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. Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans.

    PubMed

    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.

  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.

  4. 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

  5. Structured population dynamics: continuous size and discontinuous stage structures.

    PubMed

    Buffoni, Giuseppe; Pasquali, Sara

    2007-04-01

    A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

  6. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    .../Automated Credit Account File Structure This is the structure of the data file to provide information to the... remainder of the data fields defined below should be populated. For data provided in the Sweep/Automated... number. The Account Identifier may be composed of more than one physical data element. If multiple fields...

  7. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    .../Automated Credit Account File Structure This is the structure of the data file to provide information to the... remainder of the data fields defined below should be populated. For data provided in the Sweep/Automated... number. The Account Identifier may be composed of more than one physical data element. If multiple fields...

  8. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    .../Automated Credit Account File Structure This is the structure of the data file to provide information to the... remainder of the data fields defined below should be populated. For data provided in the Sweep/Automated... number. The Account Identifier may be composed of more than one physical data element. If multiple fields...

  9. 12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    .../Automated Credit Account File Structure This is the structure of the data file to provide information to the... remainder of the data fields defined below should be populated. For data provided in the Sweep/Automated... number. The Account Identifier may be composed of more than one physical data element. If multiple fields...

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

    PubMed

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

    2010-10-27

    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.

  11. Population activity structure of excitatory and inhibitory neurons

    PubMed Central

    Doiron, Brent

    2017-01-01

    Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure. PMID:28817581

  12. Accountable Care Organizations and Population Health Organizations.

    PubMed

    Casalino, Lawrence P; Erb, Natalie; Joshi, Maulik S; Shortell, Stephen M

    2015-08-01

    Accountable care organizations (ACOs) and hospitals are investing in improving "population health," by which they nearly always mean the health of the "population" of patients "attributed" by Medicare, Medicaid, or private health insurers to their organizations. But population health can and should also mean "the health of the entire population in a geographic area." We present arguments for and against ACOs and hospitals investing in affecting the socioeconomic determinants of health to improve the health of the population in their geographic area, and we provide examples of ACOs and hospitals that are doing so in a limited way. These examples suggest that ACOs and hospitals can work with other organizations in their community to improve population health. We briefly present recent proposals for such coalitions and for how they could be financed to be sustainable. Copyright © 2015 by Duke University Press.

  13. 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.

  14. 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.

  15. 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. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  16. Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation

    PubMed Central

    Chen, Jieming; Zheng, Houfeng; Bei, Jin-Xin; Sun, Liangdan; Jia, Wei-hua; Li, Tao; Zhang, Furen; Seielstad, Mark; Zeng, Yi-Xin; Zhang, Xuejun; Liu, Jianjun

    2009-01-01

    Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future. PMID:19944401

  17. Achieving Population Health in Accountable Care Organizations

    PubMed Central

    Walker, Deborah Klein

    2013-01-01

    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. PMID:23678910

  18. 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.

  19. 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.

  20. Rare variation facilitates inferences of fine-scale population structure in humans.

    PubMed

    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

    2015-03-01

    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. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  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 follows...

  2. 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 follows...

  3. 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 (F ST>0.2). Outside Central Asia F ST 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

  4. Improving Aquatic Warbler Population Assessments by Accounting for Imperfect Detection

    PubMed Central

    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

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

    PubMed

    Tompkins, Adrian M; Ermert, Volker

    2013-02-18

    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. 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. 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. 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.

  6. 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

  7. 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

  8. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    PubMed

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-04-05

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  9. 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.

  10. Genetic structure in four West African population groups

    PubMed Central

    Adeyemo, Adebowale A; Chen, Guanjie; Chen, Yuanxiu; Rotimi, Charles

    2005-01-01

    Background Africa contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for, have been reported to lead to spurious association between a putative risk allele and a disease. Within the context of the Africa America Diabetes Mellitus (AADM) Study (a genetic epidemiologic study of type 2 diabetes mellitus in West Africa), we have investigated population structure or stratification in four ethnic groups in two countries (Akan and Gaa-Adangbe from Ghana, Yoruba and Igbo from Nigeria) using data from 372 autosomal microsatellite loci typed in 493 unrelated persons (986 chromosomes). Results There was no significant population genetic structure in the overall sample. The smallest probability is associated with an inferred cluster of 1 and little of the posterior probability is associated with a higher number of inferred clusters. The distribution of members of the sample to inferred clusters is consistent with this finding; roughly the same proportion of individuals from each group is assigned to each cluster with little variation between the ethnic groups. Analysis of molecular variance (AMOVA) showed that the between-population component of genetic variance is less than 0.1% in contrast to 99.91% for the within population component. Pair-wise genetic distances between the four ethnic groups were also very similar. Nonetheless, the small between-population genetic variance was sufficient to distinguish the two Ghanaian groups from the two Nigerian groups. Conclusion There was little evidence for significant population substructure in the four major West African ethnic groups represented in the AADM

  11. 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)

  12. Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

    PubMed Central

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-01-01

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia. PMID:21483678

  13. Population Structure and Genomic Breed Composition in an Angus-Brahman Crossbred Cattle Population.

    PubMed

    Gobena, Mesfin; Elzo, Mauricio A; Mateescu, Raluca G

    2018-01-01

    Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due

  14. PyClone: statistical inference of clonal population structure in cancer.

    PubMed

    Roth, Andrew; Khattra, Jaswinder; Yap, Damian; Wan, Adrian; Laks, Emma; Biele, Justina; Ha, Gavin; Aparicio, Samuel; Bouchard-Côté, Alexandre; Shah, Sohrab P

    2014-04-01

    We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination. Single-cell sequencing validation demonstrates PyClone's accuracy.

  15. Genetic population structure of Shoal Bass within their native range

    USGS Publications Warehouse

    Taylor, Andrew T.; Tringali, Michael D.; Sammons, Steven M.; Ingram, Travis R.; O'Rouke, Patrick M.; Peterson, Douglas L.; Long, James M.

    2018-01-01

    Endemic to the Apalachicola River basin of the southeastern USA, the Shoal Bass Micropterus cataractae is a fluvial‐specialist sport fish that is imperiled because of anthropogenic habitat alteration. To counter population declines, restorative stocking efforts are becoming an increasingly relevant management strategy. However, population genetic structure within the species is currently unknown, but it could influence management decisions, such as brood source location. Leveraging a collaborative effort to collect and genotype specimens with 16 microsatellite loci, our objective was to characterize hierarchical population structure and genetic differentiation of the Shoal Bass across its native range, including an examination of structuring mechanisms, such as relatedness and inbreeding levels. Specimens identified as Shoal Bass were collected from 13 distinct sites (N ranged from 17 to 209 per location) and were then taxonomically screened to remove nonnative congeners and hybrids (pure Shoal Bass N ranged from 13 to 183 per location). Our results revealed appreciable population structure, with five distinct Shoal Bass populations identifiable at the uppermost hierarchical level that generally corresponded with natural geographic features and anthropogenic barriers. Substructure was recovered within several of these populations, wherein differences appeared related to spatial isolation and local population dynamics. An analysis of molecular variance revealed that 3.6% of the variation in our data set was accounted for among three larger river drainages, but substructure within each river drainage also explained an additional 8.9% of genetic variation, demonstrating that management at a scale lower than the river drainage level would likely best conserve genetic diversity. Results provide a population genetic framework that can inform future management decisions, such as brood source location, so that genetic diversity within and among populations is

  16. Low Genetic Diversity and Structuring of the Arapaima (Osteoglossiformes, Arapaimidae) Population of the Araguaia-Tocantins Basin.

    PubMed

    Vitorino, Carla A; Nogueira, Fabrícia; Souza, Issakar L; Araripe, Juliana; Venere, Paulo C

    2017-01-01

    The arapaima, Arapaima gigas , is a fish whose populations are threatened by both overfishing and the ongoing destruction of its natural habitats. In the Amazon basin, varying levels of population structure have been found in A. gigas , although no data are available on the genetic diversity or structure of the populations found in the Araguaia-Tocantins basin, which has a topographic profile, hydrological regime, and history of fishing quite distinct from those of the Amazon. In this context, microsatellite markers were used to assess the genetic diversity and connectivity of five wild A. gigas populations in the Araguaia-Tocantins basin. The results of the analysis indicated low levels of genetic diversity in comparison with other A. gigas populations, studied in the Amazon basin. The AMOVA revealed that the Arapaima populations of the Araguaia-Tocantins basin are structured significantly. No correlation was found between pairwise F ST values and the geographical distance among populations. The low level of genetic variability and the evidence of restricted gene flow may both be accounted for by overfishing, as well as the other human impacts that these populations have been exposed to over the years. The genetic fragility of these populations demands attention, given that future environmental changes (natural or otherwise) may further reduce these indices and eventually endanger these populations. The results of this study emphasize the need to take the genetic differences among the study populations into account when planning management measures and conservation strategies for the arapaima stocks of the Araguaia-Tocantins basin.

  17. Low Genetic Diversity and Structuring of the Arapaima (Osteoglossiformes, Arapaimidae) Population of the Araguaia-Tocantins Basin

    PubMed Central

    Vitorino, Carla A.; Nogueira, Fabrícia; Souza, Issakar L.; Araripe, Juliana; Venere, Paulo C.

    2017-01-01

    The arapaima, Arapaima gigas, is a fish whose populations are threatened by both overfishing and the ongoing destruction of its natural habitats. In the Amazon basin, varying levels of population structure have been found in A. gigas, although no data are available on the genetic diversity or structure of the populations found in the Araguaia-Tocantins basin, which has a topographic profile, hydrological regime, and history of fishing quite distinct from those of the Amazon. In this context, microsatellite markers were used to assess the genetic diversity and connectivity of five wild A. gigas populations in the Araguaia-Tocantins basin. The results of the analysis indicated low levels of genetic diversity in comparison with other A. gigas populations, studied in the Amazon basin. The AMOVA revealed that the Arapaima populations of the Araguaia-Tocantins basin are structured significantly. No correlation was found between pairwise FST values and the geographical distance among populations. The low level of genetic variability and the evidence of restricted gene flow may both be accounted for by overfishing, as well as the other human impacts that these populations have been exposed to over the years. The genetic fragility of these populations demands attention, given that future environmental changes (natural or otherwise) may further reduce these indices and eventually endanger these populations. The results of this study emphasize the need to take the genetic differences among the study populations into account when planning management measures and conservation strategies for the arapaima stocks of the Araguaia-Tocantins basin. PMID:29114261

  18. Population structure of two black Venezuelan populations studied through their mating structure and other related variables.

    PubMed

    Castro de Guerra, D; Arvelo, H; Pinto-Cisternas, J

    1999-01-01

    In order to obtain information about the population structure of two black Venezuelan populations with historical differences both in their origins and development, a variety of variables were utilized, especially on marital structure, including: frequency of surnames, isonymy, population genealogical consanguinity, multiple unions, and marital distances, all of which provided information and isolation, migration, endogamy, consanguinity, and patri-matrifocality. Results showed differences in the extent of isolation and endogamy, as well as differences in population structure, which can be directly related with historical conditions of each population. Results agree with those previously obtained with traditional genetic polymorphisms and with the historical information available. Thus, the usefulness of surnames for inferring about population structure is supported, as well as the usefulness of historical information for explaining genetic diversity.

  19. SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies

    PubMed Central

    Bouaziz, Matthieu; Paccard, Caroline; Guedj, Mickael; Ambroise, Christophe

    2012-01-01

    Inferring the structure of populations has many applications for genetic research. In addition to providing information for evolutionary studies, it can be used to account for the bias induced by population stratification in association studies. To this end, many algorithms have been proposed to cluster individuals into genetically homogeneous sub-populations. The parametric algorithms, such as Structure, are very popular but their underlying complexity and their high computational cost led to the development of faster parametric alternatives such as Admixture. Alternatives to these methods are the non-parametric approaches. Among this category, AWclust has proven efficient but fails to properly identify population structure for complex datasets. We present in this article a new clustering algorithm called Spectral Hierarchical clustering for the Inference of Population Structure (SHIPS), based on a divisive hierarchical clustering strategy, allowing a progressive investigation of population structure. This method takes genetic data as input to cluster individuals into homogeneous sub-populations and with the use of the gap statistic estimates the optimal number of such sub-populations. SHIPS was applied to a set of simulated discrete and admixed datasets and to real SNP datasets, that are data from the HapMap and Pan-Asian SNP consortium. The programs Structure, Admixture, AWclust and PCAclust were also investigated in a comparison study. SHIPS and the parametric approach Structure were the most accurate when applied to simulated datasets both in terms of individual assignments and estimation of the correct number of clusters. The analysis of the results on the real datasets highlighted that the clusterings of SHIPS were the more consistent with the population labels or those produced by the Admixture program. The performances of SHIPS when applied to SNP data, along with its relatively low computational cost and its ease of use make this method a promising

  20. Strategy selection in structured populations.

    PubMed

    Tarnita, Corina E; Ohtsuki, Hisashi; Antal, Tibor; Fu, Feng; Nowak, Martin A

    2009-08-07

    Evolutionary game theory studies frequency dependent selection. The fitness of a strategy is not constant, but depends on the relative frequencies of strategies in the population. This type of evolutionary dynamics occurs in many settings of ecology, infectious disease dynamics, animal behavior and social interactions of humans. Traditionally evolutionary game dynamics are studied in well-mixed populations, where the interaction between any two individuals is equally likely. There have also been several approaches to study evolutionary games in structured populations. In this paper we present a simple result that holds for a large variety of population structures. We consider the game between two strategies, A and B, described by the payoff matrix(abcd). We study a mutation and selection process. For weak selection strategy A is favored over B if and only if sigma a+b>c+sigma d. This means the effect of population structure on strategy selection can be described by a single parameter, sigma. We present the values of sigma for various examples including the well-mixed population, games on graphs, games in phenotype space and games on sets. We give a proof for the existence of such a sigma, which holds for all population structures and update rules that have certain (natural) properties. We assume weak selection, but allow any mutation rate. We discuss the relationship between sigma and the critical benefit to cost ratio for the evolution of cooperation. The single parameter, sigma, allows us to quantify the ability of a population structure to promote the evolution of cooperation or to choose efficient equilibria in coordination games.

  1. Geographical distance and local environmental conditions drive the genetic population structure of a freshwater microalga (Bathycoccaceae; Chlorophyta) in Patagonian lakes.

    PubMed

    Fernández, Leonardo D; Hernández, Cristián E; Schiaffino, M Romina; Izaguirre, Irina; Lara, Enrique

    2017-10-01

    The patterns and mechanisms underlying the genetic structure of microbial populations remain unresolved. Herein we investigated the role played by two non-mutually exclusive models (i.e. isolation by distance and isolation by environment) in shaping the genetic structure of lacustrine populations of a microalga (a freshwater Bathycoccaceae) in the Argentinean Patagonia. To our knowledge, this was the first study to investigate the genetic population structure in a South American microorganism. Population-level analyses based on ITS1-5.8S-ITS2 sequences revealed high levels of nucleotide and haplotype diversity within and among populations. Fixation index and a spatially explicit Bayesian analysis confirmed the occurrence of genetically distinct microalga populations in Patagonia. Isolation by distance and isolation by environment accounted for 38.5% and 17.7% of the genetic structure observed, respectively, whereas together these models accounted for 41% of the genetic differentiation. While our results highlighted isolation by distance and isolation by environment as important mechanisms in driving the genetic population structure of the microalga studied, none of these models (either alone or together) could explain the entire genetic differentiation observed. The unexplained variation in the genetic differentiation observed could be the result of founder events combined with rapid local adaptations, as proposed by the monopolisation hypothesis. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. A model for a spatially structured metapopulation accounting for within patch dynamics.

    PubMed

    Smith, Andrew G; McVinish, Ross; Pollett, Philip K

    2014-01-01

    We develop a stochastic metapopulation model that accounts for spatial structure as well as within patch dynamics. Using a deterministic approximation derived from a functional law of large numbers, we develop conditions for extinction and persistence of the metapopulation in terms of the birth, death and migration parameters. Interestingly, we observe the Allee effect in a metapopulation comprising two patches of greatly different sizes, despite there being decreasing patch specific per-capita birth rates. We show that the Allee effect is due to the way the migration rates depend on the population density of the patches. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. 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.

  4. Population Structure in Nontypeable Haemophilus influenzae

    PubMed Central

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

    2013-01-01

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

  5. Accounting for imperfect detection is critical for inferring marine turtle nesting population trends.

    PubMed

    Pfaller, Joseph B; Bjorndal, Karen A; Chaloupka, Milani; Williams, Kristina L; Frick, Michael G; Bolten, Alan B

    2013-01-01

    Assessments of population trends based on time-series counts of individuals are complicated by imperfect detection, which can lead to serious misinterpretations of data. Population trends of threatened marine turtles worldwide are usually based on counts of nests or nesting females. We analyze 39 years of nest-count, female-count, and capture-mark-recapture (CMR) data for nesting loggerhead turtles (Caretta caretta) on Wassaw Island, Georgia, USA. Annual counts of nests and females, not corrected for imperfect detection, yield significant, positive trends in abundance. However, multistate open robust design modeling of CMR data that accounts for changes in imperfect detection reveals that the annual abundance of nesting females has remained essentially constant over the 39-year period. The dichotomy could result from improvements in surveys or increased within-season nest-site fidelity in females, either of which would increase detection probability. For the first time in a marine turtle population, we compare results of population trend analyses that do and do not account for imperfect detection and demonstrate the potential for erroneous conclusions. Past assessments of marine turtle population trends based exclusively on count data should be interpreted with caution and re-evaluated when possible. These concerns apply equally to population assessments of all species with imperfect detection.

  6. 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. © 2016 John Wiley & Sons Ltd.

  7. Public Health Departments and Accountable Care Organizations: Finding Common Ground in Population Health

    PubMed Central

    Ingram, Richard; Scutchfield, F. Douglas

    2015-01-01

    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. PMID:25790392

  8. 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

  9. Dietary Differentiation and the Evolution of Population Genetic Structure in a Highly Mobile Carnivore

    PubMed Central

    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 13C and δ 15N 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

  10. 18 CFR 367.9350 - Account 935, Maintenance of structures and equipment.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... POWER ACT AND NATURAL GAS ACT Operation and Maintenance Expense Chart of Accounts § 367.9350 Account 935, Maintenance of structures and equipment. This account must include materials used and expenses incurred in the maintenance of property owned, the cost of which is included in accounts 390 through 399 (§§ 367.3900 through...

  11. Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

    PubMed Central

    Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

    2011-01-01

    An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

  12. Evolutionary dynamics on any population structure

    NASA Astrophysics Data System (ADS)

    Allen, Benjamin; Lippner, Gabor; Chen, Yu-Ting; Fotouhi, Babak; Momeni, Naghmeh; Yau, Shing-Tung; Nowak, Martin A.

    2017-03-01

    Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

  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. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

  14. The Role of Social Work Leadership: Mount Sinai Care, the Accountable Care Organization, and Population Health Management.

    PubMed

    Xenakis, Nancy

    2015-10-01

    In July 2012, The Mount Sinai Medical Center was selected by the Centers for Medicare and Medicaid to join the first cohort of Accountable Care Organizations (ACOs) in this country under its Medicare Shared Savings Program. A critical component of an ACO is care coordination of patients, which is a complex concept, intertwined with other concepts related to quality, delivery and organization of health care. This article provides an overview of the development, structure and functionality of Mount Sinai Care, the ACO of The Mount Sinai Health System, and how it was the beginning of its work in population health management. It describes the important role of social work leadership in the development and operation of its care coordination model. The model's successes and challenges and recommendations for future development of care coordination and population health management are outlined.

  15. Possible ancestral structure in human populations.

    PubMed

    Plagnol, Vincent; Wall, Jeffrey D

    2006-07-01

    Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p approximately 10(-7)), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.

  16. 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.

  17. Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul).

    PubMed

    Wang, Ian J

    2009-09-01

    Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul, which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure (F(ST) = 0.051-0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes (N(e) = 7-30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B. exsul's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.

  18. Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

    PubMed

    Cushing, J M; Henson, Shandelle M

    2018-02-03

    For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

  19. 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.

  20. Developing a tuberculosis transmission model that accounts for changes in population health.

    PubMed

    Oxlade, Olivia; Schwartzman, Kevin; Benedetti, Andrea; Pai, Madhukar; Heymann, Jody; Menzies, Dick

    2011-01-01

    Simulation models are useful in policy planning for tuberculosis (TB) control. To accurately assess interventions, important modifiers of the epidemic should be accounted for in evaluative models. Improvements in population health were associated with the declining TB epidemic in the pre-antibiotic era and may be relevant today. The objective of this study was to develop and validate a TB transmission model that accounted for changes in population health. We developed a deterministic TB transmission model, using reported data from the pre-antibiotic era in England. Change in adjusted life expectancy, used as a proxy for general health, was used to determine the rate of change of key epidemiological parameters. Predicted outcomes included risk of TB infection and TB mortality. The model was validated in the setting of the Netherlands and then applied to modern Peru. The model, developed in the setting of England, predicted TB trends in the Netherlands very accurately. The R(2) value for correlation between observed and predicted data was 0.97 and 0.95 for TB infection and mortality, respectively. In Peru, the predicted decline in incidence prior to the expansion of "Directly Observed Treatment Short Course" (The DOTS strategy) was 3.7% per year (observed = 3.9% per year). After DOTS expansion, the predicted decline was very similar to the observed decline of 5.8% per year. We successfully developed and validated a TB model, which uses a proxy for population health to estimate changes in key epidemiology parameters. Population health contributed significantly to improvement in TB outcomes observed in Peru. Changing population health should be incorporated into evaluative models for global TB control.

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

    USGS Publications Warehouse

    Koons, David N.; Holmes, Randall R.; Grand, James 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.

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

    PubMed

    Peña, Jorge; Nöldeke, Georg; Lehmann, Laurent

    2015-10-07

    Many models proposed to study the evolution of collective action rely on a formalism that represents social interactions as n-player games between individuals adopting discrete actions such as cooperate and defect. Despite the importance of spatial structure in biological collective action, the analysis of n-player games games in spatially structured populations has so far proved elusive. We address this problem by considering mixed strategies and by integrating discrete-action n-player games into the direct fitness approach of social evolution theory. This allows to conveniently identify convergence stable strategies and to capture the effect of population structure by a single structure coefficient, namely, the pairwise (scaled) relatedness among interacting individuals. As an application, we use our mathematical framework to investigate collective action problems associated with the provision of three different kinds of collective goods, paradigmatic of a vast array of helping traits in nature: "public goods" (both providers and shirkers can use the good, e.g., alarm calls), "club goods" (only providers can use the good, e.g., participation in collective hunting), and "charity goods" (only shirkers can use the good, e.g., altruistic sacrifice). We show that relatedness promotes the evolution of collective action in different ways depending on the kind of collective good and its economies of scale. Our findings highlight the importance of explicitly accounting for relatedness, the kind of collective good, and the economies of scale in theoretical and empirical studies of the evolution of collective action. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. 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

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

    PubMed

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

    2015-04-06

    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.

  5. Structural stability of nonlinear population dynamics.

    PubMed

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  6. Structural stability of nonlinear population dynamics

    NASA Astrophysics Data System (ADS)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  7. Probabilistic models of genetic variation in structured populations applied to global human studies.

    PubMed

    Hao, Wei; Song, Minsun; Storey, John D

    2016-03-01

    Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important problem is how to formulate and estimate probabilistic models of observed genotypes that account for complex population structure. The most prominent work on this problem has focused on estimating a model of admixture proportions of ancestral populations for each individual. Here, we instead focus on modeling variation of the genotypes without requiring a higher-level admixture interpretation. We formulate two general probabilistic models, and we propose computationally efficient algorithms to estimate them. First, we show how principal component analysis can be utilized to estimate a general model that includes the well-known Pritchard-Stephens-Donnelly admixture model as a special case. Noting some drawbacks of this approach, we introduce a new 'logistic factor analysis' framework that seeks to directly model the logit transformation of probabilities underlying observed genotypes in terms of latent variables that capture population structure. We demonstrate these advances on data from the Human Genome Diversity Panel and 1000 Genomes Project, where we are able to identify SNPs that are highly differentiated with respect to structure while making minimal modeling assumptions. A Bioconductor R package called lfa is available at http://www.bioconductor.org/packages/release/bioc/html/lfa.html jstorey@princeton.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  8. 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.

  9. 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

  10. Colony social organization and population genetic structure of an introduced population of formosan subterranean termite from New Orleans, Louisiana.

    PubMed

    Husseneder, Claudia; Messenger, Matthew T; Su, Nan-Yao; Grace, J Kenneth; Vargo, Edward L

    2005-10-01

    The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an invasive species in many parts of the world, including the U.S. mainland. The reasons for its invasive success may have to do with the flexible social and spatial organization of colonies. We investigated the population and breeding structure of 14 C. formosanus colonies in Louis Armstrong Park, New Orleans, LA. This population has been the focus of extensive study for many years, providing the opportunity to relate aspects of colony breeding structure to previous findings on colony characteristics such as body weight and number of workers, wood consumption, and intercolony aggression. Eight colonies were headed by a single pair of outbred reproductives (simple families), whereas six colonies were headed by low numbers of multiple kings and/or queens that were likely the neotenic descendants of the original colony (extended families). Within the foraging area of one large extended family colony, we found genetic differentiation among different collection sites, suggesting the presence of separate reproductive centers. No significant difference between simple family colonies and extended family colonies was found in worker body weight, soldier body weight, foraging area, population size, or wood consumption. However, level of inbreeding within colonies was negatively correlated with worker body weight and positively correlated with wood consumption. Also, genetic distance between colonies was positively correlated with aggression levels, suggesting a genetic basis to nestmate discrimination cues in this termite population. No obvious trait associated with colony reproductive structure was found that could account for the invasion success of this species.

  11. Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations.

    PubMed

    Chapple, David G; Birkett, Alisha; Miller, Kimberly A; Daugherty, Charles H; Gleeson, Dianne M

    2012-01-01

    Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key

  12. Population structure in Japanese rice population

    PubMed Central

    Yamasaki, Masanori; Ideta, Osamu

    2013-01-01

    It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars. PMID:23641181

  13. 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. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. Genetic diversity and population structure of Plasmodium vivax in Central China

    PubMed Central

    2014-01-01

    Background In Central China the declining incidence of Plasmodium vivax has been interrupted by epidemic expansions and imported cases. The impact of these changes on the local parasite population, and concurrent risks of future resurgence, was assessed. Methods Plasmodium vivax isolates collected from Anhui and Jiangsu provinces, Central China between 2007 and 2010 were genotyped using capillary electrophoresis at seven polymorphic short tandem repeat markers. Spatial and temporal analyses of within-host and population diversity, population structure, and relatedness were conducted on these isolates. Results Polyclonal infections were infrequent in the 94 isolates from Anhui (4%) and 25 from Jiangsu (12%), with a trend for increasing frequency from 2008 to 2010 (2 to 19%) when combined. Population diversity was high in both provinces and across the years tested (HE = 0.8 – 0.85). Differentiation between Anhui and Jiangsu was modest (F’ ST  = 0.1). Several clusters of isolates with identical multi-locus haplotypes were observed across both Anhui and Jiangsu. Linkage disequilibrium was strong in both populations and in each year tested (IAS = 0.2 – 0.4), but declined two- to four-fold when identical haplotypes were accounted for, indicative of occasional epidemic transmission dynamics. None of five imported isolates shared identical haplotypes to any of the central Chinese isolates. Conclusions The population genetic structure of P. vivax in Central China highlights unstable transmission, with limited barriers to gene flow between the central provinces. Despite low endemicity, population diversity remained high, but the reservoirs sustaining this diversity remain unclear. The challenge of imported cases and risks of resurgence emphasize the need for continued surveillance to detect early warning signals. Although parasite genotyping has potential to inform the management of outbreaks, further studies are required to identify suitable marker panels

  15. 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.

  16. Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity.

    PubMed

    Trask, Amanda E; Bignal, Eric M; McCracken, Davy I; Piertney, Stuart B; Reid, Jane M

    2017-09-01

    A population's effective size (N e ) is a key parameter that shapes rates of inbreeding and loss of genetic diversity, thereby influencing evolutionary processes and population viability. However, estimating N e , and identifying key demographic mechanisms that underlie the N e to census population size (N) ratio, remains challenging, especially for small populations with overlapping generations and substantial environmental and demographic stochasticity and hence dynamic age-structure. A sophisticated demographic method of estimating N e /N, which uses Fisher's reproductive value to account for dynamic age-structure, has been formulated. However, this method requires detailed individual- and population-level data on sex- and age-specific reproduction and survival, and has rarely been implemented. Here, we use the reproductive value method and detailed demographic data to estimate N e /N for a small and apparently isolated red-billed chough (Pyrrhocorax pyrrhocorax) population of high conservation concern. We additionally calculated two single-sample molecular genetic estimates of N e to corroborate the demographic estimate and examine evidence for unobserved immigration and gene flow. The demographic estimate of N e /N was 0.21, reflecting a high total demographic variance (σ2dg) of 0.71. Females and males made similar overall contributions to σ2dg. However, contributions varied among sex-age classes, with greater contributions from 3 year-old females than males, but greater contributions from ≥5 year-old males than females. The demographic estimate of N e was ~30, suggesting that rates of increase of inbreeding and loss of genetic variation per generation will be relatively high. Molecular genetic estimates of N e computed from linkage disequilibrium and approximate Bayesian computation were approximately 50 and 30, respectively, providing no evidence of substantial unobserved immigration which could bias demographic estimates of N e . Our analyses identify

  17. 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

  18. 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

  19. Genetic structure of Rajaka caste and affinities with other caste populations of Andhra Pradesh, India.

    PubMed

    Parvatheesam, C; Babu, B V; Babu, M C

    1997-01-01

    The present study gives an account of the genetic structure in terms of distribution of a few genetic markers, viz., A1A2B0, Rh(D), G6PD deficiency and haemoglobin among the Rajaka caste population of Andhra Pradesh, India. The genetic relationships of the Rajaka caste with other Andhra caste populations were investigated in terms of genetic distance, i.e., Sq B (mn) of Balakrishnan and Sanghvi. Relatively lesser distance was established between the Rajaka and two Panchama castes. Also, the pattern of genetic distance corroborates the hierarchical order of the Hindu varna system.

  20. 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.

  1. Spatial genetic structure in continuous and fragmented populations of Pinus pinaster Aiton.

    PubMed

    De-Lucas, A I; González-Martínez, S C; Vendramin, G G; Hidalgo, E; Heuertz, M

    2009-11-01

    Habitat fragmentation, i.e., the reduction of populations into small isolated remnants, is expected to increase spatial genetic structure (SGS) in plant populations through nonrandom mating, lower population densities and potential aggregation of reproductive individuals. We investigated the effects of population size reduction and genetic isolation on SGS in maritime pine (Pinus pinaster Aiton) using a combined experimental and simulation approach. Maritime pine is a wind-pollinated conifer which has a scattered distribution in the Iberian Peninsula as a result of forest fires and habitat fragmentation. Five highly polymorphic nuclear microsatellites were genotyped in a total of 394 individuals from two population pairs from the Iberian Peninsula, formed by one continuous and one fragmented population each. In agreement with predictions, SGS was significant and stronger in fragments (Sp = 0.020 and Sp = 0.026) than in continuous populations, where significant SGS was detected for one population only (Sp = 0.010). Simulations suggested that under fat-tailed dispersal, small population size is a stronger determinant of SGS than genetic isolation, while under normal dispersal, genetic isolation has a stronger effect. SGS was always stronger in real populations than in simulations, except if unrealistically narrow dispersal and/or high variance of reproductive success were modelled (even when accounting for potential overestimation of SGS in real populations as a result of short-distance sampling). This suggests that factors such as nonrandom mating or selection not considered in the simulations were additionally operating on SGS in Iberian maritime pine populations.

  2. 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). ...

  3. Family history and risk of breast cancer: an analysis accounting for family structure.

    PubMed

    Brewer, Hannah R; Jones, Michael E; Schoemaker, Minouk J; Ashworth, Alan; Swerdlow, Anthony J

    2017-08-01

    Family history is an important risk factor for breast cancer incidence, but the parameters conventionally used to categorize it are based solely on numbers and/or ages of breast cancer cases in the family and take no account of the size and age-structure of the woman's family. Using data from the Generations Study, a cohort of over 113,000 women from the general UK population, we analyzed breast cancer risk in relation to first-degree family history using a family history score (FHS) that takes account of the expected number of family cases based on the family's age-structure and national cancer incidence rates. Breast cancer risk increased significantly (P trend  < 0.0001) with greater FHS. There was a 3.5-fold (95% CI 2.56-4.79) range of risk between the lowest and highest FHS groups, whereas women who had two or more relatives with breast cancer, the strongest conventional familial risk factor, had a 2.5-fold (95% CI 1.83-3.47) increase in risk. Using likelihood ratio tests, the best model for determining breast cancer risk due to family history was that combining FHS and age of relative at diagnosis. A family history score based on expected as well as observed breast cancers in a family can give greater risk discrimination on breast cancer incidence than conventional parameters based solely on cases in affected relatives. Our modeling suggests that a yet stronger predictor of risk might be a combination of this score and age at diagnosis in relatives.

  4. THE SPATIAL STRUCTURE OF MONO-ABUNDANCE SUB-POPULATIONS OF THE MILKY WAY DISK

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

    Bovy, Jo; Rix, Hans-Walter; Liu Chao

    2012-07-10

    The spatial, kinematic, and elemental-abundance structure of the Milky Way's stellar disk is complex, and has been difficult to dissect with local spectroscopic or global photometric data. Here, we develop and apply a rigorous density modeling approach for Galactic spectroscopic surveys that enables investigation of the global spatial structure of stellar sub-populations in narrow bins of [{alpha}/Fe] and [Fe/H], using 23,767 G-type dwarfs from SDSS/SEGUE, which effectively sample 5 kpc < R{sub GC} < 12 kpc and 0.3 kpc {approx}< |Z| {approx}< 3 kpc. We fit models for the number density of each such ([{alpha}/Fe] and [Fe/H]) mono-abundance component, properlymore » accounting for the complex spectroscopic SEGUE sampling of the underlying stellar population, as well as for the metallicity and color distributions of the samples. We find that each mono-abundance sub-population has a simple spatial structure that can be described by a single exponential in both the vertical and radial directions, with continuously increasing scale heights ( Almost-Equal-To 200 pc to 1 kpc) and decreasing scale lengths (>4.5 kpc to 2 kpc) for increasingly older sub-populations, as indicated by their lower metallicities and [{alpha}/Fe] enhancements. That the abundance-selected sub-components with the largest scale heights have the shortest scale lengths is in sharp contrast with purely geometric 'thick-thin disk' decompositions. To the extent that [{alpha}/Fe] is an adequate proxy for age, our results directly show that older disk sub-populations are more centrally concentrated, which implies inside-out formation of galactic disks. The fact that the largest scale-height sub-components are most centrally concentrated in the Milky Way is an almost inevitable consequence of explaining the vertical structure of the disk through internal evolution. Whether the simple spatial structure of the mono-abundance sub-components and the striking correlations between age, scale length, and scale

  5. 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

  6. Influence of language and ancestry on genetic structure of contiguous populations: A microsatellite based study on populations of Orissa

    PubMed Central

    Sahoo, Sanghamitra; Kashyap, VK

    2005-01-01

    Background We have examined genetic diversity at fifteen autosomal microsatellite loci in seven predominant populations of Orissa to decipher whether populations inhabiting the same geographic region can be differentiated on the basis of language or ancestry. The studied populations have diverse historical accounts of their origin, belong to two major ethnic groups and different linguistic families. Caucasoid caste populations are speakers of Indo-European language and comprise Brahmins, Khandayat, Karan and Gope, while the three Australoid tribal populations include two Austric speakers: Juang and Saora and a Dravidian speaking population, Paroja. These divergent groups provide a varied substratum for understanding variation of genetic patterns in a geographical area resulting from differential admixture between migrants groups and aboriginals, and the influence of this admixture on population stratification. Results The allele distribution pattern showed uniformity in the studied groups with approximately 81% genetic variability within populations. The coefficient of gene differentiation was found to be significantly higher in tribes (0.014) than caste groups (0.004). Genetic variance between the groups was 0.34% in both ethnic and linguistic clusters and statistically significant only in the ethnic apportionment. Although the populations were genetically close (FST = 0.010), the contemporary caste and tribal groups formed distinct clusters in both Principal-Component plot and Neighbor-Joining tree. In the phylogenetic tree, the Orissa Brahmins showed close affinity to populations of North India, while Khandayat and Gope clustered with the tribal groups, suggesting a possibility of their origin from indigenous people. Conclusions The extent of genetic differentiation in the contemporary caste and tribal groups of Orissa is highly significant and constitutes two distinct genetic clusters. Based on our observations, we suggest that since genetic distances and

  7. How "accountable" are accountable care organizations?

    PubMed

    Addicott, Rachael; Shortell, Stephen M

    2014-01-01

    The establishment of accountable care organizations (ACOs) in the Affordable Care Act (ACA) was intended to support both cost savings and high-quality care. However, a key challenge will be to ensure that governance and accountability mechanisms are sufficient to support those twin ambitions. This exploratory study considers how recently developed ACOs have established governance structures and accountability mechanisms, particularly focusing on attempts at collaborative accountability and shared governance arrangements. Four case studies of ACOs across the United States were undertaken, with data collected throughout 2012. These involved 34 semistructured interviews with ACO administrative and clinical leaders, observation of nine meetings, and a review of documentary materials from each ACO. We identified very few examples of physicians being held to account as a collective and therefore only limited evidence of collaborative accountability impacting on behavior change. However, ACO leaders do have many mechanisms available to stimulate change across physicians. The challenge is to determine governance structure(s) and accountability mechanisms that facilitate the most effective combination of approaches, measures, incentives, and sanctions to achieve the goals of more accountable care. Accountability structures and processes will need to be tailored to local membership composition, historical evolution, and current stage of development. There are also some common lessons to be drawn. Shared goals and incentives should be reflected through performance criteria. It is important to align measures and thresholds across payers to ensure ACOs are not unnecessarily burdened or compromised by reporting on different and potentially disjointed measures. Finally, emphasis needs to be placed on the importance of credible, transparent data. This exploratory study provides early evidence regarding how ACOs are establishing their governance and accountability arrangements and

  8. A structured population model with diffusion in structure space.

    PubMed

    Pugliese, Andrea; Milner, Fabio

    2018-05-09

    A structured population model is described and analyzed, in which individual dynamics is stochastic. The model consists of a PDE of advection-diffusion type in the structure variable. The population may represent, for example, the density of infected individuals structured by pathogen density x, [Formula: see text]. The individuals with density [Formula: see text] are not infected, but rather susceptible or recovered. Their dynamics is described by an ODE with a source term that is the exact flux from the diffusion and advection as [Formula: see text]. Infection/reinfection is then modeled moving a fraction of these individuals into the infected class by distributing them in the structure variable through a probability density function. Existence of a global-in-time solution is proven, as well as a classical bifurcation result about equilibrium solutions: a net reproduction number [Formula: see text] is defined that separates the case of only the trivial equilibrium existing when [Formula: see text] from the existence of another-nontrivial-equilibrium when [Formula: see text]. Numerical simulation results are provided to show the stabilization towards the positive equilibrium when [Formula: see text] and towards the trivial one when [Formula: see text], result that is not proven analytically. Simulations are also provided to show the Allee effect that helps boost population sizes at low densities.

  9. Inference of Population Structure using Dense Haplotype Data

    PubMed Central

    Lawson, Daniel John; Hellenthal, Garrett

    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

  10. 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.

  11. Accounting for missing data in the estimation of contemporary genetic effective population size (N(e) ).

    PubMed

    Peel, D; Waples, R S; Macbeth, G M; Do, C; Ovenden, J R

    2013-03-01

    Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (N(e) ) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N(e) ). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N(e) and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed-inverse variance-weighted harmonic mean) consistently performed the best for both single-sample and two-sample (temporal) methods of estimating N(e) and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per-locus sample size components. © 2012 Blackwell Publishing Ltd.

  12. Turkish Population Structure and Genetic Ancestry Reveal Relatedness among Eurasian Populations

    PubMed Central

    Hodoğlugil, Uğur; Mahley, Robert W.

    2013-01-01

    Summary Turkey connects the Middle East, Europe, and Asia and has experienced major population movements. We examined the population structure and genetic relatedness of samples from three regions of Turkey using over 500,000 SNP genotypes. The data were analyzed together with Human Genome Diversity Panel data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analyzed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K = 3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42–49), 40% European (95% CI, 36–44), and 15% Central Asian (95% CI, 13–16), whereas at K = 4 the genetic ancestry of the Turks was 38% European (95% CI, 35–42), 35% Middle Eastern (95% CI, 33–38), 18% South Asian (95% CI, 16–19), and 9% Central Asian (95% CI, 7–11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul, and Kayseri) were superimposed, without clear subpopulation structure, suggesting the selected samples were rather homogeneous. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns. PMID:22332727

  13. Population structure of Streptococcus oralis

    PubMed Central

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

    2009-01-01

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

  14. Training set optimization under population structure in genomic selection.

    PubMed

    Isidro, Julio; Jannink, Jean-Luc; Akdemir, Deniz; Poland, Jesse; Heslot, Nicolas; Sorrells, Mark E

    2015-01-01

    Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure.

  15. Family Structure Transitions and Child Development: Instability, Selection, and Population Heterogeneity.

    PubMed

    Lee, Dohoon; McLanahan, Sara

    2015-08-01

    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.

  16. 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

  17. 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.

  18. Estimating Kinship in Admixed Populations

    PubMed Central

    Thornton, Timothy; Tang, Hua; Hoffmann, Thomas J.; Ochs-Balcom, Heather M.; Caan, Bette J.; Risch, Neil

    2012-01-01

    Genome-wide association studies (GWASs) are commonly used for the mapping of genetic loci that influence complex traits. A problem that is often encountered in both population-based and family-based GWASs is that of identifying cryptic relatedness and population stratification because it is well known that failure to appropriately account for both pedigree and population structure can lead to spurious association. A number of methods have been proposed for identifying relatives in samples from homogeneous populations. A strong assumption of population homogeneity, however, is often untenable, and many GWASs include samples from structured populations. Here, we consider the problem of estimating relatedness in structured populations with admixed ancestry. We propose a method, REAP (relatedness estimation in admixed populations), for robust estimation of identity by descent (IBD)-sharing probabilities and kinship coefficients in admixed populations. REAP appropriately accounts for population structure and ancestry-related assortative mating by using individual-specific allele frequencies at SNPs that are calculated on the basis of ancestry derived from whole-genome analysis. In simulation studies with related individuals and admixture from highly divergent populations, we demonstrate that REAP gives accurate IBD-sharing probabilities and kinship coefficients. We apply REAP to the Mexican Americans in Los Angeles, California (MXL) population sample of release 3 of phase III of the International Haplotype Map Project; in this sample, we identify third- and fourth-degree relatives who have not previously been reported. We also apply REAP to the African American and Hispanic samples from the Women's Health Initiative SNP Health Association Resource (WHI-SHARe) study, in which hundreds of pairs of cryptically related individuals have been identified. PMID:22748210

  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 in the Sherpa and neighboring Nepalese populations.

    PubMed

    Cole, Amy M; Cox, Sean; Jeong, Choongwon; Petousi, Nayia; Aryal, Dhana R; Droma, Yunden; Hanaoka, Masayuki; Ota, Masao; Kobayashi, Nobumitsu; Gasparini, Paolo; Montgomery, Hugh; Robbins, Peter; Di Rienzo, Anna; Cavalleri, Gianpiero L

    2017-01-19

    We set out to describe the fine-scale population structure across the Eastern region of Nepal. To date there is relatively little known about the genetic structure of the Sherpa residing in Nepal and their genetic relationship with the Nepalese. We assembled dense genotype data from a total of 1245 individuals representing Nepal and a variety of different populations resident across the greater Himalayan region including Tibet, China, India, Pakistan, Kazakhstan, Uzbekistan, Tajikistan and Kirghizstan. We performed analysis of principal components, admixture and homozygosity. We identified clear substructure across populations resident in the Himalayan arc, with genetic structure broadly mirroring geographical features of the region. Ethnic subgroups within Nepal show distinct genetic structure, on both admixture and principal component analysis. We detected differential proportions of ancestry from northern Himalayan populations across Nepalese subgroups, with the Nepalese Rai, Magar and Tamang carrying the greatest proportions of Tibetan ancestry. We show that populations dwelling on the Himalayan plateau have had a clear impact on the Northern Indian gene pool. We illustrate how the Sherpa are a remarkably isolated population, with little gene flow from surrounding Nepalese populations.

  1. Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L.

    PubMed Central

    Rossi, Monica; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Rau, Domenico; Attene, Giovanna; Papa, Roberto

    2009-01-01

    Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes. PMID:25567895

  2. Patient Population Loss At A Large Pioneer Accountable Care Organization And Implications For Refining The Program.

    PubMed

    Hsu, John; Price, Mary; Spirt, Jenna; Vogeli, Christine; Brand, Richard; Chernew, Michael E; Chaguturu, Sreekanth K; Mohta, Namita; Weil, Eric; Ferris, Timothy

    2016-03-01

    There is an ongoing move toward payment models that hold providers increasingly accountable for the care of their patients. The success of these new models depends in part on the stability of patient populations. We investigated the amount of population turnover in a large Medicare Pioneer accountable care organization (ACO) in the period 2012-14. We found that substantial numbers of beneficiaries became part of or left the ACO population during that period. For example, nearly one-third of beneficiaries who entered in 2012 left before 2014. Some of this turnover reflected that of ACO physicians-that is, beneficiaries whose physicians left the ACO were more likely to leave than those whose physicians remained. Some of the turnover also reflected changes in care delivery. For example, beneficiaries who were active in a care management program were less likely to leave the ACO than similar beneficiaries who had not yet started such a program. We recommend policy changes to increase the stability of ACO beneficiary populations, such as permitting lower cost sharing for care received within an ACO and requiring all beneficiaries to identify their primary care physician before being linked to an ACO. Project HOPE—The People-to-People Health Foundation, Inc.

  3. Population sub-structuring among Trypanosoma evansi stocks.

    PubMed

    Njiru, Z K; Constantine, C C

    2007-10-01

    To investigate the population genetic structure of Trypanosoma evansi from domesticated animals, we have analysed 112 stocks from camels, buffaloes, cattle and horses using the tandemly repeated coding sequence (MORF2) and minisatellite markers 292 and cysteine-rich acidic integral membrane protein (CRAM). We recorded a total of six alleles at the MORF2 locus, seven at 292 and 12 at the CRAM loci. Nei's genetic distance showed reduced allelic diversity between buffaloes and cattle stocks (1.2) as compared to the diversity between camels and buffaloes (3.75) and camels and cattle stock (1.69). The mean index of association (IA=0.92) significantly deviated from zero, and the average number of multilocus genotypes (G/N ratio) was 0.21. Twenty-four multilocus genotypes were defined from the combination of alleles at the three loci. The Kenyan sub-populations showed Fst=0.28 and analysis of molecular variance showed significant divergence (22.7%) between the Laikipia, Kulal and Galana regions. The regional and host distribution of multi-locus genotypes significant population differentiation and high Nei's genetic distances suggest existence of genetic sub-structuring within T. evansi stocks while the few multi-locus genotypes and deviation of association index from zero indicate the lack of recombination. In conclusion, this study reveals that some genetic sub-structuring does occur within T. evansi, which has a clonal population structure.

  4. Successive Invasion-Mediated Interspecific Hybridizations and Population Structure in the Endangered Cichlid Oreochromis mossambicus

    PubMed Central

    Firmat, Cyril; Alibert, Paul; Losseau, Michèle; Baroiller, Jean-François; Schliewen, Ulrich K.

    2013-01-01

    Hybridization between invasive and native species accounts among the major and pernicious threats to biodiversity. The Mozambique tilapia Oreochromis mossambicus, a widely used freshwater aquaculture species, is especially imperiled by this phenomenon since it is recognized by the IUCN as an endangered taxon due to genetic admixture with O. niloticus an invasive congeneric species. The Lower Limpopo and the intermittent Changane River (Mozambique) drain large wetlands of potentially great importance for conservation of O. mossambicus, but their populations have remained unstudied until today. Therefore we aimed (1) to estimate the autochthonous diversity and population structure among genetically pure O. mossambicus populations to provide a baseline for the conservation genetics of this endangered species, (2) to quantify and describe genetic variation of the invasive populations and investigate the most likely factors influencing their spread, (3) to identify O. mossambicus populations unaffected by hybridization. Bayesian assignment tests based on 423 AFLP loci and the distribution of 36 species-specific mitochondrial haplotypes both indicate a low frequency of invasive and hybrid genotypes throughout the system, but nevertheless reveal evidence for limited expansion of two alien species (O. niloticus and O. andersonii) and their hybrids in the Lower Limpopo. O. mossambicus populations with no traces of hybridization are identified. They exhibit a significant genetic structure. This contrasts with previously published estimates and provides rather promising auspices for the conservation of O. mossambicus. Especially, parts of the Upper Changane drainage and surrounding wetlands are identified as refugial zones for O. mossambicus populations. They should therefore receive high conservation priority and could represent valuable candidates for the development of aquaculture strains based on local genetic resources. PMID:23671704

  5. 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.

  6. Population structure and the burden of disease in the United Arab Emirates.

    PubMed

    Blair, Iain; Sharif, Amer Ahmad

    2012-06-01

    To carry out their duties more effectively, health care professionals in the UAE often ask about the population structure and the main causes of mortality and morbidity in the country. This paper summarizes what is known about these topics drawing on secondary data sources that are available in the public domain, including census data, population estimates, births and deaths, proportionate mortality, age-standardized mortality rates and disability adjusted life-years. There are inconsistencies and flaws in some of this data which this paper will highlight and attempt to explain. Since 2005, the UAE population has grown substantially owing to high natural growth and high net inward migration and is currently estimated to be about 8.2million. In 2008, injuries, heart disease, neoplasms and cerebrovascular disease accounted for 57% of deaths, and this is well known. Less is reported about the risk of death, disease, injury and disability. The population of the UAE is diverse, and there are variations in mortality and morbidity risk by age-group, sex and nationality. The authors recommend improvements in the timeliness, completeness and consistency of data. They conclude that better data will encourage more analysis which will generate health intelligence leading to health improvement for the UAE population. Copyright © 2012 Ministry of Health, Saudi Arabia. Published by Elsevier Ltd. All rights reserved.

  7. 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

  8. Accounting for sampling error when inferring population synchrony from time-series data: a Bayesian state-space modelling approach with applications.

    PubMed

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

    2014-01-01

    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. 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. 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 population size estimates.

  9. 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

  10. Population structure of Phytophthora ramorum in Oregon

    Treesearch

    Simone Prospero; Jennifer Britt; Niklaus Grünwald; Everett Hansen

    2008-01-01

    Phytophthora ramorum is infecting plants in Oregon forests and nurseries. In this study, we analyzed the population structure of the P. ramorum in Oregon from 2001 to 2004 using microsatellites. The P. ramorum population in Oregon is characterized by low genetic diversity, significant genetic differences between...

  11. The role of self-defined race/ethnicity in population structure control.

    PubMed

    Liu, X-Q; Paterson, A D; John, E M; Knight, J A

    2006-07-01

    Population-based association studies are powerful tools for the genetic mapping of complex diseases. However, this method is sensitive to potential confounding by population structure. While statistical methods that use genetic markers to detect and control for population structure have been the focus of current literature, the utility of self-defined race/ethnicity in controlling for population structure has been controversial. In this study of 1334 individuals, who self-identified as either African American, European American or Hispanic, we demonstrated that when the true underlying genetic structure and the self-defined racial/ethnic groups were roughly in agreement with each other, the self-defined race/ethnicity information was useful in the control of population structure.

  12. Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

    PubMed

    Mura-Jornet, Isidora; Pimentel, Carolina; Dantas, Gisele P M; Petry, Maria Virginia; González-Acuña, Daniel; Barbosa, Andrés; Lowther, Andrew D; Kovacs, Kit M; Poulin, Elie; Vianna, Juliana A

    2018-06-13

    Historical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species' easternmost breeding colony (Bouvetøya). Connectivity, sex-biased dispersal, diversity, genetic structure and demographic history were studied using 12 microsatellite loci and a mitochondrial DNA region (HVRI) in 12 breeding colonies in the South Shetland Islands (SSI) and the Western Antarctic Peninsula (WAP), and one previously unstudied sub-Antarctic island, 3600 km away from the WAP (Bouvetøya). High genetic diversity, evidence of female bias-dispersal and a sign of population expansion after the last glacial maximum around 10,000 mya were detected. Limited population genetic structure and lack of isolation by distance throughout the region were found, along with no differentiation between the WAP and Bouvetøya (overall microsatellite F ST  = 0.002, p = 0.273; mtDNA F ST  = - 0.004, p = 0.766), indicating long distance dispersal. Therefore, genetic assignment tests could not assign individuals to their population(s) of origin. The most differentiated location was Georges Point, one of the southernmost breeding colonies of this species in the WAP. The subtle differentiation found may be explained by some combination of low natal philopatric behavior, high rates of dispersal and/or generally high mobility among colonies of chinstrap penguins compared to other Pygoscelis species.

  13. 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

  14. Population genetic structure of Helicobacter pylori strains from Portuguese-speaking countries.

    PubMed

    Oleastro, Mónica; Rocha, Raquel; Vale, Filipa F

    2017-08-01

    The human gastric colonizer Helicobacter pylori is useful to track human migrations given the agreement between the bacterium phylogeographic distribution and human migrations. As Portugal was an African and Brazilian colonizer for over 400 years, we hypothesized that Portuguese isolates were likely genetically closer with those from countries colonized by Portuguese in the past. We aimed to characterize the population structure of several Portuguese-speaking countries, including Portugal, Brazil, Angola, and Cape Verde. We included strains isolated in Portugal from Portuguese and from former Portuguese colonies. These strains were typed by multilocus sequence typing (MLST) for seven housekeeping genes. We also retrieved from Multi Locus Sequence Typing Web site additional housekeeping gene sequences, namely from Angola and Brazil. We provided evidence that strains from Portuguese belong to hpEurope and that the introgression of hpEurope in non-European countries that speak Portuguese is low, except for Brazil and Cape Verde, where hpEurope accounted for one quarter and one half of the population, respectively. We found genetic similarity for all strains from Portuguese-speaking countries that belong to hpEurope population. Moreover, these strains showed a predominance of ancestral Europe 2 (AE2) over ancestral Europe 1 (AE1), followed by ancestral Africa 1. H. pylori is a useful marker even for relative recent human migration events and may become rapidly differentiated from founder populations. H. pylori from Portuguese-speaking countries assigned to hpEurope appears to be a hybrid population resulting from the admixture of AE1, AE2 and ancestral hpAfrica1. © 2017 John Wiley & Sons Ltd.

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

    PubMed Central

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

    2013-01-01

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

  16. Among-population variation in microbial community structure in the floral nectar of the bee-pollinated forest herb Pulmonaria officinalis L.

    PubMed

    Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

    2013-01-01

    Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0-4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2-13) OTUs0.03 and 7.9 (range 2-16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar.

  17. A general modeling framework for describing spatially structured population dynamics

    USGS Publications Warehouse

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

    2017-01-01

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

  18. Krill population dynamics in the Scotia Sea: variability in growth and mortality within a single population

    NASA Astrophysics Data System (ADS)

    Reid, K.; Murphy, E. J.; Loeb, V.; Hewitt, R. P.

    2002-07-01

    Understanding the demographics of Antarctic krill over large scales may be complicated by regional differences in the processes that govern population structure. The influence of regional differences in growth and mortality on population size structure was examined using data on the length-frequency distribution of krill in the Scotia Sea using samples from the South Shetland Islands and South Georgia collected annually from 1991 to 2000. A correction function, which took account of the higher growth rate at South Georgia, produced a consistent similarity in the position of the modal size classes that was not present in the raw data. Optimising the mortality rate, to minimise the differences in the growth corrected length-frequency distribution, suggested a higher mortality rate at South Georgia that the South Shetlands. The intra-specific variations in growth and mortality rates are consistent with published values and with other Euphausiids species. Having accounted for the demographic plasticity, it is apparent that strong recruitment of the smallest size class of krill is represented in both populations simultaneously. It appears that first-year krill are advected into different regions of the Scotia Sea where the resultant population size structure is determined by regional differences in growth and mortality. The majority of the commercial harvest of krill in the Antarctic occurs in a relatively small number of regional fisheries within the Scotia Sea and is managed using population models based on a single set of demographic parameters. Where substantial differences in these parameters exist between fishing areas, the calculation of catch limits should take these differences into account.

  19. Accountability for the Quality of Care Provided to People with Serious Illness

    PubMed Central

    Hudson Scholle, Sarah; Briefer French, Jessica

    2018-01-01

    Abstract Background: Care for patients with serious illness is an emerging practice area that has gained attention as value-based purchasing has increased. While the number of programs is growing, their impact on care quality and outcomes is unknown. Objective: With support from the Gordon and Betty Moore Foundation, the National Committee for Quality Assurance (NCQA) is assessing the feasibility of creating an accountability program focused on serious illness care. Methods: This article describes the process of developing an accountability program, findings from our initial work, and our plans to develop measures for a serious illness care accountability program. We focused on three questions: 1. What patient populations should be targeted for measurement?2. What entities have accountability for ensuring high-quality care for serious illness?3. What structures, processes, and outcomes should be evaluated in an accountability program for serious illness care? Results: Our environmental scan showed that the evidence base for specific patient populations or care models is not sufficiently mature to justify traditional structure and process measures. In visits to serious illness care programs, we observed different staffing models, care models, care settings, and payment structures. We found a gap between recommended inclusion criteria and services when compared to inclusion criteria and services offered by existing programs. Conclusions: To address the challenges, NCQA intends to develop outcome measures driven by patient and family priorities. Structure and process measures will focus on building organizations' capacity to measure outcomes, including patient engagement and outcomes, linked to patient goals. PMID:29313755

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

    PubMed

    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

    2016-04-07

    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. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  1. Pseudomonas aeruginosa Population Structure Revisited

    PubMed Central

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

    2009-01-01

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

  2. 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

  3. 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. Copyright © 2016 by the Genetics Society of America.

  4. A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations.

    PubMed

    Rosenberg, Noah A; Nordborg, Magnus

    2006-07-01

    In linkage disequilibrium mapping of genetic variants causally associated with phenotypes, spurious associations can potentially be generated by any of a variety of types of population structure. However, mathematical theory of the production of spurious associations has largely been restricted to population structure models that involve the sampling of individuals from a collection of discrete subpopulations. Here, we introduce a general model of spurious association in structured populations, appropriate whether the population structure involves discrete groups, admixture among such groups, or continuous variation across space. Under the assumptions of the model, we find that a single common principle--applicable to both the discrete and admixed settings as well as to spatial populations--gives a necessary and sufficient condition for the occurrence of spurious associations. Using a mathematical connection between the discrete and admixed cases, we show that in admixed populations, spurious associations are less severe than in corresponding mixtures of discrete subpopulations, especially when the variance of admixture across individuals is small. This observation, together with the results of simulations that examine the relative influences of various model parameters, has important implications for the design and analysis of genetic association studies in structured populations.

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

    Code of Federal Regulations, 2011 CFR

    2011-01-01

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

  6. 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. To...

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

    Code of Federal Regulations, 2014 CFR

    2014-01-01

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

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

    Code of Federal Regulations, 2013 CFR

    2013-01-01

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

  9. 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. To...

  10. 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.

  11. 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.

  12. A Comparative Study of the Perceptions of Accounting Educators and Accountants on Skills Required of Accounting Education Graduates in Automated Offices

    ERIC Educational Resources Information Center

    Nwokike, Felicia Ogonnia; Eya, Gloria Mgboyibo

    2015-01-01

    The study dealt with perception of accounting educators and senior accountants on skills required of accounting education graduates for effective job performance in automated offices. The study adopted a descriptive research design.The population consisted of 149 respondents, made up of 80 accounting educators in public tertiary institutions and…

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

    PubMed Central

    2009-01-01

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

  14. Population structure and genetic diversity in natural populations of Theobroma speciosum Willd. Ex Spreng (Malvaceae).

    PubMed

    Giustina, L D; Luz, L N; Vieira, F S; Rossi, F S; Soares-Lopes, C R A; Pereira, T N S; Rossi, A A B

    2014-02-14

    The genus Theobroma found in the Amazon region is composed of 22 species, including Theobroma speciosum, better known as cacauí. These species are constantly threatened by forest fragmentation caused by human activities and require conservation strategies and management aimed at preserving them in their natural environments. The main objective of this study was to analyze the population structure and genetic diversity within and between natural populations of T. speciosum by using ISSR molecular markers to understand the population structure of the species. Four natural populations belonging to the Amazon rainforest (BAC, CRO, FLA, and PNA), located in the State of Mato Grosso, were selected. Amplification reactions were performed using 15 ISSR primers. A total of 101 loci were found, of which 54.46% were polymorphic at the species level. The BAC population showed higher genetic diversity (H=0.095 and I=0.144) and higher percentage of polymorphism (28.71%). The populations showed an FST value of 0.604, indicating marked genetic differentiation. The highest genetic variation was found between populations. Gene flow was low between populations, indicating genetic isolation between populations.

  15. HLA-C molecular characterization of a Lebanese population and genetic structure of 39 populations from Europe to India-Pakistan.

    PubMed

    Buhler, S; Megarbane, A; Lefranc, G; Tiercy, J-M; Sanchez-Mazas, A

    2006-07-01

    Lebanon is located at a continental crossroad between Europe, Africa, and Asia. This region has been the center of wide-scale movements of populations as well as the theater of genetic and cultural trade off among neighboring populations. In this study, HLA-C alleles were characterized by a PCR-SSOP (sequence-specific oligonucleotide probes) hybridization protocol in a sample of 97 Lebanese. A total of 23 alleles were identified with four predominant, Cw*0401, Cw*0602, Cw*0701/06, and Cw*1203, accounting for almost 60% of HLA-C allele frequencies. We included the Lebanese data into a broad analysis of the HLA-C genetic structure of a large set of populations located in Europe, the Middle East, and the Indian subcontinent. Our results indicate that Lebanese exhibit an intermediate genetic profile among the populations from the Middle East, which constitute a rather homogeneous genetic group. In Europe, a high correlation coefficient is found between genetic and geographic distances. In this continent, we also identified a significant genetic frontier following a north-east to south-west axis. This frontier cuts through the Alps and the Pyrenees, thus separating the north-western European populations from those located in the eastern and Mediterranean areas. Finally, the populations from India - Pakistan are very heterogeneous, particularly the Dravidians. Their differentiation has probably been caused by rapid genetic drift under complex influences of cultural, linguistic, and/or religious barriers. Overall, the results show that the HLA-C genetic patterns of these three geographic regions, i.e., the Middle East, Europe, and India-Pakistan, have been shaped by very different genetic histories.

  16. 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

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

    PubMed

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

    2012-09-01

    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.

  18. Ethnicity and Population Structure in Personal Naming Networks

    PubMed Central

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

    2011-01-01

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

  19. 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.

  20. Spatio-temporal variation in age structure and abundance of the endangered snail kite: Pooling across regions masks a declining and aging population

    USGS Publications Warehouse

    Reichert, Brian E.; Kendall, William L.; Fletcher, Robert J.; Kitchens, Wiley M.

    2016-01-01

    While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species.

  1. Kin groups and trait groups: population structure and epidemic disease selection.

    PubMed

    Fix, A G

    1984-10-01

    A Monte Carlo simulation based on the population structure of a small-scale human population, the Semai Senoi of Malaysia, has been developed to study the combined effects of group, kin, and individual selection. The population structure resembles D.S. Wilson's structured deme model in that local breeding populations (Semai settlements) are subdivided into trait groups (hamlets) that may be kin-structured and are not themselves demes. Additionally, settlement breeding populations are connected by two-dimensional stepping-stone migration approaching 30% per generation. Group and kin-structured group selection occur among hamlets the survivors of which then disperse to breed within the settlement population. Genetic drift is modeled by the process of hamlet formation; individual selection as a deterministic process, and stepping-stone migration as either random or kin-structured migrant groups. The mechanism for group selection is epidemics of infectious disease that can wipe out small hamlets particularly if most adults become sick and social life collapses. Genetic resistance to a disease is an individual attribute; however, hamlet groups with several resistant adults are less likely to disintegrate and experience high social mortality. A specific human gene, hemoglobin E, which confers resistance to malaria, is studied as an example of the process. The results of the simulations show that high genetic variance among hamlet groups may be generated by moderate degrees of kin-structuring. This strong microdifferentiation provides the potential for group selection. The effect of group selection in this case is rapid increase in gene frequencies among the total set of populations. In fact, group selection in concert with individual selection produced a faster rate of gene frequency increase among a set of 25 populations than the rate within a single unstructured population subject to deterministic individual selection. Such rapid evolution with plausible rates of

  2. Ethical challenges for accountable care organizations: a structured review.

    PubMed

    DeCamp, Matthew; Farber, Neil J; Torke, Alexia M; George, Maura; Berger, Zackary; Keirns, Carla C; Kaldjian, Lauris C

    2014-10-01

    Accountable care organizations (ACOs) are proliferating as a solution to the cost crisis in American health care, and already involve as many as 31 million patients. ACOs hold clinicians, group practices, and in many circumstances hospitals financially accountable for reducing expenditures and improving their patients' health outcomes. The structure of health care affects the ethical issues arising in the practice of medicine; therefore, like all health care organizational structures, ACOs will experience ethical challenges. No framework exists to assist key ACO stakeholders in identifying or managing these challenges. We conducted a structured review of the medical ACO literature using qualitative content analysis to inform identification of ethical challenges for ACOs. Our analysis found infrequent discussion of ethics as an explicit concern for ACOs. Nonetheless, we identified nine critical ethical challenges, often described in other terms, for ACO stakeholders. Leaders could face challenges regarding fair resource allocation (e.g., about fairly using ACOs' shared savings), protection of professionals' ethical obligations (especially related to the design of financial incentives), and development of fair decision processes (e.g., ensuring that beneficiary representatives on the ACO board truly represent the ACO's patients). Clinicians could perceive threats to their professional autonomy (e.g., through cost control measures), a sense of dual or conflicted responsibility to their patients and the ACO, or competition with other clinicians. For patients, critical ethical challenges will include protecting their autonomy, ensuring privacy and confidentiality, and effectively engaging them with the ACO. ACOs are not inherently more or less "ethical" than other health care payment models, such as fee-for-service or pure capitation. ACOs' nascent development and flexibility in design, however, present a time-sensitive opportunity to ensure their ethical operation

  3. Disruptive innovation in academic medical centers: balancing accountable and academic care.

    PubMed

    Stein, Daniel; Chen, Christopher; Ackerly, D Clay

    2015-05-01

    Numerous academic medicine leaders have argued that academic referral centers must prepare for the growing importance of accountability-driven payment models by adopting population health initiatives. Although this shift has merit, execution of this strategy will prove significantly more problematic than most observers have appreciated. The authors describe how successful implementation of an accountable care health strategy within a referral academic medical center (AMC) requires navigating a critical tension: The academic referral business model, driven by tertiary-level care, is fundamentally in conflict with population health. Referral AMCs that create successful value-driven population health systems within their organizations will in effect disrupt their own existing tertiary care businesses. The theory of disruptive innovation suggests that balancing the push and pull of academic and accountable care within a single organization is achievable. However, it will require significant shifts in resource allocation and changes in management structure to enable AMCs to make the inherent difficult choices and trade-offs that will ensue. On the basis of the theories of disruptive innovation, the authors present recommendations for how academic health systems can successfully navigate these issues as they transition toward accountability-driven care.

  4. Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers

    PubMed Central

    Edea, Zewdu; Dessie, Tadelle; Dadi, Hailu; Do, Kyoung-Tag; Kim, Kwan-Suk

    2017-01-01

    Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin—i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered

  5. 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.

  6. 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

  7. Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification.

    PubMed

    Zhang, Z; Guillaume, F; Sartelet, A; Charlier, C; Georges, M; Farnir, F; Druet, T

    2012-10-01

    In many situations, genome-wide association studies are performed in populations presenting stratification. Mixed models including a kinship matrix accounting for genetic relatedness among individuals have been shown to correct for population and/or family structure. Here we extend this methodology to generalized linear mixed models which properly model data under various distributions. In addition we perform association with ancestral haplotypes inferred using a hidden Markov model. The method was shown to properly account for stratification under various simulated scenari presenting population and/or family structure. Use of ancestral haplotypes resulted in higher power than SNPs on simulated datasets. Application to real data demonstrates the usefulness of the developed model. Full analysis of a dataset with 4600 individuals and 500 000 SNPs was performed in 2 h 36 min and required 2.28 Gb of RAM. The software GLASCOW can be freely downloaded from www.giga.ulg.ac.be/jcms/prod_381171/software. francois.guillaume@jouy.inra.fr Supplementary data are available at Bioinformatics online.

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

    PubMed

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

    2016-09-01

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

  9. Mapping population-based structural connectomes.

    PubMed

    Zhang, Zhengwu; Descoteaux, Maxime; Zhang, Jingwen; Girard, Gabriel; Chamberland, Maxime; Dunson, David; Srivastava, Anuj; Zhu, Hongtu

    2018-05-15

    Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Comparing population structure as inferred from genealogical versus genetic information.

    PubMed

    Colonna, Vincenza; Nutile, Teresa; Ferrucci, Ronald R; Fardella, Giulio; Aversano, Mario; Barbujani, Guido; Ciullo, Marina

    2009-12-01

    Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite F(st) between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and F(st) between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when F(st) values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data.

  11. Comparing population structure as inferred from genealogical versus genetic information

    PubMed Central

    Colonna, Vincenza; Nutile, Teresa; Ferrucci, Ronald R; Fardella, Giulio; Aversano, Mario; Barbujani, Guido; Ciullo, Marina

    2009-01-01

    Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite Fst between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and Fst between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when Fst values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data. PMID:19550436

  12. Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

    PubMed Central

    Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

    2013-01-01

    Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID

  13. Dynamic changes in the population structure of Escherichia coli in the Yeongsan River basin of South Korea.

    PubMed

    Jang, Jeonghwan; Di, Doris Y W; Han, Dukki; Unno, Tatsuya; Lee, Jeom-Ho; Sadowsky, Michael J; Hur, Hor-Gil

    2015-11-01

    Although Escherichia coli has been used as an indicator to examine fecal contamination of aquatic environment, it also has been reported to become naturalized to secondary habitats, including soil, water and beach sand. A total of 2880 E. coli isolates obtained from surface water and sediment samples from the Yeongsan River in 2013 were genotyped by using the horizontal fluorophore-enhanced rep-PCR DNA fingerprinting technique. Although different E. coli genotypic groups were observed between surface water and sediments in the dry season, they were mingled and undifferentiated from each other in the rainy season. This indicates that there are frequent sediment resuspension events in the river basin. Moreover, the genotypic composition of the E. coli population in the Yeongsan River basin changes over months and years, implying that genotypic structure of E. coli populations dynamically fluctuates in the river environment. Consequently, our data suggests that the use of E. coli libraries for fecal source tracking needs to be reassessed to account for the changing structure of riverine E. coli populations. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Genetic structure among continental and island populations of gyrfalcons.

    PubMed

    Johnson, Jeff A; Burnham, Kurt K; Burnham, William A; Mindell, David P

    2007-08-01

    Little is known about the possible influence that past glacial events have had on the phylogeography and population structure of avian predators in the Arctic and sub-Arctic. In this study, we use microsatellite and mitochondrial control region DNA variation to investigate the population genetic structure of gyrfalcons (Falco rusticolus) throughout a large portion of their circumpolar distribution. In most locations sampled, the mtDNA data revealed little geographic structure; however, five out of eight mtDNA haplotypes were unique to a particular geographic area (Greenland, Iceland, or Alaska) and the Iceland population differed from others based on haplotype frequency differences (F(ST)). With the microsatellite results, significant population structure (F(ST), principal components analysis, and cluster analysis) was observed identifying Greenland and Iceland as separate populations, while Norway, Alaska and Canada were identified as a single population consistent with contemporary gene flow across Russia. Within Greenland, differing levels of gene flow between western and eastern sampling locations was indicated with apparent asymmetric dispersal in western Greenland from north to south. This dispersal bias is in agreement with the distribution of plumage colour variants with white gyrfalcons in much higher proportion in northern Greenland. Lastly, because the mtDNA control region sequence differed by only one to four nucleotides from a common haplotype among all gyrfalcons, we infer that the observed microsatellite population genetic structure has developed since the last glacial maximum. This conclusion is further supported by our finding that a closely related species, the saker falcon (Falco cherrug), has greater genetic heterogeneity, including mtDNA haplotypes differing by 1-16 nucleotide substitutions from a common gyrfalcon haplotype. This is consistent with gyrfalcons having expanded rapidly from a single glacial-age refugium to their current

  15. 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.

  16. Structure of some East African Glossina fuscipes fuscipes populations

    PubMed Central

    Krafsur, E. S.; Marquez, J. G.; Ouma, J. O.

    2008-01-01

    Glossina fuscipes fuscipes Newstead 1910 (Diptera: Glossinidae) is the primary vector of human sleeping sickness in Kenya and Uganda. This is the first report on its population structure. A total of 688 nucleotides of mitochondrial ribosomal 16S2 and cytochrome oxidase I genes were sequenced. Twenty-one variants were scored in 79 flies from three geographically diverse natural populations. Four haplotypes were shared among populations, eight were private and nine were singletons. The mean haplotype and nucleotide diversities were 0.84 and 0.009, respectively. All populations were genetically differentiated and were at demographic equilibrium. In addition, a longstanding laboratory culture originating from the Central African Republic (CAR-lab) in 1986 (or before) was examined. Haplotype and nucleotide diversities in this culture were 0.95 and 0.012, respectively. None of its 27 haplotypes were shared with the East African populations. A first approximation of relative effective population sizes was Uganda > CAR-lab > Kenya. It was concluded that the structure of G. f. fuscipes populations in East Africa is localized. PMID:18816270

  17. The mutation-drift balance in spatially structured populations.

    PubMed

    Schneider, David M; Martins, Ayana B; de Aguiar, Marcus A M

    2016-08-07

    In finite populations the action of neutral mutations is balanced by genetic drift, leading to a stationary distribution of alleles that displays a transition between two different behaviors. For small mutation rates most individuals will carry the same allele at equilibrium, whereas for high mutation rates of the alleles will be randomly distributed with frequencies close to one half for a biallelic gene. For well-mixed haploid populations the mutation threshold is μc=1/2N, where N is the population size. In this paper we study how spatial structure affects this mutation threshold. Specifically, we study the stationary allele distribution for populations placed on regular networks where connected nodes represent potential mating partners. We show that the mutation threshold is sensitive to spatial structure only if the number of potential mates is very small. In this limit, the mutation threshold decreases substantially, increasing the diversity of the population at considerably low mutation rates. Defining kc as the degree of the network for which the mutation threshold drops to half of its value in well-mixed populations we show that kc grows slowly as a function of the population size, following a power law. Our calculations and simulations are based on the Moran model and on a mapping between the Moran model with mutations and the voter model with opinion makers. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. 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.

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

    PubMed

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

    1999-10-01

    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.

  20. 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.

  1. Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure

    PubMed Central

    Chaichoompu, Kridsadakorn; Ngamphiw, Chumpol; Assawamakin, Anunchai; Nuinoon, Manit; Sripichai, Orapan; Svasti, Saovaros; Fucharoen, Suthat; Praphanphoj, Verayuth; Tongsima, Sissades

    2013-01-01

    studies to account for population-structure confounding effects. PMID:24223962

  2. Temperature-driven regime shifts in the dynamics of size-structured populations.

    PubMed

    Ohlberger, Jan; Edeline, Eric; Vøllestad, Leif Asbjørn; Stenseth, Nils C; Claessen, David

    2011-02-01

    Global warming impacts virtually all biota and ecosystems. Many of these impacts are mediated through direct effects of temperature on individual vital rates. Yet how this translates from the individual to the population level is still poorly understood, hampering the assessment of global warming impacts on population structure and dynamics. Here, we study the effects of temperature on intraspecific competition and cannibalism and the population dynamical consequences in a size-structured fish population. We use a physiologically structured consumer-resource model in which we explicitly model the temperature dependencies of the consumer vital rates and the resource population growth rate. Our model predicts that increased temperature decreases resource density despite higher resource growth rates, reflecting stronger intraspecific competition among consumers. At a critical temperature, the consumer population dynamics destabilize and shift from a stable equilibrium to competition-driven generation cycles that are dominated by recruits. As a consequence, maximum age decreases and the proportion of younger and smaller-sized fish increases. These model predictions support the hypothesis of decreasing mean body sizes due to increased temperatures. We conclude that in size-structured fish populations, global warming may increase competition, favor smaller size classes, and induce regime shifts that destabilize population and community dynamics.

  3. 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.

  4. 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

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

    PubMed

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

    2015-08-01

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

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

    PubMed

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

    2009-02-01

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

  7. Competition in size-structured populations: mechanisms inducing cohort formation and population cycles.

    PubMed

    de Roos, André M; Persson, Lennart

    2003-02-01

    In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and adults both feed on one and the same resource and hence interact by means of exploitative competition. Juvenile individuals allocate all assimilated energy into development and mature on reaching a fixed developmental threshold. The combination of this fixed threshold and the resource-dependent developmental rate, implies that the juvenile delay between birth and the onset of reproduction may vary in time. Adult individuals allocate all assimilated energy to reproduction. Mortality of both juveniles and adults is assumed to be inversely proportional to the amount of energy assimilated. In this setting we study how the dynamics of the population are influenced by the relative foraging capabilities of juveniles and adults. In line with results that we previously obtained in size-structured consumer-resource models with pulsed reproduction, population cycles primarily occur when either juveniles or adults have a distinct competitive advantage. When adults have a larger per capita feeding rate and are hence competitively superior to juveniles, population oscillations occur that are primarily induced by the fact that the duration of the juvenile period changes with changing food conditions. These cycles do not occur when the juvenile delay is a fixed parameter. When juveniles are competitively superior, two different types of population fluctuations can occur: (1) rapid, low-amplitude fluctuations having a period of half the juvenile delay and (2) slow, large-amplitude fluctuations characterized by a period, which is roughly equal to the juvenile delay. The analysis of simplified versions of the structured model indicates that these two types of oscillations also occur if

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

    PubMed Central

    Rico, Y; Wagner, H H

    2016-01-01

    Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations. PMID:27381322

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

    PubMed

    Rico, Y; Wagner, H H

    2016-11-01

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

  10. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. I: Multivariate Gaussian priors for marker effects and derivation of the joint probability mass function of genotypes.

    PubMed

    Martínez, Carlos Alberto; Khare, Kshitij; Banerjee, Arunava; Elzo, Mauricio A

    2017-03-21

    It is important to consider heterogeneity of marker effects and allelic frequencies in across population genome-wide prediction studies. Moreover, all regression models used in genome-wide prediction overlook randomness of genotypes. In this study, a family of hierarchical Bayesian models to perform across population genome-wide prediction modeling genotypes as random variables and allowing population-specific effects for each marker was developed. Models shared a common structure and differed in the priors used and the assumption about residual variances (homogeneous or heterogeneous). Randomness of genotypes was accounted for by deriving the joint probability mass function of marker genotypes conditional on allelic frequencies and pedigree information. As a consequence, these models incorporated kinship and genotypic information that not only permitted to account for heterogeneity of allelic frequencies, but also to include individuals with missing genotypes at some or all loci without the need for previous imputation. This was possible because the non-observed fraction of the design matrix was treated as an unknown model parameter. For each model, a simpler version ignoring population structure, but still accounting for randomness of genotypes was proposed. Implementation of these models and computation of some criteria for model comparison were illustrated using two simulated datasets. Theoretical and computational issues along with possible applications, extensions and refinements were discussed. Some features of the models developed in this study make them promising for genome-wide prediction, the use of information contained in the probability distribution of genotypes is perhaps the most appealing. Further studies to assess the performance of the models proposed here and also to compare them with conventional models used in genome-wide prediction are needed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Utility of R0 as a predictor of disease invasion in structured populations

    USGS Publications Warehouse

    Cross, P.C.; Johnson, P.L.F.; Lloyd-Smith, James 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.

  12. Utility of R0 as a predictor of disease invasion in structured populations.

    PubMed

    Cross, Paul C; Johnson, Philip L F; Lloyd-Smith, James O; Getz, Wayne M

    2007-04-22

    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.

  13. Inference and Analysis of Population Structure Using Genetic Data and Network Theory

    PubMed Central

    Greenbaum, Gili; Templeton, Alan R.; Bar-David, Shirli

    2016-01-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  14. Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

    PubMed

    Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

    2016-04-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  15. Spatial and population genetic structure of microsatellites in white pine

    Treesearch

    Paula E. Marquardt; Bryan K. Epperson

    2004-01-01

    We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

  16. Mitochondrial population genomic analyses reveal population structure and demography of Indian Plasmodium falciparum.

    PubMed

    Tyagi, Suchi; Das, Aparup

    2015-09-01

    Inference on the genetic diversity of Plasmodium falciparum populations could help in better management of malaria. A very recent study with mitochondrial (mt) genomes in global P. falciparum had revealed interesting evolutionary genetic patterns of Indian isolates in comparison to global ones. However, no population genetic study using the whole mt genome sequences of P. falciparum isolates collected in the entire distribution range in India has yet been performed. We herewith have analyzed 85 whole mt genomes (48 already published and 37 entirely new) sampled from eight differentially endemic Indian locations to estimate genetic diversity and infer population structure and historical demography of Indian P. falciparum. We found 19 novel Indian-specific Single Nucleotide Polymorphisms (SNPs) and 22 novel haplotypes segregating in Indian P. falciparum. Accordingly, high haplotype and nucleotide diversities were detected in Indian P. falciparum in comparison to many other global isolates. Indian P. falciparum populations were found to be moderately sub-structured with four different genetic clusters. Interestingly, group of local populations aggregate to form each cluster; while samples from Jharkhand and Odisha formed a single cluster, P. falciparum isolates from Asom formed an independent one. Similarly, Surat, Bilaspur and Betul formed a single cluster and Goa and Mangalore formed another. Interestingly, P. falciparum isolates from the two later populations were significantly genetically differentiated from isolates collected in other six Indian locations. Signature of historical population expansion was evident in five population samples, and the onset of expansion event was found to be very similar to African P. falciparum. In agreement with the previous finding, the estimated Time to Most Recent Common Ancestor (TMRCA) and the effective population size were high in Indian P. falciparum. All these genetic features of Indian P. falciparum with high mt genome

  17. Fine-scale population structure and the era of next-generation sequencing.

    PubMed

    Henn, Brenna M; Gravel, Simon; Moreno-Estrada, Andres; Acevedo-Acevedo, Suehelay; Bustamante, Carlos D

    2010-10-15

    Fine-scale population structure characterizes most continents and is especially pronounced in non-cosmopolitan populations. Roughly half of the world's population remains non-cosmopolitan and even populations within cities often assort along ethnic and linguistic categories. Barriers to random mating can be ecologically extreme, such as the Sahara Desert, or cultural, such as the Indian caste system. In either case, subpopulations accumulate genetic differences if the barrier is maintained over multiple generations. Genome-wide polymorphism data, initially with only a few hundred autosomal microsatellites, have clearly established differences in allele frequency not only among continental regions, but also within continents and within countries. We review recent evidence from the analysis of genome-wide polymorphism data for genetic boundaries delineating human population structure and the main demographic and genomic processes shaping variation, and discuss the implications of population structure for the distribution and discovery of disease-causing genetic variants, in the light of the imminent availability of sequencing data for a multitude of diverse human genomes.

  18. Structural drift: the population dynamics of sequential learning.

    PubMed

    Crutchfield, James P; Whalen, Sean

    2012-01-01

    We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream "teacher" and then pass samples from the model to their downstream "student". It extends the population dynamics of genetic drift, recasting Kimura's selectively neutral theory as a special case of a generalized drift process using structured populations with memory. We examine the diffusion and fixation properties of several drift processes and propose applications to learning, inference, and evolution. We also demonstrate how the organization of drift process space controls fidelity, facilitates innovations, and leads to information loss in sequential learning with and without memory.

  19. 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

  20. Is urbanisation scrambling the genetic structure of human populations? A case study

    PubMed Central

    Ashrafian-Bonab, Maziar; Handley, Lori Lawson; Balloux, François

    2007-01-01

    Recent population expansion and increased migration linked to urbanisation are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from twenty-two Iranian populations. Potential changes in genetic diversity (θ) and genetic distance (FST) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterised by massive immigration, increased θ and a large decrease in FST over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies. PMID:17106453

  1. Phenotypic diversity, population structure and stress protein-based capacitoring in populations of Xeropicta derbentina, a heat-tolerant land snail species.

    PubMed

    Di Lellis, Maddalena A; Sereda, Sergej; Geißler, Anna; Picot, Adrien; Arnold, Petra; Lang, Stefanie; Troschinski, Sandra; Dieterich, Andreas; Hauffe, Torsten; Capowiez, Yvan; Mazzia, Christophe; Knigge, Thomas; Monsinjon, Tiphaine; Krais, Stefanie; Wilke, Thomas; Triebskorn, Rita; Köhler, Heinz-R

    2014-11-01

    The shell colour of many pulmonate land snail species is highly diverse. Besides a genetic basis, environmentally triggered epigenetic mechanisms including stress proteins as evolutionary capacitors are thought to influence such phenotypic diversity. In this study, we investigated the relationship of stress protein (Hsp70) levels with temperature stress tolerance, population structure and phenotypic diversity within and among different populations of a xerophilic Mediterranean snail species (Xeropicta derbentina). Hsp70 levels varied considerably among populations, and were significantly associated with shell colour diversity: individuals in populations exhibiting low diversity expressed higher Hsp70 levels both constitutively and under heat stress than those of phenotypically diverse populations. In contrast, population structure (cytochrome c oxidase subunit I gene) did not correlate with phenotypic diversity. However, genetic parameters (both within and among population differences) were able to explain variation in Hsp70 induction at elevated but non-pathologic temperatures. Our observation that (1) population structure had a high explanatory potential for Hsp70 induction and that (2) Hsp70 levels, in turn, correlated with phenotypic diversity while (3) population structure and phenotypic diversity failed to correlate provides empirical evidence for Hsp70 to act as a mediator between genotypic variation and phenotype and thus for chaperone-driven evolutionary capacitance in natural populations.

  2. Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation.

    PubMed

    Atnaf, Mulugeta; Yao, Nasser; Martina, Kyalo; Dagne, Kifle; Wegary, Dagne; Tesfaye, Kassahun

    2017-01-01

    White lupin is one of the four economically important species of the Lupinus genus and is an important grain legume in the Ethiopian farming system. However, there has been limited research effort to characterize the Ethiopian white lupin landraces. Fifteen polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 212 Ethiopian white lupin (Lupinus albus) landraces and two genotypes from different species (Lupinus angustifolius and Lupinus mutabilis) were used as out-group. The SSR markers revealed 108 different alleles, 98 of them from 212 landraces and 10 from out-group genotypes, with an average of 6.5 alleles per locus. The average gene diversity was 0.31. Twenty eight landraces harbored one or more private alleles from the total of 28 private alleles identified in the 212 white lupin accessions. Seventy-seven rare alleles with a frequency of less than 5% were identified and accounted for 78.6% of the total alleles detected. Analysis of molecular variance (AMOVA) showed that 92% of allelic diversity was attributed to individual accessions within populations while only 8% was distributed among populations. At 70% similarity level, the UPGMA dendrogram resulted in the formation of 13 clusters comprised of 2 to 136 landraces, with the out-group genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and Ethiopian white lupin populations collected by Australians. A model-based population structure analysis divided the white lupin landraces into two populations. All Ethiopian white lupin landrace populations, except most of the landraces collected by Australians (77%) and about 44% from Awi, were grouped together with significant admixtures. The study also suggested that 34 accessions, as core collections, were sufficient to retain 100% of SSR diversity. These accessions (core G-34) represent 16% of the whole 212

  3. Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation

    PubMed Central

    Yao, Nasser; Martina, Kyalo; Dagne, Kifle; Wegary, Dagne; Tesfaye, Kassahun

    2017-01-01

    White lupin is one of the four economically important species of the Lupinus genus and is an important grain legume in the Ethiopian farming system. However, there has been limited research effort to characterize the Ethiopian white lupin landraces. Fifteen polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 212 Ethiopian white lupin (Lupinus albus) landraces and two genotypes from different species (Lupinus angustifolius and Lupinus mutabilis) were used as out-group. The SSR markers revealed 108 different alleles, 98 of them from 212 landraces and 10 from out-group genotypes, with an average of 6.5 alleles per locus. The average gene diversity was 0.31. Twenty eight landraces harbored one or more private alleles from the total of 28 private alleles identified in the 212 white lupin accessions. Seventy-seven rare alleles with a frequency of less than 5% were identified and accounted for 78.6% of the total alleles detected. Analysis of molecular variance (AMOVA) showed that 92% of allelic diversity was attributed to individual accessions within populations while only 8% was distributed among populations. At 70% similarity level, the UPGMA dendrogram resulted in the formation of 13 clusters comprised of 2 to 136 landraces, with the out-group genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and Ethiopian white lupin populations collected by Australians. A model-based population structure analysis divided the white lupin landraces into two populations. All Ethiopian white lupin landrace populations, except most of the landraces collected by Australians (77%) and about 44% from Awi, were grouped together with significant admixtures. The study also suggested that 34 accessions, as core collections, were sufficient to retain 100% of SSR diversity. These accessions (core G-34) represent 16% of the whole 212

  4. Limiting similarity and niche theory for structured populations.

    PubMed

    Szilágyi, András; Meszéna, Géza

    2009-05-07

    We develop the theory of limiting similarity and niche for structured populations with finite number of individual states (i-state). In line with a previously published theory for unstructured populations, the niche of a species is specified by the impact and sensitivity niche vectors. They describe the population's impact on and sensitivity towards the variables involved in the population regulation. Robust coexistence requires sufficient segregation of the impact, as well as of the sensitivity niche vectors. Connection between the population-level impact and sensitivity and the impact/sensitivity of the specific i-states is developed. Each i-state contributes to the impact of the population proportional to its frequency in the population. Sensitivity of the population is composed of the sensitivity of the rates of demographic transitions, weighted by the frequency and by the reproductive value of the initial and final i-states of the transition, respectively. Coexistence in a multi-patch environment is studied. This analysis is interpreted as spatial niche segregation.

  5. Genetic structure of Culex erraticus populations across the Americas.

    PubMed

    Mendenhall, Ian H; Bahl, Justin; Blum, Michael J; Wesson, Dawn M

    2012-05-01

    Culex erraticus (Dyar & Knab) is a potential competent vector for several arboviruses such as Eastern and Venezuelan equine encephalitis viruses and West Nile virus. It therefore may play a role in the maintenance and spread of viral populations in areas of concern, including the United States where it occurs in >33 states. However, little information is available on potential barriers to movement across the species' distribution. Here, we analyze genetic variation among Cx. erraticus collected from Colombia, Guatemala, and nine locations in the United States to better understand population structure and connectivity. Comparative sequence analysis of the second internal transcribed spacer and mitochondrial NADH dehydrogenase genes identified two major lineages of sampled populations. One lineage represented the central and eastern United States, whereas the other corresponded to Central America, South America, and the western United States. Hierarchical analysis of genetic variation provided further evidence of regional population structure, although the majority of genetic variation was found to reside within populations, suggestive of large population sizes. Although significant physical barriers such as the Chihuahuan Desert probably constrain the spread of Cx. erraticus, large population sizes and connectivity within regions remain important risk factors that probably contribute to the movement of arboviruses within and between these regions.

  6. Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain.

    PubMed

    Moreno, I M; Malpica, J M; Díaz-Pendón, J A; Moriones, E; Fraile, A; García-Arenal, F

    2004-01-05

    The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection.

  7. 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.

  8. Population structure and infectious disease risk in southern Africa.

    PubMed

    Uren, Caitlin; Möller, Marlo; van Helden, Paul D; Henn, Brenna M; Hoal, Eileen G

    2017-06-01

    The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.

  9. 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. Project HOPE—The People-to-People Health Foundation, Inc.

  10. Importance of dispersal routes that minimize open-ocean movement to the genetic structure of island populations.

    PubMed

    Harradine, E L; Andrew, M E; Thomas, J W; How, R A; Schmitt, L H; Spencer, P B S

    2015-12-01

    Islands present a unique scenario in conservation biology, offering refuge yet imposing limitations on insular populations. The Kimberley region of northwestern Australia has more than 2500 islands that have recently come into focus as substantial conservation resources. It is therefore of great interest for managers to understand the driving forces of genetic structure of species within these island archipelagos. We used the ubiquitous bar-shouldered skink (Ctenotus inornatus) as a model species to represent the influence of landscape factors on genetic structure across the Kimberley islands. On 41 islands and 4 mainland locations in a remote area of Australia, we genotyped individuals across 18 nuclear (microsatellite) markers. Measures of genetic differentiation and diversity were used in two complementary analyses. We used circuit theory and Mantel tests to examine the influence of the landscape matrix on population connectivity and linear regression and model selection based on Akaike's information criterion to investigate landscape controls on genetic diversity. Genetic differentiation between islands was best predicted with circuit-theory models that accounted for the large difference in resistance to dispersal between land and ocean. In contrast, straight-line distances were unrelated to either resistance distances or genetic differentiation. Instead, connectivity was determined by island-hopping routes that allow organisms to minimize the distance of difficult ocean passages. Island populations of C. inornatus retained varying degrees of genetic diversity (NA = 1.83 - 7.39), but it was greatest on islands closer to the mainland, in terms of resistance-distance units. In contrast, genetic diversity was unrelated to island size. Our results highlight the potential for islands to contribute to both theoretical and applied conservation, provide strong evidence of the driving forces of population structure within undisturbed landscapes, and identify the islands

  11. Population structure of Vibrio fischeri within the light organs of Euprymna scolopes squid from Two Oahu (Hawaii) populations.

    PubMed

    Wollenberg, M S; Ruby, E G

    2009-01-01

    We resolved the intraspecific diversity of Vibrio fischeri, the bioluminescent symbiont of the Hawaiian sepiolid squid Euprymna scolopes, at two previously unexplored morphological and geographical scales. These scales ranged from submillimeter regions within the host light organ to the several kilometers encompassing two host populations around Oahu. To facilitate this effort, we employed both novel and standard genetic and phenotypic assays of light-organ symbiont populations. A V. fischeri-specific fingerprinting method and five phenotypic assays were used to gauge the genetic richness of V. fischeri populations; these methods confirmed that the symbiont population present in each adult host's light organ is polyclonal. Upon statistical analysis of these genetic and phenotypic population data, we concluded that the characteristics of symbiotic populations were more similar within individual host populations than between the two distinct Oahu populations of E. scolopes, providing evidence that local geographic symbiont population structure exists. Finally, to better understand the genesis of symbiont diversity within host light organs, the process of symbiosis initiation in newly hatched juvenile squid was examined both experimentally and by mathematical modeling. We concluded that, after the juvenile hatches, only one or two cells of V. fischeri enter each of six internal epithelium-lined crypts present in the developing light organ. We hypothesize that the expansion of different, crypt-segregated, clonal populations creates the polyclonal adult light-organ population structure observed in this study. The stability of the luminous-bacterium-sepiolid squid mutualism in the presence of a polyclonal symbiont population structure is discussed in the context of contemporary evolutionary theory.

  12. Population and labour force projections for 27 European countries, 2002-052: impact of international migration on population ageing: Projections de population et de population active pour 27 pays européens 2002-052: impact de la migration internationale sur le vieillissement de la population.

    PubMed

    Bijak, Jakub; Kupiszewska, Dorota; Kupiszewski, Marek; Saczuk, Katarzyna; Kicinger, Anna

    2007-03-01

    Population and labour force projections are made for 27 selected European countries for 2002-052, focussing on the impact of international migration on population and labour force dynamics. Starting from single scenarios for fertility, mortality and economic activity, three sets of assumptions are explored regarding migration flows, taking into account probable policy developments in Europe following the enlargement of the EU. In addition to age structures, various support ratio indicators are analysed. The results indicate that plausible immigration cannot offset the negative effects of population and labour force ageing.

  13. Impacts of Population Structure and Analytical Models in Genome-Wide Association Studies of Complex Traits in Forest Trees: A Case Study in Eucalyptus globulus

    PubMed Central

    Garcia, Martín N.; Acuña, Cintia; Borralho, Nuno M. G.; Grattapaglia, Dario; Marcucci Poltri, Susana N.

    2013-01-01

    The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly

  14. Evolutionary genomics and population structure of Entamoeba histolytica

    PubMed Central

    Das, Koushik; Ganguly, Sandipan

    2014-01-01

    Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genetic diversity reveals parasite population structure has also been discussed. Queries concerning their evolution and population structure which were required to be addressed have also been highlighted. This significantly large amount of genomic data will improve our knowledge about this pathogenic species of Entamoeba. PMID:25505504

  15. Spatial and temporal aspects of the genetic structure of Juniperus communis populations.

    PubMed

    Merwe, M V; Winfield, M O; Arnold, G M; Parker, J S

    2000-04-01

    Juniperus communis is a dioecious, wind pollinated shrub or small tree that produces 'berries' (female cones) containing a small number of seeds that are thought to be dispersed by birds. The expectation, therefore, would be that populations of Juniper are genetically diverse with little structuring between them. In Britain, the species has two main centres of distribution: a highland zone in the north and west, in which populations are still large and sexually reproducing, and a southern zone on chalk downlands in which populations are small and fragmented and individuals suffer from a decline in fertility. Thus, one would expect the large sexually viable populations in the north to exhibit high levels of within-population genetic variation, while the declining southern populations would be genetically depauperate. The analysis of amplified fragment length polymorphisms (AFLPs) was used to test this hypothesis. Surprisingly, all populations studied showed high levels of genetic variation although there was clear structuring between populations. On the basis of the geographical structuring of the populations it was hypothesized that J. communis colonized Britain via three separate routes.

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

    PubMed

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

    2012-02-01

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

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

    PubMed Central

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

    2012-01-01

    Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population FST values (−0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (FCT = 0.028, p<0.05), and no genetic variation within groups (0.53%; FSC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species. PMID:25049547

  18. Social structural consequences of population growth.

    PubMed

    Adams, R E

    1981-01-01

    Estimates from archaeological data of the numbers in the elite classes, nonelite occupational specialists, density of population, city size, and size of political units in the ancient Maya civilization suggest that there was a quantum shift in rate of development in the Early Classic period, associated with intensification of agriculture, and that the social structure approximated to a generalized feudal pattern.

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

    PubMed

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

    2014-08-01

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

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

    PubMed Central

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

    2014-01-01

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

  1. 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

  2. Genetic structure of populations and differentiation in forest trees

    Treesearch

    Raymond P. Guries; F. Thomas Ledig

    1981-01-01

    Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

  3. Age structure changes and extraordinary lifespan in wild medfly populations.

    PubMed

    Carey, James R; Papadopoulos, Nikos T; Müller, Hans-Georg; Katsoyannos, Byron I; Kouloussis, Nikos A; Wang, Jane-Ling; Wachter, Kenneth; Yu, Wei; Liedo, Pablo

    2008-06-01

    The main purpose of this study was to test the hypotheses that major changes in age structure occur in wild populations of the Mediterranean fruit fly (medfly) and that a substantial fraction of individuals survive to middle age and beyond (> 3-4 weeks). We thus brought reference life tables and deconvolution models to bear on medfly mortality data gathered from a 3-year study of field-captured individuals that were monitored in the laboratory. The average time-to-death of captured females differed between sampling dates by 23.9, 22.7, and 37.0 days in the 2003, 2004, and 2005 field seasons, respectively. These shifts in average times-to-death provided evidence of changes in population age structure. Estimates indicated that middle-aged medflies (> 30 days) were common in the population. A surprise in the study was the extraordinary longevity observed in field-captured medflies. For example, 19 captured females but no reference females survived in the laboratory for 140 days or more, and 6 captured but no reference males survived in the laboratory for 170 days or more. This paper advances the study of aging in the wild by introducing a new method for estimating age structure in insect populations, demonstrating that major changes in age structure occur in field populations of insects, showing that middle-aged individuals are common in the wild, and revealing the extraordinary lifespans of wild-caught individuals due to their early life experience in the field.

  4. Genetic structure of cougar populations across the Wyoming basin: Metapopulation or megapopulation

    USGS Publications Warehouse

    Anderson, C.R.; Lindzey, F.G.; McDonald, D.B.

    2004-01-01

    We examined the genetic structure of 5 Wyoming cougar (Puma concolor) populations surrounding the Wyoming Basin, as well as a population from southwestern Colorado. When using 9 microsatellite DNA loci, observed heterozygosity was similar among populations (HO = 0.49-0.59) and intermediate to that of other large carnivores. Estimates of genetic structure (FST = 0.028, RST = 0.029) and number of migrants per generation (Nm) suggested high gene flow. Nm was lowest between distant populations and highest among adjacent populations. Examination of these data, plus Mantel test results of genetic versus geographic distance (P ??? 0.01), suggested both isolation by distance and an effect of habitat matrix. Bayesian assignment to population based on individual genotypes showed that cougars in this region were best described as a single panmictic population. Total effective population size for cougars in this region ranged from 1,797 to 4,532 depending on mutation model and analytical method used. Based on measures of gene flow, extinction risk in the near future appears low. We found no support for the existence of metapopulation structure among cougars in this region.

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

    USGS Publications Warehouse

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

    2003-01-01

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

  6. Constructing stage-structured matrix population models from life tables: comparison of methods

    PubMed Central

    Diaz-Lopez, Jasmin

    2017-01-01

    A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate (λ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the

  7. Constructing stage-structured matrix population models from life tables: comparison of methods.

    PubMed

    Fujiwara, Masami; Diaz-Lopez, Jasmin

    2017-01-01

    A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate ( λ ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism's life history type and the true values of λ . In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ . Here, the weights are given by survivorship curve after discounting with λ . To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting

  8. 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

  9. Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

    PubMed Central

    Miner, Brooks E.; Kerr, Benjamin

    2011-01-01

    Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system. PMID:20943691

  10. Stress state reassessment of Romanian offshore structures taking into account corrosion influence

    NASA Astrophysics Data System (ADS)

    Joavină, R.; Zăgan, S.; Zăgan, R.; Popa, M.

    2017-08-01

    Progressive degradation analysis for extraction or exploration offshore structure, with appraisal of failure potential and the causes that can be correlated with the service age, depends on the various sources of uncertainty that require particular attention in design, construction and exploitation phases. Romanian self erecting platforms are spatial lattice structures consist of tubular steel joints, forming a continuous system with an infinite number of dynamic degrees of freedom. Reassessment of a structure at fixed intervals of time, recorrelation of initial design elements with the actual situation encountered in location and with structural behaviour represents a major asset in lowering vulnerabilities of offshore structure. This paper proposes a comparative reassessment of the stress state for an offshore structure Gloria type, when leaving the shipyard and at the end of that interval corresponding to capital revision, taking into account sectional changes due to marine environment corrosion. The calculation was done using Newmark integration method on a 3D model, asses of the dynamic loads was made through probabilistic spectral method.

  11. Evaluating the Impact of an Accountable Care Organization on Population Health: The Quasi-Experimental Design of the German Gesundes Kinzigtal.

    PubMed

    Pimperl, Alexander; Schulte, Timo; Mühlbacher, Axel; Rosenmöller, Magdalena; Busse, Reinhard; Groene, Oliver; Rodriguez, Hector P; Hildebrandt, Helmut

    2017-06-01

    A central goal of accountable care organizations (ACOs) is to improve the health of their accountable population. No evidence currently links ACO development to improved population health. A major challenge to establishing the evidence base for the impact of ACOs on population health is the absence of a theoretically grounded, robust, operationally feasible, and meaningful research design. The authors present an evaluation study design, provide an empirical example, and discuss considerations for generating the evidence base for ACO implementation. A quasi-experimental study design using propensity score matching in combination with small-scale exact matching is implemented. Outcome indicators based on claims data were constructed and analyzed. Population health is measured by using a range of mortality indicators: mortality ratio, age at time of death, years of potential life lost/gained, and survival time. The application is assessed using longitudinal data from Gesundes Kinzigtal, one of the leading population-based ACOs in Germany. The proposed matching approach resulted in a balanced control of observable differences between the intervention (ACO) and control groups. The mortality indicators used indicate positive results. For example, 635.6 fewer years of potential life lost (2005.8 vs. 2641.4; t-test: sig. P < 0.05*) in the ACO intervention group (n = 5411) attributable to the ACO, also after controlling for a potential (indirect) immortal time bias by excluding the first half year after enrollment from the outcome measurement. This empirical example of the impact of a German ACO on population health can be extended to the evaluation of ACOs and other integrated delivery models of care.

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

    PubMed

    Van Vuuren, B J; Robinson, T J

    1997-12-01

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

  13. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Age or stage structure? A comparison of dynamic outcomes from discrete age- and stage-structured population models.

    PubMed

    Wikan, Arild

    2012-06-01

    Discrete stage-structured density-dependent and discrete age-structured density-dependent population models are considered. Regarding the former, we prove that the model at hand is permanent (i.e., that the population will neither go extinct nor exhibit explosive oscillations) and given density dependent fecundity terms we also show that species with delayed semelparous life histories tend to be more stable than species which possess precocious semelparous life histories. Moreover, our findings together with results obtained from other stage-structured models seem to illustrate a fairly general ecological principle, namely that iteroparous species are more stable than semelparous species. Our analysis of various age-structured models does not necessarily support the conclusions above. In fact, species with precocious life histories now appear to possess better stability properties than species with delayed life histories, especially in the iteroparous case. We also show that there are dynamical outcomes from semelparous age-structured models which we are not able to capture in corresponding stage-structured cases. Finally, both age- and stage-structured population models may generate periodic dynamics of low period (either exact or approximate). The important prerequisite is to assume density-dependent survival probabilities.

  15. Population structure and genomic inbreeding in nine Swiss dairy cattle populations.

    PubMed

    Signer-Hasler, Heidi; Burren, Alexander; Neuditschko, Markus; Frischknecht, Mirjam; Garrick, Dorian; Stricker, Christian; Gredler, Birgit; Bapst, Beat; Flury, Christine

    2017-11-07

    Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH ) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH : 0.027), OB (F ROH : 0.029), and SI (F ROH : 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH : 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service

  16. Genomic estimation of additive and dominance effects and impact of accounting for dominance on accuracy of genomic evaluation in sheep populations.

    PubMed

    Moghaddar, N; van der Werf, J H J

    2017-12-01

    The objectives of this study were to estimate the additive and dominance variance component of several weight and ultrasound scanned body composition traits in purebred and combined cross-bred sheep populations based on single nucleotide polymorphism (SNP) marker genotypes and then to investigate the effect of fitting additive and dominance effects on accuracy of genomic evaluation. Additive and dominance variance components were estimated in a mixed model equation based on "average information restricted maximum likelihood" using additive and dominance (co)variances between animals calculated from 48,599 SNP marker genotypes. Genomic prediction was based on genomic best linear unbiased prediction (GBLUP), and the accuracy of prediction was assessed based on a random 10-fold cross-validation. Across different weight and scanned body composition traits, dominance variance ranged from 0.0% to 7.3% of the phenotypic variance in the purebred population and from 7.1% to 19.2% in the combined cross-bred population. In the combined cross-bred population, the range of dominance variance decreased to 3.1% and 9.9% after accounting for heterosis effects. Accounting for dominance effects significantly improved the likelihood of the fitting model in the combined cross-bred population. This study showed a substantial dominance genetic variance for weight and ultrasound scanned body composition traits particularly in cross-bred population; however, improvement in the accuracy of genomic breeding values was small and statistically not significant. Dominance variance estimates in combined cross-bred population could be overestimated if heterosis is not fitted in the model. © 2017 Blackwell Verlag GmbH.

  17. Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border

    PubMed Central

    2013-01-01

    Background The Caribbean coast of Central America remains an area of malaria transmission caused by Plasmodium falciparum despite the fact that morbidity has been reduced in recent years. Parasite populations in that region show interesting characteristics such as chloroquine susceptibility and low mortality rates. Genetic structure and diversity of P. falciparum populations in the Honduras-Nicaragua border were analysed in this study. Methods Seven neutral microsatellite loci were analysed in 110 P. falciparum isolates from endemic areas of Honduras (n = 77) and Nicaragua (n = 33), mostly from the border region called the Moskitia. Several analyses concerning the genetic diversity, linkage disequilibrium, population structure, molecular variance, and haplotype clustering were conducted. Results There was a low level of genetic diversity in P. falciparum populations from Honduras and Nicaragua. Expected heterozigosity (He) results were similarly low for both populations. A moderate differentiation was revealed by the FST index between both populations, and two putative clusters were defined through a structure analysis. The main cluster grouped most of samples from Honduras and Nicaragua, while the second cluster was smaller and included all the samples from the Siuna community in Nicaragua. This result could partially explain the stronger linkage disequilibrium (LD) in the parasite population from that country. These findings are congruent with the decreasing rates of malaria endemicity in Central America. PMID:24093629

  18. Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border.

    PubMed

    Larrañaga, Nerea; Mejía, Rosa E; Hormaza, José I; Montoya, Alberto; Soto, Aida; Fontecha, Gustavo A

    2013-10-04

    The Caribbean coast of Central America remains an area of malaria transmission caused by Plasmodium falciparum despite the fact that morbidity has been reduced in recent years. Parasite populations in that region show interesting characteristics such as chloroquine susceptibility and low mortality rates. Genetic structure and diversity of P. falciparum populations in the Honduras-Nicaragua border were analysed in this study. Seven neutral microsatellite loci were analysed in 110 P. falciparum isolates from endemic areas of Honduras (n = 77) and Nicaragua (n = 33), mostly from the border region called the Moskitia. Several analyses concerning the genetic diversity, linkage disequilibrium, population structure, molecular variance, and haplotype clustering were conducted. There was a low level of genetic diversity in P. falciparum populations from Honduras and Nicaragua. Expected heterozigosity (H(e)) results were similarly low for both populations. A moderate differentiation was revealed by the F(ST) index between both populations, and two putative clusters were defined through a structure analysis. The main cluster grouped most of samples from Honduras and Nicaragua, while the second cluster was smaller and included all the samples from the Siuna community in Nicaragua. This result could partially explain the stronger linkage disequilibrium (LD) in the parasite population from that country. These findings are congruent with the decreasing rates of malaria endemicity in Central America.

  19. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

    PubMed

    Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

    2017-01-01

    The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. Copyright © 2017 Montinaro et al.

  20. 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.

  1. 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.

  2. Demographic connectivity for ursid populations at wildlife crossing structures in Banff National Park.

    PubMed

    Sawaya, Michael A; Clevenger, Anthony P; Kalinowski, Steven T

    2013-08-01

    Wildlife crossing structures are one solution to mitigating the fragmentation of wildlife populations caused by roads, but their effectiveness in providing connectivity has only been superficially evaluated. Hundreds of grizzly (Ursus arctos) and black bear (Ursus americanus) passages through under and overpasses have been recorded in Banff National Park, Alberta, Canada. However, the ability of crossing structures to allow individual and population-level movements across road networks remains unknown. In April 2006, we initiated a 3-year investigation into whether crossing structures provide demographic connectivity for grizzly and black bears in Banff National Park. We collected hair with multiple noninvasive methods to obtain genetic samples from grizzly and black bears around the Bow Valley. Our objectives were to determine the number of male and female grizzly and black bears that use crossing structures; examine spatial and temporal patterns of crossings; and estimate the proportions of grizzly and black bear populations in the Bow Valley that use crossing structures. Fifteen grizzly (7 female, 8 male) and 17 black bears (8 female, 9 male) used wildlife crossing structures. The number of individuals detected at wildlife crossing structures was highly correlated with the number of passages in space and time. Grizzly bears used open crossing structures (e.g., overpasses) more often than constricted crossings (e.g., culverts). Peak use of crossing structures for both bear species occurred in July, when high rates of foraging activity coincide with mating season. We compared the number of bears that used crossings with estimates of population abundance from a related study and determined that substantial percentages of grizzly (15.0% in 2006, 19.8% in 2008) and black bear (17.6% in 2006, 11.0% in 2008) populations used crossing structures. On the basis of our results, we concluded wildlife crossing structures provide demographic connectivity for bear populations

  3. [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.

  4. Genetic population structure analysis in New Hampshire reveals Eastern European ancestry.

    PubMed

    Sloan, Chantel D; Andrew, Angeline D; Duell, Eric J; Williams, Scott M; Karagas, Margaret R; Moore, Jason H

    2009-09-07

    Genetic structure due to ancestry has been well documented among many divergent human populations. However, the ability to associate ancestry with genetic substructure without using supervised clustering has not been explored in more presumably homogeneous and admixed US populations. The goal of this study was to determine if genetic structure could be detected in a United States population from a single state where the individuals have mixed European ancestry. Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups. We then correlated self-reported ancestry of the individuals with the Bayesian clustering results. Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure. The ancestral results were further explained and substantiated using New Hampshire census data from 1870 to 1930 when the largest waves of European immigrants came to the area. We also discerned distinct patterns of linkage disequilibrium (LD) between the genetic groups in the growth hormone receptor gene (GHR). To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population.

  5. Evidence for population bottlenecks and subtle genetic structure in the yellow rail

    USGS Publications Warehouse

    Popper, Kenneth J.; Miller, Leonard F.; Green, Michael; Haig, Susan M.; Mullins, Thomas D.

    2012-01-01

    The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. We used mitochondrial DNA sequences (mtDNA) and six microsatellite loci to characterize the Yellow Rail's genetic structure and diversity patterns in six areas. Our mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail's main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. At this time, we are unable to determine if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail's entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed.

  6. Population genetic structure of a California endemic Branchiopod, Branchinecta sandiegonensis

    USGS Publications Warehouse

    Davies, Cathleen P.; Simovich, Marie A.; Hathaway, Stacie A.

    1997-01-01

    Branchinecta sandiegonensis (Crustacea: Anostraca) is a narrow range endemic fairy shrimp discontinuously distributed in ephemeral pools on coastal mesas in San Diego County, USA. Ten populations across the range of the species were subjected to allozyme analysis for eleven loci. The species exhibits low variability (P95 =9.1–45.5) and one third of the loci tested did not conform to Hardy-Weinberg equilibrium expectations. The species also exhibited a high degree of genetic differentiation between populations. F ST values (fixation index) for most pairs of populations were above 0.25 (0.036–0.889).Low genetic variability and high genetic structure may result from low gene flow and founder effects due to habitat fragmentation and the lack of potential vectors for cyst dispersal. The unpredictable rainfall of the region also creates potential for variable population sizes which could affect structure and variability.

  7. [Population dynamics, urban structure, and production of living space in the metropolitan zone of Mexico City].

    PubMed

    Schteingart, M

    1989-01-01

    "In this article, an attempt is made to account for certain trends in the growth and distribution of the population, and in the structuring of living space in the metropolitan zone of Mexico City.... Among the important conclusions of this essay are those having to do with the huge growth of some political-administrative units and the relation of this phenomenon to the practices followed by private realtors, often articulated with the policies and programs set by the State's housing agencies, as well as those that associate urban growth and expansion with the development of habitational spaces within the so-called 'formal' and 'informal' housing sectors." Data are from Mexican censuses and other official sources. (SUMMARY IN ENG) excerpt

  8. 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

  9. 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. Copyright © 2013 Wayne State University Press, Detroit, Michigan 48201-1309.

  10. Evolutionary mechanisms shaping the genetic population structure of coastal fish: insight from populations of Coilia nasus in Northwestern Pacific.

    PubMed

    Gao, Tianxiang; Wan, Zhenzhen; Song, Na; Zhang, Xiumei; Han, Zhiqiang

    2014-12-01

    A number of evolutionary mechanisms have been suggested for generating significant genetic structuring among marine fish populations in Northwestern Pacific. We used mtDNA control region to assess the factors in shaping the genetic structure of Japanese grenadier anchovy, Coilia nasus, an anadromous and estuarine coastal species, in Northwestern Pacific. Sixty seven individuals from four locations in Northwestern Pacific were sequenced for mitochondrial control region, detecting 61 haplotypes. The length of amplified control region varied from 677 to 754 bp. This length variability was due to the presence of varying numbers of a 38-bp tandemly repeated sequence. Two distinct lineages were detected, which might have diverged during Pleistocene low sea levels. There were strong differences in the geographical distribution of the two lineages. Analyses of molecular variance and the population statistic ΦST revealed significant genetic structure between China and Ariake Bay populations. Based on the frequency distribution of tandem repeat units, significant genetic differentiation was also detected between China and Ariake Bay populations. Isolation by distance seems to be the main factor driving present genetic structuring of C. nasus populations, indicating coastal dispersal pattern in this coastal species. Such an evolutionary process agrees well with some of the biological features characterizing this species.

  11. The 1% of the population accountable for 63% of all violent crime convictions.

    PubMed

    Falk, Orjan; Wallinius, Märta; Lundström, Sebastian; Frisell, Thomas; Anckarsäter, Henrik; Kerekes, Nóra

    2014-04-01

    Population-based studies on violent crime and background factors may provide an understanding of the relationships between susceptibility factors and crime. We aimed to determine the distribution of violent crime convictions in the Swedish population 1973-2004 and to identify criminal, academic, parental, and psychiatric risk factors for persistence in violent crime. The nationwide multi-generation register was used with many other linked nationwide registers to select participants. All individuals born in 1958-1980 (2,393,765 individuals) were included. Persistent violent offenders (those with a lifetime history of three or more violent crime convictions) were compared with individuals having one or two such convictions, and to matched non-offenders. Independent variables were gender, age of first conviction for a violent crime, nonviolent crime convictions, and diagnoses for major mental disorders, personality disorders, and substance use disorders. A total of 93,642 individuals (3.9%) had at least one violent conviction. The distribution of convictions was highly skewed; 24,342 persistent violent offenders (1.0% of the total population) accounted for 63.2% of all convictions. Persistence in violence was associated with male sex (OR 2.5), personality disorder (OR 2.3), violent crime conviction before age 19 (OR 2.0), drug-related offenses (OR 1.9), nonviolent criminality (OR 1.9), substance use disorder (OR 1.9), and major mental disorder (OR 1.3). The majority of violent crimes are perpetrated by a small number of persistent violent offenders, typically males, characterized by early onset of violent criminality, substance abuse, personality disorders, and nonviolent criminality.

  12. The impact of natural transformation on adaptation in spatially structured bacterial populations.

    PubMed

    Moradigaravand, Danesh; Engelstädter, Jan

    2014-06-20

    Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.

  13. Population Genetic Structure of the Dwarf Seahorse (Hippocampus zosterae) in Florida

    PubMed Central

    Fedrizzi, Nathan; Stiassny, Melanie L. J.; Boehm, J. T.; Dougherty, Eric R.; Amato, George; Mendez, Martin

    2015-01-01

    The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as indicated by significant fixation indices. Despite an overall significant population structure, we observed evidence of interbreeding between individuals from geographically distant sites, supporting the hypothesis that rafting serves to maintain a degree of population connectivity. All individuals collected from Pensacola belong to a single distinct subpopulation, which is highly differentiated from the rest of Floridian dwarf seahorses sampled. Our findings highlight the utility of mtDNA markers in evaluating barriers to gene flow and identifying genetically distinct populations, which are vital to the development of comprehensive conservation strategies for exploited taxa. PMID:26200110

  14. Population Genetic Structure of the Dwarf Seahorse (Hippocampus zosterae) in Florida.

    PubMed

    Fedrizzi, Nathan; Stiassny, Melanie L J; Boehm, J T; Dougherty, Eric R; Amato, George; Mendez, Martin

    2015-01-01

    The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as indicated by significant fixation indices. Despite an overall significant population structure, we observed evidence of interbreeding between individuals from geographically distant sites, supporting the hypothesis that rafting serves to maintain a degree of population connectivity. All individuals collected from Pensacola belong to a single distinct subpopulation, which is highly differentiated from the rest of Floridian dwarf seahorses sampled. Our findings highlight the utility of mtDNA markers in evaluating barriers to gene flow and identifying genetically distinct populations, which are vital to the development of comprehensive conservation strategies for exploited taxa.

  15. [Genetic Structure of Urban Population of the Common Hamster (Cricetus cricetus)].

    PubMed

    Feoktistova, N Yu; Meschersky, I G; Surov, A V; Bogomolov, P L; Tovpinetz, N N; Poplavskaya, N S

    2016-02-01

    Over the past half-century, the common hamster (Cricetus cricetus), along with range-wide decline of natural populations, has actively populated the cities. The study of the genetic structure of urban populations of common hamster may shed light on features of the habitation of this species in urban landscapes. This article is focused on the genetic structure of common hamster populations in Simferopol (Crimea), one of the largest known urban populations of this species. On the basis of the analysis of nucleotide sequences of the cytochrome b gene and mtDNA control region, and the allelic composition of ten microsatellite loci of nDNA, we revealed that, despite the fact that some individuals can move throughout the city at considerable distances, the entire population of the city is represented by separate demes confined to different areas. These demes are characterized by a high degree of the genetic isolation and reduced genetic diversity compared to that found for the city as a whole.

  16. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

    PubMed Central

    Eckert, Andrew J.; van Heerwaarden, Joost; Wegrzyn, Jill L.; Nelson, C. Dana; Ross-Ibarra, Jeffrey; González-Martínez, Santíago C.; Neale, David. B.

    2010-01-01

    Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as FST outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes. PMID:20439779

  18. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae).

    PubMed

    Eckert, Andrew J; van Heerwaarden, Joost; Wegrzyn, Jill L; Nelson, C Dana; Ross-Ibarra, Jeffrey; González-Martínez, Santíago C; Neale, David B

    2010-07-01

    Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as F(ST) outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes.

  19. 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

  20. Population estimates of extended family structure and size.

    PubMed

    Garceau, Anne; Wideroff, Louise; McNeel, Timothy; Dunn, Marsha; Graubard, Barry I

    2008-01-01

    Population-based estimates of biological family size can be useful for planning genetic studies, assessing how distributions of relatives affect disease associations with family history and estimating prevalence of potential family support. Mean family size per person is estimated from a population-based telephone survey (n = 1,019). After multivariate adjustment for demographic variables, older and non-White respondents reported greater mean numbers of total, first- and second-degree relatives. Females reported more total and first-degree relatives, while less educated respondents reported more second-degree relatives. Demographic differences in family size have implications for genetic research. Therefore, periodic collection of family structure data in representative populations would be useful. Copyright 2008 S. Karger AG, Basel.

  1. 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

  2. The σ law of evolutionary dynamics in community-structured population.

    PubMed

    Tang, Changbing; Li, Xiang; Cao, Lang; Zhan, Jingyuan

    2012-08-07

    Evolutionary game dynamics in finite populations provide a new framework to understand the selection of traits with frequency-dependent fitness. Recently, a simple but fundamental law of evolutionary dynamics, which we call σ law, describes how to determine the selection between two competing strategies: in most evolutionary processes with two strategies, A and B, strategy A is favored over B in weak selection if and only if σR+S>T+σP. This relationship holds for a wide variety of structured populations with mutation rate and weak selection under certain assumptions. In this paper, we propose a model of games based on a community-structured population and revisit this law under the Moran process. By calculating the average payoffs of A and B individuals with the method of effective sojourn time, we find that σ features not only the structured population characteristics, but also the reaction rate between individuals. That is to say, an interaction between two individuals are not uniform, and we can take σ as a reaction rate between any two individuals with the same strategy. We verify this viewpoint by the modified replicator equation with non-uniform interaction rates in a simplified version of the prisoner's dilemma game (PDG). Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Genetic Population Structure Analysis in New Hampshire Reveals Eastern European Ancestry

    PubMed Central

    Sloan, Chantel D.; Andrew, Angeline D.; Duell, Eric J.; Williams, Scott M.; Karagas, Margaret R.; Moore, Jason H.

    2009-01-01

    Genetic structure due to ancestry has been well documented among many divergent human populations. However, the ability to associate ancestry with genetic substructure without using supervised clustering has not been explored in more presumably homogeneous and admixed US populations. The goal of this study was to determine if genetic structure could be detected in a United States population from a single state where the individuals have mixed European ancestry. Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups. We then correlated self-reported ancestry of the individuals with the Bayesian clustering results. Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure. The ancestral results were further explained and substantiated using New Hampshire census data from 1870 to 1930 when the largest waves of European immigrants came to the area. We also discerned distinct patterns of linkage disequilibrium (LD) between the genetic groups in the growth hormone receptor gene (GHR). To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population. PMID:19738909

  4. 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. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  6. 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.

  7. Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

    PubMed

    Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

    2017-09-01

    The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population

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

    PubMed

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

    2013-03-05

    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.

  9. A Chrysodeixis chalcites Single-Nucleocapsid Nucleopolyhedrovirus Population from the Canary Islands Is Genotypically Structured To Maximize Survival

    PubMed Central

    Bernal, Alexandra; Simón, Oihane; Williams, Trevor; Muñoz, Delia

    2013-01-01

    A Chrysodeixis chalcites single-nucleocapsid nucleopolyhedrovirus wild-type isolate from the Canary Islands, Spain, named ChchSNPV-TF1 (ChchTF1-wt), appears to have great potential as the basis for a biological insecticide for control of the pest. An improved understanding of the genotypic structure of this wild-type strain population should facilitate the selection of genotypes for inclusion in a bioinsecticidal product. Eight genetically distinct genotypes were cloned in vitro: ChchTF1-A to ChchTF1-H. Quantitative real-time PCR (qPCR) analysis confirmed that ChchTF1-A accounted for 36% of the genotypes in the wild-type population. In bioassays, ChchTF1-wt occlusion bodies (OBs) were significantly more pathogenic than any of the component single-genotype OBs, indicating that genotype interactions were likely responsible for the pathogenicity phenotype of wild-type OBs. However, the wild-type population was slower killing and produced higher OB yields than any of the single genotypes alone. These results strongly suggested that the ChchTF1-wt population is structured to maximize its transmission efficiency. Experimental OB mixtures and cooccluded genotype mixtures containing the most abundant and the rarest genotypes, at frequencies similar to those at which they were isolated, revealed a mutualistic interaction that restored the pathogenicity of OBs. In OB and cooccluded mixtures containing only the most abundant genotypes, ChchTF1-ABC, OB pathogenicity was even greater than that of wild-type OBs. The ChchTF1-ABC cooccluded mixture killed larvae 33 h faster than the wild-type population and remained genotypically and biologically stable throughout five successive passages in vivo. In conclusion, the ChchTF1-ABC mixture shows great potential as the active ingredient of a bioinsecticide to control C. chalcites in the Canary Islands. PMID:24096419

  10. 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.

  11. Population structure and inbreeding from pedigree analysis of purebred dogs.

    PubMed

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

    2008-05-01

    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 Psi 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.

  12. 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…

  13. Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China.

    PubMed

    Zhan, Aibin; Li, Cheng; Fu, Jinzhong

    2009-04-09

    Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the

  14. Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations.

    PubMed

    Ben Halim, Nizar; Hsouna, Sana; Lasram, Khaled; Chargui, Mariem; Khemira, Laaroussi; Saidane, Rachid; Abdelhak, Sonia; Kefi, Rym

    2018-02-01

    Douiret is an isolated Berber population from South-Eastern Tunisia. The strong geographic and cultural isolation characterising this population might have contributed to remarkable endogamy and consanguinity, which were practiced for several centuries. The objective of this study is to evaluate the mitochondrial DNA (mtDNA) genetic structure of Douiret and to compare it to other Mediterranean populations with a special focus on major haplogroup T. Genomic DNA was extracted from blood samples of 58 unrelated individuals collected from the different patrilineal lineages of the population. The hypervariable region 1 of the mtDNA was amplified and sequenced. For comparative analyses, additional HVS1 sequences (n = 4857) were compiled from previous studies. The maternal background of the studied sample from Douiret was mainly of Eurasian origin (74%) followed by Sub-Saharan (17%) and North African (3%) lineages. Douiret harbours the highest frequency of haplogroup T in the Mediterranean region, assigned to the unique subclade T1a (38%). Phylogenetic analysis showed an outlier position of Douiret at the Mediterranean level. The genetic structure of Douiret highlights the presence of founders, most likely of Near/Middle Eastern origin, who conquered this area during the Middle/Late Upper Palaeolithic and Neolithic dispersals.

  15. Producing genome structure populations with the dynamic and automated PGS software.

    PubMed

    Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

    2018-05-01

    Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

  16. Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico

    PubMed Central

    Ceballos-Vázquez, Bertha P.; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J.; Culver, Melanie; Reyes-Bonilla, Hector

    2018-01-01

    . bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures. PMID:29472993

  17. Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico.

    PubMed

    Domínguez-Contreras, José F; Munguia-Vega, Adrian; Ceballos-Vázquez, Bertha P; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J; Culver, Melanie; Reyes-Bonilla, Hector

    2018-01-01

    . bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.

  18. Continuous and Discrete Structured Population Models with Applications to Epidemiology and Marine Mammals

    NASA Astrophysics Data System (ADS)

    Tang, Tingting

    In this dissertation, we develop structured population models to examine how changes in the environmental affect population processes. In Chapter 2, we develop a general continuous time size structured model describing a susceptible-infected (SI) population coupled with the environment. This model applies to problems arising in ecology, epidemiology, and cell biology. The model consists of a system of quasilinear hyperbolic partial differential equations coupled with a system of nonlinear ordinary differential equations that represent the environment. We develop a second-order high resolution finite difference scheme to numerically solve the model. Convergence of this scheme to a weak solution with bounded total variation is proved. We numerically compare the second order high resolution scheme with a first order finite difference scheme. Higher order of convergence and high resolution property are observed in the second order finite difference scheme. In addition, we apply our model to a multi-host wildlife disease problem, questions regarding the impact of the initial population structure and transition rate within each host are numerically explored. In Chapter 3, we use a stage structured matrix model for wildlife population to study the recovery process of the population given an environmental disturbance. We focus on the time it takes for the population to recover to its pre-event level and develop general formulas to calculate the sensitivity or elasticity of the recovery time to changes in the initial population distribution, vital rates and event severity. Our results suggest that the recovery time is independent of the initial population size, but is sensitive to the initial population structure. Moreover, it is more sensitive to the reduction proportion to the vital rates of the population caused by the catastrophe event relative to the duration of impact of the event. We present the potential application of our model to the amphibian population dynamic

  19. Population Genetic Structure of the Tropical Two-Wing Flyingfish (Exocoetus volitans)

    PubMed Central

    Lewallen, Eric A.; Bohonak, Andrew J.; Bonin, Carolina A.; van Wijnen, Andre J.; Pitman, Robert L.; Lovejoy, Nathan R.

    2016-01-01

    Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps) from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266). AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (ΦST = 0.035, p<0.001). A spatially-unbiased Bayesian approach identified two circumtropical population clusters north and south of the Equator (ΦST = 0.026, p<0.001), a previously unknown dispersal barrier for an epipelagic fish. Bayesian demographic modeling suggested the effective population size of this species increased by at least an order of magnitude ~150,000 years ago, to more than 1 billion individuals currently. Thus, high levels of genetic similarity observed in E. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic range of the

  20. Population Genetic Structure of the Tropical Two-Wing Flyingfish (Exocoetus volitans).

    PubMed

    Lewallen, Eric A; Bohonak, Andrew J; Bonin, Carolina A; van Wijnen, Andre J; Pitman, Robert L; Lovejoy, Nathan R

    2016-01-01

    Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps) from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266). AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (ΦST = 0.035, p<0.001). A spatially-unbiased Bayesian approach identified two circumtropical population clusters north and south of the Equator (ΦST = 0.026, p<0.001), a previously unknown dispersal barrier for an epipelagic fish. Bayesian demographic modeling suggested the effective population size of this species increased by at least an order of magnitude ~150,000 years ago, to more than 1 billion individuals currently. Thus, high levels of genetic similarity observed in E. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic range of the

  1. Modeling livestock population structure: a geospatial database for Ontario swine farms.

    PubMed

    Khan, Salah Uddin; O'Sullivan, Terri L; Poljak, Zvonimir; Alsop, Janet; Greer, Amy L

    2018-01-30

    Infectious diseases in farmed animals have economic, social, and health consequences. Foreign animal diseases (FAD) of swine are of significant concern. Mathematical and simulation models are often used to simulate FAD outbreaks and best practices for control. However, simulation outcomes are sensitive to the population structure used. Within Canada, access to individual swine farm population data with which to parameterize models is a challenge because of privacy concerns. Our objective was to develop a methodology to model the farmed swine population in Ontario, Canada that could represent the existing population structure and improve the efficacy of simulation models. We developed a swine population model based on the factors such as facilities supporting farm infrastructure, land availability, zoning and local regulations, and natural geographic barriers that could affect swine farming in Ontario. Assigned farm locations were equal to the swine farm density described in the 2011 Canadian Census of Agriculture. Farms were then randomly assigned to farm types proportional to the existing swine herd types. We compared the swine population models with a known database of swine farm locations in Ontario and found that the modeled population was representative of farm locations with a high accuracy (AUC: 0.91, Standard deviation: 0.02) suggesting that our algorithm generated a reasonable approximation of farm locations in Ontario. In the absence of a readily accessible dataset providing details of the relative locations of swine farms in Ontario, development of a model livestock population that captures key characteristics of the true population structure while protecting privacy concerns is an important methodological advancement. This methodology will be useful for individuals interested in modeling the spread of pathogens between farms across a landscape and using these models to evaluate disease control strategies.

  2. Surprisingly little population genetic structure in a fungus-associated beetle despite its exploitation of multiple hosts

    PubMed Central

    Wood, Corlett W; Donald, Hannah M; Formica, Vincent A; Brodie, Edmund D

    2013-01-01

    In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource-associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource-associated population genetic structure. PMID:23789061

  3. Population genetic structure of moose (Alces alces) of South-central Alaska

    USGS Publications Warehouse

    Wilson, Robert E.; McDonough, John T.; Barboza, Perry S.; Talbot, Sandra L.; Farley, Sean D.

    2015-01-01

    The location of a population can influence its genetic structure and diversity by impacting the degree of isolation and connectivity to other populations. Populations at range margins are often thought to have less genetic variation and increased genetic structure, and a reduction in genetic diversity can have negative impacts on the health of a population. We explored the genetic diversity and connectivity between 3 peripheral populations of moose (Alces alces) with differing potential for connectivity to other areas within interior Alaska. Populations on the Kenai Peninsula and from the Anchorage region were found to be significantly differentiated (FST= 0.071, P < 0.0001) with lower levels of genetic diversity observed within the Kenai population. Bayesian analyses employing assignment methodologies uncovered little evidence of contemporary gene flow between Anchorage and Kenai, suggesting regional isolation. Although gene flow outside the peninsula is restricted, high levels of gene flow were detected within the Kenai that is explained by male-biased dispersal. Furthermore, gene flow estimates differed across time scales on the Kenai Peninsula which may have been influenced by demographic fluctuations correlated, at least in part, with habitat change.

  4. 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

  5. Continental-scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides)

    Treesearch

    Colin M. Callahan; Carol A. Rowe; Ronald J. Ryel; John D. Shaw; Michael D. Madritch; Karen E. Mock

    2013-01-01

    Aspen populations in the south-western portion of the range are consistent with expectations for a historically stable edge, with low within-population diversity, significant geographical population structuring, and little evidence of northward expansion. Structuring within the southwestern cluster may result from distinct gene pools separated during the Pleistocene...

  6. 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 COMMISSION (CONTINUED) UNIFORM SYSTEM OF ACCOUNTS FOR MUTUAL SERVICE COMPANIES AND SUBSIDIARY SERVICE... accounting system. (a) The accounts provided herein are in two general categories: Balance sheet accounts and...

  7. 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. © 2013 Society for Conservation Biology.

  8. 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

  9. 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.

  10. Population structure of giraffes is affected by management in the Great Rift Valley, Kenya

    PubMed Central

    2018-01-01

    Giraffe populations in East Africa have declined in the past thirty years yet there has been limited research on this species. This study had four objectives: i) to provide a baseline population assessment for the two largest populations of Rothschild’s giraffes in Kenya, ii) to assess whether there are differences in population structure between the two enclosed populations, iii) to assess the potential and possible implications of different management practices on enclosed giraffe populations to inform future decision-making, and iv) to add to the availability of information available about giraffes in the wild. I used individual identification to assess the size and structure of the two populations; in Soysambu Conservancy between May 2010 and January 2011, I identified 77 giraffes; in Lake Nakuru National Park between May 2011 and January 2012, I identified 89. Population structure differed significantly between the two sites; Soysambu Conservancy contained a high percentage of juveniles (34%) and subadults (29%) compared to Lake Nakuru NP, which contained fewer juveniles (5%) and subadults (15%). During the time of this study Soysambu Conservancy contained no lions while Lake Nakuru NP contained a high density of lions (30 lions per 100km2). Lions are the main predator of giraffes, and preferential predation on juvenile giraffes has previously been identified in Lake Nakuru NP. My results suggest that high lion density in Lake Nakuru NP may have influenced the structure of the giraffe population by removing juveniles and, consequently, may affect future population growth. I suggest that wildlife managers consider lion densities alongside breeding plans for Endangered species, since the presence of lions appears to influence the population structure of giraffes in enclosed habitats. PMID:29298338

  11. Population structure of giraffes is affected by management in the Great Rift Valley, Kenya.

    PubMed

    Muller, Zoe

    2018-01-01

    Giraffe populations in East Africa have declined in the past thirty years yet there has been limited research on this species. This study had four objectives: i) to provide a baseline population assessment for the two largest populations of Rothschild's giraffes in Kenya, ii) to assess whether there are differences in population structure between the two enclosed populations, iii) to assess the potential and possible implications of different management practices on enclosed giraffe populations to inform future decision-making, and iv) to add to the availability of information available about giraffes in the wild. I used individual identification to assess the size and structure of the two populations; in Soysambu Conservancy between May 2010 and January 2011, I identified 77 giraffes; in Lake Nakuru National Park between May 2011 and January 2012, I identified 89. Population structure differed significantly between the two sites; Soysambu Conservancy contained a high percentage of juveniles (34%) and subadults (29%) compared to Lake Nakuru NP, which contained fewer juveniles (5%) and subadults (15%). During the time of this study Soysambu Conservancy contained no lions while Lake Nakuru NP contained a high density of lions (30 lions per 100km2). Lions are the main predator of giraffes, and preferential predation on juvenile giraffes has previously been identified in Lake Nakuru NP. My results suggest that high lion density in Lake Nakuru NP may have influenced the structure of the giraffe population by removing juveniles and, consequently, may affect future population growth. I suggest that wildlife managers consider lion densities alongside breeding plans for Endangered species, since the presence of lions appears to influence the population structure of giraffes in enclosed habitats.

  12. Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina

    PubMed Central

    McCartney-Melstad, Evan; Waller, Tomás; Micucci, Patricio A.; Barros, Mariano; Draque, Juan; Amato, George; Mendez, Martin

    2012-01-01

    Yellow anacondas (Eunectes notaeus) are large, semiaquatic boid snakes found in wetland systems in South America. These snakes are commercially harvested under a sustainable management plan in Argentina, so information regarding population structuring can be helpful for determination of management units. We evaluated genetic structure and migration using partial sequences from the mitochondrial control region and mitochondrial genes cyt-b and ND4 for 183 samples collected within northern Argentina. A group of landscape features and environmental variables including several treatments of temperature and precipitation were explored as potential drivers of observed genetic patterns. We found significant population structure between most putative population comparisons and bidirectional but asymmetric migration in several cases. The configuration of rivers and wetlands was found to be significantly associated with yellow anaconda population structure (IBD), and important for gene flow, although genetic distances were not significantly correlated with the environmental variables used here. More in-depth analyses of environmental data may be needed to fully understand the importance of environmental conditions on population structure and migration. These analyses indicate that our putative populations are demographically distinct and should be treated as such in Argentina's management plan for the harvesting of yellow anacondas. PMID:22675425

  13. iNJclust: Iterative Neighbor-Joining Tree Clustering Framework for Inferring Population Structure.

    PubMed

    Limpiti, Tulaya; Amornbunchornvej, Chainarong; Intarapanich, Apichart; Assawamakin, Anunchai; Tongsima, Sissades

    2014-01-01

    Understanding genetic differences among populations is one of the most important issues in population genetics. Genetic variations, e.g., single nucleotide polymorphisms, are used to characterize commonality and difference of individuals from various populations. This paper presents an efficient graph-based clustering framework which operates iteratively on the Neighbor-Joining (NJ) tree called the iNJclust algorithm. The framework uses well-known genetic measurements, namely the allele-sharing distance, the neighbor-joining tree, and the fixation index. The behavior of the fixation index is utilized in the algorithm's stopping criterion. The algorithm provides an estimated number of populations, individual assignments, and relationships between populations as outputs. The clustering result is reported in the form of a binary tree, whose terminal nodes represent the final inferred populations and the tree structure preserves the genetic relationships among them. The clustering performance and the robustness of the proposed algorithm are tested extensively using simulated and real data sets from bovine, sheep, and human populations. The result indicates that the number of populations within each data set is reasonably estimated, the individual assignment is robust, and the structure of the inferred population tree corresponds to the intrinsic relationships among populations within the data.

  14. Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

    PubMed Central

    Shringarpure, Suyash; Xing, Eric P.

    2014-01-01

    Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

  15. Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

    PubMed

    Vickruck, J L; Richards, M H

    2017-05-01

    While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance. © 2017 John Wiley & Sons Ltd.

  16. Dynamics of climate-based malaria transmission model with age-structured human population

    NASA Astrophysics Data System (ADS)

    Addawe, Joel; Pajimola, Aprimelle Kris

    2016-10-01

    In this paper, we proposed to study the dynamics of malaria transmission with periodic birth rate of the vector and an age-structure for the human population. The human population is divided into two compartments: pre-school (0-5 years) and the rest of the human population. We showed the existence of a disease-free equilibrium point. Using published epidemiological parameters, we use numerical simulations to show potential effect of climate change in the dynamics of age-structured malaria transmission. Numerical simulations suggest that there exists an asymptotically attractive solution that is positive and periodic.

  17. The effect of seasonal harvesting on stage-structured population models.

    PubMed

    Tang, Sanyi; Chen, Lansun

    2004-04-01

    In most models of population dynamics, increases in population due to birth are assumed to be time-independent, but many species reproduce only during a single period of the year. We propose an exploited single-species model with stage structure for the dynamics in a fish population for which births occur in a single pulse once per time period. Since birth pulse populations are often characterized with a discrete time dynamical system determined by its Poincaré map, we explore the consequences of harvest timing to equilibrium population sizes under seasonal dependence and obtain threshold conditions for their stability, and show that the timing of harvesting has a strong impact on the persistence of the fish population, on the volume of mature fish stock and on the maximum annual-sustainable yield. Moreover, our results imply that the population can sustain much higher harvest rates if the mature fish is removed as early in the season (after the birth pulse) as possible. Further, the effects of harvesting effort and harvest timing on the dynamical complexity are also investigated. Bifurcation diagrams are constructed with the birth rate (or harvesting effort or harvest timing) as the bifurcation parameter, and these are observed to display rich structure, including chaotic bands with periodic windows, pitch-fork and tangent bifurcations, non-unique dynamics (meaning that several attractors coexist) and attractor crisis. This suggests that birth pulse, in effect, provides a natural period or cyclicity that makes the dynamical behavior more complex.

  18. Insular Celtic population structure and genomic footprints of migration

    PubMed Central

    Hellenthal, Garrett

    2018-01-01

    Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits. PMID:29370172

  19. The Population Care Coordination Process.

    PubMed

    Rushton, Sharron

    2015-01-01

    The purpose of the article was to outline a population-based approach to providing care coordination. The Population Care Coordination Process provides a framework for each provider and/or organization to provide multilevel care based on population- and patient-centered principles. The Population Care Coordination Process is scalable. It can be utilized in a smaller scale such as single provider office or in a larger scale such as an accountable care organization. There are many issues within our current health care structure that must be addressed. Care coordination has been identified as a potential solution to address the needs of complex patients within the system. The expansion to consider populations allows for a more targeted and efficient approach. The population care process entails a data-driven approach to care coordination. The inclusion of populations in the care coordination process provides an opportunity to maximize efforts and improve outcomes.

  20. Distance, dams and drift: What structures populations of an endangered, benthic stream fish?

    USGS Publications Warehouse

    Roberts, James H.; Angermeier, Paul; Hallerman, Eric M.

    2013-01-01

    Spatial population structure plays an important role in species persistence, evolution and conservation. Benthic stream fishes are diverse and frequently imperilled, yet the determinants and spatial scaling of their population structure are understudied. We investigated the range-wide population genetic structure of Roanoke logperch (Percina rex), an endangered, benthic stream fish of the eastern United States. Fish were sampled from 35 sites and analysed at 11 microsatellite DNA loci. Clustering models were used to sort individuals into genetically cohesive groups and thereby estimate the spatial scaling of population structure. We then used Bayesian generalized linear mixed models (BGLMMs) to test alternative hypotheses about the environmental factors most responsible for generating structure, as measured by the differentiation statistic FST. Clustering models delineated seven discrete populations, whose boundaries coincided with agents of fragmentation, including hydroelectric dams and tailwaters. In the absence of hydrological barriers, gene flow was extensive throughout catchments, whereas there was no evidence for contemporary dispersal between catchments across barriers. In the best-supported BGLMM, FST was positively related to the spatial distance and degree of hydrological alteration between sites and negatively related to genetic diversity within sites. Whereas the effect of tailwaters was equivocal, dams strongly influenced differentiation: the effect of a dam on FST was comparable to that of a between-site distance of over 1200 km of unimpounded river. Overall, the effect of distance-mediated dispersal was negligible compared to the combined effects of fragmentation and genetic drift. The contemporary population structure of P. rex comprises a few geographically extensive ‘islands’ that are fragmented by hydroelectric projects. This information clarifies the importance of a catchment-scale perspective on conserving the species and

  1. Population structure in the Island of Ugljan--demographic processes and marital migration.

    PubMed

    Malnar, Ana

    2008-12-01

    This research on the basic demographic processes and marital migrations of the population on Ugljan Island in the period from 1857 to 2001 was conducted within the context of the long-term anthropological research of the population structure of Croatia's islands. The analysis was based on the study of the origin of 5 244 married couples from Preko, Kali, Kukljica, Lukoran and Ugljan and carried out using data preserved in the old Registers of Marriages. The results show a high level of endogamy and reproductive isolation of the population in all the villages and they also confirm the importance of using historical and demographic sources for researching the shaping of population structures.

  2. Accountability and Primary Healthcare

    PubMed Central

    Mukhi, Shaheena; Barnsley, Jan; Deber, Raisa B.

    2014-01-01

    This paper examines the accountability structures within primary healthcare (PHC) in Ontario; in particular, who is accountable for what and to whom, and the policy tools being used. Ontario has implemented a series of incremental reforms, using expenditure policy instruments, enforced through contractual agreements to provide a defined set of publicly financed services that are privately delivered, most often by family physicians. The findings indicate that reporting, funding, evaluation and governance accountability requirements vary across service provider models. Accountability to the funder and patients is most common. Agreements, incentives and compensation tools have been used but may be insufficient to ensure parties are being held responsible for their activities related to stated goals. Clear definitions of various governance structures, a cohesive approach to monitoring critical performance indicators and associated improvement strategies are important elements in operationalizing accountability and determining whether goals are being met. PMID:25305392

  3. 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. Copyright © 2010 Elsevier B.V. All rights reserved.

  4. The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines.

    PubMed

    Williams, Rachel C; Jackson, Benjamin C; Duvaux, Ludovic; Dawson, Deborah A; Burke, Terry; Sinclair, William

    2015-07-01

    Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST  = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST  = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks. © 2015 John Wiley & Sons Ltd.

  5. Earliest evidence for the structure of Homo sapiens populations in Africa

    NASA Astrophysics Data System (ADS)

    Scerri, Eleanor M. L.; Drake, Nick A.; Jennings, Richard; Groucutt, Huw S.

    2014-10-01

    Understanding the structure and variation of Homo sapiens populations in Africa is critical for interpreting multiproxy evidence of their subsequent dispersals into Eurasia. However, there is no consensus on early H. sapiens demographic structure, or its effects on intra-African dispersals. Here, we show how a patchwork of ecological corridors and bottlenecks triggered a successive budding of populations across the Sahara. Using a temporally and spatially explicit palaeoenvironmental model, we found that the Sahara was not uniformly ameliorated between ∼130 and 75 thousand years ago (ka), as has been stated. Model integration with multivariate analyses of corresponding stone tools then revealed several spatially defined technological clusters which correlated with distinct palaeobiomes. Similarities between technological clusters were such that they decreased with distance except where connected by palaeohydrological networks. These results indicate that populations at the Eurasian gateway were strongly structured, which has implications for refining the demographic parameters of dispersals out of Africa.

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

    PubMed

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

    2008-12-02

    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. 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. 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 populations in particular. This

  7. 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

  8. Can the Accountable Care Organization model facilitate integrated care in England?

    PubMed

    Ahmed, Faheem; Mays, Nicholas; Ahmed, Naeem; Bisognano, Maureen; Gottlieb, Gary

    2015-10-01

    Following the global economic recession, health care systems have experienced intense political pressure to contain costs without compromising quality. One response is to focus on improving the continuity and coordination of care, which is seen as beneficial for both patients and providers. However, cultural and structural barriers have proved difficult to overcome in the quest to provide integrated care for entire populations. By holding groups of providers responsible for the health outcomes of a designated population, in the United States, Accountable Care Organizations are regarded as having the potential to foster collaboration across the continuum of care. They could have a similar role in England's National Health Service. However, it is important to consider the difference in context before implementing a similar model, adapted to suit the system's strengths. Working together, general practice federations and the Academic Health Science Networks could form the basis of accountable care in England. © The Author(s) 2015.

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

    PubMed Central

    Lutz, Wolfgang; KC, Samir

    2010-01-01

    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

  10. Genetic structure among greater white-fronted goose populations of the Pacific Flyway

    USGS Publications Warehouse

    Ely, Craig R.; Wilson, Robert E.; Talbot, Sandra L.

    2017-01-01

    An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine-scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long-lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population-specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white-fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.

  11. Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries

    PubMed Central

    Uren, Caitlin; Kim, Minju; Martin, Alicia R.; Bobo, Dean; Gignoux, Christopher R.; van Helden, Paul D.; Möller, Marlo; Hoal, Eileen G.; Henn, Brenna M.

    2016-01-01

    Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa. PMID:27474727

  12. Biophysical connectivity explains population genetic structure in a highly dispersive marine species

    NASA Astrophysics Data System (ADS)

    Truelove, Nathan K.; Kough, Andrew S.; Behringer, Donald C.; Paris, Claire B.; Box, Stephen J.; Preziosi, Richard F.; Butler, Mark J.

    2017-03-01

    Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster ( Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F ST of 0.0016 ( P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus ( P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation ( P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

  13. 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 accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes. PMID:22152676

  14. 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.

  15. Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series

    PubMed Central

    Ferguson, Jake M; Ponciano, José M

    2014-01-01

    Predicting population extinction risk is a fundamental application of ecological theory to the practice of conservation biology. Here, we compared the prediction performance of a wide array of stochastic, population dynamics models against direct observations of the extinction process from an extensive experimental data set. By varying a series of biological and statistical assumptions in the proposed models, we were able to identify the assumptions that affected predictions about population extinction. We also show how certain autocorrelation structures can emerge due to interspecific interactions, and that accounting for the stochastic effect of these interactions can improve predictions of the extinction process. We conclude that it is possible to account for the stochastic effects of community interactions on extinction when using single-species time series. PMID:24304946

  16. Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure.

    PubMed

    Bohmann, Kristine; Gopalakrishnan, Shyam; Nielsen, Martin; Nielsen, Luisa Dos Santos Bay; Jones, Gareth; Streicker, Daniel G; Gilbert, M Thomas P

    2018-04-19

    Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large-scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks. However, previously used methods are not cost-effective and efficient for large-scale applications. Using bloodmeal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be incorporated into metabarcoding diet studies of other animals to couple information on diet and population structure. © 2018 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  17. Temperature-dependent body size effects determine population responses to climate warming.

    PubMed

    Lindmark, Max; Huss, Magnus; Ohlberger, Jan; Gårdmark, Anna

    2018-02-01

    Current understanding of animal population responses to rising temperatures is based on the assumption that biological rates such as metabolism, which governs fundamental ecological processes, scale independently with body size and temperature, despite empirical evidence for interactive effects. Here, we investigate the consequences of interactive temperature- and size scaling of vital rates for the dynamics of populations experiencing warming using a stage-structured consumer-resource model. We show that interactive scaling alters population and stage-specific responses to rising temperatures, such that warming can induce shifts in population regulation and stage-structure, influence community structure and govern population responses to mortality. Analysing experimental data for 20 fish species, we found size-temperature interactions in intraspecific scaling of metabolic rate to be common. Given the evidence for size-temperature interactions and the ubiquity of size structure in animal populations, we argue that accounting for size-specific temperature effects is pivotal for understanding how warming affects animal populations and communities. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

  18. Aligning for accountable care: Strategic practices for change in accountable care organizations.

    PubMed

    Hilligoss, Brian; Song, Paula H; McAlearney, Ann Scheck

    Alignment within accountable care organizations (ACOs) is crucial if these new entities are to achieve their lofty goals. However, the concept of alignment remains underexamined, and we know little about the work entailed in creating alignment. The aim of this study was to develop the concept of aligning by identifying and describing the strategic practices administrators use to align the structures, processes, and behaviors of their organizations and individual providers in pursuit of accountable care. We conducted 2-year qualitative case studies of four ACOs that have assumed full risk for the costs and quality of care for defined populations. Five strategic aligning practices were used by all four ACOs. Informing both aligns providers' understandings with the goals and value proposition of the ACO and aligns the providers' attention with the drivers of performance. Involving both aligns ACO leaders' understandings with the realities facing providers and aligns the policies of the ACO with the needs of providers. Enhancing both aligns the operations of individual provider practices with the operations of the ACO and aligns the trust of providers with the ACO. Motivating aligns what providers value with the goals of the ACO. Finally, evolving is a metapractice of learning and adapting that guides the execution of the other four practices. Our findings suggest that there are second-order cognitive (e.g., understandings and attention) and cultural (e.g., trust and values) levels of alignment, as well as a first-order operational level (organizational structures, processes, and incentives). A well-aligned organization may require ongoing repositioning at each of these levels, as well as attention to both cooperative and coordinative dimensions of alignment. Implications for research and practice are discussed.

  19. Population structure and genetic diversity of Fusicladium effusum in the USA

    USDA-ARS?s Scientific Manuscript database

    Scab (Fusicladium effusum) is the most destructive disease of pecan in the Southeast US. Infection is thought to occur solely through asexually produced conidia. To explore the population structure and genetic diversity of F. effusum, populations were hierarchically sampled from 11 orchards in Alaba...

  20. 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

  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. Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

    PubMed

    Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

    2016-06-17

    In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

  3. Relatedness in spatially structured populations with empty sites: An approach based on spatial moment equations.

    PubMed

    Lion, Sébastien

    2009-09-07

    Taking into account the interplay between spatial ecological dynamics and selection is a major challenge in evolutionary ecology. Although inclusive fitness theory has proven to be a very useful tool to unravel the interactions between spatial genetic structuring and selection, applications of the theory usually rely on simplifying demographic assumptions. In this paper, I attempt to bridge the gap between spatial demographic models and kin selection models by providing a method to compute approximations for relatedness coefficients in a spatial model with empty sites. Using spatial moment equations, I provide an approximation of nearest-neighbour relatedness on random regular networks, and show that this approximation performs much better than the ordinary pair approximation. I discuss the connection between the relatedness coefficients I define and those used in population genetics, and sketch some potential extensions of the theory.

  4. Genetic structure of typical and atypical populations of Candida albicans from Africa.

    PubMed

    Forche, A; Schönian, G; Gräser, Y; Vilgalys, R; Mitchell, T G

    1999-11-01

    Atypical isolates of the pathogenic yeast Candida albicans have been reported with increasing frequency. To investigate the origin of a set of atypical isolates and their relationship to typical isolates, we employed a combination of molecular phylogenetic and population genetic analyses using rDNA sequencing, PCR fingerprinting, and analysis of co-dominant DNA nucleotide polymorphisms to characterize the population structure of one typical and two atypical populations of C. albicans from Angola and Madagascar. The extent of clonality and recombination was assessed in each population. The analyses revealed that the structure of all three populations of C. albicans was predominantly clonal but, as in previous studies, there was also evidence for recombination. Allele frequencies differed significantly between the typical and the atypical populations, suggesting very low levels of gene flow between them. However, allele frequencies were quite similar in the two atypical C. albicans populations, suggesting that they are closely related. Phylogenetic analysis of partial sequences encoding the nuclear 26S rDNA demonstrated that all three populations belong to a single monophyletic group, which includes the type strain of C. albicans. Copyright 1999 Academic Press.

  5. 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.

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

    PubMed

    Poterba, J M

    1998-10-01

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

  7. Characterization of the genetic diversity and population structure for the yellow cattle in Taiwan based on microsatellite markers.

    PubMed

    Tu, Po-An; Lin, Der-Yuh; Li, Guang-Fu; Huang, Jan-Chi; Wang, De-Chi; Wang, Pei-Hwa

    2014-01-01

    In recent years, the population size of Taiwan yellow cattle has drastically declined, even become endangered. A preservation project, Taiwan Yellow Cattle Genetic Preservation Project (TYCGPP), was carried out at the Livestock Research Institute (LRI) Hengchun branch (1988-present). An analysis of intra- and inter- population variability was performed to be the first step to preserve this precious genetic resource. In this work, a total number of 140 individuals selected from the five Taiwan yellow cattle populations were analyzed using 12 microsatellite markers (loci). These markers determined the level of genetic variation within and among populations as well as the phylogenetic structure. The total number of alleles detected (122, 10.28 per locus) and the expected heterozygosity (0.712) indicated that these five populations had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups was 2 (K = 2). Genetic differentiation among clusters was moderate (F ST = 0.095). The result of AMOVA showed that yellow cattle in Taiwan had maintained a high level of within-population genetic differentiation (91%), the remainder being accounted for by differentiation among subpopulations (4%), and by differentiation among regions (5%). The results of STRUCTURE and principal component analysis (PCA) revealed two divergent clusters. The individual unrooted phylogenetic tree showed that some Kinmen yellow cattle in the Hengchun facility (KMHC individuals) were overlapped with Taiwan yellow cattle (TW) and Taiwan yellow cattle Hengchun (HC) populations. Also, they were overlapped with Kinmen × Taiwan (KT) and Kinmen yellow cattle (KM) populations. It is possible that KMHC kept similar phenotypic characteristics and analogous genotypes between TW and KM. A significant inbreeding coefficient (F IS = 0.185; P < 0.01) was detected, suggesting a medium level of inbreeding for yellow cattle in Taiwan. The hypothesis that yellow cattle

  8. Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

    PubMed Central

    Ball, R. Martin; Freeman, Scott; James, Frances C.; Bermingham, Eldredge; Avise, John C.

    1988-01-01

    A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P ≈ 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow. PMID:16593914

  9. Multi-layered population structure in Island Southeast Asians

    PubMed Central

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

    2016-01-01

    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 recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years. PMID:27302840

  10. A Malthusian curb on spatial structure in microorganism populations.

    PubMed

    Martin, A P

    2004-10-07

    That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry. It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population. Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food. The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population. Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death. The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material. Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

  11. Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus

    PubMed Central

    Gascuel, Fanny; Choisy, Marc; Duplantier, Jean-Marc; Débarre, Florence; Brouat, Carine

    2013-01-01

    Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar. PMID:23675291

  12. Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus.

    PubMed

    Gascuel, Fanny; Choisy, Marc; Duplantier, Jean-Marc; Débarre, Florence; Brouat, Carine

    2013-01-01

    Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.

  13. 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.

  14. Study of the matrimonial structure of the population of central Sardinia (Italy).

    PubMed

    Vona, G; Francalacci, P; Paoli, G; Latini, V; Salis, M

    1996-12-01

    Temporal changes in the matrimonial structure of four Sardinian populations (Bitti, Lula, Lodè and Gavoi) have been studied. The endogamy rates and the average marriage distances indicate that the four villages experienced a long period of isolation. Only in recent decades endogamous marriages have fallen shortly. The trends of marital isonymy and inbreeding, evaluated both from isonymy and dispensation for consanguineous marriages, are similar to those of endogamy. The kinship values between pairs of populations show some preferential relationship (Bitti-Lodè, Lodè-Lula) and an evident differentiation between Gavoi and Bitti. The results also indicate that the values of kinship are not associated with the geographic distances. The possible impact of the matrimonial structure on the genetic structure and the relationships among the studied populations will be examined in further investigations, in which the genetic markers will be considered.

  15. Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country.

    PubMed

    Pumpaibool, Tepanata; Arnathau, Céline; Durand, Patrick; Kanchanakhan, Naowarat; Siripoon, Napaporn; Suegorn, Aree; Sitthi-Amorn, Chitr; Renaud, François; Harnyuttanakorn, Pongchai

    2009-07-14

    The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites). Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 +/- 0.17), where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai populations during this study. Comparison of the genetic

  16. A Study of Upper Error Limits in Accounting Populations.

    DTIC Science & Technology

    1986-09-01

    The error amount intensity is a population characteristic obtained by dividing the total...423.36/$763,931.19). This population characteristic is of interest because the results of the simulation done for research questions four through v.o

  17. The evolution of antibiotic resistance in a structured host population.

    PubMed

    Blanquart, François; Lehtinen, Sonja; Lipsitch, Marc; Fraser, Christophe

    2018-06-01

    The evolution of antibiotic resistance in opportunistic pathogens such as Streptococcus pneumoniae , Escherichia coli or Staphylococcus aureus is a major public health problem, as infection with resistant strains leads to prolonged hospital stay and increased risk of death. Here, we develop a new model of the evolution of antibiotic resistance in a commensal bacterial population adapting to a heterogeneous host population composed of untreated and treated hosts, and structured in different host classes with different antibiotic use. Examples of host classes include age groups and geographic locations. Explicitly modelling the antibiotic treatment reveals that the emergence of a resistant strain is favoured by more frequent but shorter antibiotic courses, and by higher transmission rates. In addition, in a structured host population, localized transmission in host classes promotes both local adaptation of the bacterial population and the global maintenance of coexistence between sensitive and resistant strains. When transmission rates are heterogeneous across host classes, resistant strains evolve more readily in core groups of transmission. These findings have implications for the better management of antibiotic resistance: reducing the rate at which individuals receive antibiotics is more effective to reduce resistance than reducing the duration of treatment. Reducing the rate of treatment in a targeted class of the host population allows greater reduction in resistance, but determining which class to target is difficult in practice. © 2018 The Authors.

  18. Emotional decisions in structured populations for the evolution of public cooperation

    NASA Astrophysics Data System (ADS)

    Wang, Yongjie; Chen, Tong; Chen, Qiao; Si, Guangrun

    2017-02-01

    The behaviors of humans are not always profit-driven in public goods games (PGG). In addition, social preference and decision-making might be influenced, even changed by heuristics and conformity in the real life. Motivated by the facts, we would like to investigate the role of emotional system in cooperative behaviors of structured population in PGG. Meantime, the effects of diffusion of influence are studied in structured population. Numerical simulation results are indicated that emotions play very significant role indeed in emergence and maintenance of cooperation in structured populations in PGG. However, the influences of emotions on others are limited due to diminishing of influence diffusion and the existence of pure defectors. What is more, conformity, to some extent, could drive potentially more people to accept cooperative strategy with higher probability. Higher-level cooperation could be promoted as increasing values of synergy factors, but while the effects might diminish gradually as increasing number of positive heuristic players and conformist. Our work may be beneficial to address the social dilemmas in PGG.

  19. Individual movement behavior, matrix heterogeneity, and the dynamics of spatially structured populations.

    PubMed

    Revilla, Eloy; Wiegand, Thorsten

    2008-12-09

    The dynamics of spatially structured populations is characterized by within- and between-patch processes. The available theory describes the latter with simple distance-dependent functions that depend on landscape properties such as interpatch distance or patch size. Despite its potential role, we lack a good mechanistic understanding of how the movement of individuals between patches affects the dynamics of these populations. We used the theoretical framework provided by movement ecology to make a direct representation of the processes determining how individuals connect local populations in a spatially structured population of Iberian lynx. Interpatch processes depended on the heterogeneity of the matrix where patches are embedded and the parameters defining individual movement behavior. They were also very sensitive to the dynamic demographic variables limiting the time moving, the within-patch dynamics of available settlement sites (both spatiotemporally heterogeneous) and the response of individuals to the perceived risk while moving. These context-dependent dynamic factors are an inherent part of the movement process, producing connectivities and dispersal kernels whose variability is affected by other demographic processes. Mechanistic representations of interpatch movements, such as the one provided by the movement-ecology framework, permit the dynamic interaction of birth-death processes and individual movement behavior, thus improving our understanding of stochastic spatially structured populations.

  20. Role of E-Payment System in Promoting Accountability in Government Ministries as Perceived by Accounting Education Graduates and Accountants in Ministry of Finance of Ebonyi State

    ERIC Educational Resources Information Center

    Azih, Nonye; Nwagwu, Lazarus

    2015-01-01

    This paper identified the role of electronic payment system in promoting accountability in government ministries as well as the challenges facing the implementation of e-payment in government ministries in Ebonyi State. The study was guided by two research questions and two hypotheses. The population of the study comprised of 112 accountants as…

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

    PubMed

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

    2014-01-07

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

  2. 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

  3. An account of the Speech-to-Song Illusion using Node Structure Theory.

    PubMed

    Castro, Nichol; Mendoza, Joshua M; Tampke, Elizabeth C; Vitevitch, Michael S

    2018-01-01

    In the Speech-to-Song Illusion, repetition of a spoken phrase results in it being perceived as if it were sung. Although a number of previous studies have examined which characteristics of the stimulus will produce the illusion, there is, until now, no description of the cognitive mechanism that underlies the illusion. We suggest that the processes found in Node Structure Theory that are used to explain normal language processing as well as other auditory illusions might also account for the Speech-to-Song Illusion. In six experiments we tested whether the satiation of lexical nodes, but continued priming of syllable nodes may lead to the Speech-to-Song Illusion. The results of these experiments provide evidence for the role of priming, activation, and satiation as described in Node Structure Theory as an explanation of the Speech-to-Song Illusion.

  4. Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

    PubMed

    Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

    2017-09-01

    Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

  5. Clostridium perfringens: insight into virulence evolution and population structure.

    PubMed

    Sawires, Youhanna S; Songer, J Glenn

    2006-02-01

    Clostridium perfringens is an important pathogen in veterinary and medical fields. Diseases caused by this organism are in many cases life threatening or fatal. At the same time, it is part of the ecological community of the intestinal tract of man and animals. Virulence in this species is not fully understood and it does seem that there is erratic distribution of the toxin/enzyme genes within C. perfringens population. We used the recently developed multiple-locus variable-number tandem repeat analysis (MLVA) scheme to investigate the evolution of virulence and population structure of this species. Analysis of the phylogenetic signal indicates that acquisition of the major toxin genes as well as other plasmid-borne toxin genes is a recent evolutionary event and their maintenance is essentially a function of the selective advantage they confer in certain niches under different conditions. In addition, it indicates the ability of virulent strains to cause disease in different host species. More interestingly, there is evidence that certain normal flora strains are virulent when they gain access to a different host species. Analysis of the population structure indicates that recombination events are the major tool that shapes the population and this panmixia is interrupted by frequent clonal expansion that mostly corresponds to disease processes. The signature of positive selection was detected in alpha toxin gene, suggesting the possibility of adaptive alleles on the other chromosomally encoded determinants. Finally, C. perfringens proved to have a dynamic population and availability of more genome sequences and use of comparative proteomics and animal modeling would provide more insight into the virulence of this organism.

  6. Population genetic diversity and structure of a naturally isolated plant species, Rhodiola dumulosa (Crassulaceae).

    PubMed

    Hou, Yan; Lou, Anru

    2011-01-01

    Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations.

  7. Population Genetic Diversity and Structure of a Naturally Isolated Plant Species, Rhodiola dumulosa (Crassulaceae)

    PubMed Central

    Hou, Yan; Lou, Anru

    2011-01-01

    Aims Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Methods Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. Important Findings The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations. PMID:21909437

  8. Accountable Care Organizations: roles and opportunities for hospitals.

    PubMed

    Schoenbaum, Stephen C

    2011-08-01

    Federal health reform has established Medicare Accountable Care Organizations (ACOs) as a new program, and some states and private payers have been independently developing ACO pilot projects. The objective is to hold provider groups accountable for the quality and cost of care to a population. The financial models for providers generally build off of shared savings between the payers and providers or some type of global payment that includes the possibility of partial or full capitation. For ACOs to achieve the same outcomes with lower costs or, better yet, improved outcomes with the same or lower costs, the delivery system will need to become more oriented toward primary care and care coordination than is currently the case. Providers of clinical services, in order to be more effective, efficient, and coordinated, will need to be supported by a variety of shared services, such as off-hours care, easy access to specialties, and information exchanges. These services can be organized by an ACO as a medical neighborhood or community. Hospitals, because they have a management structure, history of developing programs and services, and accessibility 24/7/365, are logical leaders of this enhancement of health care delivery for populations and other providers.

  9. 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.

  10. Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations.

    PubMed

    Wang, Yuchen; Lu, Dongsheng; Chung, Yeun-Jun; Xu, Shuhua

    2018-01-01

    Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied. We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant. These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies.

  11. Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs.

    PubMed

    Viengkone, Michelle; Derocher, Andrew Edward; Richardson, Evan Shaun; Malenfant, René Michael; Miller, Joshua Moses; Obbard, Martyn E; Dyck, Markus G; Lunn, Nick J; Sahanatien, Vicki; Davis, Corey S

    2016-12-01

    Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single-nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine-scale structure. In Hudson Bay, Canada, three polar bear ( Ursus maritimus ) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark-recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine-scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western-including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern-individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast-individuals from SH (Akimiski Island in James Bay); and (iv) Northeast-individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine-scale population delineation in polar bears.

  12. [Analysis of the population structure of the Black Forest Draught Horse].

    PubMed

    Aberle, Kerstin; Wrede, Jörn; Distl, Ottmar

    2003-01-01

    Gene contributions of foreign populations as well as coefficients of inbreeding and relationship were evaluated in 699 Black Forest Draught horses of Baden-Württemberg actually registered in the year 2002. Based on nearly complete 5-generation-pedigrees and after taking into account the remaining incompleteness, the mean coefficient of inbreeding for the total population was 6.5%. The recently by incrossing with different breeds newly established lines of stallions showed significantly lower mean coefficients of inbreeding. High rates of inbreeding of about 1.6% in the last five generations could also be faced by incrossing stallions of foreign coldblooded populations what resulted in a decrease of inbreeding in the last generation. In the total population the mean degree of relationship was 16%. The mean degree of relationships within lines of stallions was between 18.3 and 26.8%. The coefficients of relationships between lines of stallions varied between 5.1 and 16.6%. Especially, the newly established lines of stallions showed a lower mean degree of relationships to the other different lines of stallions. The proportion of purebred Black Forest Draught horses in the total population was nearly 70%. Assuming that most animals of unknown origin were purebred, the proportion of purebred Black Forest Draught horses reached about 90%. Austrian Noric, Swiss Freiberg and South German Coldblood stallions were the most important contributors to the Black Forest Draught horse population.

  13. 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

    2010-07-09

    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. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  14. Population Genetic Structure of the People of Qatar

    PubMed Central

    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.

    2010-01-01

    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. PMID:20579625

  15. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia.

    PubMed

    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

    2011-12-09

    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 accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  16. Genetic variation and structure in remnant population of critically endangered Melicope zahlbruckneri

    USGS Publications Warehouse

    Raji, J. A.; Atkinson, Carter T.

    2016-01-01

    The distribution and amount of genetic variation within and between populations of plant species are important for their adaptability to future habitat changes and also critical for their restoration and overall management. This study was initiated to assess the genetic status of the remnant population of Melicope zahlbruckneri–a critically endangered species in Hawaii, and determine the extent of genetic variation and diversity in order to propose valuable conservation approaches. Estimated genetic structure of individuals based on molecular marker allele frequencies identified genetic groups with low overall differentiation but identified the most genetically diverse individuals within the population. Analysis of Amplified Fragment Length Polymorphic (AFLP) marker loci in the population based on Bayesian model and multivariate statistics classified the population into four subgroups. We inferred a mixed species population structure based on Bayesian clustering and frequency of unique alleles. The percentage of Polymorphic Fragment (PPF) ranged from 18.8 to 64.6% for all marker loci with an average of 54.9% within the population. Inclusion of all surviving M. zahlbruckneri trees in future restorative planting at new sites are suggested, and approaches for longer term maintenance of genetic variability are discussed. To our knowledge, this study represents the first report of molecular genetic analysis of the remaining population of M. zahlbruckneri and also illustrates the importance of genetic variability for conservation of a small endangered population.

  17. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

    PubMed Central

    Larson, Wesley A; Seeb, Lisa W; Everett, Meredith V; Waples, Ryan K; Templin, William D; Seeb, James E

    2014-01-01

    Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure. PMID:24665338

  18. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    USGS Publications Warehouse

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  19. Population genetics related to adaptation in elite oat germplasm

    USDA-ARS?s Scientific Manuscript database

    Six hundred thirty five oat lines and 2,635 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 2...

  20. Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations.

    PubMed

    Saville, Amanda; Charles, Melodi; Chavan, Suchitra; Muñoz, Miguel; Gómez-Alpizar, Luis; Ristaino, Jean Beagle

    2017-12-01

    Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas.

  1. Insights into Platypus Population Structure and History from Whole-Genome Sequencing.

    PubMed

    Martin, Hilary C; Batty, Elizabeth M; Hussin, Julie; Westall, Portia; Daish, Tasman; Kolomyjec, Stephen; Piazza, Paolo; Bowden, Rory; Hawkins, Margaret; Grant, Tom; Moritz, Craig; Grutzner, Frank; Gongora, Jaime; Donnelly, Peter

    2018-05-01

    The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

  2. Insights into Platypus Population Structure and History from Whole-Genome Sequencing

    PubMed Central

    Martin, Hilary C; Hussin, Julie; Westall, Portia; Daish, Tasman; Kolomyjec, Stephen; Piazza, Paolo; Bowden, Rory; Hawkins, Margaret; Grant, Tom; Moritz, Craig; Grutzner, Frank; Gongora, Jaime; Donnelly, Peter

    2018-01-01

    Abstract The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10−9/bp/generation (95% CI 4.1 × 10−9–1.2 × 10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species. PMID:29688544

  3. Global population structure and adaptive evolution of aflatoxin-producing fungi.

    PubMed

    Moore, Geromy G; Olarte, Rodrigo A; Horn, Bruce W; Elliott, Jacalyn L; Singh, Rakhi; O'Neal, Carolyn J; Carbone, Ignazio

    2017-11-01

    Aflatoxins produced by several species in Aspergillus section Flavi are a significant problem in agriculture and a continuous threat to human health. To provide insights into the biology and global population structure of species in section Flavi , a total of 1,304 isolates were sampled across six species ( A. flavus, A. parasiticus, A. nomius, A. caelatus, A. tamarii, and A. alliaceus ) from single fields in major peanut-growing regions in Georgia (USA), Australia, Argentina, India, and Benin (Africa). We inferred maximum-likelihood phylogenies for six loci, both combined and separately, including two aflatoxin cluster regions ( aflM/alfN and aflW/aflX ) and four noncluster regions ( amdS, trpC, mfs and MAT ), to examine population structure and history. We also employed principal component and STRUCTURE analysis to identify genetic clusters and their associations with six different categories (geography, species, precipitation, temperature, aflatoxin chemotype profile, and mating type). Overall, seven distinct genetic clusters were inferred, some of which were more strongly structured by G chemotype diversity than geography. Populations of A. flavus S in Benin were genetically distinct from all other section Flavi species for the loci examined, which suggests genetic isolation. Evidence of trans-speciation within two noncluster regions, whereby A. flavus S BG strains from Australia share haplotypes with either A. flavus or A. parasiticus , was observed. Finally, while clay soil and precipitation may influence species richness in Aspergillus section Flavi , other region-specific environmental and genetic parameters must also be considered.

  4. Population dynamics of bowfin in a south Georgia reservoir: latitudinal comparisons of population structure, growth, and mortality

    USGS Publications Warehouse

    Porter, Nicholas J.; Bonvechio, Timothy F.; McCormick, Joshua L.; Quist, Michael

    2014-01-01

    The objectives of this study were to evaluate the population dynamics of bowfin (Amia calva) in Lake Lindsay Grace, Georgia, and to compare those dynamics to other bowfin populations. Relative abundance of bowfin sampled in 2010 in Lake Lindsay Grace was low and variable (mean±SD; 2.7±4.7 fish per hour of electrofishing). Total length (TL) of bowfin collected in Lake Lindsay Grace varied from 233–683 mm. Age of bowfin in Lake Lindsay Grace varied from 0–5 yr. Total annual mortality (A) was estimated at 68%. Both sexes appeared to be fully mature by age 2 with gonadosomatic index values above 8 for females and close to 1 for males. The majority of females were older, longer, and heavier than males. Bowfin in Lake Lindsay Grace had fast growth up to age 4 and higher total annual mortality than the other populations examined in this study. A chi-square test indicated that size structure of bowfin from Lake Lindsay Grace was different than those of a Louisiana population and two bowfin populations from the upper Mississippi River. To further assess bowfin size structure, we proposed standard length (i.e., TL) categories: stock (200 mm, 8 inches), quality (350 mm, 14 inches), preferred (460 mm, 18 inches), memorable (560 mm, 22, inches), and trophy (710 mm, 28 inches). Because our knowledge of bowfin ecology is limited, additional understanding of bowfin population dynamics provides important insight that can be used in management of bowfin across their distribution.

  5. Medicare Accountable Care Organizations of Diverse Structures Achieve Comparable Quality and Cost Performance.

    PubMed

    Comfort, Leeann N; Shortell, Stephen M; Rodriguez, Hector P; Colla, Carrie H

    2018-01-31

    To examine whether an empirically derived taxonomy of Accountable Care Organizations (ACOs) is associated with quality and spending performance among patients of ACOs in the Medicare Shared Savings Program (MSSP). Three waves of the National Survey of ACOs and corresponding publicly available Centers for Medicare & Medicaid Services performance data for NSACO respondents participating in the MSSP (N = 204); SK&A Office Based Physicians Database from QuintilesIMS. We compare the performance of three ACO types (physician-led, integrated, and hybrid) for three domains: quality, spending, and likelihood of achieving savings. Sources of performance variation within and between ACO types are compared for each performance measure. There is greater heterogeneity within ACO types than between ACO types. There were no consistent differences in quality by ACO type, nor were there differences in likelihood of achieving savings or overall spending per-person-year. There was evidence for higher spending on physician services for physician-led ACOs. ACOs of diverse structures perform comparably on core MSSP quality and spending measures. CMS should maintain its flexibility and continue to support participation of diverse ACOs. Future research to identify modifiable organizational factors that account for performance variation within ACO types may provide insight as to how best to improve ACO performance based on organizational structure and ownership. © Health Research and Educational Trust.

  6. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

    PubMed

    Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

    2017-08-01

    Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

  7. Fixation Times in Deme Structured, Finite Populations with Rare Migration

    NASA Astrophysics Data System (ADS)

    Hauert, Christoph; Chen, Yu-Ting; Imhof, Lorens A.

    2014-08-01

    Population structure affects both the outcome and the speed of evolutionary dynamics. Here we consider a finite population that is divided into subpopulations called demes. The dynamics within the demes are stochastic and frequency-dependent. Individuals can adopt one of two strategic types, or . The fitness of each individual is determined by interactions with other individuals in the same deme. With small probability, proportional to fitness, individuals migrate to other demes. The outcome of these dynamics has been studied earlier by analyzing the fixation probability of a single mutant in an otherwise homogeneous population. These results give only a partial picture of the dynamics, because the time when fixation occurs can be exceedingly large. In this paper, we study the impact of deme structures on the speed of evolution. We derive analytical approximations of fixation times in the limit of rare migration and rare mutation. In this limit, the conditional fixation time of a single mutant in a population is the same as that of a single in an population. For the prisoner's dilemma game, simulation results fit very well with our analytical predictions and demonstrate that fixation takes place in a moderate amount of time as compared to the expected waiting time until a mutant successfully invades and fixates. The simulations also confirm that the conditional fixation time of a single cooperator is indeed the same as that of a single defector.

  8. Duelling timescales of host mixing and disease spread determine invasion of disease in structured populations

    USGS Publications Warehouse

    Cross, P.C.; Lloyd-Smith, James O.; Johnson, P.L.F.; Getz, W.M.

    2005-01-01

    The epidemic potential of a disease is traditionally assessed using the basic reproductive number, R0. However, in populations with social or spatial structure a chronic disease is more likely to invade than an acute disease with the same R0, because it persists longer within each group and allows for more host movement between groups. Acute diseases ‘perceive’ a more structured host population, and it is more important to consider host population structure in analyses of these diseases. The probability of a pandemic does not arise independently from characteristics of either the host or disease, but rather from the interaction of host movement and disease recovery timescales. The R* statistic, a group-level equivalent of R0, is a better indicator of disease invasion in structured populations than the individual-level R0.

  9. 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

  10. Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

    PubMed

    Pressoir, G; Berthaud, J

    2004-02-01

    To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

  11. Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.

    PubMed

    Hawksworth, Joseph; Levy, Max; Smale, Chloe; Cheung, Dean; Whittle, Alice; Longhurst, Denise; Muir, Peter; Gibson, Wendy

    2015-08-01

    The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, an extremely common, but non-life-threatening, sexually-transmitted disease throughout the world. Recent population genetics studies of T. vaginalis have detected high genetic diversity and revealed a two-type population structure, associated with phenotypic differences in sensitivity to metronidazole, the drug commonly used for treatment, and presence of T. vaginalis virus. There is currently a lack of data on UK isolates; most isolates examined to date are from the US. Here we used a recently described system for multilocus sequence typing (MLST) of T. vaginalis to study diversity of clinical isolates from Bristol, UK. We used MLST to characterise 23 clinical isolates of T. vaginalis collected from female patients during 2013. Seven housekeeping genes were PCR-amplified for each isolate and sequenced. The concatenated sequences were then compared with data from other MLST-characterised isolates available from http://tvaginalis.mlst.net/ to analyse the population structure and construct phylogenetic trees. Among the 23 isolates from the Bristol population of T. vaginalis, we found 23 polymorphic nucleotide sites, 25 different alleles and 19 sequence types (genotypes). Most isolates had a unique genotype, in agreement with the high levels of heterogeneity observed elsewhere in the world. A two-type population structure was evident from population genetic analysis and phylogenetic reconstruction split the isolates into two major clades. Tests for recombination in the Bristol population of T. vaginalis gave conflicting results, suggesting overall a clonal pattern of reproduction. We conclude that the Bristol population of T. vaginalis parasites conforms to the two-type population structure found in most other regions of the world. We found the MLST scheme to be an efficient genotyping method. The online MLST database provides a useful repository and resource that will prove

  12. 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. © 2014 WILEY PERIODICALS, INC.

  13. Population Modeling of Modified Risk Tobacco Products Accounting for Smoking Reduction and Gradual Transitions of Relative Risk.

    PubMed

    Poland, Bill; Teischinger, Florian

    2017-11-01

    As suggested by the Food and Drug Administration (FDA) Modified Risk Tobacco Product (MRTP) Applications Draft Guidance, we developed a statistical model based on public data to explore the effect on population mortality of an MRTP resulting in reduced conventional cigarette smoking. Many cigarette smokers who try an MRTP persist as dual users while smoking fewer conventional cigarettes per day (CPD). Lower-CPD smokers have lower mortality risk based on large cohort studies. However, with little data on the effect of smoking reduction on mortality, predictive modeling is needed. We generalize prior assumptions of gradual, exponential decay of Excess Risk (ER) of death, relative to never-smokers, after quitting or reducing CPD. The same age-dependent slopes are applied to all transitions, including initiation to conventional cigarettes and to a second product (MRTP). A Monte Carlo simulation model generates random individual product use histories, including CPD, to project cumulative deaths through 2060 in a population with versus without the MRTP. Transitions are modeled to and from dual use, which affects CPD and cigarette quit rates, and to MRTP use only. Results in a hypothetical scenario showed high sensitivity of long-run mortality to CPD reduction levels and moderate sensitivity to ER transition rates. Models to project population effects of an MRTP should account for possible mortality effects of reduced smoking among dual users. In addition, studies should follow dual-user CPD histories and quit rates over long time periods to clarify long-term usage patterns and thereby improve health impact projections. We simulated mortality effects of a hypothetical MRTP accounting for cigarette smoking reduction by smokers who add MRTP use. Data on relative mortality risk versus CPD suggest that this reduction may have a substantial effect on mortality rates, unaccounted for in other models. This effect is weighed with additional hypothetical effects in an example.

  14. How does the host population's network structure affect the estimation accuracy of epidemic parameters?

    NASA Astrophysics Data System (ADS)

    Yashima, Kenta; Ito, Kana; Nakamura, Kazuyuki

    2013-03-01

    When an Infectious disease where to prevail throughout the population, epidemic parameters such as the basic reproduction ratio, initial point of infection etc. are estimated from the time series data of infected population. However, it is unclear how does the structure of host population affects this estimation accuracy. In other words, what kind of city is difficult to estimate its epidemic parameters? To answer this question, epidemic data are simulated by constructing a commuting network with different network structure and running the infection process over this network. From the given time series data for each network structure, we would like to analyzed estimation accuracy of epidemic parameters.

  15. Genetic diversity and structure in two species of Leavenworthia with self-incompatible and self-compatible populations

    PubMed Central

    Koelling, V A; Hamrick, J L; Mauricio, R

    2011-01-01

    Self-fertilization is a common mating system in plants and is known to reduce genetic diversity, increase genetic structure and potentially put populations at greater risk of extinction. In this study, we measured the genetic diversity and structure of two cedar glade endemic species, Leavenworthia alabamica and L. crassa. These species have self-incompatible (SI) and self-compatible (SC) populations and are therefore ideal for understanding how the mating system affects genetic diversity and structure. We found that L. alabamica and L. crassa had high species-level genetic diversity (He=0.229 and 0.183, respectively) and high genetic structure among their populations (FST=0.45 and 0.36, respectively), but that mean genetic diversity was significantly lower in SC compared with SI populations (SC vs SI, He for L. alabamica was 0.065 vs 0.206 and for L. crassa was 0.084 vs 0.189). We also found significant genetic structure using maximum-likelihood clustering methods. These data indicate that the loss of SI leads to the loss of genetic diversity within populations. In addition, we examined genetic distance relationships between SI and SC populations to analyze possible population history and origins of self-compatibility. We find there may have been multiple origins of self-compatibility in L. alabamica and L. crassa. However, further work is required to test this hypothesis. Finally, given their high genetic structure and that individual populations harbor unique alleles, conservation strategies seeking to maximize species-level genetic diversity for these or similar species should protect multiple populations. PMID:20485327

  16. No population genetic structure in a widespread aquatic songbird from the Neotropics

    USGS Publications Warehouse

    Cadena, Carlos Daniel; Gutierrez-Pinto, Natalia; Davila, Nicolas; Chesser, R. Terry

    2011-01-01

    Neotropical lowland organisms often show marked population genetic structure, suggesting restricted migration among populations. However, most phylogeographic studies have focused on species inhabiting humid forest interior. Little attention has been devoted to the study of species with ecologies conducive to dispersal, such as those of more open and variable environments associated with watercourses. Using mtDNA sequences, we examined patterns of genetic variation in a widely distributed Neotropical songbird of aquatic environments, the Yellow-hooded Blackbird (Icteridae, Chrysomus icterocephalus). In contrast to many forest species, Yellow-hooded Blackbirds showed no detectable genetic structure across their range, which includes lowland populations on both sides of the Andes, much of northeastern South America, Amazonia, as well as a phenotypically distinct highland population in Colombia. A coalescent-based analysis of the species indicated that its effective population size has increased considerably, suggesting a range expansion. Our results support the hypothesis that species occurring in open habitats and tracking temporally dynamic environments should show increased dispersal propensities (hence gene flow) relative to species from closed and more stable environments. The phenotypic and behavioral variation among populations of our study species appears to have arisen recently and perhaps in the face of gene flow.

  17. Leveraging Hierarchical Population Structure in Discrete Association Studies

    PubMed Central

    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. PMID:17611623

  18. Strong population structure in the marine sponge Crambe crambe (Poecilosclerida) as revealed by microsatellite markers.

    PubMed

    Duran, S; Pascual, M; Estoup, A; Turon, X

    2004-03-01

    Different categories of molecular markers have been used so far to study the population structure of sponges. However, these markers often did not have the resolution power to address precisely questions on structuring processes, especially at the intrapopulational level. In this study we show that microsatellites fulfil these expectations, allowing a fine description of population structure at different geographical scales in the marine sponge Crambe crambe. Specimens were collected in 11 locations, representing most of the Atlanto-Mediterranean range of the species, and were analysed at six loci. As expected for a sessile invertebrate with lecitotrophic larvae, high levels of between-population structure were found (FST = 0.18) and a significant isolation-by-distance pattern was observed. A strong genetic structure was also found within sampled sites (FIS = 0.21) that may be explained by several factors including inbreeding, selfing and the Wahlund effect. In spite of a sampling design planned to avoid the sampling of clones, genotypically identical individuals for the six loci were found in some locations. The significance of these potential clones is discussed and their effect on the observed pattern of population structure assessed. Patterns of allelic distribution within populations suggest the possibility of a recent colonization of the Atlantic range from the Mediterranean Sea.

  19. ParallelStructure: A R Package to Distribute Parallel Runs of the Population Genetics Program STRUCTURE on Multi-Core Computers

    PubMed Central

    Besnier, Francois; Glover, Kevin A.

    2013-01-01

    This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/. PMID:23923012

  20. Impact of Insertion Sequences and Recombination on the Population Structure of Staphylococcus haemolyticus.

    PubMed

    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.

  1. 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

  2. Learning to account for the social determinants of health affecting homeless persons.

    PubMed

    McNeil, Ryan; Guirguis-Younger, Manal; Dilley, Laura B; Turnbull, Jeffrey; Hwang, Stephen W

    2013-05-01

    Intersecting social determinants of health constrain access to care and treatment adherence among homeless populations. Because clinicians seldom receive training in the social determinants of health, they may be unprepared to account for or address these factors when developing treatment strategies for homeless individuals. This study explored: (i) clinicians' preparedness to provide care responsive to the social determinants of health in homeless populations, and (ii) the steps taken by clinicians to overcome shortcomings in their clinical training in regard to the social determinants of health. Qualitative interviews were conducted with doctors (n = 6) and nurses (n = 18) in six Canadian cities. Participants had at least 2 years of experience in providing care to homeless populations. Interview transcripts were analysed using methods of constant comparison. Participants highlighted how, when first providing care to this population, they were unprepared to account for or address social determinants shaping the health of homeless persons. However, participants recognised the necessity of addressing these factors to situate care within the social and structural contexts of homelessness. Participants' accounts illustrated that experiential learning was critical to increasing capacity to provide care responsive to the social determinants of health. Experiential learning was a continuous process that involved: (i) engaging with homeless persons in multiple settings and contexts to inform treatment strategies; (ii) evaluating the efficacy of treatment strategies through continued observation and critical reflection, and (iii) adjusting clinical practice to reflect observations and new knowledge. This study underscores the need for greater emphasis on the social determinants of health in medical education in the context of homelessness. These insights may help to inform the development and design of service-learning initiatives that integrate understandings of the

  3. Characterizing spatial structure of sediment E. coli populations to inform sampling design.

    PubMed

    Piorkowski, Gregory S; Jamieson, Rob C; Hansen, Lisbeth Truelstrup; Bezanson, Greg S; Yost, Chris K

    2014-01-01

    Escherichia coli can persist in streambed sediments and influence water quality monitoring programs through their resuspension into overlying waters. This study examined the spatial patterns in E. coli concentration and population structure within streambed morphological features during baseflow and following stormflow to inform sampling strategies for representative characterization of E. coli populations within a stream reach. E. coli concentrations in bed sediments were significantly different (p = 0.002) among monitoring sites during baseflow, and significant interactive effects (p = 0.002) occurred among monitoring sites and morphological features following stormflow. Least absolute shrinkage and selection operator (LASSO) regression revealed that water velocity and effective particle size (D 10) explained E. coli concentration during baseflow, whereas sediment organic carbon, water velocity and median particle diameter (D 50) were important explanatory variables following stormflow. Principle Coordinate Analysis illustrated the site-scale differences in sediment E. coli populations between disconnected stream segments. Also, E. coli populations were similar among depositional features within a reach, but differed in relation to high velocity features (e.g., riffles). Canonical correspondence analysis resolved that E. coli population structure was primarily explained by spatial (26.9–31.7 %) over environmental variables (9.2–13.1 %). Spatial autocorrelation existed among monitoring sites and morphological features for both sampling events, and gradients in mean particle diameter and water velocity influenced E. coli population structure for the baseflow and stormflow sampling events, respectively. Representative characterization of streambed E. coli requires sampling of depositional and high velocity environments to accommodate strain selectivity among these features owing to sediment and water velocity heterogeneity.

  4. Marked population structure and recent migration in the critically endangered Sumatran orangutan (Pongo abelii).

    PubMed

    Nater, Alexander; Arora, Natasha; Greminger, Maja P; van Schaik, Carel P; Singleton, Ian; Wich, Serge A; Fredriksson, Gabriella; Perwitasari-Farajallah, Dyah; Pamungkas, Joko; Krützen, Michael

    2013-01-01

    A multitude of factors influence how natural populations are genetically structured, including dispersal barriers, inhomogeneous habitats, and social organization. Such population subdivision is of special concern in endangered species, as it may lead to reduced adaptive potential and inbreeding in local subpopulations, thus increasing the risk of future extinctions. With only 6600 animals left in the wild, Sumatran orangutans (Pongo abelii) are among the most endangered, but also most enigmatic, great ape species. In order to infer the fine-scale population structure and connectivity of Sumatran orangutans, we analyzed the most comprehensive set of samples to date, including mitochondrial hyper-variable region I haplotypes for 123 individuals and genotypes of 27 autosomal microsatellite markers for 109 individuals. For both mitochondrial and autosomal markers, we found a pronounced population structure, caused by major rivers, mountain ridges, and the Toba caldera. We found that genetic diversity and corresponding long-term effective population size estimates vary strongly among sampling regions for mitochondrial DNA, but show remarkable similarity for autosomal markers, hinting at male-driven long-distance gene flow. In support of this, we identified several individuals that were most likely sired by males originating from other genetic clusters. Our results highlight the effect of natural barriers in shaping the genetic structure of great ape populations, but also point toward important dispersal corridors on northern Sumatra that allow for genetic exchange.

  5. British Columbia's health reform: "new directions" and accountability.

    PubMed

    Davidson, A R

    1999-01-01

    The health policy New Directions committed the British Columbia government to a population health perspective and extensive community involvement in the health services reform process. The policy envisaged elected citizen boards with authority to raise revenues and exercise a significant degree of local autonomy. Academic and public attention has been paid to the decision in November 1996 to collapse New Directions' two-tier governance structure into a single level. Less attention has been paid to the profound changes that occurred prior to the government's reversal on the question of governance. This paper focuses on those changes. During the critical three years between the 1993 launch of the reform and its formal revision in 1996, the government's positions on elections, taxation power, local autonomy and scope of action for regional boards all changed. Those changes marked a retreat from political accountability to the community and an advance towards managerial accountability to the government.

  6. Population genetic structure of endangered Mongolian racerunner (Eremias argus) from the Korean Peninsula.

    PubMed

    Park, Han-Chan; Suk, Ho Young; Jeong, Eu-Jin; Park, Dae-Sik; Lee, Hang; Min, Mi-Sook

    2014-11-01

    The Mongolian racerunner (Eremias argus) is a small lacertid lizard species, and its distribution range encompasses the Korean Peninsula, Mongolia, China and Russia. Eremias argus is widespread, but populations on the Korean Peninsula are small and declining, provoking concerns that genetic diversity is being lost. This species is currently listed under the Protection of Wild Fauna and Flora Act in South Korea. In this study, nine novel microsatellites for E. argus were developed with a biotin-enrichment method and used to understand its population genetic structure and delineate conservation units on the Korean Peninsula. Overall, low intrapopulation genetic diversity was observed (mean number of alleles per locus = 2.463; mean H E = 0.398) from 10 populations investigated (n = 110). Two populations (among five with n≥ 10) showed an excess of heterozygosity expected under HWE relative to that expected at mutation-drift equilibrium, indicating severe reduction in population sizes. With only a few exceptions, the overall genetic differentiation among populations was substantial with the high levels of pairwise-F ST (0.006-0.746) and -R ST (0.034-0.940) values. The results of Bayesian STRUCTURE analysis showed that E. argus populations on the Korean Peninsula were most likely partitioned into three genetic clusters. Taken all together, such low levels of gene flow and strong genetic structuring have critical implications for the conservation of this endangered species and its management.

  7. Accounting for age structure and spatial structure in eco-evolutionary analyses of a large, mobile vertebrate.

    PubMed

    Waples, Robin S; Scribner, Kim; Moore, Jennifer; Draheim, Hope; Etter, Dwayne; Boersen, Mark

    2018-04-14

    The idealized concept of a population is integral to ecology, evolutionary biology, and natural resource management. To make analyses tractable, most models adopt simplifying assumptions, which almost inevitably are violated by real species in nature. Here we focus on both demographic and genetic estimates of effective population size per generation (Ne), the effective number of breeders per year (Nb), and Wright's neighborhood size (NS) for black bears (Ursus americanus) that are continuously distributed in the northern lower peninsula of Michigan, USA. We illustrate practical application of recently-developed methods to account for violations of two common, simplifying assumptions about populations: 1) reproduction occurs in discrete generations, and 2) mating occurs randomly among all individuals. We use a 9-year harvest dataset of >3300 individuals, together with genetic determination of 221 parent-offspring pairs, to estimate male and female vital rates, including age-specific survival, age-specific fecundity, and age-specific variance in fecundity (for which empirical data are rare). We find strong evidence for overdispersed variance in reproductive success of same-age individuals in both sexes, and we show that constraints on litter size have a strong influence on results. We also estimate that another life-history trait that is often ignored (skip breeding by females) has a relatively modest influence, reducing Nb by 9% and increasing Ne by 3%. We conclude that isolation by distance depresses genetic estimates of Nb, which implicitly assume a randomly-mating population. Estimated demographic NS (100, based on parent-offspring dispersal) was similar to genetic NS (85, based on regression of genetic distance and geographic distance), indicating that the >36,000 km2 study area includes about 4-5 black-bear neighborhoods. Results from this expansive data set provide important insight into effects of violating assumptions when estimating evolutionary parameters

  8. Cityscape genetics: structural vs. functional connectivity of an urban lizard population.

    PubMed

    Beninde, Joscha; Feldmeier, Stephan; Werner, Maike; Peroverde, Daniel; Schulte, Ulrich; Hochkirch, Axel; Veith, Michael

    2016-10-01

    Functional connectivity is essential for the long-term persistence of populations. However, many studies assess connectivity with a focus on structural connectivity only. Cityscapes, namely urban landscapes, are particularly dynamic and include numerous potential anthropogenic barriers to animal movements, such as roads, traffic or buildings. To assess and compare structural connectivity of habitats and functional connectivity of gene flow of an urban lizard, we here combined species distribution models (SDMs) with an individual-based landscape genetic optimization procedure. The most important environmental factors of the SDMs are structural diversity and substrate type, with high and medium levels of structural diversity as well as open and rocky/gravel substrates contributing most to structural connectivity. By contrast, water cover was the best model of all environmental factors following landscape genetic optimization. The river is thus a major barrier to gene flow, while of the typical anthropogenic factors only buildings showed an effect. Nonetheless, using SDMs as a basis for landscape genetic optimization provided the highest ranked model for functional connectivity. Optimizing SDMs in this way can provide a sound basis for models of gene flow of the cityscape, and elsewhere, while presence-only and presence-absence modelling approaches showed differences in performance. Additionally, interpretation of results based on SDM factor importance can be misleading, dictating more thorough analyses following optimization of SDMs. Such approaches can be adopted for management strategies, for example aiming to connect native common wall lizard populations or disconnect them from non-native introduced populations, which are currently spreading in many cities in Central Europe. © 2016 John Wiley & Sons Ltd.

  9. Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae).

    PubMed

    Batista, Philip D; Janes, Jasmine K; Boone, Celia K; Murray, Brent W; Sperling, Felix A H

    2016-09-01

    Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

  10. Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model.

    PubMed

    Johnson, Eric G; Swenarton, Mary Katherine

    2016-01-01

    The effective management of invasive species requires detailed understanding of the invader's life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish ( Pterois volitans/miles ) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates; (2) distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3) the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water.

  11. Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model

    PubMed Central

    2016-01-01

    The effective management of invasive species requires detailed understanding of the invader’s life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish (Pterois volitans/miles) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates; (2) distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3) the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water. PMID:27920953

  12. Population structure and landscape genetics of two endangered frog species of genus Odorrana: different scenarios on two islands

    PubMed Central

    Igawa, T; Oumi, S; Katsuren, S; Sumida, M

    2013-01-01

    Isolation by distance and landscape connectivity are fundamental factors underlying speciation and evolution. To understand how landscapes affect gene flow and shape population structures, island species provide intrinsic study objects. We investigated the effects of landscapes on the population structure of the endangered frog species, Odorrana ishikawae and O. splendida, which each inhabit an island in southwest Japan. This was done by examining population structure, gene flow and demographic history of each species by analyzing 12 microsatellite loci and exploring causal environmental factors through ecological niche modeling (ENM) and the cost-distance approach. Our results revealed that the limited gene flow and multiple-population structure in O. splendida and the single-population structure in O. ishikawae were maintained after divergence of the species through ancient vicariance between islands. We found that genetic distance correlated with geographic distance between populations of both species. Our landscape genetic analysis revealed that the connectivity of suitable habitats influences gene flow and leads to the formation of specific population structures. In particular, different degrees of topographical complexity between islands are the major determining factor for shaping contrasting population structures of two species. In conclusion, our results illustrate the diversification mechanism of organisms through the interaction with space and environment. Our results also present an ENM approach for identifying the key factors affecting demographic history and population structures of target species, especially endangered species. PMID:22990312

  13. Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations

    PubMed Central

    Bilton, Timothy P.; Schofield, Matthew R.; Black, Michael A.; Chagné, David; Wilcox, Phillip L.; Dodds, Ken G.

    2018-01-01

    Next-generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high-density genetic linkage maps, which facilitate the development of nonmodel species’ genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sibling family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sibling populations of diploid species, implemented in a package called GUSMap. Our model is based on the Lander–Green hidden Markov model but extended to account for errors present in sequencing data. We were able to obtain accurate estimates of the recombination fractions and overall map distance using GUSMap, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model. PMID:29487138

  14. Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations.

    PubMed

    Bilton, Timothy P; Schofield, Matthew R; Black, Michael A; Chagné, David; Wilcox, Phillip L; Dodds, Ken G

    2018-05-01

    Next-generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high-density genetic linkage maps, which facilitate the development of nonmodel species' genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology ( e.g. , genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sibling family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sibling populations of diploid species, implemented in a package called GUSMap. Our model is based on the Lander-Green hidden Markov model but extended to account for errors present in sequencing data. We were able to obtain accurate estimates of the recombination fractions and overall map distance using GUSMap, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model. Copyright © 2018 Bilton et al.

  15. 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

  16. 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

    2016-07-07

    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.

  17. Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series.

    PubMed

    Ferguson, Jake M; Ponciano, José M

    2014-02-01

    Predicting population extinction risk is a fundamental application of ecological theory to the practice of conservation biology. Here, we compared the prediction performance of a wide array of stochastic, population dynamics models against direct observations of the extinction process from an extensive experimental data set. By varying a series of biological and statistical assumptions in the proposed models, we were able to identify the assumptions that affected predictions about population extinction. We also show how certain autocorrelation structures can emerge due to interspecific interactions, and that accounting for the stochastic effect of these interactions can improve predictions of the extinction process. We conclude that it is possible to account for the stochastic effects of community interactions on extinction when using single-species time series. © 2013 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

  18. Novelty-seeking DRD4 polymorphisms are associated with human migration distance out-of-Africa after controlling for neutral population gene structure.

    PubMed

    Matthews, Luke J; Butler, Paul M

    2011-07-01

    Numerous lines of evidence suggest that Homo sapiens evolved as a distinct species in Africa by 150,000 years before the present (BP) and began major migrations out-of-Africa ∼50,000 BP. By 20,000 BP, our species had effectively colonized the entire Old World, and by 12,000 BP H. sapiens had a global distribution. We propose that this rapid migration into new habitats selected for individuals with low reactivity to novel stressors. Certain dopamine receptor D4 (DRD4) polymorphisms are associated with low neuronal reactivity and increased exploratory behavior, novelty seeking, and risk taking, collectively considered novelty-seeking trait (NS). One previous report (Chen et al.: Evol Hum Behav 20 (1999) 309-324) demonstrated a correlation between migratory distance and the seven-repeat (7R) VNTR DRD4 allele at exon 3 for human populations. This study, however, failed to account for neutral genetic processes (drift and admixture) that might create such a correlation in the absence of natural selection. Furthermore, additional loci surrounding DRD4 are now recognized to influence NS. Herein we account for neutral genetic structure by modeling the nonindependence of neutral allele frequencies between human populations. We retest the DRD4 exon 3 alleles, and also test two other loci near DRD4 that are associated with NS. We conclude there is an association between migratory distance and DRD4 exon 3 2R and 7R alleles that cannot be accounted for by neutral genetic processes alone. Copyright © 2011 Wiley-Liss, Inc.

  19. Population genetic structure in migratory sandhill cranes and the role of Pleistocene glaciations.

    PubMed

    Jones, Kenneth L; Krapu, Gary L; Brandt, David A; Ashley, Mary V

    2005-08-01

    Previous studies of migratory sandhill cranes (Grus canadensis) have made significant progress explaining evolution of this group at the species scale, but have been unsuccessful in explaining the geographically partitioned variation in morphology seen on the population scale. The objectives of this study were to assess the population structure and gene flow patterns among migratory sandhill cranes using microsatellite DNA genotypes and mitochondrial DNA haplotypes of a large sample of individuals across three populations. In particular, we were interested in evaluating the roles of Pleistocene glaciation events and postglaciation gene flow in shaping the present-day population structure. Our results indicate substantial gene flow across regions of the Midcontinental population that are geographically adjacent, suggesting that gene flow for most of the region follows an isolation-by-distance model. Male-mediated gene flow and strong female philopatry may explain the differing patterns of nuclear and mitochondrial variation. Taken in context with precise geographical information on breeding locations, the morphologic and microsatellite DNA variation shows a gradation from the Arctic-nesting subspecies G. c. canadensis to the nonArctic subspecies G. c. tabida. Analogous to other Arctic-nesting birds, it is probable that the population structure seen in Midcontinental sandhill cranes reflects the result of postglacial secondary contact. Our data suggest that subspecies of migratory sandhills experience significant gene flow and therefore do not represent distinct and independent genetic entities.

  20. A unified genetic association test robust to latent population structure for a count phenotype.

    PubMed

    Song, Minsun

    2018-06-04

    Confounding caused by latent population structure in genome-wide association studies has been a big concern despite the success of genome-wide association studies at identifying genetic variants associated with complex diseases. In particular, because of the growing interest in association mapping using count phenotype data, it would be interesting to develop a testing framework for genetic associations that is immune to population structure when phenotype data consist of count measurements. Here, I propose a solution for testing associations between single nucleotide polymorphisms and a count phenotype in the presence of an arbitrary population structure. I consider a classical range of models for count phenotype data. Under these models, a unified test for genetic associations that protects against confounding was derived. An algorithm was developed to efficiently estimate the parameters that are required to fit the proposed model. I illustrate the proposed approach using simulation studies and an empirical study. Both simulated and real-data examples suggest that the proposed method successfully corrects population structure. Copyright © 2018 John Wiley & Sons, Ltd.

  1. Vector-borne disease risk indexes in spatially structured populations

    PubMed Central

    Anzo-Hernández, Andrés; Bonilla-Capilla, Beatriz; Soto-Bajo, Moisés; Fraguela-Collar, Andrés

    2018-01-01

    There are economic and physical limitations when applying prevention and control strategies for urban vector borne diseases. Consequently, there are increasing concerns and interest in designing efficient strategies and regulations that health agencies can follow in order to reduce the imminent impact of viruses like Dengue, Zika and Chikungunya. That includes fumigation, abatization, reducing the hatcheries, picking up trash, information campaigns. A basic question that arise when designing control strategies is about which and where these ones should focus. In other words, one would like to know whether preventing the contagion or decrease vector population, and in which area of the city, is more efficient. In this work, we propose risk indexes based on the idea of secondary cases from patch to patch. Thus, they take into account human mobility and indicate which patch has more chance to be a corridor for the spread of the disease and which is more vulnerable, i.e. more likely to have cases?. They can also indicate the neighborhood where hatchery control will reduce more the number of potential cases. In order to illustrate the usefulness of these indexes, we run a set of numerical simulations in a mathematical model that takes into account the urban mobility and the differences in population density among the areas of a city. If we label by i a particular neighborhood, the transmission risk index (TRi) measures the potential secondary cases caused by a host in that neighborhood. The vector transmission risk index (VTRi) measures the potential secondary cases caused by a vector. Finally, the vulnerability risk index (VRi) measures the potential secondary cases in the neighborhood. Transmission indexes can be used to give geographical priority to some neighborhoods when applying prevention and control measures. On the other hand, the vulnerability index can be useful to implement monitoring campaigns or public health investment. PMID:29432455

  2. Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations.

    PubMed

    Grilo, Clara; Del Cerro, Irene; Centeno-Cuadros, Alejandro; Ramiro, Victor; Román, Jacinto; Molina-Vacas, Guillem; Fernández-Aguilar, Xavier; Rodríguez, Juan; Porto-Peter, Flávia; Fonseca, Carlos; Revilla, Eloy; Godoy, José A

    2016-09-15

    Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L.) in China

    PubMed Central

    Li, Ming; Zhao, Zhong; Miao, Xingjun; Zhou, Jingjing

    2014-01-01

    The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program) analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG) 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY. PMID:24384840

  4. 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…

  5. Hierarchical Population Genetic Structure in a Direct Developing Antarctic Marine Invertebrate

    PubMed Central

    Hoffman, Joseph I.; Clarke, Andrew; Clark, Melody S.; Peck, Lloyd S.

    2013-01-01

    Understanding the relationship between life-history variation and population structure in marine invertebrates is not straightforward. This is particularly true of polar species due to the difficulty of obtaining samples and a paucity of genomic resources from which to develop nuclear genetic markers. Such knowledge, however, is essential for understanding how different taxa may respond to climate change in the most rapidly warming regions of the planet. We therefore used over two hundred polymorphic Amplified Fragment Length Polymorphisms (AFLPs) to explore population connectivity at three hierachical spatial scales in the direct developing Antarctic topshell Margarella antarctica. To previously published data from five populations spanning a 1500 km transect along the length of the Western Antarctic Peninsula, we added new AFLP data for four populations separated by up to 6 km within Ryder Bay, Adelaide Island. Overall, we found a nonlinear isolation-by-distance pattern, suggestive of weaker population structure within Ryder Bay than is present over larger spatial scales. Nevertheless, significantly positive F st values were obtained in all but two of ten pairwise population comparisons within the bay following Bonferroni correction for multiple tests. This is in contrast to a previous study of the broadcast spawner Nacella concinna that found no significant genetic differences among several of the same sites. By implication, the topshell's direct-developing lifestyle may constrain its ability to disperse even over relatively small geographic scales. PMID:23691125

  6. Addressing wild turkey population declines using structured decision making

    USGS Publications Warehouse

    Robinson, Kelly F.; Fuller, Angela K.; Schiavone, Michael V.; Swift, Bryan L.; Diefenbach, Duane R.; Siemer, William F.; Decker, Daniel J.

    2017-01-01

    We present a case study from New York, USA, of the use of structured decision making (SDM) to identify fall turkey harvest regulations that best meet stakeholder objectives, in light of recent apparent declines in abundance of wild turkeys in the northeastern United States. We used the SDM framework to incorporate the multiple objectives associated with turkey hunting, stakeholder desires, and region-specific ecological and environmental factors that could influence fall harvest. We identified a set of 4 fall harvest regulations, composed of different season lengths and bag limits, and evaluated their relative achievement of the objectives. We used a stochastic turkey population model, statistical modeling, and expert elicitation to evaluate the consequences of each harvest regulation on each of the objectives. We conducted a statewide mail survey of fall turkey hunters in New York to gather the necessary information to evaluate tradeoffs among multiple objectives associated with hunter satisfaction. The optimal fall harvest regulation was a 2-week season and allowed for the harvest of 1 bird/hunter. This regulation was the most conservative of those evaluated, reflecting the concerns about recent declines in turkey abundance among agency wildlife biologists and the hunting public. Depending on the region of the state, the 2-week, 1-bird regulation was predicted to result in 7–32% more turkeys on the landscape after 5 years. The SDM process provided a transparent framework for setting fall turkey harvest regulations and reduced potential stakeholder conflict by explicitly taking the multiple objectives of different stakeholder groups into account.

  7. Genetic population structure in an equatorial sparrow: roles for culture and geography.

    PubMed

    Danner, J E; Fleischer, R C; Danner, R M; Moore, I T

    2017-06-01

    Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  8. Types of provincial structure and population health.

    PubMed

    Young, Frank W; Rodriguez, Eunice

    2005-01-01

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

  9. Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.

    PubMed

    Xiao, Yongshuang; Zhang, Yan; Yanagimoto, Takashi; Li, Jun; Xiao, Zhizhong; Gao, Tianxiang; Xu, Shihong; Ma, Daoyuan

    2011-02-01

    Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

  10. Accounting for methodological, structural, and parameter uncertainty in decision-analytic models: a practical guide.

    PubMed

    Bilcke, Joke; Beutels, Philippe; Brisson, Marc; Jit, Mark

    2011-01-01

    Accounting for uncertainty is now a standard part of decision-analytic modeling and is recommended by many health technology agencies and published guidelines. However, the scope of such analyses is often limited, even though techniques have been developed for presenting the effects of methodological, structural, and parameter uncertainty on model results. To help bring these techniques into mainstream use, the authors present a step-by-step guide that offers an integrated approach to account for different kinds of uncertainty in the same model, along with a checklist for assessing the way in which uncertainty has been incorporated. The guide also addresses special situations such as when a source of uncertainty is difficult to parameterize, resources are limited for an ideal exploration of uncertainty, or evidence to inform the model is not available or not reliable. for identifying the sources of uncertainty that influence results most are also described. Besides guiding analysts, the guide and checklist may be useful to decision makers who need to assess how well uncertainty has been accounted for in a decision-analytic model before using the results to make a decision.

  11. Cannibals in space: the coevolution of cannibalism and dispersal in spatially structured populations.

    PubMed

    Rudolf, Volker H W; Kamo, Masashi; Boots, Mike

    2010-05-01

    The propensity for cannibalism varies considerably both within and between species. Currently we have little understanding of both the causes of this variation and its evolutionary consequences for other life-history traits. We examine how different levels of spatial structure affect the evolution of cannibalism and how cannibalism in turn drives the evolution of dispersal. Using pair approximations and simulations, we show that cannibalism can easily evolve in spatially structured populations as long as some dispersal exists. Furthermore, for a wide range of intermediate levels of spatial structure, we find the possibility of evolutionary branching leading to polymorphism in cannibalism. We also show that cannibalism itself can have important evolutionary consequences and select for increased dispersal rates, thus helping to determine the spatial structure of populations. The coevolution of cannibalism and dispersal results in the evolution of various alternative life-history strategies with different dispersal and cannibalism regimes. Which strategy evolves depends on the environmental conditions that determine initial cannibalism rates. Our results therefore suggest that differences in spatial structure could explain variation in the propensity for cannibalism and cannibalistic polyphenism. Furthermore, results emphasize that cannibalism can drive the evolution of other life-history traits and determine the spatial structure of natural populations.

  12. GENETIC STRUCTURE OF TRIATOMA INFESTANS POPULATIONS IN RURAL COMMUNITIES OF SANTIAGO DEL ESTERO, NORTHERN ARGENTINA

    PubMed Central

    Marcet, PL; Mora, MS; Cutrera, AP; Jones, L; Gürtler, RE; Kitron, U; Dotson, EM

    2008-01-01

    To gain an understanding of the genetic structure and dispersal dynamics of T. infestans populations, we analyzed the multilocus genotype of 10 microsatellite loci for 352 T. infestans collected in 21 houses of 11 rural communities in October 2002. Genetic structure was analyzed at the community and house compound levels. Analysis revealed that vector control actions affected the genetic structure of T. infestans populations. Bug populations from communities under sustained vector control (core area) were highly structured and genetic differentiation between neighboring house compounds was significant. In contrast, bug populations from communities with sporadic vector control actions were more homogeneous and lacked defined genetic clusters. Genetic differentiation between population pairs did not fit a model of isolation by distance at the microgeographical level. Evidence consistent with flight or walking bug dispersal was detected within and among communities, dispersal was more female-biased in the core area and results suggested that houses received immigrants from more than one source. Putative sources and mechanisms of re-infestation are described. These data may be use to design improved vector control strategies PMID:18773972

  13. What can otolith shape analysis tell us about population structure of the European sardine, Sardina pilchardus, from Atlantic and Mediterranean waters?

    NASA Astrophysics Data System (ADS)

    Jemaa, Sharif; Bacha, Mahmoud; Khalaf, Gaby; Dessailly, David; Rabhi, Khalef; Amara, Rachid

    2015-02-01

    The European sardine, Sardina pilchardus, exhibits a complex population structure, which has produced conflicting results in previous genetic studies. Despite its importance in the fisheries industry, stock delineation for management and conservation purposes is still a matter of debate throughout the distribution range of the species. This study examines whether otolith shapes are more efficient than genetic markers to detect population structure in pelagic species with large population sizes. Sardines were analyzed from 15 sampling localities in the Northeast Atlantic and Mediterranean Sea covering almost the whole distribution range of the species. A combination of otolith shape indices and elliptic Fourier descriptors was investigated by multivariate statistical procedures. Within the studied area, three distinct groups were identified with an overall correct classification of 77%. Group A: northern Mediterranean Sea and Gulf of Gabès; group B: Atlantic Morocco-south Alboran-Algero-provençal coasts; and group C: European Atlantic coast. The Almeria-Oran front and the Gibraltar strait are not an efficient barrier for sardine population separation as there seems to be exchanges between populations of the south-western Mediterranean Sea and those of the Moroccan Atlantic Ocean coast or Gulf of Cadiz. The results are discussed in relation to environmental conditions, oceanographic features, and physical barriers to dispersal in the study area, and compared with those obtained by previous genetic, morphometric, and meristic data. For pelagic species with high gene flow, present results highlighted the need to take into account the identification of phenotypic stocks to ensure sustainable fishery benefits and efficient conservation as they may have unique demographic properties and responses to exploitation.

  14. Population Genetic Structure of Rock Bream (Oplegnathus fasciatus Temminck & Schlegel, 1884) Revealed by mtDNA COI Sequence in Korea and China

    NASA Astrophysics Data System (ADS)

    Park, Hyun Suk; Kim, Choong-Gon; Kim, Sung; Park, Yong-Joo; Choi, Hee-Jung; Xiao, Zhizhong; Li, Jun; Xiao, Yongshuang; Lee, Youn-Ho

    2018-04-01

    The rock bream, Oplegnathus fasciatus, is a common rocky reef game fish in East Asia and recently has become an aquaculture species. Despite its commercial importance, the population genetic structure of this fish species remains poorly understood. In this study, 163 specimens were collected from 6 localities along the coastal waters of Korea and China and their genetic variation was analyzed with mtDNA COI sequences. A total of 34 polymorphic sites were detected which determined 30 haplotypes. The genetic pattern reveals a low level of nucleotide diversity (0.04 ± 0.003) but a high level of haplotype diversity (0.83 ± 0.02). The 30 haplotypes are divided into two major genealogical clades: one that consists of only Zhoushan (ZS, East China Sea) specific haplotypes from the southern East China Sea and the other that consists of the remaining haplotypes from the northern East China Sea, Yellow Sea, Korea Strait, and East Sea/Sea of Japan. The two clades are separated by approximately 330 435 kyBP. Analyses of AMOVA and F st show a significant population differentiation between the ZS sample and the other ones, corroborating separation of the two genealogical clades. Larval dispersal and the fresh Yangtze River plume are invoked as the main determining factors for this population genetic structure of O. fasciatus. Neutrality tests and mismatch distribution analyses indicate late Pleistocene population expansion along the coastal waters of Korea and China approximately 133-183 kyBP during which there were periodic cycles of glaciations and deglaciations. Such population information needs to be taken into account when stock enhancement and conservation measures are implemented for this fisheries species.

  15. Genetic diversity and population structure of the endangered Namaqua Afrikaner sheep.

    PubMed

    Qwabe, Sithembele O; van Marle-Köster, Este; Visser, Carina

    2013-02-01

    The Namaqua Afrikaner is an endangered sheep breed indigenous to South Africa, primarily used in smallholder farming systems. Genetic characterization is essential for the breed's conservation and utilization. In this study, a genetic characterization was performed on 144 Namaqua Afrikaner sheep kept at the Karakul Experimental Station (KES), Carnarvon Experimental Station (CES), and a private farm Welgeluk (WGK) using 22 microsatellite markers. The mean number of alleles observed was low (3.7 for KES, 3.9 for CES, and 4.2 for WGK). Expected heterozygosity values across loci ranged between 46 % for WGK, 48 % for KES, and 55 % for CES, indicating low to moderate genetic variation. The analysis of molecular variance revealed that 89.5 % of the genetic variation was due to differences within populations. The population structure confirmed the differentiation of three clusters with high relationships between the CES and WGK populations. In the population structure comparison with Pedi and South African Mutton Merino sheep, limited hybridization between the Namaqua Afrikaner sheep and both of these breeds was observed. The results of this study will serve as a reference for genetic management and conservation of Namaqua Afrikaner sheep.

  16. Pulses of movement across the sea ice: population connectivity and temporal genetic structure in the arctic fox.

    PubMed

    Norén, Karin; Carmichael, Lindsey; Fuglei, Eva; Eide, Nina E; Hersteinsson, Pall; Angerbjörn, Anders

    2011-08-01

    Lemmings are involved in several important functions in the Arctic ecosystem. The Arctic fox (Vulpes lagopus) can be divided into two discrete ecotypes: "lemming foxes" and "coastal foxes". Crashes in lemming abundance can result in pulses of "lemming fox" movement across the Arctic sea ice and immigration into coastal habitats in search for food. These pulses can influence the genetic structure of the receiving population. We have tested the impact of immigration on the genetic structure of the "coastal fox" population in Svalbard by recording microsatellite variation in seven loci for 162 Arctic foxes sampled during the summer and winter over a 5-year period. Genetic heterogeneity and temporal genetic shifts, as inferred by STRUCTURE simulations and deviations from Hardy-Weinberg proportions, respectively, were recorded. Maximum likelihood estimates of movement as well as STRUCTURE simulations suggested that both immigration and genetic mixture are higher in Svalbard than in the neighbouring "lemming fox" populations. The STRUCTURE simulations and AMOVA revealed there are differences in genetic composition of the population between summer and winter seasons, indicating that immigrants are not present in the reproductive portion of the Svalbard population. Based on these results, we conclude that Arctic fox population structure varies with time and is influenced by immigration from neighbouring populations. The lemming cycle is likely an important factor shaping Arctic fox movement across sea ice and the subsequent population genetic structure, but is also likely to influence local adaptation to the coastal habitat and the prevalence of diseases.

  17. Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

    PubMed

    Lesser, M R; Parchman, T L; Jackson, S T

    2013-05-01

    Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century. © 2013 Blackwell Publishing Ltd.

  18. Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum

    PubMed Central

    Artzy-Randrup, Yael; Rorick, Mary M; Day, Karen; Chen, Donald; Dobson, Andrew P; Pascual, Mercedes

    2012-01-01

    The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier ‘strain theory’ by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression. It tracks the dynamics of all unique var repertoires in a population of hosts, and shows that even under high levels of sexual recombination, strain competition mediated through cross-immunity structures the parasite population into a subset of coexisting dominant repertoires of var genes whose degree of antigenic overlap depends on transmission intensity. Empirical comparison of patterns of genetic variation at antigenic and neutral sites supports this role for immune selection in structuring parasite diversity. DOI: http://dx.doi.org/10.7554/eLife.00093.001 PMID:23251784

  19. 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

  20. Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

    PubMed Central

    Kunene, Nokuthula Winfred

    2018-01-01

    The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69) and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu) had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep. PMID:29698497

  1. Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds.

    PubMed

    Selepe, Mokhethi Matthews; Ceccobelli, Simone; Lasagna, Emiliano; Kunene, Nokuthula Winfred

    2018-01-01

    The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69) and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu) had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

  2. Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe.

    PubMed

    Skovrind, Mikkel; Olsen, Morten Tange; Vieira, Filipe Garrett; Pacheco, George; Carl, Henrik; Gilbert, M Thomas P; Møller, Peter Rask

    2016-02-01

    Climate change experts largely agree that future climate change and associated rises in oceanic water levels over the upcoming decades, will affect marine salinity levels. The subsequent effects on fish communities in estuarine ecosystems however, are less clear. One species that is likely to become increasingly affected by changes in salinity is the ide (Leuciscus idus). The ide is a stenohaline freshwater fish that primarily inhabits rivers, with frequent anadromous behavior when sea salinity does not exceed 15%. Unlike most other anadromous Baltic Sea fish species, the ide has yet to be subjected to large-scale stocking programs, and thus provides an excellent opportunity for studying the natural population structure across the current salinity gradient in the Danish Belts. To explore this, we used Genotyping-by-Sequencing to determine genomic population structure of both freshwater resident and anadromous ide populations in the western Baltic Sea region, and relate the results to the current salinity gradient and the demographic history of ide in the region. The sample sites separate into four clusters, with all anadromous populations in one cluster and the freshwater resident populations in the remaining three. Results demonstrate high level of differentiation between sites hosting freshwater resident populations, but little differentiation among anadromous populations. Thus ide exhibit the genomic population structure of both a typical freshwater species, and a typical anadromous species. In addition to providing a first insight into the population structure of north-western European ide, our data also (1) provide indications of a single illegal introduction by man; (2) suggest limited genetic effects of heavy pollution in the past; and (3) indicate possible historical anadromous behavior in a now isolated freshwater population.

  3. 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.

  4. Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

    PubMed

    Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

    2016-01-01

    The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

  5. Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp)

    PubMed Central

    Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

    2016-01-01

    The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research. PMID:27509049

  6. 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…

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

    PubMed Central

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

    2013-01-01

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

  8. Population structure in the Arab world and its impact on integration and development trends.

    PubMed

    El-hallak, M N

    1986-12-01

    The author examines three issues: "population structure in the Arab world; trends making for integration and unity among the Arab countries; and economic and social development trends." Data from the United Nations for 1985 and from recent censuses are used to discuss population size, growth, and spatial distribution; the labor force; age and sex distribution; and fertility, mortality, and natural increase. Figures are presented separately for 22 Arab countries. Attention is then given to the relationships between population structure and economic and social development and between development and Arab unity and integration. excerpt

  9. Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda

    PubMed Central

    Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D.; Goffredo, Stefano

    2015-01-01

    Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa. PMID:26544963

  10. Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda.

    PubMed

    Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D; Goffredo, Stefano

    2015-01-01

    Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa.

  11. 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.

  12. 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.

  13. Population genetic structure of Patagonian toothfish (Dissostichus eleginoides) in the Southeast Pacific and Southwest Atlantic Ocean

    PubMed Central

    Canales-Aguirre, Cristian B.; Galleguillos, Ricardo; Oyarzun, Fernanda X.; Hernández, Cristián E.

    2018-01-01

    Previous studies of population genetic structure in Dissostichus eleginoides have shown that oceanographic and geographic discontinuities drive in this species population differentiation. Studies have focused on the genetics of D. eleginoides in the Southern Ocean; however, there is little knowledge of their genetic variation along the South American continental shelf. In this study, we used a panel of six microsatellites to test whether D. eleginoides shows population genetic structuring in this region. We hypothesized that this species would show zero or very limited genetic structuring due to the habitat continuity along the South American shelf from Peru in the Pacific Ocean to the Falkland Islands in the Atlantic Ocean. We used Bayesian and traditional analyses to evaluate population genetic structure, and we estimated the number of putative migrants and effective population size. Consistent with our predictions, our results showed no significant genetic structuring among populations of the South American continental shelf but supported two significant and well-defined genetic clusters of D. eleginoides between regions (South American continental shelf and South Georgia clusters). Genetic connectivity between these two clusters was 11.3% of putative migrants from the South American cluster to the South Georgia Island and 0.7% in the opposite direction. Effective population size was higher in locations from the South American continental shelf as compared with the South Georgia Island. Overall, our results support that the continuity of the deep-sea habitat along the continental shelf and the biological features of the study species are plausible drivers of intraspecific population genetic structuring across the distribution of D. eleginoides on the South American continental shelf. PMID:29362690

  14. Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae).

    PubMed

    Cosendai, A-C; Wagner, J; Ladinig, U; Rosche, C; Hörandl, E

    2013-06-01

    Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations.

  15. Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae)

    PubMed Central

    Cosendai, A-C; Wagner, J; Ladinig, U; Rosche, C; Hörandl, E

    2013-01-01

    Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations. PMID:23403961

  16. Population genetic structure and direct observations reveal sex-reversed patterns of dispersal in a cooperative bird.

    PubMed

    Harrison, Xavier A; York, Jennifer E; Young, Andrew J

    2014-12-01

    Sex-biased dispersal is pervasive and has diverse evolutionary implications, but the fundamental drivers of dispersal sex biases remain unresolved. This is due in part to limited diversity within taxonomic groups in the direction of dispersal sex biases, which leaves hypothesis testing critically dependent upon identifying rare reversals of taxonomic norms. Here, we use a combination of observational and genetic data to demonstrate a rare reversal of the avian sex bias in dispersal in the cooperatively breeding white-browed sparrow weaver (Plocepasser mahali). Direct observations revealed that (i) natal philopatry was rare, with both sexes typically dispersing locally to breed, and (ii), unusually for birds, males bred at significantly greater distances from their natal group than females. Population genetic analyses confirmed these patterns, as (i) corrected Assignment index (AIc), FST tests and isolation-by-distance metrics were all indicative of longer dispersal distances among males than females, and (ii) spatial autocorrelation analysis indicated stronger within-group genetic structure among females than males. Examining the spatial scale of extra-group mating highlighted that the resulting 'sperm dispersal' could have acted in concert with individual dispersal to generate these genetic patterns, but gamete dispersal alone cannot account entirely for the sex differences in genetic structure observed. That leading hypotheses for the evolution of dispersal sex biases cannot readily account for these sex-reversed patterns of dispersal in white-browed sparrow weavers highlights the continued need for attention to alternative explanations for this enigmatic phenomenon. We highlight the potential importance of sex differences in the distances over which dispersal opportunities can be detected. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  17. Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

    USGS Publications Warehouse

    Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

    2004-01-01

    Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

  18. Historical habitat connectivity affects current genetic structure in a grassland species.

    PubMed

    Münzbergová, Z; Cousins, S A O; Herben, T; Plačková, I; Mildén, M; Ehrlén, J

    2013-01-01

    Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co-dominant markers to estimate genetic diversity and deviation from Hardy-Weinberg equilibrium in 31 populations distributed within a 5 km(2) agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  19. Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population.

    PubMed

    Hoffman, J I; Kowalski, G J; Klimova, A; Eberhart-Phillips, L J; Staniland, I J; Baylis, A M M

    2016-07-01

    Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.

  20. Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

    PubMed Central

    Hoffman, J. I.; Kowalski, G. J.; Klimova, A.; Staniland, I. J.; Baylis, A. M. M.

    2016-01-01

    Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations. PMID:27493782

  1. Genetic structuring among silverside fish (Atherinella brasiliensis) populations from different Brazilian regions

    NASA Astrophysics Data System (ADS)

    da Silva Cortinhas, Maria Cristina; Kersanach, Ralf; Proietti, Maíra; Dumont, Luiz Felipe Cestari; D'Incao, Fernando; Lacerda, Ana Luzia F.; Prata, Pedro Sanmartin; Matoso, Daniele Aparecida; Noleto, Rafael Bueno; Ramsdorf, Wanessa; Boni, Talge Aiex; Prioli, Alberto José; Cestari, Marta Margarete

    2016-09-01

    Estuaries are dynamic environments, key for the survival of innumerous ecologically or economically important fish species. Among these species are Neotropical silversides (Atherinella brasiliensis), which are resident and abundant in Brazilian estuaries and used as a complementary source of income and food for local communities. To better understand silverside populations in Brazil, we evaluated the genetic diversity, structure and demography of fish sampled at six estuaries from the northeastern to the southern coast, using Random Amplified Polymorphic DNA and mitochondrial DNA (D-loop) markers. High haplotype diversities (h ranging from 0.75 to 0.99) were found in all populations except Carapebus, located in Southeast Brazil (h = 0.54). A total of 69 mtDNA haplotypes were found, with Itaparica (Northeast Brazil) and Carapebus presenting only exclusive haplotypes, while some were shared among populations in the South. Strong regional structure was observed, with very high differentiation between Itaparica and Carapebus, as well as among these two populations and the ones from the Southern region (Paranaguá, Conceição, Camacho and Patos). Among southern areas, low/moderate structure was detected. Most populations showed unimodal mismatch distributions indicating recent demographic expansion, while Carapebus presented a multimodal distribution characteristic of a stable or bottlenecked population. Times since possible population expansion were highest in Itaparica (32,500 ya) and Carapebus (29,540 ya), while in the Southern region longest time was observed at Conceição (25,540 ya) and shortest at Patos (9720 ya). In a general manner, haplotype diversities were directly related to times since population expansions; again, Carapebus was the exception, displaying long time since expansion but low diversity, possibly due to a recent bottleneck caused by the isolation and human impacts this lagoon is subject to. Isolation by Distance was significant for Itaparica

  2. 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.

  3. Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India.

    PubMed

    Gaur, Uma; Tantia, Madhu Sudan; Mishra, Bina; Bharani Kumar, Settypalli Tirumala; Vijh, Ramesh Kumar; Chaudhury, Ashok

    2018-03-01

    The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise F ST value among populations was 0.4243 (p < .01) and the range of nucleotide substitution per site (Dxy) between the five Indian duck populations was 0.00034-0.00555, and the net divergence (Da) was 0-0.00355. The phylogenetic analysis in the present study unveiled three clades. The analysis revealed genetic continuity among ducks of coastal region of the country which formed a separate group from the ducks of the inland area. Both coastal as well as the land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.

  4. Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus.

    PubMed

    Ball, Sarah E; Bovero, Stefano; Sotgiu, Giuseppe; Tessa, Giulia; Angelini, Claudio; Bielby, Jon; Durrant, Christopher; Favelli, Marco; Gazzaniga, Enrico; Garner, Trenton W J

    2017-02-01

    The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus . Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.

  5. Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

    USGS Publications Warehouse

    Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

    2018-01-01

    Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or

  6. Plasmodium falciparum population structure in Sudan post artemisinin-based combination therapy.

    PubMed

    Bakhiet, Amani M A; Abdel-Muhsin, Abdel-Muhsin A; Elzaki, Salah-Eldin G; Al-Hashami, Zainab; Albarwani, Hamida S; AlQamashoui, Badar A; Al-Hamidhi, Salama; Idris, Mohamed A; Elagib, Atif A; Beja-Pereira, Albano; Babiker, Hamza A

    2015-08-01

    Over the past decade, Sudan has stepped up malaria control backed by WHO, and this has resulted in significant reduction in parasite rate, malaria morbidity and mortality. The present study analyzed Plasmodium falciparum parasites in four geographical separated areas, to examine whether the success in malaria control following the use of artemisinin-based combination therapy (ACT) has disrupted the population structure and evolution of the parasite. We examined 319 P. falciparum isolates collected between October 2009 and October 2012 in four different areas in Sudan (Jazira [central Sudan], Southern Darfur [western Sudan], Upper Nile [southern Sudan] and Kasala [eastern Sudan]). Twelve microsatellites were analyzed for allelic diversity, multi-locus haplotype and inter-population differentiation. Level of diversity was compared to that detected for three of the above microsatellites among P. falciparum parasites in central and eastern Sudan in 1999, prior to introduction of ACT. Diversity at each locus (unbiased heterozygosity [H]) was high in all areas (Jazira, H=0.67), (Southern Darfur, H=0.71), (Upper Nile, H=0.71), and (Kasala, H=0.63). Microsatellites were distributed widely and private alleles, detected in a single population, were rare. The extent of diversity in the above sites was similar to that seen, in 1999, in central (Khartoum, H=0.73) and eastern Sudan (Gedaref, H=0.75). Significant Linkage disequilibrium (LD) was observed between the microsatellites in all populations. Pairwise FST analysis revealed that parasites in the four areas could be considered as one population. However, the parasites in Sudan clustered away from parasites in West Africa and the Arabian Peninsula. Despite marked reduction in malaria risk in Sudan, the extent of diversity and parasite genetic structure are indicative of a large population size. Further considerable reduction in transmission would be needed before fragmented sub-population can be seen. In addition, the large

  7. 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

  8. History and structure of sub-Saharan populations of Drosophila melanogaster.

    PubMed

    Pool, John E; Aquadro, Charles F

    2006-10-01

    Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of genetic differentiation within sub-Saharan Africa. A clear geographic pattern is observed, with eastern and western African populations composing two genetically distinct groups. This pattern may have resulted from a relatively recent establishment of D. melanogaster in western Africa. Eastern populations show greater evidence for long-term stability, consistent with the hypothesis that eastern Africa contains the ancestral range of the species. Three sub-Saharan populations show evidence for cosmopolitan introgression. Apart from those cases, the closest relationships between Palearctic and sub-Saharan populations involve a sample from the rift zone (Uganda), suggesting that the progenitors of Palearctic D. melanogaster might have come from this region. Finally, we find a large excess of singleton polymorphisms in the full data set, which is best explained by a combination of population growth and purifying selection.

  9. The role of population inertia in predicting the outcome of stage-structured biological invasions.

    PubMed

    Guiver, Chris; Dreiwi, Hanan; Filannino, Donna-Maria; Hodgson, Dave; Lloyd, Stephanie; Townley, Stuart

    2015-07-01

    Deterministic dynamic models for coupled resident and invader populations are considered with the purpose of finding quantities that are effective at predicting when the invasive population will become established asymptotically. A key feature of the models considered is the stage-structure, meaning that the populations are described by vectors of discrete developmental stage- or age-classes. The vector structure permits exotic transient behaviour-phenomena not encountered in scalar models. Analysis using a linear Lyapunov function demonstrates that for the class of population models considered, a large so-called population inertia is indicative of successful invasion. Population inertia is an indicator of transient growth or decline. Furthermore, for the class of models considered, we find that the so-called invasion exponent, an existing index used in models for invasion, is not always a reliable comparative indicator of successful invasion. We highlight these findings through numerical examples and a biological interpretation of why this might be the case is discussed. Copyright © 2015. Published by Elsevier Inc.

  10. An agent-based computational model for tuberculosis spreading on age-structured populations

    NASA Astrophysics Data System (ADS)

    Graciani Rodrigues, C. C.; Espíndola, Aquino L.; Penna, T. J. P.

    2015-06-01

    In this work we present an agent-based computational model to study the spreading of the tuberculosis (TB) disease on age-structured populations. The model proposed is a merge of two previous models: an agent-based computational model for the spreading of tuberculosis and a bit-string model for biological aging. The combination of TB with the population aging, reproduces the coexistence of health states, as seen in real populations. In addition, the universal exponential behavior of mortalities curves is still preserved. Finally, the population distribution as function of age shows the prevalence of TB mostly in elders, for high efficacy treatments.

  11. Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation

    PubMed Central

    Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun

    2018-01-01

    Abstract Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice (Oryza rufipogon) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars (O. sativa), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression. PMID:29308123

  12. Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation.

    PubMed

    Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun; Lu, Bao-Rong

    2018-02-01

    Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice ( Oryza rufipogon ) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars ( O. sativa ), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression.

  13. Hierarchical spatial genetic structure in a distinct population segment of greater sage-grouse

    USGS Publications Warehouse

    Oyler-McCance, Sara J.; Casazza, Michael L.; Fike, Jennifer A.; Coates, Peter S.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus) within the Bi-State Management Zone (area along the border between Nevada and California) are geographically isolated on the southwestern edge of the species’ range. Previous research demonstrated that this population is genetically unique, with a high proportion of unique mitochondrial DNA (mtDNA) haplotypes and with significant differences in microsatellite allele frequencies compared to populations across the species’ range. As a result, this population was considered a distinct population segment (DPS) and was recently proposed for listing as threatened under the U.S. Endangered Species Act. A more comprehensive understanding of the boundaries of this genetically unique population (where the Bi-State population begins) and an examination of genetic structure within the Bi-State is needed to help guide effective management decisions. We collected DNA from eight sampling locales within the Bi-State (N = 181) and compared those samples to previously collected DNA from the two most proximal populations outside of the Bi-State DPS, generating mtDNA sequence data and amplifying 15 nuclear microsatellites. Both mtDNA and microsatellite analyses support the idea that the Bi-State DPS represents a genetically unique population, which has likely been separated for thousands of years. Seven mtDNA haplotypes were found exclusively in the Bi-State population and represented 73 % of individuals, while three haplotypes were shared with neighboring populations. In the microsatellite analyses both STRUCTURE and FCA separate the Bi-State from the neighboring populations. We also found genetic structure within the Bi-State as both types of data revealed differences between the northern and southern part of the Bi-State and there was evidence of isolation-by-distance. STRUCTURE revealed three subpopulations within the Bi-State consisting of the northern Pine Nut Mountains (PNa), mid Bi-State, and White Mountains (WM) following a

  14. Genetic variation and population structure of the mixed-mating cactus, Melocactus curvispinus (Cactaceae).

    PubMed

    Nassar, J M; Hamrick, J L; Fleming, T H

    2001-07-01

    Genetic diversity was measured in the mixed-mating cactus, Melocactus curvispinus, in Venezuela. Allozyme diversity was surveyed in 19 putative loci over 18 populations. Compared to other plant taxa, this cactus is rich in polymorphic loci (Ps=89.5%), with high numbers of alleles per polymorphic locus (APs=3.82), but moderate levels of heterozygosity (Hes=0.145). Substantial levels of inbreeding were detected across loci and populations at macrogeographic (FIS=0.348) and regional levels (FIS=0.194-0.402). Moderate levels of genetic differentiation among populations were detected at macrogeographical (FST=0.193) and regional (FST=0.084-0.187) scales, suggesting that gene flow is relatively restricted, but increases within regions without topographic barriers. The population genetic structure observed for this cactus was attributed to, at least, three factors: short-distance pollination and seed dispersal, the mixed-mating condition of the species, and genetic drift. High genetic identities between populations (I=0.942) supported the conspecific nature of all populations surveyed. The levels and patterns of genetic structure observed for M. curvispinus were consistent with its mating system and gene dispersal mechanisms.

  15. Population genetic structure of the prairie dog flea and plague vector, Oropsylla hirsuta.

    PubMed

    Brinkerhoff, R Jory; Martin, Andrew P; Jones, Ryan T; Collinge, Sharon K

    2011-01-01

    Oropsylla hirsuta is the primary flea of the black-tailed prairie dog and is a vector of the plague bacterium, Yersinia pestis. We examined the population genetic structure of O. hirsuta fleas collected from 11 prairie dog colonies, 7 of which had experienced a plague-associated die-off in 1994. In a sample of 332 O. hirsuta collected from 226 host individuals, we detected 24 unique haplotype sequences in a 480 nucleotide segment of the cytochrome oxidase II gene. We found significant overall population structure but we did not detect a signal of isolation by distance, suggesting that O. hirsuta may be able to disperse relatively quickly at the scale of this study. All 7 colonies that were recently decimated by plague showed signs of recent population expansion, whereas 3 of the 4 plague-negative colonies showed haplotype patterns consistent with stable populations. These results suggest that O. hirsuta populations are affected by plague-induced prairie dog die-offs and that flea dispersal among prairie dog colonies may not be dependent exclusively on dispersal of prairie dogs. Re-colonization following plague events from plague-free refugia may allow for rapid flea population expansion following plague epizootics.

  16. Analysis of Genetic Diversity and Population Structure of Rice Germplasm from North-Eastern Region of India and Development of a Core Germplasm Set

    PubMed Central

    Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Ahmad, Altaf; Singh, N. K.; Singh, Rakesh

    2014-01-01

    The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a

  17. 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

  18. A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe

    PubMed Central

    Gubili, Chrysoula; Sims, David W.; Veríssimo, Ana; Domenici, Paolo; Ellis, Jim; Grigoriou, Panagiotis; Johnson, Andrew F.; McHugh, Matthew; Neat, Francis; Satta, Andrea; Scarcella, Giuseppe; Serra-Pereira, Bárbara; Soldo, Alen; Genner, Martin J.; Griffiths, Andrew M.

    2014-01-01

    Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species. PMID:26064555

  19. A Genomic View of the Peopling and Population Structure of India

    PubMed Central

    Majumder, Partha P.; Basu, Analabha

    2015-01-01

    Recent advances in molecular and statistical genetics have enabled the reconstruction of human history by studying living humans. The ability to sequence and study DNA by calibrating the rate of accumulation of changes with evolutionary time has enabled robust inferences about how humans have evolved. These data indicate that modern humans evolved in Africa about 150,000 years ago and, consistent with paleontological evidence, migrated out of Africa. And through a series of settlements, demographic expansions, and further migrations, they populated the entire world. One of the first waves of migration from Africa was into India. Subsequent, more recent, waves of migration from other parts of the world have resulted in India being a genetic melting pot. Contemporary India has a rich tapestry of cultures and ecologies. There are about 400 tribal groups and more than 4000 groups of castes and subcastes, speaking dialects of 22 recognized languages belonging to four major language families. The contemporary social structure of Indian populations is characterized by endogamy with different degrees of porosity. The social structure, possibly coupled with large ecological heterogeneity, has resulted in considerable genetic diversity and local genetic differences within India. In this essay, we provide genetic evidence of how India may have been peopled, the nature and extent of its genetic diversity, and genetic structure among the extant populations of India. PMID:25147176

  20. Bipartite graphs as models of population structures in evolutionary multiplayer games.

    PubMed

    Peña, Jorge; Rochat, Yannick

    2012-01-01

    By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

  1. Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

    PubMed Central

    Peña, Jorge; Rochat, Yannick

    2012-01-01

    By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures. PMID:22970237

  2. 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

  3. Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae).

    PubMed

    Pometti, Carolina; Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

    2018-01-01

    The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees.

  4. Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae)

    PubMed Central

    Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

    2018-01-01

    The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees. PMID:29389969

  5. Dissecting gene-environment interactions: A penalized robust approach accounting for hierarchical structures.

    PubMed

    Wu, Cen; Jiang, Yu; Ren, Jie; Cui, Yuehua; Ma, Shuangge

    2018-02-10

    Identification of gene-environment (G × E) interactions associated with disease phenotypes has posed a great challenge in high-throughput cancer studies. The existing marginal identification methods have suffered from not being able to accommodate the joint effects of a large number of genetic variants, while some of the joint-effect methods have been limited by failing to respect the "main effects, interactions" hierarchy, by ignoring data contamination, and by using inefficient selection techniques under complex structural sparsity. In this article, we develop an effective penalization approach to identify important G × E interactions and main effects, which can account for the hierarchical structures of the 2 types of effects. Possible data contamination is accommodated by adopting the least absolute deviation loss function. The advantage of the proposed approach over the alternatives is convincingly demonstrated in both simulation and a case study on lung cancer prognosis with gene expression measurements and clinical covariates under the accelerated failure time model. Copyright © 2017 John Wiley & Sons, Ltd.

  6. 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

  7. Global population structure of the tope (Galeorhinus galeus) inferred by mitochondrial control region sequence data.

    PubMed

    Chabot, C L; Allen, L G

    2009-02-01

    In order to properly manage and conserve exploited shark species, detailed analyses of their population structure is needed. Global populations of Galeorhinus galeus are in decline due to the exploitation of the fishery over the past 80 years. Currently, the genetic structure of eastern Pacific populations of G. galeus is not known and recent observations in the northeastern Pacific suggest an increase in numbers. To evaluate gene flow among populations of G. galeus, 116 samples were collected and analysed from six geographically dispersed locations: Australia, North America, South Africa, South America (Argentina and Peru), and the UK. Analysis of 968 to 1006 bp of the 1068-bp mitochondrial control region revealed 38 unique haplotypes that were largely restricted to their collecting locality. Significant genetic structure was detected among populations (Phi(ST) = 0.84; P < 0.000001) and migration estimates were low (Nm = 0.05-0.97). Due to an apparent lack of migration, populations of G. galeus appear to be isolated from each other with little to no gene flow occurring among them. As a consequence of this isolation, increasing numbers of G. galeus in the northeastern Pacific can be best explained by local recruitment and not by input from geographically distant populations.

  8. On the structure-bounded growth processes in plant populations.

    PubMed

    Kilian, H G; Kazda, M; Király, F; Kaufmann, D; Kemkemer, R; Bartkowiak, D

    2010-07-01

    If growing cells in plants are considered to be composed of increments (ICs) an extended version of the law of mass action can be formulated. It evidences that growth of plants runs optimal if the reaction-entropy term (entropy times the absolute temperature) matches the contact energy of ICs. Since these energies are small, thermal molecular movements facilitate via relaxation the removal of structure disturbances. Stem diameter distributions exhibit extra fluctuations likely to be caused by permanent constraints. Since the signal-response system enables in principle perfect optimization only within finite-sized cell ensembles, plants comprising relatively large cell numbers form a network of size-limited subsystems. The maximal number of these constituents depends both on genetic and environmental factors. Accounting for logistical structure-dynamics interrelations, equations can be formulated to describe the bimodal growth curves of very different plants. The reproduction of the S-bended growth curves verifies that the relaxation modes with a broad structure-controlled distribution freeze successively until finally growth is fully blocked thus bringing about "continuous solidification".

  9. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus).

    PubMed

    Schield, Drew R; Adams, Richard H; Card, Daren C; Corbin, Andrew B; Jezkova, Tereza; Hales, Nicole R; Meik, Jesse M; Perry, Blair W; Spencer, Carol L; Smith, Lydia L; García, Gustavo Campillo; Bouzid, Nassima M; Strickland, Jason L; Parkinson, Christopher L; Borja, Miguel; Castañeda-Gaytán, Gamaliel; Bryson, Robert W; Flores-Villela, Oscar A; Mackessy, Stephen P; Castoe, Todd A

    2018-06-15

    The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scutulatus. We used mitochondrial DNA and thousands of nuclear loci from double-digest restriction site associated DNA sequencing to infer population genetic structure throughout the range of C. scutulatus, and to evaluate divergence times and gene flow between populations. We find strong support for several divergent mitochondrial and nuclear clades of C. scutulatus, including splits coincident with two major phylogeographic barriers: the Continental Divide and the elevational increase associated with the Central Mexican Plateau. We apply Bayesian clustering, phylogenetic inference, and coalescent-based species delimitation to our nuclear genetic data to test hypotheses of population structure. We also performed demographic analyses to test hypotheses relating to population divergence and gene flow. Collectively, our results support the existence of four distinct lineages within C. scutulatus, and genetically defined populations do not correspond with currently recognized subspecies ranges. Finally, we use approximate Bayesian computation to test hypotheses of divergence among multiple rattlesnake species groups distributed across the Continental Divide, and find evidence for co-divergence at this boundary during the mid-Pleistocene. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Genetic Diversity, Population Structure, and Resistance to Phytophthora capsici of a Worldwide Collection of Eggplant Germplasm

    PubMed Central

    Naegele, Rachel P.; Boyle, Samantha; Quesada-Ocampo, Lina M.; Hausbeck, Mary K.

    2014-01-01

    Eggplant (Solanum melongena L.) is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo), landraces and heirloom cultivars) from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluated for resistance to two Phytophthora capsici isolates seven days post inoculation. Only one accession (PI 413784) was completely resistant to both isolates evaluated. Partial resistance to Phytophthora fruit rot was found in accessions from all four eggplant species evaluated in this study. Genetic diversity and population structure were assessed using 22 polymorphic simple sequence repeats (SSRs). The polymorphism information content (PIC) for the population was moderate (0.49) in the population. Genetic analyses using the program STRUCTURE indicated the existence of four genetic clusters within the eggplant collection. Population structure was detected when eggplant lines were grouped by species, continent of origin, country of origin, fruit shape and disease resistance. PMID:24819601

  11. Population structure, spatial distribution and life-history traits of blacktip reef sharks Carcharhinus melanopterus.

    PubMed

    Mourier, J; Mills, S C; Planes, S

    2013-03-01

    During a survey of the population of blacktip reef shark Carcharhinus melanopterus in Moorea (French Polynesia) between 2007 and 2011, population structural characteristics were estimated from 268 individuals. Total length (LT ) ranged from 48 to 139 cm and 48 to 157 cm for males and females, respectively, demonstrating that the average LT of females was larger than that of males. The C. melanopterus population at Moorea showed an apparent spatial sexual segregation with females preferentially frequenting lagoons and males the fore-reefs. Mean growth rate was c. 6 cm year(-1) . Males reached sexual maturity at 111 cm LT . This study reports on the population characteristics of this widespread carcharhinid shark species and makes comparisons with other locations, confirming high geographic variability in the population structure of the species. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

  12. Blue cheese-making has shaped the population genetic structure of the mould Penicillium roqueforti

    PubMed Central

    Ropars, Jeanne; López-Villavicencio, Manuela; Snirc, Alodie; Lacoste, Sandrine; Giraud, Tatiana

    2017-01-01

    Background Penicillium roqueforti is a filamentous fungus used for making blue cheeses worldwide. It also occurs as a food spoiler and in silage and wood. Previous studies have revealed a strong population genetic structure, with specific traits associated with the different populations. Here, we used a large strain collection from worldwide cheeses published recently to investigate the genetic structure of P. roqueforti. Principal findings We found a genetic population structure in P. roqueforti that was consistent with previous studies, with two main genetic clusters (W+C+ and W-C-, i.e., with and without horizontal gene transferred regions CheesyTer and Wallaby). In addition, we detected a finer genetic subdivision that corresponded to the environment and to protected designation of origin (PDO), namely the Roquefort PDO. We indeed found evidence for eight genetic clusters, one of the cluster including only strains from other environments than cheeses, and another cluster encompassing only strains from the Roquefort PDO. The W-C- and W+C+ cheese clusters were not the most closely related ones, suggesting that there may have been two independent domestication events of P. roqueforti for making blue cheeses. Significance The additional population structure revealed here may be relevant for cheese-makers and for understanding the history of domestication in P. roqueforti. PMID:28248964

  13. Blue cheese-making has shaped the population genetic structure of the mould Penicillium roqueforti.

    PubMed

    Ropars, Jeanne; López-Villavicencio, Manuela; Snirc, Alodie; Lacoste, Sandrine; Giraud, Tatiana

    2017-01-01

    Penicillium roqueforti is a filamentous fungus used for making blue cheeses worldwide. It also occurs as a food spoiler and in silage and wood. Previous studies have revealed a strong population genetic structure, with specific traits associated with the different populations. Here, we used a large strain collection from worldwide cheeses published recently to investigate the genetic structure of P. roqueforti. We found a genetic population structure in P. roqueforti that was consistent with previous studies, with two main genetic clusters (W+C+ and W-C-, i.e., with and without horizontal gene transferred regions CheesyTer and Wallaby). In addition, we detected a finer genetic subdivision that corresponded to the environment and to protected designation of origin (PDO), namely the Roquefort PDO. We indeed found evidence for eight genetic clusters, one of the cluster including only strains from other environments than cheeses, and another cluster encompassing only strains from the Roquefort PDO. The W-C- and W+C+ cheese clusters were not the most closely related ones, suggesting that there may have been two independent domestication events of P. roqueforti for making blue cheeses. The additional population structure revealed here may be relevant for cheese-makers and for understanding the history of domestication in P. roqueforti.

  14. Population genetic structure and demographic history of the black fly vector, Simulium nodosum in Thailand.

    PubMed

    Chaiyasan, P; Pramual, P

    2016-09-01

    An understanding of the genetic structure and diversity of vector species is crucial for effective control and management. In this study, mitochondrial DNA sequences were used to examine the genetic structure, diversity and demographic history of a black fly vector, Simulium nodosum Puri (Diptera: Simuliidae), in Thailand. A total of 145 sequences were obtained from 10 sampling locations collected across geographical ranges in the country. Low genetic diversity was found in populations of S. nodosum that could be explained by the recent population history of this species. Demographic history analysis revealed a signature of demographic expansion dating back to only 2600-5200 years ago. Recent population expansion in S. nodosum possibly followed an increase in agriculture that enabled its hosts', humans and domestic animals, densities to increase. Alternatively, the Thai populations could be a derivative of an older expansion event in the more northern populations. Mitochondrial DNA genealogy revealed no genetically divergent lineages, which agrees with the previous cytogenetic study. Genetic structure analyses found that only 27% of the pairwise comparisons were significantly different. The most likely explanation for the pattern of genetic structuring is the effect of genetic drift because of recent colonization. © 2016 The Royal Entomological Society.

  15. Population structure of Aphis spiraecola (Hemiptera: Aphididae) on pear trees in China identified using microsatellites.

    PubMed

    Cao, Jinjun; Li, Jie; Niu, Jianqun; Liu, Xiaoxia; Zhang, Qingwen

    2012-04-01

    The spiraea aphid (Aphis spiraecola Patch) is a primary pest of fruit trees, particularly pear trees in China. Despite the economic importance of this pest, little is known about its genetic structure or its patterns of dispersal at local and regional scales; however, knowledge of these characteristics is important for establishing effective control strategies for this pest. The genetic variability of 431 individuals from 21 populations on pear trees in China was investigated using eight polymorphic microsatellite loci. The high polymorphism of these markers was evident from the expected heterozygosity value (He = 0.824) and the Polymorphism Information Content (PIC = 0.805), indicating that the spiraea aphid maintains a high level of genetic diversity. The analysis of molecular variance revealed a middle level of population differentiation (F(ST) = 0.1478) among A. spiraecola populations. This result is consistent with the results of the STRUCTURE analysis (K = 3), the unweighted pair-group method with arithmetic average tree and the Mantel test (r = 0.6392; P < 0.05). Our results indicate high levels of genetic exchange in the spiraea aphid, possibly facilitated by geography and climate. Our findings emphasize the importance of considering regional differences in studies of population structure, even when strong isolation-by-distance influences the genetic population structure of species.

  16. 12 CFR 715.8 - Requirements for verification of accounts and passbooks.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... selection: (ii) A sample which is representative of the population from which it was selected; (iii) An equal chance of selecting each dollar in the population; (iv) Sufficient accounts in both number and... consistent with GAAS if such methods provide for: (i) Sufficient accounts in both number and scope on which...

  17. Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean.

    PubMed

    Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

    2011-10-01

    Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species.

  18. Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

    PubMed Central

    Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

    2011-01-01

    Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species. PMID:21427750

  19. The Coach-Team Approach: An Introductory Accounting Instructional Alternative

    ERIC Educational Resources Information Center

    Wood, Lynette I.

    2012-01-01

    Many students approach the introductory accounting course with a great deal of apprehension. For the most part, the course is populated by non-accounting majors who often perceive accounting to be extremely difficult and may view the instructor-student relationship as adversarial. As a result, such students may be inclined to express their…

  20. Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): Natural replicate tests of post-Pleistocene evolution

    USGS Publications Warehouse

    Morris-Pocock, J. A.; Taylor, S.A.; Birt, T.P.; Damus, M.; Piatt, John F.; Warheit, K.I.; Friesen, Vicki L.

    2008-01-01

    Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east-west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east-west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa. ?? 2008 The Authors.

  1. A parametric ribcage geometry model accounting for variations among the adult population.

    PubMed

    Wang, Yulong; Cao, Libo; Bai, Zhonghao; Reed, Matthew P; Rupp, Jonathan D; Hoff, Carrie N; Hu, Jingwen

    2016-09-06

    The objective of this study is to develop a parametric ribcage model that can account for morphological variations among the adult population. Ribcage geometries, including 12 pair of ribs, sternum, and thoracic spine, were collected from CT scans of 101 adult subjects through image segmentation, landmark identification (1016 for each subject), symmetry adjustment, and template mesh mapping (26,180 elements for each subject). Generalized procrustes analysis (GPA), principal component analysis (PCA), and regression analysis were used to develop a parametric ribcage model, which can predict nodal locations of the template mesh according to age, sex, height, and body mass index (BMI). Two regression models, a quadratic model for estimating the ribcage size and a linear model for estimating the ribcage shape, were developed. The results showed that the ribcage size was dominated by the height (p=0.000) and age-sex-interaction (p=0.007) and the ribcage shape was significantly affected by the age (p=0.0005), sex (p=0.0002), height (p=0.0064) and BMI (p=0.0000). Along with proper assignment of cortical bone thickness, material properties and failure properties, this parametric ribcage model can directly serve as the mesh of finite element ribcage models for quantifying effects of human characteristics on thoracic injury risks. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

    PubMed

    Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

    2016-01-01

    Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat

  3. Population genetic structure in a social landscape: barley in a traditional Ethiopian agricultural system

    PubMed Central

    Samberg, Leah H; Fishman, Lila; Allendorf, Fred W

    2013-01-01

    Conservation strategies are increasingly driven by our understanding of the processes and patterns of gene flow across complex landscapes. The expansion of population genetic approaches into traditional agricultural systems requires understanding how social factors contribute to that landscape, and thus to gene flow. This study incorporates extensive farmer interviews and population genetic analysis of barley landraces (Hordeum vulgare) to build a holistic picture of farmer-mediated geneflow in an ancient, traditional agricultural system in the highlands of Ethiopia. We analyze barley samples at 14 microsatellite loci across sites at varying elevations and locations across a contiguous mountain range, and across farmer-identified barley types and management strategies. Genetic structure is analyzed using population-based and individual-based methods, including measures of population differentiation and genetic distance, multivariate Principal Coordinate Analysis, and Bayesian assignment tests. Phenotypic analysis links genetic patterns to traits identified by farmers. We find that differential farmer management strategies lead to markedly different patterns of population structure across elevation classes and barley types. The extent to which farmer seed management appears as a stronger determinant of spatial structure than the physical landscape highlights the need for incorporation of social, landscape, and genetic data for the design of conservation strategies in human-influenced landscapes. PMID:24478796

  4. 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…

  5. Temporal genetic population structure and interannual variation in migration behavior of Pacific Lamprey Entosphenus tridentatus

    USGS Publications Warehouse

    Clemens, Benjamin J.; Wyss, Lance A.; McCoun, Rebecca; Courter, Ian; Schwabe, Lawrence; Peery, Christopher; Schreck, Carl B.; Spice, Erin K.; Docker, Margaret F.

    2017-01-01

    Studies using neutral loci suggest that Pacific lamprey, Entosphenus tridentatus, lack strong spatial genetic population structure. However, it is unknown whether temporal genetic population structure exists. We tested whether adult Pacific lamprey: (1) show temporal genetic population structure; and (2) migrate different distances between years. We non-lethally sampled lamprey for DNA in 2009 and 2010 and used eight microsatellite loci to test for genetic population structure. We used telemetry to record the migration behaviors of these fish. Lamprey were assignable to three moderately differentiated genetic clusters (FST = 0.16–0.24 for all pairwise comparisons): one cluster was composed of individuals from 2009, and the other two contained individuals from 2010. The FST value between years was 0.13 and between genetic clusters within 2010 was 0.20. A total of 372 (72.5%) fish were detected multiple times during their migrations. Most fish (69.9%) remained in the mainstem Willamette River; the remaining 30.1% migrated into tributaries. Eighty-two lamprey exhibited multiple back-and-forth movements among tributaries and the mainstem, which may indicate searching behaviors. All migration distances were significantly greater in 2010, when the amplitude of river discharge was greater. Our data suggest genetic structuring between and within years that may reflect different cohorts.

  6. Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

    PubMed

    Xie, Guo-Wen; Wang, De-Lian; Yuan, Yong-Ming; Ge, Xue-Jun

    2005-04-01

    Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

  7. Microsatellites Reveal a High Population Structure in Triatoma infestans from Chuquisaca, Bolivia

    PubMed Central

    Pizarro, Juan Carlos; Gilligan, Lauren M.; Stevens, Lori

    2008-01-01

    Background For Chagas disease, the most serious infectious disease in the Americas, effective disease control depends on elimination of vectors through spraying with insecticides. Molecular genetic research can help vector control programs by identifying and characterizing vector populations and then developing effective intervention strategies. Methods and Findings The population genetic structure of Triatoma infestans (Hemiptera: Reduviidae), the main vector of Chagas disease in Bolivia, was investigated using a hierarchical sampling strategy. A total of 230 adults and nymphs from 23 localities throughout the department of Chuquisaca in Southern Bolivia were analyzed at ten microsatellite loci. Population structure, estimated using analysis of molecular variance (AMOVA) to estimate FST (infinite alleles model) and RST (stepwise mutation model), was significant between western and eastern regions within Chuquisaca and between insects collected in domestic and peri-domestic habitats. Genetic differentiation at three different hierarchical geographic levels was significant, even in the case of adjacent households within a single locality (R ST = 0.14, F ST = 0.07). On the largest geographic scale, among five communities up to 100 km apart, R ST = 0.12 and F ST = 0.06. Cluster analysis combined with assignment tests identified five clusters within the five communities. Conclusions Some houses are colonized by insects from several genetic clusters after spraying, whereas other households are colonized predominately by insects from a single cluster. Significant population structure, measured by both R ST and F ST, supports the hypothesis of poor dispersal ability and/or reduced migration of T. infestans. The high degree of genetic structure at small geographic scales, inferences from cluster analysis and assignment tests, and demographic data suggest reinfesting vectors are coming from nearby and from recrudescence (hatching of eggs that were laid

  8. Significant demographic and fine-scale genetic structure in expanding and senescing populations of the terrestrial orchid Cymbidium goeringii (Orchidaceae).

    PubMed

    Chung, Mi Yoon; Nason, John D; Chung, Myong Gi

    2011-12-01

    Fine-scale genetic structure (FSGS) in plants is influenced by variation in spatial and temporal demographic processes. To determine how demographic structure and FSGS change with stages of population succession, we studied replicate expanding and senescing populations of the Asian terrestrial orchid Cymbidium goeringii. We used spatial autocorrelation methods (O-ring and kinship statistics) to quantify spatial demographic structure and FSGS in two expanding and two senescing populations, also measuring genetic diversity and inbreeding in each. All populations exhibited significant aggregation of individuals and FSGS at short spatial scales. In expanding populations, this finding was associated with high recruitment rates, suggesting restricted seed dispersal. In senescing populations, recruitment was minimal, suggesting alternative mechanisms of aggregation, perhaps including spatial associations with mycorrhizal fungi. All populations had significant evidence of genetic bottlenecks, and inbreeding levels were consistently high. Our results indicate that different successional stages can generate similar patterns of spatial demographic and genetic structure, but as a consequence of different processes. These results contrast with the only other study of senescence effects on population genetic structure in an herbaceous perennial, which found little to no FSGS in senescing populations. With the exception of populations subject to mass collection by orchid sellers, significant FSGS is characteristic of the 16 terrestrial orchid species examined to date. From a conservation perspective, this result suggests that inference of orchid population history will benefit from analyses of both FSGS and demographic structure in combination with other ecological field data.

  9. Reclaiming Accountability in Teacher Education

    ERIC Educational Resources Information Center

    Cochran-Smith, Marilyn; Carney, Molly Cummings; Keefe, Elizabeth Stringer; Burton, Stephani; Chang, Wen-Chia; Fernández, M. Beatriz; Miller, Andrew F.; Sánchez, Juan Gabriel; Baker, Megina

    2018-01-01

    Teacher accountability has been a major strategy for "fixing" education for the last 2 decades. In this book, Cochran-Smith and her research team argue that it is time for teacher educators to reclaim accountability by adopting a new approach that features intelligent professional responsibility, challenges the structures and processes…

  10. Open Book Professional Accountancy Examinations

    ERIC Educational Resources Information Center

    Rowlands, J. E.; Forsyth, D.

    2006-01-01

    This article describes the structure and rationale for an open-book approach in professional accountancy examinations. The concept of knowledge management and the recognition that some knowledge ought to be embedded in the minds of professional accountants while other knowledge ought to be readily accessible and capable of application forms the…

  11. Evolutionary mixed games in structured populations: Cooperation and the benefits of heterogeneity

    NASA Astrophysics Data System (ADS)

    Amaral, Marco A.; Wardil, Lucas; Perc, Matjaž; da Silva, Jafferson K. L.

    2016-04-01

    Evolutionary games on networks traditionally involve the same game at each interaction. Here we depart from this assumption by considering mixed games, where the game played at each interaction is drawn uniformly at random from a set of two different games. While in well-mixed populations the random mixture of the two games is always equivalent to the average single game, in structured populations this is not always the case. We show that the outcome is, in fact, strongly dependent on the distance of separation of the two games in the parameter space. Effectively, this distance introduces payoff heterogeneity, and the average game is returned only if the heterogeneity is small. For higher levels of heterogeneity the distance to the average game grows, which often involves the promotion of cooperation. The presented results support preceding research that highlights the favorable role of heterogeneity regardless of its origin, and they also emphasize the importance of the population structure in amplifying facilitators of cooperation.

  12. Investigating the population structure and genetic differentiation of livestock guard dog breeds.

    PubMed

    Bigi, D; Marelli, S P; Liotta, L; Frattini, S; Talenti, A; Pagnacco, G; Polli, M; Crepaldi, P

    2018-01-14

    Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila's Dog, Maremma and Abruzzese Sheepdog and Mannara's Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Nei's and Reynold's genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

  13. Evolutionary mixed games in structured populations: Cooperation and the benefits of heterogeneity.

    PubMed

    Amaral, Marco A; Wardil, Lucas; Perc, Matjaž; da Silva, Jafferson K L

    2016-04-01

    Evolutionary games on networks traditionally involve the same game at each interaction. Here we depart from this assumption by considering mixed games, where the game played at each interaction is drawn uniformly at random from a set of two different games. While in well-mixed populations the random mixture of the two games is always equivalent to the average single game, in structured populations this is not always the case. We show that the outcome is, in fact, strongly dependent on the distance of separation of the two games in the parameter space. Effectively, this distance introduces payoff heterogeneity, and the average game is returned only if the heterogeneity is small. For higher levels of heterogeneity the distance to the average game grows, which often involves the promotion of cooperation. The presented results support preceding research that highlights the favorable role of heterogeneity regardless of its origin, and they also emphasize the importance of the population structure in amplifying facilitators of cooperation.

  14. RAPD variation and population genetic structure of Physalaemus cuvieri (Anura: Leptodactylidae) in Central Brazil.

    PubMed

    Telles, Mariana Pires de Campos; Bastos, Rogério Pereira; Soares, Thannya Nascimento; Resende, Lucileide Vilela; Diniz-Filho, José Alexandre Felizola

    2006-01-01

    Studies about the organization of the genetic variability and population structure in natural populations are used either to understand microevolutionary processes or the effects of isolation by human-inducted landscape modifications. In this paper, we analyzed patterns of genetic population structure using 126 RAPD loci scored for 214 individuals of Physalaemus cuvieri, sampled from 18 local populations. Around 97% of these loci were polymorphic. The among-population variation component (Phi(ST)) obtained by AMOVA was equal to 0.101 and theta B obtained using a Bayesian approach for dominant markers was 0.103. Genetic divergence, analyzed by Mantel spatial correlogram, revealed only a short-distance significant correlation between genetic and geographic distances. This is expected if low levels of population differentiation, due to high abundance buffering the effect of stochastic processes, are combined with low spatially restricted gene flow. Although this may be consistent with the current knowledge of species' biology, the spatial distribution of local populations observed in this study also suggest that, at least in part, recent human occupation and habitat fragmentation may also explain part of the interpopulational component of the genetic variation.

  15. Using ancestry-informative markers to identify fine structure across 15 populations of European origin.

    PubMed

    Huckins, Laura M; Boraska, Vesna; Franklin, Christopher S; Floyd, James A B; Southam, Lorraine; Sullivan, Patrick F; Bulik, Cynthia M; Collier, David A; Tyler-Smith, Chris; Zeggini, Eleftheria; Tachmazidou, Ioanna

    2014-10-01

    The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.

  16. Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian Oceans.

    PubMed

    Rosenbaum, Howard C; Pomilla, Cristina; Mendez, Martin; Leslie, Matthew S; Best, Peter B; Findlay, Ken P; Minton, Gianna; Ersts, Peter J; Collins, Timothy; Engel, Marcia H; Bonatto, Sandro L; Kotze, Deon P G H; Meÿer, Mike; Barendse, Jaco; Thornton, Meredith; Razafindrakoto, Yvette; Ngouessono, Solange; Vely, Michel; Kiszka, Jeremy

    2009-10-08

    Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.

  17. Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans

    PubMed Central

    Rosenbaum, Howard C.; Pomilla, Cristina; Mendez, Martin; Leslie, Matthew S.; Best, Peter B.; Findlay, Ken P.; Minton, Gianna; Ersts, Peter J.; Collins, Timothy; Engel, Marcia H.; Bonatto, Sandro L.; Kotze, Deon P. G. H.; Meÿer, Mike; Barendse, Jaco; Thornton, Meredith; Razafindrakoto, Yvette; Ngouessono, Solange; Vely, Michel; Kiszka, Jeremy

    2009-01-01

    Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region. PMID:19812698

  18. CONTRIBUTIONS OF SEXUAL AND ASEXUAL REPRODUCTION TO POPULATION STRUCTURE IN THE CLONAL SOFT CORAL, ALCYONIUM RUDYI.

    PubMed

    McFadden, Catherine S

    1997-02-01

    Numerous studies of population structure in sessile clonal marine invertebrates have demonstrated low genotypic diversity and nonequilibrium genotype frequencies within local populations that are monopolized by relatively few, highly replicated genets. All of the species studied to date produce planktonic sexual propagules capable of dispersing long distances; despite local genotypic disequilibria, populations are often panmictic over large geographic areas. The population structure paradigm these species represent may not be typical of the majority of clonal invertebrate groups, however, which are believed to produce highly philopatric sexual propagules. I used allozyme variation to examine the population structure of the temperate soft coral, Alcyonium rudyi, a typical clonal species whose sexually produced larvae and asexually produced ramets both have very low dispersal capabilities. Like other clonal plants and invertebrates, the local population dynamics of A. rudyi are dominated by asexual reproduction, and recruitment of new sexually produced genets occurs infrequently. As expected from its philopatric larval stage, estimates of genetic differentiation among populations of A. rudyi were highly significant at all spatial scales examined (mean θ = 0.300 among 20 populations spanning a 1100-km range), suggesting that genetic exchange seldom occurs among populations separated by as little as a few hundred meters. Mapping of multilocus allozyme genotypes within a dense aggregation of A. rudyi ramets confirmed that dispersal of asexual propagules is also very limited: members of the same genet usually remain within < 50 cm of one another on the same rock surface. Unlike most previously studied clonal invertebrates, populations of A. rudyi do not appear to be dominated by a few widespread genets: estimates of genotypic diversity (G o ) within 20 geographically distinct populations did not differ from expectations for outcrossing, sexual populations. Despite

  19. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus) population in north-eastern Europe.

    PubMed

    Hindrikson, Maris; Remm, Jaanus; Männil, Peep; Ozolins, Janis; Tammeleht, Egle; Saarma, Urmas

    2013-01-01

    Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus) population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  20. Retrospect and prospect of China's population.

    PubMed

    Liu, G

    1985-03-01

    This discussion of the population of China covers the reproductive pattern and fertility rate, the death pattern and mortality, age-sex structure of the population, population and employment, urbanization, migration, and the aging of the population. During the 1949-83 period, China almost doubled her population with an annual natural growth rate of 19/1000. China's reproductive pattern developed from early childbearing, short birth spacing and many births to later childbearing, longer birth spacing and fewer births. China's total fertility rate (TFR) was 5.8 in 1950 and 2.1 in 1983 with an annual decrease of 3%. The annual national income grew at a rate of 7.1%, while the annual growth rate of population 1.9% from 1950-82. Consequently, the national income per capita increased from 50 yuan in 1950 to 338 yuan in 1982. The major factor responsible for the changes is the remarkable decline in the rural fertility rate. The crude death rate dropped from 27.1/1000 in 1963 to 7.1 in 1983 and the infant mortality rate from 179.4/1000 live births in 1936 to 36.6 in 1981. There was also a significant change in the causes of death. Population aged 0-14 in China account for 33.6%, 15-49 for 51.3%, and 50 and over for 15.1% of the total population. China is in the process of transition from an expansive to a stationary population. The age-dependency ratio declined from 68.6% in 1953 and 79.4% in 1964 to 62.6% in 1982. Sex ratios recorded in the 3 population censuses are 105.99 in 1953, 105.45 in 1964, and 105.46 in 1982. Employment in both collective and individual economies did not expand until 1978. Sectoral, occupational, and industrial structures of population started to change rationally with the adjustment and reform of economic management system in 1978. The strategic stress on the employment of China's economically active population should be shifted from farming to diversified economy and urban industry and commerce, from sectors of industrial-agricultural production

  1. Accountable care organization readiness and academic medical centers.

    PubMed

    Berkowitz, Scott A; Pahira, Jennifer J

    2014-09-01

    As academic medical centers (AMCs) consider becoming accountable care organizations (ACOs) under Medicare, they must assess their readiness for this transition. Of the 253 Medicare ACOs prior to 2014, 51 (20%) are AMCs. Three critical components of ACO readiness are institutional and ACO structure, leadership, and governance; robust information technology and analytic systems; and care coordination and management to improve care delivery and health at the population level. All of these must be viewed through the lens of unique AMC mission-driven goals.There is clear benefit to developing and maintaining a centralized internal leadership when it comes to driving change within an ACO, yet there is also the need for broad stakeholder involvement. Other important structural features are an extensive primary care foundation; concomitant operation of a managed care plan or risk-bearing entity; or maintaining a close relationship with post-acute-care or skilled nursing facilities, which provide valuable expertise in coordinating care across the continuum. ACOs also require comprehensive and integrated data and analytic systems that provide meaningful population data to inform care teams in real time, promote quality improvement, and monitor spending trends. AMCs will require proven care coordination and management strategies within a population health framework and deployment of an innovative workforce.AMC core functions of providing high-quality subspecialty and primary care, generating new knowledge, and training future health care leaders can be well aligned with a transition to an ACO model. Further study of results from Medicare-related ACO programs and commercial ACOs will help define best practices.

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

    PubMed

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

    2017-01-01

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

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

    PubMed Central

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

    2017-01-01

    This study describes the genetic diversity and population structure of 194 native maize populations from 23 countries of Latin America and the Caribbean. The germplasm, representing 131 distinct landraces, was genetically characterized as population bulks using 28 SSR markers. Three main groups of maize germplasm were identified. The first, the Mexico and Southern Andes group, highlights the Pre-Columbian and modern exchange of germplasm between North and South America. The second group, Mesoamerica lowland, supports the hypothesis that two separate human migration events could have contributed to Caribbean maize germplasm. The third, the Andean group, displayed early introduction of maize into the Andes, with little mixing since then, other than a regional interchange zone active in the past. Events and activities in the pre- and post-Columbian Americas including the development and expansion of pre-Columbian cultures and the arrival of Europeans to the Americas are discussed in relation to the history of maize migration from its point of domestication in Mesoamerica to South America and the Caribbean through sea and land routes. PMID:28403177

  4. Consumptive and nonconsumptive effects of cannibalism in fluctuating age-structured populations.

    PubMed

    Wissinger, Scott A; Whiteman, Howard H; Denoël, Mathieu; Mumford, Miranda L; Aubee, Catherine B

    2010-02-01

    Theory and empirical studies suggest that cannibalism in age-structured populations can regulate recruitment depending on the intensity of intraspecific competition between cannibals and victims and the nature of the cannibalism window, i.e., which size classes interact as cannibals and victims. Here we report on a series of experiments that quantify that window for age-structured populations of salamander larvae and paedomorphic adults. We determined body size limits on cannibalism in microcosms and then the consumptive and nonconsumptive (injuries, foraging and activity, diet, growth) effects on victims in mesocosms with seminatural levels of habitat complexity and alternative prey. We found that cannibalism by the largest size classes (paedomorphs and > or = age 3+ yr larvae) occurs mainly on young-of-the-year (YOY) victims. Surviving YOY and other small larvae had increased injuries, reduced activity levels, and reduced growth rates in the presence of cannibals. Data on YOY survival in an experiment in which we manipulated the density of paedomorphs combined with historical data on the number of cannibals in natural populations indicate that dominant cohorts of paedomorphs can cause observed recruitment failures. Dietary data indicate that ontogenetic shifts in diet should preclude strong intraspecific competition between YOY and cannibals in this species. Thus our results are consistent with previous empirical and theoretical work that suggests that recruitment regulation by cannibalism is most likely when YOY are vulnerable to cannibalism but have low dietary overlap with cannibals. Understanding the role of cannibalism in regulating recruitment in salamander populations is timely, given the widespread occurrences of amphibian decline. Previous studies have focused on extrinsic (including anthropogenic) factors that affect amphibian population dynamics, whereas the data presented here combined with long-term field observations suggest the potential for

  5. Genetic structure of Chinese indigenous goats and the special geographical structure in the Southwest China as a geographic barrier driving the fragmentation of a large population.

    PubMed

    Wei, Caihong; Lu, Jian; Xu, Lingyang; Liu, Gang; Wang, Zhigang; Zhao, Fuping; Zhang, Li; Han, Xu; Du, Lixin; Liu, Chousheng

    2014-01-01

    China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demographic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers. Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (H(S) of 0.644) and high population diversity at the species level (H(T) value of 0.737) were estimated. Significant moderate population differentiation was detected (F(ST) value of 0.129). Significant excess homozygosity (F(IS) of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China. Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human's migration history throughout China. This study provides a fundamental genetic profile for the conservation of

  6. Role of stochastic processes in maintaining discrete strain structure in antigenically diverse pathogen populations.

    PubMed

    Buckee, Caroline O; Recker, Mario; Watkins, Eleanor R; Gupta, Sunetra

    2011-09-13

    Many highly diverse pathogen populations appear to exist stably as discrete antigenic types despite evidence of genetic exchange. It has been shown that this may arise as a consequence of immune selection on pathogen populations, causing them to segregate permanently into discrete nonoverlapping subsets of antigenic variants to minimize competition for available hosts. However, discrete antigenic strain structure tends to break down under conditions where there are unequal numbers of allelic variants at each locus. Here, we show that the inclusion of stochastic processes can lead to the stable recovery of discrete strain structure through loss of certain alleles. This explains how pathogen populations may continue to behave as independently transmitted strains despite inevitable asymmetries in allelic diversity of major antigens. We present evidence for this type of structuring across global meningococcal isolates in three diverse antigens that are currently being developed as vaccine components.

  7. Population dynamics and rural poverty.

    PubMed

    Fong, M S

    1985-01-01

    An overview of the relationship between demographic factors and rural poverty in developing countries is presented. The author examines both the micro- and macro-level perspectives of this relationship and the determinants and consequences of population growth. The author notes the prospects for a rapid increase in the rural labor force and considers its implications for the agricultural production structure and the need for institutional change. Consideration is also given to the continuing demand for high fertility at the family level and the role of infant and child mortality in the poverty cycle. "The paper concludes by drawing attention to the need for developing the mechanism for reconciliation of social and individual optima with respect to family size and population growth." The need for rural development projects that take demographic factors into account is stressed as is the need for effective population programs. (summary in FRE, ITA) excerpt

  8. Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies.

    PubMed

    Hoh, Boon-Peng; Deng, Lian; Julia-Ashazila, Mat Jusoh; Zuraihan, Zakaria; Nur-Hasnah, Ma'amor; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Endom, Ismail; Zilfalil, Bin Alwi; Khalid, Yusoff; Xu, Shuhua

    2015-07-22

    Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.

  9. Detection of stable community structures within gut microbiota co-occurrence networks from different human populations.

    PubMed

    Jackson, Matthew A; Bonder, Marc Jan; Kuncheva, Zhana; Zierer, Jonas; Fu, Jingyuan; Kurilshikov, Alexander; Wijmenga, Cisca; Zhernakova, Alexandra; Bell, Jordana T; Spector, Tim D; Steves, Claire J

    2018-01-01

    Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.

  10. Writing across the Accounting Curriculum: An Experiment.

    ERIC Educational Resources Information Center

    Riordan, Diane A.; Riordan, Michael P.; Sullivan, M. Cathy

    2000-01-01

    Develops a structured writing effectiveness program across three junior level courses in the accounting major (tax, cost, and financial accounting) to improve the writing skills of accounting students. Provides evidence that the writing across the curriculum project significantly improved the students' writing skills. (SC)

  11. Government Accounting Standards: Past, Present and Future.

    ERIC Educational Resources Information Center

    Harmer, W. Gary

    1993-01-01

    States that government accounting is the product of mixing together budget-oriented and accounting-oriented voices. Presents a history of governmental accounting including the groups involved. An organization chart describes the current standard-setting structure. Accomplishments that improve reporting operations results are listed. (MLF)

  12. The genetic structure of a Venturia inaequalis population in a heterogeneous host population composed of different Malus species

    PubMed Central

    2013-01-01

    Background Adaptation, which induces differentiation between populations in relation to environmental conditions, can initiate divergence. The balance between gene flow and selection determines the maintenance of such a structure in sympatry. Studying these two antagonistic forces in plant pathogens is made possible because of the high ability of pathogens to disperse and of the strong selective pressures exerted by their hosts. In this article, we analysed the genetic structure of the population of the apple scab fungus, Venturia inaequalis, in a heterogeneous environment composed of various Malus species. Inferences were drawn from microsatellite and AFLP data obtained from 114 strains sampled in a single orchard on nine different Malus species to determine the forces that shape the genetic structure of the pathogen. Results Using clustering methods, we first identified two specialist subpopulations: (i) a virulent subpopulation sampled on Malus trees carrying the Rvi6 resistance gene; and (ii) a subpopulation infecting only Malus trees that did not carry this resistance gene. A genome scan of loci on these two subpopulations did not detect any locus under selection. Additionally, we did not detect any other particular substructure linked to different hosts. However, an isolation-by-distance (IBD) pattern at the orchard scale revealed free gene flow within each subpopulation. Conclusions Our work shows a rare example of a very strong effect of a resistance gene on pathogen populations. Despite the high diversity of Malus hosts, the presence of Rvi6 seems sufficient to explain the observed genetic structure. Moreover, detection of an IBD pattern at the orchard scale revealed a very low average dispersal distance that is particularly significant for epidemiologists and landscape managers for the design of scab control strategies PMID:23497223

  13. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

    PubMed Central

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification. PMID:27535707

  14. Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure

    PubMed Central

    De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J.; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E. Richard; Soriani, Marco; Donati, Claudio

    2014-01-01

    One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen. PMID:24706866

  15. Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.

    PubMed

    De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E Richard; Soriani, Marco; Donati, Claudio

    2014-04-08

    One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen.

  16. Structure and genetic diversity of natural populations of Morus alba in the trans-Himalayan Ladakh region.

    PubMed

    Bajpai, Prabodh K; Warghat, Ashish R; Sharma, Ram Kumar; Yadav, Ashish; Thakur, Anil K; Srivastava, Ravi B; Stobdan, Tsering

    2014-04-01

    Sequence-related amplified polymorphism markers were used to assess the genetic structure in three natural populations of Morus alba from trans-Himalaya. Multilocation sampling was conducted across 14 collection sites. The overall genetic diversity estimates were high: percentage polymorphic loci 89.66%, Nei's gene diversity 0.2286, and Shannon's information index 0.2175. At a regional level, partitioning of variability assessed using analysis of molecular variance (AMOVA), revealed 80% variation within and 20% among collection sites. Pattern appeared in STRUCTURE, BARRIER, and AMOVA, clearly demonstrating gene flow between the Indus and Suru populations and a geographic barrier between the Indus-Suru and Nubra populations, which effectively hinders gene flow. The results showed significant genetic differentiation, population structure, high to restricted gene flow, and high genetic diversity. The assumption that samples collected from the three valleys represent three different populations does not hold true. The fragmentation present in trans-Himalaya was more natural and less anthropogenic.

  17. Microsatellite variation and genetic structuring in Mugil liza (Teleostei: Mugilidae) populations from Argentina and Brazil

    NASA Astrophysics Data System (ADS)

    Mai, Ana C. G.; Miño, Carolina I.; Marins, Luis F. F.; Monteiro-Neto, Cassiano; Miranda, Laura; Schwingel, Paulo R.; Lemos, Valéria M.; Gonzalez-Castro, Mariano; Castello, Jorge P.; Vieira, João P.

    2014-08-01

    The mullet Mugil liza is distributed along the Atlantic coast of South America, from Argentina to Venezuela, and it is heavily exploited in Brazil. We assessed patterns of distribution of neutral nuclear genetic variation in 250 samples from the Brazilian states of Rio de Janeiro, São Paulo, Santa Catarina and Rio Grande do Sul (latitudinal range of 23-31°S) and from Buenos Aires Province in Argentina (36°S). Nine microsatellite loci revealed 131 total alleles, 3-23 alleles per locus, He: 0.69 and Ho: 0.67. Significant genetic differentiation was observed between Rio de Janeiro samples (23°S) and those from all other locations, as indicated by FST, hierarchical analyses of genetic structure, Bayesian cluster analyses and assignment tests. The presence of two different demographic clusters better explains the allelic diversity observed in mullets from the southernmost portion of the Atlantic coast of Brazil and from Argentina. This may be taken into account when designing fisheries management plans involving Brazilian, Uruguayan and Argentinean M. liza populations.

  18. Homogenous Population Genetic Structure of the Non-Native Raccoon Dog (Nyctereutes procyonoides) in Europe as a Result of Rapid Population Expansion

    PubMed Central

    Drygala, Frank; Korablev, Nikolay; Ansorge, Hermann; Fickel, Joerns; Isomursu, Marja; Elmeros, Morten; Kowalczyk, Rafał; Baltrunaite, Laima; Balciauskas, Linas; Saarma, Urmas; Schulze, Christoph; Borkenhagen, Peter; Frantz, Alain C.

    2016-01-01

    The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species’ dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large ‘central’ population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations. PMID:27064784

  19. Effects of recruitment, growth, and exploitation on walleye population size structure in northern Wisconsin lakes

    USGS Publications Warehouse

    Hansen, Michael J.; Nate, Nancy A.

    2014-01-01

    We evaluated the dynamics of walleye Sander vitreus population size structure, as indexed by the proportional size distribution (PSD) of quality-length fish, in Escanaba Lake during 1967–2003 and in 204 other lakes in northern Wisconsin during 1990–2011. We estimated PSD from angler-caught walleyes in Escanaba Lake and from spring electrofishing in 204 other lakes, and then related PSD to annual estimates of recruitment to age-3, length at age 3, and annual angling exploitation rate. In Escanaba Lake during 1967–2003, annual estimates of PSD were highly dynamic, growth (positively) explained 35% of PSD variation, recruitment explained only 3% of PSD variation, and exploitation explained only 7% of PSD variation. In 204 other northern Wisconsin lakes during 1990–2011, PSD varied widely among lakes, recruitment (negatively) explained 29% of PSD variation, growth (positively) explained 21% of PSD variation, and exploitation explained only 4% of PSD variation. We conclude that population size structure was most strongly driven by recruitment and growth, rather than exploitation, in northern Wisconsin walleye populations. Studies of other species over wide spatial and temporal ranges of recruitment, growth, and mortality are needed to determine which dynamic rate most strongly influences population size structure of other species. Our findings indicate a need to be cautious about assuming exploitation is a strong driver of walleye population size structure.

  20. Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker.

    PubMed

    Zeng, Wei; Zhang, Limin; Fan, Pengchao; Guo, Jingjing; Peng, Yongzhen

    2018-05-01

    Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A 2 O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×10 9 cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A 2 O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter. Copyright © 2017. Published by Elsevier B.V.