Genomic Prediction of Gene Bank Wheat Landraces.

PubMed

Crossa, José; Jarquín, Diego; Franco, Jorge; Pérez-Rodríguez, Paulino; Burgueño, Juan; Saint-Pierre, Carolina; Vikram, Prashant; Sansaloni, Carolina; Petroli, Cesar; Akdemir, Deniz; Sneller, Clay; Reynolds, Matthew; Tattaris, Maria; Payne, Thomas; Guzman, Carlos; Peña, Roberto J; Wenzl, Peter; Singh, Sukhwinder

2016-07-07

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% testing (TST) (TRN20-TST80) sets, and (2) two types of core sets, "diversity" and "prediction", including 10% and 20%, respectively, of the total collections. Accounting for population structure decreased prediction accuracy by 15-20% as compared to prediction accuracy obtained when not accounting for population structure. Accounting for population structure gave prediction accuracies for traits evaluated in one environment for TRN20-TST80 that ranged from 0.407 to 0.677 for Mexican landraces, and from 0.166 to 0.662 for Iranian landraces. Prediction accuracy of the 20% diversity core set was similar to accuracies obtained for TRN20-TST80, ranging from 0.412 to 0.654 for Mexican landraces, and from 0.182 to 0.647 for Iranian landraces. The predictive core set gave similar prediction accuracy as the diversity core set for Mexican collections, but slightly lower for Iranian collections. Prediction accuracy when incorporating G × E for DTH and DTM for Mexican landraces for TRN20-TST80 was around 0.60, which is greater than without the G × E term. For Iranian landraces, accuracies were 0.55 for the G × E model with TRN20-TST80. Results show promising prediction accuracies for potential use in germplasm enhancement and rapid introgression of exotic germplasm into elite materials. Copyright © 2016 Crossa et al.

Genomic Prediction of Gene Bank Wheat Landraces

PubMed Central

Crossa, José; Jarquín, Diego; Franco, Jorge; Pérez-Rodríguez, Paulino; Burgueño, Juan; Saint-Pierre, Carolina; Vikram, Prashant; Sansaloni, Carolina; Petroli, Cesar; Akdemir, Deniz; Sneller, Clay; Reynolds, Matthew; Tattaris, Maria; Payne, Thomas; Guzman, Carlos; Peña, Roberto J.; Wenzl, Peter; Singh, Sukhwinder

2016-01-01

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% testing (TST) (TRN20-TST80) sets, and (2) two types of core sets, “diversity” and “prediction”, including 10% and 20%, respectively, of the total collections. Accounting for population structure decreased prediction accuracy by 15–20% as compared to prediction accuracy obtained when not accounting for population structure. Accounting for population structure gave prediction accuracies for traits evaluated in one environment for TRN20-TST80 that ranged from 0.407 to 0.677 for Mexican landraces, and from 0.166 to 0.662 for Iranian landraces. Prediction accuracy of the 20% diversity core set was similar to accuracies obtained for TRN20-TST80, ranging from 0.412 to 0.654 for Mexican landraces, and from 0.182 to 0.647 for Iranian landraces. The predictive core set gave similar prediction accuracy as the diversity core set for Mexican collections, but slightly lower for Iranian collections. Prediction accuracy when incorporating G × E for DTH and DTM for Mexican landraces for TRN20-TST80 was around 0.60, which is greater than without the G × E term. For Iranian landraces, accuracies were 0.55 for the G × E model with TRN20-TST80. Results show promising prediction accuracies for potential use in germplasm enhancement and rapid introgression of exotic germplasm into elite materials. PMID:27172218

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.

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.

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

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.

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

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.

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

Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations.

PubMed

Venables, Samantha J; Daniel, Runa; Sarre, Stephen D; Soedarsono, Nurtami; Sudoyo, Herawati; Suryadi, Helena; van Oorschot, Roland A H; Walsh, Simon J; Widodo, Putut T; McNevin, Dennis

2016-01-01

Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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.

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.

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

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...

The structural and functional connectivity of the grassland plant Lychnis flos-cuculi

PubMed Central

Aavik, T; Holderegger, R; Bolliger, J

2014-01-01

Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among populations as a measurement of functional connectivity. Second, we examined the effect of structural graph-theoretic connectivity measures on gene flow among populations and on genetic diversity within populations of L. flos-cuculi. Among landscape elements, forests hindered gene flow in L. flos-cuculi, whereas gene flow was independent of geographic distance. Among the structural graph-theoretic connectivity variables, only intrapopulation connectivity, which was based on population size, had a significant positive effect on gene flow, that is, more gene flow took place among larger populations. Unexpectedly, interpopulation connectivity of populations, which takes into account the spatial location and distance among populations, did not influence gene flow in L. flos-cuculi. However, higher observed heterozygosity and lower inbreeding was observed in populations characterised by higher structural interpopulation connectivity. This finding shows that a spatially coherent network of populations is significant for maintaining the genetic diversity of populations. Nevertheless, lack of significant relationships between gene flow and most of the structural connectivity measures suggests that structural connectivity does not necessarily correspond to functional connectivity. PMID:24253937

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.

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.

Sewall Wright, shifting balance theory, and the hardening of the modern synthesis.

PubMed

Ishida, Yoichi

2017-02-01

The period between the 1940s and 1960s saw the hardening of the modern synthesis in evolutionary biology. Gould and Provine argue that Wright's shifting balance theory of evolution hardened during this period. But their account does not do justice to Wright, who always regarded selection as acting together with drift. This paper presents a more adequate account of the development of Wright's shifting balance theory, paying particular attention to his application of the theory to the geographical distribution of flower color dimorphism in Linanthus parryae. The account shows that even in the heyday of the hardened synthesis, the balance or interaction of evolutionary factors, such as drift, selection, and migration, occupied pride of place in Wright's theory, and that between the 1940s and 1970s, Wright developed the theory of isolation by distance to quantitatively represent the structure of the Linanthus population, which he argued had the kind of structure posited by his shifting balance theory. In the end, Wright arrived at a sophisticated description of the structure of the Linanthus population, where the interaction between drift and selection varied spatially. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Coherent structure diffusivity in the edge region of Reversed Field Pinch experiments

NASA Astrophysics Data System (ADS)

Spolaore, M.; Antoni, V.; Spada, E.; Bergsåker, H.; Cavazzana, R.; Drake, J. R.; Martines, E.; Regnoli, G.; Serianni, G.; Vianello, N.

2005-01-01

Coherent structures emerging from the background turbulence have been detected by electrostatic measurements in the edge region of two Reversed Field Pinch experiments, RFX (Padua) and Extrap-T2R (Stockholm). Measurements have been performed by arrays of Langmuir probes which allowed simultaneous measurements of temperature, potential and density to be carried out. These structures have been interpreted as a dynamic balance of dipolar and monopolar vortices, whose relative population are found to depend on the local mean E × B flow shear. The contribution to the anomalous transport of these structures has been investigated and it has been found that the corresponding diffusion coeffcient accounts up to 50% of the total diffusivity. The experimental findings indicate that the diffusion coeffcient associated to the coherent structures depends on the relative population of the two types of vortices and is minimum when the two populations are equal. An interpretative model is proposed to explain this feature.

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.

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth.

PubMed

de la Cruz, Roberto; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás

2017-12-01

The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of front, which cannot be accounted for by the coarse-grained model. Such fluctuations have non-trivial effects on the wave velocity. Beyond the development of a new hybrid method, we thus conclude that birth-rate fluctuations are central to a quantitatively accurate description of invasive phenomena such as tumour growth.

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

NASA Astrophysics Data System (ADS)

de la Cruz, Roberto; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás

2017-12-01

The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of front, which cannot be accounted for by the coarse-grained model. Such fluctuations have non-trivial effects on the wave velocity. Beyond the development of a new hybrid method, we thus conclude that birth-rate fluctuations are central to a quantitatively accurate description of invasive phenomena such as tumour growth.

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.

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.

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.

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.

Origins and Divergence of the Roma (Gypsies)

PubMed Central

Gresham, David; Morar, Bharti; Underhill, Peter A.; Passarino, Giuseppe; Lin, Alice A.; Wise, Cheryl; Angelicheva, Dora; Calafell, Francesc; Oefner, Peter J.; Shen, Peidong; Tournev, Ivailo; de Pablo, Rosario; Kuĉinskas, Vaidutis; Perez-Lezaun, Anna; Marushiakova, Elena; Popov, Vesselin; Kalaydjieva, Luba

2001-01-01

The identification of a growing number of novel Mendelian disorders and private mutations in the Roma (Gypsies) points to their unique genetic heritage. Linguistic evidence suggests that they are of diverse Indian origins. Their social structure within Europe resembles that of the jatis of India, where the endogamous group, often defined by profession, is the primary unit. Genetic studies have reported dramatic differences in the frequencies of mutations and neutral polymorphisms in different Romani populations. However, these studies have not resolved ambiguities regarding the origins and relatedness of Romani populations. In this study, we examine the genetic structure of 14 well-defined Romani populations. Y-chromosome and mtDNA markers of different mutability were analyzed in a total of 275 individuals. Asian Y-chromosome haplogroup VI-68, defined by a mutation at the M82 locus, was present in all 14 populations and accounted for 44.8% of Romani Y chromosomes. Asian mtDNA-haplogroup M was also identified in all Romani populations and accounted for 26.5% of female lineages in the sample. Limited diversity within these two haplogroups, measured by the variation at eight short-tandem-repeat loci for the Y chromosome, and sequencing of the HVS1 for the mtDNA are consistent with a small group of founders splitting from a single ethnic population in the Indian subcontinent. Principal-components analysis and analysis of molecular variance indicate that genetic structure in extant endogamous Romani populations has been shaped by genetic drift and differential admixture and correlates with the migrational history of the Roma in Europe. By contrast, social organization and professional group divisions appear to be the product of a more recent restitution of the caste system of India. PMID:11704928

Origins and divergence of the Roma (gypsies).

PubMed

Gresham, D; Morar, B; Underhill, P A; Passarino, G; Lin, A A; Wise, C; Angelicheva, D; Calafell, F; Oefner, P J; Shen, P; Tournev, I; de Pablo, R; Kuĉinskas, V; Perez-Lezaun, A; Marushiakova, E; Popov, V; Kalaydjieva, L

2001-12-01

The identification of a growing number of novel Mendelian disorders and private mutations in the Roma (Gypsies) points to their unique genetic heritage. Linguistic evidence suggests that they are of diverse Indian origins. Their social structure within Europe resembles that of the jatis of India, where the endogamous group, often defined by profession, is the primary unit. Genetic studies have reported dramatic differences in the frequencies of mutations and neutral polymorphisms in different Romani populations. However, these studies have not resolved ambiguities regarding the origins and relatedness of Romani populations. In this study, we examine the genetic structure of 14 well-defined Romani populations. Y-chromosome and mtDNA markers of different mutability were analyzed in a total of 275 individuals. Asian Y-chromosome haplogroup VI-68, defined by a mutation at the M82 locus, was present in all 14 populations and accounted for 44.8% of Romani Y chromosomes. Asian mtDNA-haplogroup M was also identified in all Romani populations and accounted for 26.5% of female lineages in the sample. Limited diversity within these two haplogroups, measured by the variation at eight short-tandem-repeat loci for the Y chromosome, and sequencing of the HVS1 for the mtDNA are consistent with a small group of founders splitting from a single ethnic population in the Indian subcontinent. Principal-components analysis and analysis of molecular variance indicate that genetic structure in extant endogamous Romani populations has been shaped by genetic drift and differential admixture and correlates with the migrational history of the Roma in Europe. By contrast, social organization and professional group divisions appear to be the product of a more recent restitution of the caste system of India.

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.

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

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.

State dependence of noise correlations in macaque primary visual cortex

PubMed Central

Ecker, Alexander S.; Berens, Philipp; Cotton, R. James; Subramaniyan, Manivannan; Denfield, George H.; Cadwell, Cathryn R.; Smirnakis, Stelios M.; Bethge, Matthias; Tolias, Andreas S.

2014-01-01

Shared, trial-to-trial variability in neuronal populations has a strong impact on the accuracy of information processing in the brain. Estimates of the level of such noise correlations are diverse, ranging from 0.01 to 0.4, with little consensus on which factors account for these differences. Here we addressed one important factor that varied across studies, asking how anesthesia affects the population activity structure in macaque primary visual cortex. We found that under opioid anesthesia, activity was dominated by strong coordinated fluctuations on a timescale of 1–2 Hz, which were mostly absent in awake, fixating monkeys. Accounting for these global fluctuations markedly reduced correlations under anesthesia, matching those observed during wakefulness and reconciling earlier studies conducted under anesthesia and in awake animals. Our results show that internal signals, such as brain state transitions under anesthesia, can induce noise correlations, but can also be estimated and accounted for based on neuronal population activity. PMID:24698278

State dependence of noise correlations in macaque primary visual cortex.

PubMed

Ecker, Alexander S; Berens, Philipp; Cotton, R James; Subramaniyan, Manivannan; Denfield, George H; Cadwell, Cathryn R; Smirnakis, Stelios M; Bethge, Matthias; Tolias, Andreas S

2014-04-02

Shared, trial-to-trial variability in neuronal populations has a strong impact on the accuracy of information processing in the brain. Estimates of the level of such noise correlations are diverse, ranging from 0.01 to 0.4, with little consensus on which factors account for these differences. Here we addressed one important factor that varied across studies, asking how anesthesia affects the population activity structure in macaque primary visual cortex. We found that under opioid anesthesia, activity was dominated by strong coordinated fluctuations on a timescale of 1-2 Hz, which were mostly absent in awake, fixating monkeys. Accounting for these global fluctuations markedly reduced correlations under anesthesia, matching those observed during wakefulness and reconciling earlier studies conducted under anesthesia and in awake animals. Our results show that internal signals, such as brain state transitions under anesthesia, can induce noise correlations but can also be estimated and accounted for based on neuronal population activity. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

A kinetic theory for age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Chou, Tom; Greenman, Chris

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but they are structurally unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Conversely, current theories that include size-dependent population dynamics (e.g., carrying capacity) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a BBGKY-like hierarchy. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution. NSF.

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

Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

PubMed Central

Barbeau, Myriam A.

2016-01-01

Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

Quantifying inter- and intra-population niche variability using hierarchical bayesian stable isotope mixing models.

PubMed

Semmens, Brice X; Ward, Eric J; Moore, Jonathan W; Darimont, Chris T

2009-07-09

Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population.

Past climate change drives current genetic structure of an endangered freshwater mussel species.

PubMed

Inoue, Kentaro; Lang, Brian K; Berg, David J

2015-04-01

Historical-to-recent climate change and anthropogenic disturbance affect species distributions and genetic structure. The Rio Grande watershed of the United States and Mexico encompasses ecosystems that are intensively exploited, resulting in substantial degradation of aquatic habitats. While significant anthropogenic disturbances in the Rio Grande are recent, inhospitable conditions for freshwater organisms likely existed prior to such disturbances. A combination of anthropogenic and past climate factors may contribute to current distributions of aquatic fauna in the Rio Grande basin. We used mitochondrial DNA and 18 microsatellite loci to infer evolutionary history and genetic structure of an endangered freshwater mussel, Popenaias popeii, throughout the Rio Grande drainage. We estimated spatial connectivity and gene flow across extant populations of P. popeii and used ecological niche models (ENMs) and approximate Bayesian computation (ABC) to infer its evolutionary history during the Pleistocene. structure results recovered regional and local population clusters in the Rio Grande. ENMs predicted drastic reductions in suitable habitat during the last glacial maximum. ABC analyses suggested that regional population structure likely arose in this species during the mid-to-late Pleistocene and was followed by a late Pleistocene population bottleneck in New Mexico populations. The local population structure arose relatively recently, perhaps due to anthropogenic factors. Popenaias popeii, one of the few freshwater mussel species native to the Rio Grande basin, is a case study for understanding how both geological and anthropogenic factors shape current population genetic structure. Conservation strategies for this species should account for the fragmented nature of contemporary populations. © 2015 John Wiley & Sons Ltd.

Micro- and macro-geographic scale effect on the molecular imprint of selection and adaptation in Norway spruce.

PubMed

Scalfi, Marta; Mosca, Elena; Di Pierro, Erica Adele; Troggio, Michela; Vendramin, Giovanni Giuseppe; Sperisen, Christoph; La Porta, Nicola; Neale, David B

2014-01-01

Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and south-east Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based F(ST)-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the F(ST)-outlier methods detected together 11 F(ST)-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with F(ST)-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and environmental variation at both geographic scales. It also suggests that an integrative approach combining different outlier detection methods and population sampling at different geographic scales is useful to identify loci potentially involved in adaptation.

Micro- and Macro-Geographic Scale Effect on the Molecular Imprint of Selection and Adaptation in Norway Spruce

PubMed Central

Scalfi, Marta; Mosca, Elena; Di Pierro, Erica Adele; Troggio, Michela; Vendramin, Giovanni Giuseppe; Sperisen, Christoph; La Porta, Nicola; Neale, David B.

2014-01-01

Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and south-east Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based F ST-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the F ST-outlier methods detected together 11 F ST-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with F ST-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and environmental variation at both geographic scales. It also suggests that an integrative approach combining different outlier detection methods and population sampling at different geographic scales is useful to identify loci potentially involved in adaptation. PMID:25551624

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.

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

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.

Robust Identification of Local Adaptation from Allele Frequencies

PubMed Central

Günther, Torsten; Coop, Graham

2013-01-01

Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

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.

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.

Phenotypic variation as an indicator of pesticide stress in gudgeon: Accounting for confounding factors in the wild.

PubMed

Shinn, Cândida; Blanchet, Simon; Loot, Géraldine; Lek, Sovan; Grenouillet, Gaël

2015-12-15

The response of organisms to environmental stress is currently used in the assessment of ecosystem health. Morphological changes integrate the multiple effects of one or several stress factors upon the development of the exposed organisms. In a natural environment, many factors determine the patterns of morphological differentiation between individuals. However, few studies have sought to distinguish and measure the independent effect of these factors (genetic diversity and structure, spatial structuring of populations, physical-chemical conditions, etc.). Here we investigated the relationship between pesticide levels measured at 11 sites sampled in rivers of the Garonne river basin (SW France) and morphological changes of a freshwater fish species, the gudgeon (Gobio gobio). Each individual sampled was genotyped using 8 microsatellite markers and their phenotype characterized via 17 morphological traits. Our analysis detected a link between population genetic structure (revealed by a Bayesian method) and morphometry (linear discriminant analysis) of the studied populations. We then developed an original method based on general linear models using distance matrices, an extension of the partial Mantel test beyond 3 matrices. This method was used to test the relationship between contamination (toxicity index) and morphometry (PST of morphometric traits), taking into account (1) genetic differentiation between populations (FST), (2) geographical distances between sites, (3) site catchment area, and (4) various physical-chemical parameters for each sampling site. Upon removal of confounding effects, 3 of the 17 morphological traits studied were significantly correlated with pesticide toxicity, suggesting a response of these traits to the anthropogenic stress. These results underline the importance of taking into account the different sources of phenotypic variability between organisms when identifying the stress factors involved. The separation and quantification of the independent effect of such factors provides an interesting outlook regarding the use of these evaluation metrics as indicators of ecosystem health. Copyright © 2015 Elsevier B.V. All rights reserved.

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 heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus. PMID:24282578

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

Galactic gamma-ray observations and galactic structure

NASA Technical Reports Server (NTRS)

Stecker, F. W.

1975-01-01

Recent observations of gamma-rays originating in the galactic disk together with radio observations, support an emerging picture of the overall structure of our galaxy with higher interstellar gas densities and star formation rates in a region which corresponds to that of the inner arms. The emerging picture is one where molecular clouds make up the dominant constituent of the interstellar gas in the inner galaxy and play a key role in accounting for the gamma-rays and phenomena associated with the production of young stars and other population 1 objects. In this picture, cosmic rays are associated with supernovae and are primarily of galactic origin. These newly observed phenomena can be understood as consequences of the density wave theories of spiral structure. Based on these new developments, the suggestion is made that a new galactic population class, Population O, be added to the standard Populations 1 and 2 in order to recognize important differences in dynamics and distribution between diffuse galactic H1 and interstellar molecular clouds.

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.

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

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.

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 solution to infer fine-scale genetic patterns. PMID:23077494

Evidence that Magnetic Navigation and Geomagnetic Imprinting Shape Spatial Genetic Variation in Sea Turtles.

PubMed

Brothers, J Roger; Lohmann, Kenneth J

2018-04-23

The canonical drivers of population genetic structure, or spatial genetic variation, are isolation by distance and isolation by environment. Isolation by distance predicts that neighboring populations will be genetically similar and geographically distant populations will be genetically distinct [1]. Numerous examples also exist of isolation by environment, a phenomenon in which populations that inhabit similar environments (e.g., same elevation, temperature, or vegetation) are genetically similar even if they are distant, whereas populations that inhabit different environments are genetically distinct even when geographically close [2-4]. These dual models provide a widely accepted conceptual framework for understanding population structure [5-8]. Here, we present evidence for an additional, novel process that we call isolation by navigation, in which the navigational mechanism used by a long-distance migrant influences population structure independently of isolation by either distance or environment. Specifically, we investigated the population structure of loggerhead sea turtles (Caretta caretta) [9], which return to nest on their natal beaches by seeking out unique magnetic signatures along the coast-a behavior known as geomagnetic imprinting [10-12]. Results reveal that spatial variation in Earth's magnetic field strongly predicts genetic differentiation between nesting beaches, even when environmental similarities and geographic proximity are taken into account. The findings provide genetic corroboration of geomagnetic imprinting [10, 13]. Moreover, they provide strong evidence that geomagnetic imprinting and magnetic navigation help shape the population structure of sea turtles and perhaps numerous other long-distance migrants that return to their natal areas to reproduce [13-17]. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ecotoxicology and spatial modeling in population dynamics: an illustration with brown trout.

PubMed

Chaumot, Arnaud; Charles, Sandrine; Flammarion, Patrick; Auger, Pierre

2003-05-01

We developed a multiregion matrix population model to explore how the demography of a hypothetical brown trout population living in a river network varies in response to different spatial scenarios of cadmium contamination. Age structure, spatial distribution, and demographic and migration processes are taken into account in the model. Chronic or acute cadmium concentrations affect the demographic parameters at the scale of the river range. The outputs of the model constitute population-level end points (the asymptotic population growth rate, the stable age structure, and the asymptotic spatial distribution) that allow comparing the different spatial scenarios of contamination regarding the demographic response at the scale of the whole river network. An analysis of the sensitivity of these end points to lower order parameters enables us to link the local effects of cadmium to the global demographic behavior of the brown trout population. Such a link is of broad interest in the point of view of ecotoxicological management.

Individualism in plant populations: using stochastic differential equations to model individual neighbourhood-dependent plant growth.

PubMed

Lv, Qiming; Schneider, Manuel K; Pitchford, Jonathan W

2008-08-01

We study individual plant growth and size hierarchy formation in an experimental population of Arabidopsis thaliana, within an integrated analysis that explicitly accounts for size-dependent growth, size- and space-dependent competition, and environmental stochasticity. It is shown that a Gompertz-type stochastic differential equation (SDE) model, involving asymmetric competition kernels and a stochastic term which decreases with the logarithm of plant weight, efficiently describes individual plant growth, competition, and variability in the studied population. The model is evaluated within a Bayesian framework and compared to its deterministic counterpart, and to several simplified stochastic models, using distributional validation. We show that stochasticity is an important determinant of size hierarchy and that SDE models outperform the deterministic model if and only if structural components of competition (asymmetry; size- and space-dependence) are accounted for. Implications of these results are discussed in the context of plant ecology and in more general modelling situations.

Is Low Fertility Really a Problem? Population Aging, Dependency, and Consumption*

PubMed Central

2015-01-01

Longer lives and fertility far below the replacement level of 2.1 births per woman are leading to rapid population aging in many countries. Many observers are concerned that aging will adversely affect public finances and standards of living. Analysis of newly available National Transfer Accounts data for 40 countries shows that fertility well above replacement would typically be most beneficial for government budgets. However, fertility near replacement would be most beneficial for standards of living when the analysis includes the effects of age structure on families as well as governments. And fertility below replacement would maximize per capita consumption when the cost of providing capital for a growing labor force is taken into account. While low fertility will indeed challenge government programs and very low fertility undermines living standards, we find that moderately low fertility and population decline favor the broader material standard of living PMID:25301626

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.

Data integration for inference about spatial processes: A model-based approach to test and account for data inconsistency

PubMed Central

Pedrini, Paolo; Bragalanti, Natalia; Groff, Claudio

2017-01-01

Recently-developed methods that integrate multiple data sources arising from the same ecological processes have typically utilized structured data from well-defined sampling protocols (e.g., capture-recapture and telemetry). Despite this new methodological focus, the value of opportunistic data for improving inference about spatial ecological processes is unclear and, perhaps more importantly, no procedures are available to formally test whether parameter estimates are consistent across data sources and whether they are suitable for integration. Using data collected on the reintroduced brown bear population in the Italian Alps, a population of conservation importance, we combined data from three sources: traditional spatial capture-recapture data, telemetry data, and opportunistic data. We developed a fully integrated spatial capture-recapture (SCR) model that included a model-based test for data consistency to first compare model estimates using different combinations of data, and then, by acknowledging data-type differences, evaluate parameter consistency. We demonstrate that opportunistic data lend itself naturally to integration within the SCR framework and highlight the value of opportunistic data for improving inference about space use and population size. This is particularly relevant in studies of rare or elusive species, where the number of spatial encounters is usually small and where additional observations are of high value. In addition, our results highlight the importance of testing and accounting for inconsistencies in spatial information from structured and unstructured data so as to avoid the risk of spurious or averaged estimates of space use and consequently, of population size. Our work supports the use of a single modeling framework to combine spatially-referenced data while also accounting for parameter consistency. PMID:28973034

[Biologically active food supplements: legislative and regulator basis. Report 2].

PubMed

Sukhanov, B P; Kerimova, M G

2004-01-01

The article presents the history of food supplements' origin. The main requirements to them are given an account of the main legislative and normative documents, regulating the composition and considered as an important instrument for improving the structure and quality of nutrition of the population.

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 conserved and overall adaptability of the species is maintained.

River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community.

PubMed

Pilger, Tyler J; Gido, Keith B; Propst, David L; Whitney, James E; Turner, Thomas F

2017-05-01

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species' genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise F ST ) while explicitly accounting for intraspecific demographic influences on effective population size (N e ). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of N e was a strong predictor of pairwise F ST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases. © 2017 John Wiley & Sons Ltd.

Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish.

PubMed

Coleman, R A; Gauffre, B; Pavlova, A; Beheregaray, L B; Kearns, J; Lyon, J; Sasaki, M; Leblois, R; Sgro, C; Sunnucks, P

2018-06-01

Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (<13 km) genetic structure within reaches unimpeded by barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (F ST  = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (<100). Our study highlights that, in structured populations, the ability to detect short-term genetic effects from barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.

Plague circulation and population genetics of the reservoir Rattus rattus: the influence of topographic relief on the distribution of the disease within the Madagascan focus.

PubMed

Brouat, Carine; Rahelinirina, Soanandrasana; Loiseau, Anne; Rahalison, Lila; Rajerison, Minoariso; Laffly, Dominique; Handschumacher, Pascal; Duplantier, Jean-Marc

2013-01-01

Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150-200 km(2) within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations.

Estimating temporal trend in the presence of spatial complexity: A Bayesian hierarchical model for a wetland plant population undergoing restoration

USGS Publications Warehouse

Rodhouse, T.J.; Irvine, K.M.; Vierling, K.T.; Vierling, L.A.

2011-01-01

Monitoring programs that evaluate restoration and inform adaptive management are important for addressing environmental degradation. These efforts may be well served by spatially explicit hierarchical approaches to modeling because of unavoidable spatial structure inherited from past land use patterns and other factors. We developed Bayesian hierarchical models to estimate trends from annual density counts observed in a spatially structured wetland forb (Camassia quamash [camas]) population following the cessation of grazing and mowing on the study area, and in a separate reference population of camas. The restoration site was bisected by roads and drainage ditches, resulting in distinct subpopulations ("zones") with different land use histories. We modeled this spatial structure by fitting zone-specific intercepts and slopes. We allowed spatial covariance parameters in the model to vary by zone, as in stratified kriging, accommodating anisotropy and improving computation and biological interpretation. Trend estimates provided evidence of a positive effect of passive restoration, and the strength of evidence was influenced by the amount of spatial structure in the model. Allowing trends to vary among zones and accounting for topographic heterogeneity increased precision of trend estimates. Accounting for spatial autocorrelation shifted parameter coefficients in ways that varied among zones depending on strength of statistical shrinkage, autocorrelation and topographic heterogeneity-a phenomenon not widely described. Spatially explicit estimates of trend from hierarchical models will generally be more useful to land managers than pooled regional estimates and provide more realistic assessments of uncertainty. The ability to grapple with historical contingency is an appealing benefit of this approach.

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:23536759

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.

Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

PubMed

Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

2017-03-15

Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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.

Modeling Chagas Disease at Population Level to Explain Venezuela's Real Data

PubMed Central

González-Parra, Gilberto; Chen-Charpentier, Benito M.; Bermúdez, Moises

2015-01-01

Objectives In this paper we present an age-structured epidemiological model for Chagas disease. This model includes the interactions between human and vector populations that transmit Chagas disease. Methods The human population is divided into age groups since the proportion of infected individuals in this population changes with age as shown by real prevalence data. Moreover, the age-structured model allows more accurate information regarding the prevalence, which can help to design more specific control programs. We apply this proposed model to data from the country of Venezuela for two periods, 1961–1971, and 1961–1991 taking into account real demographic data for these periods. Results Numerical computer simulations are presented to show the suitability of the age-structured model to explain the real data regarding prevalence of Chagas disease in each of the age groups. In addition, a numerical simulation varying the death rate of the vector is done to illustrate prevention and control strategies against Chagas disease. Conclusion The proposed model can be used to determine the effect of control strategies in different age groups. PMID:26929912

Social network analysis of the genetic structure of Pacific islanders.

PubMed

Terrell, John Edward

2010-05-01

Social network analysis (SNA) is a body of theory and a set of relatively new computer-aided techniques used in the analysis and study of relational data. Recent studies of autosomal markers from over 40 human populations in the south-western Pacific have further documented the remarkable degree of genetic diversity in this part of the world. I report additional analysis using SNA methods contributing new controlled observations on the structuring of genetic diversity among these islanders. These SNA mappings are then compared with model-based network expectations derived from the geographic distances among the same populations. Previous studies found that genetic divergence among island Melanesian populations is organised by island, island size/topography, and position (coastal vs. inland), and that similarities observed correlate only weakly with an isolation-by-distance model. Using SNA methods, however, improves the resolution of among population comparison, and suggests that isolation by distance constrained by social networks together with position (coastal/inland) accounts for much of the population structuring observed. The multilocus data now available is also in accord with current thinking on the impact of major biogeographical transformations on prehistoric colonisation and post-settlement human interaction in Oceania.

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.

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.

Kinetic theory of age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Greenman, Chris D.; Chou, Tom

2016-01-01

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but are unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Stochastic theories that treat semi-Markov age-dependent processes using, e.g., the Bellman-Harris equation do not resolve a population's age structure and are unable to quantify population-size dependencies. Conversely, current theories that include size-dependent population dynamics (e.g., mathematical models that include carrying capacity such as the logistic equation) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new, fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a Bogoliubov--Born--Green--Kirkwood--Yvon-like hierarchy. Explicit solutions are derived in three limits: no birth, no death, and steady state. These are then compared with their corresponding mean-field results. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution.

Stochastic differential equations in NONMEM: implementation, application, and comparison with ordinary differential equations.

PubMed

Tornøe, Christoffer W; Overgaard, Rune V; Agersø, Henrik; Nielsen, Henrik A; Madsen, Henrik; Jonsson, E Niclas

2005-08-01

The objective of the present analysis was to explore the use of stochastic differential equations (SDEs) in population pharmacokinetic/pharmacodynamic (PK/PD) modeling. The intra-individual variability in nonlinear mixed-effects models based on SDEs is decomposed into two types of noise: a measurement and a system noise term. The measurement noise represents uncorrelated error due to, for example, assay error while the system noise accounts for structural misspecifications, approximations of the dynamical model, and true random physiological fluctuations. Since the system noise accounts for model misspecifications, the SDEs provide a diagnostic tool for model appropriateness. The focus of the article is on the implementation of the Extended Kalman Filter (EKF) in NONMEM for parameter estimation in SDE models. Various applications of SDEs in population PK/PD modeling are illustrated through a systematic model development example using clinical PK data of the gonadotropin releasing hormone (GnRH) antagonist degarelix. The dynamic noise estimates were used to track variations in model parameters and systematically build an absorption model for subcutaneously administered degarelix. The EKF-based algorithm was successfully implemented in NONMEM for parameter estimation in population PK/PD models described by systems of SDEs. The example indicated that it was possible to pinpoint structural model deficiencies, and that valuable information may be obtained by tracking unexplained variations in parameters.

[Genetic polymorphism of Gentiana lutea L. (Gentianaceae) populations from Chornohora Ridge of Ukrainian Carpathians].

PubMed

Mosula, M Z; Konvaliuk, I I; Mel'nyk, V M; Drobyk, N M; Tsaryk, I V; Nesteruk, Iu I; Kunakh, V A

2014-01-01

The features of genetic structure and level of diversity were investigated for G. lutea populations from Chornohora Ridge of Ukrainian Carpathians using RAPD- and ISSR-PCR. We have shown a high level of genetic diversity for investigated populations. The differences between populations account for 59-72% of the total genetic variation, whereas intrapopulation polymorphism makes up 28-41%. The relationships among genetic variability level and ecological-geographical conditions as well as biological features of the species were assumed to be possible. The obtained results indicate the genetic isolation of G. lutea Chornohora populations from Ukrainian Carpathians. Pozhyzhevska agropopulation was characterized by a high level of polymorphism that means the possibility to use artificial plantings of the investigated species for its conservation.

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.

Integrating macro- and micro-level approaches in the explanation of population change

PubMed Central

Billari, Francesco C.

2015-01-01

Demographers study population change across time and place, and traditionally they place a strong emphasis on a long-range view of population change. This paper builds on current reflections on how to structure the study of population change and proposes a two-stage perspective. The first stage, discovery, focuses on the production of novel evidence at the population level. The second stage, explanation, develops accounts of demographic change and tests how the action and interaction of individuals generate what is discovered in the first stage. This explanatory stage also provides the foundation for the prediction of demographic change. The transformation of micro-level actions and interactions into macro-level population outcomes is identified as a key challenge for the second stage. Specific instances of research are discussed. PMID:25912913

Recombination Processes and Nonlinear Markov Chains.

PubMed

Pirogov, Sergey; Rybko, Alexander; Kalinina, Anastasia; Gelfand, Mikhail

2016-09-01

Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.

Plague Circulation and Population Genetics of the Reservoir Rattus rattus: The Influence of Topographic Relief on the Distribution of the Disease within the Madagascan Focus

PubMed Central

Brouat, Carine; Rahelinirina, Soanandrasana; Loiseau, Anne; Rahalison, Lila; Rajerison, Minoariso; Laffly, Dominique; Handschumacher, Pascal; Duplantier, Jean-Marc

2013-01-01

Background Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. Methodology/Principal Findings We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150–200 km2 within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Conclusions/Significance Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations. PMID:23755317

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 diminishing barrier effect of mountain ridges. Additionally, a significant decrease in genetic diversity in the peripheral populations supports Mayr's central-peripheral population hypothesis.

Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease

PubMed Central

Brüniche-Olsen, Anna; Austin, Jeremy J.; Jones, Menna E.; Holland, Barbara R.; Burridge, Christopher P.

2016-01-01

Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer—devil facial tumor disease (DFTD)—that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series ‘restriction site associated DNA’ (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results. PMID:26930198

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.

Is it necessary to assume an apartheid-like social structure in Early Anglo-Saxon England?

PubMed

Pattison, John E

2008-11-07

It has recently been argued that there was an apartheid-like social structure operating in Early Anglo-Saxon England. This was proposed in order to explain the relatively high degree of similarity between Germanic-speaking areas of northwest Europe and England. Opinions vary as to whether there was a substantial Germanic invasion or only a relatively small number arrived in Britain during this period. Contrary to the assumption of limited intermarriage made in the apartheid simulation, there is evidence that significant mixing of the British and Germanic peoples occurred, and that the early law codes, such as that of King Ine of Wessex, could have deliberately encouraged such mixing. More importantly, the simulation did not take into account any northwest European immigration that arrived both before and after the Early Anglo-Saxon period. In view of the uncertainty of the places of origin of the various Germanic peoples, and their numbers and dates of arrival, the present study adopts an alternative approach to estimate the percentage of indigenous Britons in the current British population. It was found unnecessary to introduce any special social structure among the diverse Anglo-Saxon people in order to account for the estimates of northwest European intrusion into the British population.

Is it necessary to assume an apartheid-like social structure in Early Anglo-Saxon England?

PubMed Central

Pattison, John E

2008-01-01

It has recently been argued that there was an apartheid-like social structure operating in Early Anglo-Saxon England. This was proposed in order to explain the relatively high degree of similarity between Germanic-speaking areas of northwest Europe and England. Opinions vary as to whether there was a substantial Germanic invasion or only a relatively small number arrived in Britain during this period. Contrary to the assumption of limited intermarriage made in the apartheid simulation, there is evidence that significant mixing of the British and Germanic peoples occurred, and that the early law codes, such as that of King Ine of Wessex, could have deliberately encouraged such mixing. More importantly, the simulation did not take into account any northwest European immigration that arrived both before and after the Early Anglo-Saxon period. In view of the uncertainty of the places of origin of the various Germanic peoples, and their numbers and dates of arrival, the present study adopts an alternative approach to estimate the percentage of indigenous Britons in the current British population. It was found unnecessary to introduce any special social structure among the diverse Anglo-Saxon people in order to account for the estimates of northwest European intrusion into the British population. PMID:18430641

Consumption dynamics of the adult piscivorous fish community in Spirit Lake, Iowa

USGS Publications Warehouse

Liao, H.; Pierce, C.L.; Larscheid, J.G.

2004-01-01

At Spirit Lake, one of Iowa's most important fisheries, walleye Sander vitreus (formerly Stizostedion vitreum) is one of the most popular species with anglers. Despite a century of walleye stocking and management in Spirit Lake, walleye growth rate, size structure, and angler harvest continue to decline. Our purpose was to determine the magnitude and dynamics of walleye population consumption relative to those of other piscivorous species in Spirit Lake, which would allow managers to judge the feasibility of increasing the abundance, growth rate, and size structure of the walleye population. We quantified food consumption by the adult piscivorous fish community in Spirit Lake over a 3-year period. Data on population dynamics, diet, energy density, and water temperature from 1995 to 1997 were used in bioenergetics models to estimate total consumption by walleye, yellow perch Perca flavescens, smallmouth bass Micropterus dolomieu, largemouth bass Micropterus salmoides, black crappie Pomoxis nigromaculatus, and northern pike Esox lucius. Estimated annual consumption by the piscivorous community varied roughly fourfold, ranging from 154,752 kg in 1995 to 662,776 kg in 1997. Walleyes dominated total consumption, accounting for 68, 73, and 90% (1995-1997, respectively) of total food consumption. Walleyes were also the dominant consumers of fish, accounting for 76, 86, and 97% of piscivorous consumption; yellow perch followed, accounting for 16% of piscivorous consumption in 1995 and 12% in 1996. Yellow perch were the predominant fish prey species in all 3 years, accounting for 68, 52, and 36% of the total prey consumed. Natural reproduction is weak, so high walleye densities are maintained by intensive stocking. Walleye stocking drives piscivorous consumption in Spirit Lake, and yearly variation in the cannibalism of stocked walleye fry may be an important determinant of walleye year-class strength and angler success. Reducing walleye stocking intensity, varying stocking intensity from year to year, and attempting to match stocking intensity with the abundance of prey species other than walleye may improve the walleye fishery in Spirit Lake.

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.

Wherever I may roam: social viscosity and kin affiliation in a wild population despite natal dispersal

PubMed Central

Hinde, Camilla A.; Garroway, Colin J.; Sheldon, Ben C.

2016-01-01

Dispersal affects the social contexts individuals experience by redistributing individuals in space, and the nature of social interactions can have important fitness consequences. During the vagrancy stage of natal dispersal, after an individual has left its natal site and before it has settled to breed, social affiliations might be predicted by opportunities to associate (e.g., distance in space and time between natal points of origin) or kin preferences. We investigated the social structure of a population of juvenile great tits (Parus major) and asked whether social affiliations during vagrancy were predicted by 1) the distance between natal nest-boxes, 2) synchrony in fledge dates, and 3) accounting for spatial and temporal predictors, whether siblings tended to stay together. We show that association strength was affected predominantly by spatial proximity at fledging and, to a lesser extent, temporal proximity in birth dates. Independently of spatial and temporal effects, sibling pairs associated more often than expected by chance. Our results suggest that the structure of the winter population is shaped primarily by limits to dispersal through incomplete population mixing. In addition, our results reveal kin structure, and hence the scope for fitness-related interactions between particular classes of kin. Both spatial-mediated and socially mediated population structuring can have implications for our understanding of the evolution of sociality. PMID:27418755

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 discussed.

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.

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 to inaccuracies in the pedigree-based estimation of breed composition, which supported the case for using genomic information to complement and/or replace pedigree information when estimating breed composition. Comparison with a supervised analysis where purebreds are used as the training set suggest that accurate predictions can be achieved even in the absence of purebred population information.

Robust permanence for ecological equations with internal and external feedbacks.

PubMed

Patel, Swati; Schreiber, Sebastian J

2018-07-01

Species experience both internal feedbacks with endogenous factors such as trait evolution and external feedbacks with exogenous factors such as weather. These feedbacks can play an important role in determining whether populations persist or communities of species coexist. To provide a general mathematical framework for studying these effects, we develop a theorem for coexistence for ecological models accounting for internal and external feedbacks. Specifically, we use average Lyapunov functions and Morse decompositions to develop sufficient and necessary conditions for robust permanence, a form of coexistence robust to large perturbations of the population densities and small structural perturbations of the models. We illustrate how our results can be applied to verify permanence in non-autonomous models, structured population models, including those with frequency-dependent feedbacks, and models of eco-evolutionary dynamics. In these applications, we discuss how our results relate to previous results for models with particular types of feedbacks.

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

PubMed

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

Do Institutional Audits Stifle the Academic Enterprise or Enhance Accountability?

ERIC Educational Resources Information Center

Monnapula-Mapesela, M. L. E.; Moraka, T. S.

2008-01-01

The birth of democracy in South Africa resulted in the mammoth task of transforming the higher education sector. Policies, structures, procedures and processes underwent a review that hoped to align the system with the needs of the wider population of the country. Among other strategies that are used for this process are quality assurance…

[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

Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

PubMed

Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

2015-09-25

In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

Heterogeneous Structure of Stem Cells Dynamics: Statistical Models and Quantitative Predictions

PubMed Central

Bogdan, Paul; Deasy, Bridget M.; Gharaibeh, Burhan; Roehrs, Timo; Marculescu, Radu

2014-01-01

Understanding stem cell (SC) population dynamics is essential for developing models that can be used in basic science and medicine, to aid in predicting cells fate. These models can be used as tools e.g. in studying patho-physiological events at the cellular and tissue level, predicting (mal)functions along the developmental course, and personalized regenerative medicine. Using time-lapsed imaging and statistical tools, we show that the dynamics of SC populations involve a heterogeneous structure consisting of multiple sub-population behaviors. Using non-Gaussian statistical approaches, we identify the co-existence of fast and slow dividing subpopulations, and quiescent cells, in stem cells from three species. The mathematical analysis also shows that, instead of developing independently, SCs exhibit a time-dependent fractal behavior as they interact with each other through molecular and tactile signals. These findings suggest that more sophisticated models of SC dynamics should view SC populations as a collective and avoid the simplifying homogeneity assumption by accounting for the presence of more than one dividing sub-population, and their multi-fractal characteristics. PMID:24769917

The disease profile of poverty: morbidity and mortality in northern Uganda in the context of war, population displacement and HIV/AIDS.

PubMed

Accorsi, S; Fabiani, M; Nattabi, B; Corrado, B; Iriso, R; Ayella, E O; Pido, B; Onek, P A; Ogwang, M; Declich, S

2005-03-01

The population of Gulu District (northern Uganda) has been severely incapacitated by war, epidemics and social disruption. This study is aimed at describing disease patterns and trends in this area through a retrospective analysis of discharge records for 155205 in-patients of Lacor Hospital in the period 1992-2002. The burden of infectious diseases in childhood is overwhelming, with malaria accounting for the steepest increase in admissions. Admissions for war-related injuries and malnutrition fluctuated with the intensity of the war and the severity of famine. Emerging and re-emerging infections, such as HIV/AIDS, tuberculosis and Ebola, accounted for a heavy disease burden; however, there has been a trend for admissions related to HIV/AIDS and tuberculosis to decrease since the implementation of community-based services. Vulnerable groups (infants, children and women) accounted for 79.8% of admissions. Long-term war, population displacement, the collapse of social structures and the breakdown of the health system place people at a much greater risk of persistent, emerging and re-emerging infectious diseases, malnutrition and war-related injuries, shaping the 'disease profile of poverty'. Most of the disease burden results from infectious diseases of childhood, whose occurrence could be dramatically reduced by low-cost and effective preventive and curative interventions.

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

Ecological and genetic determinants of plasmid distribution in Escherichia coli.

PubMed

Medaney, Frances; Ellis, Richard J; Raymond, Ben

2016-11-01

Bacterial plasmids are important carriers of virulence and antibiotic resistance genes. Nevertheless, little is known of the determinants of plasmid distribution in bacterial populations. Here the factors affecting the diversity and distribution of the large plasmids of Escherichia coli were explored in cattle grazing on semi-natural grassland, a set of populations with low frequencies of antibiotic resistance genes. Critically, the population genetic structure of bacterial hosts was chararacterized. This revealed structured E. coli populations with high diversity between sites and individuals but low diversity within cattle hosts. Plasmid profiles, however, varied considerably within the same E. coli genotype. Both ecological and genetic factors affected plasmid distribution: plasmid profiles were affected by site, E. coli diversity, E. coli genotype and the presence of other large plasmids. Notably 3/26 E. coli serotypes accounted for half the observed plasmid-free isolates indicating that within species variation can substantially affect carriage of the major conjugative plasmids. The observed population structure suggest that most of the opportunities for within species plasmid transfer occur between different individuals of the same genotype and support recent experimental work indicating that plasmid-host coevolution, and epistatic interactions on fitness costs are likely to be important in determining occupancy. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

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.

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.

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.

Genetic Structure of First Nation Communities in the Pacific Northwest.

PubMed

Hughes, Cris E; Rogers, Mary P; Owings, Amanda C; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; Williams, Theresa; Goldberg, Dena; Labuda, Damian; Smith, David Glenn; Cybulski, Jerome S; Malhi, Ripan S

2016-10-01

This study presents genetic data for nine Native American populations from northern North America. Analyses of genetic variation focus on the Pacific Northwest (PNW). Using mitochondrial, Y chromosomal, and autosomal DNA variants, we aimed to more closely address the relationships of geography and language with present genetic diversity among the regional PNW Native American populations. Patterns of genetic diversity exhibited by the three genetic systems were consistent with our hypotheses: genetic variation was more strongly explained by geographic proximity than by linguistic structure. Our findings were corroborated through a variety on analytic approaches, with the unrooted trees for the three genetic systems consistently separating inland from coastal PNW populations. Furthermore, analyses of molecular variance support the trends exhibited by the unrooted trees, with geographic partitioning of PNW populations (F CT = 19.43%, p = 0.010 ± 0.009) accounting for over twice as much of the observed genetic variation as linguistic partitioning of the same populations (F CT = 9.15%, p = 0.193 ± 0.013). These findings demonstrate a consensus with previous PNW population studies examining the relationships of genome-wide variation, mitochondrial haplogroup frequencies, and skeletal morphology with geography and language.

Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

PubMed Central

2013-01-01

Background Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. Conclusions When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied. PMID:23281913

Beyond sex differences: new approaches for thinking about variation in brain structure and function

PubMed Central

Joel, Daphna; Fausto-Sterling, Anne

2016-01-01

In the study of variation in brain structure and function that might relate to sex and gender, language matters because it frames our research questions and methods. In this article, we offer an approach to thinking about variation in brain structure and function that pulls us outside the sex differences formulation. We argue that the existence of differences between the brains of males and females does not unravel the relations between sex and the brain nor is it sufficient to characterize a population of brains. Such characterization is necessary for studying sex effects on the brain as well as for studying brain structure and function in general. Animal studies show that sex interacts with environmental, developmental and genetic factors to affect the brain. Studies of humans further suggest that human brains are better described as belonging to a single heterogeneous population rather than two distinct populations. We discuss the implications of these observations for studies of brain and behaviour in humans and in laboratory animals. We believe that studying sex effects in context and developing or adopting analytical methods that take into account the heterogeneity of the brain are crucial for the advancement of human health and well-being. PMID:26833844

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 study sample. Ethnicity apparently did not introduce differential allele frequencies that may affect analysis and interpretation of linkage and association studies. These findings, although not entirely surprising given the geographical proximity of these groups, provide important insights into the genetic relationships between the ethnic groups studied and confirm previous results that showed close genetic relationship between most studied West African groups. PMID:15978124

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 social determinants of health, and thus potentially improve the readiness of clinicians to address the complex factors that shape the health of homeless populations. © Blackwell Publishing Ltd 2013.

Ecological Modeling of Aedes aegypti (L.) Pupal Production in Rural Kamphaeng Phet, Thailand

PubMed Central

Aldstadt, Jared; Koenraadt, Constantianus J. M.; Fansiri, Thanyalak; Kijchalao, Udom; Richardson, Jason; Jones, James W.; Scott, Thomas W.

2011-01-01

Background Aedes aegypti (L.) is the primary vector of dengue, the most important arboviral infection globally. Until an effective vaccine is licensed and rigorously administered, Ae. aegypti control remains the principal tool in preventing and curtailing dengue transmission. Accurate predictions of vector populations are required to assess control methods and develop effective population reduction strategies. Ae. aegypti develops primarily in artificial water holding containers. Release recapture studies indicate that most adult Ae. aegypti do not disperse over long distances. We expect, therefore, that containers in an area of high development site density are more likely to be oviposition sites and to be more frequently used as oviposition sites than containers that are relatively isolated from other development sites. After accounting for individual container characteristics, containers more frequently used as oviposition sites are likely to produce adult mosquitoes consistently and at a higher rate. To this point, most studies of Ae. aegypti populations ignore the spatial density of larval development sites. Methodology Pupal surveys were carried out from 2004 to 2007 in rural Kamphaeng Phet, Thailand. In total, 84,840 samples of water holding containers were used to estimate model parameters. Regression modeling was used to assess the effect of larval development site density, access to piped water, and seasonal variation on container productivity. A varying-coefficients model was employed to account for the large differences in productivity between container types. A two-part modeling structure, called a hurdle model, accounts for the large number of zeroes and overdispersion present in pupal population counts. Findings The number of suitable larval development sites and their density in the environment were the primary determinants of the distribution and abundance of Ae. aegypti pupae. The productivity of most container types increased significantly as habitat density increased. An ecological approach, accounting for development site density, is appropriate for predicting Ae. aegypti population levels and developing efficient vector control programs. PMID:21267055

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.

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

[Polymorphic biochemical systems in the population of immigrant inhabitants of the northeastern USSR. II. Genotypic distances between groups of persons with a varying duration of living under extreme environmental conditions].

PubMed

Solovenchuk, L L

1983-08-01

Analysis of the differences in the groups examined for phenotypes and genes has shown that the longer dwelling in the regions of the extreme conditions, the greater changes are in the genetic structure of separate selections with "retreating" from middle latitudes'population and "approaching" the aboriginal one of the North-East. This "dynamics" is mostly pronounced in men and groups characterized by very long dwelling in the region; the differences between representatives of both sexes are maximal. A slightly more isolated position is occupied by the genetic structure of individuals living in the North from the birth. The data obtained allow to assume that the genetic structure of the man's population being formed in the extreme conditions, tends to the ecological fit on account of the selectivity of migratory behaviour. The ecological fit of separate genotypes may well be assumed to be different for representatives of both sexes and on different stages of ontogenesis.

Modeling the effects of space structure and combination therapies on phenotypic heterogeneity and drug resistance in solid tumors.

PubMed

Lorz, Alexander; Lorenzi, Tommaso; Clairambault, Jean; Escargueil, Alexandre; Perthame, Benoît

2015-01-01

Histopathological evidence supports the idea that the emergence of phenotypic heterogeneity and resistance to cytotoxic drugs can be considered as a process of selection in tumor cell populations. In this framework, can we explain intra-tumor heterogeneity in terms of selection driven by the local cell environment? Can we overcome the emergence of resistance and favor the eradication of cancer cells by using combination therapies? Bearing these questions in mind, we develop a model describing cell dynamics inside a tumor spheroid under the effects of cytotoxic and cytostatic drugs. Cancer cells are assumed to be structured as a population by two real variables standing for space position and the expression level of a phenotype of resistance to cytotoxic drugs. The model takes explicitly into account the dynamics of resources and anticancer drugs as well as their interactions with the cell population under treatment. We analyze the effects of space structure and combination therapies on phenotypic heterogeneity and chemotherapeutic resistance. Furthermore, we study the efficacy of combined therapy protocols based on constant infusion and bang-bang delivery of cytotoxic and cytostatic drugs.

Body Dissatisfaction and Eating-Related Problems on the College Campus: Usefulness of the Eating Disorder Inventory with a Nonclinical Population.

ERIC Educational Resources Information Center

Klemchuk, Helen P.; And Others

1990-01-01

Administered Eating Disorder Inventory (EDI) to 1,506 female undergraduates. Found very high rates of body dissatisfaction. EDI factor analysis yielded six-factor structure accounting for 41 percent of variance. Two risk groups were identified on basis of extreme EDI factor scores: body-dissatisfied group and binge-purge group with poor…

Invasion and Persistence of Infectious Agents in Fragmented Host Populations

PubMed Central

Jesse, Marieke; Mazzucco, Rupert; Dieckmann, Ulf; Heesterbeek, Hans; Metz, Johan A. J.

2011-01-01

One of the important questions in understanding infectious diseases and their prevention and control is how infectious agents can invade and become endemic in a host population. A ubiquitous feature of natural populations is that they are spatially fragmented, resulting in relatively homogeneous local populations inhabiting patches connected by the migration of hosts. Such fragmented population structures are studied extensively with metapopulation models. Being able to define and calculate an indicator for the success of invasion and persistence of an infectious agent is essential for obtaining general qualitative insights into infection dynamics, for the comparison of prevention and control scenarios, and for quantitative insights into specific systems. For homogeneous populations, the basic reproduction ratio plays this role. For metapopulations, defining such an ‘invasion indicator’ is not straightforward. Some indicators have been defined for specific situations, e.g., the household reproduction number . However, these existing indicators often fail to account for host demography and especially host migration. Here we show how to calculate a more broadly applicable indicator for the invasion and persistence of infectious agents in a host metapopulation of equally connected patches, for a wide range of possible epidemiological models. A strong feature of our method is that it explicitly accounts for host demography and host migration. Using a simple compartmental system as an example, we illustrate how can be calculated and expressed in terms of the key determinants of epidemiological dynamics. PMID:21980339

Relative importance of pollen and seed dispersal across a Neotropical mountain landscape for an epiphytic orchid.

PubMed

Kartzinel, Tyler R; Shefferson, Richard P; Trapnell, Dorset W

2013-12-01

Populations of many species are isolated within narrow elevation bands of Neotropical mountain habitat, and how well dispersal maintains genetic connectivity is unknown. We asked whether genetic structure of an epiphytic orchid, Epidendrum firmum, corresponds to gaps between Costa Rican mountain ranges, and how these gaps influence pollen and seed flow. We predicted that significant genetic structure exists among mountain ranges due to different colonization histories and limited gene flow. Furthermore, we predicted that pollen movement contributes more to gene flow than seeds because seeds are released into strong winds perpendicular to the narrow northwest-southeast species distribution, while the likely pollinators are strong fliers. Individuals from 12 populations and three mountain ranges were genotyped with nuclear microsatellites (nDNA) and chloroplast sequences (cpDNA). Genetic diversity was high for both markers, while nDNA genetic structure was low (FSTn  = 0.020) and cpDNA structure was moderate (FSTc  = 0.443). Significant cpDNA barriers occurred within and among mountain ranges, but nDNA barriers were not significant after accounting for geographic distance. Consistent with these contrasting patterns of genetic structure, pollen contributes substantially more to gene flow among populations than seed (mp /ms  = 46). Pollinators mediated extensive gene flow, eroding nDNA colonization footprints, while seed flow was comparatively limited, possibly due to directional prevailing winds across linearly distributed populations. Dispersal traits alone may not accurately inform predictions about gene flow or genetic structure, supporting the need for research into the potentially crucial role of pollinators and landscape context in gene flow among isolated populations. © 2013 John Wiley & Sons Ltd.

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.

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.

Radiation exposure in the remote period after the Chernobyl accident caused oxidative stress and genetic effects in Scots pine populations

NASA Astrophysics Data System (ADS)

Volkova, Polina Yu.; Geras'Kin, Stanislav A.; Kazakova, Elizaveta A.

2017-02-01

Even 30 years after the Chernobyl accident, biological effects of irradiation are observed in the chronically exposed Scots pine populations. Chronic radiation exposure at dose rates above 50 mGy•yr-1 caused oxidative stress and led to the increase of antioxidants concentrations in these populations. Genetic variability was examined for 6 enzymes and 14 enzymatic loci of 6 Scots pine populations. Dose rates over 10 mGy•yr-1 caused the increased frequency of mutations and changes in genetic structure of Scots pine populations. However, the same dose rates had no effect on enzymatic activities. The results indicate that even relatively low dose rates of radiation can be considered as an ecological factor which should be taken into account for ecological management and radiation protection of biota species.

A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population

PubMed Central

Tashi, Tsewang; Lorenzo, Felipe Ramos; Feusier, Julie Ellen; Mir, Hyder

2016-01-01

The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas. PMID:27490348

Ionization competition effects on population distribution and radiative opacity of mixture plasmas

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

Li, Yongjun; Gao, Cheng; Tian, Qinyun

2015-11-15

Ionization competition arising from the electronic shell structures of various atomic species in the mixture plasmas was investigated, taking SiO{sub 2} as an example. Using a detailed-level-accounting approximation, we studied the competition effects on the charge state population distribution and spectrally resolved and Planck and Rosseland mean radiative opacities of mixture plasmas. A set of coupled equations for ionization equilibria that include all components of the mixture plasmas are solved to determine the population distributions. For a given plasma density, competition effects are found at three distinct temperature ranges, corresponding to the ionization of M-, L-, and K-shell electrons ofmore » Si. Taking the effects into account, the spectrally resolved and Planck and Rosseland mean opacities are systematically investigated over a wide range of plasma densities and temperatures. For a given mass density, the Rosseland mean decreases monotonically with plasma temperature, whereas Planck mean does not. Although the overall trend is a decrease, the Planck mean increases over a finite intermediate temperature regime. A comparison with the available experimental and theoretical results is made.« less

Veridical mapping in savant abilities, absolute pitch, and synesthesia: an autism case study

PubMed Central

Bouvet, Lucie; Donnadieu, Sophie; Valdois, Sylviane; Caron, Chantal; Dawson, Michelle; Mottron, Laurent

2014-01-01

An enhanced role and autonomy of perception are prominent in autism. Furthermore, savant abilities, absolute pitch, and synesthesia are all more commonly found in autistic individuals than in the typical population. The mechanism of veridical mapping has been proposed to account for how enhanced perception in autism leads to the high prevalence of these three phenomena and their structural similarity. Veridical mapping entails functional rededication of perceptual brain regions to higher order cognitive operations, allowing the enhanced detection and memorization of isomorphisms between perceptual and non-perceptual structures across multiple scales. In this paper, we present FC, an autistic individual who possesses several savant abilities in addition to both absolute pitch and synesthesia-like associations. The co-occurrence in FC of abilities, some of them rare, which share the same structure, as well as FC’s own accounts of their development, together suggest the importance of veridical mapping in the atypical range and nature of abilities displayed by autistic people. PMID:24600416

GENETIC STRUCTURE OF NORWAY SPRUCE (PICEA ABIES): CONCORDANCE OF MORPHOLOGICAL AND ALLOZYMIC VARIATION.

PubMed

Lagercrantz, Ulf; Ryman, Nils

1990-02-01

This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (G ST = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases. We suggest that the population structure largely reflects relatively recent historical events related to the last glaciation and that Norway spruce is still in a process of adaptation and differentiation. There is a clear geographic pattern in the variation of allele frequencies. A major part of the allelefrequency variation can be accounted for by a few synthetic variables (principal components), and 80% of the variation of the first principal component is "explained" by latitude and longitude. The central European populations are consistently depauperate of genetic variability, most likely as an effect of severe restrictions of population size during the last glaciation. The pattern of differentiation at protein loci is very similar to that observed for seven morphological traits examined. This similarity suggests that the same evolutionary forces have acted upon both sets of characters. © 1990 The Society for the Study of Evolution.

Italy of censuses.

PubMed

Rey, G M

1983-06-01

To supplement census data on Italy's economy, Istat conducted a sample survey of 2% of households. This paper reports survey findings in 3 areas: age structure of the population, employment and unemployment patterns by region, and structure of the productive system. Those over age 65 years have increased from 11% of the population in 1971 to 13% in 1981 and are forecast to constitute 14.5% in 1991. Women accounted for 51.3% of the total population in 1981 but 58.5% of those over age 65. 12% of households have a member over age 75. The 0-14 year age group has declined from 24.4% of the population in 1971 to 21.5% in 1981 and is projected to comprise 17.4% in 1991. The labor force activity rate was 39.8% in 1981. Unemployment was set at 14.7% in the census sample compared with 9.1% in Istat's quarterly survey of the labor force. 60% of the difference between these 2 figures was accounted for by Campania, Sicily, Puglia, Calabria, and Latium. These 5 regions, which account for only 30% of total employment, are the areas with the most acute employment problems and highest proportions of casual employment in agriculture and traditional services. Agriculture accounted for 22% of total unemployment, construction for 18.5%, and traditional industry for 14%--percentages that are higher than the share of total employment represented by these sectors. In the South, 20.4% of employment is in agriculture, 18.1% in industry, 12.6% in construction, and 48.9% in services. The average worker in the South supports 3.3 persons compared with 2.5 persons in the North. Survey results indicate a substantial shift in the sectoral composition of employment as well as a change in the size of productive units. There has been an increase in the highly specialized components of the economy, including services to firms. The average size of factories has declined, with a proliferation of small and medium sized units. These findings suggest a need to broaden and deepen Italy's industrial base. Also needed is a consistent plan for labor and capital accumulation. The growth of medium sized firms should be supported until they reach a size compatible with investment and technical progress, thereby permitting greater employment and productivity.

Challenges to assessing connectivity between massive populations of the Australian plague locust

PubMed Central

Chapuis, Marie-Pierre; Popple, Julie-Anne M.; Berthier, Karine; Simpson, Stephen J.; Deveson, Edward; Spurgin, Peter; Steinbauer, Martin J.; Sword, Gregory A.

2011-01-01

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera, is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m, that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations. PMID:21389030

Land-use classification map of the greater Denver area, Front Range Urban Corridor, Colorado

USGS Publications Warehouse

Driscoll, L.B.

1975-01-01

The Greater Denver area, in the Front Range Urban Corridor of Colorado, is an area of rapid population growth and expanding land development. At present no overall land-use policy exists for this area, although man individuals and groups are concerned about environmental, economic, and social stresses caused by population pressures. A well-structured land-use policy for the entire Front Range Urban Corridor, in which compatible land uses are taken into account, could lead to overall improvements in land values. A land classification map is the first step toward implementing such a policy.

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

PubMed

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

2014-11-01

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

'Lonely within the mother': An exploratory study of first-time mothers' experiences of loneliness.

PubMed

Lee, Katharine; Vasileiou, Konstantina; Barnett, Julie

2017-08-01

Loneliness is associated with life transitions such as new motherhood, yet there are few studies investigating the issue in this population. Using data from semi-structured interviews and an interpretative phenomenological analysis, this exploratory study sought to understand seven new mothers' experiences of loneliness. Experiences were organised around three themes, reflecting loneliness arising from making unfavourable self-comparisons with perceived mothering 'norms', from reduced social contact and relationships lacking in empathy. Accounts were homogeneous and point to potential solutions to ameliorate loneliness in new mothers; encouraging empathy in new mothers' partners and countering prevalent unrealistic representations of motherhood with more pragmatic accounts.

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

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.

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.

Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan.

PubMed

Badgley, Brian D; Ferguson, John; Vanden Heuvel, Amy; Kleinheinz, Gregory T; McDermott, Colleen M; Sandrin, Todd R; Kinzelman, Julie; Junion, Emily A; Byappanahalli, Muruleedhara N; Whitman, Richard L; Sadowsky, Michael J

2011-01-01

High concentrations of Escherichia coli in mats of Cladophora in the Great Lakes have raised concern over the continued use of this bacterium as an indicator of microbial water quality. Determining the impacts of these environmentally abundant E. coli, however, necessitates a better understanding of their ecology. In this study, the population structure of 4285 Cladophora-borne E. coli isolates, obtained over multiple three day periods from Lake Michigan Cladophora mats in 2007-2009, was examined by using DNA fingerprint analyses. In contrast to previous studies that have been done using isolates from attached Cladophora obtained over large time scales and distances, the extensive sampling done here on free-floating mats over successive days at multiple sites provided a large dataset that allowed for a detailed examination of changes in population structure over a wide range of spatial and temporal scales. While Cladophora-borne E. coli populations were highly diverse and consisted of many unique isolates, multiple clonal groups were also present and accounted for approximately 33% of all isolates examined. Patterns in population structure were also evident. At the broadest scales, E. coli populations showed some temporal clustering when examined by year, but did not show good spatial distinction among sites. E. coli population structure also showed significant patterns at much finer temporal scales. Populations were distinct on an individual mat basis at a given site, and on individual days within a single mat. Results of these studies indicate that Cladophora-borne E. coli populations consist of a mixture of stable, and possibly naturalized, strains that persist during the life of the mat, and more unique, transient strains that can change over rapid time scales. It is clear that further study of microbial processes at fine spatial and temporal scales is needed, and that caution must be taken when interpolating short term microbial dynamics from results obtained from weekly or monthly samples. Copyright © 2010 Elsevier Ltd. All rights reserved.

Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan

USGS Publications Warehouse

Badgley, B.D.; Ferguson, J.; Heuvel, A.V.; Kleinheinz, G.T.; McDermott, C.M.; Sandrin, T.R.; Kinzelman, J.; Junion, E.A.; Byappanahalli, M.N.; Whitman, R.L.; Sadowsky, M.J.

2011-01-01

High concentrations of Escherichia coli in mats of Cladophora in the Great Lakes have raised concern over the continued use of this bacterium as an indicator of microbial water quality. Determining the impacts of these environmentally abundant E. coli, however, necessitates a better understanding of their ecology. In this study, the population structure of 4285 Cladophora-borne E. coli isolates, obtained over multiple three day periods from Lake Michigan Cladophora mats in 2007-2009, was examined by using DNA fingerprint analyses. In contrast to previous studies that have been done using isolates from attached Cladophora obtained over large time scales and distances, the extensive sampling done here on free-floating mats over successive days at multiple sites provided a large dataset that allowed for a detailed examination of changes in population structure over a wide range of spatial and temporal scales. While Cladophora-borne E. coli populations were highly diverse and consisted of many unique isolates, multiple clonal groups were also present and accounted for approximately 33% of all isolates examined. Patterns in population structure were also evident. At the broadest scales, E. coli populations showed some temporal clustering when examined by year, but did not show good spatial distinction among sites. E. coli population structure also showed significant patterns at much finer temporal scales. Populations were distinct on an individual mat basis at a given site, and on individual days within a single mat. Results of these studies indicate that Cladophora-borne E. coli populations consist of a mixture of stable, and possibly naturalized, strains that persist during the life of the mat, and more unique, transient strains that can change over rapid time scales. It is clear that further study of microbial processes at fine spatial and temporal scales is needed, and that caution must be taken when interpolating short term microbial dynamics from results obtained from weekly or monthly samples.

Analysis of the HLA population data (AHPD) submitted to the 15th International Histocompatibility/Immunogenetics Workshop by using the Gene[rate] computer tools accommodating ambiguous data (AHPD project report).

PubMed

Nunes, J M; Riccio, M E; Buhler, S; Di, D; Currat, M; Ries, F; Almada, A J; Benhamamouch, S; Benitez, O; Canossi, A; Fadhlaoui-Zid, K; Fischer, G; Kervaire, B; Loiseau, P; de Oliveira, D C M; Papasteriades, C; Piancatelli, D; Rahal, M; Richard, L; Romero, M; Rousseau, J; Spiroski, M; Sulcebe, G; Middleton, D; Tiercy, J-M; Sanchez-Mazas, A

2010-07-01

During the 15th International Histocompatibility and Immunogenetics Workshop (IHIWS), 14 human leukocyte antigen (HLA) laboratories participated in the Analysis of HLA Population Data (AHPD) project where 18 new population samples were analyzed statistically and compared with data available from previous workshops. To that aim, an original methodology was developed and used (i) to estimate frequencies by taking into account ambiguous genotypic data, (ii) to test for Hardy-Weinberg equilibrium (HWE) by using a nested likelihood ratio test involving a parameter accounting for HWE deviations, (iii) to test for selective neutrality by using a resampling algorithm, and (iv) to provide explicit graphical representations including allele frequencies and basic statistics for each series of data. A total of 66 data series (1-7 loci per population) were analyzed with this standard approach. Frequency estimates were compliant with HWE in all but one population of mixed stem cell donors. Neutrality testing confirmed the observation of heterozygote excess at all HLA loci, although a significant deviation was established in only a few cases. Population comparisons showed that HLA genetic patterns were mostly shaped by geographic and/or linguistic differentiations in Africa and Europe, but not in America where both genetic drift in isolated populations and gene flow in admixed populations led to a more complex genetic structure. Overall, a fruitful collaboration between HLA typing laboratories and population geneticists allowed finding useful solutions to the problem of estimating gene frequencies and testing basic population diversity statistics on highly complex HLA data (high numbers of alleles and ambiguities), with promising applications in either anthropological, epidemiological, or transplantation studies.

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.

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.

Population turnover and adaptation in heterogeneous environments

NASA Astrophysics Data System (ADS)

Campos, Paulo R. A.; de Oliveira, Viviane M.

2012-02-01

We study adaptive dynamics in a structured population model of asexual individuals which takes into account environmental heterogeneity among the subpopulations. The key purpose of the present work is to address how population turnovers, i.e. extinction events followed by recolonization, affect the rate of fixation of advantageous mutations. This model is a generalization of our previous model to address the interplay between environmental correlation and evolutionary forces on the adaptive process. The incorporation of population turnovers into the model enables us to make a direct correspondence between the model and host-parasite dynamics (epidemiological models). Strikingly, contrary to the intuitive and usual deleterious effect associated to extinction events, it is observed that population turnovers can in fact speed up adaptation as heterogeneity rises. On the other side, in nearly homogeneous population turnovers have a neutral effect on fixation rates, but a detrimental outcome is also achieved when extinction events become very common. In resume, population turnover outcomes on fixation rates of advantageous mutations are strongly influenced by the selective correlation among the subpopulations (demes).

Variation in Age and Size in Fennoscandian Three-Spined Sticklebacks (Gasterosteus aculeatus)

PubMed Central

DeFaveri, Jacquelin; Merilä, Juha

2013-01-01

Average age and maximum life span of breeding adult three-spined sticklebacks (Gasterosteus aculeatus) were determined in eight Fennoscandian localities with the aid of skeletochronology. The average age varied from 1.8 to 3.6 years, and maximum life span from three to six years depending on the locality. On average, fish from marine populations were significantly older than those from freshwater populations, but variation within habitat types was large. We also found significant differences in mean body size among different habitat types and populations, but only the population differences remained significant after accounting for variation due to age effects. These results show that generation length and longevity in three-spined sticklebacks can vary significantly from one locality to another, and that population differences in mean body size cannot be explained as a simple consequence of differences in population age structure. We also describe a nanistic population from northern Finland exhibiting long life span and small body size. PMID:24260496

Variation in age and size in Fennoscandian three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

DeFaveri, Jacquelin; Merilä, Juha

2013-01-01

Average age and maximum life span of breeding adult three-spined sticklebacks (Gasterosteus aculeatus) were determined in eight Fennoscandian localities with the aid of skeletochronology. The average age varied from 1.8 to 3.6 years, and maximum life span from three to six years depending on the locality. On average, fish from marine populations were significantly older than those from freshwater populations, but variation within habitat types was large. We also found significant differences in mean body size among different habitat types and populations, but only the population differences remained significant after accounting for variation due to age effects. These results show that generation length and longevity in three-spined sticklebacks can vary significantly from one locality to another, and that population differences in mean body size cannot be explained as a simple consequence of differences in population age structure. We also describe a nanistic population from northern Finland exhibiting long life span and small body size.

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.

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

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides . These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. 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.

Beyond sex differences: new approaches for thinking about variation in brain structure and function.

PubMed

Joel, Daphna; Fausto-Sterling, Anne

2016-02-19

In the study of variation in brain structure and function that might relate to sex and gender, language matters because it frames our research questions and methods. In this article, we offer an approach to thinking about variation in brain structure and function that pulls us outside the sex differences formulation. We argue that the existence of differences between the brains of males and females does not unravel the relations between sex and the brain nor is it sufficient to characterize a population of brains. Such characterization is necessary for studying sex effects on the brain as well as for studying brain structure and function in general. Animal studies show that sex interacts with environmental, developmental and genetic factors to affect the brain. Studies of humans further suggest that human brains are better described as belonging to a single heterogeneous population rather than two distinct populations. We discuss the implications of these observations for studies of brain and behaviour in humans and in laboratory animals. We believe that studying sex effects in context and developing or adopting analytical methods that take into account the heterogeneity of the brain are crucial for the advancement of human health and well-being. © 2016 The Author(s).

Psychometric properties of the Interpersonal Relationship Inventory-Short Form for active duty female service members.

PubMed

Nayback-Beebe, Ann M; Yoder, Linda H

2011-06-01

The Interpersonal Relationship Inventory-Short Form (IPRI-SF) has demonstrated psychometric consistency across several demographic and clinical populations; however, it has not been psychometrically tested in a military population. The purpose of this study was to psychometrically evaluate the reliability and component structure of the IPRI-SF in active duty United States Army female service members (FSMs). The reliability estimates were .93 for the social support subscale and .91 for the conflict subscale. Principal component analysis demonstrated an obliquely rotated three-component solution that accounted for 58.9% of the variance. The results of this study support the reliability and validity of the IPRI-SF for use in FSMs; however, a three-factor structure emerged in this sample of FSMs post-deployment that represents "cultural context." Copyright © 2011 Wiley Periodicals, Inc.

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 to those of non-material production, and from expansion of employment to the rise of employment efficiency. The proportion of urban population in China accounted for 20.8% in 1982 with an annual growth rate of 4% during the 1949-82 period. The 1982 population census reveals that 94.4% of China's population resides on the southeast side of Aihui-Tengchong Line. Compared with the statistics in 1953, there was no notable change of the unbalanced population distribution on each side of the Line over the last 50 years. China is comparatively young in its population age structure. 1982 census data show that there were 49.29 million people at age 65 and over in 1982, representing 4.91% of the whole population. It is estimated from the age composition of 1982 and age-specific mortality rate of 1981 that there will be 88 million elderly persons by 2000, 150 million by 2020, and about 300 million as a maximum around 2040.

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

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

PubMed Central

Watkins, WS; Thara, R; Mowry, BJ; Zhang, Y; Witherspoon, DJ; Tolpinrud, W; Bamshad, MJ; Tirupati, S; Padmavati, R; Smith, H; Nancarrow, D; Filippich, C; Jorde, LB

2008-01-01

Background Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations. Results We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST = 0.96%, Andhra Pradesh RST = 0.77%) exceeds the estimate of variation between these geographically separated groups (RST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data. Conclusion Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions. PMID:19077280

A selfsimilar behavior of the urban structure in the spatially inhomogeneous model

NASA Astrophysics Data System (ADS)

Echkina, E. Y.; Inovenkov, O. I.; Kostomarov, D. P.

2006-03-01

At present there is a strong tendency to use new methods for the description of the regional and spatial economy. In increasing frequency we consider that any economic activity is spatially dependent. The problem of the evolution of internal urban formation can be described with the exact supposition. So that is why we use partial derivative equations set with the appropriate boundary and initial conditions for the solving the problem of the urban evolution. Here we describe the model of urban population's density modification taking into account a modification of the housing quality. A program has been created which realizes difference method of mixed problem solution for population's density. For the wide class of coefficients it has been shown that the problem's solution “quickly forgets” the parts of the initial conditions and comes out to the intermediate asymptotic form, which nature depends only on the problem's operator. Actually it means that the urban structure does not depend on external circumstances and is formed by the internal structure of the model.

Breeding system and demography shape population genetic structure across ecological and climatic zones in the African freshwater snail, Bulinus forskalii (Gastropoda, Pulmonata), intermediate host for schistosomes.

PubMed

Gow, J L; Noble, L R; Rollinson, D; Mimpfoundi, R; Jones, C S

2004-11-01

The role of breeding system and population bottlenecks in shaping the distribution of neutral genetic variation among populations inhabiting patchily distributed, ephemeral water bodies was examined for the hermaphroditic freshwater snail Bulinus forskalii, intermediate host for the medically important trematode Schistosoma guineensis. Levels of genetic variation at 11 microsatellite loci were assessed for 600 individuals sampled from 19 populations that span three ecological and climatic zones (ecozones) in Cameroon, West Africa. Significant heterozygote deficiencies and linkage disequilibria indicated very high selfing rates in these populations. Despite this and the large genetic differentiation detected between populations, high levels of genetic variation were harboured within these populations. The high level of gene flow inferred from assignment tests may be responsible for this pattern. Indeed, metapopulation dynamics, including high levels of gene flow as well as extinction/contraction and recolonization events, are invoked to account for the observed population structuring, which was not a consequence of isolation-by-distance. Because B. forskalii populations inhabiting the northern, Sahelian area are subject to more pronounced annual cycles of drought and flood than the southern equatorial ones, they were expected to be subject to population bottlenecks of increased frequency and severity and, therefore, show reduced genetic variability and elevated population differentiation. Contrary to predictions, the populations inhabiting the most northerly ecozone exhibited higher genetic diversity and lower genetic differentiation than those in the most southerly one, suggesting that elevated gene flow in this region is counteracting genetic drift.

Domestic dog demographic structure and dynamics relevant to rabies control planning in urban areas in Africa: the case of Iringa, Tanzania

PubMed Central

2012-01-01

Background Mass vaccinations of domestic dogs have been shown to effectively control canine rabies and hence human exposure to rabies. Knowledge of dog population demography is essential for planning effective rabies vaccination programmes; however, such information is still rare for African domestic dog populations, particularly so in urban areas. This study describes the demographic structure and population dynamics of a domestic dog population in an urban sub-Saharan African setting. In July to November 2005, we conducted a full household-level census and a cross-sectional dog demography survey in four urban wards of Iringa Municipality, Tanzania. The achievable vaccination coverage was assessed by a two-stage vaccination campaign, and the proportion of feral dogs was estimated by a mark-recapture transect study. Results The estimated size of the domestic dog population in Iringa was six times larger than official town records assumed, however, the proportion of feral dogs was estimated to account for less than 1% of the whole population. An average of 13% of all households owned dogs which equalled a dog:human ratio of 1:14, or 0.31 dogs per household or 334 dogs km-2. Dog female:male ratio was 1:1.4. The average age of the population was 2.2 years, 52% of all individuals were less than one year old. But mortality within the first year was high (72%). Females became fertile at the age of 10 months and reportedly remained fertile up to the age of 11 years. The average number of litters whelped per fertile female per year was 0.6 with an average of 5.5 pups born per litter. The population growth was estimated at 10% y-1. Conclusions Such high birth and death rates result in a rapid replacement of anti-rabies immunised individuals with susceptible ones. This loss in herd immunity needs to be taken into account in the design of rabies control programmes. The very small proportion of truly feral dogs in the population implies that vaccination campaigns aimed at the owned dog population are sufficient to control rabies in urban Iringa, and the same may be valid in other, comparable urban settings. PMID:23217194

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.

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.

Pollen, wind and fire: how to investigate genetic effects of disturbance-induced change in forest trees.

PubMed

Bacles, Cecile F E

2014-01-01

Understanding the consequences of habitat disturbance on mating patterns although pollen and seed dispersal in forest trees has been a long-standing theme of forest and conservation genetics. Forest ecosystems face global environmental pressures from timber exploitation to genetic pollution and climate change, and it is therefore essential to comprehend how disturbances may alter the dispersal of genes and their establishment in tree populations in order to formulate relevant recommendations for sustainable resource management practices and realistic predictions of potential adaptation to climate change by means of range shift or expansion (Kremer et al. 2012). However, obtaining reliable evidence of disturbance-induced effects on gene dispersal processes from empirical evaluation of forest tree populations is difficult. Indeed, tree species share characteristics such as high longevity, long generation time and large reproductive population size, which may impede the experimenter's ability to assess parameters at the spatial and time scales at which any change may occur (Petit and Hampe 2006). It has been suggested that appropriate study designs should encompass comparison of populations before and after disturbance as well as account for demonstrated variation in conspecific density, that is, the spatial distribution of mates, and forest density, including all species and relating to alteration in landscape openness (Bacles & Jump 2011). However, more often than not, empirical studies aiming to assess the consequences of habitat disturbance on genetic processes in tree populations assume rather than quantify a change in tree densities in forests under disturbance and generally fail to account for population history, which may lead to inappropriate interpretation of a causal relationship between population genetic structure and habitat disturbance due to effects of unmonitored confounding variables (Gauzere et al. 2013). In this issue, Shohami and Nathan (2014) take advantage of the distinctive features of the fire-adapted wind-pollinated Aleppo pine Pinus halepensis (Fig. 1) to provide an elegant example of best practice. Thanks to long-term monitoring of the study site, a natural stand in Israel, Shohami and Nathan witnessed the direct impact of habitat disturbance, here taking the shape of fire, on conspecific and forest densities and compared pre- and postdisturbance mating patterns estimated from cones of different ages sampled on the same surviving maternal individuals (Fig. 2). This excellent study design is all the more strong that Shohami and Nathan took further analytical steps to account for confounding variables, such as historical population genetic structure and possible interannual variation in wind conditions, thus giving high credibility to their findings of unequivocal fire-induced alteration of mating patterns in P. halepensis. Most notably, the authors found, at the pollen pool level, a disruption of local genetic structure which, furthermore, they were able to attribute explicitly to enhanced pollen-mediated gene immigration into the low-density fire-disturbed stand. This cleverly designed research provides a model approach to be followed if we are to advance our understanding of disturbance-induced dispersal and genetic change in forest trees. © 2013 John Wiley & Sons Ltd.

Structural interventions to prevent HIV/sexually transmitted disease: are they cost-effective for women in the southern United States?

PubMed

Cohen, Deborah A; Wu, Shin-Yi; Farley, Thomas A

2006-07-01

Structural interventions are theoretically promising for populations with a low prevalence of HIV, because they can reach large numbers of people to influence their social norms and collective risky behaviors for a relatively low cost per person. Because HIV transmission is continuing to increase among women in the southern United States, interventions to stem this epidemic are particularly warranted. This study explores whether structural interventions may be a cost-effective way to prevent HIV in this population. We used the cost-effectiveness estimator, "Maximizing the Benefit" to determine the relative cost-effectiveness of 6 structural HIV prevention interventions. "Maximizing the Benefit" is a spreadsheet tool using mathematical models to estimate the cost per HIV infection prevented taking into account the epidemiologic contexts, behavioral change as a result of an intervention, and the costs of intervention. We applied estimates of HIV prevalence related to blacks in the southern United States. All the structural interventions were cost-effective compared with average lifetime treatment costs of HIV, but mass media, condom availability, and alcohol taxes theoretically prevented the largest numbers of HIV infections. Although the assumptions used in cost-effectiveness estimates have many limitations, they do allow for a relative comparison of different interventions and help to inform policy decisions related to the allocation of HIV prevention resources. Structural interventions hold the greatest promise in reducing HIV transmission among low-prevalence populations.

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data

PubMed Central

Jewett, Ethan M.; Steinrücken, Matthias; Song, Yun S.

2016-01-01

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright–Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes. PMID:27550904

Developing Tomorrow's Integrated Community Health Systems: A Leadership Challenge for Public Health and Primary Care

PubMed Central

Welton, William E.; Kantner, Theodore A.; Katz, Sheila Moriber

1997-01-01

As the nation's health system moves away from earlier models to one grounded in population health and market-based systems of care, new challenges arise for public health professionals, primary care practitioners, health plan and institutional managers, and community leaders. Among the challenges are the need to develop creative concepts of organization and accountability and to assure that dynamic, system-oriented structures support the new kind of leadership that is required. Developing tomorrow's integrated community health systems will challenge the leadership skills and integrative abilities of public health professionals, primary care practitioners, and managers. These leaders and their new organizations must, in turn, assume increased accountability for improving community health. PMID:9184684

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions.

PubMed

Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z; Gao, Xin

2017-01-01

Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil

PubMed Central

Kajdacsi, Brittney; Costa, Federico; Hyseni, Chaz; Porter, Fleur; Brown, Julia; Rodrigues, Gorete; Farias, Helena; Reis, Mitermeyer G.; Childs, James E.; Ko, Albert I.; Caccone, Adalgisa

2013-01-01

Throughout the developing world, urban centers with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers, and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus), are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure, and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from 9 sites in the city of Salvador, Brazil. These sites were divided between three neighborhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographic distances. Most FST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighborhoods or valleys within neighborhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies. PMID:24118116

Tailored combination prevention packages and PrEP for young key populations

PubMed Central

Pettifor, Audrey; Nguyen, Nadia L; Celum, Connie; Cowan, Frances M; Go, Vivian; Hightow-Weidman, Lisa

2015-01-01

Introduction Young key populations, defined in this article as men who have sex with men, transgender persons, people who sell sex and people who inject drugs, are at particularly high risk for HIV. Due to the often marginalized and sometimes criminalized status of young people who identify as members of key populations, there is a need for HIV prevention packages that account for the unique and challenging circumstances they face. Pre-exposure prophylaxis (PrEP) is likely to become an important element of combination prevention for many young key populations. Objective In this paper, we discuss important challenges to HIV prevention among young key populations, identify key components of a tailored combination prevention package for this population and examine the role of PrEP in these prevention packages. Methods We conducted a comprehensive review of the evidence to date on prevention strategies, challenges to prevention and combination prevention packages for young key populations. We focused specifically on the role of PrEP in these prevention packages and on young people under the age of 24, and 18 in particular. Results and discussion Combination prevention packages that include effective, acceptable and scalable behavioural, structural and biologic interventions are needed for all key populations to prevent new HIV infections. Interventions in these packages should meaningfully involve beneficiaries in the design and implementation of the intervention, and take into account the context in which the intervention is being delivered to thoughtfully address issues of stigma and discrimination. These interventions will likely be most effective if implemented in conjunction with strategies to facilitate an enabling environment, including increasing access to HIV testing and health services for PrEP and other prevention strategies, decriminalizing key populations’ practices, increasing access to prevention and care, reducing stigma and discrimination, and fostering community empowerment. PrEP could offer a highly effective, time-limited primary prevention for young key populations if it is implemented in combination with other programs to increase access to health services and encourage the reliable use of PrEP while at risk of HIV exposure. Conclusions Reductions in HIV incidence will only be achieved through the implementation of combinations of interventions that include biomedical and behavioural interventions, as well as components that address social, economic and other structural factors that influence HIV prevention and transmission. PMID:25724507

Redistribution population data across a regular spatial grid according to buildings characteristics

NASA Astrophysics Data System (ADS)

Calka, Beata; Bielecka, Elzbieta; Zdunkiewicz, Katarzyna

2016-12-01

Population data are generally provided by state census organisations at the predefined census enumeration units. However, these datasets very are often required at userdefined spatial units that differ from the census output levels. A number of population estimation techniques have been developed to address these problems. This article is one of those attempts aimed at improving county level population estimates by using spatial disaggregation models with support of buildings characteristic, derived from national topographic database, and average area of a flat. The experimental gridded population surface was created for Opatów county, sparsely populated rural region located in Central Poland. The method relies on geolocation of population counts in buildings, taking into account the building volume and structural building type and then aggregation the people total in 1 km quadrilateral grid. The overall quality of population distribution surface expressed by the mean of RMSE equals 9 persons, and the MAE equals 0.01. We also discovered that nearly 20% of total county area is unpopulated and 80% of people lived on 33% of the county territory.

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.

Sampling intraspecific variability in leaf functional traits: Practical suggestions to maximize collected information.

PubMed

Petruzzellis, Francesco; Palandrani, Chiara; Savi, Tadeja; Alberti, Roberto; Nardini, Andrea; Bacaro, Giovanni

2017-12-01

The choice of the best sampling strategy to capture mean values of functional traits for a species/population, while maintaining information about traits' variability and minimizing the sampling size and effort, is an open issue in functional trait ecology. Intraspecific variability (ITV) of functional traits strongly influences sampling size and effort. However, while adequate information is available about intraspecific variability between individuals (ITV BI ) and among populations (ITV POP ), relatively few studies have analyzed intraspecific variability within individuals (ITV WI ). Here, we provide an analysis of ITV WI of two foliar traits, namely specific leaf area (SLA) and osmotic potential (π), in a population of Quercus ilex L. We assessed the baseline ITV WI level of variation between the two traits and provided the minimum and optimal sampling size in order to take into account ITV WI , comparing sampling optimization outputs with those previously proposed in the literature. Different factors accounted for different amount of variance of the two traits. SLA variance was mostly spread within individuals (43.4% of the total variance), while π variance was mainly spread between individuals (43.2%). Strategies that did not account for all the canopy strata produced mean values not representative of the sampled population. The minimum size to adequately capture the studied functional traits corresponded to 5 leaves taken randomly from 5 individuals, while the most accurate and feasible sampling size was 4 leaves taken randomly from 10 individuals. We demonstrate that the spatial structure of the canopy could significantly affect traits variability. Moreover, different strategies for different traits could be implemented during sampling surveys. We partially confirm sampling sizes previously proposed in the recent literature and encourage future analysis involving different traits.

Greater Melbourne.

PubMed

Wulff, M; Burke, T; Newton, P

1986-03-01

With more than a quarter of its population born overseas, Melbourne, Australia, is rapidly changing from an all-white British outpost to a multicultural, multilingual community. Since the "white" Australian policy was abandoned after World War II, 3 million immigrants from 100 different countries have moved to Australia. Most of the immigrants come from New Zealand, Rhodesia, South Africa, Britain, Ireland, Greece, Turkey, Yugoslavia, Poland, and Indochina. Melbourne is Australia's 2nd largest city and houses 1 out of 5 Australians. Its 1984 population was 2,888,400. Melbourne's housing pattern consists of subdivisions; 75% of the population live in detached houses. Between 1954 and 1961 Melbourne grew at an annual rate of 3.5%; its growth rate between 1961 and 1971 still averaged 2.5%. In the 1970s the growth rate slowed to 1.4%. Metropolitan Melbourne has no central government but is divided into 56 councils and 8 regions. Both Australia's and Melbourne's fertility rates are high compared to the rest of the developed world, partly because of their younger age structure. 41% of Melbourne's population was under age 24 in 1981. Single-person households are growing faster than any other type. 71% of the housing is owner-occupied; in 1981 the median sized dwelling had 5.2 rooms. Public housing only accounts for 2.6% of all dwellings. Fewer students graduate from high school in Australia than in other developed countries, and fewer graduates pursue higher education. Melbourne's suburban sprawl promotes private car travel. In 1980 Melbourne contained more than 28,000 retail establishments and 4200 restaurants and hotels. Industry accounts for 30% of employment, and services account for another 30%. Its largest industries are motor vehicles, clothing, and footware. Although unemployment reached 10% after the 1973 energy crisis, by 1985 it was down to 6%.

A neuronal network model for context-dependence of pitch change perception.

PubMed

Huang, Chengcheng; Englitz, Bernhard; Shamma, Shihab; Rinzel, John

2015-01-01

Many natural stimuli have perceptual ambiguities that can be cognitively resolved by the surrounding context. In audition, preceding context can bias the perception of speech and non-speech stimuli. Here, we develop a neuronal network model that can account for how context affects the perception of pitch change between a pair of successive complex tones. We focus especially on an ambiguous comparison-listeners experience opposite percepts (either ascending or descending) for an ambiguous tone pair depending on the spectral location of preceding context tones. We developed a recurrent, firing-rate network model, which detects frequency-change-direction of successively played stimuli and successfully accounts for the context-dependent perception demonstrated in behavioral experiments. The model consists of two tonotopically organized, excitatory populations, E up and E down, that respond preferentially to ascending or descending stimuli in pitch, respectively. These preferences are generated by an inhibitory population that provides inhibition asymmetric in frequency to the two populations; context dependence arises from slow facilitation of inhibition. We show that contextual influence depends on the spectral distribution of preceding tones and the tuning width of inhibitory neurons. Further, we demonstrate, using phase-space analysis, how the facilitated inhibition from previous stimuli and the waning inhibition from the just-preceding tone shape the competition between the E up and E down populations. In sum, our model accounts for contextual influences on the pitch change perception of an ambiguous tone pair by introducing a novel decoding strategy based on direction-selective units. The model's network architecture and slow facilitating inhibition emerge as predictions of neuronal mechanisms for these perceptual dynamics. Since the model structure does not depend on the specific stimuli, we show that it generalizes to other contextual effects and stimulus types.

From Curves to Trees: A Tree-like Shapes Distance Using the Elastic Shape Analysis Framework.

PubMed

Mottini, A; Descombes, X; Besse, F

2015-04-01

Trees are a special type of graph that can be found in various disciplines. In the field of biomedical imaging, trees have been widely studied as they can be used to describe structures such as neurons, blood vessels and lung airways. It has been shown that the morphological characteristics of these structures can provide information on their function aiding the characterization of pathological states. Therefore, it is important to develop methods that analyze their shape and quantify differences between their structures. In this paper, we present a method for the comparison of tree-like shapes that takes into account both topological and geometrical information. This method, which is based on the Elastic Shape Analysis Framework, also computes the mean shape of a population of trees. As a first application, we have considered the comparison of axon morphology. The performance of our method has been evaluated on two sets of images. For the first set of images, we considered four different populations of neurons from different animals and brain sections from the NeuroMorpho.org open database. The second set was composed of a database of 3D confocal microscopy images of three populations of axonal trees (normal and two types of mutations) of the same type of neurons. We have calculated the inter and intra class distances between the populations and embedded the distance in a classification scheme. We have compared the performance of our method against three other state of the art algorithms, and results showed that the proposed method better distinguishes between the populations. Furthermore, we present the mean shape of each population. These shapes present a more complete picture of the morphological characteristics of each population, compared to the average value of certain predefined features.

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

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.

Structural validity and reliability of the Spanish version of the White Bear Suppression Inventory (WBSI) in a sample of the general Spanish population.

PubMed

González Rodríguez, Manuel; Avero Delgado, Pedro; Rovella, Anna Teresa; Cubas León, Rosario

2008-11-01

This paper introduces the validation of the Spanish adaptation of the White Bear Suppression Inventory (WBSI) by Wegner and Zanakos (1994). A sample of 833 people from the general population completed the WBSI along with other questionnaires. The exploratory factor analysis and the confirmatory factor analysis supported a two-factor solution accounting for 51.8% of the cumulative variance. This structure is comprised of the two following factors: unwanted intrusive thoughts (alpha = .87, r = .70) and actions of distraction and suppression of thoughts (alpha = .80, r = .60). Both internal consistency reliability (alpha = .89) and test-retest reliability (r = .71) showed adequate homogeneity, sound consistency, and stability over time. The results are discussed bearing in mind both isolated factors and the possible relationships of the suppression factor with automatic negative thoughts and insomnia.

Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe

PubMed Central

Veličković, N; Ferreira, E; Djan, M; Ernst, M; Obreht Vidaković, D; Monaco, A; Fonseca, C

2016-01-01

Wild boar (Sus scrofa), one of the most widespread wildlife species, has entered a stage of continuous growth in Europe, and could even be considered a pest species. We analysed microsatellite variability in 723 wild boars from across Europe, including the northern Dinaric Balkans. Our aims were: (1) to define the population structure of wild boars in the Balkans and its relation with other European populations; (2) to estimate effective populations sizes, levels of intra- and inter-population diversity, inbreeding migration and gene flow patterns; (3) to test subpopulations for bottlenecks; (4) to interpret these results in light of current knowledge about the demographic history of wild boars in Europe; and (5) to discuss the relevance of these findings for management and conservation. Strong population structuring was observed and 14 subpopulations were revealed. High genetic diversity was found, and besides the well-known identity of the Italian populations of Sardinia and Castelporziano, we bring new insights into other potential relevant, refugial populations such as Littoral Slovenia, South Portugal, North-western Iberia and an entire cluster in the Balkans. There was evidence of gene flow going from these refugial subpopulations towards less peripheral and more admixed subpopulations. Recent population bottlenecks and expansions were detected, mostly in the peninsular refuge subpopulations. The results are consistent with the fluctuations of wild boar numbers in Europe since the beginning of the twentieth century. These results should be taken into account in future conservation and management plans for wild boar populations in Europe. PMID:27436523

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 Ethiopian white lupin accessions and populations from West Gojam, Awi and Australian collections contributed more accessions to the core collection.

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 Ethiopian white lupin accessions and populations from West Gojam, Awi and Australian collections contributed more accessions to the core collection. PMID:29190792

Simple deterministic models and applications. Comment on "Coupled disease-behavior dynamics on complex networks: A review" by Z. Wang et al.

NASA Astrophysics Data System (ADS)

Yang, Hyun Mo

2015-12-01

Currently, discrete modellings are largely accepted due to the access to computers with huge storage capacity and high performance processors and easy implementation of algorithms, allowing to develop and simulate increasingly sophisticated models. Wang et al. [7] present a review of dynamics in complex networks, focusing on the interaction between disease dynamics and human behavioral and social dynamics. By doing an extensive review regarding to the human behavior responding to disease dynamics, the authors briefly describe the complex dynamics found in the literature: well-mixed populations networks, where spatial structure can be neglected, and other networks considering heterogeneity on spatially distributed populations. As controlling mechanisms are implemented, such as social distancing due 'social contagion', quarantine, non-pharmaceutical interventions and vaccination, adaptive behavior can occur in human population, which can be easily taken into account in the dynamics formulated by networked populations.

How congestion shapes cities: from mobility patterns to scaling

PubMed Central

Louf, Rémi; Barthelemy, Marc

2014-01-01

The recent availability of data for cities has allowed scientists to exhibit scalings which present themselves in the form of a power-law dependence on population of various socio-economical and structural indicators. We propose here a stochastic theory of urban growth which accounts for some of the observed scalings and we confirm these predictions on US and OECD empirical data. In particular, we show that the dependence on population size of the total number of miles driven daily, the total length of the road network, the total traffic delay, the total consumption of gasoline, the quantity of CO2 emitted and the relation between area and population of cities, are all governed by a single parameter which characterizes the sensitivity to congestion. Our results suggest that diseconomies associated with congestion scale superlinearly with population size, implying that –despite polycentrism– cities whose transportation infrastructure rely heavily on traffic sensitive modes are unsustainable. PMID:24990624

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

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data.

PubMed

Jewett, Ethan M; Steinrücken, Matthias; Song, Yun S

2016-11-01

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright-Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

[The application of National AIDS spending assessment in a county of Dehong prefecture, Yunnan province, China].

PubMed

Shan, Duo; Sun, Jiang-ping; Yakusik, Anna; Chen, Zhong-dan; Yuan, Jian-hua; Li, Tao; Duan, Song; Yang, Xing; Wei, Mei; Michael, Sante; Ye, Run-hua; Xiang, Li-fen; Yang, Yue-cheng; Ren, Da

2012-11-01

To calculate the actual expenditures in a county of Dehong prefecture, Yunnan province, China by using the method of National AIDS Spending Assessment (NASA) in 2010. Data were collected through NASA data collection form based on adapted NASA classification in the county of Dehong prefecture from October to December, 2011, and complemented by semi-structured interview with 16 well trained programmatic and financial representatives in 8 spending units. Data were entered in Resource Tracking Software (RTS) V 2009.3.0, and SPSS 13.0 was used for data processing and analysis. The NASA estimations showed that the county spent a total of ¥16 235 954 on HIV/AIDS in 2010. Public funds constituted 96.3% of the total expenditure (¥15 630 937), followed by Global Fund which accounted for 3.0% (¥484 585) and private sources which accounted for 0.7% (¥120 432). Findings based on NASA categories showed that AIDS spendings were mainly on 4 areas, and expenditure on Care & Treatment was ¥12 401 382 (76.4% of total expenditure), followed by Prevention which accounted for 14.3% (¥2 325 707), Program Management & Administration which accounted for 7.8% (¥1 268 523) and human resources which accounted for 1.5% (¥240 342). The most beneficial population group was People Living with HIV (PLHIV), accounting for 84.7% of total expenditure. (¥13 753 428), followed by 4.8% for high risk population, including female sex workers and their partners (¥297 333), injection drug users and their partners (¥293 143), men having sex with men and their partners (¥185 136) and 1.5% (¥241 429) for the general population. The local funds for HIV/AIDS in this county was insufficient. The local government should increase corresponding funds based on central government funding. Care and treatment was the first spending priority in the county and the investment of prevention services needs to be increased. Prevention and treatment and care should be combined to ensure the effectiveness of comprehensive prevention and treatment of AIDS.

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.

Turnover, account value and diversification of real traders: evidence of collective portfolio optimizing behavior

NASA Astrophysics Data System (ADS)

Morton de Lachapelle, David; Challet, Damien

2010-07-01

Despite the availability of very detailed data on financial markets, agent-based modeling is hindered by the lack of information about real trader behavior. This makes it impossible to validate agent-based models, which are thus reverse-engineering attempts. This work is a contribution towards building a set of stylized facts about the traders themselves. Using the client database of Swissquote Bank SA, the largest online Swiss broker, we find empirical relationships between turnover, account values and the number of assets in which a trader is invested. A theory based on simple mean-variance portfolio optimization that crucially includes variable transaction costs is able to reproduce faithfully the observed behaviors. We finally argue that our results bring to light the collective ability of a population to construct a mean-variance portfolio that takes into account the structure of transaction costs.

Containment of Ebola and Polio in Low-Resource Settings Using Principles and Practices of Emergency Operations Centers in Public Health.

PubMed

Shuaib, Faisal M; Musa, Philip F; Muhammad, Ado; Musa, Emmanuel; Nyanti, Sara; Mkanda, Pascal; Mahoney, Frank; Corkum, Melissa; Durojaiye, Modupeoluwa; Nganda, Gatei Wa; Sani, Samuel Usman; Dieng, Boubacar; Banda, Richard; Ali Pate, Muhammad

Emergency Operations Centers (EOCs) have been credited with driving the recent successes achieved in the Nigeria polio eradication program. EOC concept was also applied to the Ebola virus disease outbreak and is applicable to a range of other public health emergencies. This article outlines the structure and functionality of a typical EOC in addressing public health emergencies in low-resource settings. It ascribes the successful polio and Ebola responses in Nigeria to several factors including political commitment, population willingness to engage, accountability, and operational and strategic changes made by the effective use of an EOC and Incident Management System. In countries such as Nigeria where the central or federal government does not directly hold states accountable, the EOC provides a means to improve performance and use data to hold health workers accountable by using innovative technologies such as geographic position systems, dashboards, and scorecards.

Balancing income and cost in red deer management.

PubMed

Skonhoft, Anders; Veiberg, Vebjørn; Gauteplass, Asle; Olaussen, Jon Olaf; Meisingset, Erling L; Mysterud, Atle

2013-01-30

This paper presents a bioeconomic analysis of a red deer population within a Norwegian institutional context. This population is managed by a well-defined manager, typically consisting of many landowners operating in a cooperative manner, with the goal of maximizing the present-value hunting related income while taking browsing and grazing damages into account. The red deer population is structured in five categories of animals (calves, female and male yearlings, adult females and adult males). It is shown that differences in the per-animal meat values and survival rates ('biological discounted' values) are instrumental in determining the optimal harvest composition. Fertility plays no direct role. It is argued that this is a general result working in stage-structured models with harvest values. In the numerical illustration it is shown that the optimal harvest pattern stays quite stable under various parameter changes. It is revealed which parameters and harvest restrictions that is most important. We also show that the current harvest pattern involves too much yearling harvest compared with the economically efficient level. Copyright © 2012 Elsevier Ltd. All rights reserved.

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.

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

PubMed Central

2017-01-01

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

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

PubMed

Thomas, Philipp

2017-11-01

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

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 height can be plausibly explained by satellite accretion or other external heating remains to be seen.« less

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

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. 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

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

Genetic Variation of Beet Armyworm (Lepidoptera: Noctuidae) Populations Detected Using Microsatellite Markers in Iran.

PubMed

Golikhajeh, Neshat; Naseri, Bahram; Razmjou, Jabraeil; Hosseini, Reza; Aghbolaghi, Marzieh Asadi

2018-05-28

In order to understand the population genetic diversity and structure of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), a serious pest of sugar beet in Iran and the world, we genotyped 133 individuals from seven regions in Iran using four microsatellite loci. Significant difference was seen between the observed and expected heterozygosity in all loci. A lower observed heterozygosity than expected heterozygosity indicated a low heterozygosity in these populations. The value of F showed a high genetic differentiation, so that the mean of Fst was 0.21. Molecular analysis variance showed significant differences within and among populations with group variance accounted for 71 and 21%, respectively. No correlation was found between pair-wise Fst and geographic distance by Mantel test. Bayesian clustering analysis grouped all regions to two clusters. These data suggested that a combination of different factors, such as geographic distance, environmental condition, and physiological behavior in addition to genetic factors, could play an important role in forming variation within and between S. exigua populations.

Demographic aspects of climate change mitigation and adaptation.

PubMed

Lutz, Wolfgang; Striessnig, Erich

2015-01-01

This paper addresses the contribution of changes in population size and structures to greenhouse gas emissions and to the capacity to adapt to climate change. The paper goes beyond the conventional focus on the changing composition by age and sex. It does so by addressing explicitly the changing composition of the population by level of educational attainment, taking into account new evidence about the effect of educational attainment in reducing significantly the vulnerability of populations to climatic challenges. This evidence, which has inspired a new generation of socio-economic climate change scenarios, is summarized. While the earlier IPCC-SRES (Intergovernmental Panel on Climate Change-Special Report on Emissions Scenarios) scenarios only included alternative trajectories for total population size (treating population essentially as a scaling parameter), the Shared Socio-economic Pathways (SSPs) in the new scenarios were designed to capture the socio-economic challenges to climate change mitigation and adaptation, and include full age, sex, and education details for all countries.

Conservation genetics of the endangered Iberian steppe plant Ferula loscosii (Apiaceae).

PubMed

Pérez-Collazos, E; Catalán, P

2008-07-01

Ferula loscosii (Lange) Willk (Apiaceae) is a threatened endemic species native to the Iberian Peninsula. The plant has a narrow and disjunct distribution in three regions, NE, C and SE Spain. Genetic variability within and among 11 populations from its natural distribution was assessed using allozymes. Intermediate levels of genetic diversity were detected in F. loscosii (P(99%) = 36.83; H(E) = 0.125; H(T) = 0.152). However, the highest genetic diversity (58%) corresponded to the threatened populations from SE and C Spain (H(T) = 0.169) rather than the more abundant and larger populations from NE Spain (Ebro valley) (H(T) = 0.122). Low to moderate levels of genetic structure were found among regional ranges (G(ST) = 0.134), and several statistical spatial correlation analyses corroborated substantial genetic differentiation among the three main regional ranges. However, no significant genetic differentiation was found among the NE Spain populations, except for a northernmost population that is geographically isolated. Outcrossing mating and other biological traits of the species could account for the maintenance of the present values of genetic diversity within populations. The existence of an ancestral late Tertiary wider distribution of the species in SE and C Spain, followed by the maintenance of different Quaternary refugia in these warmer areas, together with a more recent and rapid post-glacial expansion towards NE Spain, are arguments that could explain the low genetic variability and structure found in the Ebro valley and the higher levels of diversity in the southern Iberian populations.

Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species.

PubMed

Murray-Dickson, Gillian; Ghazali, Muhammad; Ogden, Rob; Brown, Rafe; Auliya, Mark

2017-01-01

As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.

Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds’ most traded snake species

PubMed Central

Ghazali, Muhammad; Ogden, Rob; Brown, Rafe; Auliya, Mark

2017-01-01

As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins—which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python’s native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley’s modification of Wallace’s line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans. PMID:28817588

Y Chromosome Haplogroup Distribution in Indo-European Speaking Tribes of Gujarat, Western India

PubMed Central

Aggarwal, Aastha; Mitra, Siuli; Italia, Yazdi M.; Saraswathy, Kallur N.; Chandrasekar, Adimoolam

2014-01-01

The present study was carried out in the Indo-European speaking tribal population groups of Southern Gujarat, India to investigate and reconstruct their paternal population structure and population histories. The role of language, ethnicity and geography in determining the observed pattern of Y haplogroup clustering in the study populations was also examined. A set of 48 bi-allelic markers on the non-recombining region of Y chromosome (NRY) were analysed in 284 males; representing nine Indo-European speaking tribal populations. The genetic structure of the populations revealed that none of these groups was overtly admixed or completely isolated. However, elevated haplogroup diversity and FST value point towards greater diversity and differentiation which suggests the possibility of early demographic expansion of the study groups. The phylogenetic analysis revealed 13 paternal lineages, of which six haplogroups: C5, H1a*, H2, J2, R1a1* and R2 accounted for a major portion of the Y chromosome diversity. The higher frequency of the six haplogroups and the pattern of clustering in the populations indicated overlapping of haplogroups with West and Central Asian populations. Other analyses undertaken on the population affiliations revealed that the Indo-European speaking populations along with the Dravidian speaking groups of southern India have an influence on the tribal groups of Gujarat. The vital role of geography in determining the distribution of Y lineages was also noticed. This implies that although language plays a vital role in determining the distribution of Y lineages, the present day linguistic affiliation of any population in India for reconstructing the demographic history of the country should be considered with caution. PMID:24614885

Y chromosome haplogroup distribution in Indo-European speaking tribes of Gujarat, western India.

PubMed

Khurana, Priyanka; Aggarwal, Aastha; Mitra, Siuli; Italia, Yazdi M; Saraswathy, Kallur N; Chandrasekar, Adimoolam; Kshatriya, Gautam K

2014-01-01

The present study was carried out in the Indo-European speaking tribal population groups of Southern Gujarat, India to investigate and reconstruct their paternal population structure and population histories. The role of language, ethnicity and geography in determining the observed pattern of Y haplogroup clustering in the study populations was also examined. A set of 48 bi-allelic markers on the non-recombining region of Y chromosome (NRY) were analysed in 284 males; representing nine Indo-European speaking tribal populations. The genetic structure of the populations revealed that none of these groups was overtly admixed or completely isolated. However, elevated haplogroup diversity and FST value point towards greater diversity and differentiation which suggests the possibility of early demographic expansion of the study groups. The phylogenetic analysis revealed 13 paternal lineages, of which six haplogroups: C5, H1a*, H2, J2, R1a1* and R2 accounted for a major portion of the Y chromosome diversity. The higher frequency of the six haplogroups and the pattern of clustering in the populations indicated overlapping of haplogroups with West and Central Asian populations. Other analyses undertaken on the population affiliations revealed that the Indo-European speaking populations along with the Dravidian speaking groups of southern India have an influence on the tribal groups of Gujarat. The vital role of geography in determining the distribution of Y lineages was also noticed. This implies that although language plays a vital role in determining the distribution of Y lineages, the present day linguistic affiliation of any population in India for reconstructing the demographic history of the country should be considered with caution.

Driving force analysis of the agricultural water footprint in China based on the LMDI method.

PubMed

Zhao, Chunfu; Chen, Bin

2014-11-04

China's water scarcity problems have become more severe because of the unprecedented economic development and population explosion. Considering agriculture's large share of water consumption, obtaining a clear understanding of Chinese agricultural consumptive water use plays a key role in addressing China's water resource stress and providing appropriate water mitigation policies. We account for the Chinese agricultural water footprint from 1990 to 2009 based on bottom up approach. Then, the underlying driving forces are decomposed into diet structure effect, efficiency effect, economic activity effect, and population effect, and analyzed by applying a log-mean Divisia index (LMDI) model. The results reveal that the Chinese agricultural water footprint has risen from the 94.1 Gm3 in 1990 to 141 Gm3 in 2009. The economic activity effect is the largest positive contributor to promoting the water footprint growth, followed by the population effect and diet structure effect. Although water efficiency improvement as a significant negative effect has reduced overall water footprint, the water footprint decline from water efficiency improvement cannot compensate for the huge increase from the three positive driving factors. The combination of water efficiency improvement and dietary structure adjustment is the most effective approach for controlling the Chinese agricultural water footprint's further growth.

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.

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

Informing conservation management about structural versus functional connectivity: a case-study of Cross River gorillas.

PubMed

Imong, Inaoyom; Robbins, Martha M; Mundry, Roger; Bergl, Richard; Kühl, Hjalmar S

2014-10-01

Connectivity among subpopulations is vital for the persistence of small and fragmented populations. For management interventions to be effective conservation planners have to make the critical distinction between structural connectivity (based on landscape structure) and functional connectivity (which considers both landscape structure and organism-specific behavioral attributes) which can differ considerably within a given context. We assessed spatial and temporal changes in structural and functional connectivity of the Cross River gorilla Gorilla gorilla diehli (CRG) population in a 12,000 km(2) landscape in the Nigeria-Cameroon border region over a 23-year period, comparing two periods: 1987-2000 and 2000-2010. Despite substantial forest connections between occupied areas, genetic evidence shows that only limited dispersal occurs among CRG subpopulations. We used remotely sensed land-cover data and simulated human pressure (using a spatially explicit agent-based model) to assess human impact on connectivity of the CRG population. We calculated cost-weighted distances between areas occupied by gorillas as measures of connectivity (structural based on land-cover only, functional based on both land-cover and simulated human pressure). Whereas structural connectivity decreased by 5% over the 23-year period, functional connectivity decreased by 11%, with both decreasing more during the latter compared to the earlier period. Our results highlight the increasing threat of isolation of CRG subpopulations due to human disturbance, and provide insight into how increasing human influence may lead to functional isolation of wildlife populations despite habitat continuity, a pressing and common issue in tropical Africa often not accounted for when deciding management interventions. In addition to quantifying threats to connectivity, our study provides crucial evidence for management authorities to identify actions that are more likely to be effective for conservation of species in human-dominated landscapes. Our approach can be easily applied to other species, regions, and scales. © 2014 Wiley Periodicals, Inc.

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...

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...

Global demographic trends and future carbon emissions.

PubMed

O'Neill, Brian C; Dalton, Michael; Fuchs, Regina; Jiang, Leiwen; Pachauri, Shonali; Zigova, Katarina

2010-10-12

Substantial changes in population size, age structure, and urbanization are expected in many parts of the world this century. Although such changes can affect energy use and greenhouse gas emissions, emissions scenario analyses have either left them out or treated them in a fragmentary or overly simplified manner. We carry out a comprehensive assessment of the implications of demographic change for global emissions of carbon dioxide. Using an energy-economic growth model that accounts for a range of demographic dynamics, we show that slowing population growth could provide 16-29% of the emissions reductions suggested to be necessary by 2050 to avoid dangerous climate change. We also find that aging and urbanization can substantially influence emissions in particular world regions.

The effects of landscape modifications on the long-term persistence of animal populations.

PubMed

Nabe-Nielsen, Jacob; Sibly, Richard M; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

2010-01-28

The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

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.

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.

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.

Survival, cause-specific mortality, and harvesting of male black-tailed deer in washington

USGS Publications Warehouse

Bender, L.C.; Schirato, G.A.; Spencer, R.D.; McAllister, K.R.; Murphie, B.L.

2004-01-01

We determined survival rates, causes of mortality, and documented impacts of harvest on ???1.5-year-old male (hereafter, male) Columbian black-tailed deer (Odocoileus hemionus columbianus) in 2 Washington, USA, game management units (GMUs; Skookumchuck and Snoqualmie) characterized by different hunting-season structures. We monitored 66 males (n = 28 and 38 annually) in Skookumchuck and 58 males (n = 26 and 32 annually) in Snoqualmie, September 1999-September 2001. Annual survival rates were 0.498 (SE = 0.066) in Skookumchuck and 0.519 (SE = 0.067) in Snoqualmie. Survival rates derived from population age structure did not differ from rates derived from radiotelemetry. Harvest was the primary mortality factor for each population, accounting for 67% (SE = 7; Skookumchuck) to 44% (SE = 9; Snoqualmie) of total annual mortality. Annual harvest-specific mortality rates were 0.317 (SE = 0.032) in Skookumchuck and 0.211 (SE = 0.021) in Snoqualmie, likely due to longer hunting seasons and greater hunter effort in Skookumchuck. Following the elimination of a late buck season centered on the rut in Snoqualmie, male harvest declined 56% and annual survival increased 60%, indicating that male harvest was largely additive to other mortality. Our results indicated that harvest was the primary influence on male black-tailed deer populations in Washington, was additive, and that the effect of harvest varied with hunting-season structure and hunter effort. Managers should not assume that harvesting removes a constant proportion of the male population annually, and management models that assume compensatory mortality in adult harvest may result in over-harvest of male populations.

Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil.

PubMed

Kajdacsi, Brittney; Costa, Federico; Hyseni, Chaz; Porter, Fleur; Brown, Julia; Rodrigues, Gorete; Farias, Helena; Reis, Mitermayer G; Childs, James E; Ko, Albert I; Caccone, Adalgisa

2013-10-01

Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from nine sites in the city of Salvador, Brazil. These sites were divided between three neighbourhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most F(ST) comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighbourhoods or valleys within neighbourhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies. © 2013 John Wiley & Sons Ltd.

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...

Accounting for connectivity and spatial correlation in the optimal placement of wildlife habitat

Treesearch

John Hof; Curtis H. Flather

1996-01-01

This paper investigates optimization approaches to simultaneously modelling habitat fragmentation and spatial correlation between patch populations. The problem is formulated with habitat connectivity affecting population means and variances, with spatial correlations accounted for in covariance calculations. Population with a pre-specifled confidence level is then...

Fine- and hyperfine-structure effects in molecular photoionization. II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

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

Germann, Matthias; Willitsch, Stefan, E-mail: stefan.willitsch@unibas.ch

2016-07-28

Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine-structure effects in one-photon ionization of molecules presented in Paper I [M. Germann and S. Willitsch, J. Chem. Phys. 145, 044314 (2016)]. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including the hyperfine structuremore » that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments.« less

Demographic Histories, Isolation and Social Factors as Determinants of the Genetic Structure of Alpine Linguistic Groups

PubMed Central

Coia, Valentina; Capocasa, Marco; Anagnostou, Paolo; Pascali, Vincenzo; Scarnicci, Francesca; Boschi, Ilaria; Battaggia, Cinzia; Crivellaro, Federica; Ferri, Gianmarco; Alù, Milena; Brisighelli, Francesca; Busby, George B. J.; Capelli, Cristian; Maixner, Frank; Cipollini, Giovanna; Viazzo, Pier Paolo; Zink, Albert; Destro Bisol, Giovanni

2013-01-01

Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations. PMID:24312576

Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.

PubMed

Coia, Valentina; Capocasa, Marco; Anagnostou, Paolo; Pascali, Vincenzo; Scarnicci, Francesca; Boschi, Ilaria; Battaggia, Cinzia; Crivellaro, Federica; Ferri, Gianmarco; Alù, Milena; Brisighelli, Francesca; Busby, George B J; Capelli, Cristian; Maixner, Frank; Cipollini, Giovanna; Viazzo, Pier Paolo; Zink, Albert; Destro Bisol, Giovanni

2013-01-01

Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of "local ethnicity" on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.

A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

PubMed

Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

2017-11-22

Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.

A qualitative study into the perceived barriers of accessing healthcare among a vulnerable population involved with a community centre in Romania.

PubMed

George, Siân; Daniels, Katy; Fioratou, Evridiki

2018-04-03

Minority vulnerable communities, such as the European Roma, often face numerous barriers to accessing healthcare services, resulting in negative health outcomes. Both these barriers and outcomes have been reported extensively in the literature. However, reports on barriers faced by European non-Roma native communities are limited. The "Health Care Access Barriers" (HCAB) model identifies pertinent financial, structural and cognitive barriers that can be measured and potentially modified. The present study thus aims to explore the barriers to accessing healthcare for a vulnerable population of mixed ethnicity from a charity community centre in Romania, as perceived by the centre's family users and staff members, and assess whether these reflect the barriers identified from the HCAB model. Eleven community members whose children attend the centre and seven staff members working at the centre participated in face-to-face semi-structured interviews, exploring personal experiences and views on accessing healthcare. The interviews were transcribed and analysed using an initial deductive and secondary inductive approach to identify HCAB themes and other emerging themes and subthemes. Identified themes from both groups aligned with HCAB's themes of financial, structural and cognitive barriers and emergent subthemes important to the specific population were identified. Specifically, financial barriers related mostly to health insurance and bribery issues, structural barriers related mostly to service availability and accessibility, and cognitive barriers related mostly to healthcare professionals' attitudes and discrimination and the vulnerable population's lack of education and health literacy. A unique theme of psychological barriers emerged from both groups with associated subthemes of mistrust, hopelessness, fear and anxiety of this vulnerable population. The current study highlights healthcare access barriers to a vulnerable non-Roma native population involved with a charity community centre in Romania. The "Healthcare Access Barriers for Vulnerable Populations" (HABVP) model is proposed as an adaption to the existing HCAB model to account for the unique perceived barriers to healthcare for this population. Recommendations for future resolution of these identified barriers are proposed.

Darwinism without populations: a more inclusive understanding of the "Survival of the Fittest".

PubMed

Bouchard, Frédéric

2011-03-01

Following Wallace's suggestion, Darwin framed his theory using Spencer's expression "survival of the fittest". Since then, fitness occupies a significant place in the conventional understanding of Darwinism, even though the explicit meaning of the term 'fitness' is rarely stated. In this paper I examine some of the different roles that fitness has played in the development of the theory. Whereas the meaning of fitness was originally understood in ecological terms, it took a statistical turn in terms of reproductive success throughout the 20th Century. This has lead to the ever-increasing importance of sexually reproducing organisms and the populations they compose in evolutionary explanations. I will argue that, moving forward, evolutionary theory should look back at its ecological roots in order to be more inclusive in the type of systems it examines. Many biological systems (e.g. clonal species, colonial species, multi-species communities) can only be satisfactorily accounted for by offering a non-reproductive account of fitness. This argument will be made by examining biological systems with very small or transient population structures. I argue this has significant consequences for how we define Darwinism, increasing the significance of survival (or persistence) over that of reproduction. Copyright © 2010 Elsevier Ltd. All rights reserved.

Comparative study of local atomic structures in Zr2CuxNi1-x (x = 0, 0.5, 1) metallic glasses

NASA Astrophysics Data System (ADS)

Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

2015-11-01

Extensive analysis has been performed to understand the key structural motifs accounting for the difference in glass forming ability in the Zr-Cu and Zr-Ni binary alloy systems. Here, the reliable atomic structure models of Zr2CuxNi1-x (x = 0, 0.5, 1) are constructed using the combination of X-ray diffraction experiments, ab initio molecular dynamics simulations and a constrained reverse Monte Carlo method. We observe a systematic variation of the interatomic distance of different atomic pairs with respect to the alloy composition. The ideal icosahedral content in all samples is limited, despite the high content of five-fold symmetry motifs. We also demonstrate that the population of Z-clusters in Zr2Cu glass is much higher than that in the Zr2Ni and Zr2Cu0.5Ni0.5 samples. And Z12 ⟨0, 0, 12, 0⟩ Voronoi polyhedra clusters prefer to form around Cu atoms, while Ni-centered clusters are more like Z11 ⟨0, 2, 8, 1⟩ clusters, which is less energetically stable compared to Z12 clusters. These two different structural properties may account for the higher glass forming ability of Zr2Cu alloy than that of Zr2Ni alloy.

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 recovery action for the species.

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 for resolving local from imported P. vivax isolates. PMID:25008859

Energetic and ecological constraints on population density of reef fishes.

PubMed

Barneche, D R; Kulbicki, M; Floeter, S R; Friedlander, A M; Allen, A P

2016-01-27

Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction. © 2016 The Author(s).

Energetic and ecological constraints on population density of reef fishes

PubMed Central

Barneche, D. R.; Kulbicki, M.; Floeter, S. R.; Friedlander, A. M.; Allen, A. P.

2016-01-01

Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction. PMID:26791611

Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.)

PubMed Central

Abebe, Tiegist D.; Naz, Ali A.; Léon, Jens

2015-01-01

Land plants are sessile organisms that cannot escape the adverse climatic conditions of a given environment. Hence, adaptation is one of the solutions to surviving in a challenging environment. This study was aimed at detecting adaptive loci in barley landraces that are affected by selection. To that end, a diverse population of barley landraces was analyzed using the genotyping by sequencing approach. Climatic data for altitude, rainfall and temperature were collected from 61 weather sites near the origin of selected landraces across Ethiopia. Population structure analysis revealed three groups whereas spatial analysis accounted significant similarities at shorter geographic distances (< 40 Km) among barley landraces. Partitioning the variance between climate variables and geographic distances indicated that climate variables accounted for most of the explainable genetic variation. Markers by climatic variables association analysis resulted in altogether 18 and 62 putative adaptive loci using Bayenv and latent factor mixed model (LFMM), respectively. Subsequent analysis of the associated SNPs revealed putative candidate genes for plant adaptation. This study highlights the presence of putative adaptive loci among barley landraces representing original gene pool of the farming communities. PMID:26483825

Genetic Diversity and Association Studies in US Hispanic/Latino Populations: Applications in the Hispanic Community Health Study/Study of Latinos

PubMed Central

Conomos, Matthew P.; Laurie, Cecelia A.; Stilp, Adrienne M.; Gogarten, Stephanie M.; McHugh, Caitlin P.; Nelson, Sarah C.; Sofer, Tamar; Fernández-Rhodes, Lindsay; Justice, Anne E.; Graff, Mariaelisa; Young, Kristin L.; Seyerle, Amanda A.; Avery, Christy L.; Taylor, Kent D.; Rotter, Jerome I.; Talavera, Gregory A.; Daviglus, Martha L.; Wassertheil-Smoller, Sylvia; Schneiderman, Neil; Heiss, Gerardo; Kaplan, Robert C.; Franceschini, Nora; Reiner, Alex P.; Shaffer, John R.; Barr, R. Graham; Kerr, Kathleen F.; Browning, Sharon R.; Browning, Brian L.; Weir, Bruce S.; Avilés-Santa, M. Larissa; Papanicolaou, George J.; Lumley, Thomas; Szpiro, Adam A.; North, Kari E.; Rice, Ken; Thornton, Timothy A.; Laurie, Cathy C.

2016-01-01

US Hispanic/Latino individuals are diverse in genetic ancestry, culture, and environmental exposures. Here, we characterized and controlled for this diversity in genome-wide association studies (GWASs) for the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). We simultaneously estimated population-structure principal components (PCs) robust to familial relatedness and pairwise kinship coefficients (KCs) robust to population structure, admixture, and Hardy-Weinberg departures. The PCs revealed substantial genetic differentiation within and among six self-identified background groups (Cuban, Dominican, Puerto Rican, Mexican, and Central and South American). To control for variation among groups, we developed a multi-dimensional clustering method to define a “genetic-analysis group” variable that retains many properties of self-identified background while achieving substantially greater genetic homogeneity within groups and including participants with non-specific self-identification. In GWASs of 22 biomedical traits, we used a linear mixed model (LMM) including pairwise empirical KCs to account for familial relatedness, PCs for ancestry, and genetic-analysis groups for additional group-associated effects. Including the genetic-analysis group as a covariate accounted for significant trait variation in 8 of 22 traits, even after we fit 20 PCs. Additionally, genetic-analysis groups had significant heterogeneity of residual variance for 20 of 22 traits, and modeling this heteroscedasticity within the LMM reduced genomic inflation for 19 traits. Furthermore, fitting an LMM that utilized a genetic-analysis group rather than a self-identified background group achieved higher power to detect previously reported associations. We expect that the methods applied here will be useful in other studies with multiple ethnic groups, admixture, and relatedness. PMID:26748518

A Hierarchical Approach Embedding Hydrologic and Population Modeling for a West Nile Virus Vector Prediction

NASA Astrophysics Data System (ADS)

Jian, Y.; Silvestri, S.; Marani, M.; Saltarin, A.; Chillemi, G.

2012-12-01

We applied a hierarchical state space model to predict the abundance of Cx.pipiens (a West Nile Virus vector) in the Po River Delta Region, Northeastern Italy. The study area has large mosquito abundance, due to a favorable environment and climate as well as dense human population. Mosquito data were collected on a weekly basis at more than 20 sites from May to September in 2010 and 2011. Cx.pipiens was the dominant species in our samples, accounting for about 90% of the more than 300,000 total captures. The hydrological component of the model accounted for evapotranspiration, infiltration and deep percolation to infer, in a 0D context, the local dynamics of soil moisture as a direct exogenous forcing of mosquito dynamics. The population model had a Gompertz structure, which included exogenous meteorological forcings and delayed internal dynamics. The models were coupled within a hierarchical statistical structure to overcome the relatively short length of the samples by exploiting the large number of concurrent observations available. The results indicated that Cx.pipiens abundance had significant density dependence at 1 week lag, which approximately matched its development time from larvae to adult. Among the exogenous controls, temperature, daylight hours, and soil moisture explained most of the dynamics. Longer daylight hours and lower soil moisture values resulted in higher abundance. The negative correlation of soil moisture and mosquito population can be explained with the abundance of water in the region (e.g. due to irrigation) and the preference for eutrophic habitats by Cx.pipien. Variations among sites were explained by land use factors as represented by distance to the nearest rice field and NDVI values: the carrying capacity decreased with increased distance to the nearest rice filed, while the maximum growth rate was positively related with NDVI. The model shows a satisfactory performance in predicting (potentially one week in advance) mosquito abundance and particularly its peak timing and magnitude.

America's Minorities--The Demographics of Diversity.

ERIC Educational Resources Information Center

O'Hare, William P.

1992-01-01

The four largest racial and ethnic minorities--African Americans, Hispanics, Asians/Pacific Islanders, and American Indians--accounted for 25 percent of the U.S. population in 1992. By 2050, these minorities may account for 47 percent of the U.S. population. The U.S. minority population is also becoming more diverse because of high rates of…

Climate and population density drive changes in cod body size throughout a century on the Norwegian coast

PubMed Central

Rogers, Lauren A.; Stige, Leif C.; Olsen, Esben M.; Knutsen, Halvor; Chan, Kung-Sik; Stenseth, Nils Chr.

2011-01-01

Understanding how populations respond to changes in climate requires long-term, high-quality datasets, which are rare for marine systems. We estimated the effects of climate warming on cod lengths and length variability using a unique 91-y time series of more than 100,000 individual juvenile cod lengths from surveys that began in 1919 along the Norwegian Skagerrak coast. Using linear mixed-effects models, we accounted for spatial population structure and the nested structure of the survey data to reveal opposite effects of spring and summer warming on juvenile cod lengths. Warm summer temperatures in the coastal Skagerrak have limited juvenile growth. In contrast, warmer springs have resulted in larger juvenile cod, with less variation in lengths within a cohort, possibly because of a temperature-driven contraction in the spring spawning period. A density-dependent reduction in length was evident only at the highest population densities in the time series, which have rarely been observed in the last decade. If temperatures rise because of global warming, nonlinearities in the opposing temperature effects suggest that negative effects of warmer summers will increasingly outweigh positive effects of warmer springs, and the coastal Skagerrak will become ill-suited for Atlantic cod. PMID:21245301

Using novel descriptor accounting for ligand-receptor interactions to define and visually explore biologically relevant chemical space.

PubMed

Rabal, Obdulia; Oyarzabal, Julen

2012-05-25

The definition and pragmatic implementation of biologically relevant chemical space is critical in addressing navigation strategies in the overlapping regions where chemistry and therapeutically relevant targets reside and, therefore, also key to performing an efficient drug discovery project. Here, we describe the development and implementation of a simple and robust method for representing biologically relevant chemical space as a general reference according to current knowledge, independently of any reference space, and analyzing chemical structures accordingly. Underlying our method is the generation of a novel descriptor (LiRIf) that converts structural information into a one-dimensional string accounting for the plausible ligand-receptor interactions as well as for topological information. Capitalizing on ligand-receptor interactions as a descriptor enables the clustering, profiling, and comparison of libraries of compounds from a chemical biology and medicinal chemistry perspective. In addition, as a case study, R-groups analysis is performed to identify the most populated ligand-receptor interactions according to different target families (GPCR, kinases, etc.), as well as to evaluate the coverage of biologically relevant chemical space by structures annotated in different databases (ChEMBL, Glida, etc.).

HOW THE FIRST STARS SHAPED THE FAINTEST GAS-DOMINATED DWARF GALAXIES

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

Verbeke, R.; Vandenbroucke, B.; Rijcke, S. De, E-mail: robbert.verbeke@UGent.be

2015-12-20

Low-mass dwarf galaxies are very sensitive test-beds for theories of cosmic structure formation since their weak gravitational fields allow the effects of the relevant physical processes to clearly stand out. Up to now, no unified account has existed of the sometimes seemingly conflicting properties of the faintest isolated dwarfs in and around the Local Group, such as Leo T and the recently discovered Leo P and Pisces A systems. Using new numerical simulations, we show that this serious challenge to our understanding of galaxy formation can be effectively resolved by taking into account the regulating influence of the ultraviolet radiation of themore » first population of stars on a dwarf’s star formation rate while otherwise staying within the standard cosmological paradigm for structure formation. These simulations produce faint, gas-dominated, star-forming dwarf galaxies that lie on the baryonic Tully–Fisher relation and that successfully reproduce a broad range of chemical, kinematical, and structural observables of real late-type dwarf galaxies. Furthermore, we stress the importance of obtaining properties of simulated galaxies in a manner as close as possible to the typically employed observational techniques.« less

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

Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata.

PubMed

Sork, Victoria L; Squire, Kevin; Gugger, Paul F; Steele, Stephanie E; Levy, Eric D; Eckert, Andrew J

2016-01-01

The ability of California tree populations to survive anthropogenic climate change will be shaped by the geographic structure of adaptive genetic variation. Our goal is to test whether climate-associated candidate genes show evidence of spatially divergent selection in natural populations of valley oak, Quercus lobata, as preliminary indication of local adaptation. Using DNA from 45 individuals from 13 localities across the species' range, we sequenced portions of 40 candidate genes related to budburst/flowering, growth, osmotic stress, and temperature stress. Using 195 single nucleotide polymorphisms (SNPs), we estimated genetic differentiation across populations and correlated allele frequencies with climate gradients using single-locus and multivariate models. The top 5% of FST estimates ranged from 0.25 to 0.68, yielding loci potentially under spatially divergent selection. Environmental analyses of SNP frequencies with climate gradients revealed three significantly correlated SNPs within budburst/flowering genes and two SNPs within temperature stress genes with mean annual precipitation, after controlling for multiple testing. A redundancy model showed a significant association between SNPs and climate variables and revealed a similar set of SNPs with high loadings on the first axis. In the RDA, climate accounted for 67% of the explained variation, when holding climate constant, in contrast to a putatively neutral SSR data set where climate accounted for only 33%. Population differentiation and geographic gradients of allele frequencies in climate-associated functional genes in Q. lobata provide initial evidence of adaptive genetic variation and background for predicting population response to climate change. © 2016 Botanical Society of America.

Diversifying Selection Underlies the Origin of Allozyme Polymorphism at the Phosphoglucose Isomerase Locus in Tigriopus californicus

PubMed Central

Schoville, Sean D.; Flowers, Jonathan M.; Burton, Ronald S.

2012-01-01

The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations. PMID:22768211

Beyond localized and distributed accounts of brain functions. Comment on “Understanding brain networks and brain organization” by Pessoa

NASA Astrophysics Data System (ADS)

Cauda, Franco; Costa, Tommaso; Tamietto, Marco

2014-09-01

Recent evidence in cognitive neuroscience lends support to the idea that network models of brain architecture provide a privileged access to the understanding of the relation between brain organization and cognitive processes [1]. The core perspective holds that cognitive processes depend on the interactions among distributed neuronal populations and brain structures, and that the impact of a given region on behavior largely depends on its pattern of anatomical and functional connectivity [2,3].

A Population Genetic Signal of Polygenic Adaptation

PubMed Central

Berg, Jeremy J.; Coop, Graham

2014-01-01

Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed knowledge about the specific loci underlying polygenic traits has begun to emerge from genome-wide association studies (GWAS). Here we combine this knowledge from GWAS with robust population genetic modeling to identify traits that may have been influenced by local adaptation. We exploit the fact that GWAS provide an estimate of the additive effect size of many loci to estimate the mean additive genetic value for a given phenotype across many populations as simple weighted sums of allele frequencies. We use a general model of neutral genetic value drift for an arbitrary number of populations with an arbitrary relatedness structure. Based on this model, we develop methods for detecting unusually strong correlations between genetic values and specific environmental variables, as well as a generalization of comparisons to test for over-dispersion of genetic values among populations. Finally we lay out a framework to identify the individual populations or groups of populations that contribute to the signal of overdispersion. These tests have considerably greater power than their single locus equivalents due to the fact that they look for positive covariance between like effect alleles, and also significantly outperform methods that do not account for population structure. We apply our tests to the Human Genome Diversity Panel (HGDP) dataset using GWAS data for height, skin pigmentation, type 2 diabetes, body mass index, and two inflammatory bowel disease datasets. This analysis uncovers a number of putative signals of local adaptation, and we discuss the biological interpretation and caveats of these results. PMID:25102153

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.

Structure coefficients and strategy selection in multiplayer games.

PubMed

McAvoy, Alex; Hauert, Christoph

2016-01-01

Evolutionary processes based on two-player games such as the Prisoner's Dilemma or Snowdrift Game are abundant in evolutionary game theory. These processes, including those based on games with more than two strategies, have been studied extensively under the assumption that selection is weak. However, games involving more than two players have not received the same level of attention. To address this issue, and to relate two-player games to multiplayer games, we introduce a notion of reducibility for multiplayer games that captures what it means to break down a multiplayer game into a sequence of interactions with fewer players. We discuss the role of reducibility in structured populations, and we give examples of games that are irreducible in any population structure. Since the known conditions for strategy selection, otherwise known as [Formula: see text]-rules, have been established only for two-player games with multiple strategies and for multiplayer games with two strategies, we extend these rules to multiplayer games with many strategies to account for irreducible games that cannot be reduced to those simpler types of games. In particular, we show that the number of structure coefficients required for a symmetric game with [Formula: see text]-player interactions and [Formula: see text] strategies grows in [Formula: see text] like [Formula: see text]. Our results also cover a type of ecologically asymmetric game based on payoff values that are derived not only from the strategies of the players, but also from their spatial positions within the population.

The Strengths and Difficulties Questionnaire (SDQ): Factor Structure and Gender Equivalence in Norwegian Adolescents.

PubMed

Bøe, Tormod; Hysing, Mari; Skogen, Jens Christoffer; Breivik, Kyrre

2016-01-01

Although frequently used with older adolescents, few studies of the factor structure, internal consistency and gender equivalence of the SDQ exists for this age group, with inconsistent findings. In the present study, confirmatory factor analysis (CFA) was used to evaluate the five-factor structure of the SDQ in a population sample of 10,254 16-18 year-olds from the youth@hordaland study. Measurement invariance across gender was assessed using multigroup CFA. A modestly modified five-factor solution fitted the data acceptably, accounting for one cross loading and some local dependencies. Importantly, partial measurement non-invariance was identified, with differential item functioning in eight items, and higher correlations between emotional and conduct problems for boys compared to girls. Implications for use clinically and in research are discussed.

Ancestral populations perform better in a novel environment: domestication of medfly populations from five global regions

PubMed Central

Diamantidis, Alexandros D.; Carey, James R.; Nakas, Christos T.; Papadopoulos, Nikos T.

2010-01-01

Geographically isolated populations of a species may differ in several aspects of life-history, morphology, behavior, and genetic structure as a result of adaptation in ecologically diverse habitats. We used a global invasive species, the Mediterranean fruit fly to investigate, whether adaptation to a novel environment differs among geographically isolated populations that vary in major life history components such as life span and reproduction. We used wild populations from five global regions (Kenya, Hawaii, Guatemala, Portugal, and Greece). Adult demographic traits were monitored in F2, F5, F7 and F9 generations in captivity. Although domestication in constant laboratory conditions had a different effect on the mortality and reproductive rates of the different populations, a general trend of decreasing life span and age of first reproduction was observed for most medfly populations tested. However, taking into account longevity of both sexes, age-specific reproductive schedules, and average reproductive rates we found that the ancestral Kenyan population kept the above life history traits stable during domestication compared to the other populations tested. These findings provide important insights in the life-history evolution of this model species, and suggest that ancestral medfly populations perform better than the derived – invasive ones in a novel environment. PMID:21278856

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 coefficient of gene differentiation were fairly small, the studied populations are indeed genetically similar and that the genetic structure of populations in a geographical region is primarily influenced by their ancestry and not by socio-cultural hierarchy or language. The scenario of genetic structure, however, might be different for other regions of the subcontinent where populations have more similar ethnic and linguistic backgrounds and there might be variations in the patterns of genomic and socio-cultural affinities in different geographical regions. PMID:15694006

Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic.

PubMed

Coscia, I; Vogiatzi, E; Kotoulas, G; Tsigenopoulos, C S; Mariani, S

2012-05-01

Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here, we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 expressed sequence tag-linked markers, as well as a portion of the mitochondrial DNA (mtDNA) control region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, although the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.

Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens

PubMed Central

McDougall, Craig A.; Welsh, Amy B.; Gosselin, Thierry; Anderson, W. Gary; Nelson, Patrick A.

2017-01-01

Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525–750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013–0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways. PMID:28329005

Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens.

PubMed

McDougall, Craig A; Welsh, Amy B; Gosselin, Thierry; Anderson, W Gary; Nelson, Patrick A

2017-01-01

Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525-750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013-0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways.

Social and spatial effects on genetic variation between foraging flocks in a wild bird population.

PubMed

Radersma, Reinder; Garroway, Colin J; Santure, Anna W; de Cauwer, Isabelle; Farine, Damien R; Slate, Jon; Sheldon, Ben C

2017-10-01

Social interactions are rarely random. In some instances, animals exhibit homophily or heterophily, the tendency to interact with similar or dissimilar conspecifics, respectively. Genetic homophily and heterophily influence the evolutionary dynamics of populations, because they potentially affect sexual and social selection. Here, we investigate the link between social interactions and allele frequencies in foraging flocks of great tits (Parus major) over three consecutive years. We constructed co-occurrence networks which explicitly described the splitting and merging of 85,602 flocks through time (fission-fusion dynamics), at 60 feeding sites. Of the 1,711 birds in those flocks, we genotyped 962 individuals at 4,701 autosomal single nucleotide polymorphisms (SNPs). By combining genomewide genotyping with repeated field observations of the same individuals, we were able to investigate links between social structure and allele frequencies at a much finer scale than was previously possible. We explicitly accounted for potential spatial effects underlying genetic structure at the population level. We modelled social structure and spatial configuration of great tit fission-fusion dynamics with eigenvector maps. Variance partitioning revealed that allele frequencies were strongly affected by group fidelity (explaining 27%-45% of variance) as individuals tended to maintain associations with the same conspecifics. These conspecifics were genetically more dissimilar than expected, shown by genomewide heterophily for pure social (i.e., space-independent) grouping preferences. Genomewide homophily was linked to spatial configuration, indicating spatial segregation of genotypes. We did not find evidence for homophily or heterophily for putative socially relevant candidate genes or any other SNP markers. Together, these results demonstrate the importance of distinguishing social and spatial processes in determining population structure. © 2017 John Wiley & Sons Ltd.

The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

PubMed Central

2011-01-01

Background While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m) may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes) across its wide distributional range in Chile and Argentina. Results Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. Conclusions Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations. PMID:21672266

Ising-based model of opinion formation in a complex network of interpersonal interactions

NASA Astrophysics Data System (ADS)

Grabowski, A.; Kosiński, R. A.

2006-03-01

In our work the process of opinion formation in the human population, treated as a scale-free network, is modeled and investigated numerically. The individuals (nodes of the network) are characterized by their authorities, which influence the interpersonal interactions in the population. Hierarchical, two-level structures of interpersonal interactions and spatial localization of individuals are taken into account. The effect of the mass media, modeled as an external stimulation acting on the social network, on the process of opinion formation is investigated. It was found that in the time evolution of opinions of individuals critical phenomena occur. The first one is observed in the critical temperature of the system TC and is connected with the situation in the community, which may be described by such quantifiers as the economic status of people, unemployment or crime wave. Another critical phenomenon is connected with the influence of mass media on the population. As results from our computations, under certain circumstances the mass media can provoke critical rebuilding of opinions in the population.

What happens to the heart in chronic kidney disease?

PubMed

Rutherford, E; Mark, P B

2017-03-01

Cardiovascular disease is common in patients with chronic kidney disease. The increased risk of cardiovascular disease seen in this population is attributable to both traditional and novel vascular risk factors. Risk of sudden cardiac or arrhythmogenic death is greatly exaggerated in chronic kidney disease, particularly in patients with end stage renal disease where the risk is roughly 20 times that of the general population. The reasons for this increased risk are not entirely understood and while atherosclerosis is accelerated in the presence of chronic kidney disease, premature myocardial infarction does not solely account for the excess risk. Recent work demonstrates that the structure and function of the heart starts to alter early in chronic kidney disease, independent of other risk factors. The implications of cardiac remodelling and hypertrophy may predispose chronic kidney disease patients to heart failure, arrhythmia and myocardial ischaemia. Further research is needed to minimise cardiovascular risk associated with structural and functional heart disease associated with chronic kidney disease.

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 valuable resource for future genomic studies and crop improvement strategies. PMID:25412256

Beyond Population and Environment: Household Life Cycle Demography and Land Use Allocation among Small Farm Colonists in the Amazon

NASA Technical Reports Server (NTRS)

Perz, Stephen G.; Walker, Robert T.; Caldas, Marcellus M.

2006-01-01

Most research featuring demographic factors in environmental change has focused on processes operating at the level of national or global populations. This paper focuses on household-level demographic life cycles among colonists in the Amazon, and evaluates the impacts on land use allocation. The analysis goes beyond prior research by including a broader suite of demographic variables, and by simultaneously assessing their impacts on multiple land uses with different economic and ecological implications. We estimate a system of structural equations that accounts for endogeneity among land uses, and the findings indicate stronger demographic effects than previous work. These findings bear implications for modeling land use, and the place of demography in environmental research.

Do Canadian Civil Servants Care About the Health of Populations?

PubMed Central

Lavis, John N.; Ross, Suzanne E.; Stoddart, Gregory L.; Hohenadel, Joanne M.; McLeod, Christopher B.; Evans, Robert G.

2003-01-01

Objectives. This article describes Canadian civil servants’ awareness of, attitudes toward, and self-reported use of ideas about the determinants of health. Methods. Federal and provincial civil servants in departments of finance, labor, social services, and health were surveyed. Results. With civil servants in finance departments a notable exception, most Canadian civil servants see the health of populations as a relevant outcome for their sectors. Many (65%) report that ideas about the determinants of health have already influenced policymaking in their sector, but most (83%) say they need more information about the health consequences of the policy alternatives their departments face. Conclusions. Civil servants should consider developing accountability structures for health and researchers should consider producing and transferring more policy-relevant research. PMID:12660214

Human behavior in Prisoner's Dilemma experiments suppresses network reciprocity

NASA Astrophysics Data System (ADS)

Gracia-Lázaro, Carlos; Cuesta, José A.; Sánchez, Angel; Moreno, Yamir

2012-03-01

During the last few years, much research has been devoted to strategic interactions on complex networks. In this context, the Prisoner's Dilemma has become a paradigmatic model, and it has been established that imitative evolutionary dynamics lead to very different outcomes depending on the details of the network. We here report that when one takes into account the real behavior of people observed in the experiments, both at the mean-field level and on utterly different networks, the observed level of cooperation is the same. We thus show that when human subjects interact in a heterogeneous mix including cooperators, defectors and moody conditional cooperators, the structure of the population does not promote or inhibit cooperation with respect to a well mixed population.

Understanding the demographic drivers of realized population growth rates.

PubMed

Koons, David N; Arnold, Todd W; Schaub, Michael

2017-10-01

Identifying the demographic parameters (e.g., reproduction, survival, dispersal) that most influence population dynamics can increase conservation effectiveness and enhance ecological understanding. Life table response experiments (LTRE) aim to decompose the effects of change in parameters on past demographic outcomes (e.g., population growth rates). But the vast majority of LTREs and other retrospective population analyses have focused on decomposing asymptotic population growth rates, which do not account for the dynamic interplay between population structure and vital rates that shape realized population growth rates (λt=Nt+1/Nt) in time-varying environments. We provide an empirical means to overcome these shortcomings by merging recently developed "transient life-table response experiments" with integrated population models (IPMs). IPMs allow for the estimation of latent population structure and other demographic parameters that are required for transient LTRE analysis, and Bayesian versions additionally allow for complete error propagation from the estimation of demographic parameters to derivations of realized population growth rates and perturbation analyses of growth rates. By integrating available monitoring data for Lesser Scaup over 60 yr, and conducting transient LTREs on IPM estimates, we found that the contribution of juvenile female survival to long-term variation in realized population growth rates was 1.6 and 3.7 times larger than that of adult female survival and fecundity, respectively. But a persistent long-term decline in fecundity explained 92% of the decline in abundance between 1983 and 2006. In contrast, an improvement in adult female survival drove the modest recovery in Lesser Scaup abundance since 2006, indicating that the most important demographic drivers of Lesser Scaup population dynamics are temporally dynamic. In addition to resolving uncertainty about Lesser Scaup population dynamics, the merger of IPMs with transient LTREs will strengthen our understanding of demography for many species as we aim to conserve biodiversity during an era of non-stationary global change. © 2017 by the Ecological Society of America.

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.

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

There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects. PMID:24223962

Pollinator community structure and sources of spatial variation in plant--pollinator interactions in Clarkia xantiana ssp. xantiana.

PubMed

Moeller, David A

2005-01-01

The structure of diverse floral visitor assemblages and the nature of spatial variation in plant-pollinator interactions have important consequences for floral evolution and reproductive interactions among pollinator-sharing plant species. In this study, I use surveys of floral visitor communities across the geographic range of Clarkia xantiana ssp. xantiana (hereafter C. x. xantiana) (Onagraceae) to examine the structure of visitor communities, the specificity of the pollination system, and the role of variation in the abiotic vs. biotic environment in contributing to spatial variation in pollinator abundance and community composition. Although the assemblage of bee visitors to C. x. xantiana is very diverse (49 species), few were regular visitors and likely to act as pollinators. Seventy-four percent of visitor species accounted for only 11% of total visitor abundance and 69% were collected in three or fewer plant populations (of ten). Of the few reliable visitors, Clarkia pollen specialist bees were the most frequent visitors, carried more Clarkia pollen compared to generalist foragers, and were less likely to harbor foreign pollen. Overall, the core group of pollinators was obscured by high numbers of incidental visitors that are unlikely to contribute to pollination. In a geographic context, the composition of specialist pollinator assemblages varied considerably along the abiotic gradient spanning the subspecies' range. However, the overall abundance of specialist pollinators in plant populations was not influenced by the broad-scale abiotic gradient but strongly affected by local plant community associations. C. x. xantiana populations sympatric with pollinator-sharing congeners were visited twice as often by specialists compared to populations occurring alone. These positive indirect interactions among plant species may promote population persistence and species coexistence by enhancing individual reproductive success.

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory.

PubMed

Herrera, C M; Bazaga, P

2011-04-01

Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions. © 2011 Blackwell Publishing Ltd.

Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn Disease

PubMed Central

Jiang, Duo; Zhong, Sheng; McPeek, Mary Sara

2016-01-01

In genetic association testing, failure to properly control for population structure can lead to severely inflated type 1 error and power loss. Meanwhile, adjustment for relevant covariates is often desirable and sometimes necessary to protect against spurious association and to improve power. Many recent methods to account for population structure and covariates are based on linear mixed models (LMMs), which are primarily designed for quantitative traits. For binary traits, however, LMM is a misspecified model and can lead to deteriorated performance. We propose CARAT, a binary-trait association testing approach based on a mixed-effects quasi-likelihood framework, which exploits the dichotomous nature of the trait and achieves computational efficiency through estimating equations. We show in simulation studies that CARAT consistently outperforms existing methods and maintains high power in a wide range of population structure settings and trait models. Furthermore, CARAT is based on a retrospective approach, which is robust to misspecification of the phenotype model. We apply our approach to a genome-wide analysis of Crohn disease, in which we replicate association with 17 previously identified regions. Moreover, our analysis on 5p13.1, an extensively reported region of association, shows evidence for the presence of multiple independent association signals in the region. This example shows how CARAT can leverage known disease risk factors to shed light on the genetic architecture of complex traits. PMID:26833331

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.

Constructing fertility tables for Soviet populations.

PubMed

Mazur, D P

1976-02-01

Because the 1970 Soviet Union census does not provide information on the age structure of men and women separately by sex and according to their ethnic affiliation, the 1959 USSR census data serve as the basis to infer knowledge about ethnic fertility. The model takes into account (1) the total number of births in 1960, estimated from the child-woman ratio in 1959, (2) the age structure of women in 1959, and (3) the assumed pattern of age-specific birth rates structured in terms of the modal age at childbearing and the length of the fertility age span. The results show that Ukrainians among the Slav populations ranked as the lowest with 2.07 children born per woman. Their total fertility contrasts with that of Kazakhs native to Central Asia, who reportedly according to Soviet sources had 7.46 children per woman in 1958-1959, and whose estimated rate is around 8.59 children. Extreme variations appear in the estimates of fertility among nationalities of the Caucasus region, Volga Basin, and to a lesser degree in Siberia. Official Soviet calculations of crude birth rates and age-specific rates for 15 Union Republics in 1967-1968 are transcribed and compared with the estimates for nationalities in 1959-1960. The same theoretical model used to generate the Soviet rates may be adapted under different assumptions to non-Soviet populations in other situations where the data are scanty or incomplete.

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.

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 key sex-age classes contributing to demographic variance and thus decreasing N e /N in a small age-structured population inhabiting a variable environment. They thereby demonstrate how assessments of N e can incorporate stochastic sex- and age-specific demography and elucidate key demographic processes affecting a population's evolutionary trajectory and viability. Furthermore, our analyses show that N e for the focal chough population is critically small, implying that management to re-establish genetic connectivity may be required to ensure population viability. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

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.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

PubMed Central

Roth, Andrew; Khattra, Jaswinder; Ho, Julie; Yap, Damian; Prentice, Leah M.; Melnyk, Nataliya; McPherson, Andrew; Bashashati, Ali; Laks, Emma; Biele, Justina; Ding, Jiarui; Le, Alan; Rosner, Jamie; Shumansky, Karey; Marra, Marco A.; Gilks, C. Blake; Huntsman, David G.; McAlpine, Jessica N.; Aparicio, Samuel

2014-01-01

The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational landscapes. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting evolutionary dynamics of copy number alterations (CNA) and loss of heterozygosity (LOH) in whole-genome sequencing data remain underdeveloped. We present a novel probabilistic model, TITAN, to infer CNA and LOH events while accounting for mixtures of cell populations, thereby estimating the proportion of cells harboring each event. We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature of the evolving cancer genome. Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key modeling assumptions of TITAN. PMID:25060187

Galactic dual population models of gamma-ray bursts

NASA Technical Reports Server (NTRS)

Higdon, J. C.; Lingenfelter, R. E.

1994-01-01

We investigate in more detail the properties of two-population models for gamma-ray bursts in the galactic disk and halo. We calculate the gamma-ray burst statistical properties, mean value of (V/V(sub max)), mean value of cos Theta, and mean value of (sin(exp 2) b), as functions of the detection flux threshold for bursts coming from both Galactic disk and massive halo populations. We consider halo models inferred from the observational constraints on the large-scale Galactic structure and we compare the expected values of mean value of (V/V(sub max)), mean value of cos Theta, and mean value of (sin(exp 2) b), with those measured by Burst and Transient Source Experiment (BATSE) and other detectors. We find that the measured values are consistent with solely Galactic populations having a range of halo distributions, mixed with local disk distributions, which can account for as much as approximately 25% of the observed BATSE bursts. M31 does not contribute to these modeled bursts. We also demonstrate, contrary to recent arguments, that the size-frequency distributions of dual population models are quite consistent with the BATSE observations.

Ultrashort electromagnetic pulse control of intersubband quantum well transitions

PubMed Central

2012-01-01

We study the creation of high-efficiency controlled population transfer in intersubband transitions of semiconductor quantum wells. We give emphasis to the case of interaction of the semiconductor quantum well with electromagnetic pulses with a duration of few cycles and even a single cycle. We numerically solve the effective nonlinear Bloch equations for a specific double GaAs/AlGaAs quantum well structure, taking into account the ultrashort nature of the applied field, and show that high-efficiency population inversion is possible for specific pulse areas. The dependence of the efficiency of population transfer on the electron sheet density and the carrier envelope phase of the pulse is also explored. For electromagnetic pulses with a duration of several cycles, we find that the change in the electron sheet density leads to a very different response of the population in the two subbands to pulse area. However, for pulses with a duration equal to or shorter than 3 cycles, we show that efficient population transfer between the two subbands is possible, independent of the value of electron sheet density, if the pulse area is Π. PMID:22916956

Ultrashort electromagnetic pulse control of intersubband quantum well transitions.

PubMed

Paspalakis, Emmanuel; Boviatsis, John

2012-08-23

: We study the creation of high-efficiency controlled population transfer in intersubband transitions of semiconductor quantum wells. We give emphasis to the case of interaction of the semiconductor quantum well with electromagnetic pulses with a duration of few cycles and even a single cycle. We numerically solve the effective nonlinear Bloch equations for a specific double GaAs/AlGaAs quantum well structure, taking into account the ultrashort nature of the applied field, and show that high-efficiency population inversion is possible for specific pulse areas. The dependence of the efficiency of population transfer on the electron sheet density and the carrier envelope phase of the pulse is also explored. For electromagnetic pulses with a duration of several cycles, we find that the change in the electron sheet density leads to a very different response of the population in the two subbands to pulse area. However, for pulses with a duration equal to or shorter than 3 cycles, we show that efficient population transfer between the two subbands is possible, independent of the value of electron sheet density, if the pulse area is Π.

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 most valuable for conservation based on their contributions to gene flow and genetic diversity. © 2015 Society for Conservation Biology.

Indirect estimates of natal dispersal distance from genetic data in a stream-dwelling fish (Mogurnda adspersa).

PubMed

Shipham, Ashlee; Schmidt, Daniel J; Hughes, Jane M

2013-01-01

Recent work has highlighted the need to account for hierarchical patterns of genetic structure when estimating evolutionary and ecological parameters of interest. This caution is particularly relevant to studies of riverine organisms, where hierarchical structure appears to be commonplace. Here, we indirectly estimate dispersal distance in a hierarchically structured freshwater fish, Mogurnda adspersa. Microsatellite and mitochondrial DNA (mtDNA) data were obtained for 443 individuals across 27 sites separated by an average of 1.3 km within creeks of southeastern Queensland, Australia. Significant genetic structure was found among sites (mtDNA Φ(ST) = 0.508; microsatellite F(ST) = 0.225, F'(ST) = 0.340). Various clustering methods produced congruent patterns of hierarchical structure reflecting stream architecture. Partial mantel tests identified contiguous sets of sample sites where isolation by distance (IBD) explained F(ST) variation without significant contribution of hierarchical structure. Analysis of mean natal dispersal distance (σ) within sets of IBD-linked sample sites suggested most dispersal occurs over less than 1 km, and the average effective density (D(e)) was estimated at 11.5 individuals km(-1); indicating sedentary behavior and small effective population size are responsible for the remarkable patterns of genetic structure observed. Our results demonstrate that Rousset's regression-based method is applicable to estimating the scale of dispersal in riverine organisms and that identifying contiguous populations that satisfy the assumptions of this model is achievable with genetic clustering methods and partial correlations.

Applying Organizational Learning Research to Accountable Care Organizations.

PubMed

Nembhard, Ingrid M; Tucker, Anita L

2016-12-01

To accomplish the goal of improving quality of care while simultaneously reducing cost, Accountable Care Organizations (ACOs) need to find new and better ways of providing health care to populations of patients. This requires implementing best practices and improving collaboration across the multiple entities involved in care delivery, including patients. In this article, we discuss seven lessons from the organizational learning literature that can help ACOs overcome the inherent challenges of learning how to work together in radically new ways. The lessons involve setting expectations, creating a supportive culture, and structuring the improvement efforts. For example, with regard to setting expectations, framing the changes as learning experiences rather than as implementation projects encourages the teams to utilize helpful activities, such as dry runs and pilot tests. It is also important to create an organizational culture where employees feel safe pointing out improvement opportunities and experimenting with new ways of working. With regard to structure, stable, cross-functional teams provide a powerful building block for effective improvement efforts. The article concludes by outlining opportunities for future research on organizational learning in ACOs. © The Author(s) 2016.

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.

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

Genetic diversity and structure of Megabalanus azoricus in the Azores: Implications for aquaculture management

NASA Astrophysics Data System (ADS)

De Girolamo, Mirko; Torboli, Valentina; Pallavicini, Alberto; Isidro, Eduardo

2017-11-01

Megabalanus azoricus giant barnacles are the most traditional seafood of the Azores archipelago (NE Atlantic). This valuable commercial species has been highly exploited in the past and it is considered one of the key species for the development of aquaculture in the region. Despite the importance for conservation and aquaculture there is still a lack of basic information about M. azoricus genetic diversity and population structure. Here we used seven microsatellites markers to analyse 300 samples collected at six out of nine islands of the Azores archipelago, including also different locations from a single island, to provide information on the scale of genetic diversity and population structure of this species. Parameters like heterozygosity, allelic richness and effective number of alleles indicated a high genetic diversity and variability among islands. Pairwise comparisons and PCoA analysis on FST and Jost's DEST showed significant and evident differentiation among sampling locations. Additionally, AMOVA allocates a small (6.02%) but statistically significant portion of the variance to the among Island level revealing also a weak resolution (1.87%) at finer scale. Additionally Monte Carlo resampling methods indicated the most likely sources of the recruits were the local or adjacent populations. Genetic risks associated with the giant barnacle potential production scheme should be taken into account in a future management plan delimiting, as precautionary measure, this culture at a single island or at groups of islands here identified. Moreover a monitoring strategy should be implemented with the aim to evaluate possible changes in genetic parameters of native populations.

Dynamics and management of stage-structured fish stocks.

PubMed

Meng, Xinzhu; Lundström, Niklas L P; Bodin, Mats; Brännström, Åke

2013-01-01

With increasing fishing pressures having brought several stocks to the brink of collapse, there is a need for developing efficient harvesting methods that account for factors beyond merely yield or profit. We consider the dynamics and management of a stage-structured fish stock. Our work is based on a consumer-resource model which De Roos et al. (in Theor. Popul. Biol. 73, 47-62, 2008) have derived as an approximation of a physiologically-structured counterpart. First, we rigorously prove the existence of steady states in both models, that the models share the same steady states, and that there exists at most one positive steady state. Furthermore, we carry out numerical investigations which suggest that a steady state is globally stable if it is locally stable. Second, we consider multiobjective harvesting strategies which account for yield, profit, and the recovery potential of the fish stock. The recovery potential is a measure of how quickly a fish stock can recover from a major disturbance and serves as an indication of the extinction risk associated with a harvesting strategy. Our analysis reveals that a small reduction in yield or profit allows for a disproportional increase in recovery potential. We also show that there exists a harvesting strategy with yield close to the maximum sustainable yield (MSY) and profit close to that associated with the maximum economic yield (MEY). In offering a good compromise between MSY and MEY, we believe that this harvesting strategy is preferable in most instances. Third, we consider the impact of harvesting on population size structure and analytically determine the most and least harmful harvesting strategies. We conclude that the most harmful harvesting strategy consists of harvesting both adults and juveniles, while harvesting only adults is the least harmful strategy. Finally, we find that a high percentage of juvenile biomass indicates elevated extinction risk and might therefore serve as an early-warning signal of impending stock collapse.

Protocol and practice in the adaptive management of waterfowl harvests

USGS Publications Warehouse

Johnson, F.; Williams, K.

1999-01-01

Waterfowl harvest management in North America, for all its success, historically has had several shortcomings, including a lack of well-defined objectives, a failure to account for uncertain management outcomes, and inefficient use of harvest regulations to understand the effects of management. To address these and other concerns, the U.S. Fish and Wildlife Service began implementation of adaptive harvest management in 1995. Harvest policies are now developed using a Markov decision process in which there is an explicit accounting for uncontrolled environmental variation, partial controllability of harvest, and structural uncertainty in waterfowl population dynamics. Current policies are passively adaptive, in the sense that any reduction in structural uncertainty is an unplanned by-product of the regulatory process. A generalization of the Markov decision process permits the calculation of optimal actively adaptive policies, but it is not yet clear how state-specific harvest actions differ between passive and active approaches. The Markov decision process also provides managers the ability to explore optimal levels of aggregation or "management scale" for regulating harvests in a system that exhibits high temporal, spatial, and organizational variability. Progress in institutionalizing adaptive harvest management has been remarkable, but some managers still perceive the process as a panacea, while failing to appreciate the challenges presented by this more explicit and methodical approach to harvest regulation. Technical hurdles include the need to develop better linkages between population processes and the dynamics of landscapes, and to model the dynamics of structural uncertainty in a more comprehensive fashion. From an institutional perspective, agreement on how to value and allocate harvests continues to be elusive, and there is some evidence that waterfowl managers have overestimated the importance of achievement-oriented factors in setting hunting regulations. Indeed, it is these unresolved value judgements, and the lack of an effective structure for organizing debate, that present the greatest threat to adaptive harvest management as a viable means for coping with management uncertainty. Copyright ?? 1999 by The Resilience Alliance.

Measuring the attitudes of dental students towards social accountability following dental education - Qualitative findings.

PubMed

Chen, Vivian; Foster Page, Lyndie; McMillan, John; Lyons, Karl; Gibson, Barry

2016-06-01

The term social accountability has gained increased interest in medical education, but is relatively unexplored in dentistry. The aim of this study is to explore dental students' attitudes towards social accountability. A qualitative study utilizing focus groups with University of Otago final year (5th year) Bachelor of Dental Surgery (BDS) students was carried out. A questionnaire designed to measure medical students' attitudes towards social responsibility was used as a guide. Following data collection, framework analysis was used to analyze each of the three focus groups, and repeating themes were noted. Analysis of the focus groups discovered recurring themes, such that participants believed that dentists should be accountable to society in a professional context and that they are responsible for patients who present at their clinic but that there is no professional obligation to help reduce oral health inequalities by working with populations facing inequalities. There was strong agreement that there needs to be change to the dental health care system from a structural and political level to address oral health inequalities, rather than individual dentists assuming greater responsibility. Our findings show that dental education may not be accountable to society in the sense that it is not producing graduates who believe that they have an obligation to address the priority oral health concerns of society.

Psychopathology in Bariatric Surgery Candidates: A Review of Studies Using Structured Diagnostic Interviews

PubMed Central

Malik, Sarah; Mitchell, James E.; Engel, Scott; Crosby, Ross; Wonderlich, Steve

2014-01-01

Psychiatric disorders are not uncommon among severely obese patients who present for bariatric surgery. This paper (1) reviews the results of the published studies using the structured interviews to assess psychopathology in bariatric surgery candidates; (2) compares the prevalence rates of psychiatric disorders across these studies with the data from other population samples; and (3) assesses whether sociodemographic variables appear to affect these prevalence rates. We searched online resources, PubMed, PsychINFO and reference lists of all the relevant articles to provide an overview of evidence so far and highlight some details in the assessment and comparisons of different samples in different countries. The prevalence estimates in the non- treatment obese group did not appear to differ substantially from the general population group in the US or the Italian population samples, although they were relatively higher for the German population. However, the rates of psychopathology in the bariatric surgery candidates were considerably higher than the other two population groups in all the samples. Overall, the most common category of lifetime Axis I disorders in all the studies was affective disorders, with anxiety disorders being the most common category of current Axis I disorders. Certain demographic characteristics are also associated with higher rates of psychopathology, such as, female gender, low socioeconomic status, higher BMI. Overall, methodological and sociodemographic differences make these studies difficult to compare and these differences should be taken into account when interpreting the results. PMID:24290079

Racial and Socioeconomic Variation in Genetic Markers of Telomere Length: A Cross-Sectional Study of U.S. Older Adults.

PubMed

Hamad, Rita; Tuljapurkar, Shripad; Rehkopf, David H

2016-09-01

Shorter telomere length (TL) has been associated with stress and adverse socioeconomic conditions, yet U.S. blacks have longer TL than whites. The role of genetic versus environmental factors in explaining TL by race and socioeconomic position (SEP) remains unclear. We used data from the U.S. Health and Retirement Study (N=11,934) to test the hypothesis that there are differences in TL-associated SNPs by race and SEP. We constructed a TL polygenic risk score (PRS) and examined its association with race/ethnicity, educational attainment, assets, gender, and age. U.S. blacks were more likely to have a lower PRS for TL, as were older individuals and men. Racial differences in TL were statistically accounted for when controlling for population structure using genetic principal components. The GWAS-derived SNPs for TL, however, may not have consistent associations with TL across different racial/ethnic groups. This study showed that associations of race/ethnicity with TL differed when accounting for population stratification. The role of race/ethnicity for TL remains uncertain, however, as the genetic determinants of TL may differ by race/ethnicity. Future GWAS samples should include racially diverse participants to allow for better characterization of the determinants of TL in human populations. Copyright © 2016 Forschungsgesellschaft für Arbeitsphysiologie und Arbeitschutz e.V. Published by Elsevier B.V. All rights reserved.

A reduced number of mtSNPs saturates mitochondrial DNA haplotype diversity of worldwide population groups.

PubMed

Salas, Antonio; Amigo, Jorge

2010-05-03

The high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population. Applications of the selected mtSNP panel range from anthropologic and medical studies to forensic genetic casework. This study proposes a new simulation-based method that explores the ability of different mtSNP panels to yield the maximum levels of discrimination power. The method explores subsets of mtSNPs of different sizes randomly chosen from a preselected panel of mtSNPs based on frequency. More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations ("African-Americans" and "Hispanics") were collected from GenBank and the literature, and were used as training sets. Haplotype diversity was measured for each combination of mtSNP and compared with existing mtSNP panels available in the literature. The data indicates that only a reduced number of mtSNPs ranging from six to 22 are needed to account for 95% of the maximum haplotype diversity of a given population sample. However, only a small proportion of the best mtSNPs are shared between populations, indicating that there is not a perfect set of "universal" mtSNPs suitable for all population contexts. The discrimination power provided by these mtSNPs is much higher than the power of the mtSNP panels proposed in the literature to date. Some mtSNP combinations also yield high diversity values in admixed populations. The proposed computational approach for exploring combinations of mtSNPs that optimise the discrimination power of a given set of mtSNPs is more efficient than previous empirical approaches. In contrast to precedent findings, the results seem to indicate that only few mtSNPs are needed to reach high levels of discrimination power in a population, independently of its ancestral background.

A Reduced Number of mtSNPs Saturates Mitochondrial DNA Haplotype Diversity of Worldwide Population Groups

PubMed Central

Salas, Antonio; Amigo, Jorge

2010-01-01

Background The high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population. Applications of the selected mtSNP panel range from anthropologic and medical studies to forensic genetic casework. Methodology/Principal Findings This study proposes a new simulation-based method that explores the ability of different mtSNP panels to yield the maximum levels of discrimination power. The method explores subsets of mtSNPs of different sizes randomly chosen from a preselected panel of mtSNPs based on frequency. More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations (“African-Americans” and “Hispanics”) were collected from GenBank and the literature, and were used as training sets. Haplotype diversity was measured for each combination of mtSNP and compared with existing mtSNP panels available in the literature. The data indicates that only a reduced number of mtSNPs ranging from six to 22 are needed to account for 95% of the maximum haplotype diversity of a given population sample. However, only a small proportion of the best mtSNPs are shared between populations, indicating that there is not a perfect set of “universal” mtSNPs suitable for all population contexts. The discrimination power provided by these mtSNPs is much higher than the power of the mtSNP panels proposed in the literature to date. Some mtSNP combinations also yield high diversity values in admixed populations. Conclusions/Significance The proposed computational approach for exploring combinations of mtSNPs that optimise the discrimination power of a given set of mtSNPs is more efficient than previous empirical approaches. In contrast to precedent findings, the results seem to indicate that only few mtSNPs are needed to reach high levels of discrimination power in a population, independently of its ancestral background. PMID:20454657

Digital Curation: Learning and Legacy in Later Life

ERIC Educational Resources Information Center

Manchester, Helen; Facer, Keri

2015-01-01

The world population is ageing. In the UK alone, it is projected that by 2035 those aged 65 and over will account for 23 per cent of the total population whilst the number of people aged 85 and over will account for 5 per cent of the total population. At the same time, the digital transformations of the last few decades are leaving behind many…

An examination of social capital and social disorganisation in neighbourhoods in the British household panel study.

PubMed

McCulloch, Andrew

2003-04-01

Recent developments in social science research suggest that social environmental factors may be important for explaining community variations in health. We investigate the structural sources of two mechanisms that produce community variations in health. Using survey data collected from a representative cross-section of British households we examine variations in neighbourhood social capital and neighbourhood social disorganisation across a sample of British neighbourhoods. Adjusting for respondent's attributes, we assess the effects of neighbourhood characteristics measured by the 1991 census in Britain. The results show that concentrated affluence, residential instability and ethnic heterogeneity predict social capital for women. Population density is the only neighbourhood characteristic to predict social capital for men. For both men and women concentrated disadvantage and population density are associated with social disorganisation. Residential instability is additionally associated with social disorganisation for women. For women it was found that neighbourhood characteristics interact with individual social class in accounting for variations in social capital, the effects of neighbourhood characteristics being larger for those in professional and managerial and skilled non-manual occupations. The results show that neighbourhood structural characteristics influence social organisation processes. This helps establish a link between the structural characteristics of neighbourhoods and individual health outcomes.

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.

Rhizobium etli and Rhizobium gallicum Nodulate Common Bean (Phaseolus vulgaris) in a Traditionally Managed Milpa Plot in Mexico: Population Genetics and Biogeographic Implications

PubMed Central

Silva, Claudia; Vinuesa, Pablo; Eguiarte, Luis E.; Martínez-Romero, Esperanza; Souza, Valeria

2003-01-01

The stability of the genetic structure of rhizobial populations nodulating Phaseolus vulgaris cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial rrs, glnII, nifH, and nodB sequences), along with host range experiments, placed the isolates examined in Rhizobium etli bv. phaseoli and Rhizobium gallicum bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the R. etli and R. gallicum populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis, nifH copy number determination, and host range experiments. Plasmid profiles and nifH hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an R. gallicum bv. gallicum population nodulating common bean in America are discussed. PMID:12571008

Population size vs. social connectedness - A gene-culture coevolutionary approach to cumulative cultural evolution.

PubMed

Kobayashi, Yutaka; Ohtsuki, Hisashi; Wakano, Joe Y

2016-10-01

It has long been debated if population size is a crucial determinant of the level of culture. While empirical results are mixed, recent theoretical studies suggest that social connectedness between people may be a more important factor than the size of the entire population. These models, however, do not take into account evolutionary responses of learning strategies determining the mode of transmission and innovation and are hence not suitable for predicting the long-term implications of parameters of interest. In the present paper, to address this issue, we provide a gene-culture coevolution model, in which the microscopic learning process of each individual is explicitly described as a continuous-time stochastic process and time allocation to social and individual learning is allowed to evolve. We have found that social connectedness has a larger impact on the equilibrium level of culture than population size especially when connectedness is weak and population size is large. This result, combined with those of previous culture-only models, points to the importance of studying separate effects of population size and internal social structure to better understand spatiotemporal variation in the level of culture. Copyright © 2016 Elsevier Inc. All rights reserved.

The Strengths and Difficulties Questionnaire (SDQ): Factor Structure and Gender Equivalence in Norwegian Adolescents

PubMed Central

Hysing, Mari; Skogen, Jens Christoffer; Breivik, Kyrre

2016-01-01

Although frequently used with older adolescents, few studies of the factor structure, internal consistency and gender equivalence of the SDQ exists for this age group, with inconsistent findings. In the present study, confirmatory factor analysis (CFA) was used to evaluate the five-factor structure of the SDQ in a population sample of 10,254 16–18 year-olds from the youth@hordaland study. Measurement invariance across gender was assessed using multigroup CFA. A modestly modified five-factor solution fitted the data acceptably, accounting for one cross loading and some local dependencies. Importantly, partial measurement non-invariance was identified, with differential item functioning in eight items, and higher correlations between emotional and conduct problems for boys compared to girls. Implications for use clinically and in research are discussed. PMID:27138259

Investigation of Nuclear Structure and Quasi-Discrete Features in 150,152Sm via the (p,t) Reaction

NASA Astrophysics Data System (ADS)

Humby, Peter James Charnall

The (p,t) reaction was used to identify new levels and gamma-ray transitions in 150,152Sm utilising the particle-gamma and particle-gamma-gamma coincidence techniques. The experiment was performed using the STARLiTeR array located at the Cyclotron Institute of Texas A&M University. The relative partial cross sections for the observed levels, angle averaged between 34 and 58 degrees, were measured. A narrow peak-like structure was observed between 2.3-3.0 MeV excitation energy, in between the region of strongly populated discrete states at low energy and the high energy continuum region. In 150Sm, 39(4)% of the strength of the peak-like structure could be accounted for by the observed discrete states, which compares to a value of 93(15)% for 152Sm. The orbital angular-momentum transfer was probed by comparison of the experimental angular distributions to those calculated using the DWBA theory. The experimental angular distributions for the population of the peak-like structures are very similar in the two reactions, and significantly different to both the angular distribution of the background under the structures, and to the distribution obtained from the nearby continuum region at higher excitation energy. Post irradiation, the half-lives of isomeric states in 152Eu, populated in the 154Sm(p,3n) reaction, were obtained by measuring the decrease in intensity of the gamma rays emitted in the decay of these long lived levels. The half-life of the Jpi = 8- isomer 152m2Eu was measured to be 95.8(4) min, which is a factor of 2.5 reduction in uncertainty compared to the previous literature value of 96(1) min.

Accounting for female space sharing in St. Kilda Soay sheep (Ovis aries) results in little change in heritability estimates.

PubMed

Regan, C E; Pilkington, J G; Bérénos, C; Pemberton, J M; Smiseth, P T; Wilson, A J

2017-01-01

When estimating heritability in free-living populations, it is common practice to account for common environment effects, because of their potential to generate phenotypic covariance among relatives thereby biasing heritability estimates. In quantitative genetic studies of natural populations, however, philopatry, which results in relatives being clustered in space, is rarely accounted for. The two studies that have been carried out so far suggest absolute declines in heritability estimates of up to 43% when accounting for space sharing by relatives. However, due to methodological limitations these estimates may not be representative. We used data from the St. Kilda Soay sheep population to estimate heritabilities with and without accounting for space sharing for five traits for which there is evidence for additive genetic variance (birthweight, birth date, lamb August weight, and female post-mortem jaw and metacarpal length). We accounted for space sharing by related females by separately incorporating spatial autocorrelation, and a home range similarity matrix. Although these terms accounted for up to 18% of the variance in these traits, heritability estimates were only reduced by up to 7%. Our results suggest that the bias caused by not accounting for space sharing may be lower than previously thought. This suggests that philopatry does not inevitably lead to a large bias if space sharing by relatives is not accounted for. We hope our work stimulates researchers to model shared space when relatives in their study population share space, as doing so will enable us to better understand when bias may be of particular concern. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Study of relationship between the organizational structure and market orientation from the viewpoint of nurse managers.

PubMed

Bahadori, Mohammadkarim; Yaghoubi, Maryam; Javadi, Marzieh; Rahimi, Zahreh Agha

2015-01-01

Considering globalization of health care and quality improvement trend to respond to competition and customer orientation, attention to organizational structure and its relationship with market orientation is essential. Therefore, this study reviews the relationship between organizational structure and market orientation in selected hospitals of Isfahan (Iran). This study was a descriptive survey. The study population comprised nurse managers from selected hospitals (n = 80). Data collection tools were two questionnaires (market orientation questionnaire and organizational structure) that the validity and reliability were confirmed (r = 0.83 for market orientation questionnaire and r = 0.87 for organizational structure). SPSS (Ver. 16) software was used for the analyses. The mean score of organizational structure was 65.4 (11.2) and total mean of market orientation was 51.14 (17.6). All aspects of the organizational structure (Organization Centralization, Formalization in Organization, and Organization Complication) and market orientation (responding to competition, accountability, customer satisfaction, intelligent organization)-except by responding to clients with Formalization in Organization-as well as all aspects of the Systemic attitude (the system of internal coordination and communication systems_ and market orientation (responding to competition, accountability, customer satisfaction, intelligent organization), there was a meaningful relationship (P < 0.05). Market orientation and its dimensions have a significant relationship with organizational structure and can lead managers' view to the analysis and recognizing elements of success and achievement to goals. With increasing competition in markets, globalization of health services, and presence in international markets and more attention to patients' satisfaction, hospitals need to understand and use of market orientation in order to promote quality and services in the health care system.

Study of relationship between the organizational structure and market orientation from the viewpoint of nurse managers

PubMed Central

Bahadori, Mohammadkarim; Yaghoubi, Maryam; Javadi, Marzieh; Rahimi, Zahreh Agha

2015-01-01

Background: Considering globalization of health care and quality improvement trend to respond to competition and customer orientation, attention to organizational structure and its relationship with market orientation is essential. Therefore, this study reviews the relationship between organizational structure and market orientation in selected hospitals of Isfahan (Iran). Materials and Methods: This study was a descriptive survey. The study population comprised nurse managers from selected hospitals (n = 80). Data collection tools were two questionnaires (market orientation questionnaire and organizational structure) that the validity and reliability were confirmed (r = 0.83 for market orientation questionnaire and r = 0.87 for organizational structure). SPSS (Ver. 16) software was used for the analyses. Results: The mean score of organizational structure was 65.4 (11.2) and total mean of market orientation was 51.14 (17.6). All aspects of the organizational structure (Organization Centralization, Formalization in Organization, and Organization Complication) and market orientation (responding to competition, accountability, customer satisfaction, intelligent organization)—except by responding to clients with Formalization in Organization—as well as all aspects of the Systemic attitude (the system of internal coordination and communication systems_ and market orientation (responding to competition, accountability, customer satisfaction, intelligent organization), there was a meaningful relationship (P < 0.05). Conclusion: Market orientation and its dimensions have a significant relationship with organizational structure and can lead managers’ view to the analysis and recognizing elements of success and achievement to goals. With increasing competition in markets, globalization of health services, and presence in international markets and more attention to patients’ satisfaction, hospitals need to understand and use of market orientation in order to promote quality and services in the health care system. PMID:25861660

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.

Genetic variability in the Florida manatee (Trichechus manatus)

USGS Publications Warehouse

McClenaghan, Leroy R.; O'Shea, Thomas J.

1988-01-01

Tissue was obtained from 59 manatee (Trichechus manatus) carcasses salvaged from 20 counties in Florida. Allozyme phenotypes at 24 structural loci were determined by gel electrophoresis. Averages for the proportion of polymorphic loci and mean heterozygosity were 0.300 (range, 0.167-0.417) and 0.050 (range, 0.028-0.063), respectively. These estimates are equivalent to or higher than those generally reported for other species of marine mammals and do not support the hypothesis that body size and heterozygosity in mammals are related inversely. Among-region gene diversity accounted for only 4% of the total diversity. High rates of gene flow probably account for genetic homogeneity across regions. An F-statistic analysis revealed a general tendency toward excess homozygosity within regions. Management efforts to prevent future reductions in population size that would erode existing genic diversity should continue.

India's Proposed Universal Health Coverage Policy: Evidence for Age Structure Transition Effect and Fiscal Sustainability.

PubMed

Narayana, Muttur Ranganathan

2016-12-01

India's High Level Expert Group on Universal Health Coverage in 2011 recommended a universal, public-funded and national health coverage policy. As a plausible forward-looking macroeconomic reform in the health sector, this policy proposal on universal health coverage (UHC) needs to be evaluated for age structure transition effect and fiscal sustainability to strengthen its current design and future implementation. Macroeconomic analyses of the long-term implications of age structure transition and fiscal sustainability on India's proposed UHC policy. A new measure of age-specific UHC is developed by combining the age profile of public and private health consumption expenditure by using the National Transfer Accounts methodology. Different projections of age-specific public health expenditure are calculated over the period 2005-2100 to account for the age structure transition effect. The projections include changes in: (1) levels of the expenditure as gross domestic product grows, (2) levels and shape of the expenditure as gross domestic product grows and expenditure converges to that of developed countries (or convergence scenario) based on the Lee-Carter model of forecasting mortality rates, and (3) levels of the expenditure as India moves toward a UHC policy. Fiscal sustainability under each health expenditure projection is determined by using the measures of generational imbalance and sustainability gap in the Generational Accounting methodology. Public health expenditure is marked by age specificities and the elderly population is costlier to support for their healthcare needs in the future. Given the discount and productivity growth rates, the proposed UHC is not fiscally sustainable under India's current fiscal policies except for the convergence scenario. However, if the income elasticity of public expenditure on social welfare and health expenditure is less than one, fiscal sustainability of the UHC policy is attainable in all scenarios of projected public health expenditures. These new results strengthen the proposed UHC policy by accounting for age structure transition effect and justifying its sustainability within the framework of India's current fiscal policies. The age structure transition effect is important to incorporate the age-specific cost and benefit of the proposed UHC policy, especially as India moves toward an ageing society. Fiscal sustainability is essential to ensure that the proposed UHC is implementable on a long-term basis and within the framework of current fiscal policies.

Advancing Community–Based Research with Urban American Indian Populations: Multidisciplinary Perspectives

PubMed Central

Hartmann, William E.; Wendt, Dennis C.; Saftner, Melissa A.; Marcus, John; Momper, Sandra L.

2014-01-01

The U.S. has witnessed significant growth among urban AI populations in recent decades, and concerns have been raised that these populations face equal or greater degrees of disadvantage than their reservation counterparts. Surprisingly little urban AI research or community work has been documented in the literature, and even less has been written about the influences of urban settings on community-based work with these populations. Given the deep commitments of community psychology to empowering disadvantaged groups and understanding the impact of contextual factors on the lives of individuals and groups, community psychologists are well suited to fill these gaps in the literature. Toward informing such efforts, this work offers multidisciplinary insights from distinct idiographic accounts of community-based behavioral health research with urban AI populations. Accounts are offered by three researchers and one urban AI community organization staff member, and particular attention is given to issues of community heterogeneity, geography, membership, and collaboration. Each first-person account provides “lessons learned” from the urban context in which the research occurred. Together, these accounts suggest several important areas of consideration in research with urban AIs, some of which also seem relevant to reservation-based work. Finally, the potential role of research as a tool of empowerment for urban AI populations is emphasized, suggesting future research attend to the intersections of identity, sense of community, and empowerment in urban AI populations. PMID:24659391

On the decline of the Rusty Blackbird and the use of ornithological literature to document long-term population trends

USGS Publications Warehouse

Greenberg, R.; Droege, S.

1999-01-01

Unlike most North American blackbirds, Rusty Blackbirds (Euphagus carolensis) have shown steep population declines. Declines of approximately 90% are indicated for three recent decades from the Breeding Bird Survey, Christmas Bird Counts, and Quebec Checklist Program. Analyses of abundance classifications in bird distribution books and annotated checklists reveal an overlooked but long-term decline dating back to at least the early part of this century. Rusty Blackbirds were described as very common to abundant in 5656 of the pre-192O published accounts, 19% of the 1921-1950 accounts, and only 7% of the post-1950 accounts. Rusty Blackbirds were described as uncommon in none of the pre-1950 accounts, 18% of the 1951-1980 accounts, and 43% of the post-1980 accounts. A similar pattern was found for analyses based on local checklists. Destruction of wooded wetlands on wintering grounds, acid precipitation, and the conversion of boreal forest wetlands could have contributed to these declines. Systematic analysis of regional guides and checklists provides a valuable tool for examining large-scale and long-term population changes in birds.

[Simulation of administrative influence on a public health under conditions of changing the terminal values during the process of society transformation].

PubMed

Fed'ko, O A

2010-01-01

The article is devoted to the study of interrelation between terminal values and subjective health in the context of community development and modeling of possible directions of administrative influence on a public health taking into account such interrelation. The structural model of influence of terminal values on a subjective health is presented and the assessment of possible changes of health on the population level under condition of the introduction of the proper administrative interventions is given.

Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia

PubMed Central

Balazik, Matthew T.; Farrae, Daniel J.; Darden, Tanya L.; Garman, Greg C.

2017-01-01

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species. In the James River, VA specifically, captures of spawning Atlantic sturgeon and accompanying telemetry data suggest there are two discrete spawning groups of Atlantic sturgeon. The two putative spawning groups were genetically evaluated using a powerful microsatellite marker suite to determine if they are genetically distinct. Specifically, this study evaluates the genetic structure, characterizes the genetic diversity, estimates effective population size, and measures inbreeding of Atlantic sturgeon in the James River. The results indicate that fall and spring spawning James River Atlantic sturgeon groups are genetically distinct (overall FST = 0.048, F’ST = 0.181) with little admixture between the groups. The observed levels of genetic diversity and effective population sizes along with the lack of detected inbreeding all indicated that the James River has two genetically healthy populations of Atlantic sturgeon. The study also demonstrates that samples from adult Atlantic sturgeon, with proper sample selection criteria, can be informative when creating reference population databases. The presence of two genetically-distinct spawning groups of Atlantic sturgeon within the James River raises concerns about the current genetic assignment used by managers. Other nearby rivers may also have dual spawning groups that either are not accounted for or are pooled in reference databases. Our results represent the second documentation of genetically distinct dual spawning groups of Atlantic sturgeon in river systems along the U.S. Atlantic coast, suggesting that current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history. PMID:28686610

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

Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties.

PubMed

Thomaz, A T; Malabarba, L R; Knowles, L L

2017-10-01

Past shifts in connectivity in riverine environments (for example, sea-level changes) and the properties of current drainages can act as drivers of genetic structure and demographic processes in riverine population of fishes. However, it is unclear whether the same river properties that structure variation on recent timescales will also leave similar genomic signatures that reflect paleodrainage properties. By characterizing genetic structure in a freshwater fish species (Hollandichthys multifasciatus) from a system of basins along the Atlantic coast of Brazil we test for the effects of paleodrainages caused by sea-level changes during the Pleistocene. Given that the paleodrainage properties differ along the Brazilian coast, we also evaluate whether estimated genetic diversity within paleodrainages can be explained by past riverine properties (i.e., area and number of rivers in a paleodrainage). Our results demonstrate that genetic structure between populations is not just highly concordant with paleodrainages, but that differences in the genetic diversity among paleodrainages correspond to the joint effect of differences in the area encompassed by, and the number of rivers, within a paleodrainage. Our findings extend the influence of current riverine properties on genetic diversity to those associated with past paleodrainage properties. We discuss how these findings may explain the inconsistent support for paleodrainages in structuring divergence from different global regions and the importance of taking into account past conditions for understanding the high species diversity of freshwater fish that we currently observe in the world, and especially in the Neotropics.

[Modern principles of the geriatric analysis in medicine].

PubMed

Volobuev, A N; Zaharova, N O; Romanchuk, N P; Romanov, D V; Romanchuk, P I; Adyshirin-Zade, K A

2016-01-01

The offered methodological principles of the geriatric analysis in medicine enables to plan economic parameters of social protection of the population, necessary amount of medical help financing, to define a structure of the qualified medical personnel training. It is shown that personal health and cognitive longevity of the person depend on the adequate system geriatric analysis and use of biological parameters monitoring in time. That allows estimate efficiency of the combined individual treatment. The geriatric analysis and in particular its genetic-mathematical component aimed at reliability and objectivity of an estimation of the person life expectancy in the country and in region due to the account of influence of mutagen factors as on a gene of the person during his live, and on a population as a whole.

Diversity and population structure of Plasmodium falciparum in Thailand based on the spatial and temporal haplotype patterns of the C-terminal 19-kDa domain of merozoite surface protein-1.

PubMed

Simpalipan, Phumin; Pattaradilokrat, Sittiporn; Siripoon, Napaporn; Seugorn, Aree; Kaewthamasorn, Morakot; Butcher, Robert D J; Harnyuttanakorn, Pongchai

2014-02-12

The 19-kDa C-terminal region of the merozoite surface protein-1 of the human malaria parasite Plasmodium falciparum (PfMSP-119) constitutes the major component on the surface of merozoites and is considered as one of the leading candidates for asexual blood stage vaccines. Because the protein exhibits a level of sequence variation that may compromise the effectiveness of a vaccine, the global sequence diversity of PfMSP-119 has been subjected to extensive research, especially in malaria endemic areas. In Thailand, PfMSP-119 sequences have been derived from a single parasite population in Tak province, located along the Thailand-Myanmar border, since 1995. However, the extent of sequence variation and the spatiotemporal patterns of the MSP-119 haplotypes along the Thai borders with Laos and Cambodia are unknown. Sixty-three isolates of P. falciparum from five geographically isolated populations along the Thai borders with Myanmar, Laos and Cambodia in three transmission seasons between 2002 and 2008 were collected and culture-adapted. The msp-1 gene block 17 was sequenced and analysed for the allelic diversity, frequency and distribution patterns of PfMSP-119 haplotypes in individual populations. The PfMSP-119 haplotype patterns were then compared between parasite populations to infer the population structure and genetic differentiation of the malaria parasite. Five conserved polymorphic positions, which accounted for five distinct haplotypes, of PfMSP-119 were identified. Differences in the prevalence of PfMSP-119 haplotypes were detected in different geographical regions, with the highest levels of genetic diversity being found in the Kanchanaburi and Ranong provinces along the Thailand-Myanmar border and Trat province located at the Thailand-Cambodia border. Despite this variability, the distribution patterns of individual PfMSP-119 haplotypes seemed to be very similar across the country and over the three malarial transmission seasons, suggesting that gene flow may operate between parasite populations circulating in Thailand and the three neighboring countries. The major MSP-119 haplotypes of P. falciparum populations in all endemic populations during three transmission seasons in Thailand were identified, providing basic information on the common haplotypes of MSP-119 that is of use for malaria vaccine development and inferring the population structure of P. falciparum populations in Thailand.

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…

The structure of galaxies : the division of stellar mass by morphological type and structural component

NASA Astrophysics Data System (ADS)

Kelvin, Lee Steven

This thesis explores the relation between galaxy structure, morphology and stellar mass. In the first part I present single-Sersic two-dimensional model fits to 167,600 galaxies modelled independently in the ugrizYJHK bandpasses using reprocessed Sloan Digital Sky Survey Data Release Seven (SDSS DR7) and UKIRT Infrared Deep Sky Survey Large Area Survey (UKIDSS LAS) imaging data available via the Galaxy and Mass Assembly (GAMA) data base. In order to facilitate this study, we developed Structural Investigation of Galaxies via Model Analysis (SIGMA): an automated wrapper around several contemporary astronomy software packages. We confirm that variations in global structural measurements with wavelength arise due to the effects of dust attenuation and stellar population/metallicity gradients within galaxies. In the second part of this thesis we establish a volume-limited sample of 3,845 galaxies in the local Universe and visually classify these galaxies according to their morphological Hubble type. We find that single-Sersic photometry accurately reproduces the morphology luminosity functions predicted in the literature. We employ multi-component Sersic profiling to provide bulge-disk decompositions for this sample, allowing for the luminosity and stellar mass to be divided between the key structural components: spheroids and disks. Grouping the stellar mass in these structures by the evolutionary mechanisms that formed them, we find that hot-mode collapse, merger or otherwise turbulent mechanisms account for ~46% of the total stellar mass budget, cold-mode gas accretion and splashback mechanisms account for ~48% of the total stellar mass budget and secular evolutionary processes for ~6.5% of the total stellar mass budget in the local (z<0.06) Universe.

Economic distress and cause-of-death patterns for black and non-black men in Chicago: reconsidering the relevance of classic epidemiological transition theory.

PubMed

Palazzo, Lorella; Guest, Avery; Almgren, Gunnar

2003-01-01

The mortality disadvantage of African Americans is well documented, but previous studies have not considered its implications for population theory in the general case of industrialized nation states with high levels of income inequality. This paper examines the relevance of classic epidemiological theory to the extremes of income and mortality observed in Chicago, one of America's most racially divided cities. We analyze cause-specific death rates for black and non-black male populations residing in Chicago's community areas by using linked data from the 1990 Census and from 1989-1991 individual death certificates. The same cause-of-death patterns explain much of the mortality of black and non-black men. These two major structures include one, degenerative diseases, the other, "tough-living" causes (accidents, homicides, and liver disease). Community socioeconomic status is strongly related to tough-living deaths within each racial group, and to degenerative deaths for African Americans. Black men's tough-living mortality is much greater than non-blacks', but their younger age structure suppresses their degenerative death rates. Aggregate unemployment and social disorganization account for the most salient disparities in mortality across racial groups. This patterning of mortality along a socioeconomic continuum supports epidemiological theory and extends its applicability to highly unequal populations within industrialized countries.

Inter-Individual Variability in High-Throughput Risk ...

EPA Pesticide Factsheets

We incorporate realistic human variability into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of thousands of environmental chemicals, most which have little or no existing TK data. Chemicals are prioritized based on model estimates of hazard and exposure, to decide which chemicals should be first in line for further study. Hazard may be estimated with in vitro HT screening assays, e.g., U.S. EPA’s ToxCast program. Bioactive ToxCast concentrations can be extrapolated to doses that produce equivalent concentrations in body tissues using a reverse TK approach in which generic TK models are parameterized with 1) chemical-specific parameters derived from in vitro measurements and predicted from chemical structure; and 2) with physiological parameters for a virtual population. Here we draw physiological parameters from realistic estimates of distributions of demographic and anthropometric quantities in the modern U.S. population, based on the most recent CDC NHANES data. A Monte Carlo approach, accounting for the correlation structure in physiological parameters, is used to estimate ToxCast equivalent doses for the most sensitive portion of the population. To quantify risk, ToxCast equivalent doses are compared to estimates of exposure rates based on Bayesian inferences drawn from NHANES urinary analyte biomonitoring data. The inclusion

The development of universal health insurance coverage in Thailand: Challenges of population aging and informal economy.

PubMed

Hsu, Minchung; Huang, Xianguo; Yupho, Somrasri

2015-11-01

This paper quantitatively investigates the sustainability of the universal health insurance coverage (UHI) system in Thailand while taking into account the country's rapidly aging population and large informal labor sector. We examine the effects of population aging and informal employment across three tax options for financing the UHI. A modern dynamic general equilibrium framework is utilized to conduct policy experiments and welfare analysis. In the case of labor income tax being used to finance the cost of UHI, an additional 11-15% of labor tax will be required with the 2050 population age structure, compared with the 2005 benchmark economy. We also find that an expansion of income tax base to the informal sector can substantially alleviate the tax burden. Based on welfare comparisons across the alternative tax options, the labor income tax is the most preferred because the inequality between formal/informal sectors is large. If the informal sector cannot avoid labor income tax, capital tax will be preferred over labor and consumption taxes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Copy Number Variations in Tilapia Genomes.

PubMed

Li, Bi Jun; Li, Hong Lian; Meng, Zining; Zhang, Yong; Lin, Haoran; Yue, Gen Hua; Xia, Jun Hong

2017-02-01

Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2  > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.

Changes in breeding bird populations in North Dakota: 1967 to 1992-93

USGS Publications Warehouse

Igl, L.D.; Johnson, D.H.

1997-01-01

We compared breeding bird populations in North Dakota using surveys conducted in 1967 and 1992-93. In decreasing order, the five most frequently occurring species were Horned Lark (Eremophila alpestris), Brown-headed Cowbird (Molothrus ater), Western Meadowlark (Sturnella neglecta), Red-winged Blackbird (Agelaius phoeniceus), and Eastern Kingbird (Tyrannus tyrannus). The five most abundant species - Horned Lark, Chestnut-collared Longspur (Calcarius ornatus), Red-winged Blackbird, Western Meadowlark, and Brown-headed Cowbird - accounted for 31-41% of the estimated statewide breeding bird population in the three years. Although species composition remained relatively similar among years, between-year patterns in abundance and frequency varied considerably among species. Data from this survey and the North American Breeding Bird Survey indicated that species exhibiting significant declines were primarily grassland- and wetland-breeding birds, whereas species exhibiting significant increases primarily were those associated with human structures and woody vegetation. Population declines and increases for species with similar habitat associations paralleled breeding habitat changes, providing evidence that factors on the breeding grounds are having a detectable effect on breeding birds in the northern Great Plains.

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

PubMed

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

2017-12-01

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

Population dynamics of minimally cognitive individuals. Part I: Introducing knowledge into the dynamics

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

Schmieder, R.W.

The author presents a new approach for modeling the dynamics of collections of objects with internal structure. Based on the fact that the behavior of an individual in a population is modified by its knowledge of other individuals, a procedure for accounting for knowledge in a population of interacting objects is presented. It is assumed that each object has partial (or complete) knowledge of some (or all) other objects in the population. The dynamical equations for the objects are then modified to include the effects of this pairwise knowledge. This procedure has the effect of projecting out what the populationmore » will do from the much larger space of what it could do, i.e., filtering or smoothing the dynamics by replacing the complex detailed physical model with an effective model that produces the behavior of interest. The procedure therefore provides a minimalist approach for obtaining emergent collective behavior. The use of knowledge as a dynamical quantity, and its relationship to statistical mechanics, thermodynamics, information theory, and cognition microstructure are discussed.« less

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 for long-lived, free-ranging species. In conjunction with recently-developed analytical methodology, the ready availability of non-lethal DNA sampling methods and the ability to rapidly and cheaply survey many thousands of molecular markers should facilitate eco-evolutionary studies like this for many more species in nature.

Consanguinity and its socio-biological parameters in Rahim Yar Khan District, Southern Punjab, Pakistan.

PubMed

Riaz, Hafiza Fizzah; Mannan, Shaheen; Malik, Sajid

2016-05-20

Rahim Yar Khan (RYK) District is a multi-ethnic assemblage of both ancient and migrated communities in Southern Punjab, Pakistan. There is a paucity of knowledge on the bio-demographic structure of this endogamous population. We have carried out a cross-sectional epidemiological study in RYK District and recruited 2174 random Muslim married females. Detailed account of marital union types, level of consanguinity, and subject's fertility, was taken. The analyses of these data revealed that consanguineous unions (CU) were 58.46 %, rendering an inbreeding coefficient (IC-F) = 0.0355. The CU were observed to be significantly higher in subjects originating from rural areas, speaking Saraiki language, illiterate or having a religious/Madarsa education only, and belonging to nuclear family type. The rate of consanguinity was also higher in subjects whose husbands were engaged in unskilled manual or skilled manual jobs, and had consanguinity in the parental generation. Multivariate logistic regression analyses revealed that variables like Saraiki language, illiteracy, reciprocal marriages, and parental consanguinity, were the significant predictors of CU in the subject. Among the first cousin unions (which constituted 52 % of all marriages), parallel-cousin and patrilineal unions were in the majority (54 and 57 %, respectively), and father's brother's daughter type had the highest representation (31 %). The analyses further demonstrated that fertility and mean live-births were significantly higher in women who had CU compared to the non-consanguineous (NCU) group (p < 0.006); and significantly higher number of sons per women were born to the mothers who had CU compared with the NCU sample (p = 0.0002). However, there were no differences in the CU and NCU samples with respect to pre- or post-natal mortalities and child morbidities. The scientific findings in RYK District are distinct from the observations in other Pakistani populations and clue to a unique nature of this population. This study presents a comprehensive account of consanguinity and IC-F in RYK District and would be helpful in getting an insight into the structure of this population.

Barriers and facilitators affecting African Americans continuation into graduate programs in nursing.

PubMed

Mingo, Aunderia Doreen

2008-01-01

The population in the United States (US) is becoming more and more diverse. With each year the minority population in the US continues to grow. In the year 2000 there were over 281 million Americans with approximately 23% of them being minorities (US Census, 2000). African-Americans accounted for 34.6 million of the population or 12.3% in the 2000 census. Yet despite their growing numbers in the general population African-American Registered Nurses (RNs) only accounted for 4.9% of the total nurse population in the 2002 National Sample Survey of RN's (Health Resources Services Administration [HRSA], 2002).

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 in Taiwan were derived from two different clusters was also supported by the phylogenetic tree constructed by the UPGMA, indicating that the yellow cattle in Taiwan and in Kinmen should be treated as two different management units. This result will be applied to maintain a good level of genetic variability and rusticity (stress-resistance) and to avoid further inbreeding for yellow cattle population in Taiwan.

Structural brain development between childhood and adulthood: Convergence across four longitudinal samples.

PubMed

Mills, Kathryn L; Goddings, Anne-Lise; Herting, Megan M; Meuwese, Rosa; Blakemore, Sarah-Jayne; Crone, Eveline A; Dahl, Ronald E; Güroğlu, Berna; Raznahan, Armin; Sowell, Elizabeth R; Tamnes, Christian K

2016-11-01

Longitudinal studies including brain measures acquired through magnetic resonance imaging (MRI) have enabled population models of human brain development, crucial for our understanding of typical development as well as neurodevelopmental disorders. Brain development in the first two decades generally involves early cortical grey matter volume (CGMV) increases followed by decreases, and monotonic increases in cerebral white matter volume (CWMV). However, inconsistencies regarding the precise developmental trajectories call into question the comparability of samples. This issue can be addressed by conducting a comprehensive study across multiple datasets from diverse populations. Here, we present replicable models for gross structural brain development between childhood and adulthood (ages 8-30years) by repeating analyses in four separate longitudinal samples (391 participants; 852 scans). In addition, we address how accounting for global measures of cranial/brain size affect these developmental trajectories. First, we found evidence for continued development of both intracranial volume (ICV) and whole brain volume (WBV) through adolescence, albeit following distinct trajectories. Second, our results indicate that CGMV is at its highest in childhood, decreasing steadily through the second decade with deceleration in the third decade, while CWMV increases until mid-to-late adolescence before decelerating. Importantly, we show that accounting for cranial/brain size affects models of regional brain development, particularly with respect to sex differences. Our results increase confidence in our knowledge of the pattern of brain changes during adolescence, reduce concerns about discrepancies across samples, and suggest some best practices for statistical control of cranial volume and brain size in future studies. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species.

PubMed

Rodríguez-Quilón, Isabel; Santos-Del-Blanco, Luis; Serra-Varela, María Jesús; Koskela, Jarkko; González-Martínez, Santiago C; Alía, Ricardo

2016-10-01

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. © 2016 by the Ecological Society of America.

Association between Y haplogroups and autosomal AIMs reveals intra-population substructure in Bolivian populations.

PubMed

Vullo, Carlos; Gomes, Verónica; Romanini, Carola; Oliveira, Andréa M; Rocabado, Omar; Aquino, Juliana; Amorim, António; Gusmão, Leonor

2015-07-01

For the correct evaluation of the weight of genetic evidence in a forensic context, databases must reflect the structure of the population, with all possible groups being represented. Countries with a recent history of admixture between strongly differentiated populations are usually highly heterogeneous and sub-structured. Bolivia is one of these countries, with a high diversity of ethnic groups and different levels of admixture (among Native Americans, Europeans and Africans) across the territory. For a better characterization of the male lineages in Bolivia, 17 Y-STR and 42 Y-SNP loci were genotyped in samples from La Paz and Chuquisaca. Only European and Native American Y-haplogroups were detected, and no sub-Saharan African chromosomes were found. Significant differences were observed between the two samples, with a higher frequency of European lineages in Chuquisaca than in La Paz. A sample belonging to haplogroup Q1a3a1a1-M19 was detected in La Paz, in a haplotype background different from those previously found in Argentina. This result supports an old M19 North-south dispersion in South America, possibly via two routes. When comparing the ancestry of each individual assessed through his Y chromosome with the one estimated using autosomal AIMs, (a) increased European ancestry in individuals with European Y chromosomes and (b) higher Native American ancestry in the carriers of Native American Y-haplogroups were observed, revealing an association between autosomal and Y-chromosomal markers. The results of this study demonstrate that a sub-structure does exist in Bolivia at both inter- and intrapopulation levels, a fact which must be taken into account in the evaluation of forensic genetic evidence.

A case against an X-shaped structure in the Milky Way young bulge

NASA Astrophysics Data System (ADS)

López-Corredoira, Martín

2016-09-01

Context. A number of recent papers have claimed the discovery of an X-shape structure in the bulge of our Galaxy in the population of the red clumps. Aims: We endeavor to analyze the stellar density of bulge stars in the same regions using a different stellar population that is characteristic of the young bulge (≲ 5 Gyr). Particularly, we use F0-F5 main-sequence stars with distances derived through photometric parallax. Methods: We extract these stars from extinction-corrected color-magnitude diagrams in the near-infrared of VISTA-VVV data in some bulge regions and calculate the densities along the line of sight. We take the uncertaintity in the photometric parallax and the contamination of other sources into account, and we see that these errors do not avoid the detection of a possible double peak along some lines of sight as expected for a X-shape bulge if it existed. Results: Only a single peak in the density distribution along the line of sight is observed, so apparently there is no X-shape structure for this population of stars. Nonetheless, the effects of the dispersion of absolute magnitudes in the selected population might be an alternative explanation, although in principle these effects are insufficient to explain this lack of double peak according to our calculations. Conclusions: The results of the present paper do not demonstrate that previous claims of X-shaped bulge using only red clump stars are incorrect, but there are apparently some puzzling questions if we want to maintain the validity of both the red-clump results and the results of this paper.

Long term persistence of clonal malaria parasite Plasmodium falciparum lineages in the Colombian Pacific region.

PubMed

Echeverry, Diego F; Nair, Shalini; Osorio, Lyda; Menon, Sanjay; Murillo, Claribel; Anderson, Tim J C

2013-01-07

Resistance to chloroquine and antifolate drugs has evolved independently in South America, suggesting that genotype - phenotype studies aimed at understanding the genetic basis of resistance to these and other drugs should be conducted in this continent. This research was conducted to better understand the population structure of Colombian Plasmodium falciparum in preparation for such studies. A set of 384 SNPs were genotyped in blood spot DNA samples from 447 P. falciparum infected subjects collected over a ten year period from four provinces of the Colombian Pacific coast to evaluate clonality, population structure and linkage disequilibrium (LD). Most infections (81%) contained a single predominant clone. These clustered into 136 multilocus genotypes (MLGs), with 32% of MLGs recovered from multiple (2 - 28) independent subjects. We observed extremely low genotypic richness (R = 0.42) and long persistence of MLGs through time (median = 537 days, range = 1 - 2,997 days). There was a high probability (>5%) of sampling parasites from the same MLG in different subjects within 28 days, suggesting caution is needed when using genotyping methods to assess treatment success in clinical drug trials. Panmixia was rejected as four well differentiated subpopulations (FST = 0.084 - 0.279) were identified. These occurred sympatrically but varied in frequency within the four provinces. Linkage disequilibrium (LD) decayed more rapidly (r2 = 0.17 for markers <10 kb apart) than observed previously in South American samples. We conclude that Colombian populations have several advantages for association studies, because multiple clone infections are uncommon and LD decays over the scale of one or a few genes. However, the extensive population structure and low genotype richness will need to be accounted for when designing and analyzing association studies.

Long term persistence of clonal malaria parasite Plasmodium falciparum lineages in the Colombian Pacific region

PubMed Central

2013-01-01

Background Resistance to chloroquine and antifolate drugs has evolved independently in South America, suggesting that genotype - phenotype studies aimed at understanding the genetic basis of resistance to these and other drugs should be conducted in this continent. This research was conducted to better understand the population structure of Colombian Plasmodium falciparum in preparation for such studies. Results A set of 384 SNPs were genotyped in blood spot DNA samples from 447 P. falciparum infected subjects collected over a ten year period from four provinces of the Colombian Pacific coast to evaluate clonality, population structure and linkage disequilibrium (LD). Most infections (81%) contained a single predominant clone. These clustered into 136 multilocus genotypes (MLGs), with 32% of MLGs recovered from multiple (2 – 28) independent subjects. We observed extremely low genotypic richness (R = 0.42) and long persistence of MLGs through time (median = 537 days, range = 1 – 2,997 days). There was a high probability (>5%) of sampling parasites from the same MLG in different subjects within 28 days, suggesting caution is needed when using genotyping methods to assess treatment success in clinical drug trials. Panmixia was rejected as four well differentiated subpopulations (FST = 0.084 - 0.279) were identified. These occurred sympatrically but varied in frequency within the four provinces. Linkage disequilibrium (LD) decayed more rapidly (r2 = 0.17 for markers <10 kb apart) than observed previously in South American samples. Conclusions We conclude that Colombian populations have several advantages for association studies, because multiple clone infections are uncommon and LD decays over the scale of one or a few genes. However, the extensive population structure and low genotype richness will need to be accounted for when designing and analyzing association studies. PMID:23294725

Using Social Network Methods to Test for Assortment of Prosociality among Korean High School Students.

PubMed

Kim, Jun-Hong; Holman, Darryl J; Goodreau, Steven M

2015-01-01

Assortative interaction among altruistic individuals is a necessary condition for the evolution of cooperation. The requirement for assortment holds regardless of whether a meta-population is subdivided into distinct and isolated subgroups or has ephemeral boundaries with a high migration rate. The assumption, however, is rarely tested directly. In this paper, we develop a method to test for assortment of prosociality in network-structured data. The method is applied to a friendship network collected from 238 Korean students attending the same high school. A mixing matrix was used to explore the presence of assortative friendship among more prosocial individuals. An exponential random graph model of network structure that accounts for additional observed relational propensities (higher-than-expected number of people nominating no friends) and sampling constraints (upper bound on friendship nominations) found that individual prosociality predicted friendship propensity, and that individuals with higher prosocial scores had a higher probability of befriending other more prosocial individuals. The results reveal that a considerable level of assortment of prosociality characterizes this population.

Collective influence in evolutionary social dilemmas

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Perc, Matjaž

2016-03-01

When evolutionary games are contested in structured populations, the degree of each player in the network plays an important role. If they exist, hubs often determine the fate of the population in remarkable ways. Recent research based on optimal percolation in random networks has shown, however, that the degree is neither the sole nor the best predictor of influence in complex networks. Low-degree nodes may also be optimal influencers if they are hierarchically linked to hubs. Taking this into account leads to the formalism of collective influence in complex networks, which as we show here, has far-reaching implications for the favorable resolution of social dilemmas. In particular, there exists an optimal hierarchical depth for the determination of collective influence that we use to describe the potency of players for passing their strategies, which depends on the strength of the social dilemma. Interestingly, the degree, which corresponds to the baseline depth zero, is optimal only when the temptation to defect is small. Our research reveals that evolutionary success stories are related to spreading processes which are rooted in favorable hierarchical structures that extend beyond local neighborhoods.

Failures no More: The Radical Consequences of Realistic Stellar Feedback for Dwarf Galaxies, the Milky Way, and Reionization

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.

2016-06-01

Many of the most fundamental unsolved questions in star and galaxy formation revolve around star formation and "feedback" from massive stars, in-extricably linking galaxy formation and stellar evolution. I'll present simulations with un-precedented resolution of Milky-Way (MW) mass galaxies, followed cosmologically to redshift zero. For the first time, these simulations resolve the internal structure of small dwarf satellites around a MW-like host, with detailed models for stellar evolution including radiation pressure, supernovae, stellar winds, and photo-heating. I'll show that, without fine-tuning, these feedback processes naturally resolve the "missing satellites," "too big to fail," and "cusp-core" problems, and produce realistic galaxy populations. At high redshifts however, the realistic ISM structure predicted, coupled to standard stellar population models, naively leads to the prediction that only ~1-2% of ionizing photons can ever escape galaxies, insufficient to ionize the Universe. But these models assume all stars are single: if we account for binary evolution, the escape fraction increases dramatically to ~20% for the small, low-metallicity galaxies believed to ionize the Universe.

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.

Using Social Network Methods to Test for Assortment of Prosociality among Korean High School Students

PubMed Central

Kim, Jun-Hong; Holman, Darryl J.; Goodreau, Steven M.

2015-01-01

Assortative interaction among altruistic individuals is a necessary condition for the evolution of cooperation. The requirement for assortment holds regardless of whether a meta-population is subdivided into distinct and isolated subgroups or has ephemeral boundaries with a high migration rate. The assumption, however, is rarely tested directly. In this paper, we develop a method to test for assortment of prosociality in network-structured data. The method is applied to a friendship network collected from 238 Korean students attending the same high school. A mixing matrix was used to explore the presence of assortative friendship among more prosocial individuals. An exponential random graph model of network structure that accounts for additional observed relational propensities (higher-than-expected number of people nominating no friends) and sampling constraints (upper bound on friendship nominations) found that individual prosociality predicted friendship propensity, and that individuals with higher prosocial scores had a higher probability of befriending other more prosocial individuals. The results reveal that a considerable level of assortment of prosociality characterizes this population. PMID:25915508

Phylodynamics of vampire bat-transmitted rabies in Argentina

PubMed Central

DOHMEN, F. GURY; BELTRAN, F.; NOVARO, L.; RUSSO, S.; FREIRE, M. C.; VELASCO-VILLA, A.; MBAYED, V. A.; CISTERNA, D. M.

2016-01-01

Common vampire bat populations distributed from Mexico to Argentina are important rabies reservoir hosts in Latin America. The aim of this work was to analyse the population structure of the rabies virus (RABV) variants associated with vampire bats in the Americas and to study their phylodynamic pattern within Argentina. The phylogenetic analysis based on all available vampire bat-related N gene sequences showed both a geographical and a temporal structure. The two largest groups of RABV variants from Argentina were isolated from northwestern Argentina and from the central western zone of northeastern Argentina, corresponding to livestock areas with different climatic, topographic and biogeographical conditions, which determined their dissemination and evolutionary patterns. In addition, multiple introductions of the infection into Argentina, possibly from Brazil, were detected. The phylodynamic analysis suggests that RABV transmission dynamics is characterized by initial epizootic waves followed by local enzootic cycles with variable persistence. Anthropogenic interventions in the ecosystem should be assessed taking into account not only the environmental impact but also the potential risk of disease spreading through dissemination of current RABV lineages or the emergence of novel ones associated with vampire bats. PMID:24661865

The biogeodynamics of microbial landscapes

NASA Astrophysics Data System (ADS)

Battin, T. J.; Hödl, I.; Bertuzzo, E.; Mari, L.; Suweis, S. S.; Rinaldo, A.

2011-12-01

Spatial configuration is fundamental in defining the structural and functional properties of biological systems. Biofilms, surface-attached and matrix-enclosed microorganisms, are a striking example of spatial organisation. Coupled biotic and abiotic processes shape the spatial organisation across scales of the landscapes formed by these benthic biofilms in streams and rivers. Experimenting with such biofilms in streams, we found that, depending on the streambed topography and the related hydrodynamic microenvironment, biofilm landscapes form increasingly diverging spatial patterns as they grow. Strikingly, however, cluster size distributions tend to converge even in contrasting hydrodynamic microenvironments. To reproduce the observed cluster size distributions we used a continuous, size-structured population model. The model accounts for the formation, growth, erosion and merging of biofilm clusters. Our results suggest not only that hydrodynamic forcing induce the diverging patterning of the microbial landscape, but also that microorganisms have developed strategies to equally exploit spatial resources independently of the physical structure of the microenvironment where they live.

Quantifying Adventitious Error in a Covariance Structure as a Random Effect

PubMed Central

Wu, Hao; Browne, Michael W.

2017-01-01

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

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

PubMed

Ha, Gavin; Roth, Andrew; Khattra, Jaswinder; Ho, Julie; Yap, Damian; Prentice, Leah M; Melnyk, Nataliya; McPherson, Andrew; Bashashati, Ali; Laks, Emma; Biele, Justina; Ding, Jiarui; Le, Alan; Rosner, Jamie; Shumansky, Karey; Marra, Marco A; Gilks, C Blake; Huntsman, David G; McAlpine, Jessica N; Aparicio, Samuel; Shah, Sohrab P

2014-11-01

The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational landscapes. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting evolutionary dynamics of copy number alterations (CNA) and loss of heterozygosity (LOH) in whole-genome sequencing data remain underdeveloped. We present a novel probabilistic model, TITAN, to infer CNA and LOH events while accounting for mixtures of cell populations, thereby estimating the proportion of cells harboring each event. We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature of the evolving cancer genome. Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key modeling assumptions of TITAN. © 2014 Ha et al.; Published by Cold Spring Harbor Laboratory Press.

Developing a conservation strategy to maximize persistence of an endangered freshwater mussel species while considering management effectiveness and cost

USGS Publications Warehouse

Smith, David R.; McRae, Sarah E.; Augspurger, Tom; Ratcliffe, Judith A.; Nichols, Robert B.; Eads, Chris B.; Savidge, Tim; Bogan, Arthur E.

2015-01-01

We used a structured decision-making process to develop conservation strategies to increase persistence of Dwarf Wedgemussel (Alasmidonta heterodon) in North Carolina, USA, while accounting for uncertainty in management effectiveness and considering costs. Alternative conservation strategies were portfolios of management actions that differed by location of management actions on the landscape. Objectives of the conservation strategy were to maximize species persistence, maintain genetic diversity, maximize public support, and minimize management costs. We compared 4 conservation strategies: 1) the ‘status quo’ strategy represented current management, 2) the ‘protect the best’ strategy focused on protecting the best populations in the Tar River basin, 3) the ‘expand the distribution’ strategy focused on management of extant populations and establishment of new populations in the Neuse River basin, and 4) the ‘hybrid’ strategy combined elements of each strategy to balance conservation in the Tar and Neuse River basins. A population model informed requirements for population management, and experts projected performance of alternative strategies over a 20-y period. The optimal strategy depended on the relative value placed on competing objectives, which can vary among stakeholders. The protect the best and hybrid strategies were optimal across a wide range of relative values with 2 exceptions: 1) if minimizing management cost was of overriding concern, then status quo was optimal, or 2) if maximizing population persistence in the Neuse River basin was emphasized, then expand the distribution strategy was optimal. The optimal strategy was robust to uncertainty in management effectiveness. Overall, the structured decision process can help identify the most promising strategies for endangered species conservation that maximize conservation benefit given the constraint of limited funding.

FRED (a Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations.

PubMed

Grefenstette, John J; Brown, Shawn T; Rosenfeld, Roni; DePasse, Jay; Stone, Nathan T B; Cooley, Phillip C; Wheaton, William D; Fyshe, Alona; Galloway, David D; Sriram, Anuroop; Guclu, Hasan; Abraham, Thomas; Burke, Donald S

2013-10-08

Mathematical and computational models provide valuable tools that help public health planners to evaluate competing health interventions, especially for novel circumstances that cannot be examined through observational or controlled studies, such as pandemic influenza. The spread of diseases like influenza depends on the mixing patterns within the population, and these mixing patterns depend in part on local factors including the spatial distribution and age structure of the population, the distribution of size and composition of households, employment status and commuting patterns of adults, and the size and age structure of schools. Finally, public health planners must take into account the health behavior patterns of the population, patterns that often vary according to socioeconomic factors such as race, household income, and education levels. FRED (a Framework for Reconstructing Epidemic Dynamics) is a freely available open-source agent-based modeling system based closely on models used in previously published studies of pandemic influenza. This version of FRED uses open-access census-based synthetic populations that capture the demographic and geographic heterogeneities of the population, including realistic household, school, and workplace social networks. FRED epidemic models are currently available for every state and county in the United States, and for selected international locations. State and county public health planners can use FRED to explore the effects of possible influenza epidemics in specific geographic regions of interest and to help evaluate the effect of interventions such as vaccination programs and school closure policies. FRED is available under a free open source license in order to contribute to the development of better modeling tools and to encourage open discussion of modeling tools being used to evaluate public health policies. We also welcome participation by other researchers in the further development of FRED.

Intrabreed Stratification Related to Divergent Selection Regimes in Purebred Dogs May Affect the Interpretation of Genetic Association Studies

PubMed Central

Chang, Melanie L.; Yokoyama, Jennifer S.; Branson, Nick; Dyer, Donna J.; Hitte, Christophe; Overall, Karen L.

2009-01-01

Until recently, canine genetic research has not focused on population structure within breeds, which may confound the results of case–control studies by introducing spurious correlations between phenotype and genotype that reflect population history. Intrabreed structure may exist when geographical origin or divergent selection regimes influence the choices of potential mates for breeding dogs. We present evidence for intrabreed stratification from a genome-wide marker survey in a sample of unrelated dogs. We genotyped 76 Border Collies, 49 Australian Shepherds, 17 German Shepherd Dogs, and 17 Portuguese Water Dogs for our primary analyses using Affymetrix Canine v2.0 single-nucleotide polymorphism (SNP) arrays. Subsets of autosomal markers were examined using clustering algorithms to facilitate assignment of individuals to populations and estimation of the number of populations represented in the sample. SNPs passing stringent quality control filters were employed for explicitly phylogenetic analyses reconstructing relationships between individuals using maximum parsimony and Bayesian methods. We used simulation studies to explore the possible effects of intrabreed stratification on genome-wide association studies. These analyses demonstrate significant stratification in at least one of our primary breeds of interest, the Border Collie. Demographic and pedigree data suggest that this population substructure may result from geographic isolation or divergent selection regimes practiced by breeders with different breeding program goals. Simulation studies indicate that such stratification could result in false discovery rates significant enough to confound genome-wide association analyses. Intrabreed stratification should be accounted for when designing and interpreting the results of case–control association studies using purebred dogs.

Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon Slender Salamander (Batrachoseps wrighti): implications for conservation efforts and species management

USGS Publications Warehouse

Miller, Mark; Haig, Susan M.; Wagner, R.S.

2005-01-01

Endemic to Oregon in the northwestern US, the Oregon slender salamander (Batrachoseps wrighti) is a terrestrial plethodontid found associated with late successional mesic forests. Consequently, forest management practices such as timber harvesting may impact their persistence. Therefore, to infer possible future effects of these practices on population structure and differentiation, we used mitochondrial DNA sequences (cytochrome b) and RAPD markers to analyze 22 populations across their range. Phylogenetic analyses of sequence data (774 bp) revealed two historical lineages corresponding to northern and southern-distributed populations. Relationships among haplotypes and haplotype diversity within lineages suggested that the northern region may have more recently been colonized compared to the southern region. In contrast to the mitochondrial data, analyses of 46 RAPD loci suggested an overall pattern of isolation-by-distance in the set of populations examined and no particularly strong clustering of populations based on genetic distances. We propose two non-exclusive hypotheses to account for discrepancies between mitochondrial and nuclear data sets. First, our data may reflect an overall ancestral pattern of isolation-by-distance that has subsequently been influenced by vicariance. Alternately, our analyses may suggest that male-mediated gene flow and female philopatry are important contributors to the pattern of genetic diversity. We discuss the importance of distinguishing between these two hypotheses for the purposes of identifying conservation units and note that, regardless of the relative contribution of each mechanism towards the observed pattern of diversity, protection of habitat will likely prove critical for the long-term persistence of this species.

Gender and risk of depression in Saudi Arabia, a systematic review and meta-analysis

PubMed Central

Alibrahim, Osama A.; Al-Sadat, Nabilla; Elawad, Nagi A. M.

2010-01-01

Depression is one of the leading causes of mortality and morbidity worldwide. In the year 2000 depression accounted for 4.4% of the global disability adjusted life years (DALYs). The Kingdom of Saudi Arabia (KSA) has a population of 28 million people and is one of the countries experiencing demographic transition in its population structure. Improvements in socioeconomic status have been shown to be associated with increased chronic diseases including chronic mental diseases like depression, but still there is no comprehensive review summarizing the various reports currently existing in the literature. Although individual studies within Saudi Arabia have reported prevalence rates and risks, the quality of such studies need to be subjected to rigorous assessment and their findings pooled to give combined weighted evidence that will provide basis for targeted intervention. Pooled risks have the advantage of adjusting inherent variations within sampled populations and therefore providing more reliable estimates even though there are concerns about possible magnification of smaller individual risks. PMID:28299041

Using planned adaptation to implement evidence-based programs with new populations.

PubMed

Lee, Shawna J; Altschul, Inna; Mowbray, Carol T

2008-06-01

The Interactive Systems Framework (ISF) for Dissemination and Implementation (Wandersman et al. 2008) elaborates the functions and structures that move evidence-based programs (EBPs) from research to practice. Inherent in that process is the tension between implementing programs with fidelity and the need to tailor programs to fit the target population. We propose Planned Adaptation as one approach to resolve this tension, with the goal of guiding practitioners in adapting EBPs so that they maintain core components of program theory while taking into account the needs of particular populations. Planned Adaptation is a form of capacity building within the Prevention Support System that provides a framework to guide practitioners in adapting programs while encouraging researchers to provide information relevant to adaptation as a critical aspect of dissemination research, with the goal of promoting wider dissemination and better implementation of EBPs. We illustrate Planned Adaptation using the JOBS Program (Caplan et al. 1989), which was developed for recently laid-off, working- and middle-class workers and subsequently implemented with welfare recipients.

Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm.

PubMed

Teh, Chee-Keng; Ong, Ai-Ling; Kwong, Qi-Bin; Apparow, Sukganah; Chew, Fook-Tim; Mayes, Sean; Mohamed, Mohaimi; Appleton, David; Kulaveerasingam, Harikrishna

2016-01-08

GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10(-4)) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential.

Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties

PubMed Central

Rostoks, Nils; Ramsay, Luke; MacKenzie, Katrin; Cardle, Linda; Bhat, Prasanna R.; Roose, Mikeal L.; Svensson, Jan T.; Stein, Nils; Varshney, Rajeev K.; Marshall, David F.; Graner, Andreas; Close, Timothy J.; Waugh, Robbie

2006-01-01

Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD, and consequently, a very large number of markers are required for effective whole-genome association genetic scans. In contrast, several of the world's major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudooutbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1,524 genomewide SNPs we demonstrate that, after accounting for population substructure, the level of LD exhibited in elite northwest European barley, a typical inbred cereal crop, can be effectively exploited to map traits by using whole-genome association scans with several hundred to thousands of biallelic SNPs. PMID:17085595

Effect of temperature on the population dynamics of Aedes aegypti

NASA Astrophysics Data System (ADS)

Yusoff, Nuraini; Tokachil, Mohd Najir

2015-10-01

Aedes aegypti is one of the main vectors in the transmission of dengue fever. Its abundance may cause the spread of the disease to be more intense. In the study of its biological life cycle, temperature was found to increase the development rate of each stage of this species and thus, accelerate the process of the development from egg to adult. In this paper, a Lefkovitch matrix model will be used to study the stage-structured population dynamics of Aedes aegypti. In constructing the transition matrix, temperature will be taken into account. As a case study, temperature recorded at the Subang Meteorological Station for year 2006 until 2010 will be used. Population dynamics of Aedes aegypti at maximum, average and minimum temperature for each year will be simulated and compared. It is expected that the higher the temperature, the faster the mosquito will breed. The result will be compared to the number of dengue fever incidences to see their relationship.

Detection of genomic loci associated with environmental variables using generalized linear mixed models.

PubMed

Lobréaux, Stéphane; Melodelima, Christelle

2015-02-01

We tested the use of Generalized Linear Mixed Models to detect associations between genetic loci and environmental variables, taking into account the population structure of sampled individuals. We used a simulation approach to generate datasets under demographically and selectively explicit models. These datasets were used to analyze and optimize GLMM capacity to detect the association between markers and selective coefficients as environmental data in terms of false and true positive rates. Different sampling strategies were tested, maximizing the number of populations sampled, sites sampled per population, or individuals sampled per site, and the effect of different selective intensities on the efficiency of the method was determined. Finally, we apply these models to an Arabidopsis thaliana SNP dataset from different accessions, looking for loci associated with spring minimal temperature. We identified 25 regions that exhibit unusual correlations with the climatic variable and contain genes with functions related to temperature stress. Copyright © 2014 Elsevier Inc. All rights reserved.

Gender and risk of depression in Saudi Arabia, a systematic review and meta-analysis.

PubMed

Alibrahim, Osama A; Al-Sadat, Nabilla; Elawad, Nagi A M

2010-09-01

Depression is one of the leading causes of mortality and morbidity worldwide. In the year 2000 depression accounted for 4.4% of the global disability adjusted life years (DALYs). The Kingdom of Saudi Arabia (KSA) has a population of 28 million people and is one of the countries experiencing demographic transition in its population structure. Improvements in socioeconomic status have been shown to be associated with increased chronic diseases including chronic mental diseases like depression, but still there is no comprehensive review summarizing the various reports currently existing in the literature. Although individual studies within Saudi Arabia have reported prevalence rates and risks, the quality of such studies need to be subjected to rigorous assessment and their findings pooled to give combined weighted evidence that will provide basis for targeted intervention. Pooled risks have the advantage of adjusting inherent variations within sampled populations and therefore providing more reliable estimates even though there are concerns about possible magnification of smaller individual risks.

Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe.

PubMed

Chamaillé-Jammes, Simon; Charbonnel, Anaïs; Dray, Stéphane; Madzikanda, Hillary; Fritz, Hervé

2016-01-01

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes.

Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe

PubMed Central

Chamaillé-Jammes, Simon; Charbonnel, Anaïs; Dray, Stéphane; Madzikanda, Hillary; Fritz, Hervé

2016-01-01

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes. PMID:27074044

Correlation of soil and sediment organic matter polarity to aqueous sorption of nonionic compounds

USGS Publications Warehouse

Kile, D.E.; Wershaw, R. L.; Chiou, C.T.

1999-01-01

Polarities of the soiL/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment sam pies were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (K(oc)) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxylamide-ester carbons. A plot of the measured partition coefficients (K(oc)) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of K(oc) values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in K(oc) between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with K(oc) illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.Polarities of the soil/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment samples were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (Koc) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxyl-amide-ester carbons. A plot of the measured partition coefficients (Koc) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of Koc values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in Koc between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with Koc illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.

A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

PubMed Central

Khrunin, Andrey V.; Khokhrin, Denis V.; Filippova, Irina N.; Esko, Tõnu; Nelis, Mari; Bebyakova, Natalia A.; Bolotova, Natalia L.; Klovins, Janis; Nikitina-Zake, Liene; Rehnström, Karola; Ripatti, Samuli; Schreiber, Stefan; Franke, Andre; Macek, Milan; Krulišová, Veronika; Lubinski, Jan; Metspalu, Andres; Limborska, Svetlana A.

2013-01-01

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations. PMID:23505534

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 populations in particular. This confirms the important role that migratory movements have had in the European gene pool, at least since Neolithic times. In turn, the MDS and NJ analyses place Galicia within the group comprised of Western-Central European populations, which is justified by the influence of Germanic peoples on the Galician population during the Middle Ages. However, it should also be noted that some of the markers analysed have a certain degree of differentiation, possibly due to the region's position as a 'cul-de-sac' in terms of Iberian population dynamics. PMID:19055739

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 confirms the important role that migratory movements have had in the European gene pool, at least since Neolithic times. In turn, the MDS and NJ analyses place Galicia within the group comprised of Western-Central European populations, which is justified by the influence of Germanic peoples on the Galician population during the Middle Ages. However, it should also be noted that some of the markers analysed have a certain degree of differentiation, possibly due to the region's position as a 'cul-de-sac' in terms of Iberian population dynamics.

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...

Estimating population density and connectivity of American mink using spatial capture-recapture

USGS Publications Warehouse

Fuller, Angela K.; Sutherland, Christopher S.; Royle, Andy; Hare, Matthew P.

2016-01-01

Estimating the abundance or density of populations is fundamental to the conservation and management of species, and as landscapes become more fragmented, maintaining landscape connectivity has become one of the most important challenges for biodiversity conservation. Yet these two issues have never been formally integrated together in a model that simultaneously models abundance while accounting for connectivity of a landscape. We demonstrate an application of using capture–recapture to develop a model of animal density using a least-cost path model for individual encounter probability that accounts for non-Euclidean connectivity in a highly structured network. We utilized scat detection dogs (Canis lupus familiaris) as a means of collecting non-invasive genetic samples of American mink (Neovison vison) individuals and used spatial capture–recapture models (SCR) to gain inferences about mink population density and connectivity. Density of mink was not constant across the landscape, but rather increased with increasing distance from city, town, or village centers, and mink activity was associated with water. The SCR model allowed us to estimate the density and spatial distribution of individuals across a 388 km2 area. The model was used to investigate patterns of space usage and to evaluate covariate effects on encounter probabilities, including differences between sexes. This study provides an application of capture–recapture models based on ecological distance, allowing us to directly estimate landscape connectivity. This approach should be widely applicable to provide simultaneous direct estimates of density, space usage, and landscape connectivity for many species.

Estimating population density and connectivity of American mink using spatial capture-recapture.

PubMed

Fuller, Angela K; Sutherland, Chris S; Royle, J Andrew; Hare, Matthew P

2016-06-01

Estimating the abundance or density of populations is fundamental to the conservation and management of species, and as landscapes become more fragmented, maintaining landscape connectivity has become one of the most important challenges for biodiversity conservation. Yet these two issues have never been formally integrated together in a model that simultaneously models abundance while accounting for connectivity of a landscape. We demonstrate an application of using capture-recapture to develop a model of animal density using a least-cost path model for individual encounter probability that accounts for non-Euclidean connectivity in a highly structured network. We utilized scat detection dogs (Canis lupus familiaris) as a means of collecting non-invasive genetic samples of American mink (Neovison vison) individuals and used spatial capture-recapture models (SCR) to gain inferences about mink population density and connectivity. Density of mink was not constant across the landscape, but rather increased with increasing distance from city, town, or village centers, and mink activity was associated with water. The SCR model allowed us to estimate the density and spatial distribution of individuals across a 388 km² area. The model was used to investigate patterns of space usage and to evaluate covariate effects on encounter probabilities, including differences between sexes. This study provides an application of capture-recapture models based on ecological distance, allowing us to directly estimate landscape connectivity. This approach should be widely applicable to provide simultaneous direct estimates of density, space usage, and landscape connectivity for many species.

Age structure is critical to the population dynamics and survival of honeybee colonies.

PubMed

Betti, M I; Wahl, L M; Zamir, M

2016-11-01

Age structure is an important feature of the division of labour within honeybee colonies, but its effects on colony dynamics have rarely been explored. We present a model of a honeybee colony that incorporates this key feature, and use this model to explore the effects of both winter and disease on the fate of the colony. The model offers a novel explanation for the frequently observed phenomenon of 'spring dwindle', which emerges as a natural consequence of the age-structured dynamics. Furthermore, the results indicate that a model taking age structure into account markedly affects the predicted timing and severity of disease within a bee colony. The timing of the onset of disease with respect to the changing seasons may also have a substantial impact on the fate of a honeybee colony. Finally, simulations predict that an infection may persist in a honeybee colony over several years, with effects that compound over time. Thus, the ultimate collapse of the colony may be the result of events several years past.

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".

The Barley Phytomer

PubMed Central

Forster, Brian P.; Franckowiak, Jerome D.; Lundqvist, Udda; Lyon, Jackie; Pitkethly, Ian; Thomas, William T. B.

2007-01-01

Background and Aims Morphological mutants have been useful in elucidating the phytomeric structure of plants. Recently described mutants have shed new light on the ontogeny (development of plant structures) and the phytomeric system of barley (Hordeum vulgare). Since the current model for barley phytomers was not adequate to explain the nature of some mutants, a new model is proposed. Methods New phytomer mutants were detected by visual assessment of mutant families in the Optic barley mutation grid population. This was done at various growth stages using laboratory, glasshouse and field screens. Simple explanations were adopted to account for aberrant phytomer phenotypes and a thesis for a new phytomer model was developed. Key Results and Conclusions A barley phytomer model is presented, in which the origins of vegetative and generative structures can be explained by a single repeating phytomer unit. Organs on the barley plant are divided into two classes, single or paired, depending on their origin. Paired structures are often fused together to create specific organs. The model can be applied to wheat (Triticum aestivum) and related grasses. PMID:17901062

Investigation of discrete states and quasidiscrete structures observed in 150Sm and 152Sm using the ( p,tγ) reaction

DOE PAGES

Peter, Humby; Simon, Anna; Beausang, C. W.; ...

2016-01-01

New levels and γ-ray transitions were identified in 150,152Sm utilizing the (p,t) reaction and particle-γ coincidence data. A large, peak-like structure observed between 2.3–3.0 MeV in excitation energy in the triton energy spectra was also investigated. The orbital angular-momentum transfer was probed by comparing the experimental angular distributions of the outgoing tritons to calculated distorted wave Born approximation curves. The angular distributions of the outgoing tritons populating the peak-like structure are remarkably similar in the two reactions and are significantly different from the angular distributions associated with the nearby continuum region. Relative partial cross sections for the observed levels, anglemore » averaged between 34 and 58 degrees, were measured. In 150Sm, 39(4)% of the strength of the peak-like structure could be accounted for by the observed discrete states. This compares with a value of 93(15)% for 152Sm« less

Investigation of discrete states and quasidiscrete structures observed in 150Sm and 152Sm using the ( p,tγ) reaction

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

Peter, Humby; Simon, Anna; Beausang, C. W.

New levels and γ-ray transitions were identified in 150,152Sm utilizing the (p,t) reaction and particle-γ coincidence data. A large, peak-like structure observed between 2.3–3.0 MeV in excitation energy in the triton energy spectra was also investigated. The orbital angular-momentum transfer was probed by comparing the experimental angular distributions of the outgoing tritons to calculated distorted wave Born approximation curves. The angular distributions of the outgoing tritons populating the peak-like structure are remarkably similar in the two reactions and are significantly different from the angular distributions associated with the nearby continuum region. Relative partial cross sections for the observed levels, anglemore » averaged between 34 and 58 degrees, were measured. In 150Sm, 39(4)% of the strength of the peak-like structure could be accounted for by the observed discrete states. This compares with a value of 93(15)% for 152Sm« less

Age structured dynamical model for an endangered lizard Eulamprus leuraensis

NASA Astrophysics Data System (ADS)

Supriatna, A. K.; Rachmadani, Q.; Ilahi, F.; Anggriani, N.; Nuraini, N.

2014-02-01

The Blue Mountains Water Skink, Eulamprus leuraensis, is listed as an endangered species under the IUCN Red List. This lizard species has a typical characteristic of growth with a low fecundity. It is known that the offspring quality may decline with maternal age of the parents despite they can grow rapidly from neonatal size to adult size within two to three years. It is also believed that low adult survival rates and specialization on rare and fragmented type of habitat are the main cause leading to the endangered status of the lizard. A mathematical model with age structure for Eulamprus leuraensis, taking into account the variation of survival rate in each structure and the declining of offspring quality with respect to maternal age is considered here. Stable coexistence of non-trivial equilibriumis shown. It is also shown that an endangered status is due to combination oflow reproductive output and low rates of adult survival. Further, understanding the age structure within populations can facilitate efective management of the endangered species.

Combined effects of fishing and oil spills on marine fish: Role of stock demographic structure for offspring overlap with oil.

PubMed

Stige, Leif Chr; Ottersen, Geir; Yaragina, Natalia A; Vikebø, Frode B; Stenseth, Nils Chr; Langangen, Øystein

2018-04-01

It has been proposed that the multiple pressures of fishing and petroleum activities impact fish stocks in synergy, as fishing-induced demographic changes in a stock may lead to increased sensitivity to detrimental effects of acute oil spills. High fishing pressure may erode the demographic structure of fish stocks, lead to less diverse spawning strategies, and more concentrated distributions of offspring in space and time. Hence an oil spill may potentially hit a larger fraction of a year-class of offspring. Such a link between demographic structure and egg distribution was recently demonstrated for the Northeast Arctic stock of Atlantic cod for years 1959-1993. We here estimate that this variation translates into a two-fold variation in the maximal proportion of cod eggs potentially exposed to a large oil spill. With this information it is possible to quantitatively account for demographic structure in prospective studies of population effects of possible oil spills. Copyright © 2018 Elsevier Ltd. All rights reserved.

[Integration of demographic variables into development plans in the Sahel].

PubMed

Wane, H R

1992-07-01

A founding principle of the Program of Action of N'Djamena is the interdependence of population and development and the need for development strategies to take demographic factors into account. The concept of integration of population variables into development has evolved since its introduction in the 1974 World Population Plan of Action from a simple description of population size, growth rates, and distribution to a stress on harmonizing population policies and development policies with macroeconomic variables. The essence of the concept is the consideration given by development policies and programs to the interrelations between population, resources, the environment, and development factors. Population variables and goals should ideally be treated as endogenous variables in development planning, but in practice the extreme complexity of such a systematic approach limits its ability to be made operational. Usually the most crucial problems only are included. Integrated planning is composed of explicit or implicit population policies intended to influence demographic variables and of socioeconomic policies intended to adapt to demographic change. In the Sahel, only Senegal, Burkina Faso, and Mali have formal population policies, but around 1980 several countries of the region began to show interest in influencing demographic variables as they did economic variables. Fundamental principles for developing an integration strategy can be applied regardless or whether the plan is based on projections, analysis of interaction of a demographic variable with factors specific to a sector, or a monosectorial or multisectorial demoeconomic planning model. Demographic data is used more frequently in diagnosing problems than in developing projections or formulating objectives. The level of disaggregation of demographic projections and estimates tends to be low, despite the great potential utility of demographic projections in planning. Demographic projections can be useful in analyses of the extent of changes and the implications of alternative scenarios of development planning. The most frequently used demographic variables in development planning have been spatial distribution of the population and mortality. An examination of past development plans in Mali relating to population and nutrition and population and health reveals several inconsistencies between stated goals and strategies intended to achieve them. The incoherence can be explained in part by the absence of a coherent national population policy, the failure to translate the population policy into programs that take into account reciprocal effects of demographic trends and economic perspectives and their social effects, and the absence of disaggregated population projections. An example from Senegal demonstrates the constraints imposed by structural adjustment programs on the entire planning process.

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.

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 population size estimates. PMID:24489839

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

PubMed Central

Bickhart, Derek M.; Xu, Lingyang; Hutchison, Jana L.; Cole, John B.; Null, Daniel J.; Schroeder, Steven G.; Song, Jiuzhou; Garcia, Jose Fernando; Sonstegard, Tad S.; Van Tassell, Curtis P.; Schnabel, Robert D.; Taylor, Jeremy F.; Lewin, Harris A.; Liu, George E.

2016-01-01

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. PMID:27085184

Spectroscopic Manifestation of Vibrationally-Mediated Structure Change in the Isolated Formate Monohydrate

NASA Astrophysics Data System (ADS)

Denton, Joanna K.; Wolke, Conrad T.; Gorlova, Olga; Gerardi, Helen; McCoy, Anne B.; Johnson, Mark

2016-06-01

The breadth of the OH stretching manifold observed in the IR for bulk water is commonly attributed to the thermal population of excited states and the presence of many configurations within the water network. Here, I use carboxylate species as a rigid framework to isolate a single water molecule in the gas phase and cold ion vibrational pre-dissociation spectroscopy to explore excited state contributions to bandwidth. The spectrum of the carboxylate monohydrate exhibits a signature series of peaks in the OH stretching region of this system, providing an archetypal model to study vibrationally adiabatic mode separation. Previous analysis of this behavior accounts for the extensive progression in a Franck-Condon formalism involving displaced vibrationally adiabatic potentials. In this talk I will challenge this prediction by using isotopic substation to systematically change the level structure within these potentials. This picture quantitatively accounts for the diffuse spectrum of this complex at elevated temperature providing a convenient spectroscopic reporter for the temperature of ions in a trap. E. M. Myshakin, K. D. Jordan, E. L. Sibert III, M. A. Johnson J. Chem. Phys. 119, 10138 (2003) W.H. Robertson, et al. J. Phys Chem. 107, 6527 (2003)

The Changing Safety Net for Low-Income Parents and Their Children: Structural or Cyclical Changes in Income Support Policy?

PubMed

Hardy, Bradley; Smeeding, Timothy; Ziliak, James P

2018-02-01

Refundable tax credits and food assistance are the largest transfer programs available to able-bodied working poor and near-poor families in the United States, and simultaneous participation in these programs has more than doubled since the early 2000s. To understand this growth, we construct a series of two-year panels from the 1981-2013 waves of the Current Population Survey Annual Social and Economic Supplement to estimate the effect of state labor-market conditions, federal and state transfer program policy choices, and household demographics governing joint participation in food and refundable tax credit programs. Overall, changing policy drives much of the increase in the simultaneous, biennial use of food assistance and refundable tax credits. This stands in stark contrast from the factors accounting for the growth in food assistance alone, where cyclical and structural labor market factors account for at least one-half of the growth, and demographics play a more prominent role. Moreover, since 2000, the business cycle factors as the leading determinant in biennial participation decisions in food programs and refundable tax credits, suggesting a recent strengthening in the relationship between economic conditions and transfer programs.

The Promise and Perils of Population Research on Same-Sex Families.

PubMed

Reczek, Corinne; Spiker, Russell; Liu, Hui; Crosnoe, Robert

2017-12-01

As a follow-up to our 2016 study, this article presents new findings examining the relationship between same-sex family structure and child health using the 2008-2015 National Health Interview Survey (NHIS). After discussing NIHS data problems, we examine the relationship between family structure and a broad range of child well-being outcomes, including school days lost, behavior, parent-rated health, emotional difficulties, and activity limitations. We find both similarities (school days lost, behavior, parent-rated health) and differences (emotional difficulties and activity limitations) across our two studies using different survey years, but our overall conclusions are robust. We further discuss the implications of our findings for future research on this topic, including how to account for biological relatedness in a study on child health in same-sex families.

Epidemic spreading in a hierarchical social network.

PubMed

Grabowski, A; Kosiński, R A

2004-09-01

A model of epidemic spreading in a population with a hierarchical structure of interpersonal interactions is described and investigated numerically. The structure of interpersonal connections is based on a scale-free network. Spatial localization of individuals belonging to different social groups, and the mobility of a contemporary community, as well as the effectiveness of different interpersonal interactions, are taken into account. Typical relations characterizing the spreading process, like a range of epidemic and epidemic curves, are discussed. The influence of preventive vaccinations on the spreading process is investigated. The critical value of preventively vaccinated individuals that is sufficient for the suppression of an epidemic is calculated. Our results are compared with solutions of the master equation for the spreading process and good agreement of the character of this process is found.

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert

PubMed Central

Luebert, Federico; Jacobs, Pit; Hilger, Hartmut H; Muller, Ludo A H

2014-01-01

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (FST = 0.35), and FST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times. PMID:24558582

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert.

PubMed

Luebert, Federico; Jacobs, Pit; Hilger, Hartmut H; Muller, Ludo A H

2014-02-01

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (F ST = 0.35), and F ST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.

Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes.

PubMed

Zeng, Qian-Qian; He, Ke; Sun, Dan-Dan; Ma, Mei-Ying; Ge, Yun-Fa; Fang, Sheng-Guo; Wan, Qiu-Hong

2016-02-18

The major histocompatibility complex (MHC) genes are vital partners in the acquired immune processes of vertebrates. MHC diversity may be directly associated with population resistance to infectious pathogens. Here, we screened for polymorphisms in exons 2 and 3 of the IA1 and IA2 genes in 12 golden pheasant populations across the Chinese mainland to characterize their genetic variation levels, to understand the effects of historical positive selection and recombination in shaping class I diversity, and to investigate the genetic structure of wild golden pheasant populations. Among 339 individual pheasants, we identified 14 IA1 alleles in exon 2 (IA1-E2), 11 IA1-E3 alleles, 27 IA2-E2 alleles, and 28 IA2-E3 alleles. The non-synonymous substitution rate was significantly greater than the synonymous substitution rate at sequences in the IA2 gene encoding putative peptide-binding sites but not in the IA1 gene; we also found more positively selected sites in IA2 than in IA1. Frequent recombination events resulted in at least 9 recombinant IA2 alleles, in accordance with the intermingling pattern of the phylogenetic tree. Although some IA alleles are widely shared among studied populations, large variation occurs in the number of IA alleles across these populations. Allele frequency analysis across 2 IA loci showed low levels of genetic differentiation among populations on small geographic scales; however, significant genetic differentiation was observed between pheasants from the northern and southern regions of the Yangtze River. Both STRUCTURE analysis and F-statistic (F ST ) value comparison classified those populations into 2 major groups: the northern region of the Yangtze River (NYR) and the southern region of the Yangtze River (SYR). More extensive polymorphisms in IA2 than IA1 indicate that IA2 has undergone much stronger positive-selection pressure during evolution. Moreover, the recombination events detected between the genes and the intermingled phylogenetic pattern indicate that interlocus recombination accounts for much of the allelic variation in IA2. Analysis of the population differentiation implied that homogenous balancing selection plays an important part in maintaining an even distribution of MHC variations. The natural barrier of the Yangtze River and heterogeneous balancing selection might help shape the NYR-SYR genetic structure in golden pheasants.

Transforming healthcare delivery: Why and how accountable care organizations must evolve.

PubMed

Chen, Christopher T; Ackerly, D Clay; Gottlieb, Gary

2016-09-01

Accountable care organizations (ACOs) have shown promise in reducing healthcare spending growth, but have proven to be financially unsustainable for many healthcare organizations. Even ACOs with shared savings have experienced overall losses because the shared savings bonuses have not covered the costs of delivering population health. As physicians and former ACO leaders, we believe in the concept of accountable care, but ACOs need to evolve if they are to have a viable future. We propose the novel possibility of allowing ACOs to bill fee-for-service for their population health interventions, a concept we call population health billing. Journal of Hospital Medicine 2016;11:658-661. © 2016 Society of Hospital Medicine. © 2016 Society of Hospital Medicine.

Re-colonization by common eiders Somateria mollissima in the Aleutian Archipelago following removal of introduced arctic foxes Vulpes lagopus

USGS Publications Warehouse

Petersen, Margaret R.; Sonsthagen, Sarah A.; Sexson, Matthew G.

2015-01-01

Islands provide refuges for populations of many species where they find safety from predators, but the introduction of predators frequently results in elimination or dramatic reductions in island-dwelling organisms. When predators are removed, re-colonization for some species occurs naturally, and inter-island phylogeographic relationships and current movement patterns can illuminate processes of colonization. We studied a case of re-colonization of common eiders Somateria mollissima following removal of introduced arctic foxes Vulpes lagopus in the Aleutian Archipelago, Alaska. We expected common eiders to resume nesting on islands cleared of foxes and to re-colonize from nearby islets, islands, and island groups. We thus expected common eiders to show limited genetic structure indicative of extensive mixing among island populations. Satellite telemetry was used to record current movement patterns of female common eiders from six islands across three island groups. We collected genetic data from these and other nesting common eiders at 14 microsatellite loci and the mitochondrial DNA control region to examine population genetic structure, historical fluctuations in population demography, and gene flow. Our results suggest recent interchange among islands. Analysis of microsatellite data supports satellite telemetry data of increased dispersal of common eiders to nearby areas and little between island groups. Although evidence from mtDNA is suggestive of female dispersal among island groups, gene flow is insufficient to account for recolonization and rapid population growth. Instead, near-by remnant populations of common eiders contributed substantially to population expansion, without which re-colonization would have likely occurred at a much lower rate. Genetic and morphometric data of common eiders within one island group two and three decades after re-colonization suggests reduced movement of eiders among islands and little movement between island groups after populations were re-established. We predict that re-colonization of an island group where all common eiders are extirpated could take decades.

Genetic structure of Flores island (Azores, Portugal) in the 19th century and in the present day: evidence from surname analysis.

PubMed

Santos, Cristina; Abade, Augusto; Cantons, Jordi; Mayer, Francine M; Aluja, M Pilar; Lima, Manuela

2005-06-01

The island of Flores is the most westerly of the Azores archipelago (Portugal). Despite its marked geographic isolation and reduced population size, biodemographic and genetic studies conducted so far do not support the idea that its population constitutes a genetic isolate. In this study we conducted a surname analysis of the Flores population for two time periods: the second half of the 19th century and the present day. Our main purposes were (1) to biodemographically and genetically characterize the island, taking into account the strong reduction in population observed from the middle of the 19th century to the present day; and (2) to analyze the influence that the effective population size and geographic distance have on the genetic structure of populations. For both periods analyzed, all indicators of diversity revealed a high level of surname diversity. Our results are in accordance with the diversity estimates obtained from both monoparental genetic markers located in the Y chromosome and frequencies of mtDNA haplogroups. Contrary to what could be expected, considering the strong reduction of population in the last 150 years, we observed that diversity was maintained and that microdifferentiation decreased. Both observations support a higher openness of parishes as a consequence of the increase in communication routes. From the first to the second period analyzed, a change in surname composition is evident, although the more frequent surnames in Flores are almost the same for both periods and some of them are reported to be surnames present in the first settlers of Flores. This result testifies to the impact of founders on the present-day gene pool of Flores island and allows us to infer that the genetic characterization of the present-day population of Flores could provide reliable information about the history of the peopling of the Azores.

Environmental and Genetic Contribution to Hypertension Prevalence: Data from an Epidemiological Survey on Sardinian Genetic Isolates

PubMed Central

Biino, Ginevra; Parati, Gianfranco; Concas, Maria Pina; Adamo, Mauro; Angius, Andrea; Vaccargiu, Simona; Pirastu, Mario

2013-01-01

Background and Objectives Hypertension represents a major cause of cardiovascular morbidity and mortality worldwide but its prevalence has been shown to vary in different countries. The reasons for such differences are still matter of debate, the relative contributions given by environmental and genetic factors being still poorly defined. We estimated the current prevalence, distribution and determinants of hypertension in isolated Sardinian populations and also investigated the environmental and genetic contribution to hypertension prevalence taking advantage of the characteristics of such populations. Methods and Results An epidemiological survey with cross-sectional design was carried out measuring blood pressure in 9845 inhabitants of 10 villages of Ogliastra region between 2002 and 2008. Regression analysis for assessing blood pressure determinants and variance component models for estimating heritability were performed. Overall 38.8% of this population had hypertension, its prevalence varying significantly by age, sex and among villages taking into account age and sex structure of their population. About 50% of hypertensives had prior cardiovascular disease. High blood pressure was independently associated with age, obesity related factors, heart rate, total cholesterol, alcohol consumption, low education and smoking status, all these factors contributing more in women than in men. Heritability was 27% for diastolic and 36% for systolic blood pressure, its contribution being significantly higher in men (57%) than in women (46%). Finally, the genetic correlation between systolic and diastolic blood pressure was 0.74, indicating incomplete pleiotropy. Conclusion Genetic factors involved in the expression of blood pressure traits account for about 30% of the phenotypic variance, but seem to play a larger role in men; comorbidities and environmental factors remain of predominant importance, but seem to contribute much more in women. PMID:23527229

PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County

PubMed Central

2010-01-01

Background Because they are a closed founder population, the Old Order Amish (OOA) of Lancaster County have been the subject of many medical genetics studies. We constructed four versions of Anabaptist Genealogy Database (AGDB) using three sources of genealogies and multiple updates. In addition, we developed PedHunter, a suite of query software that can solve pedigree-related problems automatically and systematically. Methods We report on how we have used new features in PedHunter to quantify the number and expected genetic contribution of founders to the OOA. The queries and utility of PedHunter programs are illustrated by examples using AGDB in this paper. For example, we calculated the number of founders expected to be contributing genetic material to the present-day living OOA and estimated the mean relative founder representation for each founder. New features in PedHunter also include pedigree trimming and pedigree renumbering, which should prove useful for studying large pedigrees. Results With PedHunter version 2.0 querying AGDB version 4.0, we identified 34,160 presumed living OOA individuals and connected them into a 14-generation pedigree descending from 554 founders (332 females and 222 males) after trimming. From the analysis of cumulative mean relative founder representation, 128 founders (78 females and 50 males) accounted for over 95% of the mean relative founder contribution among living OOA descendants. Discussion/Conclusions The OOA are a closed founder population in which a modest number of founders account for the genetic variation present in the current OOA population. Improvements to the PedHunter software will be useful in future studies of both the OOA and other populations with large and computerized genealogies. PMID:20433770

Differences between immigrant and non-immigrant groups in the use of primary medical care; a systematic review

PubMed Central

Uiters, Ellen; Devillé, Walter; Foets, Marleen; Spreeuwenberg, Peter; Groenewegen, Peter P

2009-01-01

Background Studies on differences between immigrant and non-immigrant groups in health care utilization vary with respect to the extent and direction of differences in use. Therefore, our study aimed to provide a systematic overview of the existing research on differences in primary care utilization between immigrant groups and the majority population. Methods For this review PubMed, PsycInfo, Cinahl, Sociofile, Web of Science and Current Contents were consulted. Study selection and quality assessment was performed using a predefined protocol by 2 reviewers independently of each other. Only original, quantitative, peer-reviewed papers were taken into account. To account for this hierarchical structure, logistic multilevel analyses were performed to examine the extent to which differences are found across countries and immigrant groups. Differences in primary care use were related to study characteristics, strength of the primary care system and methodological quality. Results A total of 37 studies from 7 countries met all inclusion criteria. Remarkably, studies performed within the US more often reported a significant lower use among immigrant groups as compared to the majority population than the other countries. As studies scored higher on methodological quality, the likelihood of reporting significant differences increased. Adjustment for health status and use of culture-/language-adjusted procedures during the data collection were negatively related to reporting significant differences in the studies. Conclusion Our review underlined the need for careful design in studies of differences in health care use between immigrant groups and the majority population. The results from studies concerning differences between immigrant and the majority population in primary health care use performed within the US might be interpreted as a reflection of a weaker primary care system in the US compared to Europe and Canada. PMID:19426567

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.

A personality theory of U.S. migration geography.

PubMed

Stetzer, F C

1985-01-01

"Neoclassical models of migration fail to account adequately for individual differences in propensity to migrate, rates of emigration from states and cities, and the generally high rates of population circulation common in the United States. This article proposes that migration propensity is related to an individual's personality. Using the facts that personality traits are generationally regenerative, both through inheritance and culture, and that the United States was settled in a series of migration waves from east to west, this theory predicts a spatial structuring of emigration rates which closely correspond to actual rates for states and major cities." excerpt

Deconstructing national leadership: politicians' accounts of electoral success and failure in the Irish Lisbon Treaty referenda.

PubMed

Burns, Michele; Stevenson, Clifford

2013-03-01

The Self Categorization approach to national leadership proposes that leaders rhetorically construct national identity as essentialized and inevitable in order to consensualize and mobilize the population. In contrast, discursive studies have demonstrated how national politicians flexibly construct the nation to manage their own accountability in local interactions, though this in turn has neglected broader leadership processes. The present paper brings both approaches together to examine how and when national politicians construct versions of national identity in order to account for their failure as well as success in mobilizing the electorate. Eight semi-structured conversational style interviews were conducted with a strategic sample of eight leading Irish politicians on the subject of the 2008/2009 Irish Lisbon Treaty referenda. Using a Critical Discourse Psychology approach, the hegemonic repertoire of the 'settled will' of the informed and consensualized Irish nation was identified across all interviews. Politicians either endorsed the 'settled will' repertoire as evidence of their successful leadership, or rejected the repertoire by denying the rationality or unity of the populace to account for their failure. Our results suggest national identity is only constructed as essentialized and inevitable to the extent that it serves a strategic political purpose. © 2011 The British Psychological Society.

Linguistic, geographic and genetic isolation: a collaborative study of Italian populations.

PubMed

Capocasa, Marco; Anagnostou, Paolo; Bachis, Valeria; Battaggia, Cinzia; Bertoncini, Stefania; Biondi, Gianfranco; Boattini, Alessio; Boschi, Ilaria; Brisighelli, Francesca; Caló, Carla Maria; Carta, Marilisa; Coia, Valentina; Corrias, Laura; Crivellaro, Federica; De Fanti, Sara; Dominici, Valentina; Ferri, Gianmarco; Francalacci, Paolo; Franceschi, Zelda Alice; Luiselli, Donata; Morelli, Laura; Paoli, Giorgio; Rickards, Olga; Robledo, Renato; Sanna, Daria; Sanna, Emanuele; Sarno, Stefania; Sineo, Luca; Taglioli, Luca; Tagarelli, Giuseppe; Tofanelli, Sergio; Vona, Giuseppe; Pettener, Davide; Destro Bisol, Giovanni

2014-01-01

The animal and plant biodiversity of the Italian territory is known to be one of the richest in the Mediterranean basin and Europe as a whole, but does the genetic diversity of extant human populations show a comparable pattern? According to a number of studies, the genetic structure of Italian populations retains the signatures of complex peopling processes which took place from the Paleolithic to modern era. Although the observed patterns highlight a remarkable degree of genetic heterogeneity, they do not, however, take into account an important source of variation. In fact, Italy is home to numerous ethnolinguistic minorities which have yet to be studied systematically. Due to their difference in geographical origin and demographic history, such groups not only signal the cultural and social diversity of our country, but they are also potential contributors to its bio-anthropological heterogeneity. To fill this gap, research groups from four Italian Universities (Bologna, Cagliari, Pisa and Roma Sapienza) started a collaborative study in 2007, which was funded by the Italian Ministry of Education, University and Research and received partial support by the Istituto Italiano di Antropologia. In this paper, we present an account of the results obtained in the course of this initiative. Four case-studies relative to linguistic minorities from the Eastern Alps, Sardinia, Apennines and Southern Italy are first described and discussed, focusing on their micro-evolutionary and anthropological implications. Thereafter, we present the results of a systematic analysis of the relations between linguistic, geographic and genetic isolation. Integrating the data obtained in the course of the long-term study with literature and unpublished results on Italian populations, we show that a combination of linguistic and geographic factors is probably responsible for the presence of the most robust signatures of genetic isolation. Finally, we evaluate the magnitude of the diversity of Italian populations in the European context. The human genetic diversity of our country was found to be greater than observed throughout the continent at short (0-200 km) and intermediate (700-800km) distances, and accounted for most of the highest values of genetic distances observed at all geographic ranges. Interestingly, an important contribution to this pattern comes from the "linguistic islands"( e.g. German speaking groups of Sappada and Luserna from the Eastern Italian Alps), further proof of the importance of considering social and cultural factors when studying human genetic variation.

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.

Testing the environmental Kuznets curve hypothesis with bird populations as habitat-specific environmental indicators: evidence from Canada.

PubMed

Lantz, Van; Martínez-Espiñeira, Roberto

2008-04-01

The traditional environmental Kuznets curve (EKC) hypothesis postulates that environmental degradation follows an inverted U-shaped relationship with gross domestic product (GDP) per capita. We tested the EKC hypothesis with bird populations in 5 different habitats as environmental quality indicators. Because birds are considered environmental goods, for them the EKC hypothesis would instead be associated with a U-shaped relationship between bird populations and GDP per capita. In keeping with the literature, we included other variables in the analysis-namely, human population density and time index variables (the latter variable captured the impact of persistent and exogenous climate and/or policy changes on bird populations over time). Using data from 9 Canadian provinces gathered over 37 years, we used a generalized least-squares regression for each bird habitat type, which accounted for the panel structure of the data, the cross-sectional dependence across provinces in the residuals, heteroskedasticity, and fixed- or random-effect specifications of the models. We found evidence that supports the EKC hypothesis for 3 of the 5 bird population habitat types. In addition, the relationship between human population density and the different bird populations varied, which emphasizes the complex nature of the impact that human populations have on the environment. The relationship between the time-index variable and the different bird populations also varied, which indicates there are other persistent and significant influences on bird populations over time. Overall our EKC results were consistent with those found for threatened bird species, indicating that economic prosperity does indeed act to benefit some bird populations.

Differential expression analysis for RNAseq using Poisson mixed models

PubMed Central

Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny

2017-01-01

Abstract Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. PMID:28369632

Gender equality in university sportspeople's drinking.

PubMed

O'Brien, Kerry S; Hunter, Jackie; Kypri, Kypros; Ali, Ajmol

2008-11-01

In large population-based alcohol studies males are shown consistently to drink more, and more hazardously, than females. However, research from some countries suggests that gender differences in drinking are converging, with females drinking more than in the past. Large population-based research may miss gender-based changes in drinking behaviours that occur in sub-populations most at risk of hazardous drinking. We examine gender differences in a sub-population where hazardous drinking is common and endorsed, namely university sportspeople. The Alcohol Use Disorders Identification Test (AUDIT) and a drinking motives measure were used to assess hazardous drinking behaviours and drinking motives in 631 university sportspeople (females = 331, 52%). There were no gender differences in AUDIT scores. However, drinking motives differed between genders, with coping motives being a significant predictor of hazardous drinking in females but not males. Hazardous drinking, including binge drinking (46.3%) and frequent binge drinking (35%), in New Zealand university sportspeople is high for both males and females. New Zealand university sportspeople are one population where gender differences in drinking are not apparent and run counter to European population based research and research in US sporting populations. Gender role equality in the university systems, and endorsement of drinking in sporting culture, may account for the lack of gender differences in this New Zealand sporting population. Future research on gender differences in drinking should examine sub-populations where gender role differentiation is low, and socio-cultural/structural factors supporting gender equality are high.

Characteristics of Populations of the Russian Federation over the Panel of Fifteen Loci Used for DNA Identification and in Forensic Medical Examination

PubMed Central

A Stepanov, V.; Balanovsky, O.P.; Melnikov, A.V.; Lash-Zavada, A.Yu.; Khar’kov, V.N.; Tyazhelova, T.V.; Akhmetova, V.L.; Zhukova, O.V.; Shneider, Yu.V.; Shil’nikova, I.N.; Borinskaya, S.A.; Marusin, A.V.; Spiridonova, M.G.; Simonova, K.V.; Khitrinskaya, I.Yu.; Radzhabov, M.O.; Romanov, A.G.; Shtygasheva, O.V.; Koshel’, S.M.; Balanovskaya, E.V.; Rybakova, A.V.; Khusnutdinova, E.K.; Puzyrev, V.P.; Yankovsky, N.K.

2011-01-01

Seventeen population groups within the Russian Federation were characterized for the first time using a panel of 15 genetic markers that are used for DNA identification and in forensic medical examinations. The degree of polymorphism and population diversity of microsatellite loci within the Power Plex system (Promega) in Russian populations; the distribution of alleles and genotypes within the populations of six cities and 11 ethnic groups of the Russian Federation; the levels of intra- and interpopulation genetic differentiation of population; genetic relations between populations; and the identification and forensic medical characteristics of the system of markers under study were determined. Significant differences were revealed between the Russian populations and the U.S. reference base that was used recently in the forensic medical examination of the RF. A database of the allelic frequencies of 15 microsatellite loci that are used for DNA identification and forensic medical examination was created; the database has the potential of becoming the reference for performing forensic medical examinations in Russia. The spatial organization of genetic diversity over the panel of the STR markers that are used for DNA identification was revealed. It represents the general regularities of geographical clusterization of human populations over various types of genetic markers. The necessity to take into account a population’s genetic structure during forensic medical examinations and DNA identification of criminal suspects was substantiated. PMID:22649684

[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.

Morphological analysis of Trichomycterus areolatus Valenciennes, 1846 from southern Chilean rivers using a truss-based system (Siluriformes, Trichomycteridae).

PubMed

Colihueque, Nelson; Corrales, Olga; Yáñez, Miguel

2017-01-01

Trichomycterus areolatus Valenciennes, 1846 is a small endemic catfish inhabiting the Andean river basins of Chile. In this study, the morphological variability of three T. areolatus populations, collected in two river basins from southern Chile, was assessed with multivariate analyses, including principal component analysis (PCA) and discriminant function analysis (DFA). It is hypothesized that populations must segregate morphologically from each other based on the river basin that they were sampled from, since each basin presents relatively particular hydrological characteristics. Significant morphological differences among the three populations were found with PCA (ANOSIM test, r = 0.552, p < 0.0001) and DFA (Wilks's λ = 0.036, p < 0.01). PCA accounted for a total variation of 56.16% by the first two principal components. The first Principal Component (PC1) and PC2 explained 34.72 and 21.44% of the total variation, respectively. The scatter-plot of the first two discriminant functions (DF1 on DF2) also validated the existence of three different populations. In group classification using DFA, 93.3% of the specimens were correctly-classified into their original populations. Of the total of 22 transformed truss measurements, 17 exhibited highly significant ( p < 0.01) differences among populations. The data support the existence of T. areolatus morphological variation across different rivers in southern Chile, likely reflecting the geographic isolation underlying population structure of the species.

Assessing the Risk of Invasion by Tephritid Fruit Flies: Intraspecific Divergence Matters

PubMed Central

Godefroid, Martin; Cruaud, Astrid; Rossi, Jean-Pierre; Rasplus, Jean-Yves

2015-01-01

Widely distributed species often show strong phylogeographic structure, with lineages potentially adapted to different biotic and abiotic conditions. The success of an invasion process may thus depend on the intraspecific identity of the introduced propagules. However, pest risk analyses are usually performed without accounting for intraspecific diversity. In this study, we developed bioclimatic models using MaxEnt and boosted regression trees approaches, to predict the potential distribution in Europe of six economically important Tephritid pests (Ceratitis fasciventris (Bezzi), Bactrocera oleae (Rossi), Anastrepha obliqua (Macquart), Anastrepha fraterculus (Wiedemann), Rhagoletis pomonella (Walsh) and Bactrocera cucurbitae (Coquillet)). We considered intraspecific diversity in our risk analyses by independently modeling the distributions of conspecific lineages. The six species displayed different potential distributions in Europe. A strong signal of intraspecific climate envelope divergence was observed in most species. In some cases, conspecific lineages differed strongly in potential distributions suggesting that taxonomic resolution should be accounted for in pest risk analyses. No models (lineage- and species-based approaches) predicted high climatic suitability in the entire invaded range of B. oleae—the only species whose intraspecific identity of invading populations has been elucidated—in California. Host availability appears to play the most important role in shaping the geographic range of this specialist pest. However, climatic suitability values predicted by species-based models are correlated with population densities of B. oleae globally reported in California. Our study highlights how classical taxonomic boundaries may lead to under- or overestimation of the potential pest distributions and encourages accounting for intraspecific diversity when assessing the risk of biological invasion. PMID:26274582

Redesigning Care Delivery with Patient Support Personnel: Learning from Accountable Care Organizations

PubMed Central

Gorbenko, Ksenia O.; Fraze, Taressa; Lewis, Valerie A.

2017-01-01

INTRODUCTION Accountable care organizations (ACOs) are a value-based payment model in the United States rooted in holding groups of healthcare providers financially accountable for the quality and total cost of care of their attributed population. To succeed in reaching their quality and efficiency goals, ACOs implement a variety of care delivery changes, including workforce redesign. Patient support personnel (PSP)—non-physician staff such as care coordinators, community health workers, and others—are critical to restructuring care delivery. Little is known about how ACOs are redesigning their patient support personnel in terms of responsibilities, location, and evaluation. METHODS We conducted semi-structured one-hour interviews with 25 executives at 16 distinct ACOs. The interviews were recorded, transcribed, and coded for themes, using a qualitative coding and analysis process. RESULTS ACOs deployed PSP to perform four clusters of responsibilities: care provision, care coordination, logistical help with transportation, and social and emotional support. ACOs deployed these personnel strategically across settings (primary care, inpatient services, emergency department, home care and community) depending on their population needs. Most ACOs used personnel with the same level of training across settings. Few ACOs planned to conduct a comprehensive evaluation of their PSP to optimize their value. DISCUSSION ACO strategies in workforce redesign indicate a shift from a physician-centered to a team-based approach. Employing personnel with varying levels of clinical training to perform different tasks can help further optimize care delivery. More robust evaluation of the deployment of PSP and their performance is needed to demonstrate cost-saving benefits of workforce redesign. PMID:28217305

The Situation of Children and the Quality of the Human Potential in Russia

ERIC Educational Resources Information Center

Rimashevskaia, N. M.

2004-01-01

From 1992 through 2001, Russia lost more than 7 million people as a result of natural population loss or, with the positive migration balance taken into account, 4.7 million. These statistics show that the size of Russia's population is diminishing steadily. This article reports the findings of a study examining the factors that account for the…

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…

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.

Figurative language processing in atypical populations: the ASD perspective

PubMed Central

Vulchanova, Mila; Saldaña, David; Chahboun, Sobh; Vulchanov, Valentin

2015-01-01

This paper is intended to provide a critical overview of experimental and clinical research documenting problems in figurative language processing in atypical populations with a focus on the Autistic Spectrum. Research in the comprehension and processing of figurative language in autism invariably documents problems in this area. The greater paradox is that even at the higher end of the spectrum or in the cases of linguistically talented individuals with Asperger syndrome, where structural language competence is intact, problems with extended language persist. If we assume that figurative and extended uses of language essentially depend on the perception and processing of more concrete core concepts and phenomena, the commonly observed failure in atypical populations to understand figurative language remains a puzzle. Various accounts have been offered to explain this issue, ranging from linking potential failure directly to overall structural language competence (Norbury, 2005; Brock et al., 2008) to right-hemispheric involvement (Gold and Faust, 2010). We argue that the dissociation between structural language and figurative language competence in autism should be sought in more general cognitive mechanisms and traits in the autistic phenotype (e.g., in terms of weak central coherence, Vulchanova et al., 2012b), as well as failure at on-line semantic integration with increased complexity and diversity of the stimuli (Coulson and Van Petten, 2002). This perspective is even more compelling in light of similar problems in a number of conditions, including both acquired (e.g., Aphasia) and developmental disorders (Williams Syndrome). This dissociation argues against a simple continuity view of language interpretation. PMID:25741261

Figurative language processing in atypical populations: the ASD perspective.

PubMed

Vulchanova, Mila; Saldaña, David; Chahboun, Sobh; Vulchanov, Valentin

2015-01-01

This paper is intended to provide a critical overview of experimental and clinical research documenting problems in figurative language processing in atypical populations with a focus on the Autistic Spectrum. Research in the comprehension and processing of figurative language in autism invariably documents problems in this area. The greater paradox is that even at the higher end of the spectrum or in the cases of linguistically talented individuals with Asperger syndrome, where structural language competence is intact, problems with extended language persist. If we assume that figurative and extended uses of language essentially depend on the perception and processing of more concrete core concepts and phenomena, the commonly observed failure in atypical populations to understand figurative language remains a puzzle. Various accounts have been offered to explain this issue, ranging from linking potential failure directly to overall structural language competence (Norbury, 2005; Brock et al., 2008) to right-hemispheric involvement (Gold and Faust, 2010). We argue that the dissociation between structural language and figurative language competence in autism should be sought in more general cognitive mechanisms and traits in the autistic phenotype (e.g., in terms of weak central coherence, Vulchanova et al., 2012b), as well as failure at on-line semantic integration with increased complexity and diversity of the stimuli (Coulson and Van Petten, 2002). This perspective is even more compelling in light of similar problems in a number of conditions, including both acquired (e.g., Aphasia) and developmental disorders (Williams Syndrome). This dissociation argues against a simple continuity view of language interpretation.

Development and validation of a nutrition knowledge questionnaire for a Canadian population.

PubMed

Bradette-Laplante, Maude; Carbonneau, Élise; Provencher, Véronique; Bégin, Catherine; Robitaille, Julie; Desroches, Sophie; Vohl, Marie-Claude; Corneau, Louise; Lemieux, Simone

2017-05-01

The present study aimed to develop and validate a nutrition knowledge questionnaire in a sample of French Canadians from the province of Quebec, taking into account dietary guidelines. A thirty-eight-item questionnaire was developed by the research team and evaluated for content validity by an expert panel, and then administered to respondents. Face validity and construct validity were measured in a pre-test. Exploratory factor analysis and covariance structure analysis were performed to verify the structure of the questionnaire and identify problematic items. Internal consistency and test-retest reliability were evaluated through a validation study. Online survey. Six nutrition and psychology experts, fifteen registered dietitians (RD) and 180 lay people participated. Content validity evaluation resulted in the removal of two items and reformulation of one item. Following face validity, one item was reformulated. Construct validity was found to be adequate, with higher scores for RD v. non-RD (21·5 (sd 2·1) v. 15·7 (sd 3·0) out of 24, P<0·001). Exploratory factor analysis revealed that the questionnaire contained only one factor. Covariance structure analysis led to removal of sixteen items. Internal consistency for the overall questionnaire was adequate (Cronbach's α=0·73). Assessment of test-retest reliability resulted in significant associations for the total knowledge score (r=0·59, P<0·001). This nutrition knowledge questionnaire was found to be a suitable instrument which can be used to measure levels of nutrition knowledge in a Canadian population. It could also serve as a model for the development of similar instruments in other populations.

Interaction Between the Environment and Animals in Urban Settings: Integrated and Participatory Planning

NASA Astrophysics Data System (ADS)

Tarsitano, Elvira

2006-11-01

In urban ecosystems, the ecological system has become completely unbalanced; this, in turn, has led to an increase in well-known problems such as air pollution, ground pollution, and water pollution. This imbalance has also led to the growth and spread of pathogens harmful to man, animals, and plants. Urban sustainability indicators, both global and local, also “indicate” the percentage of population, but these refer only to the human population, not the animal population. Cities need good waste, water, and air management, effective traffic planning, and good zoning of businesses, crafts, and services; over and above these activities, cities also need for planning to take into account the existence of pets (dogs, cats, and etc.) and nonpet animals (insects, birds, mice, etc.). Cities tend to be designed around humans and “on a human scale,” without taking into account the fact that a huge animal population is living side by side with people. That explains why overcrowding tends to go hand in hand with urbanization; all these populations, including humans, need to adapt to new spaces and often need to drastically change their behavior. This is a fact that must be included when drafting sustainable city plans. The supposed strategy is that of “integrated-participatory” control of the interactions between the environment and animals in the cities. Strategy will focus on the development of integrated approaches and tools for environment and animal management in the context of urban settings. This will require such specific methods as ecological balance sheets and ecoplans for the planning, management, and control of the interrelation among environment, animal, and public health. The objective is to develop a better understanding of urban biodiversity and of urban ecosystem functioning, in order to understand and minimize the negative impacts of human activities on them. The research will focus on assessing and forecasting changes in urban biodiversity, structure, function, and dynamics of urban ecosystems, with relationships among society, economy, biodiversity, and habitats.

Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

PubMed Central

Gupta, Vinod K.; Paul, Sandip; Dutta, Chitra

2017-01-01

One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics or his environment. Some of the geographical/racial variations in microbiome structure have been attributed to differences in host genetics and innate/adaptive immunity, while in many other cases, cultural/behavioral features like diet, hygiene, parasitic load, environmental exposure etc. overshadow genetics. The ethnicity or population-specific variations in human microbiome composition, as reviewed in this report, question the universality of the microbiome-based therapeutic strategies and recommend for geographically tailored community-scale approaches to microbiome engineering. PMID:28690602

Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima).

PubMed

Nayfa, Maria G; Zenger, Kyall R

2016-08-01

Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G×E effects) among populations in this region. Global Fst values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise Fst comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAFavg=0.144, Ho=0.238 and MAFavg=0.232, Ho=0.369, respectively) compared to Aru (MAFavg=0.292, Ho=0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and Fst analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Modelling the dynamics of feral alfalfa populations and its management implications.

PubMed

Bagavathiannan, Muthukumar V; Begg, Graham S; Gulden, Robert H; Van Acker, Rene C

2012-01-01

Feral populations of cultivated crops can pose challenges to novel trait confinement within agricultural landscapes. Simulation models can be helpful in investigating the underlying dynamics of feral populations and determining suitable management options. We developed a stage-structured matrix population model for roadside feral alfalfa populations occurring in southern Manitoba, Canada. The model accounted for the existence of density-dependence and recruitment subsidy in feral populations. We used the model to investigate the long-term dynamics of feral alfalfa populations, and to evaluate the effectiveness of simulated management strategies such as herbicide application and mowing in controlling feral alfalfa. Results suggest that alfalfa populations occurring in roadside habitats can be persistent and less likely to go extinct under current roadverge management scenarios. Management attempts focused on controlling adult plants alone can be counterproductive due to the presence of density-dependent effects. Targeted herbicide application, which can achieve complete control of seedlings, rosettes and established plants, will be an effective strategy, but the seedbank population may contribute to new recruits. In regions where roadside mowing is regularly practiced, devising a timely mowing strategy (early- to mid-August for southern Manitoba), one that can totally prevent seed production, will be a feasible option for managing feral alfalfa populations. Feral alfalfa populations can be persistent in roadside habitats. Timely mowing or regular targeted herbicide application will be effective in managing feral alfalfa populations and limit feral-population-mediated gene flow in alfalfa. However, in the context of novel trait confinement, the extent to which feral alfalfa populations need to be managed will be dictated by the tolerance levels established by specific production systems for specific traits. The modelling framework outlined in this paper could be applied to other perennial herbaceous plants with similar life-history characteristics.

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

PubMed

Chotibut, Thiparat; Nelson, David R

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Evolutionary dynamics with fluctuating population sizes and strong mutualism

NASA Astrophysics Data System (ADS)

Chotibut, Thiparat; Nelson, David R.

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics.

PubMed

Hasenauer, Jan; Hasenauer, Christine; Hucho, Tim; Theis, Fabian J

2014-07-01

Functional cell-to-cell variability is ubiquitous in multicellular organisms as well as bacterial populations. Even genetically identical cells of the same cell type can respond differently to identical stimuli. Methods have been developed to analyse heterogeneous populations, e.g., mixture models and stochastic population models. The available methods are, however, either incapable of simultaneously analysing different experimental conditions or are computationally demanding and difficult to apply. Furthermore, they do not account for biological information available in the literature. To overcome disadvantages of existing methods, we combine mixture models and ordinary differential equation (ODE) models. The ODE models provide a mechanistic description of the underlying processes while mixture models provide an easy way to capture variability. In a simulation study, we show that the class of ODE constrained mixture models can unravel the subpopulation structure and determine the sources of cell-to-cell variability. In addition, the method provides reliable estimates for kinetic rates and subpopulation characteristics. We use ODE constrained mixture modelling to study NGF-induced Erk1/2 phosphorylation in primary sensory neurones, a process relevant in inflammatory and neuropathic pain. We propose a mechanistic pathway model for this process and reconstructed static and dynamical subpopulation characteristics across experimental conditions. We validate the model predictions experimentally, which verifies the capabilities of ODE constrained mixture models. These results illustrate that ODE constrained mixture models can reveal novel mechanistic insights and possess a high sensitivity.

Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers.

PubMed

Revidatti, M A; Delgado Bermejo, J V; Gama, L T; Landi Periati, V; Ginja, C; Alvarez, L A; Vega-Pla, J L; Martínez, A M

2014-11-01

Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. The overall means for genetic variability parameters based on the 24 microsatellite markers were the following: mean number of alleles per locus of 6.25 ± 2.3; effective number of alleles per locus of 3.33 ± 1.56; allelic richness per locus of 4.61 ± 1.37; expected and observed heterozygosity of 0.62 ± 0.04 and 0.57 ± 0.02, respectively; within-population inbreeding coefficient of 0.089; and proportion of genetic variability accounted for by differences among breeds of 0.11 ± 0.01. Genetic differences were not significantly associated with the geographical location to which breeds were assigned or their country of origin. Still, the NeighborNet dendrogram depicted the clustering by geographic origin of several South American breeds (Criollo Boliviano, Criollo of northeastern Argentina wet, and Criollo of northeastern Argentina dry), but some unexpected results were also observed, such as the grouping of breeds from countries as distant as El Salvador, Mexico, Ecuador, and Cuba. The results of genetic structure and admixture analyses indicated that the most likely number of ancestral populations was 11, and most breeds clustered separately when this was the number of predefined populations, with the exception of some closely related breeds that shared the same cluster and others that were admixed. These results indicate that Criollo pigs represent important reservoirs of pig genetic diversity useful for local development as well as for the pig industry.

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

PubMed Central

Städler, Thomas; Haubold, Bernhard; Merino, Carlos; Stephan, Wolfgang; Pfaffelhuber, Peter

2009-01-01

Using coalescent simulations, we study the impact of three different sampling schemes on patterns of neutral diversity in structured populations. Specifically, we are interested in two summary statistics based on the site frequency spectrum as a function of migration rate, demographic history of the entire substructured population (including timing and magnitude of specieswide expansions), and the sampling scheme. Using simulations implementing both finite-island and two-dimensional stepping-stone spatial structure, we demonstrate strong effects of the sampling scheme on Tajima's D (DT) and Fu and Li's D (DFL) statistics, particularly under specieswide (range) expansions. Pooled samples yield average DT and DFL values that are generally intermediate between those of local and scattered samples. Local samples (and to a lesser extent, pooled samples) are influenced by local, rapid coalescence events in the underlying coalescent process. These processes result in lower proportions of external branch lengths and hence lower proportions of singletons, explaining our finding that the sampling scheme affects DFL more than it does DT. Under specieswide expansion scenarios, these effects of spatial sampling may persist up to very high levels of gene flow (Nm > 25), implying that local samples cannot be regarded as being drawn from a panmictic population. Importantly, many data sets on humans, Drosophila, and plants contain signatures of specieswide expansions and effects of sampling scheme that are predicted by our simulation results. This suggests that validating the assumption of panmixia is crucial if robust demographic inferences are to be made from local or pooled samples. However, future studies should consider adopting a framework that explicitly accounts for the genealogical effects of population subdivision and empirical sampling schemes. PMID:19237689

Determinants of Social Accountability in Iranian Nursing and Midwifery Schools: A Delphi Study.

PubMed

Salehmoghaddam, Amir Reza; Mazloom, Seyed Reza; Sharafkhani, Mohammad; Gholami, Hassan; Emami Zeydi, Amir; Khorashadizadeh, Fatemeh; Emadzadeh, Ali

2017-04-01

Revising the medical education programs to meet the needs of society has become both a necessity and an important priority due to the considerable increase of population, changing patterns of diseases, and new health priorities. While this necessity has been highlighted in Iran's Fifth Development Plan as well as its National 2025 Vision Plan, the determinants of social accountability have not been explained yet. This study aimed to develop determinants of social accountability in the Iranian Nursing and Midwifery Schools. This classic Delphi study included thirty experts in Nursing and Midwifery Education, Research and Services selected based on purposive sampling and three rounds of Delphi technique and conducted in Nursing and Midwifery School of Mashhad University of Medical Sciences. The primary data were collected using an initial structured questionnaire prepared through extensive review of literature. SPSS 11.5 software was used to analyze the data. The interquartile deviation and percentage of agreement were also used to study the consensus of opinion by experts. Finding obtained from the rounds of Delphi resulted in selecting 69 determinants out of the initial pool of 128 primary determinants of social accountability. The items were selected based on experts' consensus and categorized under three main activities of Nursing and Midwifery School, namely education, research, and service. Social accountability determinants were explained by 69 items for Schools of Nursing and Midwifery in Iran. The proposed determinants can be used by managers and authorities of Nursing and Midwifery School, policy makers, and evaluating institutions associated with them to ensure realizing social accountability goals.

Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range.

PubMed

Clucas, Gemma V; Younger, Jane L; Kao, Damian; Rogers, Alex D; Handley, Jonathan; Miller, Gary D; Jouventin, Pierre; Nolan, Paul; Gharbi, Karim; Miller, Karen J; Hart, Tom

2016-10-13

Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion. We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of kilometers of open-ocean, suggesting migration among islands and archipelagos may be common. Our results show that the South Georgia population is slightly differentiated from all other colonies and suggest that the recently founded Falkland Island colony is likely to have been established by migrants from the distant Crozet Islands rather than nearby colonies on South Georgia, possibly as a result of density-dependent processes. The observed subtle differentiation among king penguin colonies must be considered in future conservation planning and monitoring of the species, and demographic models that attempt to forecast extinction risk in response to large-scale climate change must take into account migration. It is possible that migration could buffer king penguins against some of the impacts of climate change where colonies appear panmictic, although it is unlikely to protect them completely given the widespread physical changes projected for their Southern Ocean foraging grounds. Overall, large-scale population genetic studies of marine predators across the Southern Ocean are revealing more interconnection and migration than previously supposed.

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. PMID:24713994

Modelling proteins' hidden conformations to predict antibiotic resistance

NASA Astrophysics Data System (ADS)

Hart, Kathryn M.; Ho, Chris M. W.; Dutta, Supratik; Gross, Michael L.; Bowman, Gregory R.

2016-10-01

TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM's specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models' prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design.

Cost containment: the Pacific. Japan.

PubMed

Tajimi, K; Shimada, Y; Nishimura, S; Sirio, C A

1994-08-01

The Japanese healthcare system is structured to provide universal healthcare access to the entire Japanese population via a constitutional guarantee. Increasing costs within the Japanese healthcare system are largely attributable to the country's rapidly aging population. Intensive care services are provided primarily in large tertiary care hospitals by a relatively small cadre of dedicated critical care physicians. Triage pressure is high in many Japanese hospitals due to a relatively small proportion of ICU beds. As a result, few patients are admitted to the ICU at low risk of adverse outcome or monitoring. Costs associated with providing critical care are poorly understood because of current hospital cost accounting systems. Critical care costs have only recently become an area of concern. Nevertheless, critical care physicians are taking steps to more fully understand severity of illness, clinical outcome, and utilization of resources in order to effectively guide healthcare policy and resource allocation decisions impacting Japanese critical care.

Calculation of the vibration-rotational transition intensities of water molecules trapped in an argon matrix: stretching O-H vibrations spectral region

NASA Astrophysics Data System (ADS)

Pitsevich, George; Shalamberidze, Elena; Malevich, Alex; Sablinskas, Valdas; Balevicius, Vytautas; Pettersson, Lars G. M.

2017-10-01

The frequencies and intensities of vibration-rotational transitions of water molecules in an argon matrix were calculated for temperatures of 6 and 30 K. The rigid asymmetric top approximation was used with available literature values of the effective rotational constants in the ground and excited vibrational states. The calculations were carried out by taking into account the existence of a non-equilibrium population distribution between the rotational levels of ortho- and para-water isomers. It was assumed that the temperature relaxation of the population of rotational levels is independent of the ortho- and para-isomers. Comparison of the results of the theoretical calculations with experimental literature data shows good agreement for the majority of the rotational structure lines for symmetric and antisymmetric stretching vibrations both in the frequency values and in the values of the relative intensities.

Ecological determinants of divorce: a structural approach to the explanation of Japanese divorce.

PubMed

Fukurai, H; Alston, J P

1992-01-01

This paper examines the ecological determinants of contemporary Japanese divorce rates on the prefectural level. LISREL and computer-generated graphics are the analytic methods used. The aggregate level of analysis demands the use of the ecological model which posits that demographic changes, economic activities, migration patterns, and the level of urbanization are significant predictors of divorce rate. Our analysis demonstrates that sex ratio, female labor force participation, female in-migration patterns, population increase, and net household income all play a significant role in affecting the divorce rate. Our findings also confirm the well-supported hypothesis that both population density and modernization positively influence modern Japan's divorce rates. The residual analysis also points out that in order to account for the large proportion of the unexplained variance of Japanese divorce, behavioral-related variables and island- or prefecture-specific dimensions need to be included in the ecological model of divorce.

Challenges and Opportunities for Developing and Implementing Incentives to Improve Health-Related Behaviors in Older Adults

PubMed Central

Klein, Eran; Karlawish, Jason

2010-01-01

There is growing interest in using patient-directed incentives to change health-related behaviors. Advocates of incentive programs have proposed an ambitious research agenda for moving patient incentive programs forward. Older adults may pose a challenge to such a research agenda. The cognitive and psychological features of this population, in particular, age-related changes in emotional regulation, executive function and cognitive capacities, and a preference for collaborative decision-making raise questions about the suitability of these programs, particularly the structure of current financial incentives, to older adults. Differences in decision-making in older adults need to be accounted for in the design and implementation of financial incentive programs. Financial incentive programs tailored to characteristics of older adult populations may be more likely to improve the lives of older persons and the economic success of programs that serve them. PMID:20863335

Modelling proteins’ hidden conformations to predict antibiotic resistance

PubMed Central

Hart, Kathryn M.; Ho, Chris M. W.; Dutta, Supratik; Gross, Michael L.; Bowman, Gregory R.

2016-01-01

TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM’s specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models’ prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design. PMID:27708258

Emergence of cooperation with self-organized criticality

NASA Astrophysics Data System (ADS)

Park, Sangmin; Jeong, Hyeong-Chai

2012-02-01

Cooperation and self-organized criticality are two main keywords in current studies of evolution. We propose a generalized Bak-Sneppen model and provide a natural mechanism which accounts for both phenomena simultaneously. We use the prisoner's dilemma games to mimic the interactions among the members in the population. Each member is identified by its cooperation probability, and its fitness is given by the payoffs from neighbors. The least fit member with the minimum payoff is replaced by a new member with a random cooperation probability. When the neighbors of the least fit one are also replaced with a non-zero probability, a strong cooperation emerges. The Bak-Sneppen process builds a self-organized structure so that the cooperation can emerge even in the parameter region where a uniform or random population decreases the number of cooperators. The emergence of cooperation is due to the same dynamical correlation that leads to self-organized criticality in replacement activities.

Adolescent lives matter: preventing HIV in adolescents

PubMed Central

Pettifor, Audrey; Stoner, Marie; Pike, Carey; Bekker, Linda-Gail

2018-01-01

Purpose of review Many of the almost 2 million HIV infections that occurred globally in the last year occurred among adolescents and young people, particularly those from East and Southern Africa and within key populations. Global HIV epidemic control will require that new infections among these youth populations be curtailed. This review examines the most effective prevention approaches to reach these adolescent populations in the next 5 years. Recent findings Adolescents are in transition and are developmentally unique. They have specific needs and challenges, which if not addressed will result in less than successful interventions. Tailored, layered, combination prevention packages that take into account specific adolescent needs and involve biomedical, behavioural and structural components are recommended. These packages should be designed for and with the meaningful input of adolescents, and involve their peers in their implementation and execution. Where possible, age-appropriate health and social interventions that go beyond HIV should be bundled and offered in a variety of community-based venues that are already acceptable to and frequented by adolescents. Summary It is urgent that we reach adolescents globally with the most effective HIV prevention approaches. HIV prevention investment in this population has immediate and longer-term benefits. PMID:29528850

Searching for collective behavior in a large network of sensory neurons.

PubMed

Tkačik, Gašper; Marre, Olivier; Amodei, Dario; Schneidman, Elad; Bialek, William; Berry, Michael J

2014-01-01

Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such "K-pairwise" models--being systematic extensions of the previously used pairwise Ising models--provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction.

Searching for Collective Behavior in a Large Network of Sensory Neurons

PubMed Central

Tkačik, Gašper; Marre, Olivier; Amodei, Dario; Schneidman, Elad; Bialek, William; Berry, Michael J.

2014-01-01

Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction. PMID:24391485

Adapting an Evidence-Based Intervention Targeting HIV-Infected Prisoners in Malaysia

PubMed Central

Copenhaver, Michael M.; Tunku, Noor; Ezeabogu, Ifeoma; Potrepka, Jessica; Zahari, Muhammad Muhsin A.; Kamarulzaman, Adeeba; Altice, Frederick L.

2011-01-01

HIV-infected prisoners in Malaysia represent a critical target population for secondary HIV risk reduction interventions and care. We report on the process and outcome of our formative research aimed at systematically selecting and adapting an EBI designed to reduce secondary HIV risk and improve adherence to antiretroviral therapy among soon-to-be-released HIV-infected prisoners. Our formative work involved a critical examination of established EBIs and associated published reports complemented by data elicited through structured interviews and focus groups with key stakeholders, members of the target population, and their family members. Based on all information, we adapted the Holistic Health Recovery Program targeting people living with HIV (HHRP+), an EBI, to consist of eight 2-hour sessions that cover a range of specified topics so that participants may individually apply intervention content as needed to accommodate their particular substance abuse, HIV risk, and antiretroviral adherence issues. This study provides a complete example of the process of selecting and adapting an EBI—taking into account both empirical evidence and input from target organization stakeholders and target population members and their families—for use in real world prison settings where high-risk populations are concentrated. PMID:21860786

Dissection of complex adult traits in a mouse synthetic population.

PubMed

Burke, David T; Kozloff, Kenneth M; Chen, Shu; West, Joshua L; Wilkowski, Jodi M; Goldstein, Steven A; Miller, Richard A; Galecki, Andrzej T

2012-08-01

Finding the causative genetic variations that underlie complex adult traits is a significant experimental challenge. The unbiased search strategy of genome-wide association (GWAS) has been used extensively in recent human population studies. These efforts, however, typically find only a minor fraction of the genetic loci that are predicted to affect variation. As an experimental model for the analysis of adult polygenic traits, we measured a mouse population for multiple phenotypes and conducted a genome-wide search for effector loci. Complex adult phenotypes, related to body size and bone structure, were measured as component phenotypes, and each subphenotype was associated with a genomic spectrum of candidate effector loci. The strategy successfully detected several loci for the phenotypes, at genome-wide significance, using a single, modest-sized population (N = 505). The effector loci each explain 2%-10% of the measured trait variation and, taken together, the loci can account for over 25% of a trait's total population variation. A replicate population (N = 378) was used to confirm initially observed loci for one trait (femur length), and, when the two groups were merged, the combined population demonstrated increased power to detect loci. In contrast to human population studies, our mouse genome-wide searches find loci that individually explain a larger fraction of the observed variation. Also, the additive effects of our detected mouse loci more closely match the predicted genetic component of variation. The genetic loci discovered are logical candidates for components of the genetic networks having evolutionary conservation with human biology.

Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea abies (L.) Karst

PubMed Central

Heuertz, Myriam; De Paoli, Emanuele; Källman, Thomas; Larsson, Hanna; Jurman, Irena; Morgante, Michele; Lascoux, Martin; Gyllenstrand, Niclas

2006-01-01

DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico–Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively. PMID:17057229

Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.

PubMed

Lloyd-Jones, Luke R; Robinson, Matthew R; Moser, Gerhard; Zeng, Jian; Beleza, Sandra; Barsh, Gregory S; Tang, Hua; Visscher, Peter M

2017-06-01

Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye ( n = 625) and skin ( n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color ( AHRR ) and one for skin color ( DDB1 ). Copyright © 2017 by the Genetics Society of America.

Genomic evidence for the population genetic differentiation of Misgurnus anguillicaudatus in the Yangtze River basin of China.

PubMed

Yi, Shaokui; Wang, Weimin; Zhou, Xiaoyun

2018-02-21

Misgurnus anguillicaudatus, an important aquatic species, is mainly distributed in the Yangtze River basin. To reveal the population genetic structure of M. anguillicaudatus distributed in the Yangtze River basin, genotyping by sequencing (GBS) technique was employed to detect the genome wide genetic variations of M. anguillicaudatus. A total of 30.03 Gb raw data were yielded from 70 samples collected from 15 geographic sites located in the Yangtze River basin. Subsequently, 2092 high quality SNPs were genotyped across these samples and used for a series of genetic analysis. The results of genetic analysis showed that high levels of genetic diversity were observed and the populations from upper reaches (UR) were significantly differentiated from the middle and lower reaches (MLR) of Yangtze River basin. Meanwhile, no significant isolation by distance was detected among the populations. Ecological factors (e.g. complicated topography and climatic environment) and anthropogenic factors (e.g. aquaculture and agriculture cultivation) might account for the genetic disconnectivity between UR and MLR populations. This study provided valuable genetic data for the future breeding program and also for the conversation and scientific utilization of those abundant genetic resources stored in the Yangtze River basin. Copyright © 2018 Elsevier Inc. All rights reserved.

Predicting the consequences of species loss using size-structured biodiversity approaches.

PubMed

Brose, Ulrich; Blanchard, Julia L; Eklöf, Anna; Galiana, Nuria; Hartvig, Martin; R Hirt, Myriam; Kalinkat, Gregor; Nordström, Marie C; O'Gorman, Eoin J; Rall, Björn C; Schneider, Florian D; Thébault, Elisa; Jacob, Ute

2017-05-01

Understanding the consequences of species loss in complex ecological communities is one of the great challenges in current biodiversity research. For a long time, this topic has been addressed by traditional biodiversity experiments. Most of these approaches treat species as trait-free, taxonomic units characterizing communities only by species number without accounting for species traits. However, extinctions do not occur at random as there is a clear correlation between extinction risk and species traits. In this review, we assume that large species will be most threatened by extinction and use novel allometric and size-spectrum concepts that include body mass as a primary species trait at the levels of populations and individuals, respectively, to re-assess three classic debates on the relationships between biodiversity and (i) food-web structural complexity, (ii) community dynamic stability, and (iii) ecosystem functioning. Contrasting current expectations, size-structured approaches suggest that the loss of large species, that typically exploit most resource species, may lead to future food webs that are less interwoven and more structured by chains of interactions and compartments. The disruption of natural body-mass distributions maintaining food-web stability may trigger avalanches of secondary extinctions and strong trophic cascades with expected knock-on effects on the functionality of the ecosystems. Therefore, we argue that it is crucial to take into account body size as a species trait when analysing the consequences of biodiversity loss for natural ecosystems. Applying size-structured approaches provides an integrative ecological concept that enables a better understanding of each species' unique role across communities and the causes and consequences of biodiversity loss. © 2016 Cambridge Philosophical Society.

Validation of the French version of the yale food addiction scale: an examination of its factor structure, reliability, and construct validity in a nonclinical sample.

PubMed

Brunault, Paul; Ballon, Nicolas; Gaillard, Philippe; Réveillère, Christian; Courtois, Robert

2014-05-01

The concept of food addiction has recently been proposed by applying the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision, criteria for substance dependence to eating behaviour. Food addiction has received increased attention given that it may play a role in binge eating, eating disorders, and the recent increase in obesity prevalence. Currently, there is no psychometrically sound tool for assessing food addiction in French. Our study aimed to test the psychometric properties of a French version of the Yale Food Addiction Scale (YFAS) by establishing its factor structure and construct validity in a nonclinical population. A total of 553 participants were assessed for food addiction (French version of the YFAS) and binge eating behaviour (Bulimic Investigatory Test Edinburgh and Binge Eating Scale). We tested the scale's factor structure (factor analysis for dichotomous data based on tetrachoric correlation coefficients), internal consistency, and construct validity with measures of binge eating. Our results supported a 1-factor structure, which accounted for 54.1% of the variance. This tool had adequate reliability and high construct validity with measures of binge eating in this population, both in its diagnosis and symptom count version. A 2-factor structure explained an additional 9.1% of the variance, and could differentiate between patients with high, compared with low, levels of insight regarding addiction symptoms. In our study, we validated a psychometrically sound French version of the YFAS, both in its symptom count and diagnostic version. Future studies should validate this tool in clinical samples.

Interrelated structures of the transport shock and collisional relaxation layer in a multitemperature, multilevel ionized gas

NASA Technical Reports Server (NTRS)

Vinolo, A. R.; Clarke, J. H.

1972-01-01

The gas dynamic structures of the transport shock and the downstream collisional relaxation layer are evaluated for partially ionized monatomic gases. Elastic and inelastic collisional nonequilibrium effects are taken into consideration. Three electronic levels are accounted for in the microscopic model of the atom. Nonequilibrium processes with respect to population of levels and species plus temperature are considered. By using an asymptotic technique the shock morphology is found on a continuum flow basis. The asymptotic procedure gives two distinct layers in which the nonequilibrium effects to be considered are different. A transport shock appears as the inner solution to an outer collisional relaxation layer in which the gas reaches local equilibrium. A family of numerical examples is displayed for different flow regimes. Argon and helium models are used in these examples.

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…

[Analysis of cancer incidence and mortality in elderly population in China, 2013].

PubMed

Chen, W Q; Zheng, R S; Zhang, S W; Zeng, H M; Zou, X N; He, J

2017-01-23

Objective: To estimate the cancer incidence and mortality in elderly Chinese population in 2013 based on the data from local cancer registries submitted to National Central Cancer Registry (NCCR). Methods: Data from 255 cancer registries submitted to NCCR with qualified data after checked and evaluated, were selected for this estimation. Cancer incidence and mortality were stratified by areas, sex, age groups and cancer site, combined with population data of the year 2013 to estimate cancer epidemiology in older people in China. Chinese population census in 2000 and Segi's population were used for the estimation of age-standardized incidence/mortality rates. Results: All the 255 cancer registries (88 in urban and 167 in rural areas) were selected for this estimation, covered 37 407 728 elderly subjects, accounting for 17.73% of the entire national elderly population. It was estimated about 2 171.0 thousand new cancer cases in older people in China, accounting for 58.96% of all cancer incidence, with the crude incidence rate of 1 029.16/100 000 (1 297.96 per 100 000 in male, 777.18 per 100 000 in female), and the age-standardized incidence rate by Chinese standard population (ASIRC, 2000) was 1 019.25 per 100 000. It was estimated about 1 600.5 thousand deaths in older people in China, accounting for 67.70% of all cancer deaths, with the crude mortality of 758.72/100 000 (988.37 per 100 000 in males, 543.44 per 100 000 in females), and the age-standardized incidence rate by Chinese standard population (ASIRC, 2000) was 730.78 per 100 000. Lung cancer, stomach cancer, colorectal cancer, liver cancer and esophageal cancer were the most common cancers, accounting for about 67.70% of all cancer cases in China. Those cancers are also the most common cancers in China, accounting for about 73.45% of all cancer deaths. Conclusions: The cancer burden of elderly population in China is very serious. The major cancer incidence and mortality in urban and rural areas are similar, but the cancer patterns are very different in urban and rural areas. As cancer burdens for older people are different between urban and rural areas in China, more attention should be paid to the need of older people according to the actual situation.

Population size influences amphibian detection probability: implications for biodiversity monitoring programs.

PubMed

Tanadini, Lorenzo G; Schmidt, Benedikt R

2011-01-01

Monitoring is an integral part of species conservation. Monitoring programs must take imperfect detection of species into account in order to be reliable. Theory suggests that detection probability may be determined by population size but this relationship has not yet been assessed empirically. Population size is particularly important because it may induce heterogeneity in detection probability and thereby cause bias in estimates of biodiversity. We used a site occupancy model to analyse data from a volunteer-based amphibian monitoring program to assess how well different variables explain variation in detection probability. An index to population size best explained detection probabilities for four out of six species (to avoid circular reasoning, we used the count of individuals at a previous site visit as an index to current population size). The relationship between the population index and detection probability was positive. Commonly used weather variables best explained detection probabilities for two out of six species. Estimates of site occupancy probabilities differed depending on whether the population index was or was not used to model detection probability. The relationship between the population index and detectability has implications for the design of monitoring and species conservation. Most importantly, because many small populations are likely to be overlooked, monitoring programs should be designed in such a way that small populations are not overlooked. The results also imply that methods cannot be standardized in such a way that detection probabilities are constant. As we have shown here, one can easily account for variation in population size in the analysis of data from long-term monitoring programs by using counts of individuals from surveys at the same site in previous years. Accounting for variation in population size is important because it can affect the results of long-term monitoring programs and ultimately the conservation of imperiled species.

Accountable care around the world: a framework to guide reform strategies.

PubMed

McClellan, Mark; Kent, James; Beales, Stephen J; Cohen, Samuel I A; Macdonnell, Michael; Thoumi, Andrea; Abdulmalik, Mariam; Darzi, Ara

2014-09-01

Accountable care--a way to align health care payments with patient-focused reform goals--is currently being pursued in the United States, but its principles are also being applied in many other countries. In this article we review experiences with such reforms to offer a globally applicable definition of an accountable care system and propose a conceptual framework for characterizing and assessing accountable care reforms. The framework consists of five components: population, outcomes, metrics and learning, payments and incentives, and coordinated delivery. We describe how the framework applies to accountable care reforms that are already being implemented in Spain and Singapore. We also describe how it can be used to map progress through increasingly sophisticated levels of reforms. We recommend that policy makers pursuing accountable care reforms emphasize the following steps: highlight population health and wellness instead of just treating illness; pay for outcomes instead of activities; create a more favorable environment for collaboration and coordinated care; and promote interoperable data systems. Project HOPE—The People-to-People Health Foundation, Inc.

Incorporating shared savings programs into primary care: from theory to practice.

PubMed

Hayen, Arthur P; van den Berg, Michael J; Meijboom, Bert R; Struijs, Jeroen N; Westert, Gert P

2015-12-30

In several countries, health care policies gear toward strengthening the position of primary care physicians. Primary care physicians are increasingly expected to take accountability for overall spending and quality. Yet traditional models of paying physicians do not provide adequate incentives for taking on this new role. Under a so-called shared savings program physicians are instead incentivized to take accountability for spending and quality, as the program lets them share in cost savings when quality targets are met. We provide a structured approach to designing a shared savings program for primary care, and apply this approach to the design of a shared savings program for a Dutch chain of primary care providers, which is currently being piloted. Based on the literature, we defined five building blocks of shared savings models that encompass the definition of the scope of the program, the calculation of health care expenditures, the construction of a savings benchmark, the assessment of savings and the rules and conditions under which savings are shared. We apply insights from a variety of literatures to assess the relative merits of alternative design choices within these building blocks. The shared savings program uses an econometric model of provider expenditures as an input to calculating a casemix-corrected benchmark. The minimization of risk and uncertainty for both payer and provider is pertinent to the design of a shared savings program. In that respect, the primary care setting provides a number of unique opportunities for achieving cost and quality targets. Accountability can more readily be assumed due to the relatively long-lasting relationships between primary care physicians and patients. A stable population furthermore improves the confidence with which savings can be attributed to changes in population management. Challenges arise from the institutional context. The Dutch health care system has a fragmented structure and providers are typically small in size. Shared savings programs fit the concept of enhanced primary care. Incorporating a shared savings program into existing payment models could therefore contribute to the financial sustainability of this organizational form.

Accounting for selection and correlation in the analysis of two-stage genome-wide association studies.

PubMed

Robertson, David S; Prevost, A Toby; Bowden, Jack

2016-10-01

The problem of selection bias has long been recognized in the analysis of two-stage trials, where promising candidates are selected in stage 1 for confirmatory analysis in stage 2. To efficiently correct for bias, uniformly minimum variance conditionally unbiased estimators (UMVCUEs) have been proposed for a wide variety of trial settings, but where the population parameter estimates are assumed to be independent. We relax this assumption and derive the UMVCUE in the multivariate normal setting with an arbitrary known covariance structure. One area of application is the estimation of odds ratios (ORs) when combining a genome-wide scan with a replication study. Our framework explicitly accounts for correlated single nucleotide polymorphisms, as might occur due to linkage disequilibrium. We illustrate our approach on the measurement of the association between 11 genetic variants and the risk of Crohn's disease, as reported in Parkes and others (2007. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat. Gen. 39: (7), 830-832.), and show that the estimated ORs can vary substantially if both selection and correlation are taken into account. © The Author 2016. Published by Oxford University Press.

Orthopaedic injury analysis in the 2010 Yushu, China earthquake.

PubMed

Li, Ting; Jiang, Xieyuan; Chen, Hui; Yang, Zheng; Wang, Xiaobo; Wang, Manyi

2012-06-01

By analysing the injuries of the orthopaedic wounded during the 2010 Yushu earthquake, we aim to provide useful medical information for the rational application and allocation of medical resources and better implementation of medical relief in earthquake-stricken areas. Five hundred and eighty-two orthopaedic patients injured during the earthquake. The clinical data, injury conditions and epidemiological features (including age composition, gender ratio, distribution of injury, etc.) were collected and analysed. Altogether 582 orthopaedic patients were analysed. The average age for all patients was 38.8±13.08 years (0-86 years). Adults accounted for 81.62%. There was no gender difference. The most common injuries included limb fractures, pelvic/acetabular fractures and spinal fractures. Fractures accompany with nerve injury were relatively low, only 17 patients account for 2.92%. Fractures complicated by crush syndrome were even lower, only 7 patients account for 1.20%. The patients who experienced fractures in the Yushu earthquake were mostly adults. This was correlated with population composition in Yushu area. This time all the orthopaedic injuries were relative mild with less complication as nerve injury or crush syndrome mainly because of the characteristics of the house structure in Yushu area. Copyright © 2011 Elsevier Ltd. All rights reserved.

Genome-wide SNPs reveal the drivers of gene flow in an urban population of the Asian Tiger Mosquito, Aedes albopictus.

PubMed

Schmidt, Thomas L; Rašić, Gordana; Zhang, Dongjing; Zheng, Xiaoying; Xi, Zhiyong; Hoffmann, Ary A

2017-10-01

Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Aedes albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations.

Psychometric Properties of the Catastrophic Cognitions Questionnaire-Modified (CCQ-Modified) Among Community Samples in Malaysia.

PubMed

Abdul Khaiyom, Jamilah Hanum; Mukhtar, Firdaus; Ibrahim, Normala; Mohd Sidik, Sherina; Oei, Tian Po Sumantri

2016-12-01

The Catastrophic Cognitions Questionnaire-Modified (CCQ-M) is a common instrument for measuring catastrophic thoughts. In some countries, however, CCQ-M still poses concerns following the lack of appropriate validation among their populations. The current study aimed to examine the factor structure of the CCQ-M, the reliability, and the validity in community samples in Malaysia. The Malay version of CCQ-M and additional measures assessing the symptoms and cognitions relevant to anxiety disorders were completed by 682 university students and general community. Exploratory factor analysis revealed a two-factor structure accounting for 62.2% of the total variance. Confirmatory factor analysis confirmed the two-factor model by deleting four items. The Cronbach's alpha coefficients for the total and the two subscales were .94, .90, and .92, respectively. Test-retest reliability analysis was conducted on 82 university students in the interval period of 14 days, and the result was r = .58. Evidence supported the concurrent, convergent, and discriminant validity. In conclusion, the 17-item CCQ-M-Malaysia is a valid and reliable instrument for assessing catastrophic cognitions among Malaysian populations. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Fine-resolution Modeling of Urban-Energy Systems' Water Footprint in River Networks

NASA Astrophysics Data System (ADS)

McManamay, R.; Surendran Nair, S.; Morton, A.; DeRolph, C.; Stewart, R.

2015-12-01

Characterizing the interplay between urbanization, energy production, and water resources is essential for ensuring sustainable population growth. In order to balance limited water supplies, competing users must account for their realized and virtual water footprint, i.e. the total direct and indirect amount of water used, respectively. Unfortunately, publicly reported US water use estimates are spatially coarse, temporally static, and completely ignore returns of water to rivers after use. These estimates are insufficient to account for the high spatial and temporal heterogeneity of water budgets in urbanizing systems. Likewise, urbanizing areas are supported by competing sources of energy production, which also have heterogeneous water footprints. Hence, a fundamental challenge of planning for sustainable urban growth and decision-making across disparate policy sectors lies in characterizing inter-dependencies among urban systems, energy producers, and water resources. A modeling framework is presented that provides a novel approach to integrate urban-energy infrastructure into a spatial accounting network that accurately measures water footprints as changes in the quantity and quality of river flows. River networks (RNs), i.e. networks of branching tributaries nested within larger rivers, provide a spatial structure to measure water budgets by modeling hydrology and accounting for use and returns from urbanizing areas and energy producers. We quantify urban-energy water footprints for Atlanta, GA and Knoxville, TN (USA) based on changes in hydrology in RNs. Although water intakes providing supply to metropolitan areas were proximate to metropolitan areas, power plants contributing to energy demand in Knoxville and Atlanta, occurred 30 and 90km outside the metropolitan boundary, respectively. Direct water footprints from urban landcover primarily comprised smaller streams whereas indirect footprints from water supply reservoirs and energy producers included larger river systems. By using projections in urban populations for 2030 and 2050, we estimated scenarios of expansion in water footprints depending on urban growth policies and energy production technology. We provide examples of how this framework can be used to minimize water footprints and impacts to aquatic biodiversity.

Molecular Zoogeography of Freshwater Fishes in the Southeastern United States

PubMed Central

Bermingham, Eldredge; Avise, John C.

1986-01-01

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were used to reconstruct evolutionary relationships of conspecific populations in four species of freshwater fish—Amia calva, Lepomis punctatus, L. gulosus, and L. microlophus. A suite of 14-17 endonucleases was employed to assay mtDNAs from 305 specimens collected from 14 river drainages extending from South Carolina to Louisiana. Extensive mtDNA polymorphism was observed within each assayed species. In both phenograms and Wagner parsimony networks, mtDNA clones that were closely related genetically were usually geographically contiguous. Within each species, major mtDNA phylogenetic breaks also distinguished populations from separate geographic regions, demonstrating that dispersal and gene flow have not been sufficient to override geographic influences on population subdivision.—Importantly, there were strong patterns of congruence across species in the geographic placements of the mtDNA phylogenetic breaks. Three major boundary regions were characterized by concentrations of phylogenetic discontinuities, and these zones agree well with previously described zoogeographic boundaries identified by a different kind of data base—distributional limits of species—suggesting that a common set of historical factors may account for both phenomena. Repeated episodes of eustatic sea level change along a relatively static continental morphology are the likely causes of several patterns of drainage isolation and coalescence, and these are discussed in relation to the genetic data.—Overall, results exemplify the positive role that intraspecific genetic analyses may play in historical zoogeographic reconstruction. They also point out the potential inadequacies of any interpretations of population genetic structure that fail to consider the influences of history in shaping that structure. PMID:17246340

[Hygienic characteristics of the population's morbidity rate associated with iodine deficiency in the Republic of Mordovia].

PubMed

Blinov, D S; Chemova, N N; Balykova, O P; Liapina, S A; Chugunova, L A

2015-01-01

In the article there are presented the results of research on naturally conditioned insufficiency of trace elements, particularly iodine, in the Republic of Mordovia. Iodine deficiency disorders are referred to the most common non-infectious human pathology. According to WHO data, about two billion people on Earth live in conditions of in iodine deficiency. In the Russian Federation there are no areas in which the population would not be at risk for the development of iodine deficiency disorders. To these regions and the Republic of Mordovia is referred. The prevalence of diseases caused by iodine deficiency among the urban population accounted for 100-150, among rural--130-350. In some regions of endemic goiter rate reaches 800. Analysis of the morbidity rate of the population in the Republic of Mordovia, associated with the iodine deficiency, shows that in the structure of diseases related to micronutrient deficiency, by 2013 diffuse goiter plays a leading role, beingfollowed by a multi-node (endemic) goiter onward thyroiditis, subclinical hypothyroidism and hyperthyroidism. Thus, the analysis of indices of new cases of diseases associated with the iodine deficiency, allows to make the conclusion that diffuse goiter is the most significant pathology. In the structure of diseases related to the micronutrient deficiency, out of the most frequently detected iodine deficiency disorders, the greatest fraction are diffuse and multinodular goiter. The study was conducted with the support of the project, performed in the framework of the basic part of the State assignment (project 2859) and a RHSF grant.

West Asia - a demographic profile.

PubMed

1980-01-01

The average rate of population growth in the Arab region is about 3% per year, and fertility rates are high. The population aged 15 years or under accounts for 48% of the total population in most countries. The rate of economically active population is very low, ranging from 22% to 32% of the total. Infant mortality rates range from 60/1000 to 200/1000. Illiteracy rates average around 47% of the total number of males aged 15 and above, and exceeded 70% among women. Special attention is being given girls' education. The proportion of girls aged 6-24 enrolled at various educational levels rose from about 14.3% in 1960 to about 25% in 1975. Female illiteracy rates in Arab countries are among the highest in the world. Negative attitudes toward working women continue to be the major obstacle and contributes to high fertility. Demographic profiles are given for Kuwait, Qatar, Yemen, and United Arab Emirates. In the United Arab Emirates the most prominent feature of the age-sex structure is the relatively large number of males between the ages of 20 and 40. The total fertility rate and the gross reproduction rate for the entire population in 1975 were estimated to be about 5.9 and 2.9 respectively. Between 1968 and 1975 the population of the United Arab Emirates grew from 180,226 to 557,887, yielding an annual growth of 14.6%.

17 CFR 256.305 - Structures and improvements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... provided for machinery, apparatus, or other equipment of the company shall be charged to the same account... (CONTINUED) UNIFORM SYSTEM OF ACCOUNTS FOR MUTUAL SERVICE COMPANIES AND SUBSIDIARY SERVICE COMPANIES, PUBLIC UTILITY HOLDING COMPANY ACT OF 1935 Service Company Property Accounts § 256.305 Structures and...

Quantifying the health impacts of air pollution under a changing climate-a review of approaches and methodology.

PubMed

Sujaritpong, Sarunya; Dear, Keith; Cope, Martin; Walsh, Sean; Kjellstrom, Tord

2014-03-01

Climate change has been predicted to affect future air quality, with inevitable consequences for health. Quantifying the health effects of air pollution under a changing climate is crucial to provide evidence for actions to safeguard future populations. In this paper, we review published methods for quantifying health impacts to identify optimal approaches and ways in which existing challenges facing this line of research can be addressed. Most studies have employed a simplified methodology, while only a few have reported sensitivity analyses to assess sources of uncertainty. The limited investigations that do exist suggest that examining the health risk estimates should particularly take into account the uncertainty associated with future air pollution emissions scenarios, concentration-response functions, and future population growth and age structures. Knowledge gaps identified for future research include future health impacts from extreme air pollution events, interactions between temperature and air pollution effects on public health under a changing climate, and how population adaptation and behavioural changes in a warmer climate may modify exposure to air pollution and health consequences.

Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm

PubMed Central

Teh, Chee-Keng; Ong, Ai-Ling; Kwong, Qi-Bin; Apparow, Sukganah; Chew, Fook-Tim; Mayes, Sean; Mohamed, Mohaimi; Appleton, David; Kulaveerasingam, Harikrishna

2016-01-01

GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10−4) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential. PMID:26743827

GONe: Software for estimating effective population size in species with generational overlap

USGS Publications Warehouse

Coombs, J.A.; Letcher, B.H.; Nislow, K.H.

2012-01-01

GONe is a user-friendly, Windows-based program for estimating effective size (N e) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N e is estimated at each locus and over all loci. Furthermore, N e estimates are output for three different genetic drift estimators (F s, F c and F k). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N e values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at. ?? 2011 Blackwell Publishing Ltd.

Multimorbidity prevalence and patterns across socioeconomic determinants: a cross-sectional survey.

PubMed

Agborsangaya, Calypse B; Lau, Darren; Lahtinen, Markus; Cooke, Tim; Johnson, Jeffrey A

2012-03-19

Studies on the prevalence of multimorbidity, defined as having two or more chronic conditions, have predominantly focused on the elderly. We estimated the prevalence and specific patterns of multimorbidity across different adult age groups. Furthermore, we examined the associations of multimorbidity with socio-demographic factors. Using data from the Health Quality Council of Alberta (HQCA) 2010 Patient Experience Survey, the prevalence of self reported multimorbidity was assessed by telephone interview among a sample of 5010 adults (18 years and over) from the general population. Logistic regression analyses were performed to determine the association between a range of socio-demographic factors and multimorbidity. The overall age- and sex-standardized prevalence of multimorbidity was 19.0% in the surveyed general population. Of those with multimorbidity, 70.2% were aged less than 65 years. The most common pairing of chronic conditions was chronic pain and arthritis. Age, sex, income and family structure were independently associated with multimorbidity. Multimorbidity is a common occurrence in the general adult population, and is not limited to the elderly. Future prevention programs and practice guidelines should take into account the common patterns of multimorbidity.

Mechanism of biphasic charge recombination and accumulation in TiO2 mesoporous structured perovskite solar cells.

PubMed

Wang, Hao-Yi; Wang, Yi; Yu, Man; Han, Jun; Guo, Zhi-Xin; Ai, Xi-Cheng; Zhang, Jian-Ping; Qin, Yujun

2016-04-28

Organic-inorganic halide perovskite solar cells are becoming the next big thing in the photovoltaic field owing to their rapidly developing photoelectric conversion performance. Herein, mesoporous structured perovskite devices with various perovskite grain sizes are fabricated by a sequential dropping method, and the charge recombination dynamics is investigated by transient optical-electric measurements. All devices exhibit an overall power conversion efficiency around 15%. More importantly, a biphasic trap-limited charge recombination process is proposed and interpreted by taking into account the specific charge accumulation mechanism in perovskite solar cells. At low Fermi levels, photo-generated electrons predominately populate in the perovskite phase, while at high Fermi levels, most electrons occupy traps in mesoporous TiO2. As a result, the dynamics of charge recombination is, respectively, dominated by the perovskite phase and mesoporous TiO2 in these two cases. The present work would give a new perspective on the charge recombination process in meso-structured perovskite solar cells.

Interrelated structures of the transport shock and collisional relaxation layer in a multitemperature, multilevel ionized gas

NASA Technical Reports Server (NTRS)

Vinolo, A. R.; Clarke, J. H.

1973-01-01

The gas dynamic structures of the transport shock and the downstream collisional relaxation layer are evaluated for partially ionized monatomic gases. Elastic and inelastic collisional nonequilibrium effects are taken into consideration. In the microscopic model of the atom, three electronic levels are accounted for. By using an asymptotic technique, the shock morphology is found on a continuum flow basis. This procedure gives two distinct layers in which the nonequilibrium effects to be considered are different. A transport shock appears as the inner solution to an outer collisional relaxation layer. The results show four main interesting points: (1) on structuring the transport shock, ionization and excitation rates must be included in the formulation, since the flow is not frozen with respect to the population of the different electronic levels; (2) an electron temperature precursor appears at the beginning of the transport shock; (3) the collisional layer is rationally reduced to quadrature for special initial conditions, which (4) are obtained from new Rankine-Hugoniot relations for the inner shock.

HFE gene: Structure, function, mutations, and associated iron abnormalities.

PubMed

Barton, James C; Edwards, Corwin Q; Acton, Ronald T

2015-12-15

The hemochromatosis gene HFE was discovered in 1996, more than a century after clinical and pathologic manifestations of hemochromatosis were reported. Linked to the major histocompatibility complex (MHC) on chromosome 6p, HFE encodes the MHC class I-like protein HFE that binds beta-2 microglobulin. HFE influences iron absorption by modulating the expression of hepcidin, the main controller of iron metabolism. Common HFE mutations account for ~90% of hemochromatosis phenotypes in whites of western European descent. We review HFE mapping and cloning, structure, promoters and controllers, and coding region mutations, HFE protein structure, cell and tissue expression and function, mouse Hfe knockouts and knockins, and HFE mutations in other mammals with iron overload. We describe the pertinence of HFE and HFE to mechanisms of iron homeostasis, the origin and fixation of HFE polymorphisms in European and other populations, and the genetic and biochemical basis of HFE hemochromatosis and iron overload. Copyright © 2015 Elsevier B.V. All rights reserved.

Genetic and environmental structure of DSM-IV criteria for Antisocial Personality Disorder: a twin study

PubMed Central

Rosenström, Tom; Ystrom, Eivind; Torvik, Fartein Ask; Czajkowski, Nikolai Olavi; Gillespie, Nathan A.; Aggen, Steven H.; Krueger, Robert F.; Kendler, Kenneth S; Reichborn-Kjennerud, Ted

2017-01-01

Results from previous studies on DSM-IV and DSM-5 Antisocial Personality Disorder (ASPD) have suggested that the construct is etiologically multidimensional. To our knowledge, however, the structure of genetic and environmental influences in ASPD has not been examined using an appropriate range of biometric models and diagnostic interviews. The 7 ASPD criteria (section A) were assessed in a population-based sample of 2794 Norwegian twins by a structured interview for DSM-IV personality disorders. Exploratory analyses were conducted at the phenotypic level. Multivariate biometric models, including both independent and common pathways, were compared. A single phenotypic factor was found, and the best-fitting biometric model was a single-factor common pathway model, with common-factor heritability of 51% (95% CI = 40–67%). In other words, both genetic and environmental correlations between the ASPD criteria could be accounted for by a single common latent variable. The findings support the validity of ASPD as a unidimensional diagnostic construct. PMID:28108863

Genetic and Environmental Structure of DSM-IV Criteria for Antisocial Personality Disorder: A Twin Study.

PubMed

Rosenström, Tom; Ystrom, Eivind; Torvik, Fartein Ask; Czajkowski, Nikolai Olavi; Gillespie, Nathan A; Aggen, Steven H; Krueger, Robert F; Kendler, Kenneth S; Reichborn-Kjennerud, Ted

2017-05-01

Results from previous studies on DSM-IV and DSM-5 Antisocial Personality Disorder (ASPD) have suggested that the construct is etiologically multidimensional. To our knowledge, however, the structure of genetic and environmental influences in ASPD has not been examined using an appropriate range of biometric models and diagnostic interviews. The 7 ASPD criteria (section A) were assessed in a population-based sample of 2794 Norwegian twins by a structured interview for DSM-IV personality disorders. Exploratory analyses were conducted at the phenotypic level. Multivariate biometric models, including both independent and common pathways, were compared. A single phenotypic factor was found, and the best-fitting biometric model was a single-factor common pathway model, with common-factor heritability of 51% (95% CI 40-67%). In other words, both genetic and environmental correlations between the ASPD criteria could be accounted for by a single common latent variable. The findings support the validity of ASPD as a unidimensional diagnostic construct.

Impaired esophageal motor function in eosinophilic esophagitis.

PubMed

Santander, Cecilio; Chavarría-Herbozo, Carlos M; Becerro-González, Irene; Burgos-Santamaría, Diego

2015-10-01

Eosinophilic esophagitis is a chronic immunoallergic inflammatory disease of the esophagus that represents a major cause of digestive morbidity among the pediatric and young adult populations. Despite the fact that key symptoms in adults include dysphagia and food impaction, many patients lack structural changes in the esophagus to account for their complaints, which suggests the presence of underlying motor disorders and esophageal distensibility impairment. In the last few years the esophageal motility of these patients has been studied using various approaches, most particularly high-resolution manometry, ambulatory manometry, and impedance planimetry. This review focuses on the most relevant findings and scientific evidence regarding esophageal motor disorders in eosinophilic esophagitis.

Manganese Abundances in the Stars with Metallicities -1 <[Fe/H]< +0.3

NASA Astrophysics Data System (ADS)

Mishenina, T.; Gorbaneva, T.; Pignatari, M.; Thielemann, F.-K.; Korotin, S.

2018-01-01

We estimate the Mn abundances in the atmospheres of 247 F-G-K-type dwarf stars belonging to the thin and thick disk populations in the metallicity range -1 < [Fe/H] < +0.3. The observations were conducted using the 1.93 m telescope at Observatoire de Haute-Provence (OHP, France) equipped with the echelle type spectrographs ELODIE and SOPHIE. The abundances were derived under the LTE approximation; the synthetic spectrum for the Mn lines was computed accounting for the hyperfine structure. Starting from the results obtained, we discuss the evolution of the [Mn/Fe] ratio with respect to [Fe/H] in the galactic disk.

Retention in the allied health workforce: boomers, generation X, and generation Y.

PubMed

Dodd, Jenny; Saggers, Sherry; Wildy, Helen

2009-01-01

The recruitment and retention of allied health workers present challenges for organizations in Australia and internationally. Australia, in common with other developed countries, faces the prospect of a rapidly aging population and the high turnover of younger allied health workers (the majority of whom are female) from employing organizations. Emphases on the individual characteristics of Boomer, Generation X, and Generation Y workers may provide a useful starting base for recruitment and retention strategies, but our study shows that these need to be contextualized within broader political, social, and structural factors that take account of gender and the changing needs of workers over their life span.

Acidic deposition: A review of biological effects

USGS Publications Warehouse

Sparling, Donald W.; Hoffman, David J.; Rattner, Barnett A.; Burton, G. Allen; Cairns, John

1995-01-01

The problem of acidic deposition and its possible effects on habitats, organisms, materials, and human health has been recognized for centuries. Earliest accounts date to Cicero (about 100 B.C.), who linked structural damage to buildings and statues in Rome to the smokey rains of wood and charcoal burning.3 Based on estimated of human demographics and centers of population, problems caused by acidic deposition may extend back to 400 to 500 B.C., but were not fully manifested until the mid-1800s with the rise of the Industrial revolution. the term "acid rain" was apparently first coined by R.A. Smith in 1972.4

Invariant Theory for Dispersed Transverse Isotropy: An Efficient Means for Modeling Fiber Splay

NASA Technical Reports Server (NTRS)

Freed, alan D.; Einstein, Daniel R.; Vesely, Ivan

2004-01-01

Most soft tissues possess an oriented architecture of collagen fiber bundles, conferring both anisotropy and nonlinearity to their elastic behavior. Transverse isotropy has often been assumed for a subset of these tissues that have a single macroscopically-identifiable preferred fiber direction. Micro-structural studies, however, suggest that, in some tissues, collagen fibers are approximately normally distributed about a mean preferred fiber direction. Structural constitutive equations that account for this dispersion of fibers have been shown to capture the mechanical complexity of these tissues quite well. Such descriptions, however, are computationally cumbersome for two-dimensional (2D) fiber distributions, let alone for fully three-dimensional (3D) fiber populations. In this paper, we develop a new constitutive law for such tissues, based on a novel invariant theory for dispersed transverse isotropy. The invariant theory is based on a novel closed-form splay invariant that can easily handle 3D fiber populations, and that only requires a single parameter in the 2D case. The model is polyconvex and fits biaxial data for aortic valve tissue as accurately as the standard structural model. Modification of the fiber stress-strain law requires no re-formulation of the constitutive tangent matrix, making the model flexible for different types of soft tissues. Most importantly, the model is computationally expedient in a finite-element analysis.

Overhead Costs and Rates in the U.S. Defense Industrial Base. Volume 1

DTIC Science & Technology

1980-10-01

Manager rather than to establish rigidly defined cost accounting structures. The conclusions to be own from the analysis were that overhead costs have...specific costs which make up tho overhead account ; whether management is controlling them; whether these costs are "reasonable" and the external factors... cost accounting structures, . ..... ....... .... ... ............................... , , ,’" ’ .. -17- and since there is no one accounting definition of

Productivity, mortality, and population trends of wolves in northeastern Minnesota

USGS Publications Warehouse

Mech, L.D.

1977-01-01

Population parameters, mortality causes, and mechanisms of a population decline were studied in wolves (Canis lupus lycaon) from 1968 to 1976 in the Superior National Forest. The main method was aerial radio-tracking of 129 wolves and their packmates. Due to a decline in white-tailed deer (Odocoileus virginianus), the wolf population decreased during most of the study. Average annual productivity varied from 1.5 to 3.3 pups per litter, and annual mortality rates from 7 to 65 percent. Malnutrition and intraspecific strife accounted equally for 58 percent of the mortality; human causes accounted for the remainder. As wolf numbers began to decline, pup starvation became apparent, followed by lower pup production, and then by increased intraspecific strife. At higher densities, adult pack wolves were the most secure members of the population, but as the population declined, they became the least secure because of intraspecific strife.

A Re-Evaluation of the Size of the White Shark (Carcharodon carcharias) Population off California, USA

PubMed Central

Burgess, George H.; Bruce, Barry D.; Cailliet, Gregor M.; Goldman, Kenneth J.; Grubbs, R. Dean; Lowe, Christopher G.; MacNeil, M. Aaron; Mollet, Henry F.; Weng, Kevin C.; O'Sullivan, John B.

2014-01-01

White sharks are highly migratory and segregate by sex, age and size. Unlike marine mammals, they neither surface to breathe nor frequent haul-out sites, hindering generation of abundance data required to estimate population size. A recent tag-recapture study used photographic identifications of white sharks at two aggregation sites to estimate abundance in “central California” at 219 mature and sub-adult individuals. They concluded this represented approximately one-half of the total abundance of mature and sub-adult sharks in the entire eastern North Pacific Ocean (ENP). This low estimate generated great concern within the conservation community, prompting petitions for governmental endangered species designations. We critically examine that study and find violations of model assumptions that, when considered in total, lead to population underestimates. We also use a Bayesian mixture model to demonstrate that the inclusion of transient sharks, characteristic of white shark aggregation sites, would substantially increase abundance estimates for the adults and sub-adults in the surveyed sub-population. Using a dataset obtained from the same sampling locations and widely accepted demographic methodology, our analysis indicates a minimum all-life stages population size of >2000 individuals in the California subpopulation is required to account for the number and size range of individual sharks observed at the two sampled sites. Even accounting for methodological and conceptual biases, an extrapolation of these data to estimate the white shark population size throughout the ENP is inappropriate. The true ENP white shark population size is likely several-fold greater as both our study and the original published estimate exclude non-aggregating sharks and those that independently aggregate at other important ENP sites. Accurately estimating the central California and ENP white shark population size requires methodologies that account for biases introduced by sampling a limited number of sites and that account for all life history stages across the species' range of habitats. PMID:24932483

A re-evaluation of the size of the white shark (Carcharodon carcharias) population off California, USA.

PubMed

Burgess, George H; Bruce, Barry D; Cailliet, Gregor M; Goldman, Kenneth J; Grubbs, R Dean; Lowe, Christopher G; MacNeil, M Aaron; Mollet, Henry F; Weng, Kevin C; O'Sullivan, John B

2014-01-01

White sharks are highly migratory and segregate by sex, age and size. Unlike marine mammals, they neither surface to breathe nor frequent haul-out sites, hindering generation of abundance data required to estimate population size. A recent tag-recapture study used photographic identifications of white sharks at two aggregation sites to estimate abundance in "central California" at 219 mature and sub-adult individuals. They concluded this represented approximately one-half of the total abundance of mature and sub-adult sharks in the entire eastern North Pacific Ocean (ENP). This low estimate generated great concern within the conservation community, prompting petitions for governmental endangered species designations. We critically examine that study and find violations of model assumptions that, when considered in total, lead to population underestimates. We also use a Bayesian mixture model to demonstrate that the inclusion of transient sharks, characteristic of white shark aggregation sites, would substantially increase abundance estimates for the adults and sub-adults in the surveyed sub-population. Using a dataset obtained from the same sampling locations and widely accepted demographic methodology, our analysis indicates a minimum all-life stages population size of >2000 individuals in the California subpopulation is required to account for the number and size range of individual sharks observed at the two sampled sites. Even accounting for methodological and conceptual biases, an extrapolation of these data to estimate the white shark population size throughout the ENP is inappropriate. The true ENP white shark population size is likely several-fold greater as both our study and the original published estimate exclude non-aggregating sharks and those that independently aggregate at other important ENP sites. Accurately estimating the central California and ENP white shark population size requires methodologies that account for biases introduced by sampling a limited number of sites and that account for all life history stages across the species' range of habitats.

Accounting for selection bias in association studies with complex survey data.

PubMed

Wirth, Kathleen E; Tchetgen Tchetgen, Eric J

2014-05-01

Obtaining representative information from hidden and hard-to-reach populations is fundamental to describe the epidemiology of many sexually transmitted diseases, including HIV. Unfortunately, simple random sampling is impractical in these settings, as no registry of names exists from which to sample the population at random. However, complex sampling designs can be used, as members of these populations tend to congregate at known locations, which can be enumerated and sampled at random. For example, female sex workers may be found at brothels and street corners, whereas injection drug users often come together at shooting galleries. Despite the logistical appeal, complex sampling schemes lead to unequal probabilities of selection, and failure to account for this differential selection can result in biased estimates of population averages and relative risks. However, standard techniques to account for selection can lead to substantial losses in efficiency. Consequently, researchers implement a variety of strategies in an effort to balance validity and efficiency. Some researchers fully or partially account for the survey design, whereas others do nothing and treat the sample as a realization of the population of interest. We use directed acyclic graphs to show how certain survey sampling designs, combined with subject-matter considerations unique to individual exposure-outcome associations, can induce selection bias. Finally, we present a novel yet simple maximum likelihood approach for analyzing complex survey data; this approach optimizes statistical efficiency at no cost to validity. We use simulated data to illustrate this method and compare it with other analytic techniques.

Age structure is critical to the population dynamics and survival of honeybee colonies

PubMed Central

Betti, M. I.; Wahl, L. M.

2016-01-01

Age structure is an important feature of the division of labour within honeybee colonies, but its effects on colony dynamics have rarely been explored. We present a model of a honeybee colony that incorporates this key feature, and use this model to explore the effects of both winter and disease on the fate of the colony. The model offers a novel explanation for the frequently observed phenomenon of ‘spring dwindle’, which emerges as a natural consequence of the age-structured dynamics. Furthermore, the results indicate that a model taking age structure into account markedly affects the predicted timing and severity of disease within a bee colony. The timing of the onset of disease with respect to the changing seasons may also have a substantial impact on the fate of a honeybee colony. Finally, simulations predict that an infection may persist in a honeybee colony over several years, with effects that compound over time. Thus, the ultimate collapse of the colony may be the result of events several years past. PMID:28018627

Decoding the dynamic representation of musical pitch from human brain activity.

PubMed

Sankaran, N; Thompson, W F; Carlile, S; Carlson, T A

2018-01-16

In music, the perception of pitch is governed largely by its tonal function given the preceding harmonic structure of the music. While behavioral research has advanced our understanding of the perceptual representation of musical pitch, relatively little is known about its representational structure in the brain. Using Magnetoencephalography (MEG), we recorded evoked neural responses to different tones presented within a tonal context. Multivariate Pattern Analysis (MVPA) was applied to "decode" the stimulus that listeners heard based on the underlying neural activity. We then characterized the structure of the brain's representation using decoding accuracy as a proxy for representational distance, and compared this structure to several well established perceptual and acoustic models. The observed neural representation was best accounted for by a model based on the Standard Tonal Hierarchy, whereby differences in the neural encoding of musical pitches correspond to their differences in perceived stability. By confirming that perceptual differences honor those in the underlying neuronal population coding, our results provide a crucial link in understanding the cognitive foundations of musical pitch across psychological and neural domains.

Analysis of urban-rural population dynamics for China.

PubMed

Shen, J

1991-12-01

The population dynamics of China are presented in a multiregional demographic model using regional estimates or mortality and migration based on the 1% population sample survey in 1987. An open ended population account is generated for period cohort a, gender g of region i (urban) and j (rural) using population, birth, death, and migration. Demographic rates and equations for flows of nonsurviving migrants of period cohort a of gender g are estimated using the forward demographic rate definition. Out-migration rates for period cohort a of gender g are defined by migration flow divided by the initial population. The death rate for period cohort A1 and A are estimated using a single region method. Death and migration rates are simultaneously estimated with an iterative procedure. The population accounts estimates and demographic rates are provided for the period ending 1986-87 for male births, males in period cohorts 10 and 20, female births, and females in period cohorts 10 and 20. The urban and rural population projection model is based on the population accounts concept and assumes fixed rates of mortality, migration, and normal fertility for the base year 1987. The results of this projection are a population of 1090 million that will grow to 1304 million in 2000, 1720 million in 2050, and 1791 million in 2087. Urban population will expand from 44.2% in 1988 to 46.6% in 2000, and 54.7% in 2087. The labor population of males 18-65 years and females 18-60 years will increase from 58.8% in 1988 to 59.7% in 2000 and decline to 58.4% by 2087. The old age population of males 65 years and females 60 years will increase from 6.5% in 1988 to 7.9% in 2000, and 16.3% in 2087. The mean age increased from 28.3 years in 1988 to 37 in 2087. Urban population may be underprojected; migration problems are recognized. Fertility also is likely to decline. An alternative projection (B) is given to account for the U-shape distribution and urban fertility of 1.8 in 2000, increasing to and stabilizing at 2.2 in 2020, such that population estimates for 2000 are 1291 and 1524 for 2087 with a peak in 2048 of 1573. A faster fertility decline is also used to generate projection C. The author's projections A, B, and C, which are based on more recent data and a more realistic model, are than the "objective projection" and than the "warning projection" generated by China's Population Census Office based on 1982 census data.

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

Glaser, D.; Connolly, J.; Berghoffen, A.

The resident bald eagles of the lower Columbia River have lower productivity and higher contaminant levels than other bald eagles of the Pacific Northwest. The primary population stressors are believed to be habitat loss, human disturbance, p,p{prime}DDE, PCBs, dioxins and furans. The primary effect of habitat loss is to reduce the carrying capacity of the region for nesting sites, and the primary effects of human disturbance and contamination by organic compounds are to reduce productivity. The purpose of this study was to quantitatively evaluate the effects of all of, these potential stressors on the bald eagle population dynamics. A modelmore » of the population dynamics was developed. The model structure includes a physiologically-based toxicokinetic (PBTK) submodel to estimate the degree of contamination, which is linked via a toxicology submodel to a population dynamics submodel. The PBTK submodel is time-variable, incorporating species-specific bioenergetics, as well as contaminant assimilation and excretion rates for each compound of interest. Calculated body burdens and egg concentrations for each compound account for spatial and temporal variations in feeding habits and prey contaminant levels. The population submodel includes fecundity and survival information, as well as a limit to the number of breeding pairs (carrying capacity) and a population of non-breeding subadults and adults (floaters). Model simulations are performed in a Monte Carlo framework. Results include estimates of the persistence, resistance and resilience of the population: the probability of extinction, the relationship between magnitude of stress and change in population size, and the time course of recovery of a population following a reduction in stress.« less

A Spatial Statistical Model for Landscape Genetics

PubMed Central

Guillot, Gilles; Estoup, Arnaud; Mortier, Frédéric; Cosson, Jean François

2005-01-01

Landscape genetics is a new discipline that aims to provide information on how landscape and environmental features influence population genetic structure. The first key step of landscape genetics is the spatial detection and location of genetic discontinuities between populations. However, efficient methods for achieving this task are lacking. In this article, we first clarify what is conceptually involved in the spatial modeling of genetic data. Then we describe a Bayesian model implemented in a Markov chain Monte Carlo scheme that allows inference of the location of such genetic discontinuities from individual geo-referenced multilocus genotypes, without a priori knowledge on populational units and limits. In this method, the global set of sampled individuals is modeled as a spatial mixture of panmictic populations, and the spatial organization of populations is modeled through the colored Voronoi tessellation. In addition to spatially locating genetic discontinuities, the method quantifies the amount of spatial dependence in the data set, estimates the number of populations in the studied area, assigns individuals to their population of origin, and detects individual migrants between populations, while taking into account uncertainty on the location of sampled individuals. The performance of the method is evaluated through the analysis of simulated data sets. Results show good performances for standard data sets (e.g., 100 individuals genotyped at 10 loci with 10 alleles per locus), with high but also low levels of population differentiation (e.g., FST < 0.05). The method is then applied to a set of 88 individuals of wolverines (Gulo gulo) sampled in the northwestern United States and genotyped at 10 microsatellites. PMID:15520263

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)

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.

Isotropic Inelastic Collisions in a Multiterm Atom with Hyperfine Structure

NASA Astrophysics Data System (ADS)

Belluzzi, Luca; Landi Degl'Innocenti, Egidio; Trujillo Bueno, Javier

2015-10-01

A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron-atom interaction is described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D1 and D2 lines is presented.

Conspecific and Heterospecific Plant Densities at Small-Scale Can Drive Plant-Pollinator Interactions

PubMed Central

Janovský, Zdeněk; Mikát, Michael; Hadrava, Jiří; Horčičková, Eva; Kmecová, Kateřina; Požárová, Doubravka; Smyčka, Jan; Herben, Tomáš

2013-01-01

Generalist pollinators are important in many habitats, but little research has been done on small-scale spatial variation in interactions between them and the plants that they visit. Here, using a spatially explicit approach, we examined whether multiple species of flowering plants occurring within a single meadow showed spatial structure in their generalist pollinator assemblages. We report the results for eight plant species for which at least 200 individual visits were recorded. We found that for all of these species, the proportions of their general pollinator assemblages accounted for by particular functional groups showed spatial heterogeneity at the scale of tens of metres. This heterogeneity was connected either with no or only subtle changes of vegetation and flowering species composition. In five of these species, differences in conspecific plant density influenced the pollinator communities (with greater dominance of main pollinators at low-conspecific plant densities). The density of heterospecific plant individuals influenced the pollinator spectrum in one case. Our results indicate that the picture of plant-pollinator interactions provided by averaging data within large plots may be misleading and that within-site spatial heterogeneity should be accounted for in terms of sampling effort allocation and analysis. Moreover, spatially structured plant-pollinator interactions may have important ecological and evolutionary consequences, especially for plant population biology. PMID:24204818

Community structure of rare methanogenic archaea: insight from a single functional group

PubMed Central

Winkel, Matthias; Wagner, Dirk

2017-01-01

Abstract The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups. PMID:29029047

76 FR 75873 - Proposed Information Collection; Comment Request; West Coast Groundfish Trawl Economic Data...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

..., make the requests for information more consistent with the accounting/bookkeeping systems used by.... The definition of the survey population is different for 2011 data, to account for differences between... receiver and shorebased processor form was modified to better align with accounting practices and to...

Population density and phenotypic attributes influence the level of nematode parasitism in roe deer.

PubMed

Body, Guillaume; Ferté, Hubert; Gaillard, Jean-Michel; Delorme, Daniel; Klein, François; Gilot-Fromont, Emmanuelle

2011-11-01

The impact of parasites on population dynamics is well documented, but less is known on how host population density affects parasite spread. This relationship is difficult to assess because of confounding effects of social structure, population density, and environmental conditions that lead to biased among-population comparisons. Here, we analyzed the infestation by two groups of nematodes (gastro-intestinal (GI) strongyles and Trichuris) in the roe deer (Capreolus capreolus) population of Trois Fontaines (France) between 1997 and 2007. During this period, we experimentally manipulated population density through changes in removals. Using measures collected on 297 individuals, we quantified the impact of density on parasite spread after taking into account possible influences of date, age, sex, body mass, and weather conditions. The prevalence and abundance of eggs of both parasites in females were positively related to roe deer density, except Trichuris in adult females. We also found a negative relationship between parasitism and body mass, and strong age and sex-dependent patterns of parasitism. Prime-age adults were less often parasitized and had lower fecal egg counts than fawns or old individuals, and males were more heavily and more often infected than females. Trichuris parasites were not affected by weather, whereas GI strongyles were less present after dry and hot summers. In the range of observed densities, the observed effect of density likely involves a variation of the exposure rate, as opposed to variation in host susceptibility.

Morphological analysis of Trichomycterus areolatus Valenciennes, 1846 from southern Chilean rivers using a truss-based system (Siluriformes, Trichomycteridae)

PubMed Central

Colihueque, Nelson; Corrales, Olga; Yáñez, Miguel

2017-01-01

Abstract Trichomycterus areolatus Valenciennes, 1846 is a small endemic catfish inhabiting the Andean river basins of Chile. In this study, the morphological variability of three T. areolatus populations, collected in two river basins from southern Chile, was assessed with multivariate analyses, including principal component analysis (PCA) and discriminant function analysis (DFA). It is hypothesized that populations must segregate morphologically from each other based on the river basin that they were sampled from, since each basin presents relatively particular hydrological characteristics. Significant morphological differences among the three populations were found with PCA (ANOSIM test, r = 0.552, p < 0.0001) and DFA (Wilks’s λ = 0.036, p < 0.01). PCA accounted for a total variation of 56.16% by the first two principal components. The first Principal Component (PC1) and PC2 explained 34.72 and 21.44% of the total variation, respectively. The scatter-plot of the first two discriminant functions (DF1 on DF2) also validated the existence of three different populations. In group classification using DFA, 93.3% of the specimens were correctly-classified into their original populations. Of the total of 22 transformed truss measurements, 17 exhibited highly significant (p < 0.01) differences among populations. The data support the existence of T. areolatus morphological variation across different rivers in southern Chile, likely reflecting the geographic isolation underlying population structure of the species. PMID:29134012

Early experience of a safety net provider reorganizing into an accountable care organization.

PubMed

Hacker, Karen; Santos, Palmira; Thompson, Douglas; Stout, Somava S; Bearse, Adriana; Mechanic, Robert E

2014-08-01

Although safety net providers will benefit from health insurance expansions under the Affordable Care Act, they also face significant challenges in the postreform environment. Some have embraced the concept of the accountable care organization to help improve quality and efficiency while addressing financial shortfalls. The experience of Cambridge Health Alliance (CHA) in Massachusetts, where health care reform began six years ago, provides insight into the opportunities and challenges of this approach in the safety net. CHA's strategies include care redesign, financial realignment, workforce transformation, and development of external partnerships. Early results show some improvement in access, patient experience, quality, and utilization; however, the potential efficiencies will not eliminate CHA's current operating deficit. The patient population, payer mix, service mix, cost structure, and political requirements reduce the likelihood of financial sustainability without significant changes in these factors, increased public funding, or both. Thus the future of safety net institutions, regardless of payment and care redesign success, remains at risk. Copyright © 2014 by Duke University Press.

Modeling the Relations Among Morphological Awareness Dimensions, Vocabulary Knowledge, and Reading Comprehension in Adult Basic Education Students

PubMed Central

Tighe, Elizabeth L.; Schatschneider, Christopher

2016-01-01

This study extended the findings of Tighe and Schatschneider (2015) by investigating the predictive utility of separate dimensions of morphological awareness as well as vocabulary knowledge to reading comprehension in adult basic education (ABE) students. We competed two- and three-factor structural equation models of reading comprehension. A three-factor model of real word morphological awareness, pseudoword morphological awareness, and vocabulary knowledge emerged as the best fit and accounted for 79% of the reading comprehension variance. The results indicated that the constructs contributed jointly to reading comprehension; however, vocabulary knowledge was the only potentially unique predictor (p = 0.052), accounting for an additional 5.6% of the variance. This study demonstrates the feasibility of applying a latent variable modeling approach to examine individual differences in the reading comprehension skills of ABE students. Further, this study replicates the findings of Tighe and Schatschneider (2015) on the importance of differentiating among dimensions of morphological awareness in this population. PMID:26869981

Modeling the Relations Among Morphological Awareness Dimensions, Vocabulary Knowledge, and Reading Comprehension in Adult Basic Education Students.

PubMed

Tighe, Elizabeth L; Schatschneider, Christopher

2016-01-01

This study extended the findings of Tighe and Schatschneider (2015) by investigating the predictive utility of separate dimensions of morphological awareness as well as vocabulary knowledge to reading comprehension in adult basic education (ABE) students. We competed two- and three-factor structural equation models of reading comprehension. A three-factor model of real word morphological awareness, pseudoword morphological awareness, and vocabulary knowledge emerged as the best fit and accounted for 79% of the reading comprehension variance. The results indicated that the constructs contributed jointly to reading comprehension; however, vocabulary knowledge was the only potentially unique predictor (p = 0.052), accounting for an additional 5.6% of the variance. This study demonstrates the feasibility of applying a latent variable modeling approach to examine individual differences in the reading comprehension skills of ABE students. Further, this study replicates the findings of Tighe and Schatschneider (2015) on the importance of differentiating among dimensions of morphological awareness in this population.

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). ...

Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus)

PubMed Central

Carr, Steven M.; Duggan, Ana T.; Stenson, Garry B.; Marshall, H. Dawn

2015-01-01

Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on “fast ice” attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40 ~ 60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed. PMID:26301872

Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus).

PubMed

Carr, Steven M; Duggan, Ana T; Stenson, Garry B; Marshall, H Dawn

2015-01-01

Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on "fast ice" attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40~60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed.

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

Longitudinal association of short-term, metronome-paced heart rate variability and echocardiographically assessed cardiac structure at a 4-year follow-up: results from the prospective, population-based CARLA cohort.

PubMed

Medenwald, Daniel; Swenne, Cees A; Frantz, Stefan; Nuding, Sebastian; Kors, Jan A; Pietzner, Diana; Tiller, Daniel; Greiser, Karin H; Kluttig, Alexander; Haerting, Johannes

2017-12-01

To assess the value of cardiac structure/function in predicting heart rate variability (HRV) and the possibly predictive value of HRV on cardiac parameters. Baseline and 4-year follow-up data from the population-based CARLA cohort were used (790 men, 646 women, aged 45-83 years at baseline and 50-87 years at follow-up). Echocardiographic and HRV recordings were performed at baseline and at follow-up. Linear regression models with a quadratic term were used. Crude and covariate adjusted estimates were calculated. Missing values were imputed by means of multiple imputation. Heart rate variability measures taken into account consisted of linear time and frequency domain [standard deviation of normal-to-normal intervals (SDNN), high-frequency power (HF), low-frequency power (LF), LF/HF ratio] and non-linear measures [detrended fluctuation analysis (DFA1), SD1, SD2, SD1/SD2 ratio]. Echocardiographic parameters considered were ventricular mass index, diastolic interventricular septum thickness, left ventricular diastolic dimension, left atrial dimension systolic (LADS), and ejection fraction (Teichholz). A negative quadratic relation between baseline LADS and change in SDNN and HF was observed. The maximum HF and SDNN change (an increase of roughly 0.02%) was predicted at LADS of 3.72 and 3.57 cm, respectively, while the majority of subjects experienced a decrease in HRV. There was no association between further echocardiographic parameters and change in HRV, and there was no evidence of a predictive value of HRV in the prediction of changes in cardiac structure. In the general population, LADS predicts 4-year alteration in SDNN and HF non-linearly. Because of the novelty of the result, analyses should be replicated in other populations. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions please email: journals.permissions@oup.com.

Genetic variation and recombination of RdRp and HSP 70h genes of Citrus tristeza virus isolates from orange trees showing symptoms of citrus sudden death disease.

PubMed

Gomes, Clarissa P C; Nagata, Tatsuya; de Jesus, Waldir C; Neto, Carlos R Borges; Pappas, Georgios J; Martin, Darren P

2008-01-16

Citrus sudden death (CSD), a disease that rapidly kills orange trees, is an emerging threat to the Brazilian citrus industry. Although the causal agent of CSD has not been definitively determined, based on the disease's distribution and symptomatology it is suspected that the agent may be a new strain of Citrus tristeza virus (CTV). CTV genetic variation was therefore assessed in two Brazilian orange trees displaying CSD symptoms and a third with more conventional CTV symptoms. A total of 286 RNA-dependent-RNA polymerase (RdRp) and 284 heat shock protein 70 homolog (HSP70h) gene fragments were determined for CTV variants infecting the three trees. It was discovered that, despite differences in symptomatology, the trees were all apparently coinfected with similar populations of divergent CTV variants. While mixed CTV infections are common, the genetic distance between the most divergent population members observed (24.1% for RdRp and 11.0% for HSP70h) was far greater than that in previously described mixed infections. Recombinants of five distinct RdRp lineages and three distinct HSP70h lineages were easily detectable but respectively accounted for only 5.9 and 11.9% of the RdRp and HSP70h gene fragments analysed and there was no evidence of an association between particular recombinant mosaics and CSD. Also, comparisons of CTV population structures indicated that the two most similar CTV populations were those of one of the trees with CSD and the tree without CSD. We suggest that if CTV is the causal agent of CSD, it is most likely a subtle feature of population structures within mixed infections and not merely the presence (or absence) of a single CTV variant within these populations that triggers the disease.

Individual-Based Modeling of Tuberculosis in a User-Friendly Interface: Understanding the Epidemiological Role of Population Heterogeneity in a City

PubMed Central

Prats, Clara; Montañola-Sales, Cristina; Gilabert-Navarro, Joan F.; Valls, Joaquim; Casanovas-Garcia, Josep; Vilaplana, Cristina; Cardona, Pere-Joan; López, Daniel

2016-01-01

For millennia tuberculosis (TB) has shown a successful strategy to survive, making it one of the world’s deadliest infectious diseases. This resilient behavior is based not only on remaining hidden in most of the infected population, but also by showing slow evolution in most sick people. The course of the disease within a population is highly related to its heterogeneity. Thus, classic epidemiological approaches with a top-down perspective have not succeeded in understanding its dynamics. In the past decade a few individual-based models were built, but most of them preserved a top-down view that makes it difficult to study a heterogeneous population. We propose an individual-based model developed with a bottom-up approach to studying the dynamics of pulmonary TB in a certain population, considered constant. Individuals may belong to the following classes: healthy, infected, sick, under treatment, and treated with a probability of relapse. Several variables and parameters account for their age, origin (native or immigrant), immunodeficiency, diabetes, and other risk factors (smoking and alcoholism). The time within each infection state is controlled, and sick individuals may show a cavitated disease or not that conditions infectiousness. It was implemented in NetLogo because it allows non-modelers to perform virtual experiments with a user-friendly interface. The simulation was conducted with data from Ciutat Vella, a district of Barcelona with an incidence of 67 TB cases per 100,000 inhabitants in 2013. Several virtual experiments were performed to relate the disease dynamics with the structure of the infected subpopulation (e.g., the distribution of infected times). Moreover, the short-term effect of health control policies on modifying that structure was studied. Results show that the characteristics of the population are crucial for the local epidemiology of TB. The developed user-friendly tool is ready to test control strategies of disease in any city in the short-term. PMID:26793189

Individual-Based Modeling of Tuberculosis in a User-Friendly Interface: Understanding the Epidemiological Role of Population Heterogeneity in a City.

PubMed

Prats, Clara; Montañola-Sales, Cristina; Gilabert-Navarro, Joan F; Valls, Joaquim; Casanovas-Garcia, Josep; Vilaplana, Cristina; Cardona, Pere-Joan; López, Daniel

2015-01-01

For millennia tuberculosis (TB) has shown a successful strategy to survive, making it one of the world's deadliest infectious diseases. This resilient behavior is based not only on remaining hidden in most of the infected population, but also by showing slow evolution in most sick people. The course of the disease within a population is highly related to its heterogeneity. Thus, classic epidemiological approaches with a top-down perspective have not succeeded in understanding its dynamics. In the past decade a few individual-based models were built, but most of them preserved a top-down view that makes it difficult to study a heterogeneous population. We propose an individual-based model developed with a bottom-up approach to studying the dynamics of pulmonary TB in a certain population, considered constant. Individuals may belong to the following classes: healthy, infected, sick, under treatment, and treated with a probability of relapse. Several variables and parameters account for their age, origin (native or immigrant), immunodeficiency, diabetes, and other risk factors (smoking and alcoholism). The time within each infection state is controlled, and sick individuals may show a cavitated disease or not that conditions infectiousness. It was implemented in NetLogo because it allows non-modelers to perform virtual experiments with a user-friendly interface. The simulation was conducted with data from Ciutat Vella, a district of Barcelona with an incidence of 67 TB cases per 100,000 inhabitants in 2013. Several virtual experiments were performed to relate the disease dynamics with the structure of the infected subpopulation (e.g., the distribution of infected times). Moreover, the short-term effect of health control policies on modifying that structure was studied. Results show that the characteristics of the population are crucial for the local epidemiology of TB. The developed user-friendly tool is ready to test control strategies of disease in any city in the short-term.

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands.

PubMed

Gama, Luis T; Martínez, Amparo M; Carolino, Inês; Landi, Vincenzo; Delgado, Juan V; Vicente, Antonio A; Vega-Pla, José L; Cortés, Oscar; Sousa, Conceição O

2013-06-14

Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies. A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results. Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity. Native pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates

PubMed Central

Gill, Mandev S.; Lemey, Philippe; Bennett, Shannon N.; Biek, Roman; Suchard, Marc A.

2016-01-01

Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman’s coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and understanding the association between the effective population size and such factors. Building upon Bayesian nonparametric coalescent-based approaches, we introduce a flexible framework that incorporates time-varying covariates that exploit Gaussian Markov random fields to achieve temporal smoothing of effective population size trajectories. To approximate the posterior distribution, we adapt efficient Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. Incorporating covariates into the demographic inference framework enables the modeling of associations between the effective population size and covariates while accounting for uncertainty in population histories. Furthermore, it can lead to more precise estimates of population dynamics. We apply our model to four examples. We reconstruct the demographic history of raccoon rabies in North America and find a significant association with the spatiotemporal spread of the outbreak. Next, we examine the effective population size trajectory of the DENV-4 virus in Puerto Rico along with viral isolate count data and find similar cyclic patterns. We compare the population history of the HIV-1 CRF02_AG clade in Cameroon with HIV incidence and prevalence data and find that the effective population size is more reflective of incidence rate. Finally, we explore the hypothesis that the population dynamics of musk ox during the Late Quaternary period were related to climate change. [Coalescent; effective population size; Gaussian Markov random fields; phylodynamics; phylogenetics; population genetics. PMID:27368344

A Conceptual Model of Riparian Forest Response to Channel Abandonment on Meandering Rivers

NASA Astrophysics Data System (ADS)

Stella, J. C.; Hayden, M. K.; Battles, J. J.; Piegay, H.; Dufour, S.; Fremier, A. K.

2008-12-01

On alluvial rivers, hydrogeomorphic regimes exert a primary control on the regeneration of pioneer riparian forest stands and thus their composition and age structure. Seasonal flow patterns provide the necessary conditions for recruitment, and channel migration drives patterns of forest stand dynamics. To date, studies of pioneer riparian forest structure have focused primarily on point bar habitats, where woody vegetation typically recruits with decadal frequency in even-aged bands parallel to the river margin. However, there are indications that other recruitment pathways exist and can be important from a population and conservation perspective. On floodplains where channel migration occurs as infrequent cutoff or avulsion events, the geometry and position of the old channel relative to the new one determines rates and patterns of sedimentation and flood frequency. These conditions provide a brief opportunity for forest recruitment, and geomorphic evolution of the former channel habitat in turn influences forest dynamics. The population implications of this alternative forest regeneration pathway depend on the temporal dynamics of channel abandonment versus the rate of lateral channel migration. Preliminary analysis indicates that the geographic scope of this ecogeomorphological process is sizable. Along the Sacramento River (CA) and Ain River (France), for example, cottonwood-dominated stands associated with abandoned channels tend to be less frequent in number (38% of all stands) but larger in area (accounting for 53% of all forest area) relative to forest stands associated with laterally migrating point bars. Dendrochronological analysis confirms that tree ages in floodplain stands corresponds to the first decade after channel abandonment. These data indicate that changes to the rate and scale of channel abandonment due to human and climatic alterations to the flow regime will likely influence riparian corridor-wide tree population structure and forest dynamics.

Genetic variability and natural selection at the ligand domain of the Duffy binding protein in brazilian Plasmodium vivax populations

PubMed Central

2010-01-01

Background Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBPII), which is the most variable segment of the protein. Methods To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBPII in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBPII, and T- and B-cell epitopes were localized on the 3-D structure. Results The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBPII, and (ii) PvDBPII appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions This study shows that some polymorphisms of PvDBPII are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion. PMID:21092207