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Sample records for account population structure

  1. Genetic Population Structure Accounts for Contemporary Ecogeographic Patterns in Tropic and Subtropic-Dwelling Humans

    PubMed Central

    Hruschka, Daniel J.; Hadley, Craig; Brewis, Alexandra A.; Stojanowski, Christopher M.

    2015-01-01

    Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28). However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74). Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments. PMID:25816235

  2. Simultaneously accounting for population structure, genotype by environment interaction, and spatial variation in marker-trait associations in sugarcane.

    PubMed

    Wei, Xianming; Jackson, Phillip A; Hermann, Scott; Kilian, Andrzej; Heller-Uszynska, Katarzyna; Deomano, Emily

    2010-11-01

    Few association mapping studies have simultaneously accounted for population structure, genotype by environment interaction (GEI), and spatial variation. In this sugarcane association mapping study we tested models accounting for these factors and identified the impact that each model component had on the list of markers declared as being significantly associated with traits. About 480 genotypes were evaluated for cane yield and sugar content at three sites and scored with DArT markers. A mixed model was applied in analysis of the data to simultaneously account for the impacts of population structure, GEI, and spatial variation within a trial. Two forms of the DArT marker data were used in the analysis: the standard discrete data (0, 1) and a continuous DArT score, which is related to the marker dosage. A large number of markers were significantly associated with cane yield and sugar content. However, failure to account for population structure, GEI, and (or) spatial variation produced both type I and type II errors, which on the one hand substantially inflated the number of significant markers identified (especially true for failing to account for GEI) and on the other hand resulted in failure to detect markers that could be associated with cane yield or sugar content (especially when failing to account for population structure). We concluded that association mapping based on trials from one site or analysis that failed to account for GEI would produce many trial-specific associated markers that would have low value in breeding programs.

  3. Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.

    PubMed

    Sul, Jae Hoon; Bilow, Michael; Yang, Wen-Yun; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar

    2016-03-01

    Although genome-wide association studies (GWASs) have discovered numerous novel genetic variants associated with many complex traits and diseases, those genetic variants typically explain only a small fraction of phenotypic variance. Factors that account for phenotypic variance include environmental factors and gene-by-environment interactions (GEIs). Recently, several studies have conducted genome-wide gene-by-environment association analyses and demonstrated important roles of GEIs in complex traits. One of the main challenges in these association studies is to control effects of population structure that may cause spurious associations. Many studies have analyzed how population structure influences statistics of genetic variants and developed several statistical approaches to correct for population structure. However, the impact of population structure on GEI statistics in GWASs has not been extensively studied and nor have there been methods designed to correct for population structure on GEI statistics. In this paper, we show both analytically and empirically that population structure may cause spurious GEIs and use both simulation and two GWAS datasets to support our finding. We propose a statistical approach based on mixed models to account for population structure on GEI statistics. We find that our approach effectively controls population structure on statistics for GEIs as well as for genetic variants. PMID:26943367

  4. Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.

    PubMed

    Sul, Jae Hoon; Bilow, Michael; Yang, Wen-Yun; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar

    2016-03-01

    Although genome-wide association studies (GWASs) have discovered numerous novel genetic variants associated with many complex traits and diseases, those genetic variants typically explain only a small fraction of phenotypic variance. Factors that account for phenotypic variance include environmental factors and gene-by-environment interactions (GEIs). Recently, several studies have conducted genome-wide gene-by-environment association analyses and demonstrated important roles of GEIs in complex traits. One of the main challenges in these association studies is to control effects of population structure that may cause spurious associations. Many studies have analyzed how population structure influences statistics of genetic variants and developed several statistical approaches to correct for population structure. However, the impact of population structure on GEI statistics in GWASs has not been extensively studied and nor have there been methods designed to correct for population structure on GEI statistics. In this paper, we show both analytically and empirically that population structure may cause spurious GEIs and use both simulation and two GWAS datasets to support our finding. We propose a statistical approach based on mixed models to account for population structure on GEI statistics. We find that our approach effectively controls population structure on statistics for GEIs as well as for genetic variants.

  5. Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models

    PubMed Central

    Yang, Wen-Yun; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar

    2016-01-01

    Although genome-wide association studies (GWASs) have discovered numerous novel genetic variants associated with many complex traits and diseases, those genetic variants typically explain only a small fraction of phenotypic variance. Factors that account for phenotypic variance include environmental factors and gene-by-environment interactions (GEIs). Recently, several studies have conducted genome-wide gene-by-environment association analyses and demonstrated important roles of GEIs in complex traits. One of the main challenges in these association studies is to control effects of population structure that may cause spurious associations. Many studies have analyzed how population structure influences statistics of genetic variants and developed several statistical approaches to correct for population structure. However, the impact of population structure on GEI statistics in GWASs has not been extensively studied and nor have there been methods designed to correct for population structure on GEI statistics. In this paper, we show both analytically and empirically that population structure may cause spurious GEIs and use both simulation and two GWAS datasets to support our finding. We propose a statistical approach based on mixed models to account for population structure on GEI statistics. We find that our approach effectively controls population structure on statistics for GEIs as well as for genetic variants. PMID:26943367

  6. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

    PubMed Central

    Stone, Anne C.; Battistuzzi, Fabia U.; Kubatko, Laura S.; Perry, George H.; Trudeau, Evan; Lin, Hsiuman; Kumar, Sudhir

    2010-01-01

    Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human–chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1–1.5, 1.1–0.76 and 0.25–0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively. PMID:20855302

  7. Estimating diagnostic test accuracies for Brachyspira hyodysenteriae accounting for the complexities of population structure in food animals.

    PubMed

    Hartnack, Sonja; Nathues, Christina; Nathues, Heiko; Grosse Beilage, Elisabeth; Lewis, Fraser Iain

    2014-01-01

    For swine dysentery, which is caused by Brachyspira hyodysenteriae infection and is an economically important disease in intensive pig production systems worldwide, a perfect or error-free diagnostic test ("gold standard") is not available. In the absence of a gold standard, Bayesian latent class modelling is a well-established methodology for robust diagnostic test evaluation. In contrast to risk factor studies in food animals, where adjustment for within group correlations is both usual and required for good statistical practice, diagnostic test evaluation studies rarely take such clustering aspects into account, which can result in misleading results. The aim of the present study was to estimate test accuracies of a PCR originally designed for use as a confirmatory test, displaying a high diagnostic specificity, and cultural examination for B. hyodysenteriae. This estimation was conducted based on results of 239 samples from 103 herds originating from routine diagnostic sampling. Using Bayesian latent class modelling comprising of a hierarchical beta-binomial approach (which allowed prevalence across individual herds to vary as herd level random effect), robust estimates for the sensitivities of PCR and culture, as well as for the specificity of PCR, were obtained. The estimated diagnostic sensitivity of PCR (95% CI) and culture were 73.2% (62.3; 82.9) and 88.6% (74.9; 99.3), respectively. The estimated specificity of the PCR was 96.2% (90.9; 99.8). For test evaluation studies, a Bayesian latent class approach is well suited for addressing the considerable complexities of population structure in food animals.

  8. Driving population health through accountable care organizations.

    PubMed

    Devore, Susan; Champion, R Wesley

    2011-01-01

    Accountable care organizations, scheduled to become part of the Medicare program under the Affordable Care Act, have been promoted as a way to improve health care quality, reduce growth in costs, and increase patients' satisfaction. It is unclear how these organizations will develop. Yet in principle they will have to meet quality metrics, adopt improved care processes, assume risk, and provide incentives for population health and wellness. These capabilities represent a radical departure from today's health delivery system. In May 2010 the Premier healthcare alliance formed the Accountable Care Implementation Collaborative, which consists of health systems that seek to pursue accountability by forming partnerships with private payers to evolve from fee-for-service payment models to new, value-driven models. This article describes how participants in the collaborative are building models and developing best practices that can inform the implementation of accountable care organizations as well as public policies.

  9. The Use of Targeted Marker Subsets to Account for Population Structure and Relatedness in Genome-Wide Association Studies of Maize (Zea mays L.).

    PubMed

    Chen, Angela H; Lipka, Alexander E

    2016-01-01

    A typical plant genome-wide association study (GWAS) uses a mixed linear model (MLM) that includes a trait as the response variable, a marker as an explanatory variable, and fixed and random effect covariates accounting for population structure and relatedness. Although effective in controlling for false positive signals, this model typically fails to detect signals that are correlated with population structure or are located in high linkage disequilibrium (LD) genomic regions. This result likely arises from each tested marker being used to estimate population structure and relatedness. Previous work has demonstrated that it is possible to increase the power of the MLM by estimating relatedness (i.e., kinship) with markers that are not located on the chromosome where the tested marker resides. To quantify the amount of additional significant signals one can expect using this so-called K_chr model, we reanalyzed Mendelian, polygenic, and complex traits in two maize (Zea mays L.) diversity panels that have been previously assessed using the traditional MLM. We demonstrated that the K_chr model could find more significant associations, especially in high LD regions. This finding is underscored by our identification of novel genomic signals proximal to the tocochromanol biosynthetic pathway gene ZmVTE1 that are associated with a ratio of tocotrienols. We conclude that the K_chr model can detect more intricate sources of allelic variation underlying agronomically important traits, and should therefore become more widely used for GWAS. To facilitate the implementation of the K_chr model, we provide code written in the R programming language. PMID:27233668

  10. The Use of Targeted Marker Subsets to Account for Population Structure and Relatedness in Genome-Wide Association Studies of Maize (Zea mays L.)

    PubMed Central

    Chen, Angela H.; Lipka, Alexander E.

    2016-01-01

    A typical plant genome-wide association study (GWAS) uses a mixed linear model (MLM) that includes a trait as the response variable, a marker as an explanatory variable, and fixed and random effect covariates accounting for population structure and relatedness. Although effective in controlling for false positive signals, this model typically fails to detect signals that are correlated with population structure or are located in high linkage disequilibrium (LD) genomic regions. This result likely arises from each tested marker being used to estimate population structure and relatedness. Previous work has demonstrated that it is possible to increase the power of the MLM by estimating relatedness (i.e., kinship) with markers that are not located on the chromosome where the tested marker resides. To quantify the amount of additional significant signals one can expect using this so-called K_chr model, we reanalyzed Mendelian, polygenic, and complex traits in two maize (Zea mays L.) diversity panels that have been previously assessed using the traditional MLM. We demonstrated that the K_chr model could find more significant associations, especially in high LD regions. This finding is underscored by our identification of novel genomic signals proximal to the tocochromanol biosynthetic pathway gene ZmVTE1 that are associated with a ratio of tocotrienols. We conclude that the K_chr model can detect more intricate sources of allelic variation underlying agronomically important traits, and should therefore become more widely used for GWAS. To facilitate the implementation of the K_chr model, we provide code written in the R programming language. PMID:27233668

  11. Achieving population health in accountable care organizations.

    PubMed

    Hacker, Karen; Walker, Deborah Klein

    2013-07-01

    Although "population health" is one of the Institute for Healthcare Improvement's Triple Aim goals, its relationship to accountable care organizations (ACOs) remains ill-defined and lacks clarity as to how the clinical delivery system intersects with the public health system. Although defining population health as "panel" management seems to be the default definition, we called for a broader "community health" definition that could improve relationships between clinical delivery and public health systems and health outcomes for communities. We discussed this broader definition and offered recommendations for linking ACOs with the public health system toward improving health for patients and their communities.

  12. Population Size Predicts Lexical Diversity, but so Does the Mean Sea Level --Why It Is Important to Correctly Account for the Structure of Temporal Data.

    PubMed

    Koplenig, Alexander; Müller-Spitzer, Carolin

    2016-01-01

    In order to demonstrate why it is important to correctly account for the (serial dependent) structure of temporal data, we document an apparently spectacular relationship between population size and lexical diversity: for five out of seven investigated languages, there is a strong relationship between population size and lexical diversity of the primary language in this country. We show that this relationship is the result of a misspecified model that does not consider the temporal aspect of the data by presenting a similar but nonsensical relationship between the global annual mean sea level and lexical diversity. Given the fact that in the recent past, several studies were published that present surprising links between different economic, cultural, political and (socio-)demographical variables on the one hand and cultural or linguistic characteristics on the other hand, but seem to suffer from exactly this problem, we explain the cause of the misspecification and show that it has profound consequences. We demonstrate how simple transformation of the time series can often solve problems of this type and argue that the evaluation of the plausibility of a relationship is important in this context. We hope that our paper will help both researchers and reviewers to understand why it is important to use special models for the analysis of data with a natural temporal ordering. PMID:26938719

  13. Population Size Predicts Lexical Diversity, but so Does the Mean Sea Level --Why It Is Important to Correctly Account for the Structure of Temporal Data.

    PubMed

    Koplenig, Alexander; Müller-Spitzer, Carolin

    2016-01-01

    In order to demonstrate why it is important to correctly account for the (serial dependent) structure of temporal data, we document an apparently spectacular relationship between population size and lexical diversity: for five out of seven investigated languages, there is a strong relationship between population size and lexical diversity of the primary language in this country. We show that this relationship is the result of a misspecified model that does not consider the temporal aspect of the data by presenting a similar but nonsensical relationship between the global annual mean sea level and lexical diversity. Given the fact that in the recent past, several studies were published that present surprising links between different economic, cultural, political and (socio-)demographical variables on the one hand and cultural or linguistic characteristics on the other hand, but seem to suffer from exactly this problem, we explain the cause of the misspecification and show that it has profound consequences. We demonstrate how simple transformation of the time series can often solve problems of this type and argue that the evaluation of the plausibility of a relationship is important in this context. We hope that our paper will help both researchers and reviewers to understand why it is important to use special models for the analysis of data with a natural temporal ordering.

  14. Population Size Predicts Lexical Diversity, but so Does the Mean Sea Level – Why It Is Important to Correctly Account for the Structure of Temporal Data

    PubMed Central

    Koplenig, Alexander; Müller-Spitzer, Carolin

    2016-01-01

    In order to demonstrate why it is important to correctly account for the (serial dependent) structure of temporal data, we document an apparently spectacular relationship between population size and lexical diversity: for five out of seven investigated languages, there is a strong relationship between population size and lexical diversity of the primary language in this country. We show that this relationship is the result of a misspecified model that does not consider the temporal aspect of the data by presenting a similar but nonsensical relationship between the global annual mean sea level and lexical diversity. Given the fact that in the recent past, several studies were published that present surprising links between different economic, cultural, political and (socio-)demographical variables on the one hand and cultural or linguistic characteristics on the other hand, but seem to suffer from exactly this problem, we explain the cause of the misspecification and show that it has profound consequences. We demonstrate how simple transformation of the time series can often solve problems of this type and argue that the evaluation of the plausibility of a relationship is important in this context. We hope that our paper will help both researchers and reviewers to understand why it is important to use special models for the analysis of data with a natural temporal ordering. PMID:26938719

  15. Accommodating environmental variation in population models: metaphysiological biomass loss accounting.

    PubMed

    Owen-Smith, Norman

    2011-07-01

    1. There is a pressing need for population models that can reliably predict responses to changing environmental conditions and diagnose the causes of variation in abundance in space as well as through time. In this 'how to' article, it is outlined how standard population models can be modified to accommodate environmental variation in a heuristically conducive way. This approach is based on metaphysiological modelling concepts linking populations within food web contexts and underlying behaviour governing resource selection. Using population biomass as the currency, population changes can be considered at fine temporal scales taking into account seasonal variation. Density feedbacks are generated through the seasonal depression of resources even in the absence of interference competition. 2. Examples described include (i) metaphysiological modifications of Lotka-Volterra equations for coupled consumer-resource dynamics, accommodating seasonal variation in resource quality as well as availability, resource-dependent mortality and additive predation, (ii) spatial variation in habitat suitability evident from the population abundance attained, taking into account resource heterogeneity and consumer choice using empirical data, (iii) accommodating population structure through the variable sensitivity of life-history stages to resource deficiencies, affecting susceptibility to oscillatory dynamics and (iv) expansion of density-dependent equations to accommodate various biomass losses reducing population growth rate below its potential, including reductions in reproductive outputs. Supporting computational code and parameter values are provided. 3. The essential features of metaphysiological population models include (i) the biomass currency enabling within-year dynamics to be represented appropriately, (ii) distinguishing various processes reducing population growth below its potential, (iii) structural consistency in the representation of interacting populations and

  16. Accommodating environmental variation in population models: metaphysiological biomass loss accounting.

    PubMed

    Owen-Smith, Norman

    2011-07-01

    1. There is a pressing need for population models that can reliably predict responses to changing environmental conditions and diagnose the causes of variation in abundance in space as well as through time. In this 'how to' article, it is outlined how standard population models can be modified to accommodate environmental variation in a heuristically conducive way. This approach is based on metaphysiological modelling concepts linking populations within food web contexts and underlying behaviour governing resource selection. Using population biomass as the currency, population changes can be considered at fine temporal scales taking into account seasonal variation. Density feedbacks are generated through the seasonal depression of resources even in the absence of interference competition. 2. Examples described include (i) metaphysiological modifications of Lotka-Volterra equations for coupled consumer-resource dynamics, accommodating seasonal variation in resource quality as well as availability, resource-dependent mortality and additive predation, (ii) spatial variation in habitat suitability evident from the population abundance attained, taking into account resource heterogeneity and consumer choice using empirical data, (iii) accommodating population structure through the variable sensitivity of life-history stages to resource deficiencies, affecting susceptibility to oscillatory dynamics and (iv) expansion of density-dependent equations to accommodate various biomass losses reducing population growth rate below its potential, including reductions in reproductive outputs. Supporting computational code and parameter values are provided. 3. The essential features of metaphysiological population models include (i) the biomass currency enabling within-year dynamics to be represented appropriately, (ii) distinguishing various processes reducing population growth below its potential, (iii) structural consistency in the representation of interacting populations and

  17. Solution Accounts for Structural Damping

    NASA Technical Reports Server (NTRS)

    Roussos, L. A.; Hyer, M. W.; Thornton, E. A.

    1982-01-01

    New analytical technique determines dynamic response of damped structures dominated by internal structural damping mechanisms. Though structural damping is often negligible compared with damping due to air friction and friction in joints, structural damping can be of major importance in structures having heavy damping treatments or in outer-space structures. Finite-element model includes nonlinear, nonviscous internal damping.

  18. Accounting for population variation in targeted proteomics

    SciTech Connect

    Fujimoto, Grant M.; Monroe, Matthew E.; Rodriguez, Larissa M.; Wu, Chaochao; MacLean, Brendan; Smith, Richard D.; MacCoss, Michael; Payne, Samuel H.

    2014-01-03

    Individual proteomes typically differ from the reference human proteome at ~10,000 single amino acid variants. When viewed at the population scale, this individual variation results in a wide variety of protein sequences. In targeted proteomics experiments, such variability would confound accurate protein quantification. To facilitate researchers in identifying target peptides with high variability within the human population we have created the Population Variation plug-in for Skyline, which provides easy access to the polymorphisms stored in dbSNP. Given a set of peptides, the tool reports minor allele frequency for common polymorphisms. We highlight the importance of considering genetic variation by applying the tool to public datasets.

  19. Assessing Students' Accounting Knowledge: A Structural Approach.

    ERIC Educational Resources Information Center

    Boldt, Margaret N.

    2001-01-01

    Comparisons of students' representations of financial accounting concepts with the knowledge structures of experts were depicted using Pathfinder networks. This structural approach identified the level of students' understanding of concepts and knowledge gaps that need to be addressed. (SK)

  20. [Population structure and dynamics: the population matrix].

    PubMed

    Wang, C S; Gorter, D

    1990-08-01

    "This article shows an alternative way of presenting population data. The population matrix, constructed as an important part in the process of compiling socio-demographic accounts, demonstrates the close connection between stock and flow data, bringing both types of data consistently together." Official data for the Netherlands are used to illustrate the concept. (SUMMARY IN ENG) PMID:12342861

  1. Assessing population viability while accounting for demographic and environmental uncertainty.

    PubMed

    Oppel, Steffen; Hilton, Geoff; Ratcliffe, Norman; Fenton, Calvin; Daley, James; Gray, Gerard; Vickery, Juliet; Gibbons, David

    2014-07-01

    Predicting the future trend and viability of populations is an essential task in ecology. Because many populations respond to changing environments, uncertainty surrounding environmental responses must be incorporated into population assessments. However, understanding the effects of environmental variation on population dynamics requires information on several important demographic parameters that are often difficult to estimate. Integrated population models facilitate the integration of time series data on population size and all existing demographic information from a species, allowing the estimation of demographic parameters for which limited or no empirical data exist. Although these models are ideal for assessments of population viability, they have so far not included environmental uncertainty. We incorporated environmental variation in an integrated population model to account for both demographic and environmental uncertainty in an assessment of population viability. In addition, we used this model to estimate true juvenile survival, an important demographic parameter for population dynamics that is difficult to estimate empirically. We applied this model to assess the past and future population trend of a rare island endemic songbird, the Montserrat Oriole Icterus oberi, which is threatened by volcanic activity. Montserrat Orioles experienced lower survival in years with volcanic ashfall, causing periodic population declines that were compensated by higher seasonal fecundity in years with high pre-breeding season rainfall. Due to the inclusion of both demographic and environmental uncertainty in the model, the estimated population growth rate in the immediate future was highly imprecise (95% credible interval 0.844-1.105), and the probability of extinction after three generations (in the year 2028) was low (2.1%). This projection demonstrates that accounting for both demographic and environmental sources of uncertainty provides a more realistic assessment

  2. Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons

    PubMed Central

    DiCarlo, James J.; Zecchina, Riccardo; Zoccolan, Davide

    2013-01-01

    The anterior inferotemporal cortex (IT) is the highest stage along the hierarchy of visual areas that, in primates, processes visual objects. Although several lines of evidence suggest that IT primarily represents visual shape information, some recent studies have argued that neuronal ensembles in IT code the semantic membership of visual objects (i.e., represent conceptual classes such as animate and inanimate objects). In this study, we investigated to what extent semantic, rather than purely visual information, is represented in IT by performing a multivariate analysis of IT responses to a set of visual objects. By relying on a variety of machine-learning approaches (including a cutting-edge clustering algorithm that has been recently developed in the domain of statistical physics), we found that, in most instances, IT representation of visual objects is accounted for by their similarity at the level of shape or, more surprisingly, low-level visual properties. Only in a few cases we observed IT representations of semantic classes that were not explainable by the visual similarity of their members. Overall, these findings reassert the primary function of IT as a conveyor of explicit visual shape information, and reveal that low-level visual properties are represented in IT to a greater extent than previously appreciated. In addition, our work demonstrates how combining a variety of state-of-the-art multivariate approaches, and carefully estimating the contribution of shape similarity to the representation of object categories, can substantially advance our understanding of neuronal coding of visual objects in cortex. PMID:23950700

  3. Improving aquatic warbler population assessments by accounting for imperfect detection.

    PubMed

    Oppel, Steffen; Marczakiewicz, Piotr; Lachmann, Lars; Grzywaczewski, Grzegorz

    2014-01-01

    Monitoring programs designed to assess changes in population size over time need to account for imperfect detection and provide estimates of precision around annual abundance estimates. Especially for species dependent on conservation management, robust monitoring is essential to evaluate the effectiveness of management. Many bird species of temperate grasslands depend on specific conservation management to maintain suitable breeding habitat. One such species is the Aquatic Warbler (Acrocephalus paludicola), which breeds in open fen mires in Central Europe. Aquatic Warbler populations have so far been assessed using a complete survey that aims to enumerate all singing males over a large area. Because this approach provides no estimate of precision and does not account for observation error, detecting moderate population changes is challenging. From 2011 to 2013 we trialled a new line transect sampling monitoring design in the Biebrza valley, Poland, to estimate abundance of singing male Aquatic Warblers. We surveyed Aquatic Warblers repeatedly along 50 randomly placed 1-km transects, and used binomial mixture models to estimate abundances per transect. The repeated line transect sampling required 150 observer days, and thus less effort than the traditional 'full count' approach (175 observer days). Aquatic Warbler abundance was highest at intermediate water levels, and detection probability varied between years and was influenced by vegetation height. A power analysis indicated that our line transect sampling design had a power of 68% to detect a 20% population change over 10 years, whereas raw count data had a 9% power to detect the same trend. Thus, by accounting for imperfect detection we increased the power to detect population changes. We recommend to adopt the repeated line transect sampling approach for monitoring Aquatic Warblers in Poland and in other important breeding areas to monitor changes in population size and the effects of habitat management.

  4. Effective population size and population subdivision in demographically structured populations.

    PubMed Central

    Laporte, Valérie; Charlesworth, Brian

    2002-01-01

    A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results. PMID:12242257

  5. Population genetic structure and ecotoxicology.

    PubMed Central

    Guttman, S I

    1994-01-01

    Electrophoretic analyses of population genetic structure, both in the laboratory and in the field, have documented significant shifts in allozyme genotype frequencies in a variety of aquatic taxa as a result of environmental impacts. Studies are documented which indicate that contaminants may select for individuals with tolerant allozyme genotypes, causing the potential loss of individuals with sensitive genotypes. This may diminish the genetic variability and fitness of affected populations and make them more susceptible to extinction following a subsequent stress. Future research involving population genetic structure and ecotoxicology should focus on determining the mechanism of sensitivity, documenting multigenerational effects of chronic laboratory exposure on population genetic composition, investigating whether previously stressed and genetically impacted populations are more susceptible to further natural and/or anthropogenic stressors, and establishing the utility of population genetic structure as a sensitive monitor of impacts in aquatic systems and their subsequent remediation. PMID:7713044

  6. Noise in neural populations accounts for errors in working memory.

    PubMed

    Bays, Paul M

    2014-03-01

    Errors in short-term memory increase with the quantity of information stored, limiting the complexity of cognition and behavior. In visual memory, attempts to account for errors in terms of allocation of a limited pool of working memory resources have met with some success, but the biological basis for this cognitive architecture is unclear. An alternative perspective attributes recall errors to noise in tuned populations of neurons that encode stimulus features in spiking activity. I show that errors associated with decreasing signal strength in probabilistically spiking neurons reproduce the pattern of failures in human recall under increasing memory load. In particular, deviations from the normal distribution that are characteristic of working memory errors and have been attributed previously to guesses or variability in precision are shown to arise as a natural consequence of decoding populations of tuned neurons. Observers possess fine control over memory representations and prioritize accurate storage of behaviorally relevant information, at a cost to lower priority stimuli. I show that changing the input drive to neurons encoding a prioritized stimulus biases population activity in a manner that reproduces this empirical tradeoff in memory precision. In a task in which predictive cues indicate stimuli most probable for test, human observers use the cues in an optimal manner to maximize performance, within the constraints imposed by neural noise. PMID:24599462

  7. 18 CFR 367.3900 - Account 390, Structures and improvements.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... GAS ACT Service Company Property Chart of Accounts § 367.3900 Account 390, Structures and improvements. This account must include the cost in place of structures and improvements used for service company... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Account 390,...

  8. Genealogical histories in structured populations.

    PubMed

    Kumagai, Seiji; Uyenoyama, Marcy K

    2015-06-01

    In genealogies of genes sampled from structured populations, lineages coalesce at rates dependent on the states of the lineages. For migration and coalescence events occurring on comparable time scales, for example, only lineages residing in the same deme of a geographically subdivided population can have descended from a common ancestor in the immediately preceding generation. Here, we explore aspects of genealogical structure in a population comprising two demes, between which migration may occur. We use generating functions to obtain exact densities and moments of coalescence time, number of mutations, total tree length, and age of the most recent common ancestor of the sample. We describe qualitative features of the distribution of gene genealogies, including factors that influence the geographical location of the most recent common ancestor and departures of the distribution of internode lengths from exponential. PMID:25770971

  9. Origin and population structure of the Icelanders.

    PubMed

    Williams, J T

    1993-04-01

    The Norse and Celtic contributions to the founding population of Iceland have been estimated previously on a pan-Icelandic basis using gene frequency data for the entire island. Accounts of the settlement of Iceland, however, suggest that different regions received different proportions of Norse and Celtic settlers, indicating the need to incorporate geographic variation into Icelandic admixture studies. A formal likelihood ratio test rejects the null hypothesis of regional homogeneity in admixture proportions. Here, regional admixture estimates for Iceland are reported; they are in agreement with the settlement pattern inferred from historical accounts. The western, northern, and southern regions of Iceland exhibit a moderate Celtic component, consistent with historical indications that these regions were settled by Norse Vikings from the British Isles, accompanied by Celtic wives and slaves. Eastern Iceland, believed to have been settled chiefly by Vikings from Scandinavia, is characterized by a large Norse component of admixture. The northwestern peninsula is also found to be predominantly Norse. Regional genetic data are used to elucidate the contemporary population structure of Iceland. The observed structure correlates well with patterns of Icelandic geography, history, economy, marriage, urbanization, and internal migration. The northeastern region is strongly isolated, the urbanized areas of the north and southwest are representative of the overall population, and the remaining regions exhibit small-scale variation about the genetic central tendency. A high level of genetic homogeneity is indicated (RST = 0.0005), consistent with the high internal migration rate of the Icelanders. A regression of mean per-locus heterozygosity on distance from the gene frequency centroid reveals a greater than average external gene flow into the eastern region, whereas the northwestern peninsula has received less than average external gene flow. Iceland is compared with

  10. Accounting for linkage disequilibrium in association analysis of diverse populations.

    PubMed

    Charles, Bashira A; Shriner, Daniel; Rotimi, Charles N

    2014-04-01

    The National Human Genome Research Institute's catalog of published genome-wide association studies (GWAS) lists over 10,000 genetic variants collectively associated with over 800 human diseases or traits. Most of these GWAS have been conducted in European-ancestry populations. Findings gleaned from these studies have led to identification of disease-associated loci and biologic pathways involved in disease etiology. In multiple instances, these genomic findings have led to the development of novel medical therapies or evidence for prescribing a given drug as the appropriate treatment for a given individual beyond phenotypic appearances or socially defined constructs of race or ethnicity. Such findings have implications for populations throughout the globe and GWAS are increasingly being conducted in more diverse populations. A major challenge for investigators seeking to follow up genomic findings between diverse populations is discordant patterns of linkage disequilibrium (LD). We provide an overview of common measures of LD and opportunities for their use in novel methods designed to address challenges associated with following up GWAS conducted in European-ancestry populations in African-ancestry populations or, more generally, between populations with discordant LD patterns. We detail the strengths and weaknesses associated with different approaches. We also describe application of these strategies in follow-up studies of populations with concordant LD patterns (replication) or discordant LD patterns (transferability) as well as fine-mapping studies. We review application of these methods to a variety of traits and diseases.

  11. Accounting for population stratification in DNA methylation studies.

    PubMed

    Barfield, Richard T; Almli, Lynn M; Kilaru, Varun; Smith, Alicia K; Mercer, Kristina B; Duncan, Richard; Klengel, Torsten; Mehta, Divya; Binder, Elisabeth B; Epstein, Michael P; Ressler, Kerry J; Conneely, Karen N

    2014-04-01

    DNA methylation is an important epigenetic mechanism that has been linked to complex diseases and is of great interest to researchers as a potential link between genome, environment, and disease. As the scale of DNA methylation association studies approaches that of genome-wide association studies, issues such as population stratification will need to be addressed. It is well-documented that failure to adjust for population stratification can lead to false positives in genetic association studies, but population stratification is often unaccounted for in DNA methylation studies. Here, we propose several approaches to correct for population stratification using principal components (PCs) from different subsets of genome-wide methylation data. We first illustrate the potential for confounding due to population stratification by demonstrating widespread associations between DNA methylation and race in 388 individuals (365 African American and 23 Caucasian). We subsequently evaluate the performance of our PC-based approaches and other methods in adjusting for confounding due to population stratification. Our simulations show that (1) all of the methods considered are effective at removing inflation due to population stratification, and (2) maximum power can be obtained with single-nucleotide polymorphism (SNP)-based PCs, followed by methylation-based PCs, which outperform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based PCs, we find that PCs based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjust for population stratification in DNA methylation studies when genome-wide SNP data are unavailable.

  12. Accounting for population stratification in DNA methylation studies.

    PubMed

    Barfield, Richard T; Almli, Lynn M; Kilaru, Varun; Smith, Alicia K; Mercer, Kristina B; Duncan, Richard; Klengel, Torsten; Mehta, Divya; Binder, Elisabeth B; Epstein, Michael P; Ressler, Kerry J; Conneely, Karen N

    2014-04-01

    DNA methylation is an important epigenetic mechanism that has been linked to complex diseases and is of great interest to researchers as a potential link between genome, environment, and disease. As the scale of DNA methylation association studies approaches that of genome-wide association studies, issues such as population stratification will need to be addressed. It is well-documented that failure to adjust for population stratification can lead to false positives in genetic association studies, but population stratification is often unaccounted for in DNA methylation studies. Here, we propose several approaches to correct for population stratification using principal components (PCs) from different subsets of genome-wide methylation data. We first illustrate the potential for confounding due to population stratification by demonstrating widespread associations between DNA methylation and race in 388 individuals (365 African American and 23 Caucasian). We subsequently evaluate the performance of our PC-based approaches and other methods in adjusting for confounding due to population stratification. Our simulations show that (1) all of the methods considered are effective at removing inflation due to population stratification, and (2) maximum power can be obtained with single-nucleotide polymorphism (SNP)-based PCs, followed by methylation-based PCs, which outperform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based PCs, we find that PCs based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjust for population stratification in DNA methylation studies when genome-wide SNP data are unavailable. PMID:24478250

  13. Direct reciprocity in structured populations.

    PubMed

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

    2012-06-19

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

  14. The Genetic Structure of the Swedish Population

    PubMed Central

    Humphreys, Keith; Grankvist, Alexander; Leu, Monica; Hall, Per; Liu, Jianjun; Ripatti, Samuli; Rehnström, Karola; Groop, Leif; Klareskog, Lars; Ding, Bo; Grönberg, Henrik; Xu, Jianfeng; Pedersen, Nancy L.; Lichtenstein, Paul; Mattingsdal, Morten; Andreassen, Ole A.; O'Dushlaine, Colm; Purcell, Shaun M.; Sklar, Pamela; Sullivan, Patrick F.; Hultman, Christina M.; Palmgren, Juni; Magnusson, Patrik K. E.

    2011-01-01

    Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise Fst) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions

  15. Ordering structured populations in multiplayer cooperation games

    PubMed Central

    Peña, Jorge; Wu, Bin; Traulsen, Arne

    2016-01-01

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

  16. Evolution in Stage-Structured Populations

    PubMed Central

    Barfield, Michael; Holt, Robert D.; Gomulkiewicz, Richard

    2016-01-01

    For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande’s theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price’s theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations. PMID:21460563

  17. Structural dynamics and ecology of flatfish populations

    NASA Astrophysics Data System (ADS)

    Bailey, Kevin M.

    1997-11-01

    The concept of structure in populations of marine fishes is fundamental to how we manage and conduct research on these resources. The degree of population structure ranges widely among flatfishes. Although we know that large populations tend to be subdivided into local populations, based on morphological, meristic and reproductive characteristics, these data often conflict with evidence on genetic stock structure, due to the scale and organization of movement within the metapopulation. Movement of individuals between local subpopulations and colonization events on a macroecological scale are probably important to some flatfish populations. Dispersal of larvae is known to be a major factor affecting population mixing. Some flatfishes have planktonic stages of long duration and for these species there is often, but not always, little population structure; gene flow sometimes may be limited by oceanographic features, such as eddies and fronts. At the juvenile stage dispersal can result in colonization of under-utilized habitats; however, for flatfishes with strong habitat requirements, this type of event may be less likely when suitable habitats are fragmented. Complex population structure has major implications for management, e.g. lumping harvested populations with little gene flow can have detrimental local effects. Moreover, the issue of population structure and movement influences the interpretation of research data, where populations are generally treated as closed systems. There is currently a strong need for a multidisciplinary approach to study fish population dynamics and the structure of their populations. This research should involve molecular geneticists, population geneticists, animal behaviourists and ecologists. Migration mechanisms, colonization and extinction events, gene flow and density-dependent movements are subject areas of great importance to managing large harvested populations, but our understanding of them at ecological scales, at least for

  18. Determining population structure and hybridization for two iris species

    PubMed Central

    Hamlin, Jennafer A P; Arnold, Michael L

    2014-01-01

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

  19. Accountability.

    ERIC Educational Resources Information Center

    Mullen, David J., Ed.

    This monograph, prepared to assist Georgia elementary principals to better understand accountability and its implications for educational improvement, sets forth many of the theoretical and philosophical bases from which accountability is being considered. Leon M. Lessinger begins this 5-paper presentation by describing the need for accountability…

  20. Accountability.

    ERIC Educational Resources Information Center

    Lashway, Larry

    1999-01-01

    This issue reviews publications that provide a starting point for principals looking for a way through the accountability maze. Each publication views accountability differently, but collectively these readings argue that even in an era of state-mandated assessment, principals can pursue proactive strategies that serve students' needs. James A.…

  1. Accountability.

    ERIC Educational Resources Information Center

    The Newsletter of the Comprehensive Center-Region VI, 1999

    1999-01-01

    Controversy surrounding the accountability movement is related to how the movement began in response to dissatisfaction with public schools. Opponents see it as one-sided, somewhat mean-spirited, and a threat to the professional status of teachers. Supporters argue that all other spheres of the workplace have accountability systems and that the…

  2. Population Structure and Quantitative Characters

    PubMed Central

    Rogers, Alan R.; Harpending, Henry C.

    1983-01-01

    A migration matrix model is used to investigate the behavior of neutral polygenic characters in subdivided populations. It is shown that gametic disequilibrium has a large effect on the variance among groups but none at all on its expectation. The variance of among-group variance is substantial and does not depend on the number of loci contributing to variance in the character. It is just as large for polygenic characters as for single loci with the same additive variance. This implies that one polygenic character contains exactly as much information about population relationships as one single-locus marker. The theory is compared with observed differentiation of dermatoglyphic and anthropometric characters among Bougainville islanders. PMID:17246186

  3. On the Apportionment of Population Structure

    PubMed Central

    Granot, Yaron; Tal, Omri; Rosset, Saharon; Skorecki, Karl

    2016-01-01

    Measures of population differentiation, such as FST, are traditionally derived from the partition of diversity within and between populations. However, the emergence of population clusters from multilocus analysis is a function of genetic structure (departures from panmixia) rather than of diversity. If the populations are close to panmixia, slight differences between the mean pairwise distance within and between populations (low FST) can manifest as strong separation between the populations, thus population clusters are often evident even when the vast majority of diversity is partitioned within populations rather than between them. For any given FST value, clusters can be tighter (more panmictic) or looser (more stratified), and in this respect higher FST does not always imply stronger differentiation. In this study we propose a measure for the partition of structure, denoted EST, which is more consistent with results from clustering schemes. Crucially, our measure is based on a statistic of the data that is a good measure of internal structure, mimicking the information extracted by unsupervised clustering or dimensionality reduction schemes. To assess the utility of our metric, we ranked various human (HGDP) population pairs based on FST and EST and found substantial differences in ranking order. EST ranking seems more consistent with population clustering and classification and possibly with geographic distance between populations. Thus, EST may at times outperform FST in identifying evolutionary significant differentiation. PMID:27505172

  4. Stage-Structured Population Dynamics of AEDES AEGYPTI

    NASA Astrophysics Data System (ADS)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

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

  5. (Genetic structure of natural populations)

    SciTech Connect

    Not Available

    1988-01-01

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

  6. Public health departments and accountable care organizations: finding common ground in population health.

    PubMed

    Ingram, Richard; Scutchfield, F Douglas; Costich, Julia F

    2015-05-01

    We examined areas of potential collaboration between accountable care organizations and public health agencies, as well as perceived barriers and facilitators. We interviewed 9 key informants on 4 topics: advantages of public health agency involvement in accountable care organizations; services public health agencies could provide; practical, cultural, and legal barriers to accountable care organization-public health agency involvement; and business models that facilitate accountable care organization-public health agency collaboration. Public health agencies could help accountable care organizations partner with community organizations and reach vulnerable patients, provide population-based services and surveillance data, and promote policies that improve member health. Barriers include accountable care organizations' need for short-term financial yield, limited public health agency technical and financial capacity, and the absence of a financial model.

  7. Plasmodium vivax Diversity and Population Structure across Four Continents

    PubMed Central

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

    2015-01-01

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

  8. Plasmodium vivax Diversity and Population Structure across Four Continents.

    PubMed

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

    2015-01-01

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

  9. Genetic structure among Fijian island populations.

    PubMed

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

    2015-02-01

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

  10. Population structure of ice-breeding seals.

    PubMed

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

    2008-07-01

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

  11. Improving population health one person at a time? Accountable care organisations: perceptions of population health—a qualitative interview study

    PubMed Central

    Noble, Douglas J; Greenhalgh, Trisha; Casalino, Lawrence P

    2014-01-01

    Objective This qualitative interview study explored perceptions of the phrases ‘population health’, ‘public health’ and ‘community health’. Setting Accountable care organisations (ACOs), and public health or similar agencies in different parts of the USA. Participants Purposive sample of 29 interviewees at four ACOs, and 10 interviewees at six public health or similar agencies. Results Interviewees working for ACOs most often viewed ‘population health’ as referring to a defined group of their organisation's patients, though a few applied the phrase to people living in a geographical area. In contrast, interviewees working for public health agencies were more likely to consider ‘population health’ from a geographical perspective. Conclusions Conflating geographical population health with the health of ACOs’ patients may divert attention and resources away from organisations that use non-medical means to improve the health of geographical populations. As ACOs battle to control costs of their population of patients, it would be more accurate to consider using a more specific phrase, such as ‘population of attributed patients’, to refer to ACOs’ efforts to care for the health of their defined group of patients. PMID:24770586

  12. The population genetics of structural variation

    PubMed Central

    Conrad, Donald F; Hurles, Matthew E

    2009-01-01

    Population genetics is central to our understanding of human variation, and by linking medical and evolutionary themes, it enables us to understand the origins and impacts of our genomic differences. Despite current limitations in our knowledge of the locations, sizes and mutational origins of structural variants, our characterization of their population genetics is developing apace, bringing new insights into recent human adaptation, genome biology and disease. We summarize recent dramatic advances, describe the diverse mutational origins of chromosomal rearrangements and argue that their complexity necessitates a re-evaluation of existing population genetic methods. PMID:17597779

  13. Using health information technology to manage a patient population in accountable care organizations.

    PubMed

    Wu, Frances M; Rundall, Thomas G; Shortell, Stephen M; Bloom, Joan R

    2016-06-20

    Purpose - The purpose of this paper is to describe the current landscape of health information technology (HIT) in early accountable care organizations (ACOs), the different strategies ACOs are using to develop HIT-based capabilities, and how ACOs are using these capabilities within their care management processes to advance health outcomes for their patient population. Design/methodology/approach - Mixed methods study pairing data from a cross-sectional National Survey of ACOs with in-depth, semi-structured interviews with leaders from 11 ACOs (both completed in 2013). Findings - Early ACOs vary widely in their electronic health record, data integration, and analytic capabilities. The most common HIT capability was drug-drug and drug-allergy interaction checks, with 53.2 percent of respondents reporting that the ACO possessed the capability to a high degree. Outpatient and inpatient data integration was the least common HIT capability (8.1 percent). In the interviews, ACO leaders commented on different HIT development strategies to gain a more comprehensive picture of patient needs and service utilization. ACOs realize the necessity for robust data analytics, and are exploring a variety of approaches to achieve it. Research limitations/implications - Data are self-reported. The qualitative portion was based on interviews with 11 ACOs, limiting generalizability to the universe of ACOs but allowing for a range of responses. Practical implications - ACOs are challenged with the development of sophisticated HIT infrastructure. They may benefit from targeted assistance and incentives to implement health information exchanges with other providers to promote more coordinated care management for their patient population. Originality/value - Using new empirical data, this study increases understanding of the extent of ACOs' current and developing HIT capabilities to support ongoing care management.

  14. Using health information technology to manage a patient population in accountable care organizations.

    PubMed

    Wu, Frances M; Rundall, Thomas G; Shortell, Stephen M; Bloom, Joan R

    2016-06-20

    Purpose - The purpose of this paper is to describe the current landscape of health information technology (HIT) in early accountable care organizations (ACOs), the different strategies ACOs are using to develop HIT-based capabilities, and how ACOs are using these capabilities within their care management processes to advance health outcomes for their patient population. Design/methodology/approach - Mixed methods study pairing data from a cross-sectional National Survey of ACOs with in-depth, semi-structured interviews with leaders from 11 ACOs (both completed in 2013). Findings - Early ACOs vary widely in their electronic health record, data integration, and analytic capabilities. The most common HIT capability was drug-drug and drug-allergy interaction checks, with 53.2 percent of respondents reporting that the ACO possessed the capability to a high degree. Outpatient and inpatient data integration was the least common HIT capability (8.1 percent). In the interviews, ACO leaders commented on different HIT development strategies to gain a more comprehensive picture of patient needs and service utilization. ACOs realize the necessity for robust data analytics, and are exploring a variety of approaches to achieve it. Research limitations/implications - Data are self-reported. The qualitative portion was based on interviews with 11 ACOs, limiting generalizability to the universe of ACOs but allowing for a range of responses. Practical implications - ACOs are challenged with the development of sophisticated HIT infrastructure. They may benefit from targeted assistance and incentives to implement health information exchanges with other providers to promote more coordinated care management for their patient population. Originality/value - Using new empirical data, this study increases understanding of the extent of ACOs' current and developing HIT capabilities to support ongoing care management. PMID:27296880

  15. A regional-scale, high resolution dynamical malaria model that accounts for population density, climate and surface hydrology

    PubMed Central

    2013-01-01

    Background The relative roles of climate variability and population related effects in malaria transmission could be better understood if regional-scale dynamical malaria models could account for these factors. Methods A new dynamical community malaria model is introduced that accounts for the temperature and rainfall influences on the parasite and vector life cycles which are finely resolved in order to correctly represent the delay between the rains and the malaria season. The rainfall drives a simple but physically based representation of the surface hydrology. The model accounts for the population density in the calculation of daily biting rates. Results Model simulations of entomological inoculation rate and circumsporozoite protein rate compare well to data from field studies from a wide range of locations in West Africa that encompass both seasonal endemic and epidemic fringe areas. A focus on Bobo-Dioulasso shows the ability of the model to represent the differences in transmission rates between rural and peri-urban areas in addition to the seasonality of malaria. Fine spatial resolution regional integrations for Eastern Africa reproduce the malaria atlas project (MAP) spatial distribution of the parasite ratio, and integrations for West and Eastern Africa show that the model grossly reproduces the reduction in parasite ratio as a function of population density observed in a large number of field surveys, although it underestimates malaria prevalence at high densities probably due to the neglect of population migration. Conclusions A new dynamical community malaria model is publicly available that accounts for climate and population density to simulate malaria transmission on a regional scale. The model structure facilitates future development to incorporate migration, immunity and interventions. PMID:23419192

  16. Modeling structured population dynamics using data from unmarked individuals

    USGS Publications Warehouse

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

    2014-01-01

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

  17. 47 CFR 32.101 - Structure of the balance sheet accounts.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 2 2014-10-01 2014-10-01 false Structure of the balance sheet accounts. 32.101... UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES Instructions for Balance Sheet Accounts § 32.101 Structure of the balance sheet accounts. The Balance Sheet accounts shall be maintained as...

  18. 47 CFR 32.101 - Structure of the balance sheet accounts.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 2 2013-10-01 2013-10-01 false Structure of the balance sheet accounts. 32.101... UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES Instructions for Balance Sheet Accounts § 32.101 Structure of the balance sheet accounts. The Balance Sheet accounts shall be maintained as...

  19. 47 CFR 32.101 - Structure of the balance sheet accounts.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 2 2012-10-01 2012-10-01 false Structure of the balance sheet accounts. 32.101... UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES Instructions for Balance Sheet Accounts § 32.101 Structure of the balance sheet accounts. The Balance Sheet accounts shall be maintained as...

  20. 47 CFR 32.101 - Structure of the balance sheet accounts.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Structure of the balance sheet accounts. 32.101... UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES Instructions for Balance Sheet Accounts § 32.101 Structure of the balance sheet accounts. The Balance Sheet accounts shall be maintained as...

  1. 47 CFR 32.101 - Structure of the balance sheet accounts.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 2 2011-10-01 2011-10-01 false Structure of the balance sheet accounts. 32.101... UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES Instructions for Balance Sheet Accounts § 32.101 Structure of the balance sheet accounts. The Balance Sheet accounts shall be maintained as...

  2. Admixture, Population Structure, and F-Statistics.

    PubMed

    Peter, Benjamin M

    2016-04-01

    Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose isF-statistics that measure shared genetic drift between sets of two, three, and four populations and can be used to test simple and complex hypotheses about admixture between populations. This article provides context from phylogenetic and population genetic theory. I review how F-statistics can be interpreted as branch lengths or paths and derive new interpretations, using coalescent theory. I further show that the admixture tests can be interpreted as testing general properties of phylogenies, allowing extension of some ideas applications to arbitrary phylogenetic trees. The new results are used to investigate the behavior of the statistics under different models of population structure and show how population substructure complicates inference. The results lead to simplified estimators in many cases, and I recommend to replace F3 with the average number of pairwise differences for estimating population divergence.

  3. Familial Identification: Population Structure and Relationship Distinguishability

    PubMed Central

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

    2012-01-01

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

  4. Spatial population structure of Yellowstone bison

    USGS Publications Warehouse

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

    2007-01-01

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

  5. 17 CFR 256.01-3 - General structure of accounting system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... account numbers in the Uniform System of Accounts for Public Utilities and Licensees (18 CFR Part 101) of... COMPANIES, PUBLIC UTILITY HOLDING COMPANY ACT OF 1935 General Instructions § 256.01-3 General structure of... company property. (b) The income and expense accounts include, under separate divisions, accounts...

  6. The role of palliative care in population management and accountable care organizations.

    PubMed

    Smith, Grant; Bernacki, Rachelle; Block, Susan D

    2015-06-01

    By 2021, health care spending is projected to grow to 19.6% of the GDP, likely crowding out spending in other areas. The 2010 Affordable Care Act (ACA) attempts to curb health care spending by incentivizing high-value care through the creation of Accountable Care Organizations (ACOs), which assume financial risk for patient outcomes. With this financial risk, health systems creating ACOs will be motivated to pursue innovative care models that maximize the value of care. Palliative care, as an emerging field with a growing evidence base, is positioned to improve value in ACOs by increasing high-quality care and decreasing costs for the sickest patients. ACO leaders may find palliative care input valuable in optimizing high-quality patient-centered care in the accountable care environment; however, palliative care clinicians will need to adopt new models that extrapolate their direct patient care skills to population management strategies. We propose that palliative care specialists take on responsibilities for working with ACO leaders to broaden their mission for systemwide palliative care for appropriate patients by prospectively identifying patients with a high risk of death, high symptom burden, and/or significant psychosocial dysfunction, and developing targeted, "triggered" interventions to enhance patient-centered, goal-consistent, coordinated care. Developing these new population management competencies is a critical role for palliative care teams in the ACO environment.

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

    PubMed

    Peña, Jorge; Nöldeke, Georg; Lehmann, Laurent

    2015-10-01

    Many models proposed to study the evolution of collective action rely on a formalism that represents social interactions as n-player games between individuals adopting discrete actions such as cooperate and defect. Despite the importance of spatial structure in biological collective action, the analysis of n-player games games in spatially structured populations has so far proved elusive. We address this problem by considering mixed strategies and by integrating discrete-action n-player games into the direct fitness approach of social evolution theory. This allows to conveniently identify convergence stable strategies and to capture the effect of population structure by a single structure coefficient, namely, the pairwise (scaled) relatedness among interacting individuals. As an application, we use our mathematical framework to investigate collective action problems associated with the provision of three different kinds of collective goods, paradigmatic of a vast array of helping traits in nature: "public goods" (both providers and shirkers can use the good, e.g., alarm calls), "club goods" (only providers can use the good, e.g., participation in collective hunting), and "charity goods" (only shirkers can use the good, e.g., altruistic sacrifice). We show that relatedness promotes the evolution of collective action in different ways depending on the kind of collective good and its economies of scale. Our findings highlight the importance of explicitly accounting for relatedness, the kind of collective good, and the economies of scale in theoretical and empirical studies of the evolution of collective action. PMID:26151588

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

    PubMed

    Peña, Jorge; Nöldeke, Georg; Lehmann, Laurent

    2015-10-01

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

  9. Multiple-breed reaction norm animal model accounting for robustness and heteroskedastic in a Nelore-Angus crossed population.

    PubMed

    Oliveira, M M; Santana, M L; Cardoso, F F

    2016-07-01

    Our objective was to genetically characterize post-weaning weight gain (PWG), over a 345-day period after weaning, of Brangus-Ibagé (Nelore×Angus) cattle. Records (n=4016) were from the foundation herd of the Embrapa South Livestock Center. A Bayesian approach was used to assess genotype by environment (G×E) interaction and to identify a suitable model for the estimation of genetic parameters and use in genetic evaluation. A robust and heteroscedastic reaction norm multiple-breed animal model was proposed. The model accounted for heterogeneity of residual variance associated with effects of breed, heterozygosity, sex and contemporary group; and was robust with respect to outliers. Additive genetic effects were modeled for the intercept and slope of a reaction norm to changes in the environmental gradient. Inference was based on Monte Carlo Markov Chain of 110 000 cycles, after 10 000 cycles of burn-in. Bayesian model choice criteria indicated the proposed model was superior to simpler sub-models that did not account for G×E interaction, multiple-breed structure, robustness and heteroscedasticity. We conclude that, for the Brangus-Ibagé population, these factors should be jointly accounted for in genetic evaluation of PWG. Heritability estimates increased proportionally with improvement in the environmental conditions gradient. Therefore, an increased proportion of differences in performance among animals were explained by genetic factors rather than environmental factors as rearing conditions improved. As a consequence response to selection may be increased in favorable environments.

  10. Multiple-breed reaction norm animal model accounting for robustness and heteroskedastic in a Nelore-Angus crossed population.

    PubMed

    Oliveira, M M; Santana, M L; Cardoso, F F

    2016-07-01

    Our objective was to genetically characterize post-weaning weight gain (PWG), over a 345-day period after weaning, of Brangus-Ibagé (Nelore×Angus) cattle. Records (n=4016) were from the foundation herd of the Embrapa South Livestock Center. A Bayesian approach was used to assess genotype by environment (G×E) interaction and to identify a suitable model for the estimation of genetic parameters and use in genetic evaluation. A robust and heteroscedastic reaction norm multiple-breed animal model was proposed. The model accounted for heterogeneity of residual variance associated with effects of breed, heterozygosity, sex and contemporary group; and was robust with respect to outliers. Additive genetic effects were modeled for the intercept and slope of a reaction norm to changes in the environmental gradient. Inference was based on Monte Carlo Markov Chain of 110 000 cycles, after 10 000 cycles of burn-in. Bayesian model choice criteria indicated the proposed model was superior to simpler sub-models that did not account for G×E interaction, multiple-breed structure, robustness and heteroscedasticity. We conclude that, for the Brangus-Ibagé population, these factors should be jointly accounted for in genetic evaluation of PWG. Heritability estimates increased proportionally with improvement in the environmental conditions gradient. Therefore, an increased proportion of differences in performance among animals were explained by genetic factors rather than environmental factors as rearing conditions improved. As a consequence response to selection may be increased in favorable environments. PMID:26754914

  11. Population genetic structure in the Holstein breed in Brazil.

    PubMed

    Magalhães Araújo da Silva, Mário Henrique; Malhado, Carlos Henrique Mendes; Costa, José Lauro; Cobuci, Jaime Araujo; Costa, Claudio Napolis; Carneiro, Paulo Luiz Souza

    2016-02-01

    We evaluated the population genetic structure of the Holstein breed in Brazil through pedigree analysis with the aim of supporting genetic management of extant herds. We used data from genealogical records of 204,511 animals in farms from south and southeast Brazil. Pedigree records between 1943 and 2005 were divided into seven periods of 8 years to estimate the effective population size (N e ). N e varied during the study periods, ranging from 0.19 to 3016.25. There was an increase in the percentage of inbred animals over time, from 0.18 to 5.0 %. However, this figure may be an underestimate due to the low completeness of pedigree, primarily related to paternal pedigree. The effective number of founders (fe) was 473 animals and ancestors (fa) was 471. The genetic contribution of 260 ancestors (founders or not) accounted for 50 % of the genetic variability in the population. The average relatedness coefficient (AR) and inbreeding coefficient indicate that the Holstein breed in Brazil is being effectively managed, despite a moderate founder effect and the low number of animals that are responsible for the population variance.

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

    USGS Publications Warehouse

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

    2007-01-01

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

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

    PubMed

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

    2014-11-01

    population size. Results suggest that understanding the population dynamics of a species over its range may be facilitated by taking the spatial structure of population size into account as well as by considering changes in population processes as a function of position within the range of the species.

  14. Hennepin Health: a safety-net accountable care organization for the expanded Medicaid population.

    PubMed

    Sandberg, Shana F; Erikson, Clese; Owen, Ross; Vickery, Katherine D; Shimotsu, Scott T; Linzer, Mark; Garrett, Nancy A; Johnsrud, Kimry A; Soderlund, Dana M; DeCubellis, Jennifer

    2014-11-01

    Health care payment and delivery models that challenge providers to be accountable for outcomes have fueled interest in community-level partnerships that address the behavioral, social, and economic determinants of health. We describe how Hennepin Health--a county-based safety-net accountable care organization in Minnesota--has forged such a partnership to redesign the health care workforce and improve the coordination of the physical, behavioral, social, and economic dimensions of care for an expanded community of Medicaid beneficiaries. Early outcomes suggest that the program has had an impact in shifting care from hospitals to outpatient settings. For example, emergency department visits decreased 9.1 percent between 2012 and 2013, while outpatient visits increased 3.3 percent. An increasing percentage of patients have received diabetes, vascular, and asthma care at optimal levels. At the same time, Hennepin Health has realized savings and reinvested them in future improvements. Hennepin Health offers lessons for counties, states, and public hospitals grappling with the problem of how to make the best use of public funds in serving expanded Medicaid populations and other communities with high needs.

  15. Accounting for Unmeasured Population Substructure in Case-Control Studies of Genetic Association Using a Novel Latent-Class Model

    PubMed Central

    Satten, Glen A.; Flanders, W. Dana; Yang, Quanhe

    2001-01-01

    We propose a novel latent-class approach to detect and account for population stratification in a case-control study of association between a candidate gene and a disease. In our approach, population substructure is detected and accounted for using data on additional loci that are in linkage equilibrium within subpopulations but have alleles that vary in frequency between subpopulations. We have tested our approach using simulated data based on allele frequencies in 12 short tandem repeat (STR) loci in four populations in Argentina. PMID:11170894

  16. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

    PubMed Central

    Teixeira, Marcus M.

    2016-01-01

    During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

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

    PubMed

    Shen, A

    1984-01-01

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

  18. Socioeconomic and Nutritional Factors Account for the Association of Gastric Cancer with Amerindian Ancestry in a Latin American Admixed Population

    PubMed Central

    Pereira, Latife; Zamudio, Roxana; Soares-Souza, Giordano; Herrera, Phabiola; Cabrera, Lilia; Hooper, Catherine C.; Cok, Jaime; Combe, Juan M.; Vargas, Gloria; Prado, William A.; Schneider, Silvana; Kehdy, Fernanda; Rodrigues, Maira R.; Chanock, Stephen J.; Berg, Douglas E.; Gilman, Robert H.; Tarazona-Santos, Eduardo

    2012-01-01

    Gastric cancer is one of the most lethal types of cancer and its incidence varies worldwide, with the Andean region of South America showing high incidence rates. We evaluated the genetic structure of the population from Lima (Peru) and performed a case-control genetic association study to test the contribution of African, European, or Native American ancestry to risk for gastric cancer, controlling for the effect of non-genetic factors. A wide set of socioeconomic, dietary, and clinic information was collected for each participant in the study and ancestry was estimated based on 103 ancestry informative markers. Although the urban population from Lima is usually considered as mestizo (i.e., admixed from Africans, Europeans, and Native Americans), we observed a high fraction of Native American ancestry (78.4% for the cases and 74.6% for the controls) and a very low African ancestry (<5%). We determined that higher Native American individual ancestry is associated with gastric cancer, but socioeconomic factors associated both with gastric cancer and Native American ethnicity account for this association. Therefore, the high incidence of gastric cancer in Peru does not seem to be related to susceptibility alleles common in this population. Instead, our result suggests a predominant role for ethnic-associated socioeconomic factors and disparities in access to health services. Since Native Americans are a neglected group in genomic studies, we suggest that the population from Lima and other large cities from Western South America with high Native American ancestry background may be convenient targets for epidemiological studies focused on this ethnic group. PMID:22870209

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

    PubMed

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

    2011-06-01

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

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

    PubMed

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

    2009-09-01

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

  1. Understanding cooperative behavior in structurally disordered populations

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  2. Accounting for management costs in sensitivity analyses of matrix population models.

    PubMed

    Baxter, Peter W J; McCarthy, Michael A; Possingham, Hugh P; Menkhorst, Peter W; McLean, Natasha

    2006-06-01

    Traditional sensitivity and elasticity analyses of matrix population models have been used to inform management decisions, but they ignore the economic costs of manipulating vital rates. For example, the growth rate of a population is often most sensitive to changes in adult survival rate, but this does not mean that increasing that rate is the best option for managing the population because it may be much more expensive than other options. To explore how managers should optimize their manipulation of vital rates, we incorporated the cost of changing those rates into matrix population models. We derived analytic expressions for locations in parameter space where managers should shift between management of fecundity and survival, for the balance between fecundity and survival management at those boundaries, and for the allocation of management resources to sustain that optimal balance. For simple matrices, the optimal budget allocation can often be expressed as simple functions of vital rates and the relative costs of changing them. We applied our method to management of the Helmeted Honeyeater (Lichenostomus melanops cassidix; an endangered Australian bird) and the koala (Phascolarctos cinereus) as examples. Our method showed that cost-efficient management of the Helmeted Honeyeater should focus on increasing fecundity via nest protection, whereas optimal koala management should focus on manipulating both fecundity and survival simultaneously. These findings are contrary to the cost-negligent recommendations of elasticity analysis, which would suggest focusing on managing survival in both cases. A further investigation of Helmeted Honeyeater management options, based on an individual-based model incorporating density dependence, spatial structure, and environmental stochasticity, confirmed that fecundity management was the most cost-effective strategy. Our results demonstrate that decisions that ignore economic factors will reduce management efficiency.

  3. Accounting for management costs in sensitivity analyses of matrix population models.

    PubMed

    Baxter, Peter W J; McCarthy, Michael A; Possingham, Hugh P; Menkhorst, Peter W; McLean, Natasha

    2006-06-01

    Traditional sensitivity and elasticity analyses of matrix population models have been used to inform management decisions, but they ignore the economic costs of manipulating vital rates. For example, the growth rate of a population is often most sensitive to changes in adult survival rate, but this does not mean that increasing that rate is the best option for managing the population because it may be much more expensive than other options. To explore how managers should optimize their manipulation of vital rates, we incorporated the cost of changing those rates into matrix population models. We derived analytic expressions for locations in parameter space where managers should shift between management of fecundity and survival, for the balance between fecundity and survival management at those boundaries, and for the allocation of management resources to sustain that optimal balance. For simple matrices, the optimal budget allocation can often be expressed as simple functions of vital rates and the relative costs of changing them. We applied our method to management of the Helmeted Honeyeater (Lichenostomus melanops cassidix; an endangered Australian bird) and the koala (Phascolarctos cinereus) as examples. Our method showed that cost-efficient management of the Helmeted Honeyeater should focus on increasing fecundity via nest protection, whereas optimal koala management should focus on manipulating both fecundity and survival simultaneously. These findings are contrary to the cost-negligent recommendations of elasticity analysis, which would suggest focusing on managing survival in both cases. A further investigation of Helmeted Honeyeater management options, based on an individual-based model incorporating density dependence, spatial structure, and environmental stochasticity, confirmed that fecundity management was the most cost-effective strategy. Our results demonstrate that decisions that ignore economic factors will reduce management efficiency. PMID

  4. Transforming SIBTEST to Account for Multilevel Data Structures

    ERIC Educational Resources Information Center

    French, Brian F.; Finch, W. Holmes

    2015-01-01

    SIBTEST is a differential item functioning (DIF) detection method that is accurate and effective with small samples, in the presence of group mean differences, and for assessment of both uniform and nonuniform DIF. The presence of multilevel data with DIF detection has received increased attention. Ignoring such structure can inflate Type I error.…

  5. Inferring population structure and demographic history using Y-STR data from worldwide populations.

    PubMed

    Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui

    2015-02-01

    The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies.

  6. Inferring population structure and demographic history using Y-STR data from worldwide populations.

    PubMed

    Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui

    2015-02-01

    The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies. PMID:25159112

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  8. Population Structure and Genetic Diversity of Native and Invasive Populations of Solanum rostratum (Solanaceae)

    PubMed Central

    Zhao, Jiali; Solís-Montero, Lislie; Lou, Anru; Vallejo-Marín, Mario

    2013-01-01

    Aims We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1) determine the level of genetic diversity across the studied regions; (2) explore the likely origins of invasive populations in China; and (3) investigate whether there is the evidence of multiple introductions into China. Methods We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China. Important Findings We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (FIS) or population differentiation (FST). Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China. PMID:24224008

  9. Population structure of a parasitic plant and its perennial host.

    PubMed

    Mutikainen, P; Koskela, T

    2002-10-01

    Characterization of host and parasite population genetic structure and estimation of gene flow among populations are essential for the understanding of parasite local adaptation and coevolutionary interactions between hosts and parasites. We examined two aspects of population structure in a parasitic plant, the greater dodder (Cuscuta europaea) and its host plant, the stinging nettle (Urtica dioica), using allozyme data from 12 host and eight parasite populations. First, we examined whether hosts exposed to parasitism in the past contain higher levels of genetic variation. Second, we examined whether host and parasite populations differ in terms of population structure and if their population structures are correlated. There was no evidence that host populations differed in terms of gene diversity or heterozygosity according to their history of parasitism. Host populations were genetically more differentiated (F(ST) = 0.032) than parasite populations (F(ST) = 0.009). Based on these F(ST) values, gene flow was high for both host and parasite. Such high levels of gene flow could counteract selection for local adaptation of the parasite. We found no significant correlation between geographic and genetic distance (estimated as pairwise F(ST)), either for the host or for the parasite. Furthermore, host and parasite genetic distance matrices were uncorrelated, suggesting that sites with genetically similar host populations are unlikely to have genetically similar parasite populations. PMID:12242649

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

    PubMed

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

    2009-01-01

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

  11. Estimating total population size for adult female sea turtles: Accounting for non-nesters

    USGS Publications Warehouse

    Kendall, W.L.; Richardson, J.I.; Rees, Alan F.

    2008-01-01

    Assessment of population size and changes therein is important to sea turtle management and population or life history research. Investigators might be interested in testing hypotheses about the effect of current population size or density (number of animals per unit resource) on future population processes. Decision makers might want to determine a level of allowable take of individual turtles of specified life stage. Nevertheless, monitoring most stages of sea turtle life histories is difficult, because obtaining access to individuals is difficult. Although in-water assessments are becoming more common, nesting females and their hatchlings remain the most accessible life stages. In some cases adult females of a given nesting population are sufficiently philopatric that the population itself can be well defined. If a well designed tagging study is conducted on this population, survival, breeding probability, and the size of the nesting population in a given year can be estimated. However, with published statistical methodology the size of the entire breeding population (including those females skipping nesting in that year) cannot be estimated without assuming that each adult female in this population has the same probability of nesting in a given year (even those that had just nested in the previous year). We present a method for estimating the total size of a breeding population (including nesters those skipping nesting) from a tagging study limited to the nesting population, allowing for the probability of nesting in a given year to depend on an individual's nesting status in the previous year (i.e., a Markov process). From this we further develop estimators for rate of growth from year to year in both nesting population and total breeding population, and the proportion of the breeding population that is breeding in a given year. We also discuss assumptions and apply these methods to a breeding population of hawksbill sea turtles (Eretmochelys imbricata) from

  12. Extensive population genetic structure in the giraffe

    PubMed Central

    Brown, David M; Brenneman, Rick A; Koepfli, Klaus-Peter; Pollinger, John P; Milá, Borja; Georgiadis, Nicholas J; Louis, Edward E; Grether, Gregory F; Jacobs, David K; Wayne, Robert K

    2007-01-01

    Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations. PMID:18154651

  13. 49 CFR 1242.26 - Miscellaneous building and structures (account XX-19-28).

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 9 2014-10-01 2014-10-01 false Miscellaneous building and structures (account XX... XX-19-28). Separate common expenses as specific facts indicate or according to distribution of common expenses listed in § 1242.10, Administration-Track (account XX-19-02)....

  14. 49 CFR 1242.26 - Miscellaneous building and structures (account XX-19-28).

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 9 2011-10-01 2011-10-01 false Miscellaneous building and structures (account XX... XX-19-28). Separate common expenses as specific facts indicate or according to distribution of common expenses listed in § 1242.10, Administration-Track (account XX-19-02)....

  15. 49 CFR 1242.26 - Miscellaneous building and structures (account XX-19-28).

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 9 2010-10-01 2010-10-01 false Miscellaneous building and structures (account XX... XX-19-28). Separate common expenses as specific facts indicate or according to distribution of common expenses listed in § 1242.10, Administration-Track (account XX-19-02)....

  16. 49 CFR 1242.26 - Miscellaneous building and structures (account XX-19-28).

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 9 2013-10-01 2013-10-01 false Miscellaneous building and structures (account XX... XX-19-28). Separate common expenses as specific facts indicate or according to distribution of common expenses listed in § 1242.10, Administration-Track (account XX-19-02)....

  17. 49 CFR 1242.26 - Miscellaneous building and structures (account XX-19-28).

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 9 2012-10-01 2012-10-01 false Miscellaneous building and structures (account XX... XX-19-28). Separate common expenses as specific facts indicate or according to distribution of common expenses listed in § 1242.10, Administration-Track (account XX-19-02)....

  18. Evolutionary dynamics of general group interactions in structured populations

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  19. Evolutionary dynamics of general group interactions in structured populations.

    PubMed

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

    2016-02-01

    The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions. PMID:26986362

  20. Accountability with Voucher Threats, Responses, and the Test-Taking Population: Regression Discontinuity Evidence from Florida

    ERIC Educational Resources Information Center

    Chakrabarti, Rajashri

    2013-01-01

    Florida's 1999 A-plus program was a consequential accountability program that embedded vouchers in an accountability regime. Under Florida rules, scores of students in several special education (ESE) and limited English proficient (LEP) categories were not included in the computation of school grades. One might expect these rules to induce F…

  1. The Stellar Population Structure of the Galactic Disk

    NASA Astrophysics Data System (ADS)

    Bovy, Jo; Rix, Hans-Walter; Schlafly, Edward F.; Nidever, David L.; Holtzman, Jon A.; Shetrone, Matthew; Beers, Timothy C.

    2016-05-01

    The spatial structure of stellar populations with different chemical abundances in the Milky Way (MW) contains a wealth of information on Galactic evolution over cosmic time. We use data on 14,699 red-clump stars from the APOGEE survey, covering 4 {kpc}≲ R≲ 15 {kpc}, to determine the structure of mono-abundance populations (MAPs)—stars in narrow bins in [α /{Fe}] and [{Fe}/{{H}}]—accounting for the complex effects of the APOGEE selection function and the spatially variable dust obscuration. We determine that all MAPs with enhanced [α /{Fe}] are centrally concentrated and are well-described as exponentials with a scale length of 2.2+/- 0.2 {kpc} over the whole radial range of the disk. We discover that the surface-density profiles of low-[α /{Fe}] MAPs are complex: they do not monotonically decrease outwards, but rather display a peak radius ranging from ≈ 5 to ≈ 13 {kpc} at low [{Fe}/{{H}}]. The extensive radial coverage of the data allows us to measure radial trends in the thickness of each MAP. While high-[α /{Fe}] MAPs have constant scale heights, low-[α /{Fe}] MAPs flare. We confirm, now with high-precision abundances, previous results that each MAP contains only a single vertical scale height and that low-[{Fe}/{{H}}], low-[α /{Fe}] and high-[{Fe}/{{H}}], high-[α /{Fe}] MAPs have intermediate ({h}Z≈ 300{--}600 {pc}) scale heights that smoothly bridge the traditional thin- and thick-disk divide. That the high-[α /{Fe}], thick disk components do not flare is strong evidence against their thickness being caused by radial migration. The correspondence between the radial structure and chemical-enrichment age of stellar populations is clear confirmation of the inside-out growth of galactic disks. The details of these relations will constrain the variety of physical conditions under which stars form throughout the MW disk.

  2. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins.

    PubMed

    Eriksson, Anders; Manica, Andrea

    2012-08-28

    Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.

  3. Selection of Cooperation in Spatially Structured Populations

    NASA Astrophysics Data System (ADS)

    Yang, Hyunmo; Ghim, Cheol-Min

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

  4. [Marriage structure of Yakut populations: migrations].

    PubMed

    Kucher, A I; Danilova, A L; Koneva, L A; Nogovitsina, A N

    2010-05-01

    Rural and urban settlements of the Republic of Sakha (Yakutia) are characterized by intense marriage migrations: both indigenous residents of different uluses (districts) of the republic (7-30%) and migrants from outside Yakutia (7-29%) contract marriages in five administrative centers analyzed in this respect. All the populations studied are characterized by a wide geographic range of the birthplaces of persons contracted marriages there (from 14 to 24 uluses of Yakutia), without any predominant migration flow from one district to another. The proportion of homolocal marriages among indigenous ethnic groups (Evenks, Evens, and Yukagirs) is as high as 75-100%; this proportion among Yakuts varies from 26 to 68%; heterolocal marriages are more characteristic of Russian immigrants (41-95%). Positive assortative marriages among persons with the same birthplaces have been found in all populations except for Momsky ulus. PMID:20583606

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations. PMID:23450090

  7. The population genomics of begomoviruses: global scale population structure and gene flow

    PubMed Central

    2010-01-01

    Background The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. Results We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. Conclusions Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies

  8. How population structure shapes neighborhood segregation.

    PubMed

    Bruch, Elizabeth E

    2014-03-01

    This study provides a framework for understanding how population composition conditions the relationship between individuals' choices about group affiliation and aggregate patterns of social separation or integration. The substantive focus is the role of income inequality in racial residential segregation. The author identifies three population parameters--between-group inequality, within-group inequality, and relative group size--that determine how income inequality between race groups affects racial segregation. She uses data from the Panel Study of Income Dynamics to estimate models of individual-level residential mobility and incorporates these estimates into agent-based models. She then simulates segregation dynamics under alternative assumptions about (1) the relative size of minority groups and (2) the degree of correlation between race and income among individuals. The author finds that income inequality can have offsetting effects at the high and low ends of the income distribution. She demonstrates the empirical relevance of the simulation results using fixed-effects, metro-level regressions applied to 1980-2000 U.S. census data.

  9. An Individual-Based Model of Zebrafish Population Dynamics Accounting for Energy Dynamics

    PubMed Central

    Beaudouin, Rémy; Goussen, Benoit; Piccini, Benjamin; Augustine, Starrlight; Devillers, James; Brion, François; Péry, Alexandre R. R.

    2015-01-01

    Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model) was coupled to an individual based model of zebrafish population dynamics (IBM model). Next, we fitted the DEB model to new experimental data on zebrafish growth and reproduction thus improving existing models. We further analysed the DEB-model and DEB-IBM using a sensitivity analysis. Finally, the predictions of the DEB-IBM were compared to existing observations on natural zebrafish populations and the predicted population dynamics are realistic. While our zebrafish DEB-IBM model can still be improved by acquiring new experimental data on the most uncertain processes (e.g. survival or feeding), it can already serve to predict the impact of compounds at the population level. PMID:25938409

  10. An optimal decision population code that accounts for correlated variability unambiguously predicts a subject's choice.

    PubMed

    Carnevale, Federico; de Lafuente, Victor; Romo, Ranulfo; Parga, Néstor

    2013-12-18

    Decisions emerge from the concerted activity of neuronal populations distributed across brain circuits. However, the analytical tools best suited to decode decision signals from neuronal populations remain unknown. Here we show that knowledge of correlated variability between pairs of cortical neurons allows perfect decoding of decisions from population firing rates. We recorded pairs of neurons from secondary somatosensory (S2) and premotor (PM) cortices while monkeys reported the presence or absence of a tactile stimulus. We found that while populations of S2 and sensory-like PM neurons are only partially correlated with behavior, those PM neurons active during a delay period preceding the motor report predict unequivocally the animal's decision report. Thus, a population rate code that optimally reveals a subject's perceptual decisions can be implemented just by knowing the correlations of PM neurons representing decision variables.

  11. Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

    PubMed

    Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

    2014-01-01

    Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations

  12. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations. PMID:15446426

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Multini, Laura Cristina; Wilke, André Barretto Bruno; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

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

  15. Host genetics and population structure effects on parasitic disease.

    PubMed

    Williams-Blangero, Sarah; Criscione, Charles D; VandeBerg, John L; Correa-Oliveira, Rodrigo; Williams, Kimberly D; Subedi, Janardan; Kent, Jack W; Williams, Jeff; Kumar, Satish; Blangero, John

    2012-03-19

    Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for Trypanosoma cruzi infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of Ascaris worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for T. cruzi infection were found.

  16. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.

  17. Isonymy and the genetic structure of Albanian populations.

    PubMed

    Mikerezi, Ilia; Pizzetti, Paola; Lucchetti, Enzo; Ekonomi, Milva

    2003-12-01

    It is well known that in systems of surname transmission through the paternal line, surnames simulate neutral gene alleles belonging to the Y chromosome. This property of surnames was used to analyze the genetic structure of Albanian populations. Two large samples of surnames belonging to two different periods of time were analyzed. The analysis of indicators of population structure showed that geographical distance has an important effect on surname distribution. It seems that isolation by distance and genetic drift have been still important factors in the determination of the genetic structure of the Albanian population. PMID:14746137

  18. Evolution of extortion in structured populations.

    PubMed

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

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

  19. Evolution of extortion in structured populations

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

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

  20. Analysis of early accountable care organizations defines patient, structural, cost, and quality-of-care characteristics.

    PubMed

    Epstein, Arnold M; Jha, Ashish K; Orav, E John; Liebman, Daniel L; Audet, Anne-Marie J; Zezza, Mark A; Guterman, Stuart

    2014-01-01

    Accountable care organizations (ACOs) have attracted interest from many policy makers and clinical leaders because of their potential to improve the quality of care and reduce costs. Federal ACO programs for Medicare beneficiaries are now up and running, but little information is available about the baseline characteristics of early entrants. In this descriptive study we present data on the structural and market characteristics of these early ACOs and compare ACOs' patient populations, costs, and quality with those of their non-ACO counterparts at baseline. We found that ACO patients were more likely than non-ACO patients to be older than age eighty and had higher incomes. ACO patients were less likely than non-ACO patients to be black, covered by Medicaid, or disabled. The cost of care for ACO patients was slightly lower than that for non-ACO patients. Slightly fewer than half of the ACOs had a participating hospital. Hospitals that were in ACOs were more likely than non-ACO hospitals to be large, teaching, and not-for-profit, although there was little difference in their performance on quality metrics. Our findings can be useful in interpreting the early results from the federal ACO programs and in establishing a baseline to assess the programs' development.

  1. Rare Variation Facilitates Inferences of Fine-Scale Population Structure in Humans

    PubMed Central

    O’Connor, Timothy D.; Fu, Wenqing; Mychaleckyj, Josyf C.; Logsdon, Benjamin; Auer, Paul; Carlson, Christopher S.; Leal, Suzanne M.; Smith, Joshua D.; Rieder, Mark J.; Bamshad, Michael J.; Nickerson, Deborah A.; Akey, Joshua M.

    2015-01-01

    Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale resequencing studies have shown an abundance of rare variation in humans, which may be particularly useful for making inferences of fine-scale population structure. To this end, we used an information theory framework and extensive coalescent simulations to rigorously quantify the informativeness of rare and common variation to detect signatures of fine-scale population structure. We show that rare variation affords unique insights into patterns of recent population structure. Furthermore, to empirically assess our theoretical findings, we analyzed high-coverage exome sequences in 6,515 European and African American individuals. As predicted, rare variants are more informative than common polymorphisms in revealing a distinct cluster of European–American individuals, and subsequent analyses demonstrate that these individuals are likely of Ashkenazi Jewish ancestry. Our results provide new insights into the population structure using rare variation, which will be an important factor to account for in rare variant association studies. PMID:25415970

  2. Normalized Diurnal and Between-Day Trends in Illicit and Legal Drug Loads that Account for Changes in Population

    PubMed Central

    Brewer, Alex J.; Ort, Christoph; Banta-Green, Caleb J.; Berset, Jean-Daniel

    2012-01-01

    Drug concentrations in composite municipal wastewater samples and census-based estimates of population are used to derive daily loads of illicit substances that are indexed to population. However, such estimates do not provide information on the diurnal trends of substance excretion nor can they account for changes in population. To address these limitations, a series of 1 h composites created by sampling wastewater influent at 6 min intervals was collected over four consecutive days at a single wastewater treatment plant. Creatinine (a urinary indicator), caffeine, methamphetamine, benzoylecgonine (BZE), and cocaine were analyzed by liquid chromatography/tandem mass spectrometry (LC-MS/MS). Diurnal trends and between-day trends were substance specific and related to the number of estimated doses and excretory half-life. Normalization to creatinine yielded trends in substances that differed significantly from non-normalized trends by accounting for changes in population within the municipality studied. Increases in normalized substance excretion observed during early morning hours originate from individuals among the resident population of the municipality due to the absence of commuters. PMID:22804833

  3. The Demand for Higher Education: A Static Structural Approach Accounting for Individual Heterogeneity and Nesting Patterns

    ERIC Educational Resources Information Center

    Flannery, Darragh; O'Donoghue, Cathal

    2013-01-01

    In this paper we estimate a structural model of higher education participation and labour choices in a static setting that accounts for individual heterogeneity and possible nesting structures in the decision process. We assume that young people that complete upper secondary education are faced with three choices, go to higher education, not go to…

  4. A Behavior-Analytic Account of Cognitive Bias in Clinical Populations

    PubMed Central

    Wray, Alisha M; Freund, Rachel A; Dougher, Michael J

    2009-01-01

    Cognitive bias refers to a well-established finding that individuals who suffer from certain clinical problems (e.g., depression, anxiety, posttraumatic stress disorder, substance abuse, etc.) selectively attend to, remember, and interpret events relevant to their condition. Although a body of literature exists that has tried to examine this phenomenon, most existing explanations are mentalistic and mediational. In this paper we offer a behavior-analytic account of cognitive bias, its development, and how it may contribute to maintenance of clinical problems. This account is based on establishing operations or motivating events, verbal processes, and relational responding. Clinical and future research implications are also discussed. PMID:22478512

  5. Predicting meningococcal disease outbreaks in structured populations.

    PubMed

    Ranta, J; Mäkelä, P H; Arjas, E

    2004-03-30

    Rational decision making on whether some form of intervention would be necessary to control the spread of a meningococcal epidemic is based on predictions concerning its potential natural progression. Unfortunately, reliable predictions are difficult to make during the early stages of an outbreak. A stochastic discrete time epidemic model was applied to adaptively predict the development of outbreaks of meningococcal disease in 'closed' populations such as military garrisons or boarding schools, which are further divided into subgroups called 'units'. The performance of the adaptive method was assessed by using 3 simulated epidemics representing substantially different realizations in a 'garrison' of 20 units, with 68 men in each. Predictions of the weekly number of disease cases, of the number of carriers, and of the number of new infections were computed. Simulations suggest that predictions based only on the observed numbers of disease cases are generally inaccurate. These predictions can be improved if temporal observations on asymptomatic carriers in different units are utilized together with observed time series of the disease. A sample of 15 per cent from all units can be sufficient for a major improvement if the alternative is to obtain a full sample of only some units. Exploiting fully such information requires computer intensive Markov chain Monte Carlo methods. PMID:15027081

  6. HOW POPULATION STRUCTURE SHAPES NEIGHBORHOOD SEGREGATION*

    PubMed Central

    Bruch, Elizabeth E.

    2014-01-01

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

  7. Evolution of extortion in structured populations.

    PubMed

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games. PMID:25353531

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

    PubMed

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

    2013-01-01

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

  9. Social and Population Structure in the Ant Cataglyphis emmae

    PubMed Central

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

    2013-01-01

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

  10. Earthworm ecology affects the population structure of their Verminephrobacter symbionts.

    PubMed

    Viana, Flávia; Jensen, Christopher Erik; Macey, Michael; Schramm, Andreas; Lund, Marie Braad

    2016-05-01

    Earthworms carry species-specific Verminephrobacter symbionts in their nephridia (excretory organs). The symbionts are vertically transmitted via the cocoon, can only colonize the host during early embryonic development, and have co-speciated with their host for about 100 million years. Although several studies have addressed Verminephrobacter diversity between worm species, the intra-species diversity of the symbiont population has never been investigated. In this study, symbiont population structure was examined by using a multi-locus sequence typing (MLST) approach on Verminephrobacter isolated from two contrasting ecological types of earthworm hosts: the high population density, fast reproducing compost worms, Eisenia andrei and Eisenia fetida, and the low-density, slow reproducing Aporrectodea tuberculata, commonly found in garden soils. Three distinct populations were investigated for both types and, according to MLST analysis of 193 Verminephrobacter isolates, the symbiont community in each worm individual was very homogeneous. The more solitary A. tuberculata carried unique symbiont populations in 9 out of 10 host individuals, whereas the symbiont populations in the social compost worms were homogeneous across host individuals from the same population. These data suggested that host ecology shaped the population structure of Verminephrobacter symbionts. The homogeneous symbiont populations in the compost worms led to the hypothesis that Verminephrobacter could be transferred bi-parentally or via leaky horizontal transmission in high-density, frequently mating worm populations. PMID:27040820

  11. Genetic Variation and Population Structure in Native Americans

    PubMed Central

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

    2007-01-01

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

  12. Genetic variation and population structure in native Americans.

    PubMed

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

    2007-11-01

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

  13. A general population genetic framework for antagonistic selection that accounts for demography and recurrent mutation.

    PubMed

    Connallon, Tim; Clark, Andrew G

    2012-04-01

    Antagonistic selection--where alleles at a locus have opposing effects on male and female fitness ("sexual antagonism") or between components of fitness ("antagonistic pleiotropy")--might play an important role in maintaining population genetic variation and in driving phylogenetic and genomic patterns of sexual dimorphism and life-history evolution. While prior theory has thoroughly characterized the conditions necessary for antagonistic balancing selection to operate, we currently know little about the evolutionary interactions between antagonistic selection, recurrent mutation, and genetic drift, which should collectively shape empirical patterns of genetic variation. To fill this void, we developed and analyzed a series of population genetic models that simultaneously incorporate these processes. Our models identify two general properties of antagonistically selected loci. First, antagonistic selection inflates heterozygosity and fitness variance across a broad parameter range--a result that applies to alleles maintained by balancing selection and by recurrent mutation. Second, effective population size and genetic drift profoundly affect the statistical frequency distributions of antagonistically selected alleles. The "efficacy" of antagonistic selection (i.e., its tendency to dominate over genetic drift) is extremely weak relative to classical models, such as directional selection and overdominance. Alleles meeting traditional criteria for strong selection (N(e)s > 1, where N(e) is the effective population size, and s is a selection coefficient for a given sex or fitness component) may nevertheless evolve as if neutral. The effects of mutation and demography may generate population differences in overall levels of antagonistic fitness variation, as well as molecular population genetic signatures of balancing selection. PMID:22298707

  14. Statistical validation of structured population models for Daphnia magna

    PubMed Central

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

    2016-01-01

    In this study we use statistical validation techniques to verify density-dependent mechanisms hypothesized for populations of Daphnia magna. We develop structured population models that exemplify specific mechanisms, and use multi-scale experimental data in order to test their importance. We show that fecundity and survival rates are affected by both time-varying density-independent factors, such as age, and density-dependent factors, such as competition. We perform uncertainty analysis and show that our parameters are estimated with a high degree of confidence. Further, we perform a sensitivity analysis to understand how changes in fecundity and survival rates affect population size and age-structure. PMID:26092608

  15. Landscape structure and the genetic effects of a population collapse.

    PubMed

    Caplins, Serena A; Gilbert, Kimberly J; Ciotir, Claudia; Roland, Jens; Matter, Stephen F; Keyghobadi, Nusha

    2014-12-01

    Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60-100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift.

  16. Landscape structure and the genetic effects of a population collapse

    PubMed Central

    Caplins, Serena A.; Gilbert, Kimberly J.; Ciotir, Claudia; Roland, Jens; Matter, Stephen F.; Keyghobadi, Nusha

    2014-01-01

    Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift. PMID:25320176

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

    USGS Publications Warehouse

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

    2014-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2014-10-07

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

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

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control. PMID:26613662

  1. Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations.

    PubMed

    McHugh, Caitlin; Brown, Lisa; Thornton, Timothy A

    2016-09-01

    The genetic structure of human populations is often characterized by aggregating measures of ancestry across the autosomal chromosomes. While it may be reasonable to assume that population structure patterns are similar genome-wide in relatively homogeneous populations, this assumption may not be appropriate for admixed populations, such as Hispanics and African-Americans, with recent ancestry from two or more continents. Recent studies have suggested that systematic ancestry differences can arise at genomic locations in admixed populations as a result of selection and nonrandom mating. Here, we propose a method, which we refer to as the chromosomal ancestry differences (CAnD) test, for detecting heterogeneity in population structure across the genome. CAnD can incorporate either local or chromosome-wide ancestry inferred from SNP genotype data to identify chromosomes harboring genomic regions with ancestry contributions that are significantly different than expected. In simulation studies with real genotype data from phase III of the HapMap Project, we demonstrate the validity and power of CAnD. We apply CAnD to the HapMap Mexican-American (MXL) and African-American (ASW) population samples; in this analysis the software RFMix is used to infer local ancestry at genomic regions, assuming admixing from Europeans, West Africans, and Native Americans. The CAnD test provides strong evidence of heterogeneity in population structure across the genome in the MXL sample ([Formula: see text]), which is largely driven by elevated Native American ancestry and deficit of European ancestry on the X chromosomes. Among the ASW, all chromosomes are largely African derived and no heterogeneity in population structure is detected in this sample. PMID:27440868

  2. Inference of population structure using dense haplotype data.

    PubMed

    Lawson, Daniel John; Hellenthal, Garrett; Myers, Simon; Falush, Daniel

    2012-01-01

    The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. Each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals. Results of this "chromosome painting" can be summarized as a "coancestry matrix," which directly reveals key information about ancestral relationships among individuals. If markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard Principal Components Analysis (PCA) and model-based approaches such as STRUCTURE in a unified manner. Furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using PCA. In parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over PCA in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. We analyse Human Genome Diversity Panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. We present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. The software used for this article, ChromoPainter and fineSTRUCTURE, is available from http://www.paintmychromosomes.com/.

  3. Correcting for population structure and kinship using the linear mixed model: theory and extensions.

    PubMed

    Hoffman, Gabriel E

    2013-01-01

    Population structure and kinship are widespread confounding factors in genome-wide association studies (GWAS). It has been standard practice to include principal components of the genotypes in a regression model in order to account for population structure. More recently, the linear mixed model (LMM) has emerged as a powerful method for simultaneously accounting for population structure and kinship. The statistical theory underlying the differences in empirical performance between modeling principal components as fixed versus random effects has not been thoroughly examined. We undertake an analysis to formalize the relationship between these widely used methods and elucidate the statistical properties of each. Moreover, we introduce a new statistic, effective degrees of freedom, that serves as a metric of model complexity and a novel low rank linear mixed model (LRLMM) to learn the dimensionality of the correction for population structure and kinship, and we assess its performance through simulations. A comparison of the results of LRLMM and a standard LMM analysis applied to GWAS data from the Multi-Ethnic Study of Atherosclerosis (MESA) illustrates how our theoretical results translate into empirical properties of the mixed model. Finally, the analysis demonstrates the ability of the LRLMM to substantially boost the strength of an association for HDL cholesterol in Europeans.

  4. Correcting for population structure and kinship using the linear mixed model: theory and extensions.

    PubMed

    Hoffman, Gabriel E

    2013-01-01

    Population structure and kinship are widespread confounding factors in genome-wide association studies (GWAS). It has been standard practice to include principal components of the genotypes in a regression model in order to account for population structure. More recently, the linear mixed model (LMM) has emerged as a powerful method for simultaneously accounting for population structure and kinship. The statistical theory underlying the differences in empirical performance between modeling principal components as fixed versus random effects has not been thoroughly examined. We undertake an analysis to formalize the relationship between these widely used methods and elucidate the statistical properties of each. Moreover, we introduce a new statistic, effective degrees of freedom, that serves as a metric of model complexity and a novel low rank linear mixed model (LRLMM) to learn the dimensionality of the correction for population structure and kinship, and we assess its performance through simulations. A comparison of the results of LRLMM and a standard LMM analysis applied to GWAS data from the Multi-Ethnic Study of Atherosclerosis (MESA) illustrates how our theoretical results translate into empirical properties of the mixed model. Finally, the analysis demonstrates the ability of the LRLMM to substantially boost the strength of an association for HDL cholesterol in Europeans. PMID:24204578

  5. Accounting for randomness in measurement and sampling in studying cancer cell population dynamics.

    PubMed

    Ghavami, Siavash; Wolkenhauer, Olaf; Lahouti, Farshad; Ullah, Mukhtar; Linnebacher, Michael

    2014-10-01

    Knowing the expected temporal evolution of the proportion of different cell types in sample tissues gives an indication about the progression of the disease and its possible response to drugs. Such systems have been modelled using Markov processes. We here consider an experimentally realistic scenario in which transition probabilities are estimated from noisy cell population size measurements. Using aggregated data of FACS measurements, we develop MMSE and ML estimators and formulate two problems to find the minimum number of required samples and measurements to guarantee the accuracy of predicted population sizes. Our numerical results show that the convergence mechanism of transition probabilities and steady states differ widely from the real values if one uses the standard deterministic approach for noisy measurements. This provides support for our argument that for the analysis of FACS data one should consider the observed state as a random variable. The second problem we address is about the consequences of estimating the probability of a cell being in a particular state from measurements of small population of cells. We show how the uncertainty arising from small sample sizes can be captured by a distribution for the state probability. PMID:25257023

  6. Population genetic structure of mussels from the Baltic Sea

    NASA Astrophysics Data System (ADS)

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

    1988-03-01

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

  7. Comparative population structure of cavity-nesting sea ducks

    USGS Publications Warehouse

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

    2014-01-01

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

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

    USGS Publications Warehouse

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

    2015-01-01

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

  9. Assessment of Genetic Heterogeneity in Structured Plant Populations Using Multivariate Whole-Genome Regression Models

    PubMed Central

    Lehermeier, Christina; Schön, Chris-Carolin; de los Campos, Gustavo

    2015-01-01

    Plant breeding populations exhibit varying levels of structure and admixture; these features are likely to induce heterogeneity of marker effects across subpopulations. Traditionally, structure has been dealt with as a potential confounder, and various methods exist to “correct” for population stratification. However, these methods induce a mean correction that does not account for heterogeneity of marker effects. The animal breeding literature offers a few recent studies that consider modeling genetic heterogeneity in multibreed data, using multivariate models. However, these methods have received little attention in plant breeding where population structure can have different forms. In this article we address the problem of analyzing data from heterogeneous plant breeding populations, using three approaches: (a) a model that ignores population structure [A-genome-based best linear unbiased prediction (A-GBLUP)], (b) a stratified (i.e., within-group) analysis (W-GBLUP), and (c) a multivariate approach that uses multigroup data and accounts for heterogeneity (MG-GBLUP). The performance of the three models was assessed on three different data sets: a diversity panel of rice (Oryza sativa), a maize (Zea mays L.) half-sib panel, and a wheat (Triticum aestivum L.) data set that originated from plant breeding programs. The estimated genomic correlations between subpopulations varied from null to moderate, depending on the genetic distance between subpopulations and traits. Our assessment of prediction accuracy features cases where ignoring population structure leads to a parsimonious more powerful model as well as others where the multivariate and stratified approaches have higher predictive power. In general, the multivariate approach appeared slightly more robust than either the A- or the W-GBLUP. PMID:26122758

  10. Two-generation analysis of pollen flow across a landscape. III. Impact of adult population structure.

    PubMed

    Austerlitz, F; Smouse, P E

    2001-12-01

    The rate and distance of instantaneous pollen flow in a population are parameters of considerable current interest for plant population geneticists and conservation biologists. We have recently developed an estimator (phi ft) of differentiation between the inferred pollen clouds that fertilize several females, sampled within a single population. We have shown that there is a simple relation between phi ft and the average pollen dispersal distance (delta) for the case of a population with no geographic structure. Though forest trees usually show considerable pollen flow, assuming an absence of spatially distributed genetic structure is not always wise. Here, we develop analytical theory for the relation between phi ft and delta, for the case where the probability of Identity by Descent (IBD) for two individuals decreases with the physical distance between them. This analytical theory allows us to provide an effective method for estimating pollen dispersal distance in a population with adult genetic structure. Using real examples, we show that estimation errors can be large if genetic structure is not taken into account, so it is wise to evaluate adult genetic structure simultaneously with estimation of phi ft for the pollen clouds. We show that the results are only moderately affected by changes in the decay function, a result of some importance since no completely established theory is available for this function.

  11. Genetic structure of Aedes aegypti populations determined using pairwise comparisons.

    PubMed

    Patarro, T de F; Guirado, M M; Ravazzi, L M; Bicudo, H E M de C

    2013-01-01

    The biological characteristics of Aedes aegypti (Diptera, Culicidae), which is a vector of dengue and yellow fever, make this organism a good model for studying population structure and the events that may influence it under the effect of human activity. We assessed the genetic variability of five A. aegypti populations using RAPD-PCR technique and six primers. Four populations were from Brazil and one was from the USA. A total of 165 polymorphic DNA loci were generated. Considering the six primers and the five populations, the mean value of inter-population genetic diversity (Gst) was 0.277, which is considered high according to the Wright classification. However, pairwise comparisons of the populations gave variable Gst values ranging from 0.044 to 0.289. This variation followed the population's geographic distance to some extent but was also influenced by human activity. The lowest Gst values were obtained in the comparison of populations from cities with intensive commercial and medical contacts. These mosquito populations were previously classified as insecticide resistant, susceptible, or with decreased susceptibility; this parameter apparently had an effect on the Gst values obtained in the pairwise comparisons.

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

    USGS Publications Warehouse

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

    2016-01-01

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

  13. Accounting for vulnerable populations in rural hazard mitigation plans: results of a survey of emergency managers.

    PubMed

    Horney, Jennifer A; Nguyen, Mai; Cooper, John; Simon, Matthew; Ricchetti-Masterson, Kristen; Grabich, Shannon; Salvesen, David; Berke, Philip

    2013-01-01

    Rural areas of the United States are uniquely vulnerable to the impacts of natural disasters. One possible way to mitigate vulnerability to disasters in rural communities is to have a high-quality hazard mitigation plan in place. To understand the resources available for hazard mitigation planning and determine how well hazard mitigation plans in rural counties meet the needs of vulnerable populations, we surveyed the lead planning or emergency management official responsible for hazard mitigation plans in 96 rural counties in eight states in the Southeastern United States. In most counties, emergency management was responsible for implementing the county's hazard mitigation plan and the majority of counties had experienced a presidentially declared disaster in the last 5 years. Our research findings demonstrated that there were differences in subjective measures of vulnerability (as reported by survey respondents) and objective measures of vulnerability (as determined by US Census data). In addition, although few counties surveyed included outreach to vulnerable groups as a part of their hazard mitigation planning process, a majority felt that their hazard mitigation plan addressed the needs of vulnerable populations "well" or "very well." These differences could result in increased vulnerabilities in rural areas, particularly for certain vulnerable groups.

  14. Computer Simulation of Sexual Selection on Age-Structured Populations

    NASA Astrophysics Data System (ADS)

    Martins, S. G. F.; Penna, T. J. P.

    Using computer simulations of a bit-string model for age-structured populations, we found that sexual selection of older males is advantageous, from an evolutionary point of view. These results are in opposition to a recent proposal of females choosing younger males. Our simulations are based on findings from recent studies of polygynous bird species. Since secondary sex characters are found mostly in males, we could make use of asexual populations that can be implemented in a fast and efficient way.

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

    PubMed

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

    2014-01-01

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

  16. From inclusive fitness to fixation probability in homogeneous structured populations.

    PubMed

    Taylor, Peter D; Day, Troy; Wild, Geoff

    2007-11-01

    The methods of inclusive fitness provide a powerful analysis of the action of selection on social behaviour. The key component of this analysis is the concept of relatedness R. In infinite populations, a standard method of calculating relatedness coefficients is through coefficients of consanguinity using the notion of genetic identity by descent. In this paper, we show that this approach can also be made to work in finite populations and we assume here that the population has a homogeneous structure, such as an island model. We demonstrate that, under the assumption that genetic effects are small and additive, the resulting formulation of inclusive fitness is equivalent to other significant measures of selection in finite populations, including the change in average allele frequency and fixation probability. The results are illustrated for a model of the evolution of cooperation in a finite island population.

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

    PubMed Central

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

    2014-01-01

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

  18. [Age structure and growth characteristic of Castanopsis fargesii population].

    PubMed

    Song, Kun; Da, Liang-jun; Yang, Tong-hui; Yang, Xu-feng

    2007-02-01

    In this paper, the age structure and growth characteristics of Castanopsis fargesii population in a shade-tolerant broadleaved evergreen forest were studied, aimed to understand more about the regeneration patterns and dynamics of this population. The results showed that the age structure of C. fargesii population was of sporadic type, with two death peaks of a 30-year gap. This population had a good plasticity in growth to light condition. Because there were no significant differences in light condition under the canopy in vertical, the saplings came into their first suppression period when they were 5-8 years old, with a height growth rate less than 0. 1 m x a(-1) lasting for 10 years. The beginning time of the first growth suppression period was by the end of the first death peak of the population, and the ending time of the first growth suppression period was at the beginning of the second death peak of the population, demonstrating that growth characteristic was the key factor affecting the age structure of C. fargesii.

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

    SciTech Connect

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

    1995-01-01

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

  20. Age-structured optimal control in population economics.

    PubMed

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

    2004-06-01

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

  1. Error, population structure and the origin of diverse sign systems.

    PubMed

    Grassly, N C; Von Haeseler, A; Krakauer, D C

    2000-10-01

    Evolutionary models of communication are used to shed some light on the selective pressures involved in the evolution of simple referential signals, and the constraints hindering the emergence of signs. Error-prone communication results from errors in transmission (in which individuals learn the wrong associations) and communication (in which signs are mistaken for one another). We demonstrate how both classes of errors are required to generate diversity and subsequently impose limits on the sign repertoire within a population. We then explore the influence of geographic structuring of a population on the evolution of a shared sign system and the importance of such structure for the maintenance of sign diversity. Deceit tends to erode conventional signs systems thereby reducing signal diversity, we demonstrate that population structure can act as a hedge against deceit, thereby ensuring the persistence of sign systems. PMID:10988022

  2. Genetic Population Structure of Tectura paleacea: Implications for the Mechanisms Regulating Population Structure in Patchy Coastal Habitats

    PubMed Central

    Begovic, Emina; Lindberg, David R.

    2011-01-01

    The seagrass limpet Tectura paleacea (Gastropoda; Patellogastropoda) belongs to a seagrass obligate lineage that has shifted from the Caribbean in the late Miocene, across the Isthmus of Panama prior to the closing of the Panamanian seaway, and then northward to its modern Baja California – Oregon distribution. To address whether larval entrainment by seagrass beds contributes to population structuring, populations were sampled at six California/Oregon localities approximately 2 degrees latitude apart during two post-settlement periods in July 2002 and June 2003. Partial cytochrome oxidase b (Cytb) sequences were obtained from 20 individuals (10 per year) from each population in order to determine the levels of population subdivision/connectivity. From the 120 individuals sequenced, there were eighty-one unique haplotypes, with the greatest haplotype diversity occurring in southern populations. The only significant genetic break detected was consistent with a peri-Point Conception (PPC) biogeographic boundary while populations north and south of Point Conception were each panmictic. The data further indicate that populations found south of the PPC biogeographic boundary originated from northern populations. This pattern of population structure suggests that seagrass patches are not entraining the larvae of T. paleacea by altering flow regimes within their environment; a process hypothesized to produce extensive genetic subdivision on fine geographic scales. In contrast to the haplotype data, morphological patterns vary significantly over very fine geographic scales that are inconsistent with the observed patterns of genetic population structure, indicating that morphological variation in T. paleacea might be attributed to differential ecophenotypic expression in response to local habitat variability throughout its distribution. These results suggest that highly localized conservation efforts may not be as effective as large-scale conservation efforts in near

  3. Ecological connectivity assessment in a strongly structured fire salamander (Salamandra salamandra) population

    PubMed Central

    Bani, Luciano; Pisa, Giulia; Luppi, Massimiliano; Spilotros, Giulia; Fabbri, Elena; Randi, Ettore; Orioli, Valerio

    2015-01-01

    Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad-leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, DC) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoDb). Mantel tests between distance matrices highlighted how the Log-DC in PEF populations was related to log-transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log-EcoD, and particularly by the Log-EcoDb, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when

  4. Ecological connectivity assessment in a strongly structured fire salamander (Salamandra salamandra) population.

    PubMed

    Bani, Luciano; Pisa, Giulia; Luppi, Massimiliano; Spilotros, Giulia; Fabbri, Elena; Randi, Ettore; Orioli, Valerio

    2015-08-01

    Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad-leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, DC) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoDb). Mantel tests between distance matrices highlighted how the Log-DC in PEF populations was related to log-transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log-EcoD, and particularly by the Log-EcoDb, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when

  5. Population structure and genetic diversity of the perennial medicinal shrub Plumbago

    PubMed Central

    Panda, Sayantan; Naik, Dhiraj; Kamble, Avinash

    2015-01-01

    Knowledge of the natural genetic variation and structure in a species is important for developing appropriate conservation strategies. As genetic diversity analysis among and within populations of Plumbago zeylanica remains unknown, we aimed (i) to examine the patterns and levels of morphological and genetic variability within/among populations and ascertain whether these variations are dependent on geographical conditions; and (ii) to evaluate genetic differentiation and population structure within the species. A total of 130 individuals from 13 populations of P. zeylanica were collected, covering the entire distribution area of species across India. The genetic structure and variation within and among populations were evaluated using inter-simple sequence repeat (ISSR) and randomly amplified DNA polymorphism (RAPD) markers. High levels of genetic diversity and significantly high genetic differentiation were revealed by both the markers among all studied populations. High values of among-population genetic diversity were found, which accounted for 60 % of the total genetic variance. The estimators of genetic diversity were higher in northern and eastern populations than in southern and western populations indicating the possible loss of genetic diversity during the spread of this species to Southern India. Bayesian analysis, unweighted pair group method with arithmetic average cluster analysis and principal coordinates analysis all showed similar results. A significant isolation-by-distance pattern was revealed in P. zeylanica by ISSR (r = 0.413, P = 0.05) and RAPD (r = 0.279, P = 0.05) analysis. The results obtained suggest an urgent need for conservation of existing natural populations along with extensive domestication of this species for commercial purpose. PMID:25957315

  6. Seasonal Changes in Thrips tabaci Population Structure in Two Cultivated Hosts

    PubMed Central

    Nault, Brian A.; Kain, Wendy C.; Wang, Ping

    2014-01-01

    Thrips tabaci is a major pest of high-value vegetable crops and understanding its population genetics will advance our knowledge about its ecology and management. Mitochondrial cytochrome oxidase subunit I (COI) gene sequence was used as a molecular marker to analyze T. tabaci populations from onion and cabbage fields in New York. Eight COI haplotypes were identified in 565 T. tabaci individuals collected from these fields. All T. tabaci were thelytokous and genetically similar to those originating from hosts representing seven plant families spanning five continents. The most dominant haplotype was NY-HT1, accounting for 92 and 88% of the total individuals collected from onion fields in mid-summer in 2005 and 2007, respectively, and 100 and 96% of the total in early fall in 2005 and 2007, respectively. In contrast, T. tabaci collected from cabbage fields showed a dynamic change in population structure from mid-summer to early fall. In mid-summer, haplotype NY-HT2 was highly abundant, accounting for 58 and 52% of the total in 2005 and 2007, respectively, but in early fall it decreased drastically to 15 and 7% of the total in 2005 and 2007, respectively. Haplotype NY-HT1 accounted for 12 and 46% of the total in cabbage fields in mid-summer of 2005 and 2007, respectively, but became the dominant haplotype in early fall accounting for 81 and 66% of the total in 2005 and 2007, respectively. Despite the relative proximity of onion and cabbage fields in the western New York landscape, T. tabaci populations differed seasonally within each cropping system. Differences may have been attributed to better establishment of certain genotypes on specific hosts or differing colonization patterns within these cropping systems. Future studies investigating temporal changes in T. tabaci populations on their major hosts in these ecosystems are needed to better understand host-plant utilization and implications for population management. PMID:24992484

  7. A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

    PubMed

    Buckley, Ralf C; Castley, J Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C; Steven, Rochelle

    2012-01-01

    Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.

  8. A Population Accounting Approach to Assess Tourism Contributions to Conservation of IUCN-Redlisted Mammal Species

    PubMed Central

    Buckley, Ralf C.; Castley, J. Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C.; Steven, Rochelle

    2012-01-01

    Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥5% for over half of the species where relevant data exist, ≥15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species. PMID:22984467

  9. A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

    PubMed

    Buckley, Ralf C; Castley, J Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C; Steven, Rochelle

    2012-01-01

    Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species. PMID:22984467

  10. On Accounting for the Interplay of Kinetic and Non-Kinetic Aspects in Population Mobility Models

    SciTech Connect

    Perumalla, Kalyan S; Bhaduri, Budhendra L

    2006-01-01

    Several important applications are placing demands on satisfactory characterization of the bi-directional interaction between kinetic and non-kinetic aspects in the mobility of people and commodities. Example applications include: emergency planning which needs to account for strong interplay of vehicular transport with inventory levels of critical supplies and/or people's psychologies; energy planning for normal day-to-day activities which considers the relation between travel patterns and energy usage; and, policy making for futuristic scenarios which examines the correlation between transportation behaviors and environmental/economic concerns. All these require new and holistic approaches for capturing the interplay of kinetic and non-kinetic aspects of mobility, as those aspects cannot be treated separately. Accurate characterization of such interplay requires proper integration of three distinct components, namely, data, models and computation. The availability of new sources of high-resolution data, and of detailed models together with recent advances in scalable computational methods now permits accurate capture of such an important interplay. This paper serves to highlight and argue that the interplay can in fact be captured in a high level of detail in simulations, enabled by the availability of new data, models and computational capabilities. Some of the challenges that are encountered in incorporating the interplay are outlined and plausible solution approaches are described in the context of large-scale scenarios involving mobility of people and commodities.

  11. Spatial population structure of a specialist leaf-mining moth.

    PubMed

    Gripenberg, Sofia; Ovaskainen, Otso; Morriën, Elly; Roslin, Tomas

    2008-07-01

    1. The spatial structure of natural populations may profoundly influence their dynamics. Depending on the frequency of movements among local populations and the consequent balance between local and regional population processes, earlier work has attempted to classify metapopulations into clear-cut categories, ranging from patchy populations to sets of remnant populations. In an alternative, dichotomous scheme, local populations have been classified as self-sustaining populations generating a surplus of individuals (sources) and those depending on immigration for persistence (sinks). 2. In this paper, we describe the spatial population structure of the leaf-mining moth Tischeria ekebladella, a specialist herbivore of the pedunculate oak Quercus robur. We relate moth dispersal to the distribution of oaks on Wattkast, a small island (5 km(2)) off the south-western coast of Finland. 3. We build a spatially realistic metapopulation model derived from assumptions concerning the behaviour of individual moths, and show that the model is able to explain part of the variation in observed patterns of occurrence and colonization. 4. While the species was always present on large trees, a considerable proportion of the local populations associated with small oaks showed extinction-recolonization dynamics. The vast majority of moth individuals occur on large trees. 5. According to model predictions, the dominance of local vs. regional processes in tree-specific moth dynamics varies drastically across the landscape. Most local populations may be defined broadly as 'sinks', as model simulations suggest that in the absence of immigration, only the largest oaks will sustain viable moth populations. Large trees in areas of high oak density will contribute most to the overall persistence of the metapopulation by acting as sources of moths colonizing other trees. 6. No single 'metapopulation type' will suffice to describe the oak-moth system. Instead, our study supports the notion that

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

    USGS Publications Warehouse

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

    1992-01-01

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

  13. Temporal changes in population structure of a marine planktonic diatom.

    PubMed

    Tesson, Sylvie V M; Montresor, Marina; Procaccini, Gabriele; Kooistra, Wiebe H C F

    2014-01-01

    A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) over four consecutive years and explored possible changes over seasons and from year to year. A total of 525 strains were genotyped using seven microsatellite markers, for a genotypic diversity of 75.05%, comparable to that found in other Pseudo-nitzschia species. Evidence from Bayesian clustering analysis (BA) identified two genetically distinct clusters, here interpreted as populations, and several strains that could not be assigned with ≥ 90% probability to either population, here interpreted as putative hybrids. Principal Component Analysis (PCA) recovered these two clusters in distinct clouds with most of the putative hybrids located in-between. Relative proportions of the two populations and the putative hybrids remained similar within years, but changed radically between 2008 and 2009 and between 2010 and 2011, when the 2008-population apparently became the dominant one again. Strains from the two populations are inter-fertile, and so is their offspring. Inclusion of genotypes of parental strains and their offspring shows that the majority of the latter could not be assigned to any of the two parental populations. Therefore, field strains classified by BA as the putative hybrids could be biological hybrids. We hypothesize that P. multistriata population dynamics in the Gulf of Naples follows a meta-population-like model, including establishment of populations by cell inocula at the beginning of each growth season and remixing and dispersal governed by moving and mildly turbulent water masses.

  14. Temporal Changes in Population Structure of a Marine Planktonic Diatom

    PubMed Central

    Tesson, Sylvie V. M.; Montresor, Marina; Procaccini, Gabriele; Kooistra, Wiebe H. C. F.

    2014-01-01

    A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) over four consecutive years and explored possible changes over seasons and from year to year. A total of 525 strains were genotyped using seven microsatellite markers, for a genotypic diversity of 75.05%, comparable to that found in other Pseudo-nitzschia species. Evidence from Bayesian clustering analysis (BA) identified two genetically distinct clusters, here interpreted as populations, and several strains that could not be assigned with ≥90% probability to either population, here interpreted as putative hybrids. Principal Component Analysis (PCA) recovered these two clusters in distinct clouds with most of the putative hybrids located in-between. Relative proportions of the two populations and the putative hybrids remained similar within years, but changed radically between 2008 and 2009 and between 2010 and 2011, when the 2008-population apparently became the dominant one again. Strains from the two populations are inter-fertile, and so is their offspring. Inclusion of genotypes of parental strains and their offspring shows that the majority of the latter could not be assigned to any of the two parental populations. Therefore, field strains classified by BA as the putative hybrids could be biological hybrids. We hypothesize that P. multistriata population dynamics in the Gulf of Naples follows a meta-population-like model, including establishment of populations by cell inocula at the beginning of each growth season and remixing and dispersal governed by moving and mildly turbulent water masses. PMID:25506926

  15. Multiple imputation to account for measurement error in marginal structural models

    PubMed Central

    Edwards, Jessie K.; Cole, Stephen R.; Westreich, Daniel; Crane, Heidi; Eron, Joseph J.; Mathews, W. Christopher; Moore, Richard; Boswell, Stephen L.; Lesko, Catherine R.; Mugavero, Michael J.

    2015-01-01

    Background Marginal structural models are an important tool for observational studies. These models typically assume that variables are measured without error. We describe a method to account for differential and non-differential measurement error in a marginal structural model. Methods We illustrate the method estimating the joint effects of antiretroviral therapy initiation and current smoking on all-cause mortality in a United States cohort of 12,290 patients with HIV followed for up to 5 years between 1998 and 2011. Smoking status was likely measured with error, but a subset of 3686 patients who reported smoking status on separate questionnaires composed an internal validation subgroup. We compared a standard joint marginal structural model fit using inverse probability weights to a model that also accounted for misclassification of smoking status using multiple imputation. Results In the standard analysis, current smoking was not associated with increased risk of mortality. After accounting for misclassification, current smoking without therapy was associated with increased mortality [hazard ratio (HR): 1.2 (95% CI: 0.6, 2.3)]. The HR for current smoking and therapy (0.4 (95% CI: 0.2, 0.7)) was similar to the HR for no smoking and therapy (0.4; 95% CI: 0.2, 0.6). Conclusions Multiple imputation can be used to account for measurement error in concert with methods for causal inference to strengthen results from observational studies. PMID:26214338

  16. Ethnicity and population structure in personal naming networks.

    PubMed

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

    2011-01-01

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

  17. Ethnicity and population structure in personal naming networks.

    PubMed

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

    2011-01-01

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

  18. Structure of the New England herring gull population

    USGS Publications Warehouse

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

    1968-01-01

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

  19. Population genetic structure and long-distance dispersal among seabird populations: implications for colony persistence.

    PubMed

    Bicknell, A W J; Knight, M E; Bilton, D; Reid, J B; Burke, T; Votier, S C

    2012-06-01

    Dramatic local population decline brought about by anthropogenic-driven change is an increasingly common threat to biodiversity. Seabird life history traits make them particularly vulnerable to such change; therefore, understanding population connectivity and dispersal dynamics is vital for successful management. Our study used a 357-base pair mitochondrial control region locus sequenced for 103 individuals and 18 nuclear microsatellite loci genotyped for 245 individuals to investigate population structure in the Atlantic and Pacific populations of the pelagic seabird, Leach's storm-petrel Oceanodroma leucorhoa leucorhoa. This species is under intense predation pressure at one regionally important colony on St Kilda, Scotland, where a disparity between population decline and predation rates hints at immigration from other large colonies. AMOVA, F(ST), Φ(ST) and Bayesian cluster analyses revealed no genetic structure among Atlantic colonies (Global Φ(ST) = -0.02 P > 0.05, Global F(ST) = 0.003, P > 0.05, STRUCTURE K = 1), consistent with either contemporary gene flow or strong historical association within the ocean basin. The Pacific and Atlantic populations are genetically distinct (Global Φ(ST) = 0.32 P < 0.0001, Global F(ST) = 0.04, P < 0.0001, STRUCTURE K = 2), but evidence for interocean exchange was found with individual exclusion/assignment and population coalescent analyses. These findings highlight the importance of conserving multiple colonies at a number of different sites and suggest that management of this seabird may be best viewed at an oceanic scale. Moreover, our study provides an illustration of how long-distance movement may ameliorate the potentially deleterious impacts of localized environmental change, although direct measures of dispersal are still required to better understand this process. PMID:22548276

  20. Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

    PubMed Central

    Calboli, Federico C. F.; Sampson, Jeff; Fretwell, Neale; Balding, David J.

    2008-01-01

    Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Ψ for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare. PMID:18493074

  1. Population and colony structure of the carpenter ant Camponotus floridanus.

    PubMed

    Gadau, J; Heinze, J; Hölldobler, B; Schmid, M

    1996-12-01

    The colony and population structure of the carpenter ant, Camponotus floridanus, were investigated by multilocus DNA fingerprinting using simple repeat motifs as probes [e.g. (GATA)4]. The mating frequency of 15 queens was determined by comparing the fingerprint patterns of the queen and 17-33 of her progeny workers. C. floridanus queens are most probably singly mated, i.e. this species is monandrous and monogynous (one queen per colony). C. floridanus occurs in all counties of mainland Florida and also inhabits most of the Key islands in the southern part of Florida. We tested whether the two mainland populations and the island populations are genetically isolated. Wright's FST and Nei's D-value of genetic distance were calculated from intercolonial bandsharing-coefficients. The population of C. floridanus is substructured (FST = 0.19 +/- 0.09) and the highest degree of genetic distance was found between one of the mainland populations and the island populations (D = 0.35). Our fingerprinting technique could successfully be transferred to 12 other Camponotus species and here also revealed sufficient variability to analyse the genetic structure. In three of these species (C. ligniperdus, C. herculeanus and C. gigas) we could determine the mating frequency of the queen in one or two colonies, respectively.

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

    USGS Publications Warehouse

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

    1999-01-01

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

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

    USGS Publications Warehouse

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

    2012-01-01

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

  4. Population and colony structure of the carpenter ant Camponotus floridanus.

    PubMed

    Gadau, J; Heinze, J; Hölldobler, B; Schmid, M

    1996-12-01

    The colony and population structure of the carpenter ant, Camponotus floridanus, were investigated by multilocus DNA fingerprinting using simple repeat motifs as probes [e.g. (GATA)4]. The mating frequency of 15 queens was determined by comparing the fingerprint patterns of the queen and 17-33 of her progeny workers. C. floridanus queens are most probably singly mated, i.e. this species is monandrous and monogynous (one queen per colony). C. floridanus occurs in all counties of mainland Florida and also inhabits most of the Key islands in the southern part of Florida. We tested whether the two mainland populations and the island populations are genetically isolated. Wright's FST and Nei's D-value of genetic distance were calculated from intercolonial bandsharing-coefficients. The population of C. floridanus is substructured (FST = 0.19 +/- 0.09) and the highest degree of genetic distance was found between one of the mainland populations and the island populations (D = 0.35). Our fingerprinting technique could successfully be transferred to 12 other Camponotus species and here also revealed sufficient variability to analyse the genetic structure. In three of these species (C. ligniperdus, C. herculeanus and C. gigas) we could determine the mating frequency of the queen in one or two colonies, respectively. PMID:8981768

  5. Globalization and the population structure of Toxoplasma gondii.

    PubMed

    Lehmann, Tovi; Marcet, Paula L; Graham, Doug H; Dahl, Erica R; Dubey, J P

    2006-07-25

    Toxoplasma gondii is a protozoan parasite that infects nearly all mammal and bird species worldwide. Usually asymptomatic, toxoplasmosis can be severe and even fatal to many hosts, including people. Elucidating the contribution of genetic variation among parasites to patterns of disease transmission and manifestations has been the goal of many studies. Focusing on the geographic component of this variation, we show that most genotypes are locale-specific, but some are found across continents and are closely related to each other, indicating a recent radiation of a pandemic genotype. Furthermore, we show that the geographic structure of T. gondii is extraordinary in having one population that is found in all continents except South America, whereas other populations are generally confined to South America, and yet another population is found worldwide. Our evidence suggests that South American and Eurasian populations have evolved separately until recently, when ships populated by rats, mice, and cats provided T. gondii with unprecedented migration opportunities, probably during the transatlantic slave trade. Our results explain several enigmatic features of the population structure of T. gondii and demonstrate how pervasive, prompt, and elusive the impact of human globalization is on nature.

  6. New Summary Measures of Population Health and Well-Being for Implementation by Health Plans and Accountable Care Organizations.

    PubMed

    Kottke, Thomas E; Gallagher, Jason M; Rauri, Sachin; Tillema, Juliana O; Pronk, Nicolaas P; Knudson, Susan M

    2016-01-01

    Health plans and accountable care organizations measure many indicators of patient health, with standard metrics that track factors such as patient experience and cost. They lack, however, a summary measure of the third leg of the Triple Aim, population health. In response, HealthPartners has developed summary measures that align with the recommendations of the For the Public's Health series of reports from the Institute of Medicine. (The series comprises the following 3 reports: For the Public's Health: Investing in a Healthier Future, For the Public's Health: Revitalizing Law and Policy to Meet New Challenges, and For the Public's Health: The Role of Measurement in Action and Accountability.) The summary measures comprise 3 components: current health, sustainability of health, and well-being. The measure of current health is disability-adjusted life years (DALYs) calculated from health care claims and death records. The sustainability of health measure comprises member reporting of 6 behaviors associated with health plus a clinical preventive services index that indicates adherence to evidence-based preventive care guidelines. Life satisfaction represents the summary measure of subjective well-being. HealthPartners will use the summary measures to identify and address conditions and factors that have the greatest impact on the health and well-being of its patients, members, and community. The method could easily be implemented by other institutions and organizations in the United States, helping to address a persistent need in population health measurement for improvement. PMID:27390075

  7. New Summary Measures of Population Health and Well-Being for Implementation by Health Plans and Accountable Care Organizations

    PubMed Central

    Gallagher, Jason M.; Rauri, Sachin; Tillema, Juliana O.; Pronk, Nicolaas P.; Knudson, Susan M.

    2016-01-01

    Health plans and accountable care organizations measure many indicators of patient health, with standard metrics that track factors such as patient experience and cost. They lack, however, a summary measure of the third leg of the Triple Aim, population health. In response, HealthPartners has developed summary measures that align with the recommendations of the For the Public’s Health series of reports from the Institute of Medicine. (The series comprises the following 3 reports: For the Public’s Health: Investing in a Healthier Future, For the Public’s Health: Revitalizing Law and Policy to Meet New Challenges, and For the Public’s Health: The Role of Measurement in Action and Accountability.) The summary measures comprise 3 components: current health, sustainability of health, and well-being. The measure of current health is disability-adjusted life years (DALYs) calculated from health care claims and death records. The sustainability of health measure comprises member reporting of 6 behaviors associated with health plus a clinical preventive services index that indicates adherence to evidence-based preventive care guidelines. Life satisfaction represents the summary measure of subjective well-being. HealthPartners will use the summary measures to identify and address conditions and factors that have the greatest impact on the health and well-being of its patients, members, and community. The method could easily be implemented by other institutions and organizations in the United States, helping to address a persistent need in population health measurement for improvement. PMID:27390075

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

    PubMed

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

    2006-07-19

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

  9. Heterozygosity-fitness correlations in a wild mammal population: accounting for parental and environmental effects.

    PubMed

    Annavi, Geetha; Newman, Christopher; Buesching, Christina D; Macdonald, David W; Burke, Terry; Dugdale, Hannah L

    2014-06-01

    HFCs (heterozygosity-fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture-mark-recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first-year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity-related survival effects. This paternal interaction was significant in the most supported model; however, the model-averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First-year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta-analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first-year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness-related traits, which could play an important role in the evolution of mate choice. PMID:25360289

  10. Heterozygosity–fitness correlations in a wild mammal population: accounting for parental and environmental effects

    PubMed Central

    Annavi, Geetha; Newman, Christopher; Buesching, Christina D; Macdonald, David W; Burke, Terry; Dugdale, Hannah L

    2014-01-01

    HFCs (heterozygosity–fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture–mark–recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first-year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity-related survival effects. This paternal interaction was significant in the most supported model; however, the model-averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First-year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta-analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first-year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness-related traits, which could play an important role in the evolution of mate choice. PMID:25360289

  11. Heterozygosity-fitness correlations in a wild mammal population: accounting for parental and environmental effects.

    PubMed

    Annavi, Geetha; Newman, Christopher; Buesching, Christina D; Macdonald, David W; Burke, Terry; Dugdale, Hannah L

    2014-06-01

    HFCs (heterozygosity-fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture-mark-recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first-year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity-related survival effects. This paternal interaction was significant in the most supported model; however, the model-averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First-year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta-analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first-year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness-related traits, which could play an important role in the evolution of mate choice.

  12. Evolutionary snowdrift game incorporating costly punishment in structured populations

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

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

    PubMed

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

    2014-05-01

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

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

    PubMed Central

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

    2014-01-01

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

  15. Population Structure of Barley Landrace Populations and Gene-Flow with Modern Varieties

    PubMed Central

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

    2013-01-01

    Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments. PMID:24386303

  16. Accounting for environmental variability, modeling errors, and parameter estimation uncertainties in structural identification

    NASA Astrophysics Data System (ADS)

    Behmanesh, Iman; Moaveni, Babak

    2016-07-01

    This paper presents a Hierarchical Bayesian model updating framework to account for the effects of ambient temperature and excitation amplitude. The proposed approach is applied for model calibration, response prediction and damage identification of a footbridge under changing environmental/ambient conditions. The concrete Young's modulus of the footbridge deck is the considered updating structural parameter with its mean and variance modeled as functions of temperature and excitation amplitude. The identified modal parameters over 27 months of continuous monitoring of the footbridge are used to calibrate the updating parameters. One of the objectives of this study is to show that by increasing the levels of information in the updating process, the posterior variation of the updating structural parameter (concrete Young's modulus) is reduced. To this end, the calibration is performed at three information levels using (1) the identified modal parameters, (2) modal parameters and ambient temperatures, and (3) modal parameters, ambient temperatures, and excitation amplitudes. The calibrated model is then validated by comparing the model-predicted natural frequencies and those identified from measured data after deliberate change to the structural mass. It is shown that accounting for modeling error uncertainties is crucial for reliable response prediction, and accounting only the estimated variability of the updating structural parameter is not sufficient for accurate response predictions. Finally, the calibrated model is used for damage identification of the footbridge.

  17. Genetic Structure of Daphnia galeata Populations in Eastern China

    PubMed Central

    Wolinska, Justyna; Ma, Xiaolin; Yang, Zhong; Hu, Wei; Yin, Mingbo

    2015-01-01

    This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes. PMID:25768727

  18. [New view on the population genetic structure of marine fish].

    PubMed

    Salmenkova, E A

    2011-11-01

    The view on homogeneous population genetic structure in many marine fish with high mobility has changed significantly during the last ten years. Molecular genetic population studies over the whole ranges of such species as Atlantic herring and Atlantic cod showed a complex picture of spatial differentiation both on the macrogeographic and, in many areas, on the microgeographic scale, although the differentiation for neutral molecular markers was low. It was established that the migration activity of such fish is constrained in many areas of the species range by hydrological and physicochemical transition zones (environmental gradients), as well as gyres in the spawning regions. Natal homing was recorded in a number of marine fish species. Existing in marine fish constraints of gene migration and a very high variance of reproductive success determine a significantly smaller proportion of effective reproductive size of their populations in the total population size, which generates more complex abundance dynamics than assumed earlier. The various constraints on gene migration and natal homing in marine fish promote the formation of local adaptations at ecologically important phenotypic traits. Effects of selection underlying adaptations are actively investigated in marine fish on the genomic level, using approaches of population genomics. The knowledge of adaptive intraspecific structure enables understanding the ecological and evolutionary processes, that influence biodiversity and providing spatial frames for conservation of genetic resources under commercial exploitation. Contemporary views on the population genetic and adaptive structures or biocomplexity in marine fish support and develop the main principles of the conception of systemic organization of the species and its regional populations, which were advanced by Yu.P. Altukhov and Yu.G. Rychkov.

  19. The Decay of Genetic Variability in Geographically Structured Populations*

    PubMed Central

    Nagylaki, Thomas

    1974-01-01

    The geographical structure of a population distributed continuously and homogeneously along an infinite linear habitat is explored. The analysis is restricted to a single locus in the absence of selection, and every mutant is assumed to be new to the population. An explicit formula is derived for the probability that two homologous genes separated by a given distance at any time t are the same allele. The ultimate rate of approach to equilibrium is shown to be t-3/2e-2ut, where u is the mutation rate. An approximation is given for the stationary probability of allelism in an infinite two-dimensional population, which, unlike previous expressions, is finite everywhere. For a finite habitat of arbitrary shape and any number of dimensions, it is proved that if the population density is very high, then asymptotically the transient part of the probability of allelism is spatially uniform and decays at the rate e-[2u+1/(2N)]t, where N is the total population size. Thus, in this respect the population behaves as if it were panmictic. The dependence of the amount of local gene frequency differentiation on population density and habitat size and dimensionality is discussed. PMID:4528770

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

    PubMed Central

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

    2013-01-01

    Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture. PMID:23390109

  1. Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

    PubMed Central

    Szabo, Gitta; Preheim, Sarah P; Kauffman, Kathryn M; David, Lawrence A; Shapiro, Jesse; Alm, Eric J; Polz, Martin F

    2013-01-01

    How reproducibly microbial populations assemble in the wild remains poorly understood. Here, we assess evidence for ecological specialization and predictability of fine-scale population structure and habitat association in coastal ocean Vibrionaceae across years. We compare Vibrionaceae lifestyles in the bacterioplankton (combinations of free-living, particle, or zooplankton associations) measured using the same sampling scheme in 2006 and 2009 to assess whether the same groups show the same environmental association year after year. This reveals complex dynamics with populations falling primarily into two categories: (i) nearly equally represented in each of the two samplings and (ii) highly skewed, often to an extent that they appear exclusive to one or the other sampling times. Importantly, populations recovered at the same abundance in both samplings occupied highly similar habitats suggesting predictable and robust environmental association while skewed abundances of some populations may be triggered by shifts in ecological conditions. The latter is supported by difference in the composition of large eukaryotic plankton between years, with samples in 2006 being dominated by copepods, and those in 2009 by diatoms. Overall, the comparison supports highly predictable population-habitat linkage but highlights the fact that complex, and often unmeasured, environmental dynamics in habitat occurrence may have strong effects on population dynamics. PMID:23178668

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

    PubMed

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

    2013-04-01

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

  3. Population genetic structure of the people of Qatar.

    PubMed

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W; Fuller, Jennifer; Hackett, Neil R; Crystal, Ronald G; Clark, Andrew G

    2010-07-01

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari.

  4. Evolutionary dynamics for persistent cooperation in structured populations

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  5. Population Structure Shapes Copy Number Variation in Malaria Parasites

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-03-01

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

  7. Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance.

    PubMed

    Kovi, Mallikarjuna Rao; Fjellheim, Siri; Sandve, Simen R; Larsen, Arild; Rudi, Heidi; Asp, Torben; Kent, Matthew Peter; Rognli, Odd Arne

    2015-01-01

    Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L.), and freezing tolerance is a complex trait of major agronomical importance in northern and central Europe. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. The plant material investigated in this study was an experimental synthetic population derived from pair-crosses among five European perennial ryegrass genotypes, representing adaptations to a range of climatic conditions across Europe. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF], and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected (US) control population were genotyped using 278 genome-wide SNPs derived from perennial ryegrass transcriptome sequences. Our studies investigated the genetic diversity among the three experimental populations by analysis of molecular variance and population structure, and determined that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two F st outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN, both detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation, and abiotic stress. These six candidate loci under directional selection for freezing tolerance might be potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  8. Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

    PubMed

    Gholami, Mahmood; Reimer, Christian; Erbe, Malena; Preisinger, Rudolf; Weigend, Annett; Weigend, Steffen; Servin, Bertrand; Simianer, Henner

    2015-01-01

    An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red), genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10). We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  11. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations.

    PubMed

    Stopnisek, Nejc; Bodenhausen, Natacha; Frey, Beat; Fierer, Noah; Eberl, Leo; Weisskopf, Laure

    2014-06-01

    Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp.

  12. Care coordination in accountable care organizations: moving beyond structure and incentives.

    PubMed

    Press, Matthew J; Michelow, Marilyn D; MacPhail, Lucy H

    2012-12-01

    Accountable care organizations (ACOs) are considered by many to be a key component of healthcare delivery system improvement. One expectation is that the structural elements of the ACO model, including clinical integration and financial accountability, will lead to better coordination of care for patients. But, while structure and incentives may facilitate the delivery of coordinated care, they will not necessarily ensure that care coordination is done well. For that, physicians and other healthcare providers within ACOs must possess and utilize specific skills, particularly in the areas of collaboration, communication, and teamwork. In this article, we present strategies in 3 domains--training, support tools, and organizational culture--that ACOs can implement to foster the development of these skills and support their use in clinical practice.

  13. Gene flow and genetic structure in the Galician population (NW Spain) according to Alu insertions

    PubMed Central

    Varela, Tito A; Fariña, José; Diéguez, Lois Pérez; Lodeiro, Rosa

    2008-01-01

    Background The most recent Alu insertions reveal different degrees of polymorphism in human populations, and a series of characteristics that make them particularly suitable genetic markers for Human Biology studies. This has led these polymorphisms to be used to analyse the origin and phylogenetic relationships between contemporary human groups. This study analyses twelve Alu sequences in a sample of 216 individuals from the autochthonous population of Galicia (NW Spain), with the aim of studying their genetic structure and phylogenetic position with respect to the populations of Western and Central Europe and North Africa, research that is of special interest in revealing European population dynamics, given the peculiarities of the Galician population due to its geographical situation in western Europe, and its historical vicissitudes. Results The insertion frequencies of eleven of the Alu elements analysed were within the variability range of European populations, while Yb8NBC125 proved to be the lowest so far recorded to date in Europe. Taking the twelve polymorphisms into account, the GD value for the Galician population was 0.268. The comparative analyses carried out using the MDS, NJ and AMOVA methods reveal the existence of spatial heterogeneity, and identify three population groups that correspond to the geographic areas of Western-Central Europe, Eastern Mediterranean Europe and North Africa. Galicia is shown to be included in the Western-Central European cluster, together with other Spanish populations. When only considering populations from Mediterranean Europe, the Galician population revealed a degree of genetic flow similar to that of the majority of the populations from this geographic area. Conclusion The results of this study reveal that the Galician population, despite its geographic situation in the western edge of the European continent, occupies an intermediate position in relation to other European populations in general, and Iberian

  14. Fine-scale population structure in Atlantic salmon from Maine's Penobscot River drainage

    USGS Publications Warehouse

    Spidle, A.P.; Bane, Schill W.; Lubinski, B.A.; King, T.L.

    2001-01-01

    We report a survey of micro satellite DNA variation in Atlantic salmon from the unimpounded lower reaches of Maine's Penobscot River. Our analysis indicates that Atlantic salmon in the Penobscot River are distinct from other populations that have little or no history of human-mediated repopulation, including two of its tributaries, Cove Brook and Kenduskeag Stream, another Maine river, the Ducktrap, and Canada's Miramichi and Gander rivers. Significant heterogeneity was detected in allele frequency among all three subpopulations sampled in the Penobscot drainage. The high resolution of the 12-locus suite was quantified using maximum likelihood assignment tests, which correctly identified the source of 90.4-96.1% of individuals from within the Penobscot drainage. Current populations are clearly isolated from each other, however we are unable to determine from the present data whether the populations in Cove Brook and Kenduskeag Stream are recently diverged from populations stocked into the Penobscot River over the last century, or are aboriginal in origin. The degree of population structure identified in the Penobscot drainage is noteworthy in light of its lengthy history of systematic restocking, the geographic proximity of the subpopulations, and the extent of the differentiation. Similar population structure on this extremely limited geographic scale could exist among Atlantic salmon runs elsewhere in Maine and throughout the species' range and should be taken into account for future management decisions.

  15. The application of mass and energy conservation laws in physiologically structured population models of heterotrophic organisms

    PubMed

    Kooijman; Kooi; Hallam

    1999-04-01

    Rules for energy uptake, and subsequent utilization, form the basis of population dynamics and, therefore, explain the dynamics of the ecosystem structure in terms of changes in standing crops and size distributions of individuals. Mass fluxes are concomitant with energy flows and delineate functional aspects of ecosystems by defining the roles of individuals and populations. The assumption of homeostasis of body components, and an assumption about the general structure of energy budgets, imply that mass fluxes can be written as weighted sums of three organizing energy fluxes with the weight coefficients determined by the conservation law of mass. These energy fluxes are assimilation, maintenance and growth, and provide a theoretical underpinning of the widely applied empirical method of indirect calorimetry, which relates dissipating heat linearly to three mass fluxes: carbon dioxide production, oxygen consumption and N-waste production. A generic approach to the stoichiometry of population energetics from the perspective of the individual organism is proposed and illustrated for heterotrophic organisms. This approach indicates that mass transformations can be identified by accounting for maintenance requirements and overhead costs for the various metabolic processes at the population level. The theoretical background for coupling the dynamics of the structure of communities to nutrient cycles, including the water balance, as well as explicit expressions for the dissipating heat at the population level are obtained based on the conservation law of energy. Specifications of the general theory employ the Dynamic Energy Budget model for individuals. Copyright 1999 Academic Press.

  16. Genetic structure of a lotic population of Burkholderia (Pseudomonas) cepacia

    SciTech Connect

    Wise, M.G.; Shimkets, L.J.; McArthur, J.V.

    1995-05-01

    The genetic structure of a population of Burkholderia (Pseudomonas) cepacia isolated from a southeastern blackwater stream was investigated by using multilocus enzyme electrophoresis to examine the allelic variation in eight structural gene loci. Overall, 213 isolates were collected at transect points along the stream continuum, from both the sediments along the bank and the water column. Multilocus enzyme electrophoresis analysis revealed 164 distinct electrophoretic types, and the mean genetic diversity of the entire population was 0.574. Genetic diversity values did not vary spatially along the stream continuum. From a canonical discriminant analysis, Mahalonobis distances (measurements of genetic similarity between populations) revealed significant differences among the subpopulations at the sediment sampling points, suggesting bacterial adaptation to a heterogeneous (or patchy) microgeographical environment. Multilocus linkage disequilibrium analysis of the isolates revealed only limited association between alleles, suggesting frequent recombination, relative to binary fission, in this population. Furthermore, the dendrogram created from the data of this study and the allele mismatch distribution are typical of a population characterized by extensive genetic mixing. We suggest that B. cepacia be added to the growing list of bacteria that are not obligatorily clonal. 41 refs., 5 figs., 3 tabs.

  17. Population structure and genetic analysis of narrow-clawed crayfish (Astacus leptodactylus) populations in Turkey.

    PubMed

    Akhan, Suleyman; Bektas, Yusuf; Berber, Selcuk; Kalayci, Gokhan

    2014-10-01

    The genetic differentiation among Turkish populations of the narrow-clawed crayfish was investigated using a partial sequence of cytochrome oxidase subunit I gene (585 bp) of 183 specimens from 17 different crayfish populations. Median joining network and all phylogenetic analyses disclosed a strong haplotype structure with three prominent clades diverged by a range between 20 and 50 mutations and substantial inter-group pairwise sequence divergence (5.19-6.95 %), suggesting the presence of three distinct clades within the Anatolian populations of Astacus leptodactylus. The divergence times among the three clades of Turkish A. leptodactylus are estimated to be 4.96-3.70 Mya using a molecular clock of 1.4 % sequence divergence per million years, pointing to a lower Pliocene separation. The high level of genetic variability (H d = 95.8 %, π = 4.17 %) and numerous private haplotypes suggest the presence of refugial populations in Anatolia unaffected by Pleistocene habitat restrictions. The pattern of genetic variation among Turkish A. leptodactylus populations, therefore, suggests that the unrevealed intraspecific genetic structure is independent of geographic tendency and congruent with the previously reported geographic distribution and number of subspecies (A. l. leptodactylus and A. l. salinus) of A. leptodactylus.

  18. Sexual networks: measuring sexual selection in structured, polyandrous populations.

    PubMed

    McDonald, Grant C; James, Richard; Krause, Jens; Pizzari, Tommaso

    2013-03-01

    Sexual selection is traditionally measured at the population level, assuming that populations lack structure. However, increasing evidence undermines this approach, indicating that intrasexual competition in natural populations often displays complex patterns of spatial and temporal structure. This complexity is due in part to the degree and mechanisms of polyandry within a population, which can influence the intensity and scale of both pre- and post-copulatory sexual competition. Attempts to measure selection at the local and global scale have been made through multi-level selection approaches. However, definitions of local scale are often based on physical proximity, providing a rather coarse measure of local competition, particularly in polyandrous populations where the local scale of pre- and post-copulatory competition may differ drastically from each other. These limitations can be solved by social network analysis, which allows us to define a unique sexual environment for each member of a population: 'local scale' competition, therefore, becomes an emergent property of a sexual network. Here, we first propose a novel quantitative approach to measure pre- and post-copulatory sexual selection, which integrates multi-level selection with information on local scale competition derived as an emergent property of networks of sexual interactions. We then use simple simulations to illustrate the ways in which polyandry can impact estimates of sexual selection. We show that for intermediate levels of polyandry, the proposed network-based approach provides substantially more accurate measures of sexual selection than the more traditional population-level approach. We argue that the increasing availability of fine-grained behavioural datasets provides exciting new opportunities to develop network approaches to study sexual selection in complex societies.

  19. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

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

    2009-01-01

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

  20. Sexual networks: measuring sexual selection in structured, polyandrous populations

    PubMed Central

    McDonald, Grant C.; James, Richard; Krause, Jens; Pizzari, Tommaso

    2013-01-01

    Sexual selection is traditionally measured at the population level, assuming that populations lack structure. However, increasing evidence undermines this approach, indicating that intrasexual competition in natural populations often displays complex patterns of spatial and temporal structure. This complexity is due in part to the degree and mechanisms of polyandry within a population, which can influence the intensity and scale of both pre- and post-copulatory sexual competition. Attempts to measure selection at the local and global scale have been made through multi-level selection approaches. However, definitions of local scale are often based on physical proximity, providing a rather coarse measure of local competition, particularly in polyandrous populations where the local scale of pre- and post-copulatory competition may differ drastically from each other. These limitations can be solved by social network analysis, which allows us to define a unique sexual environment for each member of a population: ‘local scale’ competition, therefore, becomes an emergent property of a sexual network. Here, we first propose a novel quantitative approach to measure pre- and post-copulatory sexual selection, which integrates multi-level selection with information on local scale competition derived as an emergent property of networks of sexual interactions. We then use simple simulations to illustrate the ways in which polyandry can impact estimates of sexual selection. We show that for intermediate levels of polyandry, the proposed network-based approach provides substantially more accurate measures of sexual selection than the more traditional population-level approach. We argue that the increasing availability of fine-grained behavioural datasets provides exciting new opportunities to develop network approaches to study sexual selection in complex societies. PMID:23339246

  1. A Spatial Framework for Understanding Population Structure and Admixture.

    PubMed

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

    2016-01-01

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

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

    USGS Publications Warehouse

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

    2006-01-01

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

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

    PubMed

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

    2004-08-01

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

  4. Types of marriages, population structure and genetic disease.

    PubMed

    Machado, T M B; Bomfim, T F; Souza, L V; Soares, N; Santos, F L; Acosta, A X; Abe-Sandes, K

    2013-07-01

    A high occurrence rate of consanguineous marriages may favour the onset and increased frequency of autosomal recessive diseases in a population. The population of Monte Santo, Bahia, Brazil, has a high frequency of rare genetic diseases such as mucopolysaccharidosis type VI, whose observed frequency in this population is 1:5000, while the incidence of this disease recorded in other regions of the world varies from 1:43,261 in Turkey to 1:1,505,160 in Switzerland. To verify the influence of consanguineous marriage on the increased frequency of observed genetic diseases in this population, the population structure and frequency of different types of marriage during different time periods were evaluated. A total of 9765 marriages were found in an analysis of parish marriage records from the city. Over three periods, 1860-1895, 1950-1961 and 1975-2010, the inbreeding rates were 37.1%, 13.2% and 4.2% respectively. Although there was a high rate of inbreeding, endogamic marriages were the dominant marriage type in all three periods. In the most recent period, there was an increase in the number of exogamous marriages and those among immigrants, but most of these occurred among individuals from cities that neighbour Monte Santo. The low rate of migration and high frequency of endogamic and consanguineous marriages show that growth of this population is predominantly internal and could explain the occurrence, and increase in frequency, of recessive genetic diseases in the city.

  5. A Spatial Framework for Understanding Population Structure and Admixture

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth. PMID:21684917

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

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

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

  8. Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.

    PubMed

    Pilot, Małgorzata; Jędrzejewski, Włodzimierz; Sidorovich, Vadim E; Meier-Augenstein, Wolfram; Hoelzel, A Rus

    2012-01-01

    Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13)C and δ(15)N values) for Eastern European wolves (Canis lupus) as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure), to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation) in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores. PMID:22768075

  9. Population Structure in a Comprehensive Genomic Data Set on Human Microsatellite Variation

    PubMed Central

    Pemberton, Trevor J.; DeGiorgio, Michael; Rosenberg, Noah A.

    2013-01-01

    Over the past two decades, microsatellite genotypes have provided the data for landmark studies of human population-genetic variation. However, the various microsatellite data sets have been prepared with different procedures and sets of markers, so that it has been difficult to synthesize available data for a comprehensive analysis. Here, we combine eight human population-genetic data sets at the 645 microsatellite loci they share in common, accounting for procedural differences in the production of the different data sets, to assemble a single data set containing 5795 individuals from 267 worldwide populations. We perform a systematic analysis of genetic relatedness, detecting 240 intra-population and 92 inter-population pairs of previously unidentified close relatives and proposing standardized subsets of unrelated individuals for use in future studies. We then augment the human data with a data set of 84 chimpanzees at the 246 loci they share in common with the human samples. Multidimensional scaling and neighbor-joining analyses of these data sets offer new insights into the structure of human populations and enable a comparison of genetic variation patterns in chimpanzees with those in humans. Our combined data sets are the largest of their kind reported to date and provide a resource for use in human population-genetic studies. PMID:23550135

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

    PubMed

    Lutz, Wolfgang; K C, Samir

    2010-09-27

    The total size of the world population is likely to increase from its current 7 billion to 8-10 billion by 2050. This uncertainty is because of unknown future fertility and mortality trends in different parts of the world. But the young age structure of the population and the fact that in much of Africa and Western Asia, fertility is still very high makes an increase by at least one more billion almost certain. Virtually, all the increase will happen in the developing world. For the second half of the century, population stabilization and the onset of a decline are likely. In addition to the future size of the population, its distribution by age, sex, level of educational attainment and place of residence are of specific importance for studying future food security. The paper provides a detailed discussion of different relevant dimensions in population projections and an evaluation of the methods and assumptions used in current global population projections and in particular those produced by the United Nations and by IIASA. PMID:20713384

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

    PubMed

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

    2014-06-01

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

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

    USGS Publications Warehouse

    Link, W.A.; Royle, J. Andrew; Hatfield, J.S.

    2003-01-01

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

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

    PubMed

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2016-01-01

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

  14. Visualizing spatial population structure with estimated effective migration surfaces

    PubMed Central

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2015-01-01

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

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

    PubMed

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

    2004-11-01

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

  16. Demographic History, Population Structure, and Local Adaptation in Alpine Populations of Cardamine impatiens and Cardamine resedifolia

    PubMed Central

    Ometto, Lino; Li, Mingai; Bresadola, Luisa; Barbaro, Enrico; Neteler, Markus; Varotto, Claudio

    2015-01-01

    Species evolution depends on numerous and distinct forces, including demography and natural selection. For example, local adaptation and population structure affect the evolutionary history of species living along environmental clines. This is particularly relevant in plants, which are often characterized by limited dispersal ability and the need to respond to abiotic and biotic stress factors specific to the local environment. Here we study the demographic history and the possible existence of local adaptation in two related species of Brassicaceae, Cardamine impatiens and Cardamine resedifolia, which occupy separate habitats along the elevation gradient. Previous genome-wide analyses revealed the occurrence of distinct selective pressures in the two species, with genes involved in cold response evolving particularly fast in C. resedifolia. In this study we surveyed patterns of molecular evolution and genetic variability in a set of 19 genes, including neutral and candidate genes involved in cold response, across 10 populations each of C. resedifolia and C. impatiens from the Italian Alps (Trentino). We inferred the population structure and demographic history of the two species, and tested the occurrence of signatures of local adaptation in these genes. The results indicate that, despite a slightly higher population differentiation in C. resedifolia than in C. impatiens, both species are only weakly structured and that populations sampled at high altitude experience less gene flow than low-altitude ones. None of the genes showed signatures of positive selection, suggesting that they do not seem to play relevant roles in the current evolutionary processes of adaptation to alpine environments of these species. PMID:25933225

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

    PubMed Central

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

    2011-01-01

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

  18. Transport and mixing of microbial population by atmospheric coherent structures

    NASA Astrophysics Data System (ADS)

    Bozorg Magham, A.; Ross, S. D.

    2012-12-01

    Lagrangian coherent structures (LCSs) provide a new means for discussion of spatiotemporal characteristics of the passive transport and mixing of atmospheric pathogen populations, paving the way for new management strategies regarding the spread of infectious diseases affecting plants, domestic animals, and humans, including identification of probable source regions and forecasts of regions at high risk. We report on the relationship of coherent structures to the patchiness of pathogen populations, and the effects of imperfect forecast wind data on the resultant LCSs. Regarding forecasting LCSs, our main contributions are to quantify the accuracy and sensitivity of such predictions with respect to the forecasting parameters. To obtain more reliable atmospheric LCS features, we have incorporated two more concepts. First is the effect of unresolved turbulent motion; this consideration leads to the stochastic finite-time Lyapunov exponent (SFTLE) field and the resultant stochastic LCS. The second concept is ensemble FTLE/LCS forecasting using individual members of the ensemble wind field forecasts.

  19. Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

    PubMed Central

    Kühnert, Denise; Stadler, Tanja; Vaughan, Timothy G.; Drummond, Alexei J.

    2016-01-01

    When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters. We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group. PMID:27189573

  20. Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.

    PubMed

    Kühnert, Denise; Stadler, Tanja; Vaughan, Timothy G; Drummond, Alexei J

    2016-08-01

    When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth-death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters.We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group. PMID:27189573

  1. Testing for genetic structure in different urban Argentinian populations.

    PubMed

    Toscanini, Ulises; Gusmão, Leonor; Berardi, Gabriela; Amorim, António; Carracedo, Angel; Salas, Antonio; Raimondi, Eduardo

    2007-01-01

    Fifteen autosomal short tandem repeat (STR) markers (D3S1358, HUMTH01, D21S11, D18S51, PENTA E, D5S818, D13S317, D7S820, D16S539, CSF1PO, PENTA D, HUMvWA, D8S1179, HUMTPOX, FGA) were analyzed in 1734 individuals living in urban areas of cities from six different Argentinian provinces (Buenos Aires, Neuquén, Tucumán, La Pampa, San Luis, Santa Cruz) in order to determine if a common urban database could be used in Argentina for forensic purposes. Frequencies estimates, Hardy-Weinberg equilibrium (HWE), and other parameters of forensic interest were computed. Comparisons between the six populations, and with published data from one Native American population from Argentina and other urban populations from Argentina and Europe were also performed. Our results reveal evidences for population structure, both when testing for genetic differentiation and when comparing frequencies distributions between different pairs of populations. Therefore, caution should be taken when using a common pooled database with general forensic purposes in Argentina.

  2. Algebraic moment closure for population dynamics on discrete structures.

    PubMed

    House, Thomas

    2015-04-01

    Moment closure on general discrete structures often requires one of the following: (i) an absence of short-closed loops (zero clustering); (ii) existence of a spatial scale; (iii) ad hoc assumptions. Algebraic methods are presented to avoid the use of such assumptions for populations based on clumps and are applied to both SIR and macroparasite disease dynamics. One approach involves a series of approximations that can be derived systematically, and another is exact and based on Lie algebraic methods.

  3. Development of paradigms for the dynamics of structured populations

    SciTech Connect

    Not Available

    1994-10-01

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

  4. 17 CFR 256.01-3 - General structure of accounting system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... accounting system. 256.01-3 Section 256.01-3 Commodity and Securities Exchanges SECURITIES AND EXCHANGE... accounting system. (a) The accounts provided herein are in two general categories: Balance sheet accounts and... account numbers in the Uniform System of Accounts for Public Utilities and Licensees (18 CFR Part 101)...

  5. [Population structure and distribution pattern of rare plant communities in Houhe Nature Reserve].

    PubMed

    Dang, Haishan; Jiang, Mingxi; Tian, Yuqiang; Huang, Handong; Jin, Xia

    2004-12-01

    An investigation on the size structure and spatial pattern of 26 major tree species with a diameter at breast height (DBH) > or = 5 cm was made on a 1 hm2 fixed plot in the mixed evergreen and deciduous broad-leaved forest in Houhe National Nature Reserve of Central China. The results showed that 7 populations of the 26 species, i.e., Dipteronia sinensi, Aesculus wilsonii, Pterostyrax psilophyllus, Davidia involucrate, Euptelea pleiosperma, Tetracentron sinense and Cercidiphyllum japonicum, were rare endangered, species, and two of the 7 populations, T. sinense and C. japonicum, were very limited in numbers. The population structure of P. psilophyllus was in declining, and that of the rest was in growing. The spatial distribution pattern of P. psilophyllus, A. wilsonii and T. sinense was in random, and that of the others was clumped. Among the other 19 non-rare populations, the population structure of P. wilsonii was in declining, that of D. lotus, A. palmatum, A. wilsonii, A. franchetii, M. cuneifolia and H. dulcis was stable, and the rest was in growing. The spatial distribution pattern of D. lotus and H. dulcis was in random, and that of the others was clumped. On the whole, the growing populations were dominant, amounting to 61.54%, and the stable and declining populations accounted for 6.92% and 11.54%, respectively. The results of the two judging methods were consistent, showing that the distribution pattern of clumping (80.77%) was dominant, while the random and even distribution patterns were infrequent.

  6. The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river.

    PubMed

    Olsen, J B; Beacham, T D; Wetklo, M; Seeb, L W; Smith, C T; Flannery, B G; Wenburg, J K

    2010-04-01

    Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.

  7. Spreading speeds for stage structured plant populations in fragmented landscapes.

    PubMed

    Gilbert, Mark A; White, Steven M; Bullock, James M; Gaffney, Eamonn A

    2014-05-21

    Landscape fragmentation has huge ecological and economic implications and affects the spatial dynamics of many plant species. Determining the speed of population spread in fragmented/heterogeneous landscapes is therefore of utmost importance to ecologists. Stage-structured integrodifference equations (IDEs) are deterministic models which accurately reflect the life cycles and dispersal patterns for numerous species. Existing approximations to wave-speeds consider only particular kernels, or landscapes in which the scale of variation is much smaller than the dispersal scale. We propose an analytical approximation to the wave-speeds of IDE solutions with periodic landscapes of alternating good and bad patches, where the dispersal scale is greater than the extent of each good patch and where the ratio of the demographic rates in the good and bad patches is given by a small parameter, denoted as ε. We formulate this approximation for the Gaussian and Laplace dispersal kernels and for stage structured and non-stage structured populations, and compare the results against numerical simulations. We find that the approximation is accurate for the landscapes considered, and that the type of dispersal kernel affects the relationship between landscape structure, as classified by landscape period and good patch size, and the spreading speed. This indicates that accurately fitting a kernel to data is important in determining the relationship between landscape structure and spreading speed.

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

    PubMed Central

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

    2016-01-01

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

  9. Social structuring of mammalian populations and rate of chromosomal evolution.

    PubMed

    Wilson, A C; Bush, G L; Case, S M; King, M C

    1975-12-01

    To test the hypothesis that the evolution of organisms is dependent to a large degree on gene rearrangement, we devised a way of estimating rates of evolutionary change in karyotype. This non-biochemical method is based on consideration of chromosomal variability within taxonomic groups having a fossil record. The results show that chromosomal evolution has been faster in placental mammals than in other vertebrates or molluscs. This finding is consistent with published evidence that placentals have also been evolving unusually fast in anatomy and way of life. However, the structural genes of placentals seem not to have experienced accelerated evolution. Possibly, therefore, anatomical evolution may be facilitated by gene rearrangement. To explain how placentals achieved this rate of chromosomal evolution, we consider the process by which a new gene arrangement becomes fixed and spreads. The structure and dynamics of placental populations may be especially favorable for this process. The key factor involved seems to be the type of social behavior which produces small effective population sizes and inbreeding. As Bush points out elsewhere, such social structuring of populations may promote rapid fixation of gene rearrangements and rapid speciation.

  10. Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial.

    PubMed

    Le, Si Quang; Gascuel, Olivier

    2010-05-01

    Amino acid substitution models are essential to most methods to infer phylogenies from protein data. These models represent the ways in which proteins evolve and substitutions accumulate along the course of time. It is widely accepted that the substitution processes vary depending on the structural configuration of the protein residues. However, this information is very rarely used in phylogenetic studies, though the 3-dimensional structure of dozens of thousands of proteins has been elucidated. Here, we reinvestigate the question in order to fill this gap. We use an improved estimation methodology and a very large database comprising 1471 nonredundant globular protein alignments with structural annotations to estimate new amino acid substitution models accounting for the secondary structure and solvent accessibility of the residues. These models incorporate a confidence coefficient that is estimated from the data and reflects the reliability and usefulness of structural annotations in the analyzed sequences. Our results with 300 independent test alignments show an impressive likelihood gain compared with standard models such as JTT or WAG. Moreover, the use of these models induces significant topological changes in the inferred trees, which should be of primary interest to phylogeneticists. Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/.

  11. Finite Element Analysis of Layered Fiber Composite Structures Accounting for the Material's Microstructure and Delamination

    NASA Astrophysics Data System (ADS)

    Stier, Bertram; Simon, Jaan-Willem; Reese, Stefanie

    2015-04-01

    The present paper focuses on composite structures which consist of several layers of carbon fiber reinforced plastics (CFRP). For such layered composite structures, delamination constitutes one of the major failure modes. Predicting its initiation is essential for the design of these composites. Evaluating stress-strength relation based onset criteria requires an accurate representation of the through-the-thickness stress distribution, which can be particularly delicate in the case of shell-like structures. Thus, in this paper, a solid-shell finite element formulation is utilized which allows to incorporate a fully three-dimensional material model while still being suitable for applications involving thin structures. Moreover, locking phenomena are cured by using both the EAS and the ANS concept, and numerical efficiency is ensured through reduced integration. The proposed anisotropic material model accounts for the material's micro-structure by using the concept of structural tensors. It is validated by comparison to experimental data as well as by application to numerical examples.

  12. Punishment can promote defection in group-structured populations.

    PubMed

    Powers, Simon T; Taylor, Daniel J; Bryson, Joanna J

    2012-10-21

    Pro-social punishment, whereby cooperators punish defectors, is often suggested as a mechanism that maintains cooperation in large human groups. Importantly, models that support this idea have to date only allowed defectors to be the target of punishment. However, recent empirical work has demonstrated the existence of anti-social punishment in public goods games. That is, individuals that defect have been found to also punish cooperators. Some recent theoretical studies have found that such anti-social punishment can prevent the evolution of pro-social punishment and cooperation. However, the evolution of anti-social punishment in group-structured populations has not been formally addressed. Previous work has informally argued that group-structure must favour pro-social punishment. Here we formally investigate how two demographic factors, group size and dispersal frequency, affect selection pressures on pro- and anti-social punishment. Contrary to the suggestions of previous work, we find that anti-social punishment can prevent the evolution of pro-social punishment and cooperation under a range of group structures. Given that anti-social punishment has now been found in all studied extant human cultures, the claims of previous models showing the co-evolution of pro-social punishment and cooperation in group-structured populations should be re-evaluated.

  13. Differentiation and displacement: Unpicking the relationship between accounts of illness and social structure

    PubMed Central

    Gibson, Barry J; Paul, Ninu R

    2014-01-01

    This article seeks to unpack the relationship between social structure and accounts of illness. Taking dentine hypersensitivity as an example, this article explores the perspective that accounts of illness are sense-making processes that draw on a readily available pool of meaning. This pool of meaning is composed of a series of distinctions that make available a range of different lines of communication and action about such conditions. Such lines of communication are condensed and preserved over time and are often formed around a concept and its counter concept. The study of such processes is referred to as semantic analysis and involves drawing on the tools and techniques of conceptual history. This article goes on to explore how the semantics of dentine hypersensitivity developed. It illustrates how processes of social differentiation led to the concept being separated from the more dominant concept of dentine sensitivity and how it was medicalised, scientised and economised. In short, this study seeks to present the story of how society has developed a specific language for communicating about sensitivity and hypersensitivity in teeth. In doing so, it proposes that accounts of dentine hypersensitivity draw on lines of communication that society has preserved over time. PMID:25197262

  14. Opinion Dynamics in Populations with Implicit Community Structure

    NASA Astrophysics Data System (ADS)

    Si, Xiameng; Liu, Yun; Zhang, Zhenjiang

    Web encounter facilitate contacts between people from different communities outside space and time. Implicit Community Structure is exhibited because of highly connected links within community and sparse encounters between communities. Considering the imperceptible influence of encounter on opinions, Sznajd updating rules are used to mimic people's behaviors after encountering a stranger in another community. We introduce a model for opinion evolution, in which the interconnectivity between different communities is represented as encounter frequency, and leadership is introduced to control the strength of community's opinion guide. In this scenario, the effects of Implicit Community Structure of contact network on opinion evolution, for asymmetric and random initial distribution but with heterogeneous opinion guide, are investigated respectively. It is shown that large encounter frequency favors consensus of the whole populations and successful opinion spreading, which is qualitatively agree with the results observed in Majority model defined on substrates with predefined community structure.

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

    PubMed Central

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

    2003-01-01

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

  16. Multi-layered population structure in Island Southeast Asians

    PubMed Central

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

    2016-01-01

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

  17. Genetic and environmental determinants of insect herbivore community structure in a Betula pendula population

    PubMed Central

    Silfver, Tarja

    2014-01-01

    A number of recent studies have shown that intraspecific genetic variation of plants may have a profound effect on the herbivorous communities which depend on them. However less is known about the relative importance of intraspecific variation compared to other ecological factors, for example environmental variation or the effects of herbivore damage. We randomly selected 22 Betula pendula genotypes from a local population (< 0.9 ha), cloned them and planted cloned seedlings on two study sites separated at a regional scale (distance between sites about 30 km) to examine an insect community of 23-27 species on these genotypes. B. pendula genotypes did not differ in their species richness, but the total mean abundance and the structure of the insect herbivore community was significantly affected by the genotype, which could account for up to 27% of the total variation in community structure. B. pendula genotype accounted for two to four times more variation in the arthropod community structure than did environmental (block) variation on a local scale, while on a regional scale, genotypic and environmental (site) variation accounted for 4-14% of the arthropod community structure. The genetic effects were modified by environmental variation on both a local and regional scale over one study year, and locally, the largest part of the variation (38%) could be explained by the genotype × environment (block) interactions. Suppression of insect herbivores during one growing season led to changed arthropod community structure in the following growing season, but this effect was minimal and could explain only 4% of the total variation in insect community structure. Our results suggest that both genetic and environmental factors are important determinants of the community structure of herbivorous insects. Together these mechanisms appear to maintain the high diversity of insects in B. pendula forest ecosystems. PMID:24715977

  18. Referring expressions and structural language abilities in children with specific language impairment: A pragmatic tolerance account.

    PubMed

    Davies, Catherine; Andrés-Roqueta, Clara; Norbury, Courtenay Frazier

    2016-04-01

    Specific language impairment (SLI) has traditionally been characterized as a deficit of structural language (specifically grammar), with relative strengths in pragmatics. In this study, comprehensive assessment of production, comprehension, and metalinguistic judgment of referring expressions revealed that children with SLI have weaknesses in both structural and pragmatic language skills relative to age-matched peers. Correlational analyses highlight a relationship between their performance on the experimental tasks and their structural language ability. Despite their poor performance on the production and comprehension tasks, children with SLI were able to recognize pragmatically under-informative reference relative to other types of utterance, although they imposed a less severe penalty on such expressions than typically developing peers, a pattern that supports the pragmatic tolerance account. Our novel methodology (which probed structural abilities from both the speaker's and hearer's perspectives as well as metalinguistic and pragmatic skills in the same sample) challenges the assumption that pragmatic errors stem from deficits in social cognition and instead supports recent findings suggesting that when the impact of structural language is isolated, pragmatic deficits may be resolved.

  19. Referring expressions and structural language abilities in children with specific language impairment: A pragmatic tolerance account.

    PubMed

    Davies, Catherine; Andrés-Roqueta, Clara; Norbury, Courtenay Frazier

    2016-04-01

    Specific language impairment (SLI) has traditionally been characterized as a deficit of structural language (specifically grammar), with relative strengths in pragmatics. In this study, comprehensive assessment of production, comprehension, and metalinguistic judgment of referring expressions revealed that children with SLI have weaknesses in both structural and pragmatic language skills relative to age-matched peers. Correlational analyses highlight a relationship between their performance on the experimental tasks and their structural language ability. Despite their poor performance on the production and comprehension tasks, children with SLI were able to recognize pragmatically under-informative reference relative to other types of utterance, although they imposed a less severe penalty on such expressions than typically developing peers, a pattern that supports the pragmatic tolerance account. Our novel methodology (which probed structural abilities from both the speaker's and hearer's perspectives as well as metalinguistic and pragmatic skills in the same sample) challenges the assumption that pragmatic errors stem from deficits in social cognition and instead supports recent findings suggesting that when the impact of structural language is isolated, pragmatic deficits may be resolved. PMID:26716575

  20. Multilocus models in the infinite island model of population structure.

    PubMed

    Roze, Denis; Rousset, François

    2008-06-01

    Different methods have been developed to consider the effects of statistical associations among genes that arise in population genetics models: kin selection models deal with associations among genes present in different interacting individuals, while multilocus models deal with associations among genes at different loci. It was pointed out recently that these two types of models are very similar in essence. In this paper, we present a method to construct multilocus models in the infinite island model of population structure (where deme size may be arbitrarily small). This method allows one to compute recursions on allele frequencies, and different types of genetic associations (including associations between different individuals from the same deme), and incorporates selection. Recursions can be simplified using quasi-equilibrium approximations; however, we show that quasi-equilibrium calculations for associations that are different from zero under neutrality must include a term that has not been previously considered. The method is illustrated using simple examples.

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

    PubMed Central

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

    2013-01-01

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

  2. Evolutionary dynamics of rhizopine within spatially structured rhizobium populations

    PubMed Central

    Simms, E. L.; Bever, J. D.

    1998-01-01

    Symbiosis between legumes and nitrogen-fixing bacteria is thought to bring mutual benefit to each participant. However, it is not known how rhizobia benefit from nodulating legume hosts because they fix nitrogen only after becoming bacteroids, which are terminally differentiated cells that cannot reproduce. Because undifferentiated rhizobia in and around the nodule can reproduce, evolution of symbiotic nitrogen fixation may depend upon kin selection. In some hosts, these kin may persist in the nodule as viable, undifferentiated bacteria. In other hosts, no viable rhizobia survive to reproduce after nodule senescence. Bacteroids in these hosts may benefit their free-living kin by enhancing production of plant root exudates. However, unrelated non-mutualists may also benefit from increased plant exudates. Rhizopines, compounds produced by bacteroids in nodules and catabolized only by related free-living rhizobia, may provide a mechanism by which bacteroids can preferentially benefit kin. Despite this apparent advantage, rhizopine genotypes are relatively rare. We constructed a mathematical model to examine how mixing within rhizobium populations influences the evolution of rhizopine genotypes. Our model predicts that the success of rhizopine genotypes is strongly dependent upon the spatial genetic structure of the bacterial population; rhizopine is more likely to dominate well-mixed populations. Further, for a given level of mixing, we find that rhizopine evolves under a positive frequency-dependent process in which stochastic accumulation of rhizopine alleles is necessary for rhizopine establishment. This process leads to increased spatial structure in rhizobium populations, and suggests that rhizopine may expand the conditions under which nitrogen fixation can evolve via kin selection.

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-01-01

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

  5. Complex transition to cooperative behavior in a structured population model.

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  7. Fine resolution mapping of population age-structures for health and development applications

    PubMed Central

    Alegana, V. A.; Atkinson, P. M.; Pezzulo, C.; Sorichetta, A.; Weiss, D.; Bird, T.; Erbach-Schoenberg, E.; Tatem, A. J.

    2015-01-01

    The age-group composition of populations varies considerably across the world, and obtaining accurate, spatially detailed estimates of numbers of children under 5 years is important in designing vaccination strategies, educational planning or maternal healthcare delivery. Traditionally, such estimates are derived from population censuses, but these can often be unreliable, outdated and of coarse resolution for resource-poor settings. Focusing on Nigeria, we use nationally representative household surveys and their cluster locations to predict the proportion of the under-five population in 1 × 1 km using a Bayesian hierarchical spatio-temporal model. Results showed that land cover, travel time to major settlements, night-time lights and vegetation index were good predictors and that accounting for fine-scale variation, rather than assuming a uniform proportion of under 5 year olds can result in significant differences in health metrics. The largest gaps in estimated bednet and vaccination coverage were in Kano, Katsina and Jigawa. Geolocated household surveys are a valuable resource for providing detailed, contemporary and regularly updated population age-structure data in the absence of recent census data. By combining these with covariate layers, age-structure maps of unprecedented detail can be produced to guide the targeting of interventions in resource-poor settings. PMID:25788540

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

    PubMed

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

    2015-08-01

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

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

    PubMed

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

    2015-08-01

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

  10. Genetic Diversity and Population Structure of Theileria annulata in Oman

    PubMed Central

    Al-Hamidhi, Salama; H. Tageldin, Mohammed.; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H.; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Background Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Methods Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. Results We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST

  11. A reduced progenitor pool population accounts for the rudimentary appearance of the septum, medial pallium and dorsal pallium in birds.

    PubMed

    Charvet, Christine J

    2010-01-01

    To date, most studies comparing birds and mammals have focused on the similarities in brain development, architecture and connectivity. However, major differences in size, anatomy and organization exist in the telencephalon of adult birds and mammals. For instance, the septum, medial pallium and dorsal pallium of birds appear rudimentary compared with those of mammals. To identify the developmental processes that give rise to this difference in size and anatomy of the septum, medial pallium and dorsal pallium, the thickness of the ventricular zone that encompasses these regions was measured in embryonic birds (i.e. chickens, sparrows) and mammals (i.e. rabbits, hedgehogs, shrews, platypus). Cumulative bromodeoxyuridine (BrdU) labeling in chickens at embryonic day 7 and 8 was also used to examine levels of cell proliferation in the ventricular zone of the septum, medial pallium and dorsal pallium. The study's main finding is that the ventricular zone of the septum, medial pallium and dorsal pallium is thinner in birds than in mammals. In chickens, the septum, medial pallium and dorsal pallium ventricular zone harbor few proliferating (i.e. BrdU+) cells. Collectively, these findings suggest that a reduced progenitor pool population account for the 'rudimentary' appearance of the avian septum, medial pallium and dorsal pallium. PMID:21135539

  12. The effects of demographic change on disease transmission and vaccine impact in a household structured population.

    PubMed

    Geard, Nicholas; Glass, Kathryn; McCaw, James M; McBryde, Emma S; Korb, Kevin B; Keeling, Matt J; McVernon, Jodie

    2015-12-01

    The demographic structure of populations in both more developed and less developed countries is changing: increases in life expectancy and declining fertility have led to older populations and smaller households. The implications of these demographic changes for the spread and control of infectious diseases are not fully understood. Here we use an individual based model with realistic and dynamic age and household structure to demonstrate the marked effect that demographic change has on disease transmission at the population and household level. The decline in fertility is associated with a decrease in disease incidence and an increase in the age of first infection, even in the absence of vaccination or other control measures. Although large households become rarer as fertility decreases, we show that there is a proportionate increase in incidence of disease in these households as the accumulation of susceptible clusters increases the potential for explosive outbreaks. By modelling vaccination, we provide a direct comparison of the relative importance of demographic change and vaccination on incidence of disease. We highlight the increased risks associated with unvaccinated households in a low fertility setting if vaccine behaviour is correlated with household membership. We suggest that models that do not account for future demographic change, and especially its effect on household structure, may potentially overestimate the impact of vaccination. PMID:26616042

  13. Molecular advances in understanding social insect population structure.

    PubMed

    Crozier, R H; Oldroyd, B P; Tay, W T; Kaufmann, B E; Johnson, R N; Carew, M E; Jennings, K M

    1997-08-01

    Social insects present many phenomena seen in all organisms but in more extreme forms and with larger sample sizes than those observable in most natural populations of vertebrates. Microsatellites are proving very much more informative than allozymes for the analysis of population biological problems, and prolifically polymorphic markers are fairly readily developed. In addition, the male-haploid genetic system of many social insects facilitates genetic analysis. The ability to amplify DNA from sperm stored in a female's sperm storage device enables the determination of mating types long after the death of the short-lived males, in addition to information on the degree of mixing of sperm from different males. Mitochondrial (mt) DNA sequences are also proving important, not only in phylogenetic studies but also in molecular population genetics, as a tracer of female movements. Mitochondrial markers have definitively shown the movement of females between colonies, challenging models giving exclusive primacy to kin selection as the explanation for multiqueen colonies, in Australian meat ants, Iridomyrmex purpureus, and the aridzone queenless ant Rhytidoponera sp. 12. Microsatellite and mtDNA variation are being studied in Camponotus consobrinus sugar ants, showing an unexpected diversity of complexity in colony structure, and microsatellites have shown that transfer of ants between nests of the weaver ant Polyrhachis doddi must be slight, despite an apparent lack of hostility.

  14. Competitive intransitivity, population interaction structure, and strategy coexistence.

    PubMed

    Laird, Robert A; Schamp, Brandon S

    2015-01-21

    Intransitive competition occurs when competing strategies cannot be listed in a hierarchy, but rather form loops-as in the game rock-paper-scissors. Due to its cyclic competitive replacement, competitive intransitivity promotes strategy coexistence, both in rock-paper-scissors and in higher-richness communities. Previous work has shown that this intransitivity-mediated coexistence is strongly influenced by spatially explicit interactions, compared to when populations are well mixed. Here, we extend and broaden this line of research and examine the impact on coexistence of intransitive competition taking place on a continuum of small-world networks linking spatial lattices and regular random graphs. We use simulations to show that the positive effect of competitive intransitivity on strategy coexistence holds when competition occurs on networks toward the spatial end of the continuum. However, in networks that are sufficiently disordered, increasingly violent fluctuations in strategy frequencies can lead to extinctions and the prevalence of monocultures. We further show that the degree of disorder that leads to the transition between these two regimes is positively dependent on population size; indeed for very large populations, intransitivity-mediated strategy coexistence may even be possible in regular graphs with completely random connections. Our results emphasize the importance of interaction structure in determining strategy dynamics and diversity.

  15. Spatial structure of the spider crab, Maja brachydactyla population: Evidence of metapopulation structure

    NASA Astrophysics Data System (ADS)

    Corgos, Antonio; Bernárdez, Cristina; Sampedro, Paz; Verísimo, Patricia; Freire, Juan

    2011-08-01

    Distribution and spatial population structure of the spider crab, Maja brachydactyla, in the Ría de A Coruña (NW Spain) and adjacent coastal area was analysed. Sampling was done with experimental traps placed in three shallow bottom sampling stations and the central channel of the Ría, from December 1997 to November 1999. Crabs were tagged to study their movements on a small scale (1-10 km). Mean catches were substantially higher in the inner Ría station (Bastiagueiro) and were significantly higher in sandy substrates. Crabs inhabiting rocky bottoms moved to sandy bottoms from summer to autumn. Two local populations comprising mainly juveniles were identified —one located in Bastiagueiro and the other in Canide. There was no evidence of any major exchange between the juveniles of the two populations nor were juveniles observed to move towards deeper zones. Most of these juveniles reached maturity in summer and migrated to deeper waters. Adult catches and the recaptured specimens from both the experimental sampling and the commercial fishery indicate that the local Bastiagueiro population contributes a much greater number of individuals to the adult crab population in deep waters than does the Canide population. The spatial structure of the population of M. brachydactyla in the Ría de A Coruña may be defined as a part of a postlarval metapopulation made up of two shallow water local juvenile crab populations that migrate to deeper waters after attaining maturity. A pool of adults (and indirectly of larvae) from several local populations is formed in deeper waters. There is strong evidence that local populations are linked by larval dispersal.

  16. Structuring a Competency-Based Accounting Communication Course at the Graduate Level

    ERIC Educational Resources Information Center

    Sharifi, Mohsen; McCombs, Gary B.; Fraser, Linda Lussy; McCabe, Robert K.

    2009-01-01

    The authors describe a graduate capstone accounting class as a basis for building communication skills desired by both accounting practitioners and accounting faculty. An academic service-learning (ASL) component is included. Adopted as a required class for a master of science degree in accounting at two universities, this course supports…

  17. Estimating the Number of Subpopulations (K) in Structured Populations.

    PubMed

    Verity, Robert; Nichols, Richard A

    2016-08-01

    A key quantity in the analysis of structured populations is the parameter K, which describes the number of subpopulations that make up the total population. Inference of K ideally proceeds via the model evidence, which is equivalent to the likelihood of the model. However, the evidence in favor of a particular value of K cannot usually be computed exactly, and instead programs such as Structure make use of heuristic estimators to approximate this quantity. We show-using simulated data sets small enough that the true evidence can be computed exactly-that these heuristics often fail to estimate the true evidence and that this can lead to incorrect conclusions about K Our proposed solution is to use thermodynamic integration (TI) to estimate the model evidence. After outlining the TI methodology we demonstrate the effectiveness of this approach, using a range of simulated data sets. We find that TI can be used to obtain estimates of the model evidence that are more accurate and precise than those based on heuristics. Furthermore, estimates of K based on these values are found to be more reliable than those based on a suite of model comparison statistics. Finally, we test our solution in a reanalysis of a white-footed mouse data set. The TI methodology is implemented for models both with and without admixture in the software MavericK1.0. PMID:27317680

  18. Leveraging hierarchical population structure in discrete association studies.

    PubMed

    Carlson, Jonathan; Kadie, Carl; Mallal, Simon; Heckerman, David

    2007-01-01

    Population structure can confound the identification of correlations in biological data. Such confounding has been recognized in multiple biological disciplines, resulting in a disparate collection of proposed solutions. We examine several methods that correct for confounding on discrete data with hierarchical population structure and identify two distinct confounding processes, which we call coevolution and conditional influence. We describe these processes in terms of generative models and show that these generative models can be used to correct for the confounding effects. Finally, we apply the models to three applications: identification of escape mutations in HIV-1 in response to specific HLA-mediated immune pressure, prediction of coevolving residues in an HIV-1 peptide, and a search for genotypes that are associated with bacterial resistance traits in Arabidopsis thaliana. We show that coevolution is a better description of confounding in some applications and conditional influence is better in others. That is, we show that no single method is best for addressing all forms of confounding. Analysis tools based on these models are available on the internet as both web based applications and downloadable source code at http://atom.research.microsoft.com/bio/phylod.aspx.

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

    PubMed

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

    2013-08-01

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

  20. Population structure of a vector-borne plant parasite.

    PubMed

    Yule, Kelsey M; Koop, Jennifer A H; Alexandre, Nicolas M; Johnston, Lauren R; Whiteman, Noah K

    2016-07-01

    Parasites are among the most diverse groups of life on Earth, yet complex natural histories often preclude studies of their speciation processes. The biology of parasitic plants facilitates in situ collection of data on both genetic structure and the mechanisms responsible for that structure. Here, we studied the role of mating, dispersal and establishment in host race formation of a parasitic plant. We investigated the population genetics of a vector-borne desert mistletoe (Phoradendron californicum) across two legume host tree species (Senegalia greggii and Prosopis velutina) in the Sonoran desert using microsatellites. Consistent with host race formation, we found strong host-associated genetic structure in sympatry, little genetic variation due to geographic site and weak isolation by distance. We hypothesize that genetic differentiation results from differences in the timing of mistletoe flowering by host species, as we found initial flowering date of individual mistletoes correlated with genetic ancestry. Hybrids with intermediate ancestry were detected genetically. Individuals likely resulting from recent, successful establishment events following dispersal between the host species were detected at frequencies similar to hybrids between host races. Therefore, barriers to gene flow between the host races may have been stronger at mating than at dispersal. We also found higher inbreeding and within-host individual relatedness values for mistletoes on the more rare and isolated host species (S. greggii). Our study spanned spatial scales to address how interactions with both vectors and hosts influence parasitic plant structure with implications for parasite virulence evolution and speciation.

  1. Networks and Models with Heterogeneous Population Structure in Epidemiology

    NASA Astrophysics Data System (ADS)

    Kao, R. R.

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

  2. Causal Inference in Occupational Epidemiology: Accounting for the Healthy Worker Effect by Using Structural Nested Models

    PubMed Central

    Naimi, Ashley I.; Richardson, David B.; Cole, Stephen R.

    2013-01-01

    In a recent issue of the Journal, Kirkeleit et al. (Am J Epidemiol. 2013;177(11):1218–1224) provided empirical evidence for the potential of the healthy worker effect in a large cohort of Norwegian workers across a range of occupations. In this commentary, we provide some historical context, define the healthy worker effect by using causal diagrams, and use simulated data to illustrate how structural nested models can be used to estimate exposure effects while accounting for the healthy worker survivor effect in 4 simple steps. We provide technical details and annotated SAS software (SAS Institute, Inc., Cary, North Carolina) code corresponding to the example analysis in the Web Appendices, available at http://aje.oxfordjournals.org/. PMID:24077092

  3. Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars

    PubMed Central

    Winkler, Louisa R.; Michael Bonman, J.; Chao, Shiaoman; Admassu Yimer, B.; Bockelman, Harold; Esvelt Klos, Kathy

    2016-01-01

    Population structure and genetic architecture of phenotypic traits in oat (Avena sativa L.) remain relatively under-researched compared to other small grain species. This study explores the historic context of current elite germplasm, including phenotypic and genetic characterization, with a particular focus on identifying under-utilized areas. A diverse panel of cultivated oat accessions was assembled from the USDA National Small Grains Collection to represent a gene pool relatively unaffected by twentieth century breeding activity and unlikely to have been included in recent molecular studies. The panel was genotyped using an oat iSelect 6K beadchip SNP array. The final dataset included 759 unique individuals and 2,715 polymorphic markers. Some population structure was apparent, with the first three principal components accounting for 38.8% of variation and 73% of individuals belonging to one of three clusters. One cluster with high genetic distinctness appears to have been largely overlooked in twentieth century breeding. Classification and phenotype data provided by the Germplasm Resources Information Network were evaluated for their relationship to population structure. Of the structuring variables evaluated, improvement status (cultivar or landrace) was relatively unimportant, indicating that landraces and cultivars included in the panel were all sampled from a similar underlying population. Instead, lemma color and region of origin showed the strongest explanatory power. An exploratory association mapping study of the panel using a subset of 2,588 mapped markers generated novel indications of genomic regions associated with awn frequency, kernels per spikelet, lemma color, and panicle type. Further results supported previous findings of loci associated with barley yellow dwarf virus tolerance, crown rust (caused by Puccinia coronata f. sp. avenae) resistance, days to anthesis, and growth habit (winter/spring). In addition, two novel loci were identified for

  4. Population Structure and Genotype-Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars.

    PubMed

    Winkler, Louisa R; Michael Bonman, J; Chao, Shiaoman; Admassu Yimer, B; Bockelman, Harold; Esvelt Klos, Kathy

    2016-01-01

    Population structure and genetic architecture of phenotypic traits in oat (Avena sativa L.) remain relatively under-researched compared to other small grain species. This study explores the historic context of current elite germplasm, including phenotypic and genetic characterization, with a particular focus on identifying under-utilized areas. A diverse panel of cultivated oat accessions was assembled from the USDA National Small Grains Collection to represent a gene pool relatively unaffected by twentieth century breeding activity and unlikely to have been included in recent molecular studies. The panel was genotyped using an oat iSelect 6K beadchip SNP array. The final dataset included 759 unique individuals and 2,715 polymorphic markers. Some population structure was apparent, with the first three principal components accounting for 38.8% of variation and 73% of individuals belonging to one of three clusters. One cluster with high genetic distinctness appears to have been largely overlooked in twentieth century breeding. Classification and phenotype data provided by the Germplasm Resources Information Network were evaluated for their relationship to population structure. Of the structuring variables evaluated, improvement status (cultivar or landrace) was relatively unimportant, indicating that landraces and cultivars included in the panel were all sampled from a similar underlying population. Instead, lemma color and region of origin showed the strongest explanatory power. An exploratory association mapping study of the panel using a subset of 2,588 mapped markers generated novel indications of genomic regions associated with awn frequency, kernels per spikelet, lemma color, and panicle type. Further results supported previous findings of loci associated with barley yellow dwarf virus tolerance, crown rust (caused by Puccinia coronata f. sp. avenae) resistance, days to anthesis, and growth habit (winter/spring). In addition, two novel loci were identified for

  5. Population Structure and Genotype-Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars.

    PubMed

    Winkler, Louisa R; Michael Bonman, J; Chao, Shiaoman; Admassu Yimer, B; Bockelman, Harold; Esvelt Klos, Kathy

    2016-01-01

    Population structure and genetic architecture of phenotypic traits in oat (Avena sativa L.) remain relatively under-researched compared to other small grain species. This study explores the historic context of current elite germplasm, including phenotypic and genetic characterization, with a particular focus on identifying under-utilized areas. A diverse panel of cultivated oat accessions was assembled from the USDA National Small Grains Collection to represent a gene pool relatively unaffected by twentieth century breeding activity and unlikely to have been included in recent molecular studies. The panel was genotyped using an oat iSelect 6K beadchip SNP array. The final dataset included 759 unique individuals and 2,715 polymorphic markers. Some population structure was apparent, with the first three principal components accounting for 38.8% of variation and 73% of individuals belonging to one of three clusters. One cluster with high genetic distinctness appears to have been largely overlooked in twentieth century breeding. Classification and phenotype data provided by the Germplasm Resources Information Network were evaluated for their relationship to population structure. Of the structuring variables evaluated, improvement status (cultivar or landrace) was relatively unimportant, indicating that landraces and cultivars included in the panel were all sampled from a similar underlying population. Instead, lemma color and region of origin showed the strongest explanatory power. An exploratory association mapping study of the panel using a subset of 2,588 mapped markers generated novel indications of genomic regions associated with awn frequency, kernels per spikelet, lemma color, and panicle type. Further results supported previous findings of loci associated with barley yellow dwarf virus tolerance, crown rust (caused by Puccinia coronata f. sp. avenae) resistance, days to anthesis, and growth habit (winter/spring). In addition, two novel loci were identified for

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

    PubMed Central

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

    2014-01-01

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

  7. The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem.

    PubMed

    Puechmaille, Sebastien J

    2016-05-01

    Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of ecology, evolutionary biology and conservation biology. Such population structure inferences are routinely investigated via the program structure implementing a Bayesian algorithm to identify groups of individuals at Hardy-Weinberg and linkage equilibrium. While the method is performing relatively well under various population models with even sampling between subpopulations, the robustness of the method to uneven sample size between subpopulations and/or hierarchical levels of population structure has not yet been tested despite being commonly encountered in empirical data sets. In this study, I used simulated and empirical microsatellite data sets to investigate the impact of uneven sample size between subpopulations and/or hierarchical levels of population structure on the detected population structure. The results demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure and downward-biased estimates of the true number of subpopulations. Distinct subpopulations with reduced sampling tended to be merged together, while at the same time, individuals from extensively sampled subpopulations were generally split, despite belonging to the same panmictic population. Four new supervised methods to detect the number of clusters were developed and tested as part of this study and were found to outperform the existing methods using both evenly and unevenly sampled data sets. Additionally, a subsampling strategy aiming to reduce sampling unevenness between subpopulations is presented and tested. These results altogether demonstrate that when sampling evenness is accounted for, the detection of the correct population structure is greatly improved.

  8. Accounting for Sampling Error When Inferring Population Synchrony from Time-Series Data: A Bayesian State-Space Modelling Approach with Applications

    PubMed Central

    Santin-Janin, Hugues; Hugueny, Bernard; Aubry, Philippe; Fouchet, David; Gimenez, Olivier; Pontier, Dominique

    2014-01-01

    Background Data collected to inform time variations in natural population size are tainted by sampling error. Ignoring sampling error in population dynamics models induces bias in parameter estimators, e.g., density-dependence. In particular, when sampling errors are independent among populations, the classical estimator of the synchrony strength (zero-lag correlation) is biased downward. However, this bias is rarely taken into account in synchrony studies although it may lead to overemphasizing the role of intrinsic factors (e.g., dispersal) with respect to extrinsic factors (the Moran effect) in generating population synchrony as well as to underestimating the extinction risk of a metapopulation. Methodology/Principal findings The aim of this paper was first to illustrate the extent of the bias that can be encountered in empirical studies when sampling error is neglected. Second, we presented a space-state modelling approach that explicitly accounts for sampling error when quantifying population synchrony. Third, we exemplify our approach with datasets for which sampling variance (i) has been previously estimated, and (ii) has to be jointly estimated with population synchrony. Finally, we compared our results to those of a standard approach neglecting sampling variance. We showed that ignoring sampling variance can mask a synchrony pattern whatever its true value and that the common practice of averaging few replicates of population size estimates poorly performed at decreasing the bias of the classical estimator of the synchrony strength. Conclusion/Significance The state-space model used in this study provides a flexible way of accurately quantifying the strength of synchrony patterns from most population size data encountered in field studies, including over-dispersed count data. We provided a user-friendly R-program and a tutorial example to encourage further studies aiming at quantifying the strength of population synchrony to account for uncertainty in

  9. The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in northern populations and potential impact on management of resistance to transgenic maize.

    PubMed

    Li, Jing; Coates, Brad S; Kim, Kyung Seok; Bourguet, Denis; Ponsard, Sergine; He, Kanglai; Wang, Zhenying

    2014-01-01

    Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n=1673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST=0.020; P value<0.05). Analysis of molecular variance indicated that geographic region, number of generations or voltinism accounted for <0.38% of the total genetic variation at nuclear loci and was corroborated by clustering of co-ancestries among genotypes using the program STRUCTURE. In contrast, a mitochondrial haplotype network identified 4 distinct clusters, where 70.5% of samples from univoltine populations were within a single group. Univoltine populations were also placed into a unique cluster using Population Graph and Principal component analyses, which showed significant differentiation with multivoltine populations (φST=0.400; P value<0.01). This study suggests that gene flow among O. furnacalis in China may be high among regions, with the exception of northeastern localities. Haplotype variation may be due to random genetic drift resulting from partial reproductive isolation between univoltine and multivoltine O. furnacalis populations. Such reproductive isolation might impact the potential spread of alleles that confer resistance to transgenic maize in China.

  10. The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in northern populations and potential impact on management of resistance to transgenic maize.

    PubMed

    Li, Jing; Coates, Brad S; Kim, Kyung Seok; Bourguet, Denis; Ponsard, Sergine; He, Kanglai; Wang, Zhenying

    2014-01-01

    Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n=1673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST=0.020; P value<0.05). Analysis of molecular variance indicated that geographic region, number of generations or voltinism accounted for <0.38% of the total genetic variation at nuclear loci and was corroborated by clustering of co-ancestries among genotypes using the program STRUCTURE. In contrast, a mitochondrial haplotype network identified 4 distinct clusters, where 70.5% of samples from univoltine populations were within a single group. Univoltine populations were also placed into a unique cluster using Population Graph and Principal component analyses, which showed significant differentiation with multivoltine populations (φST=0.400; P value<0.01). This study suggests that gene flow among O. furnacalis in China may be high among regions, with the exception of northeastern localities. Haplotype variation may be due to random genetic drift resulting from partial reproductive isolation between univoltine and multivoltine O. furnacalis populations. Such reproductive isolation might impact the potential spread of alleles that confer resistance to transgenic maize in China. PMID:25024271

  11. Diverse plasma populations and structures in Jupiter's magnetotail.

    PubMed

    McComas, D J; Allegrini, F; Bagenal, F; Crary, F; Ebert, R W; Elliott, H; Stern, A; Valek, P

    2007-10-12

    Jupiter's magnetotail is the largest cohesive structure in the solar system and marks the loss of vast numbers of heavy ions from the Jupiter system. The New Horizons spacecraft traversed the magnetotail to distances exceeding 2500 jovian radii (R(J)) and revealed a remarkable diversity of plasma populations and structures throughout its length. Ions evolve from a hot plasma disk distribution at approximately 100 R(J) to slower, persistent flows down the tail that become increasingly variable in flux and mean energy. The plasma is highly structured-exhibiting sharp breaks, smooth variations, and apparent plasmoids-and contains ions from both Io and Jupiter's ionosphere with intense bursts of H(+) and H(+)(3). Quasi-periodic changes were seen in flux at approximately 450 and approximately 1500 R(J) with a 10-hour period. Other variations in flow speed at approximately 600 to 1000 R(J) with a 3- to 4-day period may be attributable to plasmoids moving down the tail. PMID:17932282

  12. Diverse plasma populations and structures in Jupiter's magnetotail.

    PubMed

    McComas, D J; Allegrini, F; Bagenal, F; Crary, F; Ebert, R W; Elliott, H; Stern, A; Valek, P

    2007-10-12

    Jupiter's magnetotail is the largest cohesive structure in the solar system and marks the loss of vast numbers of heavy ions from the Jupiter system. The New Horizons spacecraft traversed the magnetotail to distances exceeding 2500 jovian radii (R(J)) and revealed a remarkable diversity of plasma populations and structures throughout its length. Ions evolve from a hot plasma disk distribution at approximately 100 R(J) to slower, persistent flows down the tail that become increasingly variable in flux and mean energy. The plasma is highly structured-exhibiting sharp breaks, smooth variations, and apparent plasmoids-and contains ions from both Io and Jupiter's ionosphere with intense bursts of H(+) and H(+)(3). Quasi-periodic changes were seen in flux at approximately 450 and approximately 1500 R(J) with a 10-hour period. Other variations in flow speed at approximately 600 to 1000 R(J) with a 3- to 4-day period may be attributable to plasmoids moving down the tail.

  13. Microsatellite markers reveal spatial genetic structure of Tetranychus urticae (Acari: Tetranychidae) populations along a latitudinal gradient in Europe.

    PubMed

    Carbonnelle, Sabine; Hance, Thierry; Migeon, Alain; Baret, Philippe; Cros-Arteil, Sandrine; Navajas, Maria

    2007-01-01

    The genetic structure of populations of the two-spotted spider mite Tetranychus urticae was investigated along a south-north European transect spanning from southern France to The Netherlands. Mites were collected on Urtica dioica in 6 sampling zones. Microsatellite variation at 5 loci revealed considerable genetic variation with an average heterozygozity of 0.49. Significant heterozygote deficiency was found in 7 populations out of the 18 samples analyzed and one of them was completely monomorphic. Tetranychus urticae populations show some level of genetic structuring. First, genetic differentiation between localities (F (ST) estimates) was significant for all comparisons. Second, the analysis of molecular variance, AMOVA, indicates that there is an effect, albeit low (9%), of the locality in accounting for allele frequency variance. Geographic distance emerges as a factor responsible for this genetic structure. The results are discussed in relation to the biological features of the species and the known patterns of migration. Related agronomical issues are addressed.

  14. Genetic diversity and population structure of Plasmodium falciparum over space and time in an African archipelago.

    PubMed

    Salgueiro, Patrícia; Vicente, José Luís; Figueiredo, Rita Carrilho; Pinto, João

    2016-09-01

    The archipelago of São Tomé and Principe (STP), West Africa, has suffered the heavy burden of malaria since the 16th century. Until the last decade, when after a successful control program STP has become a low transmission country and one of the few nations with decreases of more than 90% in malaria admission and death rates. We carried out a longitudinal study to determine the genetic structure of STP parasite populations over time and space. Twelve microsatellite loci were genotyped in Plasmodium falciparum samples from two islands collected in 1997, 2000 and 2004. Analysis was performed on proportions of mixed genotype infections, allelic diversity, population differentiation, effective population size and bottleneck effects. We have found high levels of genetic diversity and minimal inter-population genetic differentiation typical of African continental regions with intense and stable malaria transmission. We detected significant differences between the years, with special emphasis for 1997 that showed the highest proportion of samples infected with P. falciparum and the highest mean number of haplotypes per isolate. This study establishes a comprehensive genetic data baseline of a pre-intervention scenario for future studies; taking into account the most recent and successful control intervention on the territory.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present. PMID:12919483

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

    USGS Publications Warehouse

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

    2007-01-01

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

  19. Population Genetic Structure of a Microalgal Species under Expansion

    PubMed Central

    Lebret, Karen; Kritzberg, Emma S.; Rengefors, Karin

    2013-01-01

    Biological invasions often cause major perturbations in the environment and are well studied among macroorganisms. Less is known about invasion by free-living microbes. Gonyostomum semen (Raphidophyceae) is a freshwater phytoplankton species that has increased in abundance in Northern Europe since the 1980's and has expanded its habitat range. In this study, we aimed to determine the genetic population structure of G. semen in Northern Europe and to what extent it reflects the species' recent expansion. We sampled lakes from 12 locations (11 lakes) in Norway, Sweden and Finland. Multiple strains from each location were genotyped using Amplified Fragment Length Polymorphism (AFLP). We found low differentiation between locations, and low gene diversity within each location. Moreover, there was an absence of genetic isolation with distance (Mantel test, p = 0.50). According to a Bayesian clustering method all the isolates belonged to the same genetic population. Together our data suggest the presence of one metapopulation and an overall low diversity, which is coherent with a recent expansion of G. semen. PMID:24349300

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  1. Genetic population structure of muskellunge in the Great Lakes

    USGS Publications Warehouse

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

    2013-01-01

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

  2. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... exists, then a null value for the Sweep/Automated Credit Account Identifiers should be provided, but the... be a null valueThe Sweep/Automated Credit Account Identifier may be composed of more than...

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

    USGS Publications Warehouse

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

    2005-01-01

    Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among 194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of FST or ??ST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California. ?? Springer 2005.

  4. Genetic Diversity and Population Structure of Haemonchus contortus.

    PubMed

    Gilleard, J S; Redman, E

    2016-01-01

    Haemonchus contortus is one of the most successful and problematic livestock parasites worldwide. From its apparent evolutionary origins in sub-Saharan Africa, it is now found in small ruminants in almost all regions of the globe, and can infect a range of different domestic and wildlife artiodactyl hosts. It has a remarkably high propensity to develop resistance to anthelmintic drugs, making control increasingly difficult. The success of this parasite is, at least in part, due to its extremely high levels of genetic diversity that, in turn, provide a high adaptive capacity. Understanding this genetic diversity is important for many areas of research including anthelmintic resistance, epidemiology, control, drug/vaccine development and molecular diagnostics. In this article, we review the current knowledge of H. contortus genetic diversity and population structure for both field isolates and laboratory strains. We highlight the practical relevance of this knowledge with a particular emphasis on anthelmintic resistance research. PMID:27238002

  5. Lack of Spatial Immunogenetic Structure among Wolverine (Gulo gulo) Populations Suggestive of Broad Scale Balancing Selection

    PubMed Central

    Rico, Yessica; Morris-Pocock, James; Zigouris, Joanna; Nocera, Joseph J.; Kyle, Christopher J.

    2015-01-01

    Elucidating the adaptive genetic potential of wildlife populations to environmental selective pressures is fundamental for species conservation. Genes of the major histocompatibility complex (MHC) are highly polymorphic, and play a key role in the adaptive immune response against pathogens. MHC polymorphism has been linked to balancing selection or heterogeneous selection promoting local adaptation. However, spatial patterns of MHC polymorphism are also influenced by gene flow and drift. Wolverines are highly vagile, inhabiting varied ecoregions that include boreal forest, taiga, tundra, and high alpine ecosystems. Here, we investigated the immunogenetic variation of wolverines in Canada as a surrogate for identifying local adaptation by contrasting the genetic structure at MHC relative to the structure at 11 neutral microsatellites to account for gene flow and drift. Evidence of historical positive selection was detected at MHC using maximum likelihood codon-based methods. Bayesian and multivariate cluster analyses revealed weaker population genetic differentiation at MHC relative to the increasing microsatellite genetic structure towards the eastern wolverine distribution. Mantel correlations of MHC against geographical distances showed no pattern of isolation by distance (IBD: r = -0.03, p = 0.9), whereas for microsatellites we found a relatively strong and significant IBD (r = 0.54, p = 0.01). Moreover, we found a significant correlation between microsatellite allelic richness and the mean number of MHC alleles, but we did not observe low MHC diversity in small populations. Overall these results suggest that MHC polymorphism has been influenced primarily by balancing selection and to a lesser extent by neutral processes such as genetic drift, with no clear evidence for local adaptation. This study contributes to our understanding of how vulnerable populations of wolverines may respond to selective pressures across their range. PMID:26448462

  6. Population structure and association mapping of yield contributing agronomic traits in foxtail millet.

    PubMed

    Gupta, Sarika; Kumari, Kajal; Muthamilarasan, Mehanathan; Parida, Swarup Kumar; Prasad, Manoj

    2014-06-01

    Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R (2) = 18 %) with nine agronomic traits in foxtail millet. Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R (2) = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of

  7. Lack of Spatial Immunogenetic Structure among Wolverine (Gulo gulo) Populations Suggestive of Broad Scale Balancing Selection.

    PubMed

    Rico, Yessica; Morris-Pocock, James; Zigouris, Joanna; Nocera, Joseph J; Kyle, Christopher J

    2015-01-01

    Elucidating the adaptive genetic potential of wildlife populations to environmental selective pressures is fundamental for species conservation. Genes of the major histocompatibility complex (MHC) are highly polymorphic, and play a key role in the adaptive immune response against pathogens. MHC polymorphism has been linked to balancing selection or heterogeneous selection promoting local adaptation. However, spatial patterns of MHC polymorphism are also influenced by gene flow and drift. Wolverines are highly vagile, inhabiting varied ecoregions that include boreal forest, taiga, tundra, and high alpine ecosystems. Here, we investigated the immunogenetic variation of wolverines in Canada as a surrogate for identifying local adaptation by contrasting the genetic structure at MHC relative to the structure at 11 neutral microsatellites to account for gene flow and drift. Evidence of historical positive selection was detected at MHC using maximum likelihood codon-based methods. Bayesian and multivariate cluster analyses revealed weaker population genetic differentiation at MHC relative to the increasing microsatellite genetic structure towards the eastern wolverine distribution. Mantel correlations of MHC against geographical distances showed no pattern of isolation by distance (IBD: r = -0.03, p = 0.9), whereas for microsatellites we found a relatively strong and significant IBD (r = 0.54, p = 0.01). Moreover, we found a significant correlation between microsatellite allelic richness and the mean number of MHC alleles, but we did not observe low MHC diversity in small populations. Overall these results suggest that MHC polymorphism has been influenced primarily by balancing selection and to a lesser extent by neutral processes such as genetic drift, with no clear evidence for local adaptation. This study contributes to our understanding of how vulnerable populations of wolverines may respond to selective pressures across their range. PMID:26448462

  8. Gene-drive in age-structured insect populations.

    PubMed

    Huang, Yunxin; Lloyd, Alun L; Legros, Mathieu; Gould, Fred

    2009-05-01

    To date, models of gene-drive mechanisms proposed for replacing wild-type mosquitoes with transgenic strains that cannot transmit diseases have assumed no age or mating structure. We developed a more detailed model to analyze the effects of age and mating-related factors on the number of engineered insects that must be introduced into a wild population to achieve successful gene-drive based on the Medea and engineered underdominance mechanisms. We found that models without age-structure and mating details can substantially overestimate or underestimate the numbers of engineered insects that must be introduced. In general, introduction thresholds are lowest when young adults are introduced. When both males and females are introduced, assortative mating by age has little impact on the introduction threshold unless the introduced females have diminished reproductive ability because of their age. However, when only males are introduced, assortative mating by age is generally predicted to increase introduction thresholds. In most cases, introduction thresholds are much higher for male-only introductions than for both-sex introductions, but when mating is nearly random and the introduced insects are adults with Medea constructs, male-only introductions can have somewhat lower thresholds than both-sex introductions. Results from this model suggest specific parameters that should be measured in field experiments.

  9. Coexistence of structured populations with size-based prey selection.

    PubMed

    Hartvig, Martin; Andersen, Ken Haste

    2013-11-01

    Species with a large adult-offspring size ratio and a preferred predator-prey mass ratio undergo ontogenetic trophic niche shift(s) throughout life. Trophic interactions between such species vary throughout life, resulting in different species-level interaction motifs depending on the maximum adult sizes and population size distributions. We explore the assembly and potential for coexistence of small communities where all species experience ontogenetic trophic niche shifts. The life-history of each species is described by a physiologically structured model and species identity is characterised by the trait: size at maturation. We show that a single species can exist in two different states: a 'resource driven state' and a 'cannibalistic state' with a large scope for emergent Allee effects and bistable states. Two species can coexist in two different configurations: in a 'competitive coexistence' state when the ratio between sizes at maturation of the two species is less than a predator-prey mass ratio and the resource level is low to intermediate, or in a 'trophic ladder' state if the ratio of sizes at maturation is larger than the predator-prey mass ratio at all resource levels. While there is a large scope for coexistence of two species, the scope for coexistence of three species is limited and we conclude that further trait differentiation is required for coexistence of more species-rich size-structured communities. PMID:23927897

  10. A structural account of substrate and inhibitor specificity differences between two Naphthol reductases

    SciTech Connect

    Liao, D.-I.; Thompson, J.E.; Fahnestock, S.; Valent, B.; Jordan, D.B.

    2010-03-08

    Two short chain dehydrogenase/reductases mediate naphthol reduction reactions in fungal melanin biosynthesis. An X-ray structure of 1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) complexed with NADPH and pyroquilon was determined for examining substrate and inhibitor specificities that differ from those of 1,3,8-trihydroxynaphthalene reductase (3HNR). The 1.5 {angstrom} resolution structure allows for comparisons with the 1.7 {angstrom} resolution structure of 3HNR complexed with the same ligands. The sequences of the two proteins are 46% identical, and they have the same fold. The 30-fold lower affinity of the 4HNR-NADPH complex for pyroquilon (a commercial fungicide that targets 3HNR) in comparison to that of the 3HNR-NADPH complex can be explained by unfavorable interactions between the anionic carboxyl group of the C-terminal Ile282 of 4HNR and CH and CH{sub 2} groups of the inhibitor that are countered by favorable inhibitor interactions with 3HNR. 1,3,8-Trihydroxynaphthalene (3HN) and 1,3,6,8-tetrahydroxynaphthalene (4HN) were modeled onto the cyclic structure of pyroquilon in the 4HNR-NADPH-pyroquilon complex to examine the 300-fold preference of the enzyme for 4HN over 3HN. The models suggest that the C-terminal carboxyl group of Ile282 has a favorable hydrogen bonding interaction with the C6 hydroxyl group of 4HN and an unfavorable interaction with the C6 CH group of 3HN. Models of 3HN and 4HN in the 3HNR active site suggest a favorable interaction of the sulfur atom of the C-terminal Met283 with the C6 CH group of 3HN and an unfavorable one with the C6 hydroxyl group of 4HN, accounting for the 4-fold difference in substrate specificities. Thus, the C-terminal residues of the two naphthol reductase are determinants of inhibitor and substrate specificities.

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  14. Associative Account of Self-Cognition: Extended Forward Model and Multi-Layer Structure

    PubMed Central

    Sugiura, Motoaki

    2013-01-01

    The neural correlates of “self” identified by neuroimaging studies differ depending on which aspects of self are addressed. Here, three categories of self are proposed based on neuroimaging findings and an evaluation of the likely underlying cognitive processes. The physical self, representing self-agency of action, body-ownership, and bodily self-recognition, is supported by the sensory and motor association cortices located primarily in the right hemisphere. The interpersonal self, representing the attention or intentions of others directed at the self, is supported by several amodal association cortices in the dorsomedial frontal and lateral posterior cortices. The social self, representing the self as a collection of context-dependent social-values, is supported by the ventral aspect of the medial prefrontal cortex and the posterior cingulate cortex. Despite differences in the underlying cognitive processes and neural substrates, all three categories of self are likely to share the computational characteristics of the forward model, which is underpinned by internal schema or learned associations between one’s behavioral output and the consequential input. Additionally, these three categories exist within a hierarchical layer structure based on developmental processes that updates the schema through the attribution of prediction error. In this account, most of the association cortices critically contribute to some aspect of the self through associative learning while the primary regions involved shift from the lateral to the medial cortices in a sequence from the physical to the interpersonal to the social self. PMID:24009578

  15. Plasmodium vivax population structure and transmission dynamics in Sabah Malaysia.

    PubMed

    Abdullah, Noor Rain; Barber, Bridget E; William, Timothy; Norahmad, Nor Azrina; Satsu, Umi Rubiah; Muniandy, Prem Kumar; Ismail, Zakiah; Grigg, Matthew J; Jelip, Jenarun; Piera, Kim; von Seidlein, Lorenz; Yeo, Tsin W; Anstey, Nicholas M; Price, Ric N; Auburn, Sarah

    2013-01-01

    Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (F ST  = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI  = 1.38) and KK (mean MOI  = 1.19). However, population diversity remained moderate (H E  = 0.583 in KM and H E  = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (I A (S) >0.5 [P<0.0001] in KK and KM) declined sharply when identical haplotypes were represented once (I A (S)  = 0.07 [P = 0.0076] in KM, and I A (S) = -0.003 [P = 0.606] in KK). All 8 recurrences, likely to be relapses, were homologous to the prior infection. These recurrences may promote the persistence of parasite lineages, sustaining local diversity. In summary, Sabah's shrinking P. vivax population appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for

  16. Genetic diversity and genetic structure of different types of natural populations in Osmanthus fragrans Lour. and the relationships with sex ratio, population structure, and geographic isolation.

    PubMed

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhao, Hongbo; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of N e , H e , and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity. PMID:25436228

  17. Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

    PubMed Central

    Deatherage, Daniel E.; Traverse, Charles C.; Wolf, Lindsey N.; Barrick, Jeffrey E.

    2014-01-01

    New mutations leading to structural variation (SV) in genomes—in the form of mobile element insertions, large deletions, gene duplications, and other chromosomal rearrangements—can play a key role in microbial evolution. Yet, SV is considerably more difficult to predict from short-read genome resequencing data than single-nucleotide substitutions and indels (SN), so it is not yet routinely identified in studies that profile population-level genetic diversity over time in evolution experiments. We implemented an algorithm for detecting polymorphic SV as part of the breseq computational pipeline. This procedure examines split-read alignments, in which the two ends of a single sequencing read match disjoint locations in the reference genome, in order to detect structural variants and estimate their frequencies within a sample. We tested our algorithm using simulated Escherichia coli data and then applied it to 500- and 1000-generation population samples from the Lenski E. coli long-term evolution experiment (LTEE). Knowledge of genes that are targets of selection in the LTEE and mutations present in previously analyzed clonal isolates allowed us to evaluate the accuracy of our procedure. Overall, SV accounted for ~25% of the genetic diversity found in these samples. By profiling rare SV, we were able to identify many cases where alternative mutations in key genes transiently competed within a single population. We also found, unexpectedly, that mutations in two genes that rose to prominence at these early time points always went extinct in the long term. Because it is not limited by the base-calling error rate of the sequencing technology, our approach for identifying rare SV in whole-population samples may have a lower detection limit than similar predictions of SNs in these data sets. We anticipate that this functionality of breseq will be useful for providing a more complete picture of genome dynamics during evolution experiments with haploid microorganisms

  18. Autosomal STR analyses in native Amazonian tribes suggest a population structure driven by isolation by distance.

    PubMed

    Dos Santos, Sidney E B; Ribeiro-Rodrigues, Elzemar M; Ribeiro-Dos-Santos, Andrea K C; Hutz, Mara H; Tovo-Rodrigues, Luciana; Salzano, Francisco M; Callegari-Jacques, Sidia M

    2009-02-01

    Eleven short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, TH01, and TPOX) were investigated in 232 individuals from 6 Amazonian native tribes (Tiriyó, Waiãpi, Zoé, Urubu-Kaapor, Awa-Guajá, and Parakanã). We added the new data to a database that included five previously typed native populations from the same area (Wai Wai, Gavião, Zoró, Suruí, and Xavante). The results presented here concern this new data set, which accounts for 526 individuals in total. We tested whether major geographic or linguistic barriers to gene flow exist among such human groups and tried to find a possible anthropological or ethnological explanation for such patterns. We measured the average heterozygosity (H) and the number of alleles (N(A) ) and found that both are lower than values observed in populations of different ethnic backgrounds, such as European or African descendants. Despite such a result, we found high between-population variation; lower H and/or N(A) values were obtained from four isolated tribes that came into contact with external nonnative populations in recent times (1921-1989). By applying analysis of molecular variance, generalized hierarchical modeling, and the Structure Bayesian analysis, we were not able to detect any significant geographic or linguistic barrier to gene flow. Geographic autocorrelation analysis suggests that the genetic structure of native Amazonian tribes is better explained by isolation by distance because the level of genetic similarity decreases according to linear geographic distance, reaching null or negative values at a scale of 300 km.

  19. Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models

    PubMed Central

    Chen, Han; Wang, Chaolong; Conomos, Matthew P.; Stilp, Adrienne M.; Li, Zilin; Sofer, Tamar; Szpiro, Adam A.; Chen, Wei; Brehm, John M.; Celedón, Juan C.; Redline, Susan; Papanicolaou, George J.; Thornton, Timothy A.; Laurie, Cathy C.; Rice, Kenneth; Lin, Xihong

    2016-01-01

    Linear mixed models (LMMs) are widely used in genome-wide association studies (GWASs) to account for population structure and relatedness, for both continuous and binary traits. Motivated by the failure of LMMs to control type I errors in a GWAS of asthma, a binary trait, we show that LMMs are generally inappropriate for analyzing binary traits when population stratification leads to violation of the LMM’s constant-residual variance assumption. To overcome this problem, we develop a computationally efficient logistic mixed model approach for genome-wide analysis of binary traits, the generalized linear mixed model association test (GMMAT). This approach fits a logistic mixed model once per GWAS and performs score tests under the null hypothesis of no association between a binary trait and individual genetic variants. We show in simulation studies and real data analysis that GMMAT effectively controls for population structure and relatedness when analyzing binary traits in a wide variety of study designs. PMID:27018471

  20. Genetic structure of Varroa destructor populations infesting Apis mellifera colonies in Argentina.

    PubMed

    Maggi, M; Medici, S; Quintana, S; Ruffinengo, S; Marcángeli, J; Gimenez Martinez, P; Fuselli, S; Eguaras, M

    2012-04-01

    Although mitochondrial DNA mapping of Varroa destructor revealed the presence of several haplotypes, only two of them (Korean and Japanese haplotypes) were capable to infest Apis mellifera populations. Even though the Korean haplotype is the only one that has been reported in Argentina, these conclusions were based on mites sampled in apiaries from a specific geographical place (Buenos Aires province). To study mites from several sites of Argentina could reveal the presence of the Japanese genotype, especially considering sites near to Brazil, where Japanese haplotype was already detected. The aim of this work was to study the genetic structure of V. destructor populations from apiaries located in various provinces of Argentina, in order to determine the presence of different haplotypes. The study was carried out between January 2006 and December 2009. Phoretic adult Varroa mites were collected from honey bee workers sampled from colonies of A. mellifera located in Entre Ríos, Buenos Aires, Corrientes, Río Negro, Santa Cruz and Neuquén provinces. Twenty female mites from each sampling site were used to carry out the genetic analysis. For DNA extraction a nondestructive method was used. DNA sequences were compared to Korean haplotype (AF106899) and Japanese haplotype (AF106897). All DNA sequences obtained from mite populations sampled in Argentina, share 98% of similitude with Korean Haplotype (AF106899). Taking into account these results, we are able to conclude that Korean haplotype is cosmopolite in Argentina.

  1. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

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

  2. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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

  3. 15 CFR 50.10 - Fee structure for special population censuses.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

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

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

    Code of Federal Regulations, 2011 CFR

    2011-01-01

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

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

    Code of Federal Regulations, 2014 CFR

    2014-01-01

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

  6. Rotation and internal structure of Population III protostars

    NASA Astrophysics Data System (ADS)

    Stacy, Athena; Greif, Thomas H.; Klessen, Ralf S.; Bromm, Volker; Loeb, Abraham

    2013-05-01

    We analyse the cosmological simulations performed in the recent work of Greif et al., which followed the early growth and merger history of Population III (Pop III) stars while resolving scales as small as 0.05 R⊙. This is the first set of cosmological simulations to self-consistently resolve the rotation and internal structure of Pop III protostars. We find that Pop III stars form under significant rotational support which is maintained for the duration of the simulations. The protostellar surfaces spin from ˜50 per cent to nearly 100 per cent of Keplerian rotational velocity. These rotation rates persist after experiencing multiple stellar merger events. In the brief time period simulated (˜10 yr), the protostars show little indication of convective instability, and their properties furthermore show little correlation with the properties of their host minihaloes. If Pop III protostars within this range of environments generally form with high degrees of rotational support, and if this rotational support is maintained for a sufficient amount of time, this has a number of crucial implications for Pop III evolution and nucleosynthesis, as well as the possibility for Pop III pair-instability supernovae, and the question of whether the first stars produced gamma-ray bursts.

  7. Structure and evolution of low-mass Population II stars

    NASA Astrophysics Data System (ADS)

    Montalbán, J.; D'Antona, F.; Mazzitelli, I.

    2000-08-01

    The focus of the present paper is on the detailed description of the internal structures of low mass, population II stars, to clarify some issues about these stellar models and, mainly, their present reliability for observational comparisons. We then explore 1) the role of the local convective model; 2) the differences between "grey" and "non grey" models, and between models in which the photospheric boundary conditions are set at different optical depths (τph = 3 or 100); 3) the role of the equation of state (EoS), both in the atmospheric models and in the interior. One of the major conclusions of the paper is a cautionary note about the usage of the additive volume law in EoS calculations. The dependence of the HR diagram locations and mass luminosity relations on metal and helium content are also discussed. A few comparisons with globular cluster stars show that: 1) general consistency of distance scales and morphologies in the HR diagram is found, when comparing ground based measurements in the Johnson B and V bands and observations in the HST bands; 2) a discrepancy between models and observations may exist for more metal rich clusters; 3) the plausible hypothesis that the mass function in the globular cluster NGC 6397 behaves smoothly until the lower limit of the main sequence poses constraints on the mass-luminosity relation at the lowest end of the main sequence. The evolutionary tracks are available at the WEB location http://www.mporzio.astro.it.

  8. Recombination shapes the structure of an environmental Vibrio cholerae population.

    PubMed

    Keymer, Daniel P; Boehm, Alexandria B

    2011-01-01

    Vibrio cholerae consists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shown V. cholerae to be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmental V. cholerae isolates and 13 other putative Vibrio isolates from coastal waters and sediments in central California, as well as four clinical V. cholerae isolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of our V. cholerae isolates. Despite frequent recombination, significant linkage disequilibrium was still detected among the V. cholerae sequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate in V. cholerae of 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination among V. cholerae may hinder the identification of ecotypes in this bacterioplankton population. PMID:21075874

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

    PubMed

    Martins, Suzana Cláudia Silveira; Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  11. The Acquisition of Prosodic Structure: An Investigation of Current Accounts of Children's Prosodic Development.

    ERIC Educational Resources Information Center

    Kehoe, Margaret; Stoel-Gammon, Carol

    1997-01-01

    Examines different approaches to prosodic acquisition: Gerken's S(W) production template; Fikkert's and Archibald's theories of stress acquisition and Demuth and Fee's prosodic hierarchy account. Results reveal that current approaches cannot account for findings in the data such as the increased preservation of final over nonfinal unstressed…

  12. Utility of R0 as a predictor of disease invasion in structured populations

    USGS Publications Warehouse

    Cross, P.C.; Johnson, P.L.F.; Lloyd-Smith, J. O.; Getz, W.M.

    2007-01-01

    Early theoretical work on disease invasion typically assumed large and well-mixed host populations. Many human and wildlife systems, however, have small groups with limited movement among groups. In these situations, the basic reproductive number, R0, is likely to be a poor predictor of a disease pandemic because it typically does not account for group structure and movement of individuals among groups. We extend recent work by combining the movement of hosts, transmission within groups, recovery from infection and the recruitment of new susceptibles into a stochastic model of disease in a host metapopulation. We focus on how recruitment of susceptibles affects disease invasion and how population structure can affect the frequency of superspreading events (SSEs). We show that the frequency of SSEs may decrease with the reduced movement and the group sizes due to the limited number of susceptible individuals available. Classification tree analysis of the model results illustrates the hierarchical nature of disease invasion in host metapopulations. First, the pathogen must effectively transmit within a group (R0 > 1), and then the pathogen must persist within a group long enough to allow for movement among the groups. Therefore, the factors affecting disease persistence - such as infectious period, group size and recruitment of new susceptibles - are as important as the local transmission rates in predicting the spread of pathogens across a metapopulation. ?? 2006 The Royal Society.

  13. Family Structure Transitions and Child Development: Instability, Selection, and Population Heterogeneity

    PubMed Central

    Lee, Dohoon; McLanahan, Sara

    2016-01-01

    A growing literature documents the importance of family instability for child wellbeing. In this article, we use longitudinal data from the Fragile Families and Child Wellbeing Study to examine the impacts of family instability on children’s cognitive and socioemotional development in early and middle childhood. We extend existing research in several ways: (1) by distinguishing between the number and types of family structure changes; (2) by accounting for time-varying as well as time-constant confounding; and (3) by assessing racial/ethnic and gender differences in family instability effects. Our results indicate that family instability has a causal effect on children’s development, but the effect depends on the type of change, the outcome assessed, and the population examined. Generally speaking, transitions out of a two-parent family are more negative for children’s development than transitions into a two-parent family. The effect of family instability is stronger for children’s socioemotional development than for their cognitive achievement. For socioemotional development, transitions out of a two-parent family are more negative for white children, whereas transitions into a two-parent family are more negative for Hispanic children. These findings suggest that future research should pay more attention to the type of family structure transition and to population heterogeneity. PMID:27293242

  14. Gene-drive into insect populations with age and spatial structure: a theoretical assessment.

    PubMed

    Huang, Yunxin; Lloyd, Alun L; Legros, Mathieu; Gould, Fred

    2011-05-01

    The potential benefits and risks of genetically engineered gene-drive systems for replacing wild pest strains with more benign strains must be assessed prior to any field releases. We develop a computer simulation model to assess the feasibility of using engineered underdominance constructs to drive transgenes into age- and spatially structured mosquito populations. Our practical criterion for success is the achievement of a transgene frequency of at least 0.80 within 3 years of release. The impacts of a number of parameters that may affect the success of gene-drive, such as the release area, release age, density-dependent larval survival, fitness cost of the engineered genes, and migration probability of adults, are examined. Results show that patchy release generally requires the release of fewer engineered insects to achieve success than central release. When the fitness cost is very low, central release covering 25% of the total area can be more effective than a completely uniform release over the whole area. This study demonstrates that to determine the best method of spatial release, and the total number of engineered insects that must be released, it is important to take into account the age and sex of the released insects and spatial structure of the population.

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

    PubMed Central

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

    2014-01-01

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

  16. Extensive population structure in San, Khoe, and mixed ancestry populations from southern Africa revealed by 44 short 5-SNP haplotypes.

    PubMed

    Schlebusch, Carina M; Soodyall, Himlya

    2012-12-01

    The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Genetic studies [mitochondrial deoxyribonucleic acid (DNA) and Y-chromosome] conducted on San and Khoe groups revealed that they harbor some of the most divergent lineages found in living peoples throughout the world. Recently, high-density, autosomal, single-nucleotide polymorphism (SNP)-array studies confirmed the early divergence of Khoe-San population groups from all other human populations. The present study made use of 220 autosomal SNP markers (in the format of both haplotypes and genotypes) to examine the population structure of various San and Khoe groups and their relationship to other neighboring groups. Whereas analyses based on the genotypic SNP data only supported the division of the included populations into three main groups-Khoe-San, Bantu-speakers, and non-African populations-haplotype analyses revealed finer structure within Khoe-San populations. By the use of only 44 short SNP haplotypes (compiled from a total of 220 SNPs), most of the Khoe-San groups could be resolved as separate groups by applying STRUCTURE analyses. Therefore, by carefully selecting a few SNPs and combining them into haplotypes, we were able to achieve the same level of population distinction that was achieved previously in high-density SNP studies on the same population groups. Using haplotypes proved to be a very efficient and cost-effective way to study population structure.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  18. Genetic Population Structure of Local Populations of the Endangered Saltmarsh Sesarmid Crab Clistocoeloma sinense in Japan

    PubMed Central

    Yuhara, Takeshi; Kawane, Masako; Furota, Toshio

    2014-01-01

    During recent decades, over 40% of Japanese estuarine tidal flats have been lost due to coastal developments. Local populations of the saltmarsh sesarmid crab Clistocoeloma sinense, designated as an endangered species due to the limited suitable saltmarsh habitat available, have decreased accordingly, being now represented as small remnant populations. Several such populations in Tokyo Bay, have been recognised as representing distributional limits of the species. To clarify the genetic diversity and connectivity among local coastal populations of Japanese Clistocoeloma sinense, including those in Tokyo Bay, mitochondrial DNA analyses were conducted in the hope of providing fundamental information for future conservation studies and an understanding of metapopulation dynamics through larval dispersal among local populations. All of the populations sampled indicated low levels of genetic diversity, which may have resulted from recent population bottlenecks or founder events. However, the results also revealed clear genetic differentiation between two enclosed-water populations in Tokyo Bay and Ise-Mikawa Bay, suggesting the existence of a barrier to larval transport between these two water bodies. Since the maintenance of genetic connectivity is a requirement of local population stability, the preservation of extant habitats and restoration of saltmarshes along the coast of Japan may be the most effective measures for conservation of this endangered species. PMID:24400112

  19. Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits.

    PubMed

    Alves, Joel M; Carneiro, Miguel; Afonso, Sandra; Lopes, Susana; Garreau, Hervé; Boucher, Samuel; Allain, Daniel; Queney, Guillaume; Esteves, Pedro J; Bolet, Gerard; Ferrand, Nuno

    2015-01-01

    Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies. PMID:26689909

  20. Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits

    PubMed Central

    Afonso, Sandra; Lopes, Susana; Garreau, Hervé; Boucher, Samuel; Allain, Daniel; Queney, Guillaume; Esteves, Pedro J.; Bolet, Gerard; Ferrand, Nuno

    2015-01-01

    Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies. PMID:26689909

  1. Structural and psychological empowerment climates, performance, and the moderating role of shared felt accountability: a managerial perspective.

    PubMed

    Wallace, J Craig; Johnson, Paul D; Mathe, Kimberly; Paul, Jeff

    2011-07-01

    The authors proposed and tested a model in which data were collected from managers (n = 539) at 116 corporate-owned quick service restaurants to assess the structural and psychological empowerment process as moderated by shared-felt accountability on indices of performance from a managerial perspective. The authors found that empowering leadership climate positively relates to psychological empowerment climate. In turn, psychological empowerment climate relates to performance only under conditions of high-felt accountability; it does not relate to performance under conditions of low-felt accountability. Overall, the present results indicate that the quick-service restaurant managers, who feel more empowered, operate restaurants that perform better than managers who feel less empowered, but only when those empowered managers also feel a high sense of accountability.

  2. Structural and psychological empowerment climates, performance, and the moderating role of shared felt accountability: a managerial perspective.

    PubMed

    Wallace, J Craig; Johnson, Paul D; Mathe, Kimberly; Paul, Jeff

    2011-07-01

    The authors proposed and tested a model in which data were collected from managers (n = 539) at 116 corporate-owned quick service restaurants to assess the structural and psychological empowerment process as moderated by shared-felt accountability on indices of performance from a managerial perspective. The authors found that empowering leadership climate positively relates to psychological empowerment climate. In turn, psychological empowerment climate relates to performance only under conditions of high-felt accountability; it does not relate to performance under conditions of low-felt accountability. Overall, the present results indicate that the quick-service restaurant managers, who feel more empowered, operate restaurants that perform better than managers who feel less empowered, but only when those empowered managers also feel a high sense of accountability. PMID:21381808

  3. Genetic variation among interconnected populations of Catostomus occidentalis: Implications for distinguishing impacts of contaminants from biogeographical structuring

    USGS Publications Warehouse

    Whitehead, A.; Anderson, S.L.; Kuivila, K.M.; Roach, J.L.; May, B.

    2003-01-01

    Exposure to contaminants can affect survivorship, recruitment, reproductive success, mutation rates and migration, and may play a significant role in the partitioning of genetic variation among exposed and nonexposed populations. However, the application of molecular population genetic data to evaluate such influences has been uncommon and often flawed. We tested whether patterns of genetic variation among native fish populations (Sacramento sucker, Catostomus occidentalis) in the Central Valley of California were consistent with long-term pesticide exposure history, or primarily with expectations based on biogeography. Field sampling was designed to rigorously test for both geographical and contamination influences. Fine-scale structure of these interconnected populations was detected with both amplified fragment length polymorphisms (AFLP) and microsatellite markers, and patterns of variation elucidated by the two marker systems were highly concordant. Analyses indicated that biogeographical hypotheses described the data set better than hypotheses relating to common historical pesticide exposure. Downstream populations had higher genetic diversity than upstream populations, regardless of exposure history, and genetic distances showed that populations from the same river system tended to cluster together. Relatedness among populations reflected primarily directions of gene flow, rather than convergence among contaminant-exposed populations. Watershed geography accounted for significant partitioning of genetic variation among populations, whereas contaminant exposure history did not. Genetic patterns indicating contaminant-induced selection, increased mutation rates or recent bottlenecks were weak or absent. We stress the importance of testing contaminant-induced genetic change hypotheses within a biogeographical context. Strategic application of molecular markers for analysis of fine-scale structure, and for evaluating contaminant impacts on gene pools, is

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

    PubMed

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

    1988-12-01

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

  5. Population Structure and Evolution of Pathogenicity of Yersinia pseudotuberculosis▿ †

    PubMed Central

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

    2011-01-01

    Yersinia pseudotuberculosis is an enteric human pathogen but is widespread in the environment. Pathogenicity is determined by a number of virulence factors, including the virulence plasmid pYV, the high-pathogenicity island (HPI), and the Y. pseudotuberculosis-derived mitogen (YPM), a superantigen. The presence of the 3 virulence factors varies among Y. pseudotuberculosis isolates. We developed a multilocus sequence typing (MLST) scheme to address the population structure of Y. pseudotuberculosis and the evolution of its pathogenicity. The seven housekeeping genes selected for MLST were mdh, recA, sucA, fumC, aroC, pgi, and gyrB. An MLST analysis of 83 isolates of Y. pseudotuberculosis, representing 19 different serotypes and six different genetic groups, identified 61 sequence types (STs) and 12 clonal complexes. Out of 26 allelic changes that occurred in the 12 clonal complexes, 13 were mutational events while 13 were recombinational events, indicating that recombination and mutation contributed equally to the diversification of the clonal complexes. The isolates were separated into 2 distinctive clusters, A and B. Cluster A is the major cluster, with 53 STs (including Y. pestis strains), and is distributed worldwide, while cluster B is restricted to the Far East. The YPM gene is widely distributed on the phylogenetic tree, with ypmA in cluster A and ypmB in cluster B. pYV is present in cluster A only but is sporadically absent in some cluster A isolates. In contrast, an HPI is present only in a limited number of lineages and must be gained by lateral transfer. Three STs carry all 3 virulence factors and can be regarded as high-pathogenicity clones. Isolates from the same ST may not carry all 3 virulence factors, indicating frequent gain or loss of these factors. The differences in pathogenicity among Y. pseudotuberculosis strains are likely due to the variable presence and instability of the virulence factors. PMID:21131531

  6. Population structure in Indian sheep ascertained using microsatellite information.

    PubMed

    Arora, R; Bhatia, S; Mishra, B P; Joshi, B K

    2011-06-01

    This study attempts to provide a comprehensive insight into the prevailing genetic status of Indian sheep breeds using microsatellite markers. Seventeen Indian sheep breeds from 3 agroecological zones were analysed using a panel of 25 microsatellite markers. All of the sheep breeds investigated were genetically diverse, as evident from the high allele (>6) and gene (>0.6) diversity values. The gene diversity values for all breeds ranged from 0.621 to 0.780. The within-population heterozygote deficit (F(IS)) varied from -0.098 to 0.234, reflecting significant levels for 12 of the 17 breeds investigated. The average genetic differentiation between all breeds (F(ST)) was 11.1%, revealing moderate discrimination between the indigenous sheep breeds. The genetic distance and principal component analysis revealed a separation of sheep breeds based on geographical propinquity. The Bayesian clustering approach suggested poor breed differentiation in the north-western arid and semi-arid region when compared to the breeds from the eastern and southern peninsular regions. The observed results mirror the divergent management strategies in the different agroecological regions, lack of specific selection policies, and intermixing of breeds in close proximity. Immediate steps to curb the intermixing and erosion of breed purity for some of these breeds need to be implemented, for example, by introducing measures like making proven rams available and ensuring their frequent exchange between flocks. The data generated here provides valuable information about the genetic structure of the 17 Indian sheep breeds and this can be used for designating priorities for their conservation.

  7. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. Genetic variability and population structure of endangered Panax ginseng in the Russian Primorye

    PubMed Central

    2010-01-01

    Background The natural habitat of wild P. ginseng is currently found only in the Russian Primorye and the populations are extremely exhausted and require restoration. Analysis of the genetic diversity and population structure of an endangered species is a prerequisite for conservation. The present study aims to investigate the patterns and levels of genetic polymorphism and population structures of wild P. ginseng with the AFLP method to (1) estimate the level of genetic diversity in the P. ginseng populations in the Russian Primorsky Krai, (2) calculate the distribution of variability within a population and among populations and (3) examine the genetic relationship between the populations. Methods Genetic variability and population structure of ten P. ginseng populations were investigated with Amplified Fragment Length Polymorphism (AFLP) markers. The genetic relationships among P. ginseng plants and populations were delineated. Results The mean genetic variability within populations was high. The mean level of polymorphisms was 55.68% at the population level and 99.65% at the species level. The Shannon's index ranged between 0.1602 and 0.3222 with an average of 0.2626 at the population level and 0.3967 at the species level. The analysis of molecular variances (AMOVA) showed a significant population structure in P. ginseng. The partition of genetic diversity with AMOVA suggested that the majority of the genetic variation (64.5%) was within populations of P. ginseng. The inter-population variability was approximately 36% of the total variability. The genetic relationships among P. ginseng plants and populations were reconstructed by Minimum Spanning tree (MS-tree) on the basis of Euclidean distances with ARLEQUIN and NTSYS, respectively. The MS-trees suggest that the southern Uss, Part and Nad populations may have promoted P. ginseng distribution throughout the Russian Primorye. Conclusion The P. ginseng populations in the Russian Primorye are significant in

  10. Expression of a Peroral Infection Factor Determines Pathogenicity and Population Structure in an Insect Virus

    PubMed Central

    Simón, Oihane; Williams, Trevor; Cerutti, Martine; Caballero, Primitivo; López-Ferber, Miguel

    2013-01-01

    A Nicaraguan isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus is being studied as a possible biological insecticide. This virus exists as a mixture of complete and deletion genotypes; the latter depend on the former for the production of an essential per os transmission factor (pif1) in coinfected cells. We hypothesized that the virus population was structured to account for the prevalence of pif1 defector genotypes, so that increasing the abundance of pif1 produced by a cooperator genotype in infected cells would favor an increased prevalence of the defector genotype. We tested this hypothesis using recombinant viruses with pif1 expression reprogrammed at its native locus using two exogenous promoters (egt, p10) in the pif2/pif1 intergenic region. Reprogrammed viruses killed their hosts markedly faster than the wild-type and rescue viruses, possibly due to an earlier onset of systemic infection. Group success (transmission) depended on expression of pif1, but overexpression was prejudicial to group-specific transmissibility, both in terms of reduced pathogenicity and reduced production of virus progeny from each infected insect. The presence of pif1-overproducing genotypes in the population was predicted to favor a shift in the prevalence of defector genotypes lacking pif1-expressing capabilities, to compensate for the modification in pif1 availability at the population level. As a result, defectors increased the overall pathogenicity of the virus population by diluting pif1 produced by overexpressing genotypes. These results offer a new and unexpected perspective on cooperative behavior between viral genomes in response to the abundance of an essential public good that is detrimental in excess. PMID:24223853

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

    ERIC Educational Resources Information Center

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

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

  12. When Global Structure "Explains Away" Local Grammar: A Bayesian Account of Rule-Induction in Tone Sequences

    ERIC Educational Resources Information Center

    Dawson, Colin; Gerken, LouAnn

    2011-01-01

    While many constraints on learning must be relatively experience-independent, past experience provides a rich source of guidance for subsequent learning. Discovering structure in some domain can inform a learner's future hypotheses about that domain. If a general property accounts for particular sub-patterns, a rational learner should not…

  13. Structural and Psychological Empowerment Climates, Performance, and the Moderating Role of Shared Felt Accountability: A Managerial Perspective

    ERIC Educational Resources Information Center

    Wallace, J. Craig; Johnson, Paul D.; Mathe, Kimberly; Paul, Jeff

    2011-01-01

    The authors proposed and tested a model in which data were collected from managers (n = 539) at 116 corporate-owned quick service restaurants to assess the structural and psychological empowerment process as moderated by shared-felt accountability on indices of performance from a managerial perspective. The authors found that empowering leadership…

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  16. Hydrography and population genetic structure in brook charr (Salvelinus fontinalis, Mitchill) from eastern Canada.

    PubMed

    Hébert, C; Danzman, R G; Jones, M W; Bernatchez, L

    2000-07-01

    Despite the abundance of studies of genetic diversity in freshwater fishes, few have specifically addressed the role of habitat structure in partitioning genetic variance within and among populations. In this study, we analysed the variability of six microsatellite loci among 24 brook charr population samples in order to correlate hydrographic structure with genetic organization. These populations originated from three Canadian National parks (Kouchibouguac, Fundy and Forillon) that showed distinct hydrographic structure. Considering the general characteristics of these habitats, we formulated specific hypotheses in regard to genetic structure, which were principally based on the potential for gene flow and population size associated with each habitat. The hierarchical analysis of molecular variance and the genetic distances computed among populations revealed that habitat structure analyses constitute an important, but insufficient, predictor of genetic structure. We discuss the importance of habitat complexity on genetic structure in the context of management and conservation.

  17. Projection of Young-Old and Old-Old with Functional Disability: Does Accounting for the Changing Educational Composition of the Elderly Population Make a Difference?

    PubMed Central

    Ansah, John P.; Malhotra, Rahul; Lew, Nicola; Chiu, Chi-Tsun; Chan, Angelique; Bayer, Steffen; Matchar, David B.

    2015-01-01

    This study compares projections, up to year 2040, of young-old (aged 60-79) and old-old (aged 80+) with functional disability in Singapore with and without accounting for the changing educational composition of the Singaporean elderly. Two multi-state population models, with and without accounting for educational composition respectively, were developed, parameterized with age-gender-(education)-specific transition probabilities (between active, functional disability and death states) estimated from two waves (2009 and 2011) of a nationally representative survey of community-dwelling Singaporeans aged ≥60 years (N=4,990). Probabilistic sensitivity analysis with the bootstrap method was used to obtain the 95% confidence interval of the transition probabilities. Not accounting for educational composition overestimated the young-old with functional disability by 65 percent and underestimated the old-old by 20 percent in 2040. Accounting for educational composition, the proportion of old-old with functional disability increased from 40.8 percent in 2000 to 64.4 percent by 2040; not accounting for educational composition, the proportion in 2040 was 49.4 percent. Since the health profiles, and hence care needs, of the old-old differ from those of the young-old, health care service utilization and expenditure and the demand for formal and informal caregiving will be affected, impacting health and long-term care policy. PMID:25974069

  18. Projection of young-old and old-old with functional disability: does accounting for the changing educational composition of the elderly population make a difference?

    PubMed

    Ansah, John P; Malhotra, Rahul; Lew, Nicola; Chiu, Chi-Tsun; Chan, Angelique; Bayer, Steffen; Matchar, David B

    2015-01-01

    This study compares projections, up to year 2040, of young-old (aged 60-79) and old-old (aged 80+) with functional disability in Singapore with and without accounting for the changing educational composition of the Singaporean elderly. Two multi-state population models, with and without accounting for educational composition respectively, were developed, parameterized with age-gender-(education)-specific transition probabilities (between active, functional disability and death states) estimated from two waves (2009 and 2011) of a nationally representative survey of community-dwelling Singaporeans aged ≥ 60 years (N=4,990). Probabilistic sensitivity analysis with the bootstrap method was used to obtain the 95% confidence interval of the transition probabilities. Not accounting for educational composition overestimated the young-old with functional disability by 65 percent and underestimated the old-old by 20 percent in 2040. Accounting for educational composition, the proportion of old-old with functional disability increased from 40.8 percent in 2000 to 64.4 percent by 2040; not accounting for educational composition, the proportion in 2040 was 49.4 percent. Since the health profiles, and hence care needs, of the old-old differ from those of the young-old, health care service utilization and expenditure and the demand for formal and informal caregiving will be affected, impacting health and long-term care policy.

  19. Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei.

    PubMed

    Nock, C J; Ovenden, J R; Butler, G L; Wooden, I; Moore, A; Baverstock, P R

    2011-01-01

    Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (F(ST) = 0·09 - 0·49; P < 0·05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species. PMID:21235562

  20. Natural variation of salinity response, population structure and candidate genes associated with salinity tolerance in perennial ryegrass accessions.

    PubMed

    Tang, Jinchi; Yu, Xiaoqing; Luo, Na; Xiao, Fangming; Camberato, James J; Jiang, Yiwei

    2013-11-01

    Natural variation in salinity response, effects of population structure on growth and physiological traits and gene-trait association were examined in 56 global collections of diverse perennial ryegrass (Lolium perenne L.) accessions. Three population structure groups were identified with 66 simple sequence repeat markers, which on average accounted for 9 and 11% of phenotypic variation for the control and salinity treatment at 300 mm NaCl. Group 1 (10 accessions) had greater plant height, leaf dry weight and water content, chlorophyll index, K(+) concentration and K(+) /Na(+) than group 2 (39 accessions) and group 3 (7 accessions) under salinity stress, while group 3 had higher Na(+) than groups 1 and 2. Eighty-seven single nucleotide polymorphisms were detected from four partial candidate genes encoding aquaporin and Na(+) /H(+) antiporter in both plasma and tonoplast membranes. Overall, rapid decay of linkage disequilibrium was observed within 500 bp. Significant associations were found between the putative LpTIP1 and Na(+) for the control and between the putative LpNHX1 and K(+) /Na(+) under the control and salinity treatments after controlling population structure. These results indicate that population structure influenced phenotypic traits, and allelic variation in LpNHX1 may affect salinity tolerance of perennial ryegrass.

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

    PubMed

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

    2006-08-01

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

  2. DEMOGRAPHY AND SPATIAL POPULATION STRUCTURE IN CALIFORNIA TIGER SALAMANDER

    EPA Science Inventory

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

  3. Spatially structured population dynamics in feral oilseed rape.

    PubMed Central

    Crawley, Michael J.; Brown, Susan L.

    2004-01-01

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

  4. Optimal lineage principle for age-structured populations

    NASA Astrophysics Data System (ADS)

    Kussell, Edo

    2012-02-01

    Populations whose individuals exhibit age-dependent growth have often been studied using temporal dynamics of age distributions. In this talk, I examine the dynamics of age along lineages. We will see that the lineage point-of-view provides fundamental insights into evolutionary pressures on individuals' aging profiles. I will describe a variational principle that enables exact results for lineage statistics, in a variety of models. I will also discuss measurements on continuously dividing bacterial populations growing in microfluidics devices.

  5. Impact of Insertion Sequences and Recombination on the Population Structure of Staphylococcus haemolyticus

    PubMed Central

    Bouchami, Ons; de Lencastre, Herminia; Miragaia, Maria

    2016-01-01

    Staphylococcus haemolyticus is one of the most common pathogens associated with medical-device related infections, but its molecular epidemiology is poorly explored. In the current study, we aimed to better understand the genetic mechanisms contributing to S. haemolyticus diversity in the hospital environment and their impact on the population structure and clinical relevant phenotypic traits. The analysis of a representative S. haemolyticus collection by multilocus sequence typing (MLST) has identified a single highly prevalent and diverse genetic lineage of nosocomial S. haemolyticus clonal complex (CC) 29 accounting for 91% of the collection of isolates disseminated worldwide. The examination of the sequence changes at MLST loci during clonal diversification showed that recombination had a higher impact than mutation in shaping the S. haemolyticus population. Also, we ascertained that another mechanism contributing significantly to clonal diversification and adaptation was mediated by insertion sequence (IS) elements. We found that all nosocomial S. haemolyticus, belonging to different STs, were rich in IS1272 copies, as determined by Southern hybridization of macrorestriction patterns. In particular, we observed that the chromosome of a S. haemolyticus strain within CC29 was highly unstable during serial growth in vitro which paralleled with IS1272 transposition events and changes in clinically relevant phenotypic traits namely, mannitol fermentation, susceptibility to beta-lactams, biofilm formation and hemolysis. Our results suggest that recombination and IS transposition might be a strategy of adaptation, evolution and pathogenicity of the major S. haemolyticus prevalent lineage in the hospital environment. PMID:27249649

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

    PubMed Central

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

    2012-01-01

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

  7. Auditing and accountability within the public hospital system: the need for structural reforms.

    PubMed

    Malley, A; Forde, K

    1993-01-01

    A recent report by the Independent Commission Against Corruption (ICAC) in NSW highlighted that some accounting controls for cash handling in public hospitals are inadequate. Given the number of public hospitals in Australia and the amount of cash being handled, it is essential that efficient accounting and auditing systems are established for these activities. This paper examines several major shortcomings in cash-handling methods used by NSW public hospitals and outlines how the system may be improved. The authors are currently developing a national survey to extend this analysis.

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

    PubMed

    Marschalek, Daniel A; Berres, Mark E

    2014-01-01

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

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

    PubMed

    Marschalek, Daniel A; Berres, Mark E

    2014-01-01

    Populations on the periphery of a species' range tend to contain lower genetic variation and increased genetic differentiation compared to populations at the core of a species range, although some exceptions to this generalization occur. The blister beetle Gnathium minimum (Say) exhibits a wide-ranging distribution in the western United States but has peripheral or disjunct populations in Mexico, Florida, and Wisconsin. We used amplified fragment length polymorphism (AFLP) to compare the genetic variation and magnitude of genetic differentiation of the Wisconsin peripheral population to western core populations (Colorado, Kansas, New Mexico, and Texas). The proportion of polymorphic loci was 53.6 and 54.3, and expected heterozygosity 0.1864 and 0.1933 for the Kansas/Colorado (n = 87) and New Mexico/Texas (n = 35) regions, respectively. Specimens from Wisconsin (n = 121) had a lower proportion of polymorphic loci (38.4) and expected heterozygosity (0.1475). Genetic cluster estimation with GENELAND and F ST values showed greater genetic differentiation among the sampling locations within Wisconsin compared to core regions. Significant isolation-by-distance (IBD) was also observed in Wisconsin but not within the core regions. Lower genetic variation and increased isolation may reduce the Wisconsin population's ability to respond to change, thereby increasing their susceptibility to extinction. PMID:25160848

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

    PubMed

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

    2015-01-01

    The clam Macridiscus multifarius with a planktonic larval stage of about 10 days is an ecologically and economically important species in the coastal regions of China. In this study, 3 mt-DNA markers (COI, 12S rRNA, and ND1) were used to investigate the population structure and demography of wild M. multifarius populations in 3 coastal localities of the East China Sea (ZS and ZP populations) and Beibu Gulf in the South China Sea (BH population). Sequences of 685 bp in COI, 350 bp in 12S rRNA, and 496 bp in ND1 were determined. High level and significant FST values were obtained among the different localities on the basis of either COI (FST = 0.100-0.444, p < 0.05) or 12S rRNA (FST = 0.199-0.742, p < 0.05) gene, indicating a high degree of genetic differentiation among the populations. FST values were significant but weak for the ND1 gene because it is highly conservative. The median-joining network suggested an obvious genetic differentiation between ZS and BH populations, and the finding is consistent with the results of our demographic analyses using the unweighted pair group method with arithmetic mean. Our study unraveled the extant population genetic structure of M. multifarius and explained the strong population structure of a species with a short planktonic larval stage species; this information could be useful for fishery management measures, including artificial breeding and conservation. PMID:26720602

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

    PubMed

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

    2015-01-01

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

  12. Juxtaposition between host population structures: implications for disease transmission in a sympatric cervid community

    PubMed Central

    Vander Wal, Eric; Edye, Iain; Paquet, Paul C; Coltman, David W; Bayne, Erin; Brook, Ryan K; Andrés, José A

    2013-01-01

    Sympatric populations of phylogenetically related species are often vulnerable to similar communicable diseases. Although some host populations may exhibit spatial structure, other hosts within the community may have unstructured populations. Thus, individuals from unstructured host populations may act as interspecific vectors among discrete subpopulations of sympatric alternate hosts. We used a cervid-bovine tuberculosis (Mycobacterium bovis) system to investigate the landscape-scale potential for bovine tuberculosis transmission within a nonmigratory white-tailed deer (Odocoileus virginianus) and elk (Cervus canadensis) community. Using landscape population genetics, we tested for genetic and spatial structure in white-tailed deer. We then compared these findings with the sympatric elk population that is structured and which has structure that correlates spatially and genetically to physiognomic landscape features. Despite genetic structure that indicates the white-tailed deer population forms three sympatric clusters, the absence of spatial structure suggested that intraspecific pathogen transmission is not likely to be limited by physiognomic landscape features. The potential for intraspecific transmission among subpopulations of elk is low due to spatial population structure. Given that white-tailed deer are abundant, widely distributed, and exhibit a distinct lack of spatial population structure, white-tailed deer likely pose a greater threat as bovine tuberculosis vectors among elk subpopulations than elk. PMID:24187583

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

    PubMed

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

    2015-07-01

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

  14. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    PubMed

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; p<0.0001) whereas Kisii had the least significant index of association values (0.03; p<0.0001). Our data suggest high genetic diversity in Kenyan parasite population with the exception of parasite from Malindi where malaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after

  15. An efficient multi-locus mixed model approach for genome-wide association studies in structured populations

    PubMed Central

    Segura, Vincent; Vilhjálmsson, Bjarni J.; Platt, Alexander; Korte, Arthur; Seren, Ümit; Long, Quan; Nordborg, Magnus

    2012-01-01

    Population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. Mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but do not always account for loci of larger effect. Here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. Simulations suggest that our method outperforms existing methods, in terms of power as well as false discovery rate. We apply our method to human and Arabidopsis thaliana data, identifying novel associations in known candidates as well as evidence for allelic heterogeneity. We also demonstrate how a priori knowledge from an A. thaliana linkage mapping study can be integrated into our method using a Bayesian approach. Our implementation is computationally efficient, making the analysis of large datasets (n > 10000) practicable. PMID:22706313

  16. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.

    PubMed

    Segura, Vincent; Vilhjálmsson, Bjarni J; Platt, Alexander; Korte, Arthur; Seren, Ümit; Long, Quan; Nordborg, Magnus

    2012-06-17

    Population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. Mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but they do not always account for loci of larger effect. Here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. Simulations suggest that our method outperforms existing methods in terms of power as well as false discovery rate. We apply our method to human and Arabidopsis thaliana data, identifying new associations and evidence for allelic heterogeneity. We also show how a priori knowledge from an A. thaliana linkage mapping study can be integrated into our method using a Bayesian approach. Our implementation is computationally efficient, making the analysis of large data sets (n > 10,000) practicable.

  17. Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

    NASA Astrophysics Data System (ADS)

    Costantini, Federica; Abbiati, Marco

    2016-03-01

    Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

  18. Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain.

    PubMed

    Pérez-Figueroa, A; Fernández, C; Amaro, R; Hermida, M; San Miguel, E

    2015-08-01

    Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N(e)) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N(e) estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N(e) estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30-56 and 47-56 for the Rato and Guisande Rivers, respectively. Estimated census size (N(c)) for the Rato River was 880 individuals. This yielded a N(e)/N(c) estimate of 3-6 % for temporal estimation of N(e), which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.

  19. Inbreeding rate and genetic structure of cat populations in Poland.

    PubMed

    Mucha, S; Wolc, A; Gradowska, A; Szwaczkowski, T

    2011-02-01

    The objective of the study was to analyze effective population size and inbreeding level in populations of cat breeds registered in the Polish Studbook. The Association of Purebred Cat Breeders in Poland provided access to pedigrees of 26725 cats from seven breeds. The most frequent breed was Persian, however increasing tendency in numbers of registered animals from other breeds was recorded in later years. Although the percentage of inbred individuals was increasing over time, mating of close relatives was avoided by most of the breeders, and the average inbreeding coefficient exceeded 5% only for Siberian and Russian breeds. Current analysis suggests that the Polish pedigree cat populations are not threatened by negative effects of inbreeding.

  20. Evolutionary dynamics of social dilemmas in structured heterogeneous populations

    PubMed Central

    Santos, F. C.; Pacheco, J. M.; Lenaerts, Tom

    2006-01-01

    Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations. PMID:16484371

  1. Evolutionary dynamics of social dilemmas in structured heterogeneous populations.

    PubMed

    Santos, F C; Pacheco, J M; Lenaerts, Tom

    2006-02-28

    Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations. PMID:16484371

  2. Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas.

    PubMed

    Lasker, Howard R; Porto-Hannes, Isabel

    2015-01-01

    Patterns of dispersal and connectivity of the Caribbean gorgonian Antillogorgia elisabethae in The Bahamas were assessed in both adults and recently settled recruits from 13 sites using microsatellite loci. Adult populations along the Little Bahama Bank (LBB) exhibited a clear pattern of isolation by distance (IBD) which described 86% of the variance in pairwise genetic distances. Estimates of dispersal based on the IBD model suggested dispersal distances along the LBB on the order of 100 m. Increasing the spatial scale to include sites separated by open ocean generated an apparent IBD signal but the relationship had a greater slope and explained less of the variance. This relationship with distance reflected both stepping stone based IBD and regional differentiation probably created by ocean currents and barriers to dispersal that are correlated with geographic distance. Analysis of recruits from 4 sites on the LBB from up to 6 years did not detect differences between years nor differences with adult populations. The result suggests that neither selection on recruits nor inter-annual variation in dispersal affected adult population structure. Assignment tests of recruits indicated the most likely sources of the recruits were the local or adjacent populations. Most of the patterning in population structure in the northern Bahamas can be explained by geographic distance and oceanographic connectivity. Recognition of these complex patterns is important in developing management plans for A. elisabethae and in understanding the effects of disturbance to adult populations of A. elisabethae and similar species with limited dispersal. PMID:26157606

  3. Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas

    PubMed Central

    Porto-Hannes, Isabel

    2015-01-01

    Patterns of dispersal and connectivity of the Caribbean gorgonian Antillogorgia elisabethae in The Bahamas were assessed in both adults and recently settled recruits from 13 sites using microsatellite loci. Adult populations along the Little Bahama Bank (LBB) exhibited a clear pattern of isolation by distance (IBD) which described 86% of the variance in pairwise genetic distances. Estimates of dispersal based on the IBD model suggested dispersal distances along the LBB on the order of 100 m. Increasing the spatial scale to include sites separated by open ocean generated an apparent IBD signal but the relationship had a greater slope and explained less of the variance. This relationship with distance reflected both stepping stone based IBD and regional differentiation probably created by ocean currents and barriers to dispersal that are correlated with geographic distance. Analysis of recruits from 4 sites on the LBB from up to 6 years did not detect differences between years nor differences with adult populations. The result suggests that neither selection on recruits nor inter-annual variation in dispersal affected adult population structure. Assignment tests of recruits indicated the most likely sources of the recruits were the local or adjacent populations. Most of the patterning in population structure in the northern Bahamas can be explained by geographic distance and oceanographic connectivity. Recognition of these complex patterns is important in developing management plans for A. elisabethae and in understanding the effects of disturbance to adult populations of A. elisabethae and similar species with limited dispersal. PMID:26157606

  4. Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

    PubMed

    Velo-Antón, Guillermo; Godinho, Raquel; Campos, João Carlos; Brito, José Carlos

    2014-01-01

    The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments. PMID:24740183

  5. Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

    PubMed

    Velo-Antón, Guillermo; Godinho, Raquel; Campos, João Carlos; Brito, José Carlos

    2014-01-01

    The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.

  6. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure.

    PubMed

    Möbius, Wolfram; Murray, Andrew W; Nelson, David R

    2015-12-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from

  7. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

    PubMed Central

    Möbius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2015-01-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle’s shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call ‘geometry-enhanced genetic drift’, complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects

  8. Ultrafast Population Switching of Quantum Dots in a Structured Vacuum

    SciTech Connect

    Ma Xun; John, Sajeev

    2009-12-04

    We demonstrate picosecond, high-contrast population flipping of two-level atoms interacting with femtojoule optical pulses in a 3D photonic band gap waveguide. This is the result of giant Mollow splitting caused by strong light localization and a remarkable field-dependent relaxation of the atomic Bloch vector as it evolves near an abrupt jump in the electromagnetic density of states. Unlike steady-state switching, population inversion can remain nearly complete after the pulse subsides. This may be used for multiwavelength channel, all-optical, on-chip information processing.

  9. Population dynamics of a South American rodent: seasonal structure interacting with climate, density dependence and predator effects.

    PubMed Central

    Lima, Mauricio; Stenseth, Nils Chr; Jaksic, Fabian M

    2002-01-01

    Understanding the role of interactions between intrinsic feedback loops and external climatic forces is one of the central challenges within the field of population ecology. For rodent dynamics, the seasonal structure of the environment necessitates changes between two stages: reproductive and non-reproductive. Nevertheless, the interactions between seasonality, climate, density dependence and predators have been generally ignored. We demonstrate that direct climate effects, the nonlinear effect of predators and the nonlinear first-order feedback embedded in a seasonal structure are key elements underlying the large and irregular fluctuations in population numbers exhibited by a small rodent in a semi-arid region of central Chile. We found that factors influencing population growth rates clearly differ between breeding and non-breeding seasons. In addition, we detected nonlinear density dependencies as well as nonlinear and differential effects of generalist and specialist predators. Recent climatic changes may account for dramatic perturbations of the rodent's population dynamics. Changes in the predator guild induced by climate are likely to result, through the food web, in a large impact on small rodent demography and population dynamics. Assuming such interactions to be typical of ecological systems, we conclude that appropriate predictions of the ecological consequences of climate change will depend on having an in-depth understanding of the community-weather system. PMID:12573073

  10. Population genetic structure of the Lyme disease vector Ixodes scapularis at an apparent spatial expansion front.

    PubMed

    Kelly, Rebecca R; Gaines, David; Gilliam, Will F; Brinkerhoff, R Jory

    2014-10-01

    Modeling and empirical evidence suggests that Lyme disease is undergoing geographic expansion from principal foci in the midwestern and northeastern United States. Virginia is at the southern edge of the current expansion zone and has seen dramatic rise in human Lyme disease cases since 2007, potentially owing to a recent increase in vector abundance. Ixodes scapularis is known throughout the eastern US but behavioral or physiological variation between northern and southern lineages might lead northern-variant ticks to more frequently parasitize humans. We hypothesized that recent spatial and numerical increase in Lyme disease cases is associated with demographic and/or spatial expansion of I. scapularis and that signals of these phenomena would be detectable and discernable in population genetic signals. In summer and fall 2011, we collected nymphal I. scapularis by drag sampling and adult I. scapularis from deer carcasses at hunting check stations at nine sites arranged along an east-west transect through central Virginia. We analyzed 16S mtDNA sequences data from up to 24 I. scapularis individuals collected from each site and detected a total of 24 haplotypes containing 29 segregating sites. We found no evidence for population genetic structure among these sites but we did find strong signals of both demographic and spatial expansion throughout our study system. We found two haplotypes (one individual each) representing a lineage of ticks that is only found in the southeastern United States, with the remaining individuals representing a less genetically diverse clade that is typical of the northern United States, but that has also been detected in the American South. Taken together, these results lead us to conclude that I. scapularis populations in Virginia are expanding and that this expansion may account for recent observed increases in Lyme disease. PMID:24882702

  11. Population genetic structure of the Lyme disease vector Ixodes scapularis at an apparent spatial expansion front.

    PubMed

    Kelly, Rebecca R; Gaines, David; Gilliam, Will F; Brinkerhoff, R Jory

    2014-10-01

    Modeling and empirical evidence suggests that Lyme disease is undergoing geographic expansion from principal foci in the midwestern and northeastern United States. Virginia is at the southern edge of the current expansion zone and has seen dramatic rise in human Lyme disease cases since 2007, potentially owing to a recent increase in vector abundance. Ixodes scapularis is known throughout the eastern US but behavioral or physiological variation between northern and southern lineages might lead northern-variant ticks to more frequently parasitize humans. We hypothesized that recent spatial and numerical increase in Lyme disease cases is associated with demographic and/or spatial expansion of I. scapularis and that signals of these phenomena would be detectable and discernable in population genetic signals. In summer and fall 2011, we collected nymphal I. scapularis by drag sampling and adult I. scapularis from deer carcasses at hunting check stations at nine sites arranged along an east-west transect through central Virginia. We analyzed 16S mtDNA sequences data from up to 24 I. scapularis individuals collected from each site and detected a total of 24 haplotypes containing 29 segregating sites. We found no evidence for population genetic structure among these sites but we did find strong signals of both demographic and spatial expansion throughout our study system. We found two haplotypes (one individual each) representing a lineage of ticks that is only found in the southeastern United States, with the remaining individuals representing a less genetically diverse clade that is typical of the northern United States, but that has also been detected in the American South. Taken together, these results lead us to conclude that I. scapularis populations in Virginia are expanding and that this expansion may account for recent observed increases in Lyme disease.

  12. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  13. Genetic structure among and within peripheral and central populations of three endangered floodplain violets.

    PubMed

    Eckstein, R L; O'neill, R A; Danihelka, J; Otte, A; Köhler, W

    2006-08-01

    Understanding the partitioning of genetic variance in peripheral and central populations may shed more light on the effects of genetic drift and gene flow on population genetic structure and, thereby, improve attempts to conserve genetic diversity. We analysed genetic structure of peripheral and central populations of three insect-pollinated violets (Viola elatior, Viola pumila, Viola stagnina) to evaluate to what extent these patterns can be explained by gene flow and genetic drift. Amplified fragment length polymorphism was used to analyse 930 individuals of 50 populations. Consistent with theoretical predictions, peripheral populations were smaller and more isolated, differentiation was stronger, and genetic diversity and gene flow lower in peripheral populations of V. pumila and V. stagnina. In V. elatior, probably historic fragmentation effects linked to its specific habitat type were superimposed on the plant geographic (peripheral-central) patterns, resulting in lower relative importance of gene flow in central populations. Genetic variation between regions (3-6%), among (30-37%) and within populations (60-64%) was significant. Peripheral populations lacked markers that were rare and localized in central populations. Loss of widespread markers in peripheral V. stagnina populations indicated genetic erosion. Autocorrelation within populations was statistically significant up to a distance of 10-20 m. Higher average genetic similarity in peripheral populations than in central ones indicated higher local gene flow, probably owing to management practices. Peripheral populations contributed significantly to genetic variation and contained unique markers, which made them valuable for the conservation of genetic diversity.

  14. [Genetic structure of wild Macrobrachium nipponense populations in Taihu Lake based on microsatellite analysis].

    PubMed

    Feng, Jian-Bin; Wu, Chun-Lin; Ma, Ke-Yi; Ding, Huai-Yu; Hua, Xue-Ming; Li, Jia-Le

    2011-06-01

    By using eight highly polymorphic microsatellite DNA loci, this paper analyzed the genetic structure of wild Macrobrachium nipponense populations in Taihu Lake. For the 15 M. nipponense populations in the Lake, there were at least three of the loci presenting heterozygosity deficiency and obvious deviation from Hardy-Weinberg equilibrium after Bonferroni correction. The observed heterozygosity values of the 15 populations were all above 0. 683, displaying a high genetic diversity, but the diversity varied obviously with site. For example, the genetic diversity of the eastern and southern populations at Dukou and Luxiang was higher than that of the western and northern populations at Huazhuang and Yangzhu. For the 15 populations, parts of the loci showed heterozygote excess and departure from mutation-drift equilibrium, suggesting that the population structure had experienced bottleneck effect and the population amount had declined. The AMOVA analysis across all the populations and loci showed that the genetic divergence among the 15 populations was at a lower level (F(ST) = 0.011 ). 98.9% of the genetic variation came from intra-population, and 1.1% came from inter-population, suggesting that all the M. nipponense populations in the Lake could be protected and managed as a single unit in genetic resource. However, the genetic distance between Huazhuang and Wutangmen populations reached 0.206, being close to the delimitation of species identification. Further studies would be needed for the sustainable utilization of the genetic resource of M. nipponense in Taihu Lake.

  15. Population structure of red-cockaded woodpeckers (Picoides borealis) in south Florida: RAPDs revisited

    USGS Publications Warehouse

    Haig, Susan M.; Bowman, R.; Mullins, Thomas D.

    1996-01-01

    Six south Florida populations of the endangered red-cockaded woodpecker (Picoides borealis) were sampled to examine genetic diversity and population structure in the southernmost portion of the species' range relative to 14 previously sampled populations from throughout the species range. Random amplified polymorphic DNA (RAPD) analyses were used to evaluate the populations (n= 161 individuals, 13 primers, one band/primer). Results suggested that south Florida populations have significant among-population genetic differentiation (FST= 0.17, P < 0.000), although gene flow may be adequate to offset drift (Nm= 1.26). Comparison of Florida populations with others sampled indicated differentiation was less in Florida (FST for all populations = 0.21). Cluster analyses of all 20 populations did not reflect complete geographical predictions, although clustering of distant populations resulted in a significant correlation between genetic distance and geographical distance. Overall, results suggest populations in south Florida, similar to the remainder of the species, have low genetic diversity and high population fragmentation. Exact clustering of distant populations supports the ability of RAPDs to differentiate populations accurately. Our results further support past management recommendations that translocations of birds among geographically proximate populations is preferable to movement of birds between distant populations.

  16. Genetic structure of introduced populations: 120-year-old DNA footprint of historic introduction in an insular small mammal population

    PubMed Central

    Simpson, Siobhan; Blampied, Nick; Peniche, Gabriela; Dozières, Anne; Blackett, Tiffany; Coleman, Stephen; Cornish, Nina; Groombridge, Jim J

    2013-01-01

    Wildlife populations have been introduced to new areas by people for centuries, but this human-mediated movement can disrupt natural patterns of genetic structure by altering patterns of gene flow. Insular populations are particularly prone to these influences due to limited opportunities for natural dispersal onto islands. Consequently, understanding how genetic patterns develop in island populations is important, particularly given that islands are frequently havens for protected wildlife. We examined the evolutionary origins and extent of genetic structure within the introduced island population of red squirrels (Sciurus vulgaris) on the Channel Island of Jersey using mitochondrial DNA (mtDNA) control region sequence and nuclear microsatellite genotypes. Our findings reveal two different genetic origins and a genetic architecture reflective of the introductions 120 years ago. Genetic structure is marked within the maternally inherited mtDNA, indicating slow dispersal of female squirrels. However, nuclear markers detected only weak genetic structure, indicating substantially greater male dispersal. Data from both mitochondrial and nuclear markers support historic records that squirrels from England were introduced to the west of the island and those from mainland Europe to the east. Although some level of dispersal and introgression across the island between the two introductions is evident, there has not yet been sufficient gene flow to erase this historic genetic “footprint.” We also investigated if inbreeding has contributed to high observed levels of disease, but found no association. Genetic footprints of introductions can persist for considerable periods of time and beyond traditional timeframes of wildlife management. PMID:23532702

  17. Population Structure of the North American Cranberry Fruit Rot Complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cranberry fruit rot is caused by a complex of pathogenic fungi. Variation in the populations within this complex from region to region could delay identification of the causal agents(s) and complicate management strategies. Our objective was to assess genetic variation within the four major fruit ro...

  18. mtDNA variation in Inuit populations of Greenland and Canada: migration history and population structure.

    PubMed

    Helgason, Agnar; Pálsson, Gísli; Pedersen, Henning Sloth; Angulalik, Emily; Gunnarsdóttir, Ellen Dröfn; Yngvadóttir, Bryndís; Stefánsson, Kári

    2006-05-01

    We examined 395 mtDNA control-region sequences from Greenlandic Inuit and Canadian Kitikmeot Inuit with the aim of shedding light on the migration history that underlies the present geographic patterns of genetic variation at this locus in the Arctic. In line with previous studies, we found that Inuit populations carry only sequences belonging to haplotype clusters A2 and D3. However, a comparison of Arctic populations from Siberia, Canada, and Greenland revealed considerable differences in the frequencies of these haplotypes. Moreover, large sample sizes and regional information about birthplaces of maternal grandmothers permitted the detection of notable differences in the distribution of haplotypes among subpopulations within Greenland. Our results cast doubt on the prevailing hypothesis that contemporary Inuit trace their all of their ancestry to so-called Thule groups that expanded from Alaska about 800-1,000 years ago. In particular, discrepancies in mutational divergence between the Inuit populations and their putative source mtDNA pool in Siberia/Alaska for the two predominant haplotype clusters, A2a and A2b, are more consistent with the possibility that expanding Thule groups encountered and interbred with existing Dorset populations in Canada and Greenland.

  19. Opportunities for multidisciplinary ASH clinical hypertension specialists in an era of population health and accountable care: ASH leadership message.

    PubMed

    Egan, Brent M

    2014-07-01

    The ASH hypertension specialists and ASH clinical and comprehensive hypertension centers represent a continuum of expertise and capacity positioned to play a major role in advancing the Triple Aim, which includes improving the patient care experience, population health, and value in cardiovascular health promotion and disease prevention. The ASH hypertension specialists board is dedicated to testing and designating a broad range of qualified health care professionals as clinical hypertension specialists. A continuing partnership with ASH, recognizing the need for an appropriate firewall between education and testing, is essential in providing the education and training programs required to grow and sustain the specialized workforce required to translate current evidence and future advances in personalized medicine into better care for individuals, better health for populations, and better value for payers. Moreover, growth of the ASH hypertension registry has the potential to accelerate advances in education and patient care as noted previously. The ASH hypertension specialists board is excited about the opportunities available to a well-trained and collaborative multidisciplinary group of clinical hypertension specialists in an era of ACOs pursuing the Triple Aim. PMID:25064766

  20. Evolution of aging: individual life history trade-offs and population heterogeneity account for mortality patterns across species.

    PubMed

    Le Cunff, Y; Baudisch, A; Pakdaman, K

    2014-08-01

    A broad range of mortality patterns has been documented across species, some even including decreasing mortality over age. Whether there exist a common denominator to explain both similarities and differences in these mortality patterns remains an open question. The disposable soma theory, an evolutionary theory of aging, proposes that universal intracellular trade-offs between maintenance/lifespan and reproduction would drive aging across species. The disposable soma theory has provided numerous insights concerning aging processes in single individuals. Yet, which specific population mortality patterns it can lead to is still largely unexplored. In this article, we propose a model exploring the mortality patterns which emerge from an evolutionary process including only the disposable soma theory core principles. We adapt a well-known model of genomic evolution to show that mortality curves producing a kink or mid-life plateaus derive from a common minimal evolutionary framework. These mortality shapes qualitatively correspond to those of Drosophila melanogaster, Caenorhabditis elegans, medflies, yeasts and humans. Species evolved in silico especially differ in their population diversity of maintenance strategies, which itself emerges as an adaptation to the environment over generations. Based on this integrative framework, we also derive predictions and interpretations concerning the effects of diet changes and heat-shock treatments on mortality patterns.

  1. Demography and genetic structure of a recovering grizzly bear population

    USGS Publications Warehouse

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  2. Evolution of population structure in a highly social top predator, the killer whale.

    PubMed

    Hoelzel, A Rus; Hey, Jody; Dahlheim, Marilyn E; Nicholson, Colin; Burkanov, Vladimir; Black, Nancy

    2007-06-01

    Intraspecific resource partitioning and social affiliations both have the potential to structure populations, though it is rarely possible to directly assess the impact of these mechanisms on genetic diversity and population divergence. Here, we address this for killer whales (Orcinus orca), which specialize on prey species and hunting strategy and have long-term social affiliations involving both males and females. We used genetic markers to assess the structure and demographic history of regional populations and test the hypothesis that known foraging specializations and matrifocal sociality contributed significantly to the evolution of population structure. We find genetic structure in sympatry between populations of foraging specialists (ecotypes) and evidence for isolation by distance within an ecotype. Fitting of an isolation with migration model suggested ongoing, low-level migration between regional populations (within and between ecotypes) and small effective sizes for extant local populations. The founding of local populations by matrifocal social groups was indicated by the pattern of fixed mtDNA haplotypes in regional populations. Simulations indicate that this occurred within the last 20,000 years (after the last glacial maximum). Our data indicate a key role for social and foraging behavior in the evolution of genetic structure among conspecific populations of the killer whale. PMID:17400573

  3. Reconciling nuclear microsatellite and mitochondrial marker estimates of population structure: breeding population structure of Chesapeake Bay striped bass (Morone saxatilis).

    PubMed

    Brown, K M; Baltazar, G A; Hamilton, M B

    2005-06-01

    Comparative analyses of nuclear and organelle genetic markers may help delineate evolutionarily significant units or management units, although population differentiation estimates from multiple genomes can also conflict. Striped bass (Morone saxatilis) are long-lived, highly migratory anadromous fish recently recovered from a severe decline in population size. Previous studies with protein, nuclear DNA and mitochondrial DNA (mtDNA) markers produced discordant results, and it remains uncertain if the multiple tributaries within Chesapeake Bay constitute distinct management units. Here, 196 young-of-the-year (YOY) striped bass were sampled from Maryland's Choptank, Potomac and Nanticoke Rivers and the north end of Chesapeake Bay in 1999 and from Virginia's Mataponi and Rappahannock Rivers in 2001. A total of 10 microsatellite loci exhibited between two and 27 alleles per locus with observed heterozygosities between 0.255 and 0.893. The 10-locus estimate of R(ST) among the six tributaries was -0.0065 (95% confidence interval -0.0198 to 0.0018). All R(ST) and all but one theta estimates for pairs of populations were not significantly different from zero. Reanalysis of Chesapeake Bay striped bass mtDNA data from two previous studies estimated population differentiation between theta=-0.002 and 0.160, values generally similar to mtDNA population differentiation predicted from microsatellite R(ST) after adjusting for reduced effective population size and uniparental inheritance in organelle genomes. Based on mtDNA differentiation, breeding sex ratios or gene flow may have been slightly male biased in some years. The results reconcile conflicting past studies based on different types of genetic markers, supporting a single Chesapeake Bay management unit encompassing a panmictic striped bass breeding population.

  4. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    PubMed

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists. PMID:23487323

  5. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    PubMed

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  6. Genetic diversity and population structure of Arabidopsis thaliana along an altitudinal gradient

    PubMed Central

    Tyagi, Antariksh; Singh, Shivani; Mishra, Parneeta; Singh, Akanksha; Tripathi, Abhinandan Mani; Jena, Satya Narayan; Roy, Sribash

    2016-01-01

    The natural genetic variation within a plant species is primarily a consequence of its phylogeography and evolutionary history. This variation largely determines its present-day population structure. Arabidopsis thaliana, as a model plant, has been studied in great detail including its probable origin, local as well as global genetic diversity pattern, population structure, adaptation, etc. However, no such studies have so far been reported from the Indian Himalayan region. Here, we describe a comprehensive study on the genetic diversity and population structure of A. thaliana from an altitudinal range of 700–3400 m above mean sea level the highest altitudinal range reported so far. We also compare these populations with previously reported worldwide populations. A total of 48 accessions representing six populations were analysed using 19 microsatellites and 11 chloroplast markers. Genetic diversity analysis indicated populations to be highly diverse and comparable with worldwide populations. STRUCTURE, principal coordinate and isolation by distance (IBD) analyses showed that genetic variation in different populations is structured at geographical and altitudinal level. Further analyses indicate that these populations are genetically distinct from the rest of the world populations. Different parameters of the demographic expansion model support a rapid expansion. Based on mismatch distribution, the initial time of expansion of west Himalayan populations was found to be about 130 000 years. Bayesian analysis of divergence time indicated that these populations have a long evolutionary history in this region. Based on the results of genetic diversity parameters, demographic expansion and divergence time estimation, it appears that west Himalayan populations may be the source of the west–east expansion model. PMID:26672075

  7. Population genetic structure of Anopheles gambiae mosquitoes on Lake Victoria islands, west Kenya

    PubMed Central

    Chen, Hong; Minakawa, Noboru; Beier, John; Yan, Guiyun

    2004-01-01

    Background Understanding the genetic structure of island Anopheles gambiae populations is important for the current tactics in mosquito control and for the proposed strategy using genetically-modified mosquitoes (GMM). Genetically-isolated mosquito populations on islands are a potential site for testing GMM. The objective of this study was to determine the genetic structure of A. gambiae populations on the islands in Lake Victoria, western Kenya. Methods The genetic diversity and the population genetic structures of 13 A. gambiae populations from five islands on Lake Victoria and six villages from the surrounding mainland area in the Suba District were examined using six microsatellite markers. The distance range of sampling sites varied between 2.5 and 35.1 km. Results A similar level of genetic diversity between island mosquito populations and adjacent mainland populations was found. The average number of alleles per locus was 7.3 for the island populations and 6.8 for the mainland populations. The average observed heterozygosity was 0.32 and 0.28 for the island and mainland populations, respectively. A low but statistically significant genetic structure was detected among the island populations (FST = 0.019) and between the island and mainland populations (FST = 0.003). A total of 12 private alleles were found, and nine of them were from the island populations. Conclusion A level of genetic differentiation between the island and mainland populations was found. Large extent of gene flow between the island and mainland mosquito populations may result from wind- or human-assisted dispersal. Should the islands on Lake Victoria be used as a trial site for the release program of GMM, mosquito dispersal between the islands and between the island and the mainland should be vigorously monitored. PMID:15581429

  8. Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

    PubMed

    Zhong, J; Wu, F-C; Qiu, P; Dai, L-J

    2016-01-01

    To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P < 0.05) with environmental factors. Genetic differentiation existed among populations and the populations exhibited heteroplasmy. PMID:27525953

  9. Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

    PubMed

    Zhong, J; Wu, F-C; Qiu, P; Dai, L-J

    2016-01-01

    To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P < 0.05) with environmental factors. Genetic differentiation existed among populations and the populations exhibited heteroplasmy.

  10. Reproductive isolation with a learned trait in a structured population.

    PubMed

    Yeh, Douhan Justin; Servedio, Maria R

    2015-07-01

    Assortative mating displays and/or preferences can be affected by learning across a wide range of animal taxa, but the specifics of how this learning affects speciation with gene flow are not well understood. We use population genetic models with trait learning to investigate how the identity of the tutor affects the divergence of a self-referent phenotype-matching trait. We find that oblique learning (learning from unrelated individual of the previous generation) and maternal learning mask sexual selection and therefore do not allow the maintenance of divergence. In contrast, by enhancing positive frequency-dependent sexual selection, paternal learning can maintain more divergence than genetic inheritance, but leads to the loss of polymorphism more easily. Furthermore, paternal learning inhibits the invasion of a novel self-referent phenotype-matching trait, especially in a large population.

  11. When global structure "Explains Away" local grammar: a Bayesian account of rule-induction in tone sequences.

    PubMed

    Dawson, Colin; Gerken, Louann

    2011-09-01

    While many constraints on learning must be relatively experience-independent, past experience provides a rich source of guidance for subsequent learning. Discovering structure in some domain can inform a learner's future hypotheses about that domain. If a general property accounts for particular sub-patterns, a rational learner should not stipulate separate explanations for each detail without additional evidence, as the general structure has "explained away" the original evidence. In a grammar-learning experiment using tone sequences, manipulating learners' prior exposure to a tone environment affects their sensitivity to the grammar-defining feature, in this case consecutive repeated tones. Grammar-learning performance is worse if context melodies are "smooth" -- when small intervals occur more than large ones -- as Smoothness is a general property accounting for a high rate of repetition. We present an idealized Bayesian model as a "best case" benchmark for learning repetition grammars. When context melodies are Smooth, the model places greater weight on the small-interval constraint, and does not learn the repetition rule as well as when context melodies are not Smooth, paralleling the human learners. These findings support an account of abstract grammar-induction in which learners rationally assess the statistical evidence for underlying structure based on a generative model of the environment.

  12. Populations of weedy crop-wild hybrid beets show contrasting variation in mating system and population genetic structure.

    PubMed

    Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

    2010-05-01

    Reproductive traits are key parameters for the evolution of invasiveness in weedy crop-wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop-wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop-wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management.

  13. Populations of weedy crop-wild hybrid beets show contrasting variation in mating system and population genetic structure.

    PubMed

    Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

    2010-05-01

    Reproductive traits are key parameters for the evolution of invasiveness in weedy crop-wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop-wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop-wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management. PMID:25567926

  14. Populations of weedy crop–wild hybrid beets show contrasting variation in mating system and population genetic structure

    PubMed Central

    Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

    2010-01-01

    Reproductive traits are key parameters for the evolution of invasiveness in weedy crop–wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop–wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop–wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management. PMID:25567926

  15. Size-specific sensitivity: Applying a new structured population model

    SciTech Connect

    Easterling, M.R.; Ellner, S.P.; Dixon, P.M.

    2000-03-01

    Matrix population models require the population to be divided into discrete stage classes. In many cases, especially when classes are defined by a continuous variable, such as length or mass, there are no natural breakpoints, and the division is artificial. The authors introduce the integral projection model, which eliminates the need for division into discrete classes, without requiring any additional biological assumptions. Like a traditional matrix model, the integral projection model provides estimates of the asymptotic growth rate, stable size distribution, reproductive values, and sensitivities of the growth rate to changes in vital rates. However, where the matrix model represents the size distributions, reproductive value, and sensitivities as step functions (constant within a stage class), the integral projection model yields smooth curves for each of these as a function of individual size. The authors describe a method for fitting the model to data, and they apply this method to data on an endangered plant species, northern monkshood (Aconitum noveboracense), with individuals classified by stem diameter. The matrix and integral models yield similar estimates of the asymptotic growth rate, but the reproductive values and sensitivities in the matrix model are sensitive to the choice of stage classes. The integral projection model avoids this problem and yields size-specific sensitivities that are not affected by stage duration. These general properties of the integral projection model will make it advantageous for other populations where there is no natural division of individuals into stage classes.

  16. Preferential sexual transmission of pseudorabies virus in feral swine populations may not account for observed seroprevalence in the USA

    PubMed Central

    Smith, Gary

    2013-01-01

    This paper compares the behavior of two competing models for the transmission of pseudorabies virus in feral swine in the USA. In first model, horizontal (non-sexual) density dependent transmission is the only transmission modality. In the second model, the only transmission modality is sexual transmission between mature males and females. The comparison of model behavior was carried out to test the hypothesis that preferential sexual transmission of PRV in feral swine can account for the seroprevalence observed in the field. The observed range of seroprevalence of PRV in mature feral swine in the USA is consistent with a preferential sexual transmission only if the feral swine mating system is a random mating system or a polygynous system in which there is a relatively large rate of acquisition of new mates. The observed range of seroprevalence of PRV in mature feral swine in the USA is not consistent with a preferential sexual transmission if there is mate guarding. This is important because the National Pseudorabies Surveillance Plan deems monitoring the risk of PRV introduction from feral swine to be a “minor objective” both in terms of the scope of the plan and with respect to the resources allocated. The rationale for this statement was derived from experimental studies, which suggested that the PRV indigenous to feral swine in the USA is preferentially sexually transmitted. PMID:21962753

  17. Blue whale population structure along the eastern South Pacific Ocean: evidence of more than one population.

    PubMed

    Torres-Florez, J P; Hucke-Gaete, R; LeDuc, R; Lang, A; Taylor, B; Pimper, L E; Bedriñana-Romano, L; Rosenbaum, H C; Figueroa, C C

    2014-12-01

    Blue whales (Balaenoptera musculus) were among the most intensively exploited species of whales in the world. As a consequence of this intense exploitation, blue whale sightings off the coast of Chile were uncommon by the end of the 20th century. In 2004, a feeding and nursing ground was reported in southern Chile (SCh). With the aim to investigate the genetic identity and relationship of these Chilean blue whales to those in other Southern Hemisphere areas, 60 biopsy samples were collected from blue whales in SCh between 2003 and 2009. These samples were genotyped at seven microsatellite loci and the mitochondrial control region was sequenced, allowing us to identify 52 individuals. To investigate the genetic identity of this suspected remnant population, we compared these 52 individuals to blue whales from Antarctica (ANT, n = 96), Northern Chile (NCh, n = 19) and the eastern tropical Pacific (ETP, n = 31). No significant differentiation in haplotype frequencies (mtDNA) or among genotypes (nDNA) was found between SCh, NCh and ETP, while significant differences were found between those three areas and Antarctica for both the mitochondrial and microsatellite analyses. Our results suggest at least two breeding population units or subspecies exist, which is also supported by other lines of evidence such as morphometrics and acoustics. The lack of differences detected between SCh/NCh/ETP areas supports the hypothesis that eastern South Pacific blue whales are using the ETP area as a possible breeding area. Considering the small population sizes previously reported for the SCh area, additional conservation measures and monitoring of this population should be developed and prioritized. PMID:25492593

  18. Blue whale population structure along the eastern South Pacific Ocean: evidence of more than one population.

    PubMed

    Torres-Florez, J P; Hucke-Gaete, R; LeDuc, R; Lang, A; Taylor, B; Pimper, L E; Bedriñana-Romano, L; Rosenbaum, H C; Figueroa, C C

    2014-12-01

    Blue whales (Balaenoptera musculus) were among the most intensively exploited species of whales in the world. As a consequence of this intense exploitation, blue whale sightings off the coast of Chile were uncommon by the end of the 20th century. In 2004, a feeding and nursing ground was reported in southern Chile (SCh). With the aim to investigate the genetic identity and relationship of these Chilean blue whales to those in other Southern Hemisphere areas, 60 biopsy samples were collected from blue whales in SCh between 2003 and 2009. These samples were genotyped at seven microsatellite loci and the mitochondrial control region was sequenced, allowing us to identify 52 individuals. To investigate the genetic identity of this suspected remnant population, we compared these 52 individuals to blue whales from Antarctica (ANT, n = 96), Northern Chile (NCh, n = 19) and the eastern tropical Pacific (ETP, n = 31). No significant differentiation in haplotype frequencies (mtDNA) or among genotypes (nDNA) was found between SCh, NCh and ETP, while significant differences were found between those three areas and Antarctica for both the mitochondrial and microsatellite analyses. Our results suggest at least two breeding population units or subspecies exist, which is also supported by other lines of evidence such as morphometrics and acoustics. The lack of differences detected between SCh/NCh/ETP areas supports the hypothesis that eastern South Pacific blue whales are using the ETP area as a possible breeding area. Considering the small population sizes previously reported for the SCh area, additional conservation measures and monitoring of this population should be developed and prioritized.

  19. Identifying the number of population clusters with structure: problems and solutions.

    PubMed

    Gilbert, Kimberly J

    2016-05-01

    The program structure has been used extensively to understand and visualize population genetic structure. It is one of the most commonly used clustering algorithms, cited over 11,500 times in Web of Science since its introduction in 2000. The method estimates ancestry proportions to assign individuals to clusters, and post hoc analyses of results may indicate the most likely number of clusters, or populations, on the landscape. However, as has been shown in this issue of Molecular Ecology Resources by Puechmaille (), when sampling is uneven across populations or across hierarchical levels of population structure, these post hoc analyses can be inaccurate and identify an incorrect number of population clusters. To solve this problem, Puechmaille () presents strategies for subsampling and new analysis methods that are robust to uneven sampling to improve inferences of the number of population clusters. PMID:27062588

  20. Identifying the number of population clusters with structure: problems and solutions.

    PubMed

    Gilbert, Kimberly J

    2016-05-01

    The program structure has been used extensively to understand and visualize population genetic structure. It is one of the most commonly used clustering algorithms, cited over 11,500 times in Web of Science since its introduction in 2000. The method estimates ancestry proportions to assign individuals to clusters, and post hoc analyses of results may indicate the most likely number of clusters, or populations, on the landscape. However, as has been shown in this issue of Molecular Ecology Resources by Puechmaille (), when sampling is uneven across populations or across hierarchical levels of population structure, these post hoc analyses can be inaccurate and identify an incorrect number of population clusters. To solve this problem, Puechmaille () presents strategies for subsampling and new analysis methods that are robust to uneven sampling to improve inferences of the number of population clusters.

  1. Recent physical connections may explain weak genetic structure in western Alaskan chum salmon (Oncorhynchus keta) populations

    PubMed Central

    Garvin, Michael R; Kondzela, Christine M; Martin, Patrick C; Finney, Bruce; Guyon, Jeffrey; Templin, William D; DeCovich, Nick; Gilk-Baumer, Sara; Gharrett, Anthony J

    2013-01-01

    Low genetic divergence at neutral loci among populations is often the result of high levels of contemporary gene flow. Western Alaskan summer-run chum salmon (Oncorhynchus keta) populations demonstrate weak genetic structure, but invoking contemporary gene flow as the basis for the low divergence is problematic because salmon home to their natal streams and some of the populations are thousands of kilometers apart. We used genotypes from microsatellite and single nucleotide polymorphism loci to investigate alternative explanations for the current genetic structure of chum salmon populations from western Alaska. We also estimated current levels of gene flow among Kuskokwim River populations. Our results suggest that weak genetic structure is best explained by physical connections that occurred after the Holocene Thermal Maximum among the Yukon, Kuskokwim, and Nushagak drainages that allowed gene flow to occur among now distant populations. PMID:23919176

  2. Quantifying Spatial Genetic Structuring in Mesophotic Populations of the Precious Coral Corallium rubrum

    PubMed Central

    Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

    2013-01-01

    While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58–118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations. PMID:23646109

  3. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    PubMed

    Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

    2013-01-01

    While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations. PMID:23646109

  4. Population structure of Aggarwals of north India as revealed by molecular markers.

    PubMed

    Gupta, Vipin; Khadgawat, Rajesh; Ng, Hon Keung Tony; Kumar, Satish; Rao, Vadlamudi Raghavendra; Sachdeva, Mohinder Pal

    2010-12-01

    Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.

  5. Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

    USGS Publications Warehouse

    Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

    2012-01-01

    Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

  6. Genetic Diversity and Population Structure in Polygonum cespitosum: Insights to an Ongoing Plant Invasion

    PubMed Central

    Matesanz, Silvia; Theiss, Kathryn E.; Holsinger, Kent E.; Sultan, Sonia E.

    2014-01-01

    Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America), via the analyses of 516 individuals, and asked the following questions: 1) Do populations have differing levels of within-population genetic diversity? 2) Do populations form distinct genetic clusters? 3) Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering) and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources) in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further contribute to the

  7. Genetic population structure of red snapper (Lutjanus malabaricus) and orange-spotted grouper (Epinephelus coiodes) in Brunei and Sabah.

    PubMed

    Sulaiman, Zohrah H; Abdul Rahman, Khadijah H; Ying, Teo Y; Taha, Hussein H; Muhd Taha, Nurqistina H

    2008-09-01

    The genetic population structure of red snapper Lutjanus malabaricus and orange-spotted grouper Epinephelus coiodes in Brunei and Sabah was investigated using allozyme electrophoresis. Samples were collected from three sites in Brunei for E. coiodes and from three sites in Brunei and Sabah for L. malabaricus. A total of 22 loci and 16 loci were scored, respectively. The index of fixation (F(ST) ) for the E. coiodes population was 0.176 but, in general, it lacked within-population structuring. The F(ST) was particularly high between Brunei Bay/Jerudong and Brunei Bay/ Kuala Belait, suggesting genetic subdivision on a small spatial scale. Isolation of Brunei Bay from the South China Sea may constrain the movement of adult fishes and larval dispersal, thereby reducing homogeneity among subpopulations. All variable loci for E. coiodes were in Hardy-Weinberg equilibrium except for MDH* and GTDHP* (P < 0.01), in which two subpopulations showed an excess of heterozygotes (P < 0.01). The study on the L. malabaricus population showed a heterozygote deficit of approximately 60% in variable loci (F(ST) genetic variation within population = 0.45; P < 0.05); however, the mean observed heterozygosity for the population far exceeded L. malabaricus populations in Australia and Indonesia. A F(ST) value of 0.076 revealed moderate genetic differentiation among subpopulations of L. malabaricus. The genotypes were likely to be drawn from the same distribution in Jerudong and Kuala Belait. This study infers that sustainable management of snapper and grouper resources in Brunei waters must take into account the presence of a single stock and two stocks, respectively.

  8. The Experience of Counseling Among a Singaporean Elderly Population: A Qualitative Account of What Clients Report as Beneficial.

    PubMed

    Mathews, Mathew

    2016-09-01

    Adjustments that accompany ageing pose a challenge to the mental health of the elderly. Psychologically based counseling has been documented in Western societies as an appropriate intervention for elderly persons with depressive episodes. There is however very little research documenting how Asian elderly populations experience and benefit from counseling. This study addresses this research gap through a qualitative study based on post-counseling interviews with a sample of 41 elderly persons who received counseling at a dedicated organisation catering to the elderly in Singapore. The qualitative data revealed that clients benefitted from counseling through better emotional management - they received emotional support, found emotional healing and learnt to deal with the emotions associated with grief and loss. Clients also reported that counseling assisted them in decision making processes - older persons were able to conceive of alternatives to their predicament, obtained insights to embark on change, were enabled to take the perspective of others and found validation for their decisions. While many elderly clients greatly appreciated and benefitted from this service, citing demonstrable changes, among the very old such changes were uncommon. Cultural explanations for these differential reports and possible directions for much needed future research are provided. PMID:27180171

  9. Agroecosystems shape population genetic structure of the greenhouse whitefly in Northern and Southern Europe

    PubMed Central

    2014-01-01

    Background To predict further invasions of pests it is important to understand what factors contribute to the genetic structure of their populations. Cosmopolitan pest species are ideal for studying how different agroecosystems affect population genetic structure within a species at different climatic extremes. We undertook the first population genetic study of the greenhouse whitefly (Trialeurodes vaporariorum), a cosmopolitan invasive herbivore, and examined the genetic structure of this species in Northern and Southern Europe. In Finland, cold temperatures limit whiteflies to greenhouses and prevent them from overwintering in nature, and in Greece, milder temperatures allow whiteflies to inhabit both fields and greenhouses year round, providing a greater potential for connectivity among populations. Using nine microsatellite markers, we genotyped 1274 T. vaporariorum females collected from 18 greenhouses in Finland and eight greenhouses as well as eight fields in Greece. Results Populations from Finland were less diverse than those from Greece, suggesting that Greek populations are larger and subjected to fewer bottlenecks. Moreover, there was significant population genetic structure in both countries that was explained by different factors. Habitat (field vs. greenhouse) together with longitude explained genetic structure in Greece, whereas in Finland, genetic structure was explained by host plant species. Furthermore, there was no temporal genetic structure among populations in Finland, suggesting that year-round populations are able to persist in greenhouses. Conclusions Taken together our results show that greenhouse agroecosystems can limit gene flow among populations in both climate zones. Fragmented populations in greenhouses could allow for efficient pest management. However, pest persistence in both climate zones, coupled with increasing opportunities for naturalization in temperate latitudes due to climate change, highlight challenges for the

  10. 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.

  11. 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. PMID:27135585

  12. [Population genetic variation and structure analysis on five populations of mirror carp Cyprinus carpio L. using microsatellites].

    PubMed

    Quan, Ying-Chun; Li, Da-Yu; Cao, Ding-Chen; Sun, Xiao-Wen; Liang, Li-Qun

    2006-12-01

    In this paper, population genetic variability and genetic structure of five populations of an important cultivation species, mirror carp (Cyprinus carpio L.) were analyzed using 30 microsatellite loci. The observed (Ho) and expected (He) heterozygosity values, polymorphic information content (PIC) and number of effective alleles (Ae) were all determined. The genetic similarity coefficient and Nei's standard genetic distance were computed based on the allele frequencies. The Hardy-Weinberg equilibrium was checked by chi2 test. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by FST and Nm. A dendrogram was constructed based on UPGMA methods using PHYLIP software package supported by a bootstrap value of 91.0%. Totally 7,083 fragments were procured. Their lengths were from 102 bp to 446 bp. For each locus, 1-16 alleles were amplified, adding up to 356 alleles in all the 5 populations. We found the genetic variability level was relatively high in all five populations, as shown by Ae = 1.07-2.30, He= 0.70-0.78 and PIC=0.69-0.75, respectively. The genetic similarity coefficients were all above 0.52, indicating their close genetic relationships. The UPGMA phylogenetic tree showed mirror carps sampled from Donggang, Fengcheng and Liaozhong were clustered into one group and the other two populations, both collected from Songpu, were grouped together. There were obvious relations between genetic distances and geographical distributions of the five populations. No fragments were amplified from some loci of EST-SSRs, which may suggest the loss of these loci in mirror carp genome or sequence divergence at the primer binding sites. These null alleles may result from selection because functional genes are under more selection pressure than non-encoding loci. Overall, population genetic variation is high for each of the five mirror carp, and the differentiations are also significant among populations. PMID:17138540

  13. Spatial structure and chaos in insect population dynamics

    NASA Astrophysics Data System (ADS)

    Hassell, Michael P.; Comins, Hugh N.; Mayt, Robert M.

    1991-09-01

    MOST environments are spatially subdivided, or patchy, and there has been much interest in the relationship between the dynamics of populations at the local and regional (metapopulation) scales1. Here we study mathematical models for host-parasitoid interactions, where in each generation specified fractions (µN and µp, respectively) of the host and parasitoid subpopulations in each patch move to adjacent patches; in most previous work, the movement is not localized but is to any other patch2. These simple and biologically sensible models with limited diffusive dispersal exhibit a remarkable range of dynamic behaviour: the density of the host and parasitoid subpopulations in a two-dimensional array of patches may exhibit complex patterns of spiral waves or spatially chaotic variation, they may show static 'crystal lattice' patterns, or they may become extinct. This range of behaviour is obtained with the local dynamics being deterministically unstable, with a constant host reproductive rate and no density dependence in the movement patterns. The dynamics depend on the host reproductive rate, and on the values of the parameters µN and µp. The results are relatively insensitive to the details of the interactions; we get essentially the same results from the mathematically-explicit Nicholon-Bailey model of host-parasitoid interactions, and from a very general 'cellular automaton' model in which only qualitative rules are specified. We conclude that local movement in a patchy environment can help otherwise unstable host and parasitoid populations to persist together, but that the deterministically generated spatial patterns in population density can be exceedingly complex (and sometimes indistinguishable from random environmental fluctuations).

  14. In situ population structure and ex situ representation of the endangered Amur tiger.

    PubMed

    Henry, P; Miquelle, D; Sugimoto, T; McCullough, D R; Caccone, A; Russello, M A

    2009-08-01

    The Amur tiger (Panthera tigris altaica) is a critically endangered felid that suffered a severe demographic contraction in the 1940s. In this study, we sampled 95 individuals collected throughout their native range to investigate questions relative to population genetic structure and demographic history. Additionally, we sampled targeted individuals from the North American ex situ population to assess the genetic representation found in captivity. Population genetic and Bayesian structure analyses clearly identified two populations separated by a development corridor in Russia. Despite their well-documented 20th century decline, we failed to find evidence of a recent population bottleneck, although genetic signatures of a historical contraction were detected. This disparity in signal may be due to several reasons, including historical paucity in population genetic variation associated with postglacial colonization and potential gene flow from a now extirpated Chinese population. Despite conflicting signatures of a bottleneck, our estimates of effective population size (N(e) = 27-35) and N(e)/N ratio (0.07-0.054) were substantially lower than the only other values reported for a wild tiger population. Lastly, the extent and distribution of genetic variation in captive and wild populations were similar, yet gene variants persisted ex situ that were lost in situ. Overall, our results indicate the need to secure ecological connectivity between the two Russian populations to minimize loss of genetic diversity and overall susceptibility to stochastic events, and support a previous study suggesting that the captive population may be a reservoir of gene variants lost in situ.

  15. Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

    PubMed Central

    Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

    2014-01-01

    Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

  16. Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

    PubMed

    Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

    2014-01-01

    Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

  17. Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

    PubMed

    Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

    2014-01-01

    Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

  18. Temporal analysis of genetic structure to assess population dynamics of reintroduced swift foxes.

    PubMed

    Cullingham, Catherine I; Moehrenschlager, Axel

    2013-12-01

    Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos.

  19. Population.

    ERIC Educational Resources Information Center

    International Planned Parenthood Federation, London (England).

    In an effort to help meet the growing interest and concern about the problems created by the rapid growth of population, The International Planned Parenthood Federation has prepared this booklet with the aim of assisting the study of the history and future trends of population growth and its impact on individual and family welfare, national,…

  20. Structure at every scale: A semantic network account of the similarities between unrelated concepts.

    PubMed

    De Deyne, Simon; Navarro, Daniel J; Perfors, Amy; Storms, Gert

    2016-09-01

    Similarity plays an important role in organizing the semantic system. However, given that similarity cannot be defined on purely logical grounds, it is important to understand how people perceive similarities between different entities. Despite this, the vast majority of studies focus on measuring similarity between very closely related items. When considering concepts that are very weakly related, little is known. In this article, we present 4 experiments showing that there are reliable and systematic patterns in how people evaluate the similarities between very dissimilar entities. We present a semantic network account of these similarities showing that a spreading activation mechanism defined over a word association network naturally makes correct predictions about weak similarities, whereas, though simpler, models based on direct neighbors between word pairs derived using the same network cannot. (PsycINFO Database Record PMID:27560855

  1. Structure at every scale: A semantic network account of the similarities between unrelated concepts.

    PubMed

    De Deyne, Simon; Navarro, Daniel J; Perfors, Amy; Storms, Gert

    2016-09-01

    Similarity plays an important role in organizing the semantic system. However, given that similarity cannot be defined on purely logical grounds, it is important to understand how people perceive similarities between different entities. Despite this, the vast majority of studies focus on measuring similarity between very closely related items. When considering concepts that are very weakly related, little is known. In this article, we present 4 experiments showing that there are reliable and systematic patterns in how people evaluate the similarities between very dissimilar entities. We present a semantic network account of these similarities showing that a spreading activation mechanism defined over a word association network naturally makes correct predictions about weak similarities, whereas, though simpler, models based on direct neighbors between word pairs derived using the same network cannot. (PsycINFO Database Record

  2. The fine-scale genetic structure of the British population.

    PubMed

    Leslie, Stephen; Winney, Bruce; Hellenthal, Garrett; Davison, Dan; Boumertit, Abdelhamid; Day, Tammy; Hutnik, Katarzyna; Royrvik, Ellen C; Cunliffe, Barry; Lawson, Daniel J; Falush, Daniel; Freeman, Colin; Pirinen, Matti; Myers, Simon; Robinson, Mark; Donnelly, Peter; Bodmer, Walter

    2015-03-19

    Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom. This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to southeastern England from Anglo-Saxon migrations to be under half, and identify the regions not carrying genetic material from these migrations. We suggest significant pre-Roman but post-Mesolithic movement into southeastern England from continental Europe, and show that in non-Saxon parts of the United Kingdom, there exist genetically differentiated subgroups rather than a general 'Celtic' population.

  3. The fine scale genetic structure of the British population

    PubMed Central

    Davison, Dan; Boumertit, Abdelhamid; Day, Tammy; Hutnik, Katarzyna; Royrvik, Ellen C; Cunliffe, Barry; Lawson, Daniel J; Falush, Daniel; Freeman, Colin; Pirinen, Matti; Myers, Simon; Robinson, Mark; Donnelly, Peter; Bodmer, Walter

    2015-01-01

    Summary Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide SNP data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom (UK). This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to SE England from Anglo-Saxon migrations to be under half, identify the regions not carrying genetic material from these migrations, suggest significant pre-Roman but post-Mesolithic movement into SE England from the Continent, and show that in non-Saxon parts of the UK there exist genetically differentiated subgroups rather than a general “Celtic” population. PMID:25788095

  4. The fine-scale genetic structure of the British population.

    PubMed

    Leslie, Stephen; Winney, Bruce; Hellenthal, Garrett; Davison, Dan; Boumertit, Abdelhamid; Day, Tammy; Hutnik, Katarzyna; Royrvik, Ellen C; Cunliffe, Barry; Lawson, Daniel J; Falush, Daniel; Freeman, Colin; Pirinen, Matti; Myers, Simon; Robinson, Mark; Donnelly, Peter; Bodmer, Walter

    2015-03-19

    Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom. This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to southeastern England from Anglo-Saxon migrations to be under half, and identify the regions not carrying genetic material from these migrations. We suggest significant pre-Roman but post-Mesolithic movement into southeastern England from continental Europe, and show that in non-Saxon parts of the United Kingdom, there exist genetically differentiated subgroups rather than a general 'Celtic' population. PMID:25788095

  5. Genetic drift suppresses bacterial conjugation in spatially structured populations.

    PubMed

    Freese, Peter D; Korolev, Kirill S; Jiménez, José I; Chen, Irene A

    2014-02-18

    Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.

  6. Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations

    NASA Astrophysics Data System (ADS)

    Freese, Peter D.; Korolev, Kirill S.; Jiménez, José I.; Chen, Irene A.

    2014-02-01

    Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.

  7. Population genetic structure and post-LGM expansion of the plant bug Nesidiocoris tenuis (Hemiptera: Miridae) in China.

    PubMed

    Xun, Huaizhu; Li, Hu; Li, Shujuan; Wei, Shujun; Zhang, Lijuan; Song, Fan; Jiang, Pei; Yang, Hailin; Han, Fei; Cai, Wanzhi

    2016-05-27

    The plant bug, Nesidiocoris tenuis (Hemiptera: Miridae), is one of the most thermophilous dicyphines in agroecosystems and is widely distributed in China. Little is known regarding the genetic structure of N. tenuis and the effect of historical climatic fluctuations on N. tenuis populations. We analyzed partial sequences of three mitochondrial protein-coding genes (COI, ND2 and CytB) and nuclear genes (5.8S, ITS2 and 28S) for 516 specimens collected from 37 localities across China. Analyses of the combined mitochondrial dataset indicated that the Southwestern China group (SWC) was significantly differentiated from the remaining populations, other Chinese group (OC). Asymmetric migration and high level of gene flow across a long distance within the OC group was detected. The long-distance dispersal of N. tenuis might be affected by air currents and human interference. Both the neutrality tests and mismatch distributions revealed the occurrence of historical population expansion. Bayesian skyline plot analyses with two different substitution rates indicated that N. tenuis might follow the post-LGM (the Last Glacial Maximum) expansion pattern for temperate species. Pleistocene climatic fluctuation, complicated topography and anthropogenic factors, along with other ecological factors (e.g. temperature and air current) might have accounted for the current population structure of N. tenuis.

  8. Population genetic structure and post-LGM expansion of the plant bug Nesidiocoris tenuis (Hemiptera: Miridae) in China

    PubMed Central

    Xun, Huaizhu; Li, Hu; Li, Shujuan; Wei, Shujun; Zhang, Lijuan; Song, Fan; Jiang, Pei; Yang, Hailin; Han, Fei; Cai, Wanzhi

    2016-01-01

    The plant bug, Nesidiocoris tenuis (Hemiptera: Miridae), is one of the most thermophilous dicyphines in agroecosystems and is widely distributed in China. Little is known regarding the genetic structure of N. tenuis and the effect of historical climatic fluctuations on N. tenuis populations. We analyzed partial sequences of three mitochondrial protein-coding genes (COI, ND2 and CytB) and nuclear genes (5.8S, ITS2 and 28S) for 516 specimens collected from 37 localities across China. Analyses of the combined mitochondrial dataset indicated that the Southwestern China group (SWC) was significantly differentiated from the remaining populations, other Chinese group (OC). Asymmetric migration and high level of gene flow across a long distance within the OC group was detected. The long-distance dispersal of N. tenuis might be affected by air currents and human interference. Both the neutrality tests and mismatch distributions revealed the occurrence of historical population expansion. Bayesian skyline plot analyses with two different substitution rates indicated that N. tenuis might follow the post-LGM (the Last Glacial Maximum) expansion pattern for temperate species. Pleistocene climatic fluctuation, complicated topography and anthropogenic factors, along with other ecological factors (e.g. temperature and air current) might have accounted for the current population structure of N. tenuis. PMID:27230109

  9. Genetic Diversity and Population Structure of Indian Golden Silkmoth (Antheraea assama)

    PubMed Central

    Arunkumar, Kallare P.; Sahu, Anup Kumar; Mohanty, Atish Ranjan; Awasthi, Arvind K.; Pradeep, Appukuttannair R.; Urs, S. Raje; Nagaraju, Javaregowda

    2012-01-01

    Background The Indian golden saturniid silkmoth (Antheraea assama), popularly known as muga silkmoth, is a semi-domesticated silk producing insect confined to a narrow habitat range of the northeastern region of India. Owing to the prevailing socio-political problems, the muga silkworm habitats in the northeastern region have not been accessible hampering the phylogeography studies of this rare silkmoth. Recently, we have been successful in our attempt to collect muga cocoon samples, although to a limited extent, from their natural habitats. Out of 87 microsatellite markers developed previously for A. assama, 13 informative markers were employed to genotype 97 individuals from six populations and analyzed their population structure and genetic variation. Methodology/Principal Findings We observed highly significant genetic diversity in one of the populations (WWS-1, a population derived from West Garo Hills region of Meghalaya state). Further analysis with and without WWS-1 population revealed that dramatic genetic differentiation (global FST = 0.301) was due to high genetic diversity contributed by WWS-1 population. Analysis of the remaining five populations (excluding WWS-1) showed a marked reduction in the number of alleles at all the employed loci. Structure analysis showed the presence of only two clusters: one formed by WWS-1 population and the other included the remaining five populations, inferring that there is no significant genetic diversity within and between these five populations, and suggesting that these five populations are probably derived from a single population. Patterns of recent population bottlenecks were not evident in any of the six populations studied. Conclusions/Significance A. assama inhabiting the WWS-1 region revealed very high genetic diversity, and was genetically divergent from the five populations studied. The efforts should be continued to identify and study such populations from this region as well as other muga silkworm

  10. Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia

    PubMed Central

    Metspalu, Mait; Romero, Irene Gallego; Yunusbayev, Bayazit; Chaubey, Gyaneshwer; Mallick, Chandana Basu; Hudjashov, Georgi; Nelis, Mari; Mägi, Reedik; Metspalu, Ene; Remm, Maido; Pitchappan, Ramasamy; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Kivisild, Toomas

    2011-01-01

    South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and