = 4) with clients of Crossroads Community Services (CCS), the largest distributor of North Texas Food Bank. Discussions probed participants' health status, healthcare utilization, understanding and utilization of mammography, and attitudes toward participation in research. Participants included 42 CCS clients, primarily Hispanic or African American women. Participants reported multiple comorbid conditions among household members, yet utilization of health services was often limited by cost. The majority expressed interest in participating in research to communicate their health concerns and obtain emotional support. CCS clients represent a high-need, under-reached population willing to engage in health-related research that affords them opportunity to connect with peers in group settings and obtain information to improve management of daily life challenges. The Community Assistance Research (CARe) Initiative, a community-academic collaboration, establishes a much-needed opportunity for ongoing clinical research and intervention among this underserved population. © 2015 Wiley Periodicals, Inc.

The population of natural Earth satellites

NASA Astrophysics Data System (ADS)

Granvik, Mikael; Vaubaillon, Jeremie; Jedicke, Robert

2012-03-01

We have for the first time calculated the population characteristics of the Earth’s irregular natural satellites (NESs) that are temporarily captured from the near-Earth-object (NEO) population. The steady-state NES size-frequency and residence-time distributions were determined under the dynamical influence of all the massive bodies in the Solar System (but mainly the Sun, Earth, and Moon) for NEOs of negligible mass. To this end, we compute the NES capture probability from the NEO population as a function of the latter’s heliocentric orbital elements and combine those results with the current best estimates for the NEO size-frequency and orbital distribution. At any given time there should be at least one NES of 1-m diameter orbiting the Earth. The average temporarily-captured orbiter (TCO; an object that makes at least one revolution around the Earth in a co-rotating coordinate system) completes (2.88 ± 0.82) rev around the Earth during a capture event that lasts (286 ± 18) d. We find a small preference for capture events starting in either January or July. Our results are consistent with the single known natural TCO, 2006 RH120, a few-meter diameter object that was captured for about a year starting in June 2006. We estimate that about 0.1% of all meteors impacting the Earth were TCOs.

Status and distribution of the Kittlitz's murrelet Brachyramphus brevirostris in Kenai Fjords, Alaska

USGS Publications Warehouse

Arimitsu, Mayumi L.; Piatt, John F.; Romano, Marc D.; van Pelt, Thomas I.

2011-01-01

The Kittlitz's Murrelet Brachyramphus brevirostris is a candidate species for listing under the US Endangered Species Act because of its apparent declines within core population areas of coastal Alaska. During the summers of 2006-2008, we conducted surveys in marine waters adjacent to Kenai Fjords National Park, Alaska, to estimate the current population size of Kittlitz's and Marbled murrelets B. marmoratus and examine seasonal variability in distribution within coastal fjords. We also evaluated historical data to estimate trend. Based on an average of point estimates, we find the recent population (95% CI) of Kittlitz's Murrelet to be 716 (353-1080) individuals, that of Marbled Murrelet to be 6690 (5427-7953) individuals, and all Brachyramphus murrelets combined to number 8186 (6978-9393) birds. Within-season density estimates showed Kittlitz's Murrelets generally increased between June and July, but dispersed rapidly by August, while Marbled Murrelets generally increased throughout the summer. Trends in Kittlitz's and Marbled murrelet populations were difficult to assess with confidence. Methods for counting or sampling murrelets varied in early decades of study, while in later years there is uncertainty due to highly variable counts among years, which may be due in part to timing of surveys relative to the spring bloom in coastal waters of the Gulf of Alaska.

Evidence for the Gompertz curve in the income distribution of Brazil 1978-2005

NASA Astrophysics Data System (ADS)

Moura, N. J., Jr.; Ribeiro, M. B.

2009-01-01

This work presents an empirical study of the evolution of the personal income distribution in Brazil. Yearly samples available from 1978 to 2005 were studied and evidence was found that the complementary cumulative distribution of personal income for 99% of the economically less favorable population is well represented by a Gompertz curve of the form G(x) = exp [exp (A-Bx)], where x is the normalized individual income. The complementary cumulative distribution of the remaining 1% richest part of the population is well represented by a Pareto power law distribution P(x) = βx-α. This result means that similarly to other countries, Brazil’s income distribution is characterized by a well defined two class system. The parameters A, B, α, β were determined by a mixture of boundary conditions, normalization and fitting methods for every year in the time span of this study. Since the Gompertz curve is characteristic of growth models, its presence here suggests that these patterns in income distribution could be a consequence of the growth dynamics of the underlying economic system. In addition, we found out that the percentage share of both the Gompertzian and Paretian components relative to the total income shows an approximate cycling pattern with periods of about 4 years and whose maximum and minimum peaks in each component alternate at about every 2 years. This finding suggests that the growth dynamics of Brazil’s economic system might possibly follow a Goodwin-type class model dynamics based on the application of the Lotka-Volterra equation to economic growth and cycle.

[Natural forming causes of China population distribution].

PubMed

Fang, Yu; Ouyang, Zhi-Yun; Zheng, Hua; Xiao, Yi; Niu, Jun-Feng; Chen, Sheng-Bin; Lu, Fei

2012-12-01

The diverse natural environment in China causes the spatial heterogeneity of China population distribution. It is essential to understand the interrelations between the population distribution pattern and natural environment to enhance the understanding of the man-land relationship and the realization of the sustainable management for the population, resources, and environment. This paper analyzed the China population distribution by adopting the index of population density (PD) in combining with spatial statistic method and Lorenz curve, and discussed the effects of the natural factors on the population distribution and the interrelations between the population distribution and 16 indices including average annual precipitation (AAP), average annual temperature (AAT), average annual sunshine duration (AASD), precipitation variation (PV), temperature variation (TV), sunshine duration variation (SDV), relative humidity (RH), aridity index (AI), warmth index ( WI), > or = 5 degrees C annual accumulated temperature (AACT), average elevation (AE), relative height difference (RHD), surface roughness (SR), water system density (WSD), net primary productivity (NPP), and shortest distance to seashore (SDTS). There existed an obvious aggregation phenomenon in the population distribution in China. The PD was high in east China, medium in central China, and low in west China, presenting an obvious positive spatial association. The PD was significantly positively correlated with WSD, AAT, AAP, NPP, AACT, PV, RH, and WI, and significantly negatively correlated with RHD, AE, SDV, SR, and SDTS. The climate factors (AAT, WI, PV, and NPP), topography factors (SR and RHD), and water system factor (WSD) together determined the basic pattern of the population distribution in China. It was suggested that the monitoring of the eco-environment in the east China of high population density should be strengthened to avoid the eco-environmental degradation due to the expanding population, and the conservation of the eco-environment in the central and west China with vulnerable eco-environment should also be strengthened to enhance the population carrying ability of these regions and to mitigate the eco-environmental pressure in the east China of high population density.

A probabilistic method for testing and estimating selection differences between populations

PubMed Central

He, Yungang; Wang, Minxian; Huang, Xin; Li, Ran; Xu, Hongyang; Xu, Shuhua; Jin, Li

2015-01-01

Human populations around the world encounter various environmental challenges and, consequently, develop genetic adaptations to different selection forces. Identifying the differences in natural selection between populations is critical for understanding the roles of specific genetic variants in evolutionary adaptation. Although numerous methods have been developed to detect genetic loci under recent directional selection, a probabilistic solution for testing and quantifying selection differences between populations is lacking. Here we report the development of a probabilistic method for testing and estimating selection differences between populations. By use of a probabilistic model of genetic drift and selection, we showed that logarithm odds ratios of allele frequencies provide estimates of the differences in selection coefficients between populations. The estimates approximate a normal distribution, and variance can be estimated using genome-wide variants. This allows us to quantify differences in selection coefficients and to determine the confidence intervals of the estimate. Our work also revealed the link between genetic association testing and hypothesis testing of selection differences. It therefore supplies a solution for hypothesis testing of selection differences. This method was applied to a genome-wide data analysis of Han and Tibetan populations. The results confirmed that both the EPAS1 and EGLN1 genes are under statistically different selection in Han and Tibetan populations. We further estimated differences in the selection coefficients for genetic variants involved in melanin formation and determined their confidence intervals between continental population groups. Application of the method to empirical data demonstrated the outstanding capability of this novel approach for testing and quantifying differences in natural selection. PMID:26463656

Impacts of Climate Change on Native Landcover: Seeking Future Climatic Refuges

PubMed Central

Mangabeira Albernaz, Ana Luisa

2016-01-01

Climate change is a driver for diverse impacts on global biodiversity. We investigated its impacts on native landcover distribution in South America, seeking to predict its effect as a new force driving habitat loss and population isolation. Moreover, we mapped potential future climatic refuges, which are likely to be key areas for biodiversity conservation under climate change scenarios. Climatically similar native landcovers were aggregated using a decision tree, generating a reclassified landcover map, from which 25% of the map’s coverage was randomly selected to fuel distribution models. We selected the best geographical distribution models among twelve techniques, validating the predicted distribution for current climate with the landcover map and used the best technique to predict the future distribution. All landcover categories showed changes in area and displacement of the latitudinal/longitudinal centroid. Closed vegetation was the only landcover type predicted to expand its distributional range. The range contractions predicted for other categories were intense, even suggesting extirpation of the sparse vegetation category. The landcover refuges under future climate change represent a small proportion of the South American area and they are disproportionately represented and unevenly distributed, predominantly occupying five of 26 South American countries. The predicted changes, regardless of their direction and intensity, can put biodiversity at risk because they are expected to occur in the near future in terms of the temporal scales of ecological and evolutionary processes. Recognition of the threat of climate change allows more efficient conservation actions. PMID:27618445

Impacts of Climate Change on Native Landcover: Seeking Future Climatic Refuges.

PubMed

Zanin, Marina; Mangabeira Albernaz, Ana Luisa

2016-01-01

Climate change is a driver for diverse impacts on global biodiversity. We investigated its impacts on native landcover distribution in South America, seeking to predict its effect as a new force driving habitat loss and population isolation. Moreover, we mapped potential future climatic refuges, which are likely to be key areas for biodiversity conservation under climate change scenarios. Climatically similar native landcovers were aggregated using a decision tree, generating a reclassified landcover map, from which 25% of the map's coverage was randomly selected to fuel distribution models. We selected the best geographical distribution models among twelve techniques, validating the predicted distribution for current climate with the landcover map and used the best technique to predict the future distribution. All landcover categories showed changes in area and displacement of the latitudinal/longitudinal centroid. Closed vegetation was the only landcover type predicted to expand its distributional range. The range contractions predicted for other categories were intense, even suggesting extirpation of the sparse vegetation category. The landcover refuges under future climate change represent a small proportion of the South American area and they are disproportionately represented and unevenly distributed, predominantly occupying five of 26 South American countries. The predicted changes, regardless of their direction and intensity, can put biodiversity at risk because they are expected to occur in the near future in terms of the temporal scales of ecological and evolutionary processes. Recognition of the threat of climate change allows more efficient conservation actions.

Determination of the optimal sample size for a clinical trial accounting for the population size.

PubMed

Stallard, Nigel; Miller, Frank; Day, Simon; Hee, Siew Wan; Madan, Jason; Zohar, Sarah; Posch, Martin

2017-07-01

The problem of choosing a sample size for a clinical trial is a very common one. In some settings, such as rare diseases or other small populations, the large sample sizes usually associated with the standard frequentist approach may be infeasible, suggesting that the sample size chosen should reflect the size of the population under consideration. Incorporation of the population size is possible in a decision-theoretic approach either explicitly by assuming that the population size is fixed and known, or implicitly through geometric discounting of the gain from future patients reflecting the expected population size. This paper develops such approaches. Building on previous work, an asymptotic expression is derived for the sample size for single and two-arm clinical trials in the general case of a clinical trial with a primary endpoint with a distribution of one parameter exponential family form that optimizes a utility function that quantifies the cost and gain per patient as a continuous function of this parameter. It is shown that as the size of the population, N, or expected size, N∗ in the case of geometric discounting, becomes large, the optimal trial size is O(N1/2) or O(N∗1/2). The sample size obtained from the asymptotic expression is also compared with the exact optimal sample size in examples with responses with Bernoulli and Poisson distributions, showing that the asymptotic approximations can also be reasonable in relatively small sample sizes. © 2016 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cell lineage distribution atlas of the human stomach reveals heterogeneous gland populations in the gastric antrum.

PubMed

Choi, Eunyoung; Roland, Joseph T; Barlow, Brittney J; O'Neal, Ryan; Rich, Amy E; Nam, Ki Taek; Shi, Chanjuan; Goldenring, James R

2014-11-01

The glands of the stomach body and antral mucosa contain a complex compendium of cell lineages. In lower mammals, the distribution of oxyntic glands and antral glands define the anatomical regions within the stomach. We examined in detail the distribution of the full range of cell lineages within the human stomach. We determined the distribution of gastric gland cell lineages with specific immunocytochemical markers in entire stomach specimens from three non-obese organ donors. The anatomical body and antrum of the human stomach were defined by the presence of ghrelin and gastrin cells, respectively. Concentrations of somatostatin cells were observed in the proximal stomach. Parietal cells were seen in all glands of the body of the stomach as well as in over 50% of antral glands. MIST1 expressing chief cells were predominantly observed in the body although individual glands of the antrum also showed MIST1 expressing chief cells. While classically described antral glands were observed with gastrin cells and deep antral mucous cells without any parietal cells, we also observed a substantial population of mixed type glands containing both parietal cells and G cells throughout the antrum. Enteroendocrine cells show distinct patterns of localisation in the human stomach. The existence of antral glands with mixed cell lineages indicates that human antral glands may be functionally chimeric with glands assembled from multiple distinct stem cell populations. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pauly, Tyler; Garrod, Robin T., E-mail: tap74@cornell.edu

Computational models of interstellar gas-grain chemistry have historically adopted a single dust-grain size of 0.1 micron, assumed to be representative of the size distribution present in the interstellar medium. Here, we investigate the effects of a broad grain-size distribution on the chemistry of dust-grain surfaces and the subsequent build-up of molecular ices on the grains, using a three-phase gas-grain chemical model of a quiescent dark cloud. We include an explicit treatment of the grain temperatures, governed both by the visual extinction of the cloud and the size of each individual grain-size population. We find that the temperature difference plays amore » significant role in determining the total bulk ice composition across the grain-size distribution, while the effects of geometrical differences between size populations appear marginal. We also consider collapse from a diffuse to a dark cloud, allowing dust temperatures to fall. Under the initial diffuse conditions, small grains are too warm to promote grain-mantle build-up, with most ices forming on the mid-sized grains. As collapse proceeds, the more abundant, smallest grains cool and become the dominant ice carriers; the large population of small grains means that this ice is distributed across many grains, with perhaps no more than 40 monolayers of ice each (versus several hundred assuming a single grain size). This effect may be important for the subsequent processing and desorption of the ice during the hot-core phase of star formation, exposing a significant proportion of the ice to the gas phase, increasing the importance of ice-surface chemistry and surface–gas interactions.« less

Characterizing the spatial distribution of multiple pollutants and populations at risk in Atlanta, Georgia.

PubMed

Pearce, John L; Waller, Lance A; Sarnat, Stefanie E; Chang, Howard H; Klein, Mitch; Mulholland, James A; Tolbert, Paige E

2016-08-01

Exposure metrics that identify spatial contrasts in multipollutant air quality are needed to better understand multipollutant geographies and health effects from air pollution. Our aim is to improve understanding of: (1) long-term spatial distributions of multiple pollutants; and (2) demographic characteristics of populations residing within areas of differing air quality. We obtained average concentrations for ten air pollutants (p=10) across a 12 km grid (n=253) covering Atlanta, Georgia for 2002-2008. We apply a self-organizing map (SOM) to our data to derive multipollutant patterns observed across our grid and classify locations under their most similar pattern (i.e, multipollutant spatial type (MST)). Finally, we geographically map classifications to delineate regions of similar multipollutant characteristics and characterize associated demographics. We found six MSTs well describe our data, with profiles highlighting a range of combinations, from locations experiencing generally clean air to locations experiencing conditions that were relatively dirty. Mapping MSTs highlighted that downtown areas were dominated by primary pollution and that suburban areas experienced relatively higher levels of secondary pollution. Demographics show the largest proportion of the overall population resided in downtown locations experiencing higher levels of primary pollution. Moreover, higher proportions of nonwhites and children in poverty reside in these areas when compared to suburban populations that resided in areas exhibiting relatively lower pollution. Our approach reveals the nature and spatial distribution of differential pollutant combinations across urban environments and provides helpful insights for identifying spatial exposure and demographic contrasts for future health studies. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

The orbital distribution of Near-Earth Objects inside Earth's orbit

NASA Astrophysics Data System (ADS)

Greenstreet, Sarah; Ngo, Henry; Gladman, Brett

2012-01-01

Canada's Near-Earth Object Surveillance Satellite (NEOSSat), set to launch in early 2012, will search for and track Near-Earth Objects (NEOs), tuning its search to best detect objects with a < 1.0 AU. In order to construct an optimal pointing strategy for NEOSSat, we needed more detailed information in the a < 1.0 AU region than the best current model (Bottke, W.F., Morbidelli, A., Jedicke, R., Petit, J.M., Levison, H.F., Michel, P., Metcalfe, T.S. [2002]. Icarus 156, 399-433) provides. We present here the NEOSSat-1.0 NEO orbital distribution model with larger statistics that permit finer resolution and less uncertainty, especially in the a < 1.0 AU region. We find that Amors = 30.1 ± 0.8%, Apollos = 63.3 ± 0.4%, Atens = 5.0 ± 0.3%, Atiras (0.718 < Q < 0.983 AU) = 1.38 ± 0.04%, and Vatiras (0.307 < Q < 0.718 AU) = 0.22 ± 0.03% of the steady-state NEO population. Vatiras are a previously undiscussed NEO population clearly defined in our integrations, whose orbits lie completely interior to that of Venus. Our integrations also uncovered the unexpected production of retrograde orbits from main-belt asteroid sources; this retrograde NEA population makes up ≃0.1% of the steady-state NEO population. The relative NEO impact rate onto Mercury, Venus, and Earth, as well as the normalized distribution of impact speeds, was calculated from the NEOSSat-1.0 orbital model under the assumption of a steady-state. The new model predicts a slightly higher Mercury impact flux.

Recursions for the exchangeable partition function of the seedbank coalescent.

PubMed

Kurt, Noemi; Rafler, Mathias

2017-04-01

For the seedbank coalescent with mutation under the infinite alleles assumption, which describes the gene genealogy of a population with a strong seedbank effect subject to mutations, we study the distribution of the final partition with mutation. This generalizes the coalescent with freeze by Dong et al. (2007) to coalescents where ancestral lineages are blocked from coalescing. We derive an implicit recursion which we show to have a unique solution and give an interpretation in terms of absorption problems of a random walk. Moreover, we derive recursions for the distribution of the number of blocks in the final partition. Copyright © 2017 Elsevier Inc. All rights reserved.

Clusters of poverty and disease emerge from feedbacks on an epidemiological network.

PubMed

Pluciński, Mateusz M; Ngonghala, Calistus N; Getz, Wayne M; Bonds, Matthew H

2013-03-06

The distribution of health conditions is characterized by extreme inequality. These disparities have been alternately attributed to disease ecology and the economics of poverty. Here, we provide a novel framework that integrates epidemiological and economic growth theory on an individual-based hierarchically structured network. Our model indicates that, under certain parameter regimes, feedbacks between disease ecology and economics create clusters of low income and high disease that can stably persist in populations that become otherwise predominantly rich and free of disease. Surprisingly, unlike traditional poverty trap models, these localized disease-driven poverty traps can arise despite homogeneity of parameters and evenly distributed initial economic conditions.

Direct Determination of Molecular Weight Distribution of Calf-Thymus DNAs and Study of Their Fragmentation under Ultrasonic and Low-Energy IR Irradiations. A Charge Detection Mass Spectrometry Investigation.

PubMed

Halim, Mohammad A; Bertorelle, Franck; Doussineau, Tristan; Antoine, Rodolphe

2018-06-09

Calf-thymus (CT-DNA) is widely used as binding agent. The commercial samples are known to be "highly polymerized DNA" samples. CT-DNA is known to be fragile in particular upon ultrasonic wave irradiation. Degradation products might have dramatic consequence on its bio-sensing activity, and an accurate determination of the molecular weight distribution and stability of commercial samples is highly demanded. We investigated the sensitivity of charge detection mass spectrometry (CDMS), a single-molecule MS method, both with single-pass and ion trap CDMS ("Benner" trap) modes to the determination of the composition and stability (under multiphoton IR irradiation) of calf-thymus DNAs. We also investigated the changes of molecular weight distributions in the course of sonication by irradiating ultrasonic wave to CT-DNA. We report for the first time, the direct molecular weight (MW) distribution of DNA sodium salt from calf-thymus revealing two populations at high (~10 MDa) and low (~3 MDa) molecular weights. We evidence a transition between the high-MW to the low-MW distribution, confirming that the low-MW distribution results from degradation of CT-DNA. Finally, we report also IRMPD experiments carried out on trapped single-stranded linear DNAs from calf-thymus allowing to extract their activation energy for unimolecular dissociation. We show that single-pass CDMS is a direct, efficient and accurate MS-based approach to determine the composition of calf-thymus DNAs. Furthermore, ion trap CDMS allows us to evaluate the stability (both under multiphoton IR irradiation and in the course of sonication by irradiating ultrasonic wave) of calf-thymus DNAs. This article is protected by copyright. All rights reserved.

Dissection of Insertion–Deletion Variants within Differentially Expressed Genes Involved in Wood Formation in Populus

PubMed Central

Gong, Chenrui; Du, Qingzhang; Xie, Jianbo; Quan, Mingyang; Chen, Beibei; Zhang, Deqiang

2018-01-01

Short insertions and deletions (InDels) are one of the major genetic variants and are distributed widely across the genome; however, few investigations of InDels have been conducted in long-lived perennial plants. Here, we employed a combination of RNA-seq and population resequencing to identify InDels within differentially expressed (DE) genes underlying wood formation in a natural population of Populus tomentosa (435 individuals) and utilized InDel-based association mapping to detect the causal variants under additive, dominance, and epistasis underlying growth and wood properties. In the present paper, 5,482 InDels detected from 629 DE genes showed uneven distributions throughout all 19 chromosomes, and 95.9% of these loci were diallelic InDels. Seventy-four InDels (positive false discovery rate q ≤ 0.10) from 68 genes exhibited significant additive/dominant effects on 10 growth and wood-properties, with an average of 14.7% phenotypic variance explained. Potential pleiotropy was observed in one-third of the InDels (representing 24 genes). Seven genes exhibited significantly differential expression among the genotypic classes of associated InDels, indicating possible important roles for these InDels. Epistasis analysis showed that overlapping interacting genes formed unique interconnected networks for each trait, supporting the putative biochemical links that control quantitative traits. Therefore, the identification and utilization of InDels in trees will be recognized as an effective marker system for molecular marker-assisted breeding applications, and further facilitate our understanding of quantitative genomics. PMID:29403506

Bias correction of nutritional status estimates when reported age is used for calculating WHO indicators in children under five years of age.

PubMed

Quezada, Amado D; García-Guerra, Armando; Escobar, Leticia

2016-06-01

To assess the performance of a simple correction method for nutritional status estimates in children under five years of age when exact age is not available from the data. The proposed method was based on the assumption of symmetry of age distributions within a given month of age and validated in a large population-based survey sample of Mexican preschool children. The main distributional assumption was consistent with the data. All prevalence estimates derived from the correction method showed no statistically significant bias. In contrast, failing to correct attained age resulted in an underestimation of stunting in general and an overestimation of overweight or obesity among the youngest. The proposed method performed remarkably well in terms of bias correction of estimates and could be easily applied in situations in which either birth or interview dates are not available from the data.

Pollen dispersal slows geographical range shift and accelerates ecological niche shift under climate change

PubMed Central

Aguilée, Robin; Raoul, Gaël; Rousset, François; Ronce, Ophélie

2016-01-01

Species may survive climate change by migrating to track favorable climates and/or adapting to different climates. Several quantitative genetics models predict that species escaping extinction will change their geographical distribution while keeping the same ecological niche. We introduce pollen dispersal in these models, which affects gene flow but not directly colonization. We show that plant populations may escape extinction because of both spatial range and ecological niche shifts. Exact analytical formulas predict that increasing pollen dispersal distance slows the expected spatial range shift and accelerates the ecological niche shift. There is an optimal distance of pollen dispersal, which maximizes the sustainable rate of climate change. These conclusions hold in simulations relaxing several strong assumptions of our analytical model. Our results imply that, for plants with long distance of pollen dispersal, models assuming niche conservatism may not accurately predict their future distribution under climate change. PMID:27621443

Pollen dispersal slows geographical range shift and accelerates ecological niche shift under climate change.

PubMed

Aguilée, Robin; Raoul, Gaël; Rousset, François; Ronce, Ophélie

2016-09-27

Species may survive climate change by migrating to track favorable climates and/or adapting to different climates. Several quantitative genetics models predict that species escaping extinction will change their geographical distribution while keeping the same ecological niche. We introduce pollen dispersal in these models, which affects gene flow but not directly colonization. We show that plant populations may escape extinction because of both spatial range and ecological niche shifts. Exact analytical formulas predict that increasing pollen dispersal distance slows the expected spatial range shift and accelerates the ecological niche shift. There is an optimal distance of pollen dispersal, which maximizes the sustainable rate of climate change. These conclusions hold in simulations relaxing several strong assumptions of our analytical model. Our results imply that, for plants with long distance of pollen dispersal, models assuming niche conservatism may not accurately predict their future distribution under climate change.

The influence of historical climate changes on Southern Ocean marine predator populations: a comparative analysis.

PubMed

Younger, Jane L; Emmerson, Louise M; Miller, Karen J

2016-02-01

The Southern Ocean ecosystem is undergoing rapid physical and biological changes that are likely to have profound implications for higher-order predators. Here, we compare the long-term, historical responses of Southern Ocean predators to climate change. We examine palaeoecological evidence for changes in the abundance and distribution of seabirds and marine mammals, and place these into context with palaeoclimate records in order to identify key environmental drivers associated with population changes. Our synthesis revealed two key factors underlying Southern Ocean predator population changes; (i) the availability of ice-free ground for breeding and (ii) access to productive foraging grounds. The processes of glaciation and sea ice fluctuation were key; the distributions and abundances of elephant seals, snow petrels, gentoo, chinstrap and Adélie penguins all responded strongly to the emergence of new breeding habitat coincident with deglaciation and reductions in sea ice. Access to productive foraging grounds was another limiting factor, with snow petrels, king and emperor penguins all affected by reduced prey availability in the past. Several species were isolated in glacial refugia and there is evidence that refuge populations were supported by polynyas. While the underlying drivers of population change were similar across most Southern Ocean predators, the individual responses of species to environmental change varied because of species specific factors such as dispersal ability and environmental sensitivity. Such interspecific differences are likely to affect the future climate change responses of Southern Ocean marine predators and should be considered in conservation plans. Comparative palaeoecological studies are a valuable source of long-term data on species' responses to environmental change that can provide important insights into future climate change responses. This synthesis highlights the importance of protecting productive foraging grounds proximate to breeding locations, as well as the potential role of polynyas as future Southern Ocean refugia. © 2015 John Wiley & Sons Ltd.

Analyses of Fusarium wilt race 3 resistance in Upland cotton (Gossypium hirsutum L.).

PubMed

Abdullaev, Alisher A; Salakhutdinov, Ilkhom B; Egamberdiev, Sharof Sh; Kuryazov, Zarif; Glukhova, Ludmila A; Adilova, Azoda T; Rizaeva, Sofiya M; Ulloa, Mauricio; Abdurakhmonov, Ibrokhim Y

2015-06-01

Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] represents a serious threat to cotton (Gossypium spp.) production. For the last few decades, the FOV pathogen has become a significant problem in Uzbekistan causing severe wilt disease and yield losses of G. hirsutum L. cultivars. We present the first genetic analyses of FOV race 3 resistance on Uzbek Cotton Germplasm with a series of field and greenhouse artificial inoculation-evaluations and inheritance studies. The field experiments were conducted in two different sites: the experimental station in Zangiota region-Environment (Env) 1 and the Institute of Cotton Breeding (Env-2, Tashkent province). The Env-1 was known to be free of FOV while the Env-2 was known to be a heavily FOV infested soil. In both (Env-1 and Env-2) of these sites, field soil was inoculated with FOV race 3. F2 and an F3 Upland populations ("Mebane B1" × "11970") were observed with a large phenotypic variance for plant survival and FOV disease severity within populations and among control or check Upland accessions. Wilt symptoms among studied F2 individuals and F3 families significantly differed depending on test type and evaluation site. Distribution of Mendelian rations of susceptible (S) and resistant (R) phenotypes were 1S:1R field Env-1 and 3S:1R field Env-2 in the F2 population, and 1S:3R greenhouse site in the F3 population. The different segregation distribution of the Uzbek populations may be explained by differences in FOV inoculum level and environmental conditions during assays. However, genetic analysis indicated a recessive single gene action under high inoculum levels or disease pressure for FOV race 3 resistance. Uzbek germplasm may be more susceptible than expected to FOV race 3, and sources of resistance to FOV may be limited under the FOV inoculum levels present in highly-infested fields making the breeding process more complex.

10 CFR 960.5-2-1 - Population density and distribution.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Population density and distribution. 960.5-2-1 Section 960... Population density and distribution. (a) Qualifying condition. The site shall be located such that, during... specified in § 960.5-1(a)(1). (b) Favorable conditions. (1) A low population density in the general region...

10 CFR 960.5-2-1 - Population density and distribution.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Population density and distribution. 960.5-2-1 Section 960... Population density and distribution. (a) Qualifying condition. The site shall be located such that, during... specified in § 960.5-1(a)(1). (b) Favorable conditions. (1) A low population density in the general region...

10 CFR 960.5-2-1 - Population density and distribution.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Population density and distribution. 960.5-2-1 Section 960... Population density and distribution. (a) Qualifying condition. The site shall be located such that, during... specified in § 960.5-1(a)(1). (b) Favorable conditions. (1) A low population density in the general region...

10 CFR 960.5-2-1 - Population density and distribution.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Population density and distribution. 960.5-2-1 Section 960... Population density and distribution. (a) Qualifying condition. The site shall be located such that, during... specified in § 960.5-1(a)(1). (b) Favorable conditions. (1) A low population density in the general region...

Validation of survey information on smoking and alcohol consumption against import statistics, Greenland 1993-2010.

PubMed

Bjerregaard, Peter; Becker, Ulrik

2013-01-01

Questionnaires are widely used to obtain information on health-related behaviour, and they are more often than not the only method that can be used to assess the distribution of behaviour in subgroups of the population. No validation studies of reported consumption of tobacco or alcohol have been published from circumpolar indigenous communities. The purpose of the study is to compare information on the consumption of tobacco and alcohol obtained from 3 population surveys in Greenland with import statistics. Estimates of consumption of cigarettes and alcohol using several different survey instruments in cross-sectional population studies from 1993-1994, 1999-2001 and 2005-2010 were compared with import statistics from the same years. For cigarettes, survey results accounted for virtually the total import. Alcohol consumption was significantly under-reported with reporting completeness ranging from 40% to 51% for different estimates of habitual weekly consumption in the 3 study periods. Including an estimate of binge drinking increased the estimated total consumption to 78% of the import. Compared with import statistics, questionnaire-based population surveys capture the consumption of cigarettes well in Greenland. Consumption of alcohol is under-reported, but asking about binge episodes in addition to the usual intake considerably increased the reported intake in this population and made it more in agreement with import statistics. It is unknown to what extent these findings at the population level can be inferred to population subgroups.

Elaboration of austenitic stainless steel samples with bimodal grain size distributions and investigation of their mechanical behavior

NASA Astrophysics Data System (ADS)

Flipon, B.; de la Cruz, L. Garcia; Hug, E.; Keller, C.; Barbe, F.

2017-10-01

Samples of 316L austenitic stainless steel with bimodal grain size distributions are elaborated using two distinct routes. The first one is based on powder metallurgy using spark plasma sintering of two powders with different particle sizes. The second route applies the reverse-annealing method: it consists in inducing martensitic phase transformation by plastic strain and further annealing in order to obtain two austenitic grain populations with different sizes. Microstructural analy ses reveal that both methods are suitable to generate significative grain size contrast and to control this contrast according to the elaboration conditions. Mechanical properties under tension are then characterized for different grain size distributions. Crystal plasticity finite element modelling is further applied in a configuration of bimodal distribution to analyse the role played by coarse grains within a matrix of fine grains, considering not only their volume fraction but also their spatial arrangement.

Life tables and reproductive parameters of Lutzomyia spinicrassa (Diptera: Psychodidae) under laboratory conditions.

PubMed

Escovar, Jesús; Bello, Felio J; Morales, Alberto; Moncada, Ligia; Cárdenas, Estrella

2004-10-01

Lutzomyia spinicrassa is a vector of Leishmania braziliensis in Colombia. This sand fly has a broad geographical distribution in Colombia and Venezuela and it is found mainly in coffee plantations. Baseline biological growth data of L. spinicrassa were obtained under experimental laboratory conditions. The development time from egg to adult ranged from 59 to 121 days, with 12.74 weeks in average. Based on cohorts of 100 females, horizontal life table was constructed. The following predictive parameters were obtained: net rate of reproduction (8.4 females per cohort female), generation time (12.74 weeks), intrinsic rate of population increase (0.17), and finite rate of population increment (1.18). The reproductive value for each class age of the cohort females was calculated. Vertical life tables were elaborated and mortality was described for the generation obtained of the field cohort. In addition, for two successive generations, additive variance and heritability for fecundity were estimated.

[Community structure and seasonal change of soil micro-arthropodes in the Lower Reaches of Liaohe River Plain under different land utilization].

PubMed

Ke, Xin; Liang, Wenju; Yu, Wantai; Xie, Rongdong; Weng, Chaolian; Yang, Yiming; Yin, Wenying

2004-04-01

The data on the soil micro-arthropodes under four land utilization types (fallow, forest, upland field and paddy) in the Lower Reaches of Liaohe River Plain were collected in a period from October 2000 to October 2001. Using the community parameters of population density, group richness, diversity index and evenness, the community structure and its seasonal changes were described. There were 12 groups of soil micro-arthropodes in this region, and of the groups, Collembola and Acarina were dominant, and Diptera, Coleoptera and Hymenoptera were often seen in fallow, forest and upland field, while Collembola, Acarina and Diptera were dominant in paddy. Both land utilization and seasonal change influenced the population density, group richness and diversity index of soil micro-arthropodes. The vertical distribution in both density and group number of arthropods in soil was in the order of surface > middle > bottom.

Examining the Supply of and Demand for Physiotherapy in Saskatchewan: The Relationship between Where Physiotherapists Work and Population Health Need.

PubMed

McFadden, Brighid; Jones McGrath, Kendra; Lowe, Teghan; Thiessen, Carla; Irinici, Steven; Shah, Tayyab; Milosavljevic, Stephan; Bath, Brenna

Purpose: This research examined the association between the distribution of physiotherapists in Saskatchewan relative to population health characteristics and self-reported physiotherapy use. Methods: Using a cross-sectional design, de-identified data were collected from the 2013 Saskatchewan College of Physical Therapy membership renewals ( n =643), and Saskatchewan population health characteristics data were obtained from the 2009-2012 Canadian Community Health Surveys (CCHSs). Age- and sex-adjusted proportions of selected population health characteristics were calculated and stratified by health region and rural-urban location; both were determined, for physiotherapists and CCHS participants, using postal codes. The association between physiotherapy distribution and physiotherapy use was calculated, and geospatial mapping techniques were used to display physiotherapist distribution across the province relative to population health characteristics. Results: Across health regions, a positive correlation ( r =0.655, p <0.029) was found between physiotherapist distribution and self-reported physiotherapy use. Mapping population health characteristics according to physiotherapist distribution demonstrated an imbalance between supply and distribution of physiotherapists and population health needs and demands. Conclusion: There is a discrepancy in Saskatchewan among the distribution of physiotherapists, self-reported physiotherapy use, and population health characteristics, especially in rural settings. These findings provide insight into which areas are in need of increased physiotherapy services.

Examining the Supply of and Demand for Physiotherapy in Saskatchewan: The Relationship between Where Physiotherapists Work and Population Health Need

PubMed Central

McFadden, Brighid; Jones McGrath, Kendra; Lowe, Teghan; Thiessen, Carla; Irinici, Steven; Shah, Tayyab; Milosavljevic, Stephan

2016-01-01

Purpose: This research examined the association between the distribution of physiotherapists in Saskatchewan relative to population health characteristics and self-reported physiotherapy use. Methods: Using a cross-sectional design, de-identified data were collected from the 2013 Saskatchewan College of Physical Therapy membership renewals (n=643), and Saskatchewan population health characteristics data were obtained from the 2009–2012 Canadian Community Health Surveys (CCHSs). Age- and sex-adjusted proportions of selected population health characteristics were calculated and stratified by health region and rural–urban location; both were determined, for physiotherapists and CCHS participants, using postal codes. The association between physiotherapy distribution and physiotherapy use was calculated, and geospatial mapping techniques were used to display physiotherapist distribution across the province relative to population health characteristics. Results: Across health regions, a positive correlation (r=0.655, p<0.029) was found between physiotherapist distribution and self-reported physiotherapy use. Mapping population health characteristics according to physiotherapist distribution demonstrated an imbalance between supply and distribution of physiotherapists and population health needs and demands. Conclusion: There is a discrepancy in Saskatchewan among the distribution of physiotherapists, self-reported physiotherapy use, and population health characteristics, especially in rural settings. These findings provide insight into which areas are in need of increased physiotherapy services. PMID:27904233

Characterization of demographic expansions from pairwise comparisons of linked microsatellite haplotypes.

PubMed

Navascués, Miguel; Hardy, Olivier J; Burgarella, Concetta

2009-03-01

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.

Assessment of radiation doses from residential smoke detectors that contain americium-241

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Donnell, F.R.; Etnier, E.L.; Holton, G.A.

1981-10-01

External dose equivalents and internal dose commitments were estimated for individuals and populations from annual distribution, use, and disposal of 10 million ionization chamber smoke detectors that contain 110 kBq (3 ..mu..Ci) americium-241 each. Under exposure scenarios developed for normal distribution, use, and disposal using the best available information, annual external dose equivalents to average individuals were estimated to range from 4 fSv (0.4 prem) to 20 nSv (2 ..mu..rem) for total body and from 7 fSv to 40 nSv for bone. Internal dose commitments to individuals under post disposal scenarios were estimated to range from 0.006 to 80 ..mu..Svmore » (0.0006 to 8 mrem) to total body and from 0.06 to 800 ..mu..Sv to bone. The total collective dose (the sum of external dose equivalents and 50-year internal dose commitments) for all individuals involved with distribution, use, or disposal of 10 million smoke detectors was estimated to be about 0.38 person-Sv (38 person-rem) to total body and 00 ft/sup 2/).« less

Spatial and temporal distribution of aliphatic hydrocarbons and linear alkylbenzenes in the particulate phase from a subtropical estuary (Guaratuba Bay, SW Atlantic) under seasonal population fluctuation.

PubMed

Dauner, Ana Lúcia L; Martins, César C

2015-12-01

Guaratuba Bay, a subtropical estuary located in the SW Atlantic, is under variable anthropogenic pressure throughout the year. Samples of surficial suspended particulate matter (SPM) were collected at 22 sites during three different periods to evaluate the temporal and spatial variability of aliphatic hydrocarbons (AHs) and linear alkylbenzenes (LABs). These compounds were determined by gas chromatography with flame ionization detection (GC-FID) and mass spectrometry (GC/MS). The spatial distributions of both compound classes were similar and varied among the sampling campaigns. Generally, the highest concentrations were observed during the austral summer, highlighting the importance of the increased human influence during this season. The compound distributions were also affected by the natural geochemical processes of organic matter accumulation. AHs were associated with petroleum, derived from boat and vehicle traffic, and biogenic sources, related to mangrove forests and autochthonous production. The LAB composition evidenced preferential degradation processes during the austral summer. Copyright © 2015 Elsevier B.V. All rights reserved.

The contribution of federal and nonfederal habitat to persistence of the northern spotted owl on the Olympic Peninsula, Washington: report of the reanalysis team.

Treesearch

Richard S. Holthausen; Martin G. Raphael; Kevin S. McKelvey; Eric D. Forsman; Edward E. Starkey; D. Erran Seaman

1995-01-01

We analyzed likely patterns of distribution and persistence of northern spotted owls (Strix occidentalis caurina) on the Olympic Peninsula. Analysis focused on the effects of Federal habitat under provisions of the Northwest Forest Plan; additional benefits to the owl population of different levels of habitat retention on non-Federal lands; effects of establishing a...

Post-glacial phylogeography and evolution of a wide-ranging highly-exploited keystone forest tree, eastern white pine (Pinus strobus) in North America: single refugium, multiple routes.

PubMed

Zinck, John W R; Rajora, Om P

2016-03-02

Knowledge of the historical distribution and postglacial phylogeography and evolution of a species is important to better understand its current distribution and population structure and potential fate in the future, especially under climate change conditions, and conservation of its genetic resources. We have addressed this issue in a wide-ranging and heavily exploited keystone forest tree species of eastern North America, eastern white pine (Pinus strobus). We examined the range-wide population genetic structure, tested various hypothetical population history and evolutionary scenarios and inferred the location of glacial refugium and post-glacial recolonization routes. Our hypothesis was that eastern white pine survived in a single glacial refugium and expanded through multiple post-glacial recolonization routes. We studied the range-wide genetic diversity and population structure of 33 eastern white pine populations using 12 nuclear and 3 chloroplast microsatellite DNA markers. We used Approximate Bayesian Computation approach to test various evolutionary scenarios. We observed high levels of genetic diversity, and significant genetic differentiation (F ST = 0.104) and population structure among eastern white pine populations across its range. A south to north trend of declining genetic diversity existed, consistent with repeated founder effects during post-glaciation migration northwards. We observed broad consensus from nuclear and chloroplast genetic markers supporting the presence of two main post-glacial recolonization routes that originated from a single southern refugium in the mid-Atlantic plain. One route gave rise to populations at the western margin of the species' range in Minnesota and western Ontario. The second route gave rise to central-eastern populations, which branched into two subgroups: central and eastern. We observed minimal sharing of chloroplast haplotypes between recolonization routes but there was evidence of admixture between the western and west-central populations. Our study reveals a single southern refugium, two recolonization routes and three genetically distinguishable lineages in eastern white pine that we suggest to be treated as separate Evolutionarily Significant Units. Like many wide-ranging North American species, eastern white pine retains the genetic signatures of post-glacial recolonization and evolution, and its contemporary population genetic structure reflects not just the modern distribution and effects of heavy exploitation but also routes northward from its glacial refugium.

Determination of vertebral range of motion using inertial measurement units in 27 Franches-Montagnes stallions and comparison between conditions and with a mixed population.

PubMed

Heim, C; Pfau, T; Gerber, V; Schweizer, C; Doherr, M; Schüpbach-Regula, G; Witte, S

2016-07-01

The diagnosis of equine back disorders is challenging. Objectively determining movement of the vertebral column may therefore be of value in a clinical setting. To establish whether surface-mounted inertial measurement units (IMUs) can be used to establish normal values for range of motion (ROM) of the vertebral column in a uniform population of horses trotting under different conditions. Vertebral ROM was established in Franches-Montagnes stallions and a general population of horses and the variability in measurements compared between the two groups. Repeatability and the influence of specific exercise condition (on ROM) were assessed. Finally, attempts were made to explain the findings of the study through the evaluation of factors that might influence ROM. Dorsoventral (DV) and mediolateral (ML) vertebral ROM was measured at a trot under different exercise conditions in 27 Franches-Montagnes stallions and six general population horses using IMUs distributed over the vertebral column. Variability in the ROM measurements was significantly higher for general population horses than for Franches-Montagnes stallions (both DV and ML ROM). Repeatability was strong to very strong for DV measurements and moderate for ML measurements. Trotting under saddle significantly reduced the ROM, with sitting trot resulting in a significantly lower ROM than rising trot. Age is unlikely to explain the low variability in vertebral ROM recorded in the Franches-Montagnes horses, while this may be associated with conformational factors. It was possible to establish a normal vertebral ROM for a group of Franches-Montagnes stallions. While within-breed variation was low in this population, further studies are necessary to determine variation in vertebral ROM for other breeds and to assess their utility for diagnosis of equine back disorders. © 2015 EVJ Ltd.

The Washington Needle Depot: fitting healthcare to injection drug users rather than injection drug users to healthcare: moving from a syringe exchange to syringe distribution model

PubMed Central

2010-01-01

Needle exchange programs chase political as well as epidemiological dragons, carrying within them both implicit moral and political goals. In the exchange model of syringe distribution, injection drug users (IDUs) must provide used needles in order to receive new needles. Distribution and retrieval are co-existent in the exchange model. Likewise, limitations on how many needles can be received at a time compel addicts to have multiple points of contact with professionals where the virtues of treatment and detox are impressed upon them. The centre of gravity for syringe distribution programs needs to shift from needle exchange to needle distribution, which provides unlimited access to syringes. This paper provides a case study of the Washington Needle Depot, a program operating under the syringe distribution model, showing that the distribution and retrieval of syringes can be separated with effective results. Further, the experience of IDUs is utilized, through paid employment, to provide a vulnerable population of people with clean syringes to prevent HIV and HCV. PMID:20047690

Fire management, managed relocation, and land conservation options for long-lived obligate seeding plants under global changes in climate, urbanization, and fire regime.

PubMed

Bonebrake, Timothy C; Syphard, Alexandra D; Franklin, Janet; Anderson, Kurt E; Akçakaya, H Resit; Mizerek, Toni; Winchell, Clark; Regan, Helen M

2014-08-01

Most species face multiple anthropogenic disruptions. Few studies have quantified the cumulative influence of multiple threats on species of conservation concern, and far fewer have quantified the potential relative value of multiple conservation interventions in light of these threats. We linked spatial distribution and population viability models to explore conservation interventions under projected climate change, urbanization, and changes in fire regime on a long-lived obligate seeding plant species sensitive to high fire frequencies, a dominant plant functional type in many fire-prone ecosystems, including the biodiversity hotspots of Mediterranean-type ecosystems. First, we investigated the relative risk of population decline for plant populations in landscapes with and without land protection under an existing habitat conservation plan. Second, we modeled the effectiveness of relocating both seedlings and seeds from a large patch with predicted declines in habitat area to 2 unoccupied recipient patches with increasing habitat area under 2 projected climate change scenarios. Finally, we modeled 8 fire return intervals (FRIs) approximating the outcomes of different management strategies that effectively control fire frequency. Invariably, long-lived obligate seeding populations remained viable only when FRIs were maintained at or above a minimum level. Land conservation and seedling relocation efforts lessened the impact of climate change and land-use change on obligate seeding populations to differing degrees depending on the climate change scenario, but neither of these efforts was as generally effective as frequent translocation of seeds. While none of the modeled strategies fully compensated for the effects of land-use and climate change, an integrative approach managing multiple threats may diminish population declines for species in complex landscapes. Conservation plans designed to mitigate the impacts of a single threat are likely to fail if additional threats are ignored. © 2014 Society for Conservation Biology.

Genetic Structure of Aedes aegypti in Australia and Vietnam Revealed by Microsatellite and Exon Primed Intron Crossing Markers Suggests Feasibility of Local Control Options

PubMed Central

ENDERSBY, N. M.; HOFFMANN, A. A.; WHITE, V. L.; LOWENSTEIN, S.; RITCHIE, S.; JOHNSON, P. H.; RAPLEY, L. P.; RYAN, P. A.; NAM, V. S.; YEN, N. T.; KITTIYAPONG, P.; WEEKS, A. R.

2009-01-01

The distribution of Aedes aegypti (L.) in Australia is currently restricted to northern Queensland, but it has been more extensive in the past. In this study, we evaluate the genetic structure of Ae. aegypti populations in Australia and Vietnam and consider genetic differentiation between mosquitoes from these areas and those from a population in Thailand. Six microsatellites and two exon primed intron crossing markers were used to assess isolation by distance across all populations and also within the Australian sample. Investigations of founder effects, amount of molecular variation between and within regions and comparison of FST values among Australian and Vietnamese populations were made to assess the scale of movement of Ae. aegypti. Genetic control methods are under development for mosquito vector populations including the dengue vector Ae. aegypti. The success of these control methods will depend on the population structure of the target species including population size and rates of movement among populations. Releases of modified mosquitoes could target local populations that show a high degree of isolation from surrounding populations, potentially allowing new variants to become established in one region with eventual dispersal to other regions. PMID:19769038

The Principles of Buoyancy in Marine Fish Eggs and Their Vertical Distributions across the World Oceans

PubMed Central

Sundby, Svein; Kristiansen, Trond

2015-01-01

Buoyancy acting on plankton, i.e. the difference in specific gravity between plankton and the ambient water, is a function of salinity and temperature. From specific gravity measurements of marine fish eggs salinity appears to be the only determinant of the buoyancy indicating that the thermal expansions of the fish egg and the ambient seawater are equal. We analyze the mechanisms behind thermal expansion in fish eggs in order to determine to what extent it can be justified to neglect the effects of temperature on buoyancy. Our results confirm the earlier assumptions that salinity is the basic determinant on buoyancy in marine fish eggs that, in turn, influence the vertical distributions and, consequently, the dispersal of fish eggs from the spawning areas. Fish populations have adapted accordingly by producing egg specific gravities that tune the egg buoyancy to create specific vertical distributions for each local population. A wide variety of buoyancy adaptations are found among fish populations. The ambient physical conditions at the spawning sites form a basic constraint for adaptation. In coastal regions where salinity increases with depth, and where the major fraction of the fish stocks spawns, pelagic and mesopelagic egg distributions dominate. However, in the larger part of worlds’ oceans salinity decreases with depth resulting in different egg distributions. Here, the principles of vertical distributions of fish eggs in the world oceans are presented in an overarching framework presenting the basic differences between regions, mainly coastal, where salinity increases with depth and the major part of the world oceans where salinity decreases with depth. We show that under these latter conditions, steady-state vertical distribution of mesopelagic fish eggs cannot exist as it does in most coastal regions. In fact, a critical spawning depth must exist where spawning below this depth threshold results in eggs sinking out of the water column and become lost for recruitment to the population. An example of adaptation to such conditions is Cape hake spawning above the critical layer in the Northern Benguela upwelling ecosystem. The eggs rise slowly in the onshore subsurface current below the Ekman layer, hence being advected inshore where the hatched larvae concentrate with optimal feeding conditions. PMID:26465149

Social-group identity and population substructure in admixed populations in New Mexico and Latin America

PubMed Central

Healy, Meghan E.; Hill, Deirdre; Berwick, Marianne; Edgar, Heather; Gross, Jessica

2017-01-01

We examined the relationship between continental-level genetic ancestry and racial and ethnic identity in an admixed population in New Mexico with the goal of increasing our understanding of how racial and ethnic identity influence genetic substructure in admixed populations. Our sample consists of 98 New Mexicans who self-identified as Hispanic or Latino (NM-HL) and who further categorized themselves by race and ethnic subgroup membership. The genetic data consist of 270 newly-published autosomal microsatellites from the NM-HL sample and previously published data from 57 globally distributed populations, including 13 admixed samples from Central and South America. For these data, we 1) summarized the major axes of genetic variation using principal component analyses, 2) performed tests of Hardy Weinberg equilibrium, 3) compared empirical genetic ancestry distributions to those predicted under a model of admixture that lacked substructure, 4) tested the hypotheses that individuals in each sample had 100%, 0%, and the sample-mean percentage of African, European, and Native American ancestry. We found that most NM-HL identify themselves and their parents as belonging to one of two groups, conforming to a region-specific narrative that distinguishes recent immigrants from Mexico from individuals whose families have resided in New Mexico for generations and who emphasize their Spanish heritage. The “Spanish” group had significantly lower Native American ancestry and higher European ancestry than the “Mexican” group. Positive FIS values, PCA plots, and heterogeneous ancestry distributions suggest that most Central and South America admixed samples also contain substructure, and that this substructure may be related to variation in social identity. Genetic substructure appears to be common in admixed populations in the Americas and may confound attempts to identify disease-causing genes and to understand the social causes of variation in health outcomes and social inequality. PMID:28977000

Implications of long tails in the distribution of mutant effects

NASA Astrophysics Data System (ADS)

Waxman, D.; Feng, J.

2005-07-01

Long-tailed distributions possess an infinite variance, yet a finite sample that is drawn from such a distribution has a finite variance. In this work we consider a model of a population subject to mutation, selection and drift. We investigate the implications of a long-tailed distribution of mutant allelic effects on the distribution of genotypic effects in a model with a continuum of allelic effects. While the analysis is confined to asexual populations, it does also have implications for sexual populations. We obtain analytical results for a selectively neutral population as well as one subject to selection. We supplement these analytical results with numerical simulations, to take into account genetic drift. We find that a long-tailed distribution of mutant effects may affect both the equilibrium and the evolutionary adaptive behaviour of a population.

Unique genetic variation at a species' rear edge is under threat from global climate change

PubMed Central

Provan, Jim; Maggs, Christine A.

2012-01-01

Global climate change is having a significant effect on the distributions of a wide variety of species, causing both range shifts and population extinctions. To date, however, no consensus has emerged on how these processes will affect the range-wide genetic diversity of impacted species. It has been suggested that species that recolonized from low-latitude refugia might harbour high levels of genetic variation in rear-edge populations, and that loss of these populations could cause a disproportionately large reduction in overall genetic diversity in such taxa. In the present study, we have examined the distribution of genetic diversity across the range of the seaweed Chondrus crispus, a species that has exhibited a northward shift in its southern limit in Europe over the last 40 years. Analysis of 19 populations from both sides of the North Atlantic using mitochondrial single nucleotide polymorphisms (SNPs), sequence data from two single-copy nuclear regions and allelic variation at eight microsatellite loci revealed unique genetic variation for all marker classes in the rear-edge populations in Iberia, but not in the rear-edge populations in North America. Palaeodistribution modelling and statistical testing of alternative phylogeographic scenarios indicate that the unique genetic diversity in Iberian populations is a result not only of persistence in the region during the last glacial maximum, but also because this refugium did not contribute substantially to the recolonization of Europe after the retreat of the ice. Consequently, loss of these rear-edge populations as a result of ongoing climate change will have a major effect on the overall genetic diversity of the species, particularly in Europe, and this could compromise the adaptive potential of the species as a whole in the face of future global warming. PMID:21593035

Limited evolutionary rescue of locally adapted populations facing climate change.

PubMed

Schiffers, Katja; Bourne, Elizabeth C; Lavergne, Sébastien; Thuiller, Wilfried; Travis, Justin M J

2013-01-19

Dispersal is a key determinant of a population's evolutionary potential. It facilitates the propagation of beneficial alleles throughout the distributional range of spatially outspread populations and increases the speed of adaptation. However, when habitat is heterogeneous and individuals are locally adapted, dispersal may, at the same time, reduce fitness through increasing maladaptation. Here, we use a spatially explicit, allelic simulation model to quantify how these equivocal effects of dispersal affect a population's evolutionary response to changing climate. Individuals carry a diploid set of chromosomes, with alleles coding for adaptation to non-climatic environmental conditions and climatic conditions, respectively. Our model results demonstrate that the interplay between gene flow and habitat heterogeneity may decrease effective dispersal and population size to such an extent that substantially reduces the likelihood of evolutionary rescue. Importantly, even when evolutionary rescue saves a population from extinction, its spatial range following climate change may be strongly narrowed, that is, the rescue is only partial. These findings emphasize that neglecting the impact of non-climatic, local adaptation might lead to a considerable overestimation of a population's evolvability under rapid environmental change.

Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod.

PubMed

Berg, Paul R; Star, Bastiaan; Pampoulie, Christophe; Sodeland, Marte; Barth, Julia M I; Knutsen, Halvor; Jakobsen, Kjetill S; Jentoft, Sissel

2016-03-17

Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod - historically a major marine resource - Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of several megabases long, covering approximately 4% of the Atlantic cod genome. These regions likely represent genomic inversions. The frequency of these distinct regions differ markedly between the ecotypes, spawning in the vicinity of each other, which contrasts with the low level of divergence in the rest of the genome. The observed patterns strongly suggest that these chromosomal rearrangements are instrumental in local adaptation and separation of Atlantic cod populations, leaving footprints of large genomic regions under selection. Our findings demonstrate the power of using genomic information in further understanding the population dynamics and defining management units in one of the world's most economically important marine resources.

Demographic controls of future global fire risk

NASA Astrophysics Data System (ADS)

Knorr, W.; Arneth, A.; Jiang, L.

2016-08-01

Wildfires are an important component of terrestrial ecosystem ecology but also a major natural hazard to societies, and their frequency and spatial distribution must be better understood. At a given location, risk from wildfire is associated with the annual fraction of burned area, which is expected to increase in response to climate warming. Until recently, however, only a few global studies of future fire have considered the effects of other important global environmental change factors such as atmospheric CO2 levels and human activities, and how these influence fires in different regions. Here, we contrast the impact of climate change and increasing atmospheric CO2 content on burned area with that of demographic dynamics, using ensembles of climate simulations combined with historical and projected population changes under different socio-economic development pathways for 1901-2100. Historically, humans notably suppressed wildfires. For future scenarios, global burned area will continue to decline under a moderate emissions scenario, except for low population growth and fast urbanization, but start to increase again from around mid-century under high greenhouse gas emissions. Contrary to common perception, we find that human exposure to wildfires increases in the future mainly owing to projected population growth in areas with frequent wildfires, rather than by a general increase in burned area.

The Roles of Dispersal, Fecundity, and Predation in the Population Persistence of an Oak (Quercus engelmannii) under Global Change

PubMed Central

Conlisk, Erin; Lawson, Dawn; Syphard, Alexandra D.; Franklin, Janet; Flint, Lorraine; Flint, Alan; Regan, Helen M.

2012-01-01

A species’ response to climate change depends on the interaction of biotic and abiotic factors that define future habitat suitability and species’ ability to migrate or adapt. The interactive effects of processes such as fire, dispersal, and predation have not been thoroughly addressed in the climate change literature. Our objective was to examine how life history traits, short-term global change perturbations, and long-term climate change interact to affect the likely persistence of an oak species - Quercus engelmannii (Engelmann oak). Specifically, we combined dynamic species distribution models, which predict suitable habitat, with stochastic, stage-based metapopulation models, which project population trajectories, to evaluate the effects of three global change factors – climate change, land use change, and altered fire frequency – emphasizing the roles of dispersal and seed predation. Our model predicted dramatic reduction in Q. engelmannii abundance, especially under drier climates and increased fire frequency. When masting lowers seed predation rates, decreased masting frequency leads to large abundance decreases. Current rates of dispersal are not likely to prevent these effects, although increased dispersal could mitigate population declines. The results suggest that habitat suitability predictions by themselves may under-estimate the impact of climate change for other species and locations. PMID:22623955

High resolution population distribution maps for Southeast Asia in 2010 and 2015.

PubMed

Gaughan, Andrea E; Stevens, Forrest R; Linard, Catherine; Jia, Peng; Tatem, Andrew J

2013-01-01

Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.

High Resolution Population Distribution Maps for Southeast Asia in 2010 and 2015

PubMed Central

Gaughan, Andrea E.; Stevens, Forrest R.; Linard, Catherine; Jia, Peng; Tatem, Andrew J.

2013-01-01

Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org. PMID:23418469

Regional Distribution Shifts Help Explain Local Changes in Wintering Raptor Abundance: Implications for Interpreting Population Trends

PubMed Central

Paprocki, Neil; Heath, Julie A.; Novak, Stephen J.

2014-01-01

Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975–2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr−1 and 7.74 km yr−1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as species experience changes in distribution in response to climate change. PMID:24466253

A bayesian approach to classification criteria for spectacled eiders

USGS Publications Warehouse

Taylor, B.L.; Wade, P.R.; Stehn, R.A.; Cochrane, J.F.

1996-01-01

To facilitate decisions to classify species according to risk of extinction, we used Bayesian methods to analyze trend data for the Spectacled Eider, an arctic sea duck. Trend data from three independent surveys of the Yukon-Kuskokwim Delta were analyzed individually and in combination to yield posterior distributions for population growth rates. We used classification criteria developed by the recovery team for Spectacled Eiders that seek to equalize errors of under- or overprotecting the species. We conducted both a Bayesian decision analysis and a frequentist (classical statistical inference) decision analysis. Bayesian decision analyses are computationally easier, yield basically the same results, and yield results that are easier to explain to nonscientists. With the exception of the aerial survey analysis of the 10 most recent years, both Bayesian and frequentist methods indicated that an endangered classification is warranted. The discrepancy between surveys warrants further research. Although the trend data are abundance indices, we used a preliminary estimate of absolute abundance to demonstrate how to calculate extinction distributions using the joint probability distributions for population growth rate and variance in growth rate generated by the Bayesian analysis. Recent apparent increases in abundance highlight the need for models that apply to declining and then recovering species.

Genetic history of the population of Corsica (western Mediterranean) as inferred from autosomal STR analysis.

PubMed

Tofanelli, Sergio; Taglioli, Luca; Varesi, Laurent; Paoli, Giorgio

2004-04-01

To genetically reconstruct the demographic history of the human population of Corsica (western Mediterranean), we analyzed the variability at eight autosomal STR loci (FES, VWA, CSF1PO, TH01, F13A1, TPOX, CD4, and D3S1358) in a sample of 179 native blood donors from 4 out of the 5 administrative districts. The main line of genetic discontinuity inferred from the spatial distribution of STR variability overlapped the linguistic and geographic boundaries. In the innermost areas (Corte district) several estimators had larger stochastic effects on allele frequencies. Genetic distance measures underlying different evolutionary models all pointed to a higher variability within Corsicans than within the rest of the Mediterranean reference populations. All Corsican subsamples showed the highest distance with a pooled sample from central Sardinia, thus making recent gene flow between the two neighboring islands unlikely. Hierarchical AMOVA and distance-based multivariate genetic spaces stressed the closeness of Tuscan and Corsican frequency distributions, which could reflect peopling events with different time depths. Anyway, estimated separation times well support the linguistic hypothesis that Neolithic/Chalcolithic events have been far more important than Paleolithic or historical processes in the shaping of present Corsican variability.

Probing dim point sources in the inner Milky Way using PCAT

NASA Astrophysics Data System (ADS)

Daylan, Tansu; Portillo, Stephen K. N.; Finkbeiner, Douglas P.

2017-01-01

Poisson regression of the Fermi-LAT data in the inner Milky Way reveals an extended gamma-ray excess. An important question is whether the signal is coming from a collection of unresolved point sources, possibly old recycled pulsars, or constitutes a truly diffuse emission component. Previous analyses have relied on non-Poissonian template fits or wavelet decomposition of the Fermi-LAT data, which find evidence for a population of dim point sources just below the 3FGL flux limit. In order to be able to draw conclusions about the flux distribution of point sources at the dim end, we employ a Bayesian trans-dimensional MCMC framework by taking samples from the space of catalogs consistent with the observed gamma-ray emission in the inner Milky Way. The software implementation, PCAT (Probabilistic Cataloger), is designed to efficiently explore that catalog space in the crowded field limit such as in the galactic plane, where the model PSF, point source positions and fluxes are highly degenerate. We thus generate fair realizations of the underlying MSP population in the inner galaxy and constrain the population characteristics such as the radial and flux distribution of such sources.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Athay, R.G.; House, L.L.

Comparisons of intensities of Mg I and O I emission lines in the flash- spectrum of the low chromosphere reveal evidence of marked departures from a Boltzmann distribution of populations of energy levels. These departures are in the same sense as those found earlier for He I, viz., an overpopulation of the levels connected to the ground state through optically forbidden transitions relative to the levels with permitted transitions. A search for a similar effect in the populations of the excited singlets and triplets of Ca I did not indicate a significant departure from a Boltzmann distribution for the levelsmore » studied. Evidence is found that the ratio Ca I/Ca II is much greater than would be expected in thermodynnmic equilibrium. For Mg I, the optical thickness of the chromosphere in the triplet lines is obtained directly from the observed intensity of the forbidden ibtercombination line lambda 4571 (3/sup 3/P-3/sup 1/ S). Computed populations of energy levels for a model Mg I atom under a range of temperature and density show agreement with observational data for choices of chromospheric temperatures and densities consistent with a model departing from spherical symmetry. (auth)« less

Threshold-selecting strategy for best possible ground state detection with genetic algorithms

NASA Astrophysics Data System (ADS)

Lässig, Jörg; Hoffmann, Karl Heinz

2009-04-01

Genetic algorithms are a standard heuristic to find states of low energy in complex state spaces as given by physical systems such as spin glasses but also in combinatorial optimization. The paper considers the problem of selecting individuals in the current population in genetic algorithms for crossover. Many schemes have been considered in literature as possible crossover selection strategies. We show for a large class of quality measures that the best possible probability distribution for selecting individuals in each generation of the algorithm execution is a rectangular distribution over the individuals sorted by their energy values. This means uniform probabilities have to be assigned to a group of the individuals with lowest energy in the population but probabilities equal to zero to individuals which are corresponding to energy values higher than a fixed cutoff, which is equal to a certain rank in the vector sorted by the energy of the states in the current population. The considered strategy is dubbed threshold selecting. The proof applies basic arguments of Markov chains and linear optimization and makes only a few assumptions on the underlying principles and hence applies to a large class of algorithms.

Monte Carlo simulation of spectral reflectance and BRDF of the bubble layer in the upper ocean.

PubMed

Ma, Lanxin; Wang, Fuqiang; Wang, Chengan; Wang, Chengchao; Tan, Jianyu

2015-09-21

The presence of bubbles can significantly change the radiative properties of seawater and these changes will affect remote sensing and underwater target detection. In this work, the spectral reflectance and bidirectional reflectance characteristics of the bubble layer in the upper ocean are investigated using the Monte Carlo method. The Hall-Novarini (HN) bubble population model, which considers the effect of wind speed and depth on the bubble size distribution, is used. The scattering coefficients and the scattering phase functions of bubbles in seawater are calculated using Mie theory, and the inherent optical properties of seawater for wavelengths between 300 nm and 800 nm are related to chlorophyll concentration (Chl). The effects of bubble coating, Chl, and bubble number density on the spectral reflectance of the bubble layer are studied. The bidirectional reflectance distribution function (BRDF) of the bubble layer for both normal and oblique incidence is also investigated. The results show that bubble populations in clear waters under high wind speed conditions significantly influence the reflection characteristics of the bubble layer. Furthermore, the contribution of bubble populations to the reflection characteristics is mainly due to the strong backscattering of bubbles that are coated with an organic film.

Comparison of plantar pressures and contact area between normal and cavus foot.

PubMed

Fernández-Seguín, Lourdes M; Diaz Mancha, Juan Antonio; Sánchez Rodríguez, Raquel; Escamilla Martínez, Elena; Gómez Martín, Beatriz; Ramos Ortega, Javier

2014-02-01

In pes cavus, the medial longitudinal arch elevation reduces the contact surface area and consequently increases the corresponding plantar pressure measurements. This poor distribution of loads may produce associated pathology and pain in this or other areas of the body. Normal reference values need to be established in order to determine which patterns are prone to pathology. To compare the plantar pressures and weight-bearing surface in a population with pes cavus to a population with neutral feet. The sample comprised 68 adults, 34 with pes cavus and 34 with neutral feet. The Footscan USB Gait Clinical System(®) was used as a platform to measure the total contact area and plantar pressure under the forefoot, midfoot, hindfoot, each metatarsal head, and the overall metatarsal area. A statistical analysis of the data was performed using Student's t-test for independent samples. The pes cavus subjects showed a significant reduction in their weight-bearing area [neutral feet: 165.04 ( ± 20.68) cm(2); pes cavus: 118.26 ( ± 30.31) cm(2); p < 0.001] and significantly increased pressures under all zones of the forefoot except the fifth metatarsal [metatarsal pressure: in neutral feet 503,797 ( ± 9.32) kPa; in pes cavus 656.12 ( ± 22.39) kPa; p < 0.001]. Compared to neutral feet, pes cavus feet show a reduction in total contact surface and the load under the first toe. A significant increase is present in the load under the metatarsal areas, but the relative distribution of this load is similar in both groups. Copyright © 2013 Elsevier B.V. All rights reserved.

Statistical analysis of latent generalized correlation matrix estimation in transelliptical distribution

PubMed Central

Han, Fang; Liu, Han

2016-01-01

Correlation matrix plays a key role in many multivariate methods (e.g., graphical model estimation and factor analysis). The current state-of-the-art in estimating large correlation matrices focuses on the use of Pearson’s sample correlation matrix. Although Pearson’s sample correlation matrix enjoys various good properties under Gaussian models, its not an effective estimator when facing heavy-tail distributions with possible outliers. As a robust alternative, Han and Liu (2013b) advocated the use of a transformed version of the Kendall’s tau sample correlation matrix in estimating high dimensional latent generalized correlation matrix under the transelliptical distribution family (or elliptical copula). The transelliptical family assumes that after unspecified marginal monotone transformations, the data follow an elliptical distribution. In this paper, we study the theoretical properties of the Kendall’s tau sample correlation matrix and its transformed version proposed in Han and Liu (2013b) for estimating the population Kendall’s tau correlation matrix and the latent Pearson’s correlation matrix under both spectral and restricted spectral norms. With regard to the spectral norm, we highlight the role of “effective rank” in quantifying the rate of convergence. With regard to the restricted spectral norm, we for the first time present a “sign subgaussian condition” which is sufficient to guarantee that the rank-based correlation matrix estimator attains the optimal rate of convergence. In both cases, we do not need any moment condition. PMID:28337068