Sample records for large population study
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Does source population size affect performance in new environments?
Yates, Matthew C; Fraser, Dylan J
2014-01-01
Small populations are predicted to perform poorly relative to large populations when experiencing environmental change. To explore this prediction in nature, data from reciprocal transplant, common garden, and translocation studies were compared meta-analytically. We contrasted changes in performance resulting from transplantation to new environments among individuals originating from different sized source populations from plants and salmonids. We then evaluated the effect of source population size on performance in natural common garden environments and the relationship between population size and habitat quality. In ‘home-away’ contrasts, large populations exhibited reduced performance in new environments. In common gardens, the effect of source population size on performance was inconsistent across life-history stages (LHS) and environments. When transplanted to the same set of new environments, small populations either performed equally well or better than large populations, depending on life stage. Conversely, large populations outperformed small populations within native environments, but only at later life stages. Population size was not associated with habitat quality. Several factors might explain the negative association between source population size and performance in new environments: (i) stronger local adaptation in large populations and antagonistic pleiotropy, (ii) the maintenance of genetic variation in small populations, and (iii) potential environmental differences between large and small populations. PMID:25469166
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Rosenblatt, Adam E.; Heithaus, Michael R.; Mather, Martha E.; Matich, Philip; Nifong, James C.; Ripple, William J.; Silliman, Brian R.
2013-01-01
During recent human history, human activities such as overhunting and habitat destruction have severely impacted many large top predator populations around the world. Studies from a variety of ecosystems show that loss or diminishment of top predator populations can have serious consequences for population and community dynamics and ecosystem stability. However, there are relatively few studies of the roles of large top predators in coastal ecosystems, so that we do not yet completely understand what could happen to coastal areas if large top predators are extirpated or significantly reduced in number. This lack of knowledge is surprising given that coastal areas around the globe are highly valued and densely populated by humans, and thus coastal large top predator populations frequently come into conflict with coastal human populations. This paper reviews what is known about the ecological roles of large top predators in coastal systems and presents a synthesis of recent work from three coastal eastern US Long Term Ecological Research (LTER) sites where long-term studies reveal what appear to be common themes relating to the roles of large top predators in coastal systems. We discuss three specific themes: (1) large top predators acting as mobile links between disparate habitats, (2) large top predators potentially affecting nutrient and biogeochemical dynamics through localized behaviors, and (3) individual specialization of large top predator behaviors. We also discuss how research within the LTER network has led to enhanced understanding of the ecological roles of coastal large top predators. Highlighting this work is intended to encourage further investigation of the roles of large top predators across diverse coastal aquatic habitats and to better inform researchers and ecosystem managers about the importance of large top predators for coastal ecosystem health and stability.
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Christopher P. Bloch; Michael R. Willi
2006-01-01
Large-scale natural disturbances, such as hurricanes, can have profound effects on animal populations. Nonetheless, generalizations about the effects of disturbance are elusive, and few studies consider long-term responses of a single population or community to multiple large-scale disturbance events. In the last 20 y, twomajor hurricanes (Hugo and Georges) have struck...
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[Epidemiological methods used in studies in the prevalence of Tourette syndrome].
Stefanoff, Paweł; Mazurek, Jacek
2003-01-01
Tourette syndrome (TS) prevalence was studied since the early 80-ies. Its clinical course is characterised by co-occurrence of motor and vocal tics. Results of previous epidemiological studies were surprisingly divergent: the prevalence varied from 0.5 to 115 cases per 10,000 population. The disease previously recognised as extremely rare and severe is now considered as quite common, with often moderate course. Selected methods used in studies of TS prevalence and analysis of their possible impact on study results are presented. The studies were divided into 3 groups: studies of the hospitalised population, large-scale screenings and studies involving school population, basing on characteristic and size of population, methods of selection of subjects, diagnostic and screening methods used. Studies of the hospitalised population involved patients with most severe symptoms, in different age groups, different methods of final diagnosis confirmation were used. TS prevalence varied from 0.5 up to 15 cases per 10,000 population. Procedures used in large-scale screening studies made possible the elimination of potential selection bias. Large populations were studied using transparent and repetitive confirmation of diagnoses. Their validity was additionally checked in parallel validity studies. TS prevalence was in the range 4.3 to 10 cases per 10,000 population. The highest TS prevalence was obtained in studies involving schoolchildren. Data were gathered from multiple sources: from parents, teachers and children, as well as from classroom observation. Diagnoses were made by experienced clinicians. TS prevalence obtained in school population studies was between 36.2 up to 115 per 10,000 population.
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Ward, Megan; Johnson, Steven D; Zalucki, Myron P
2013-04-01
One of the essential requirements for an introduced plant species to become invasive is an ability to reproduce outside the native range, particularly when initial populations are small. If a reproductive Allee effect is operating, plants in small populations will have reduced reproductive success relative to plants in larger populations. Alternatively, if plants in small populations experience less competition for pollination than those in large populations, they may actually have higher levels of reproductive success than plants in large populations. To resolve this uncertainty, we investigated how the per capita fecundity of plants was affected by population size in three invasive milkweed species. Field surveys of seed production in natural populations of different sizes but similar densities were conducted for three pollinator-dependent invasive species, namely Asclepias curassavica, Gomphocarpus fruticosus and G. physocarpus. Additionally, supplemental hand-pollinations were performed in small and large populations in order to determine whether reproductive output was limited by pollinator activity in these populations. Reproductive Allee effects were not detected in any of the study species. Instead, plants in small populations exhibited remarkably high levels of reproductive output compared to those in large populations. Increased fruit production following supplemental hand-pollinations suggested that the lower reproductive output of naturally pollinated plants in large populations is a consequence of pollen limitation rather than limitation due to abiotic resources. This is consistent with increased intraspecific competition for pollination amongst plants in large populations. It is likely that the invasion of these milkweed species in Australia has been enhanced because plants in small founding populations experience less intraspecific competition for pollinators than those in large populations, and thus have the ability to produce copious amounts of seeds.
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High population density enhances recruitment and survival of a harvested coral reef fish.
Wormald, Clare L; Steele, Mark A; Forrester, Graham E
2013-03-01
A negative relationship between population growth and population density (direct density dependence) is necessary for population regulation and is assumed in most models of harvested populations. Experimental tests for density dependence are lacking for large-bodied, harvested fish because of the difficulty of manipulating population density over large areas. We studied a harvested coral reef fish, Lutjanus apodus (schoolmaster snapper), using eight large, isolated natural reefs (0.4-1.6 ha) in the Bahamas as replicates. An initial observational test for density dependence was followed by a manipulation of population density. The manipulation weakened an association between density and shelter-providing habitat features and revealed a positive effect of population density on recruitment and survival (inverse density dependence), but no effect of density on somatic growth. The snappers on an individual reef were organized into a few shoals, and we hypothesize that large shoals on high-density reefs were less vulnerable to large piscivores (groupers and barracudas) than the small shoals on low-density reefs. Reductions in predation risk for individuals in large social groups are well documented, but because snapper shoals occupied reefs the size of small marine reserves, these ecological interactions may influence the outcome of management actions.
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Dart, Sara; Eckert, Christopher G
2015-02-01
Evolutionary transitions from outcrossing to self-fertilization are thought to occur because selfing provides reproductive assurance when pollinators or mates are scarce, but they could also occur via selection to reduce floral vulnerability to herbivores. This study investigated geographic covariation between floral morphology, fruit set, pollen limitation and florivory across the geographic range of Camissoniopsis cheiranthifolia, a Pacific coastal dune endemic that varies strikingly in flower size and mating system. Fruit set was quantified in 75 populations, and in 41 of these floral herbivory by larvae of a specialized moth (Mompha sp.) that consumes anthers in developing buds was also quantified. Experimental pollen supplementation was performed to quantify pollen limitation in three large-flowered, outcrossing and two small-flowered, selfing populations. These parameters were also compared between large- and small-flowered phenotypes within three mixed populations. Fruit set was much lower in large-flowered populations, and also much lower among large- than small-flowered plants within populations. Pollen supplementation increased per flower seed production in large-flowered but not small-flowered populations, but fruit set was not pollen limited. Hence inadequate pollination cannot account for the low fruit set of large-flowered plants. Floral herbivory was much more frequent in large-flowered populations and correlated negatively with fruit set. However, florivores did not preferentially attack large-flowered plants in three large-flowered populations or in two of three mixed populations. Selfing alleviated pollen limitation of seeds per fruit, but florivory better explains the marked variation in fruit set. Although florivory was more frequent in large-flowered populations, large-flowered individuals were not generally more vulnerable within populations. Rather than a causative selective factor, reduced florivory in small-flowered, selfing populations is probably an ecological consequence of mating system differentiation, with potentially significant effects on population demography and biotic interactions. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.
2018-01-01
Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence.The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations.Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.
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WKB theory of large deviations in stochastic populations
NASA Astrophysics Data System (ADS)
Assaf, Michael; Meerson, Baruch
2017-06-01
Stochasticity can play an important role in the dynamics of biologically relevant populations. These span a broad range of scales: from intra-cellular populations of molecules to population of cells and then to groups of plants, animals and people. Large deviations in stochastic population dynamics—such as those determining population extinction, fixation or switching between different states—are presently in a focus of attention of statistical physicists. We review recent progress in applying different variants of dissipative WKB approximation (after Wentzel, Kramers and Brillouin) to this class of problems. The WKB approximation allows one to evaluate the mean time and/or probability of population extinction, fixation and switches resulting from either intrinsic (demographic) noise, or a combination of the demographic noise and environmental variations, deterministic or random. We mostly cover well-mixed populations, single and multiple, but also briefly consider populations on heterogeneous networks and spatial populations. The spatial setting also allows one to study large fluctuations of the speed of biological invasions. Finally, we briefly discuss possible directions of future work.
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Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J
2015-09-01
How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.
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Argentine Population Genetic Structure: Large Variance in Amerindian Contribution
Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.
2011-01-01
Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183
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ERIC Educational Resources Information Center
Rouse, Heather L.; Fantuzzo, John W.; LeBoeuf, Whitney
2011-01-01
This population-based study investigated the unique and cumulative relations between risks that are monitored by public surveillance systems and academic and behavioral outcomes for an entire cohort of third graders in a large, urban public school system. Using integrated, administrative records from child welfare, public health, housing, and…
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Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations
Porto, Markus; Bastolla, Ugo
2010-01-01
Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction. PMID:20463869
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Genetic studies on populations of large river fishes provide a potentially useful but underutilized research and assessment tool. Population genetic research on freshwater systems has provided meaningful insight into stock structure, hybridization issues, and gene flow/migration...
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Gonzalez Murcia, Josue D; Schmutz, Cameron; Munger, Caitlin; Perkes, Ammon; Gustin, Aaron; Peterson, Michael; Ebbert, Mark T W; Norton, Maria C; Tschanz, Joann T; Munger, Ronald G; Corcoran, Christopher D; Kauwe, John S K
2013-12-01
Recent studies have identified the rs75932628 (R47H) variant in TREM2 as an Alzheimer's disease risk factor with estimated odds ratio ranging from 2.9 to 5.1. The Cache County Memory Study is a large, population-based sample designed for the study of memory and aging. We genotyped R47H in 2974 samples (427 cases and 2540 control subjects) from the Cache County study using a custom TaqMan assay. We observed 7 heterozygous cases and 12 heterozygous control subjects with an odds ratio of 3.5 (95% confidence interval, 1.3-8.8; p = 0.0076). The minor allele frequency and population attributable fraction for R47H were 0.0029 and 0.004, respectively. This study replicates the association between R47H and Alzheimer's disease risk in a large, population-based sample, and estimates the population frequency and attributable risk of this rare variant. Copyright © 2013 Elsevier Inc. All rights reserved.
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An Admittance Survey of Large Volcanoes on Venus: Implications for Volcano Growth
NASA Technical Reports Server (NTRS)
Brian, A. W.; Smrekar, S. E.; Stofan, E. R.
2004-01-01
Estimates of the thickness of the venusian crust and elastic lithosphere are important in determining the rheological and thermal properties of Venus. These estimates offer insights into what conditions are needed for certain features, such as large volcanoes and coronae, to form. Lithospheric properties for much of the large volcano population on Venus are not well known. Previous studies of elastic thickness (Te) have concentrated on individual or small groups of edifices, or have used volcano models and fixed values of Te to match with observations of volcano morphologies. In addition, previous studies use different methods to estimate lithospheric parameters meaning it is difficult to compare their results. Following recent global studies of the admittance signatures exhibited by the venusian corona population, we performed a similar survey into large volcanoes in an effort to determine the range of lithospheric parameters shown by these features. This survey of the entire large volcano population used the same method throughout so that all estimates could be directly compared. By analysing a large number of edifices and comparing our results to observations of their morphology and models of volcano formation, we can help determine the controlling parameters that govern volcano growth on Venus.
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Taylor, Nathan G A
2017-07-01
In response to the December 2016 article entitled "Vegetarian diet and all-cause mortality: Evidence from a large population-based Australian cohort - the 45 and Up Study". A brief analysis of the article with suggestions for interpretation and considerations for future research. Copyright © 2017 Elsevier Inc. All rights reserved.
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Is family size related to adolescence mental hospitalization?
Kylmänen, Paula; Hakko, Helinä; Räsänen, Pirkko; Riala, Kaisa
2010-05-15
The aim of this study was to investigate the association between family size and psychiatric disorders of underage adolescent psychiatric inpatients. The study sample consisted of 508 adolescents (age 12-17) admitted to psychiatric impatient care between April 2001 and March 2006. Diagnostic and Statistical Manual of Mental Disorders, fourth edition-based psychiatric diagnoses and variables measuring family size were obtained from the Schedule for Affective Disorder and Schizophrenia for School-Age Children Present and Lifetime (K-SADS-PL). The family size of the general Finnish population was used as a reference population. There was a significant difference between the family size of the inpatient adolescents and the general population: 17.0% of adolescents came from large families (with 6 or more children) while the percentage in the general population was 3.3. A girl from a large family had an about 4-fold risk of psychosis other than schizophrenia. However, large family size was not associated with a risk for schizophrenia. Large family size was overrepresented among underage adolescents admitted for psychiatric hospitalization in Northern Finland. Copyright 2009 Elsevier Ltd. All rights reserved.
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Ambinakudige, Shrinidhi; Parisi, Domenico
2010-01-01
In this study, migration data compiled by the Internal Revenue Serve (IRS) and the US Census Bureau for 2006-07 were used to analyse internal migration patterns using migration and income effectiveness for the counties containing the 25 most populous cities in the United States. The results indicated that both large metropolitan and rural counties have lost population and income due to migration. Small metropolitan and non-metropolitan counties closer to cities gained population and income. Counties in South Florida attracted a large number of higher-income migrants from the largest cities in the US. In the last 13 years, New York, Los Angeles and Chicago, the three most populous cities in the US, had negative migration effectiveness. Suburban areas and second-tier cities continued to attract people from large metropolitan areas.
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Holá, Eva; Košnar, Jiří; Kučera, Jan
2015-01-01
Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei's gene diversity in large populations reached high values and ranged between 4.41-4.97, 3.13-4.45, and 0.94-0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00-4.42, 1.00-2.73, and 0.00-0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at longer distances (20-80 m), suggesting effective dispersal of asexual propagules.
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Holá, Eva; Košnar, Jiří; Kučera, Jan
2015-01-01
Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei’s gene diversity in large populations reached high values and ranged between 4.41–4.97, 3.13–4.45, and 0.94–0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00–4.42, 1.00–2.73, and 0.00–0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at longer distances (20–80 m), suggesting effective dispersal of asexual propagules. PMID:26186214
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Sæther, Bernt-Erik; Visser, Marcel E; Grøtan, Vidar; Engen, Steinar
2016-04-27
Understanding the variation in selection pressure on key life-history traits is crucial in our rapidly changing world. Density is rarely considered as a selective agent. To study its importance, we partition phenotypic selection in fluctuating environments into components representing the population growth rate at low densities and the strength of density dependence, using a new stochastic modelling framework. We analysed the number of eggs laid per season in a small song-bird, the great tit, and found balancing selection favouring large clutch sizes at small population densities and smaller clutches in years with large populations. A significant interaction between clutch size and population size in the regression for the Malthusian fitness reveals that those females producing large clutch sizes at small population sizes also are those that show the strongest reduction in fitness when population size is increased. This provides empirical support for ongoing r- and K-selection in this population, favouring phenotypes with large growth rates r at small population sizes and phenotypes with high competitive skills when populations are close to the carrying capacity K This selection causes long-term fluctuations around a stable mean clutch size caused by variation in population size, implying that r- and K-selection is an important mechanism influencing phenotypic evolution in fluctuating environments. This provides a general link between ecological dynamics and evolutionary processes, operating through a joint influence of density dependence and environmental stochasticity on fluctuations in population size. © 2016 The Author(s).
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Isolation with Migration Models for More Than Two Populations
Hey, Jody
2010-01-01
A method for studying the divergence of multiple closely related populations is described and assessed. The approach of Hey and Nielsen (2007, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA. 104:2785–2790) for fitting an isolation-with-migration model was extended to the case of multiple populations with a known phylogeny. Analysis of simulated data sets reveals the kinds of history that are accessible with a multipopulation analysis. Necessarily, processes associated with older time periods in a phylogeny are more difficult to estimate; and histories with high levels of gene flow are particularly difficult with more than two populations. However, for histories with modest levels of gene flow, or for very large data sets, it is possible to study large complex divergence problems that involve multiple closely related populations or species. PMID:19955477
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Isolation with migration models for more than two populations.
Hey, Jody
2010-04-01
A method for studying the divergence of multiple closely related populations is described and assessed. The approach of Hey and Nielsen (2007, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA. 104:2785-2790) for fitting an isolation-with-migration model was extended to the case of multiple populations with a known phylogeny. Analysis of simulated data sets reveals the kinds of history that are accessible with a multipopulation analysis. Necessarily, processes associated with older time periods in a phylogeny are more difficult to estimate; and histories with high levels of gene flow are particularly difficult with more than two populations. However, for histories with modest levels of gene flow, or for very large data sets, it is possible to study large complex divergence problems that involve multiple closely related populations or species.
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Lee, Kenneth K C; Li, Shu Chuen; Kwong, Kai Sun; Chan, Thomas Y K; Lee, Vivian W Y; Lau, Joseph T F
2008-01-01
The incidence, health and economic impacts of influenza-like illness (ILI) among the working population in Hong Kong had never been studied. Due to the nature of the disease, ILIs can have a significant impact on the operation of a corporation in terms of loss of productivity and reduced work performance. The present study was undertaken to determine the health and economic impacts of ILIs under different environmental conditions on the working population of a large corporation. Over 2,000 employees of a large corporation in the travelling and tourism industry were studied with three different types of working environment (confined, typical office and well ventilated) by two structured questionnaires. The most affected group in terms of productivity and health was the group working in a confined area, whilst those working in a well-ventilated area were least affected. However, symptoms of the confined area group seemed to disappear faster. The infection rate appeared to vary according to work environment for the studied population. Policies on preventive measures and early treatment are important for a corporation to reduce loss in productivity due to ILIs.
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Vallejo, Roger L.; Liu, Sixin; Gao, Guangtu; Fragomeni, Breno O.; Hernandez, Alvaro G.; Leeds, Timothy D.; Parsons, James E.; Martin, Kyle E.; Evenhuis, Jason P.; Welch, Timothy J.; Wiens, Gregory D.; Palti, Yniv
2017-01-01
Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect quantitative trait loci (QTL) for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a 57 K SNP array and a reference genome assembly have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we conducted GWAS for BCWD resistance in two rainbow trout breeding populations using two genotyping platforms, the 57 K Affymetrix SNP array and restriction-associated DNA (RAD) sequencing. Overall, we identified 14 moderate-large effect QTL that explained up to 60.8% of the genetic variance in one of the two populations and 27.7% in the other. Four of these QTL were found in both populations explaining a substantial proportion of the variance, although major differences were also detected between the two populations. Our results confirm that BCWD resistance is controlled by the oligogenic inheritance of few moderate-large effect loci and a large-unknown number of loci each having a small effect on BCWD resistance. We detected differences in QTL number and genome location between two GWAS models (weighted single-step GBLUP and Bayes B), which highlights the utility of using different models to uncover QTL. The RAD-SNPs detected a greater number of QTL than the 57 K SNP array in one population, suggesting that the RAD-SNPs may uncover polymorphisms that are more unique and informative for the specific population in which they were discovered. PMID:29109734
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Vallejo, Roger L; Liu, Sixin; Gao, Guangtu; Fragomeni, Breno O; Hernandez, Alvaro G; Leeds, Timothy D; Parsons, James E; Martin, Kyle E; Evenhuis, Jason P; Welch, Timothy J; Wiens, Gregory D; Palti, Yniv
2017-01-01
Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect quantitative trait loci (QTL) for BCWD resistance in rainbow trout ( Oncorhynchus mykiss ). However, the recent availability of a 57 K SNP array and a reference genome assembly have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we conducted GWAS for BCWD resistance in two rainbow trout breeding populations using two genotyping platforms, the 57 K Affymetrix SNP array and restriction-associated DNA (RAD) sequencing. Overall, we identified 14 moderate-large effect QTL that explained up to 60.8% of the genetic variance in one of the two populations and 27.7% in the other. Four of these QTL were found in both populations explaining a substantial proportion of the variance, although major differences were also detected between the two populations. Our results confirm that BCWD resistance is controlled by the oligogenic inheritance of few moderate-large effect loci and a large-unknown number of loci each having a small effect on BCWD resistance. We detected differences in QTL number and genome location between two GWAS models (weighted single-step GBLUP and Bayes B), which highlights the utility of using different models to uncover QTL. The RAD-SNPs detected a greater number of QTL than the 57 K SNP array in one population, suggesting that the RAD-SNPs may uncover polymorphisms that are more unique and informative for the specific population in which they were discovered.
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iXora: exact haplotype inferencing and trait association.
Utro, Filippo; Haiminen, Niina; Livingstone, Donald; Cornejo, Omar E; Royaert, Stefan; Schnell, Raymond J; Motamayor, Juan Carlos; Kuhn, David N; Parida, Laxmi
2013-06-06
We address the task of extracting accurate haplotypes from genotype data of individuals of large F1 populations for mapping studies. While methods for inferring parental haplotype assignments on large F1 populations exist in theory, these approaches do not work in practice at high levels of accuracy. We have designed iXora (Identifying crossovers and recombining alleles), a robust method for extracting reliable haplotypes of a mapping population, as well as parental haplotypes, that runs in linear time. Each allele in the progeny is assigned not just to a parent, but more precisely to a haplotype inherited from the parent. iXora shows an improvement of at least 15% in accuracy over similar systems in literature. Furthermore, iXora provides an easy-to-use, comprehensive environment for association studies and hypothesis checking in populations of related individuals. iXora provides detailed resolution in parental inheritance, along with the capability of handling very large populations, which allows for accurate haplotype extraction and trait association. iXora is available for non-commercial use from http://researcher.ibm.com/project/3430.
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Predator cannibalism can intensify negative impacts on heterospecific prey.
Takatsu, Kunio; Kishida, Osamu
2015-07-01
Although natural populations consist of individuals with different traits, and the degree of phenotypic variation varies among populations, the impact of phenotypic variation on ecological interactions has received little attention, because traditional approaches to community ecology assume homogeneity of individuals within a population. Stage structure, which is a common way of generating size and developmental variation within predator populations, can drive cannibalistic interactions, which can affect the strength of predatory effects on the predator's heterospecific prey. Studies have shown that predator cannibalism weakens predatory effects on heterospecific prey by reducing the size of the predator population and by inducing less feeding activity of noncannibal predators. We predict, however, that predator cannibalism, by promoting rapid growth of the cannibals, can also intensify predation pressure on heterospecific prey, because large predators have large resource requirements and may utilize a wider variety of prey species. To test this hypothesis, we conducted an experiment in which we created carnivorous salamander (Hynobius retardatus) populations with different stage structures by manipulating the salamander's hatch timing (i.e., populations with large or small variation in the timing of hatching), and explored the resultant impacts on the abundance, behavior, morphology, and life history of the salamander's large heterospecific prey, Rana pirica frog tadpoles. Cannibalism was rare in salamander populations having small hatch-timing variation, but was frequent in those having large hatch-timing variation. Thus, giant salamander cannibals occurred only in the latter. We clearly showed that salamander giants exerted strong predation pressure on frog tadpoles, which induced large behavioral and morphological defenses in the tadpoles and caused them to metamorphose late at large size. Hence, predator cannibalism arising from large variation in the timing of hatching can strengthen predatory effects on heterospecific prey and can have impacts on various, traits of both predator and prey. Because animals commonly broaden their diet as they grow, such negative impacts of predator cannibalism on the heterospecific prey may be common in interactions between predators and prey species of similar size.
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Transient synchrony among populations of five foliage-feeding Lepidoptera
Maartje J. Klapwijk; Jonathan A. Walter; Anikó Hirka; György Csóka; Christer Björkman; Andrew M. Liebhold
2018-01-01
Studies of transient population dynamics have largely focused on temporal changes in dynamical behaviour, such as the transition between periods of stability and instability. This study explores a related dynamic pattern, namely transient synchrony during a 49-year period among populations of five sympatric species of forest insects that share host tree resources. The...
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Runstadler, J A; Angles, J M; Pedersen, N C
2006-11-01
The genetic polymorphism at the dog leucocyte antigen (DLA) class II loci DQA1, DQB1 and DRB1 was studied in a large genetically diverse population of feral and wild-type dogs from the large island nations of Indonesia (Bali), Australia and New Guinea (Bali street dog, dingo and New Guinea singing dog, respectively). Sequence-based typing (SBT) of the hypervariable region of DLA-DRB1, -DQA1 and -DQB1 alleles was used to determine genetic diversity. No new DQA1 alleles were recognized among the three dog populations, but five novel DLA-DRB1 and 2 novel DLA-DQB1 allele sequences were detected. Additional unknown alleles were postulated to exist in Bali street dogs, as indicated by the large percentage of individuals (15%-33%) that had indeterminate DRB1, DQA1 and DQB1 alleles by SBT. All three groups of dogs possessed alleles that were relatively uncommon in conventional purebreds. The New Guinea singing dog and dingo shared alleles that were not present in the Bali street dogs. These findings suggested that the dingo was more closely related to indigenous dogs from New Guinea. Feral dog populations, in particular large ones such as that of Bali, show genetic diversity that existed prior to phenotypic selection for breeds originating from their respective regions. This diversity needs to be identified and maintained in the face of progressive Westernization. These populations deserve further study as potential model populations for the evolution of major histocompatibility complex alleles, for the study of canine genetic diversity, for the development of dog breeds and for studies on the comigration of ancestral human and dog populations.
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ERIC Educational Resources Information Center
Beaino, Ghada; Khoshnood, Babak; Kaminski, Monique; Pierrat, Veronique; Marret, Stephane; Matis, Jacqueline; Ledesert, Bernard; Thiriez, Gerard; Fresson, Jeanne; Roze, Jean-Christophe; Zupan-Simunek, Veronique; Arnaud, Catherine; Burguet, Antoine; Larroque, Beatrice; Breart, Gerard; Ancel, Pierre-Yves
2010-01-01
Aim: The aim of this study was to assess the independent role of cerebral lesions on ultrasound scan, and several other neonatal and obstetric factors, as potential predictors of cerebral palsy (CP) in a large population-based cohort of very preterm infants. Method: As part of EPIPAGE, a population-based prospective cohort study, perinatal data…
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Genetic studies of type 2 diabetes in South Asians: a systematic overview.
Chowdhury, Ritam; Narayan, Kabayam M Venkat; Zabetian, Azadeh; Raj, Suraja; Tabassum, Rubina
2014-01-01
Diabetes Mellitus, which affects 366 million people worldwide, is a leading cause of mortality, morbidity, and loss of quality of life. South Asians, comprising 24% of the world's population, suffer a large burden of type 2 diabetes. With intriguing risk phenotypes, unique environmental triggers, and potential genetic predisposition, South Asians offer a valuable resource for investigating the pathophysiology of type 2 diabetes. Genomics has proven its potential to underpin some of the etiology of type 2 diabetes by identifying a number of susceptibility genes, but such data are scarce and unclear in South Asians. We present a systematic review of studies on the genetic basis of type 2 diabetes or its complications in South Asians published between 1987-2012, and discuss the findings and limitations of the available data. Of the 91 eligible studies meeting our inclusion criteria, a vast majority included Indian populations, followed by a few in those of Pakistani origin, while other South Asian countries were generally under-represented. Though a large number of studies focused on the replication of findings from genome-wide association studies (GWAS) in European populations, a few studies explored new genes and pathways along with GWAS in South Asians and suggested the potential to unravel population- specific susceptibility genes in this population. We find encouraging improvements in study designs, sample sizes and the numbers of genetic variants investigated over the last five years, which reflect the existing capacity and scope for large-scale genetic studies in South Asians.
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NASA Astrophysics Data System (ADS)
Fujita, Kazuhiko; Otomaru, Maki; Lopati, Paeniu; Hosono, Takashi; Kayanne, Hajime
2016-03-01
Carbonate production by large benthic foraminifers is sometimes comparable to that of corals and coralline algae, and contributes to sedimentation on reef islands and beaches in the tropical Pacific. Population dynamic data, such as population density and size structure (size-frequency distribution), are vital for an accurate estimation of shell production of foraminifers. However, previous production estimates in tropical environments were based on a limited sampling period with no consideration of seasonality. In addition, no comparisons were made of various estimation methods to determine more accurate estimates. Here we present the annual gross shell production rate of Baculogypsina sphaerulata, estimated based on population dynamics studied over a 2-yr period on an ocean reef flat of Funafuti Atoll (Tuvalu, tropical South Pacific). The population density of B. sphaerulata increased from January to March, when northwest winds predominated and the study site was on the leeward side of reef islands, compared to other seasons when southeast trade winds predominated and the study site was on the windward side. This result suggested that wind-driven flows controlled the population density at the study site. The B. sphaerulata population had a relatively stationary size-frequency distribution throughout the study period, indicating no definite intensive reproductive period in the tropical population. Four methods were applied to estimate the annual gross shell production rates of B. sphaerulata. The production rates estimated by three of the four methods (using monthly biomass, life tables and growth increment rates) were in the order of hundreds of g CaCO3 m-2 yr-1 or cm-3 m-2 yr-1, and the simple method using turnover rates overestimated the values. This study suggests that seasonal surveys should be undertaken of population density and size structure as these can produce more accurate estimates of shell productivity of large benthic foraminifers.
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Ojanen, Sami P; Nieminen, Marko; Meyke, Evgeniy; Pöyry, Juha; Hanski, Ilkka
2013-10-01
Long-term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long-term viability of species, but large-scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long-term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long-term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year-to-year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large-scale and long-term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long-term observational studies. For instance, in the case of the Glanville fritillary project, the long-term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life-history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long-term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt.
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Ojanen, Sami P; Nieminen, Marko; Meyke, Evgeniy; Pöyry, Juha; Hanski, Ilkka
2013-01-01
Long-term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long-term viability of species, but large-scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long-term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long-term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year-to-year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large-scale and long-term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long-term observational studies. For instance, in the case of the Glanville fritillary project, the long-term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life-history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long-term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt. PMID:24198935
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Large granular lymphocytosis in a patient infected with HTLV-II.
Martin, M P; Biggar, R J; Hamlin-Green, G; Staal, S; Mann, D
1993-08-01
HTLV-II has been associated with a variety of lymphoproliferative disorders, including atypical hairy cell leukemia, chronic T cell leukemia, T prolymphocytic leukemia, and large granular lymphocytic leukemia. However, a direct or indirect role for HTLV-II in these disorders is not yet firmly established. We studied a patient diagnosed as having leukemia of the large granular lymphocyte (LGL) type who was HTLV-II seropositive, to determine if the expanded cell population was infected. Two populations of CD3-CD16+ LGL were identified; one was CD8+, the other CD8-. Populations of cells with these surface markers as well as normal CD3+CD4+ and CD3+CD8+ cells were separated by flow cytometric methods, DNA extracted, and gene regions of HTLV-II pol and tax amplified, using the polymerase chain reaction, and probed after Southern blotting. HTLV-II was detected in the CD3+CD8+ population, and not in the CD3-CD16+ large granular lymphocyte population. This finding indicates that the role of HTLV-II, if any, in LGL proliferation is indirect.
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Correction of Population Stratification in Large Multi-Ethnic Association Studies
Serre, David; Montpetit, Alexandre; Paré, Guillaume; Engert, James C.; Yusuf, Salim; Keavney, Bernard; Hudson, Thomas J.; Anand, Sonia
2008-01-01
Background The vast majority of genetic risk factors for complex diseases have, taken individually, a small effect on the end phenotype. Population-based association studies therefore need very large sample sizes to detect significant differences between affected and non-affected individuals. Including thousands of affected individuals in a study requires recruitment in numerous centers, possibly from different geographic regions. Unfortunately such a recruitment strategy is likely to complicate the study design and to generate concerns regarding population stratification. Methodology/Principal Findings We analyzed 9,751 individuals representing three main ethnic groups - Europeans, Arabs and South Asians - that had been enrolled from 154 centers involving 52 countries for a global case/control study of acute myocardial infarction. All individuals were genotyped at 103 candidate genes using 1,536 SNPs selected with a tagging strategy that captures most of the genetic diversity in different populations. We show that relying solely on self-reported ethnicity is not sufficient to exclude population stratification and we present additional methods to identify and correct for stratification. Conclusions/Significance Our results highlight the importance of carefully addressing population stratification and of carefully “cleaning” the sample prior to analyses to obtain stronger signals of association and to avoid spurious results. PMID:18196181
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Korman, Josh; Yard, Micheal D.; Kennedy, Theodore A.
2017-01-01
Data from a large-scale mark-recapture study was used in an open population model to determine the cause for long-term trends in growth and abundance of a Rainbow Trout Oncorhynchus mykiss population in the tailwater of Glen Canyon Dam, AZ. Reduced growth affected multiple life stages and processes causing negative feedbacks that regulated the abundance of the population, including: higher mortality of larger fish; lower rates of recruitment (young of year) in years when growth was reduced; and lower rates of sexual maturation the following year. High and steady flows during spring and summer of 2011 resulted in very large recruitment event. The population declined 10-fold by 2016 due a combination of lower recruitment and reduced survival of larger trout. Survival rates for trout ≥ 225 mm in 2014, 2015, and 2016 were 11%, 21%, and 22% lower than average survival rates between 2012 and 2013, respectively. Abundance at the end of the study would have been three- to five-fold higher had survival rates for larger trout remained at the elevated levels estimated for 2012 and 2013. Growth declined between 2012 and 2014 owing to reduced prey availability, which led to very poor fish condition by fall of 2014 (~0.9-0.95). Poor condition in turn resulted in low survival rates of larger fish during fall of 2014 and winter of 2015, which contributed to the population collapse. In Glen Canyon, large recruitment events driven by high flows can lead to increases in the population that cannot be sustained due to limitations in prey supply. In the absence of being able to regulate prey supply, flows which reduce the probability of large recruitment events can be used to avoid boom-and-bust population cycles. Our study demonstrates that mark-recapture is a very informative approach for understanding the dynamics of tailwater trout populations.
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Environmental Factors Affecting Large-Bodied Coral Reef Fish Assemblages in the Mariana Archipelago
Richards, Benjamin L.; Williams, Ivor D.; Vetter, Oliver J.; Williams, Gareth J.
2012-01-01
Large-bodied reef fishes represent an economically and ecologically important segment of the coral reef fish assemblage. Many of these individuals supply the bulk of the reproductive output for their population and have a disproportionate effect on their environment (e.g. as apex predators or bioeroding herbivores). Large-bodied reef fishes also tend to be at greatest risk of overfishing, and their loss can result in a myriad of either cascading (direct) or indirect trophic and other effects. While many studies have investigated habitat characteristics affecting populations of small-bodied reef fishes, few have explored the relationship between large-bodied species and their environment. Here, we describe the distribution of the large-bodied reef fishes in the Mariana Archipelago with an emphasis on the environmental factors associated with their distribution. Of the factors considered in this study, a negative association with human population density showed the highest relative influence on the distribution of large-bodied reef fishes; however, depth, water temperature, and distance to deep water also were important. These findings provide new information on the ecology of large-bodied reef fishes can inform discussions concerning essential fish habitat and ecosystem-based management for these species and highlight important knowledge gaps worthy of additional research. PMID:22384014
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Environmental factors affecting large-bodied coral reef fish assemblages in the Mariana Archipelago.
Richards, Benjamin L; Williams, Ivor D; Vetter, Oliver J; Williams, Gareth J
2012-01-01
Large-bodied reef fishes represent an economically and ecologically important segment of the coral reef fish assemblage. Many of these individuals supply the bulk of the reproductive output for their population and have a disproportionate effect on their environment (e.g. as apex predators or bioeroding herbivores). Large-bodied reef fishes also tend to be at greatest risk of overfishing, and their loss can result in a myriad of either cascading (direct) or indirect trophic and other effects. While many studies have investigated habitat characteristics affecting populations of small-bodied reef fishes, few have explored the relationship between large-bodied species and their environment. Here, we describe the distribution of the large-bodied reef fishes in the Mariana Archipelago with an emphasis on the environmental factors associated with their distribution. Of the factors considered in this study, a negative association with human population density showed the highest relative influence on the distribution of large-bodied reef fishes; however, depth, water temperature, and distance to deep water also were important. These findings provide new information on the ecology of large-bodied reef fishes can inform discussions concerning essential fish habitat and ecosystem-based management for these species and highlight important knowledge gaps worthy of additional research.
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Pérez-Espona, S; Pérez-Barbería, F J; Goodall-Copestake, W P; Jiggins, C D; Gordon, I J; Pemberton, J M
2009-02-01
The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.
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Prazeres, Martina; Roberts, T Edward; Pandolfi, John M
2017-03-23
Large benthic foraminifera (LBF) are crucial marine calcifiers in coral reefs, and sensitive to environmental changes. Yet, many species successfully colonise a wide range of habitats including highly fluctuating environments. We tested the combined effects of ocean warming, local impacts and different light levels on populations of the common LBF Amphistegina lobifera collected along a cross-shelf gradient of temperature and nutrients fluctuations. We analysed survivorship, bleaching frequency, chlorophyll a content and fecundity. Elevated temperature and nitrate significantly reduced survivorship and fecundity of A. lobifera across populations studied. This pattern was exacerbated when combined with below optimum light levels. Inshore populations showed a consistent resistance to increased temperature and nitrate levels, but all populations studied were significantly affected by light reduction. These findings demonstrated the capacity of some populations of LBF to acclimate to local conditions; nonetheless improvements in local water quality can ultimately ameliorate effects of climate change in local LBF populations.
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Beaulieu, J; Doerksen, T; Clément, S; MacKay, J; Bousquet, J
2014-01-01
Genomic selection (GS) is of interest in breeding because of its potential for predicting the genetic value of individuals and increasing genetic gains per unit of time. To date, very few studies have reported empirical results of GS potential in the context of large population sizes and long breeding cycles such as for boreal trees. In this study, we assessed the effectiveness of marker-aided selection in an undomesticated white spruce (Picea glauca (Moench) Voss) population of large effective size using a GS approach. A discovery population of 1694 trees representative of 214 open-pollinated families from 43 natural populations was phenotyped for 12 wood and growth traits and genotyped for 6385 single-nucleotide polymorphisms (SNPs) mined in 2660 gene sequences. GS models were built to predict estimated breeding values using all the available SNPs or SNP subsets of the largest absolute effects, and they were validated using various cross-validation schemes. The accuracy of genomic estimated breeding values (GEBVs) varied from 0.327 to 0.435 when the training and the validation data sets shared half-sibs that were on average 90% of the accuracies achieved through traditionally estimated breeding values. The trend was also the same for validation across sites. As expected, the accuracy of GEBVs obtained after cross-validation with individuals of unknown relatedness was lower with about half of the accuracy achieved when half-sibs were present. We showed that with the marker densities used in the current study, predictions with low to moderate accuracy could be obtained within a large undomesticated population of related individuals, potentially resulting in larger gains per unit of time with GS than with the traditional approach. PMID:24781808
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4P: fast computing of population genetics statistics from large DNA polymorphism panels
Benazzo, Andrea; Panziera, Alex; Bertorelle, Giorgio
2015-01-01
Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations. PMID:25628874
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Blanco Gonzalez, Enrique; Aritaki, Masato; Knutsen, Halvor; Taniguchi, Nobuhiko
2015-01-01
Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F(ST) = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.
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Exploring Collaborative Culture and Leadership in Large High Schools
ERIC Educational Resources Information Center
Jeffers, Michael P.
2013-01-01
The purpose of this exploratory study was to analyze how high school principals approached developing a collaborative culture and providing collaborative leadership in a large high school setting. The population sample for this study was 82 principals of large comprehensive high schools of grades 9 through 12 or some combination thereof with…
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Dynamics of a recolonizing population of black bears in the Ouachita Mountains of Oklahoma
Bales, S.L.; Hellgren, E.C.; Leslie, David M.; Hemphill, J.
2005-01-01
Understanding how populations expand to recolonize former habitats is important to restoration efforts in wildlife management and conservation. Translocation of black bears (Ursus americanus) to Arkansas in the 1950s and 1960s has led to recolonization of former bear range in Oklahoma, with substantial increases in distribution and abundance of the species in Oklahoma over the last 15 years. We studied demographics of black bears in southeastern Oklahoma from May 2001 to November 2002 to provide insight into characteristics of recolonizing populations of large carnivores. We trapped 51 black bears (22 M, 29 F) 77 times and radiocollared 25 female bears. Sex ratios of adults and cubs were skewed toward females, and the age structure was younger than observed in other unharvested populations. Survival of adult females was estimated at 0.9??0.1, and fertility was estimated at 0.77 female young/female/year. Density on the study area was estimated at 0.21 bears/km2 and the current finite growth rate (??) of the study population was estimated to be 1.11/year. Demographic characteristics of the Oklahoma population of black bears were similar to those of other recolonizing populations of large carnivores.
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Efficient computation of the joint sample frequency spectra for multiple populations.
Kamm, John A; Terhorst, Jonathan; Song, Yun S
2017-01-01
A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity.
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Efficient computation of the joint sample frequency spectra for multiple populations
Kamm, John A.; Terhorst, Jonathan; Song, Yun S.
2016-01-01
A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity. PMID:28239248
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Lewis, Jesse S; Logan, Kenneth A; Alldredge, Mat W; Bailey, Larissa L; VandeWoude, Sue; Crooks, Kevin R
2015-10-01
Urbanization is a primary driver of landscape conversion, with far-reaching effects on landscape pattern and process, particularly related to the population characteristics of animals. Urbanization can alter animal movement and habitat quality, both of which can influence population abundance and persistence. We evaluated three important population characteristics (population density, site occupancy, and species detection probability) of a medium-sized and a large carnivore across varying levels of urbanization. Specifically, we studied bobcat and puma populations across wildland, exurban development, and wildland-urban interface (WUI) sampling grids to test hypotheses evaluating how urbanization affects wild felid populations and their prey. Exurban development appeared to have a greater impact on felid populations than did habitat adjacent to a major urban area (i.e., WUI); estimates of population density for both bobcats and pumas were lower in areas of exurban development compared to wildland areas, whereas population density was similar between WUI and wildland habitat. Bobcats and pumas were less likely to be detected in habitat as the amount of human disturbance associated with residential development increased at a site, which was potentially related to reduced habitat quality resulting from urbanization. However, occupancy of both felids was similar between grids in both study areas, indicating that this population metric was less sensitive than density. At the scale of the sampling grid, detection probability for bobcats in urbanized habitat was greater than in wildland areas, potentially due to restrictive movement corridors and funneling of animal movements in landscapes influenced by urbanization. Occupancy of important felid prey (cottontail rabbits and mule deer) was similar across levels of urbanization, although elk occupancy was lower in urbanized areas. Our study indicates that the conservation of medium- and large-sized felids associated with urbanization likely will be most successful if large areas of wildland habitat are maintained, even in close proximity to urban areas, and wildland habitat is not converted to low-density residential development.
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NASA Astrophysics Data System (ADS)
Nyitrai, Daniel; Martinho, Filipe; Dolbeth, Marina; Rito, João; Pardal, Miguel A.
2013-12-01
Large-scale and local climate patterns are known to influence several aspects of the life cycle of marine fish. In this paper, we used a 9-year database (2003-2011) to analyse the populations of two estuarine resident fishes, Pomatoschistus microps and Pomatoschistus minutus, in order to determine their relationships with varying environmental stressors operating over local and large scales. This study was performed in the Mondego estuary, Portugal. Firstly, the variations in abundance, growth, population structure and secondary production were evaluated. These species appeared in high densities in the beginning of the study period, with subsequent occasional high annual density peaks, while their secondary production was lower in dry years. The relationships between yearly fish abundance and the environmental variables were evaluated separately for both species using Spearman correlation analysis, considering the yearly abundance peaks for the whole population, juveniles and adults. Among the local climate patterns, precipitation, river runoff, salinity and temperature were used in the analyses, and North Atlantic Oscillation (NAO) index and sea surface temperature (SST) were tested as large-scale factors. For P. microps, precipitation and NAO were the significant factors explaining abundance of the whole population, the adults and the juveniles as well. Regarding P. minutus, for the whole population, juveniles and adults river runoff was the significant predictor. The results for both species suggest a differential influence of climate patterns on the various life cycle stages, confirming also the importance of estuarine resident fishes as indicators of changes in local and large-scale climate patterns, related to global climate change.
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Post, Eric; Forchhammer, Mads C
2004-06-22
According to ecological theory, populations whose dynamics are entrained by environmental correlation face increased extinction risk as environmental conditions become more synchronized spatially. This prediction is highly relevant to the study of ecological consequences of climate change. Recent empirical studies have indicated, for example, that large-scale climate synchronizes trophic interactions and population dynamics over broad spatial scales in freshwater and terrestrial systems. Here, we present an analysis of century-scale, spatially replicated data on local weather and the population dynamics of caribou in Greenland. Our results indicate that spatial autocorrelation in local weather has increased with large-scale climatic warming. This increase in spatial synchrony of environmental conditions has been matched, in turn, by an increase in the spatial synchrony of local caribou populations toward the end of the 20th century. Our results indicate that spatial synchrony in environmental conditions and the populations influenced by them are highly variable through time and can increase with climatic warming. We suggest that if future warming can increase population synchrony, it may also increase extinction risk.
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STUDIES ON MECHANISM OF BACTERICIDAL ACTION BY IRRADIATION WITH RADIOISOTOPE COBALT-60 (in Japanese)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Akimoto, T.
1960-04-01
E.Coli, YC-1 strain, were subjected to 40-C irradiation under various conditions and the survival ratios measured. The following results were obtained: With radiation dosage held constant, prolonged irradiation produced less bactericidal effect. Temperature and environment before irradiation had little influence on the bactericidal effect. Preirradiation washing had little effect. In the earlier stage metabolism continued but gradually decreased later. The more densely the suspension is populated, the higher the survival ratio. This ratio is decreased when a large number of bacteria is treated with a sublethal dose of streptomycin before irradiation. Treatment with chloramphenicol showed no effect in a smallmore » population, but the survival ratio decreased in a large population. Penicillin caused a decrease in a large population also, but in a small population the ratio became markedly high. It is presumed that the activity of bacterial metabolism is closely related to the bacterial action of irradiation. (P.C.H.)« less
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Malucelli, Emil; Procopio, Alessandra; Fratini, Michela; Gianoncelli, Alessandra; Notargiacomo, Andrea; Merolle, Lucia; Sargenti, Azzurra; Castiglioni, Sara; Cappadone, Concettina; Farruggia, Giovanna; Lombardo, Marco; Lagomarsino, Stefano; Maier, Jeanette A; Iotti, Stefano
2018-01-01
The quantification of elemental concentration in cells is usually performed by analytical assays on large populations missing peculiar but important rare cells. The present article aims at comparing the elemental quantification in single cells and cell population in three different cell types using a new approach for single cells elemental analysis performed at sub-micrometer scale combining X-ray fluorescence microscopy and atomic force microscopy. The attention is focused on the light element Mg, exploiting the opportunity to compare the single cell quantification to the cell population analysis carried out by a highly Mg-selective fluorescent chemosensor. The results show that the single cell analysis reveals the same Mg differences found in large population of the different cell strains studied. However, in one of the cell strains, single cell analysis reveals two cells with an exceptionally high intracellular Mg content compared with the other cells of the same strain. The single cell analysis allows mapping Mg and other light elements in whole cells at sub-micrometer scale. A detailed intensity correlation analysis on the two cells with the highest Mg content reveals that Mg subcellular localization correlates with oxygen in a different fashion with respect the other sister cells of the same strain. Graphical abstract Single cells or large population analysis this is the question!
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2013-01-01
Background The composition of the microbiota of the equine intestinal tract is complex. Determining whether the microbial composition of fecal samples is representative of proximal compartments of the digestive tract could greatly simplify future studies. The objectives of this study were to compare the microbial populations of the duodenum, ileum, cecum, colon and rectum (feces) within and between healthy horses, and to determine whether rectal (fecal) samples are representative of proximal segments of the gastrointestinal tract. Intestinal samples were collected from ten euthanized horses. 16S rRNA gene PCR-based TRFLP was used to investigate microbiota richness in various segments of the gastrointestinal tract, and dice similarity indices were calculated to compare the samples. Results Within horses large variations of microbial populations along the gastrointestinal tract were seen. The microbiota in rectal samples was only partially representative of other intestinal compartments. The highest similarity was obtained when feces were compared to the cecum. Large compartmental variations were also seen when microbial populations were compared between six horses with similar dietary and housing management. Conclusion Rectal samples were not entirely representative of intestinal compartments in the small or large intestine. This should be taken into account when designing studies using fecal sampling to assess other intestinal compartments. Similarity between horses with similar dietary and husbandry management was also limited, suggesting that parts of the intestinal microbiota were unique to each animal in this study. PMID:23497580
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Ischemic stroke subtypes: a population-based study of incidence rates among blacks and whites.
Schneider, Alexander T; Kissela, Brett; Woo, Daniel; Kleindorfer, Dawn; Alwell, Kathleen; Miller, Rosemary; Szaflarski, Jerzy; Gebel, James; Khoury, Jane; Shukla, Rakesh; Moomaw, Charles; Pancioli, Arthur; Jauch, Edward; Broderick, Joseph
2004-07-01
Blacks have an excess burden of stroke compared with whites; however, data comparing ischemic stroke subtypes among the 2 groups are limited and typically involve relative frequencies. The objective of this study is to compare the incidence rates of ischemic stroke subtypes between blacks and whites within a large, representative, biracial population. The Greater Cincinnati/Northern Kentucky Stroke Study is designed to measure incidence rates and trends of all strokes within a well-defined, large, biracial population. Hospitalized cases were ascertained by International Classification of Disease (9th revision; ICD-9) discharge codes. Out-of-hospital events were ascertained by prospective screening of emergency department admission logs, review of coroners' cases, and monitoring all public health and hospital-based primary care clinics. A sampling scheme was used to ascertain events from nursing homes and all other primary care physician offices. All potential cases underwent detailed chart abstraction and confirmed by physician review. Based on all available clinical, laboratory, and radiographic information, ischemic stroke cases were subtyped into the following categories: cardioembolic, large-vessel, small-vessel, other, and stroke of undetermined cause. Race-specific incidence rates were calculated and compared after adjusting for age and gender, and standardizing to the 1990 US population. Between July 1, 1993, and June 30, 1994, 1956 first-ever ischemic strokes occurred among blacks and whites in the study population. Small-vessel strokes and strokes of undetermined cause were nearly twice as common among blacks. Large-vessel strokes were 40% more common among blacks than whites, and there was a trend toward cardioembolic strokes being more common among blacks. The excess burden of ischemic strokes among blacks compared with whites is not uniformly spread across the different subtypes. Large-vessel strokes are more common and cardioembolic stroke are as common among blacks, traditionally thought to be more common among whites.
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Akanda, Ali Shafqat; Jutla, Antarpreet S.; Gute, David M.; Sack, R. Bradley; Alam, Munirul; Huq, Anwar; Colwell, Rita R.; Islam, Shafiqul
2013-01-01
The highly populated floodplains of the Bengal Delta have a long history of endemic and epidemic cholera outbreaks, both coastal and inland. Previous studies have not addressed the spatio-temporal dynamics of population vulnerability related to the influence of underlying large-scale processes. We analyzed spatial and temporal variability of cholera incidence across six surveillance sites in the Bengal Delta and their association with regional hydroclimatic and environmental drivers. More specifically, we use salinity and flood inundation modeling across the vulnerable districts of Bangladesh to test earlier proposed hypotheses on the role of these environmental variables. Our results show strong influence of seasonal and interannual variability in estuarine salinity on spring outbreaks and inland flooding on fall outbreaks. A large segment of the population in the Bengal Delta floodplains remain vulnerable to these biannual cholera transmission mechanisms that provide ecologic and environmental conditions for outbreaks over large geographic regions. PMID:24019441
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Measuring happiness in large population
NASA Astrophysics Data System (ADS)
Wenas, Annabelle; Sjahputri, Smita; Takwin, Bagus; Primaldhi, Alfindra; Muhamad, Roby
2016-01-01
The ability to know emotional states for large number of people is important, for example, to ensure the effectiveness of public policies. In this study, we propose a measure of happiness that can be used in large scale population that is based on the analysis of Indonesian language lexicons. Here, we incorporate human assessment of Indonesian words, then quantify happiness on large-scale of texts gathered from twitter conversations. We used two psychological constructs to measure happiness: valence and arousal. We found that Indonesian words have tendency towards positive emotions. We also identified several happiness patterns during days of the week, hours of the day, and selected conversation topics.
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Using Large Diabetes Databases for Research.
Wild, Sarah; Fischbacher, Colin; McKnight, John
2016-09-01
There are an increasing number of clinical, administrative and trial databases that can be used for research. These are particularly valuable if there are opportunities for linkage to other databases. This paper describes examples of the use of large diabetes databases for research. It reviews the advantages and disadvantages of using large diabetes databases for research and suggests solutions for some challenges. Large, high-quality databases offer potential sources of information for research at relatively low cost. Fundamental issues for using databases for research are the completeness of capture of cases within the population and time period of interest and accuracy of the diagnosis of diabetes and outcomes of interest. The extent to which people included in the database are representative should be considered if the database is not population based and there is the intention to extrapolate findings to the wider diabetes population. Information on key variables such as date of diagnosis or duration of diabetes may not be available at all, may be inaccurate or may contain a large amount of missing data. Information on key confounding factors is rarely available for the nondiabetic or general population limiting comparisons with the population of people with diabetes. However comparisons that allow for differences in distribution of important demographic factors may be feasible using data for the whole population or a matched cohort study design. In summary, diabetes databases can be used to address important research questions. Understanding the strengths and limitations of this approach is crucial to interpret the findings appropriately. © 2016 Diabetes Technology Society.
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Schrader, Matthew; Travis, Joseph
2012-01-01
Population density is an ecological variable that is hypothesized to be a major agent of selection on offspring size. In high-density populations, high levels of intraspecific competition are expected to favor the production of larger offspring. In contrast, lower levels of intraspecific competition and selection for large offspring should be weaker and more easily overridden by direct selection for increased fecundity in low-density populations. Some studies have found associations between population density and offspring size consistent with this hypothesis. However, their interpretations are often clouded by a number of issues. Here, we use data from a 10-year study of nine populations of the least killifish, Heterandria formosa, to describe the associations of offspring size with habitat type, population density, and predation risk. We found that females from spring populations generally produced larger offspring than females from ponds; however, the magnitude of this difference varied among years. Across all populations, larger offspring were associated with higher densities and lower risks of predation. Interestingly, the associations between the two ecological variables (density and predation risk) and offspring size were largely independent of one another. Our results suggest that previously described genetic differences in offspring size are due to density-dependent natural selection. PMID:22957156
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Effect of water hardness on cardiovascular mortality: an ecological time series approach.
Lake, I R; Swift, L; Catling, L A; Abubakar, I; Sabel, C E; Hunter, P R
2010-12-01
Numerous studies have suggested an inverse relationship between drinking water hardness and cardiovascular disease. However, the weight of evidence is insufficient for the WHO to implement a health-based guideline for water hardness. This study followed WHO recommendations to assess the feasibility of using ecological time series data from areas exposed to step changes in water hardness to investigate this issue. Monthly time series of cardiovascular mortality data, subdivided by age and sex, were systematically collected from areas reported to have undergone step changes in water hardness, calcium and magnesium in England and Wales between 1981 and 2005. Time series methods were used to investigate the effect of water hardness changes on mortality. No evidence was found of an association between step changes in drinking water hardness or drinking water calcium and cardiovascular mortality. The lack of areas with large populations and a reasonable change in magnesium levels precludes a definitive conclusion about the impact of this cation. We use our results on the variability of the series to consider the data requirements (size of population, time of water hardness change) for such a study to have sufficient power. Only data from areas with large populations (>500,000) are likely to be able to detect a change of the size suggested by previous studies (rate ratio of 1.06). Ecological time series studies of populations exposed to changes in drinking water hardness may not be able to provide conclusive evidence on the links between water hardness and cardiovascular mortality unless very large populations are studied. Investigations of individuals may be more informative.
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Incorporating Case Studies into a World Food and Population Course
ERIC Educational Resources Information Center
Econopouly, Bethany F.; Byrne, Patrick F.; Johnson, Marc A.
2010-01-01
The use of case studies in college courses can increase student engagement with the subject matter and improve analytical, problem-solving, and communication skills. Case studies were introduced in a relatively large (54 students) undergraduate world food and population course at Colorado State University in the spring semester of 2008 and…
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Implementation of a national near-road NO2 monitoring network--conference
In recent years, a large number of health studies have identified increased risks of adverse health effects for populations spending significant time near major roads. These studies indicate that populations living, working or going to school near major roads may be subjected to ...
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Prevalence of chronic atrophic gastritis in different parts of the world.
Weck, Melanie Nicole; Brenner, Hermann
2006-06-01
Chronic atrophic gastritis (CAG) is a well-established precursor of intestinal gastric cancer, but epidemiologic data about its occurrence are sparse. We provide an overview on studies that examined the prevalence of CAG in different parts of the world. Articles containing data about the prevalence of chronic atrophic gastritis in unselected population samples and published until November 2005 were identified by searching the MEDLINE database. Furthermore, the references in the identified publications were screened for additional suitable studies. Studies comprising at least 50 subjects were included. Forty-one studies providing data on the prevalence of CAG in unselected population samples could be identified. CAG was determined by gastroscopy in 15 studies and by pepsinogen serum levels in 26 studies. Although results are difficult to compare due to the various definitions of CAG used, a strong increase with age, the lack of major gender differences, and strong variations between populations and population groups (in particular, relatively high rates in certain Asian populations) could be observed quite consistently. We conclude that CAG is relatively common among older adults in different parts of the world, but large variations exist. Large-scale international comparative studies with standardized methodology to determine CAG are needed to provide a coherent picture of the epidemiology of CAG in various populations. Noninvasive measurements of CAG by pepsinogen levels may be particularly suited for that purpose.
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Measurement of macular pigment optical density in a healthy chinese population sample
USDA-ARS?s Scientific Manuscript database
Macular pigment may protect against age-related macular degeneration (AMD) by its capability to absorb blue light and scavenge free radicals. Current information on human macular pigment density has been largely from studies on Caucasians populations. The purpose of this study was to assess macular ...
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How Large Should a Statistical Sample Be?
ERIC Educational Resources Information Center
Menil, Violeta C.; Ye, Ruili
2012-01-01
This study serves as a teaching aid for teachers of introductory statistics. The aim of this study was limited to determining various sample sizes when estimating population proportion. Tables on sample sizes were generated using a C[superscript ++] program, which depends on population size, degree of precision or error level, and confidence…
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An Investigation of Student Psychological Wellbeing: Honors versus Nonhonors Undergraduate Education
ERIC Educational Resources Information Center
Plominski, Abigail P.; Burns, Lawrence R.
2018-01-01
The purpose of this study was to describe the current state of psychological wellbeing in gifted and nongifted undergraduate student sample populations and identify undergraduate populations experiencing heightened levels of distress within a large Midwestern public university. Study participants included 641 honors and 386 nonhonors undergraduate…
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Elhassan, Nuha; Gebremeskel, Eyoab Iyasu; Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E
2014-01-01
Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.
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African genetic diversity provides novel insights into evolutionary history and local adaptations.
Choudhury, Ananyo; Aron, Shaun; Sengupta, Dhriti; Hazelhurst, Scott; Ramsay, Michèle
2018-05-08
Genetic variation and susceptibility to disease are shaped by human demographic history. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about the origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unraveling the critical role of events like migration and admixture and environment factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa is providing historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.
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Fraser, Dylan J; Calvert, Anna M; Bernatchez, Louis; Coon, Andrew
2013-01-01
The potential of genetic, genomic, and phenotypic metrics for monitoring population trends may be especially high in isolated regions, where traditional demographic monitoring is logistically difficult and only sporadic sampling is possible. This potential, however, is relatively underexplored empirically. Over eleven years, we assessed several such metrics along with traditional ecological knowledge and catch data in a socioeconomically important trout species occupying a large, remote lake. The data revealed largely stable characteristics in two populations over 2–3 generations, but possible contemporary changes in a third population. These potential shifts were suggested by reduced catch rates, reduced body size, and changes in selection implied at one gene-associated single nucleotide polymorphism. A demographic decline in this population, however, was ambiguously supported, based on the apparent lack of temporal change in effective population size, and corresponding traditional knowledge suggesting little change in catch. We illustrate how the pluralistic approach employed has practicality for setting future monitoring efforts of these populations, by guiding monitoring priorities according to the relative merits of different metrics and availability of resources. Our study also considers some advantages and disadvantages to adopting a pluralistic approach to population monitoring where demographic data are not easily obtained. PMID:24455128
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Representation matters: quantitative behavioral variation in wild worm strains
NASA Astrophysics Data System (ADS)
Brown, Andre
Natural genetic variation in populations is the basis of genome-wide association studies, an approach that has been applied in large studies of humans to study the genetic architecture of complex traits including disease risk. Of course, the traits you choose to measure determine which associated genes you discover (or miss). In large-scale human studies, the measured traits are usually taken as a given during the association step because they are expensive to collect and standardize. Working with the nematode worm C. elegans, we do not have the same constraints. In this talk I will describe how large-scale imaging of worm behavior allows us to develop alternative representations of behavior that vary differently across wild populations. The alternative representations yield novel traits that can be used for genome-wide association studies and may reveal basic properties of the genotype-phenotype map that are obscured if only a small set of fixed traits are used.
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Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference
Shringarpure, Suyash; Xing, Eric P.
2014-01-01
Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351
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Spatial and temporal aspects of the genetic structure of Juniperus communis populations.
Merwe, M V; Winfield, M O; Arnold, G M; Parker, J S
2000-04-01
Juniperus communis is a dioecious, wind pollinated shrub or small tree that produces 'berries' (female cones) containing a small number of seeds that are thought to be dispersed by birds. The expectation, therefore, would be that populations of Juniper are genetically diverse with little structuring between them. In Britain, the species has two main centres of distribution: a highland zone in the north and west, in which populations are still large and sexually reproducing, and a southern zone on chalk downlands in which populations are small and fragmented and individuals suffer from a decline in fertility. Thus, one would expect the large sexually viable populations in the north to exhibit high levels of within-population genetic variation, while the declining southern populations would be genetically depauperate. The analysis of amplified fragment length polymorphisms (AFLPs) was used to test this hypothesis. Surprisingly, all populations studied showed high levels of genetic variation although there was clear structuring between populations. On the basis of the geographical structuring of the populations it was hypothesized that J. communis colonized Britain via three separate routes.
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Reconstructing a Large-Scale Population for Social Simulation
NASA Astrophysics Data System (ADS)
Fan, Zongchen; Meng, Rongqing; Ge, Yuanzheng; Qiu, Xiaogang
The advent of social simulation has provided an opportunity to research on social systems. More and more researchers tend to describe the components of social systems in a more detailed level. Any simulation needs the support of population data to initialize and implement the simulation systems. However, it's impossible to get the data which provide full information about individuals and households. We propose a two-step method to reconstruct a large-scale population for a Chinese city according to Chinese culture. Firstly, a baseline population is generated through gathering individuals into households one by one; secondly, social relationships such as friendship are assigned to the baseline population. Through a case study, a population of 3,112,559 individuals gathered in 1,133,835 households is reconstructed for Urumqi city, and the results show that the generated data can respect the real data quite well. The generated data can be applied to support modeling of some social phenomenon.
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Rochus, Christina Marie; Tortereau, Flavie; Plisson-Petit, Florence; Restoux, Gwendal; Moreno-Romieux, Carole; Tosser-Klopp, Gwenola; Servin, Bertrand
2018-01-23
One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs. Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species ("selection hotspots") including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds. Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.
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An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution
Birkner, Matthias; Blath, Jochen; Eldon, Bjarki
2013-01-01
A large offspring-number diploid biparental multilocus population model of Moran type is our object of study. At each time step, a pair of diploid individuals drawn uniformly at random contributes offspring to the population. The number of offspring can be large relative to the total population size. Similar “heavily skewed” reproduction mechanisms have been recently considered by various authors (cf. e.g., Eldon and Wakeley 2006, 2008) and reviewed by Hedgecock and Pudovkin (2011). Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can coalesce only when in distinct individuals. A separation-of-timescales phenomenon is thus observed. A result of Möhle (1998) is extended to obtain convergence of the ancestral process to an ancestral recombination graph necessarily admitting simultaneous multiple mergers of ancestral lineages. The usual ancestral recombination graph is obtained as a special case of our model when the parents contribute only one offspring to the population each time. Due to diploidy and large offspring numbers, novel effects appear. For example, the marginal genealogy at each locus admits simultaneous multiple mergers in up to four groups, and different loci remain substantially correlated even as the recombination rate grows large. Thus, genealogies for loci far apart on the same chromosome remain correlated. Correlation in coalescence times for two loci is derived and shown to be a function of the coalescence parameters of our model. Extending the observations by Eldon and Wakeley (2008), predictions of linkage disequilibrium are shown to be functions of the reproduction parameters of our model, in addition to the recombination rate. Correlations in ratios of coalescence times between loci can be high, even when the recombination rate is high and sample size is large, in large offspring-number populations, as suggested by simulations, hinting at how to distinguish between different population models. PMID:23150600
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Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data
Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; da Câmara Machado, Artur; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Røed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; M. Wade, Claire; McCue, Molly E.
2013-01-01
Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. PMID:23383025
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Cheetahs and wild dogs show contrasting patterns of suppression by lions.
Swanson, Alexandra; Caro, Tim; Davies-Mostert, Harriet; Mills, Michael G L; Macdonald, David W; Borner, Markus; Masenga, Emmanuel; Packer, Craig
2014-11-01
Top predators can dramatically suppress populations of smaller predators, with cascading effects throughout communities, and this pressure is often unquestioningly accepted as a constraint on mesopredator populations. In this study, we reassess whether African lions suppress populations of cheetahs and African wild dogs and examine possible mechanisms for coexistence between these species. Using long-term records from Serengeti National Park, we tested 30 years of population data for evidence of mesopredator suppression, and we examined six years of concurrent radio-telemetry data for evidence of large-scale spatial displacement. The Serengeti lion population nearly tripled between 1966 and 1998; during this time, wild dogs declined but cheetah numbers remained largely unchanged. Prior to their local extinction, wild dogs primarily occupied low lion density areas and apparently abandoned the long-term study area as the lion population 'saturated' the region. In contrast, cheetahs mostly utilized areas of high lion density, and the stability of the cheetah population indicates that neither high levels of lion-inflicted mortality nor behavioural avoidance inflict sufficient demographic consequences to translate into population-level effects. Population data from fenced reserves in southern Africa revealed a similar contrast between wild dogs and cheetahs in their ability to coexist with lions. These findings demonstrate differential responses of subordinate species within the same guild and challenge a widespread perception that lions undermine cheetah conservation efforts. Paired with several recent studies that document fine-scale lion-avoidance by cheetahs, this study further highlights fine-scale spatial avoidance as a possible mechanism for mitigating mesopredator suppression. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.
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Genetic Classification of Populations Using Supervised Learning
Bridges, Michael; Heron, Elizabeth A.; O'Dushlaine, Colm; Segurado, Ricardo; Morris, Derek; Corvin, Aiden; Gill, Michael; Pinto, Carlos
2011-01-01
There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case–control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available. In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies. PMID:21589856
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Trends in Medication Treatment for ADHD
ERIC Educational Resources Information Center
Castle, Lon; Aubert, Ronald E.; Verbrugge, Robert R.; Khalid, Mona; Epstein, Robert S.
2007-01-01
Objective: This study examines demographic trends in the use of medications to treat ADHD in adult and pediatric populations. Method: Using pharmacy claims data for a large population of commercially insured Americans, the study measures ADHD treatment prevalence and drug use from 2000 to 2005. Results: In 2005, 4.4% of children (ages 0 to 19) and…
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Carl, L.M.
2008-01-01
The objective of the study was to test the hypothesis that lake trout populations change in relation to cisco, lake whitefish, round whitefish and burbot populations in lakes in the Algonquin Highlands region of Ontario. Lake trout population change is greatest where cisco and lake whitefish are present. Lake trout populations in lakes without either coregonine tend to have small adults and many juveniles. Where cisco or lake whitefish are present, adult lake trout are large, juvenile abundance is low, and the stock-recruit relationship appears to be uncoupled likely due to a larval bottleneck. Lake trout populations in these lakes may be sensitive to overfishing and recruitment failure. Lake trout populations do not appear to change in relation to round whitefish. There appears to be an indirect positive change on juvenile lake trout abundance through reductions in the density of benthic coregonines in the presence of large, hypolimnetic burbot. ?? 2007 Springer Science+Business Media B.V.
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USDA-ARS?s Scientific Manuscript database
The stable fly, Stomoxys calcitrans L., is a cosmopolitan, major pest of livestock. Previous studies on this insect, from samples within the United States, suggested a large amount of gene flow; more genetic variation was detected within populations than between populations. To compare the genetic v...
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A Case Study: Bilingualism - The Link to International Trade in Miami.
ERIC Educational Resources Information Center
Cote, Andre; Cote, Ellyn
The metropolitan Miami area is a thriving bilingual community that uniquely exemplifies the utility of Spanish for business careers. Miami is unique in its large Latin population, the success of this population, and the proximity of Miami to the Caribbean and Latin American markets. The impact of the Latin population of Miami on education and…
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Software engineering the mixed model for genome-wide association studies on large samples
USDA-ARS?s Scientific Manuscript database
Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample siz...
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Hirota, Tadao; Hirohata, Tetsuo; Mashima, Hiroshi; Satoh, Toshiyuki; Obara, Yoshiaki
2004-11-01
Genetic structure of the large Japanese field mouse populations in suburban landscape of West Tokyo, Japan was determined using mitochondrial DNA control region sequence. Samples were collected from six habitats linked by forests and green tract along the Tama River, and from two forests segregated by urban areas from those continuous habitats. Thirty-five haplotypes were detected in 221 animals. Four to eight haplotypes were found within each local population belonging to the continuous landscape. Some haplotypes were shared by two or three adjacent local populations. On the other hand, two isolated habitats were occupied by one or two indigenous haplotypes. Significant genetic differentiation between all pairs of local populations, except for one pair in the continuous habitats, was found by analysis of molecular variance (amova). The geographical distance between habitats did not explain the large variance of pairwise F(ST)-values among local populations. F(ST)-values between local populations segregated by urban areas were higher than those between local populations in the continuous habitat, regardless of geographical distance. The results of this study demonstrated quantitatively that urban areas inhibit the migration of Apodemus speciosus, whereas a linear green tract along a river functions as a corridor. Moreover, it preserves the metapopulation structure of A. speciosus as well as the corridors in suburban landscape.
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Population size effects in evolutionary dynamics on neutral networks and toy landscapes
NASA Astrophysics Data System (ADS)
Sumedha; Martin, Olivier C.; Peliti, Luca
2007-05-01
We study the dynamics of a population subject to selective pressures, evolving either on RNA neutral networks or on toy fitness landscapes. We discuss the spread and the neutrality of the population in the steady state. Different limits arise depending on whether selection or random drift is dominant. In the presence of strong drift we show that the observables depend mainly on Mμ, M being the population size and μ the mutation rate, while corrections to this scaling go as 1/M: such corrections can be quite large in the presence of selection if there are barriers in the fitness landscape. Also we find that the convergence to the large-Mμ limit is linear in 1/Mμ. Finally we introduce a protocol that minimizes drift; then observables scale like 1/M rather than 1/(Mμ), allowing one to determine the large-M limit more quickly when μ is small; furthermore the genotypic diversity increases from O(lnM) to O(M).
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Monte Carlo simulations of parapatric speciation
NASA Astrophysics Data System (ADS)
Schwämmle, V.; Sousa, A. O.; de Oliveira, S. M.
2006-06-01
Parapatric speciation is studied using an individual-based model with sexual reproduction. We combine the theory of mutation accumulation for biological ageing with an environmental selection pressure that varies according to the individuals geographical positions and phenotypic traits. Fluctuations and genetic diversity of large populations are crucial ingredients to model the features of evolutionary branching and are intrinsic properties of the model. Its implementation on a spatial lattice gives interesting insights into the population dynamics of speciation on a geographical landscape and the disruptive selection that leads to the divergence of phenotypes. Our results suggest that assortative mating is not an obligatory ingredient to obtain speciation in large populations at low gene flow.
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Megaregion freight movements : a case study of the Texas Triangle.
DOT National Transportation Integrated Search
2011-09-01
U.S. population growth is predicted to substantially increase over the next 40 years, particularly in areas with large regional economies forecasted to contain over two-thirds of the national economic activity. In Texas, population growth from 2000 t...
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Mega-region freight movements : a case study of the Texas triangle.
DOT National Transportation Integrated Search
2011-09-01
U.S. population growth is predicted to substantially increase over the next 40 years, particularly in areas : with large regional economies forecasted to contain over two-thirds of the national economic activity. In : Texas, population growth from 20...
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ERIC Educational Resources Information Center
Schmidt, Michael D.; Blizzard, C. Leigh; Venn, Alison J.; Cochrane, Jennifer A.; Dwyer, Terence
2007-01-01
The aim of this study was to summarize both practical and methodological issues in using pedometers to assess physical activity in a large epidemiologic study. As part of a population-based survey of cardiovascular disease risk factors, physical activity was assessed using pedometers and activity diaries in 775 men and women ages 25-64 years who…
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ERIC Educational Resources Information Center
Bhaumik, S.; Watson, J. M.; Thorp, C. F.; Tyrer, F.; McGrother, C. W.
2008-01-01
Background: Previous studies of weight problems in adults with intellectual disability (ID) have generally been small or selective and given conflicting results. The objectives of our large-scale study were to identify inequalities in weight problems between adults with ID and the general adult population, and to investigate factors associated…
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Clark, Deborah J.; Clark, Thomas O.; Duniway, Michael C.; Flagg, Cody B.
2015-01-01
Population dynamics and effects of large ungulate disturbances on Winkler cactus (Pediocactus winkleri K.D. Heil) were documented annually over a 20-year time span at one plot within Capitol Reef National Park, Utah. This cactus species was federally listed as threatened in 1998. The study began in 1995 to gain a better understanding of life history aspects and threats to this species. Data were collected annually in early spring and included diameter, condition, reproductive structures, mortality, recruitment, and disturbance by large ungulates. We used odds ratio and probability model analyses to determine effects of large ungulate trampling and weather on these cacti. During the study, plot population declined by 18%, with trampling of cactus, low precipitation, and cold spring temperatures implicated as causal factors. Precipitation and temperature affected flowering, mortality, and recruitment. Large ungulate disturbances increased mortality and reduced the probability of flowering. These results suggest that large ungulate disturbances and recent climate regimes have had an adverse impact on long-term persistence of this cactus.
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Kleindorfer, Dawn O; Khoury, Jane; Moomaw, Charles J; Alwell, Kathleen; Woo, Daniel; Flaherty, Matthew L; Khatri, Pooja; Adeoye, Opeolu; Ferioli, Simona; Broderick, Joseph P; Kissela, Brett M
2010-07-01
Although other studies (in largely white populations) have found that stroke incidence declined during the 1990s, we previously reported that stroke incidence in our population (18% of which was black) did not change during that decade and that incidence rates in blacks were significantly higher than in whites. We sought to update temporal trends in stroke incidence by adding new data obtained from our large, biracial population in 2005. The objective of this study was to examine temporal trends in stroke incidence and case-fatality within a large biracial population over time by comparing stroke incidence rates from 1993 to 1994, 1999, and 2005. Within the Greater Cincinnati/Northern Kentucky population of 1.3 million, all strokes among area residents were ascertained at all local hospitals during July 1993 to June 19/94 and calendar years 1999 and 2005. A sampling scheme was used to ascertain cases in the out-of-hospital setting. Only first-ever strokes were included in this analysis. Race-specific incidence rates, standardized to the 2000 US Census population, and case-fatality rates were calculated. The number of physician-confirmed first-ever strokes in patients >or=20 years of age was 1942 in 1993 to 1994, 2041 in 1999, and 1921 in 2005. In all study periods, blacks had higher stroke incidence than whites, and case-fatality rates were similar between races. In contrast to previous study periods, we found a significant decrease in overall stroke incidence in 2005. When stratified by race and stroke subtype, this change was driven by a decrease in ischemic stroke incidence among whites, whereas ischemic stroke incidence in blacks was unchanged. Hemorrhagic stroke incidence was unchanged in both races. For the first time, we report a significant decrease in stroke incidence within our population, which is consistent with other reports in the literature. This decrease was found only among whites, which suggests a worsening of the racial disparity in stroke incidence.
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Wang, Guiming; Hobbs, N Thompson; Galbraith, Hector; Giesen, Kenneth M
2002-09-01
Global climate change may impact wildlife populations by affecting local weather patterns, which, in turn, can impact a variety of ecological processes. However, it is not clear that local variations in ecological processes can be explained by large-scale patterns of climate. The North Atlantic oscillation (NAO) is a large-scale climate phenomenon that has been shown to influence the population dynamics of some animals. Although effects of the NAO on vertebrate population dynamics have been studied, it remains uncertain whether it broadly predicts the impact of weather on species. We examined the ability of local weather data and the NAO to explain the annual variation in population dynamics of white-tailed ptarmigan ( Lagopus leucurus) in Rocky Mountain National Park, USA. We performed canonical correlation analysis on the demographic subspace of ptarmigan and local-climate subspace defined by the empirical orthogonal function (EOF) using data from 1975 to 1999. We found that two subspaces were significantly correlated on the first canonical variable. The Pearson correlation coefficient of the first EOF values of the demographic and local-climate subspaces was significant. The population density and the first EOF of local-climate subspace influenced the ptarmigan population with 1-year lags in the Gompertz model. However, the NAO index was neither related to the first two EOF of local-climate subspace nor to the first EOF of the demographic subspace of ptarmigan. Moreover, the NAO index was not a significant term in the Gompertz model for the ptarmigan population. Therefore, local climate had stronger signature on the demography of ptarmigan than did a large-scale index, i.e., the NAO index. We conclude that local responses of wildlife populations to changing climate may not be adequately explained by models that project large-scale climatic patterns.
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Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando
2017-09-01
The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population differentiation highlight the conservation value of large populations throughout the species' range, particularly in light of climate change and direct human threats.
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Zubair, Niha; Luis Ambite, Jose; Bush, William S.; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H.; Absher, Devin; Assimes, Themistocles L.; Bielinski, Suzette J.; Bottinger, Erwin P.; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W.; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A.; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J.; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H.; Martin, Lisa W.; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P.; Robinson, Jennifer; Rotter, Jerome I.; Ryckman, Kelli K.; Schreiner, Pamela J.; Stahl, Eli; Tao, Ran; Tsai, Michael Y.; Waite, Lindsay L.; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C.; Loos, Ruth J.F.; Rich, Stephen S.; Fornage, Myriam; North, Kari E.; Kooperberg, Charles; Carty, Cara L.
2016-01-01
Abstract Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. PMID:28426890
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INFERENCE FOR INDIVIDUAL-LEVEL MODELS OF INFECTIOUS DISEASES IN LARGE POPULATIONS.
Deardon, Rob; Brooks, Stephen P; Grenfell, Bryan T; Keeling, Matthew J; Tildesley, Michael J; Savill, Nicholas J; Shaw, Darren J; Woolhouse, Mark E J
2010-01-01
Individual Level Models (ILMs), a new class of models, are being applied to infectious epidemic data to aid in the understanding of the spatio-temporal dynamics of infectious diseases. These models are highly flexible and intuitive, and can be parameterised under a Bayesian framework via Markov chain Monte Carlo (MCMC) methods. Unfortunately, this parameterisation can be difficult to implement due to intense computational requirements when calculating the full posterior for large, or even moderately large, susceptible populations, or when missing data are present. Here we detail a methodology that can be used to estimate parameters for such large, and/or incomplete, data sets. This is done in the context of a study of the UK 2001 foot-and-mouth disease (FMD) epidemic.
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EVALUATING THE EFFECTS OF NEAR ROAD SOLID AND VEGETATION BARRIERS ON MSAT EXPOSURES
Public health concerns for populations living, working and going to school near high-traffic roadways has increased substantially in recent years. Air quality measurement studies indicate high pollutant concentrations can occur near these large roads, impacting population exposu...
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Coon, Andrew; Carson, Robert; Debes, Paul V.
2016-01-01
The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists. PMID:27680019
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Is urbanisation scrambling the genetic structure of human populations? A case study
Ashrafian-Bonab, Maziar; Handley, Lori Lawson; Balloux, François
2007-01-01
Recent population expansion and increased migration linked to urbanisation are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from twenty-two Iranian populations. Potential changes in genetic diversity (θ) and genetic distance (FST) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterised by massive immigration, increased θ and a large decrease in FST over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies. PMID:17106453
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PedNavigator: a pedigree drawing servlet for large and inbred populations.
Mancosu, Gianmaria; Ledda, Giuseppe; Melis, Paola M
2003-03-22
PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to 'walk' through family ties by point-and-clicking on person's symbols. The application is able to enrich the pedigree drawings with genotypic and phenotypic information taken from the underlying relational database.
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Kas'ianov, V I
2005-01-01
The paper presents the results of a study of the impact of large-scale solid waste storage on ascariasis morbidity in the population. The use of sewage sediments as an organic soil fertilizer to grow strawberries and table greens is shown to substantially increase the risk of Ascaris infection in the population. Storage of solid domestic garbage on specialized dumping grounds does not lead to mass environmental pollution with geohelminthic eggs.
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Density of large snags and logs in northern Arizona mixed-conifer and ponderosa pine forests
Joseph L. Ganey; Benjamin J. Bird; L. Scott Baggett; Jeffrey S. Jenness
2015-01-01
Large snags and logs provide important biological legacies and resources for native wildlife, yet data on populations of large snags and logs and factors influencing those populations are sparse. We monitored populations of large snags and logs in mixed-conifer and ponderosa pine (Pinus ponderosa) forests in northern Arizona from 1997 through 2012. We modeled density...
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Distribution of Usutu Virus in Germany and Its Effect on Breeding Bird Populations
Jöst, Hanna; Cadar, Daniel; Thomas, Stephanie Margarete; Bosch, Stefan; Tannich, Egbert; Becker, Norbert; Ziegler, Ute; Lachmann, Lars; Schmidt-Chanasit, Jonas
2017-01-01
Usutu virus (USUV) is an emerging mosquitoborne flavivirus with an increasing number of reports from several countries in Europe, where USUV infection has caused high avian mortality rates. However, 20 years after the first observed outbreak of USUV in Europe, there is still no reliable assessment of the large-scale impact of USUV outbreaks on bird populations. In this study, we identified the areas suitable for USUV circulation in Germany and analyzed the effects of USUV on breeding bird populations. We calculated the USUV-associated additional decline of common blackbird (Turdus merula) populations as 15.7% inside USUV-suitable areas but found no significant effect for the other 14 common bird species investigated. Our results show that the emergence of USUV is a further threat for birds in Europe and that the large-scale impact on population levels, at least for common blackbirds, must be considered. PMID:29148399
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Fixation of slightly beneficial mutations: effects of life history.
Vindenes, Yngvild; Lee, Aline Magdalena; Engen, Steinar; Saether, Bernt-Erik
2010-04-01
Recent studies of rates of evolution have revealed large systematic differences among organisms with different life histories, both within and among taxa. Here, we consider how life history may affect the rate of evolution via its influence on the fixation probability of slightly beneficial mutations. Our approach is based on diffusion modeling for a finite, stage-structured population with stochastic population dynamics. The results, which are verified by computer simulations, demonstrate that even with complex population structure just two demographic parameters are sufficient to give an accurate approximation of the fixation probability of a slightly beneficial mutation. These are the reproductive value of the stage in which the mutation first occurs and the demographic variance of the population. The demographic variance also determines what influence population size has on the fixation probability. This model represents a substantial generalization of earlier models, covering a large range of life histories.
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Chronic Physical Illness and Mental Health in Children. Results from a Large-Scale Population Study
ERIC Educational Resources Information Center
Hysing, Mari; Elgen, Irene; Gillberg, Christopher; Lie, Stein Atle; Lundervold, Astri J.
2007-01-01
Background: The aim of the present study was to evaluate the sensitivity and specificity of the Strengths and Difficulties Questionnaire (SDQ) in detecting emotional and behavioural problems among children with chronic illness (CI). Methods: Parents and teachers of a population of primary school children in Norway (n = 9430) completed a…
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ERIC Educational Resources Information Center
Walters, Carmen Hawkins
2009-01-01
Faculty facing challenges of teaching students in a post-Katrina environment used learning-centered approaches to restore educational opportunities to its populations of hurricane-displaced students, the growing population of Hispanic students, and the business community. The study sought to determine if the faculty members had made progress…
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Monitoring human exposure to urban air pollutants
Barale, R.; Barrai, I.; Sbrana, I.; Migliore, L.; Marrazzini, A.; Scarcelli, V.; Bacci, E.; Di Sibio, A.; Tessa, A.; Cocchi, L.; Lubrano, V.; Vassalle, C.; He, J.
1993-01-01
A multidisciplinary study on a general population exposed to vehicle exhaust was undertaken in Pisa in 1991. Environmental factors such as air pollution and those associated with lifestyle were studied. Meanwhile, biological and medical indicators of health condition were investigated. Chromosomal aberrations, sister chromatid exchanges (SCEs), and micronuclei in lymphocytes were included for the assessment of the genotoxic risk. Because of the large number (3800) of subjects being investigated, standardization of protocols was compulsory. The results on data reproducibility are reported. To assess the reliability of the protocol on a large scale, the population of Porto Tolle, a village located in northeast Italy, was studied and compared to a subset of the Pisa population. Preliminary results showed that probable differences between the two populations and invididuals were present in terms of SCE frequencies. The study was potentially able to detect the effects of several factors such as age, smoking, genetics, and environment. The in vitro treatment of lymphocytes with diepoxybutane confirmed the presence of more responsive individuals and permitted us to investigate the genetic predisposition to genetic damage. The possible influence of environmental factors was studied by correlation analyses with external exposure to air pollutants as well as with several lifestyle factors. PMID:8143653
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Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data
Oetjens, Matthew T.; Brown-Gentry, Kristin; Goodloe, Robert; Dilks, Holli H.; Crawford, Dana C.
2016-01-01
Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES), population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n = 14,998) were extracted from biospecimens from consented NHANES participants between 1991–1994 (NHANES III, phase 2) and 1999–2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We as the Epidemiologic Architecture for Genes Linked to Environment study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999–2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants, although less so for ethnicity. Overall, the strategies outlined here for a large epidemiologic study can be applied to other datasets accessible for genotype–phenotype studies but are sans genome-wide data. PMID:27200085
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Fedy, Bradley C.; O'Donnell, Michael; Bowen, Zachary H.
2015-01-01
Human impacts on wildlife populations are widespread and prolific and understanding wildlife responses to human impacts is a fundamental component of wildlife management. The first step to understanding wildlife responses is the documentation of changes in wildlife population parameters, such as population size. Meaningful assessment of population changes in potentially impacted sites requires the establishment of monitoring at similar, nonimpacted, control sites. However, it is often difficult to identify appropriate control sites in wildlife populations. We demonstrated use of Geographic Information System (GIS) data across large spatial scales to select biologically relevant control sites for population monitoring. Greater sage-grouse (Centrocercus urophasianus; hearafter, sage-grouse) are negatively affected by energy development, and monitoring of sage-grouse population within energy development areas is necessary to detect population-level responses. Weused population data (1995–2012) from an energy development area in Wyoming, USA, the Atlantic Rim Project Area (ARPA), and GIS data to identify control sites that were not impacted by energy development for population monitoring. Control sites were surrounded by similar habitat and were within similar climate areas to the ARPA. We developed nonlinear trend models for both the ARPA and control sites and compared long-term trends from the 2 areas. We found little difference between the ARPA and control sites trends over time. This research demonstrated an approach for control site selection across large landscapes and can be used as a template for similar impact-monitoring studies. It is important to note that identification of changes in population parameters between control and treatment sites is only the first step in understanding the mechanisms that underlie those changes. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
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Child Demographics Associated with Outcomes in a Community-Based Pivotal Response Training Program
ERIC Educational Resources Information Center
Baker-Ericzen, Mary J.; Stahmer, Aubyn C.; Burns, Amelia
2007-01-01
Although knowledge about the efficacy of treatments such as pivotal response training (PRT) for children with autism is increasing, studies of large-scale effectiveness for and transportability to diverse community populations are needed. The current study provides a large-scale preliminary assessment of (a) the effectiveness of a community-based…
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Large-scale replication and heterogeneity in Parkinson disease genetic loci
Ioannidis, John P.A.; Aasly, Jan O.; Annesi, Grazia; Brice, Alexis; Van Broeckhoven, Christine; Bertram, Lars; Bozi, Maria; Crosiers, David; Clarke, Carl; Facheris, Maurizio; Farrer, Matthew; Garraux, Gaetan; Gispert, Suzana; Auburger, Georg; Vilariño-Güell, Carles; Hadjigeorgiou, Georgios M.; Hicks, Andrew A.; Hattori, Nobutaka; Jeon, Beom; Lesage, Suzanne; Lill, Christina M.; Lin, Juei-Jueng; Lynch, Timothy; Lichtner, Peter; Lang, Anthony E.; Mok, Vincent; Jasinska-Myga, Barbara; Mellick, George D.; Morrison, Karen E.; Opala, Grzegorz; Pramstaller, Peter P.; Pichler, Irene; Park, Sung Sup; Quattrone, Aldo; Rogaeva, Ekaterina; Ross, Owen A.; Stefanis, Leonidas; Stockton, Joanne D.; Satake, Wataru; Silburn, Peter A.; Theuns, Jessie; Tan, Eng-King; Toda, Tatsushi; Tomiyama, Hiroyuki; Uitti, Ryan J.; Wirdefeldt, Karin; Wszolek, Zbigniew; Xiromerisiou, Georgia; Yueh, Kuo-Chu; Zhao, Yi; Gasser, Thomas; Maraganore, Demetrius; Krüger, Rejko
2012-01-01
Objective: Eleven genetic loci have reached genome-wide significance in a recent meta-analysis of genome-wide association studies in Parkinson disease (PD) based on populations of Caucasian descent. The extent to which these genetic effects are consistent across different populations is unknown. Methods: Investigators from the Genetic Epidemiology of Parkinson's Disease Consortium were invited to participate in the study. A total of 11 SNPs were genotyped in 8,750 cases and 8,955 controls. Fixed as well as random effects models were used to provide the summary risk estimates for these variants. We evaluated between-study heterogeneity and heterogeneity between populations of different ancestry. Results: In the overall analysis, single nucleotide polymorphisms (SNPs) in 9 loci showed significant associations with protective per-allele odds ratios of 0.78–0.87 (LAMP3, BST1, and MAPT) and susceptibility per-allele odds ratios of 1.14–1.43 (STK39, GAK, SNCA, LRRK2, SYT11, and HIP1R). For 5 of the 9 replicated SNPs there was nominally significant between-site heterogeneity in the effect sizes (I2 estimates ranged from 39% to 48%). Subgroup analysis by ethnicity showed significantly stronger effects for the BST1 (rs11724635) in Asian vs Caucasian populations and similar effects for SNCA, LRRK2, LAMP3, HIP1R, and STK39 in Asian and Caucasian populations, while MAPT rs2942168 and SYT11 rs34372695 were monomorphic in the Asian population, highlighting the role of population-specific heterogeneity in PD. Conclusion: Our study allows insight to understand the distribution of newly identified genetic factors contributing to PD and shows that large-scale evaluation in diverse populations is important to understand the role of population-specific heterogeneity. Neurology® 2012;79:659–667 PMID:22786590
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Large-scale replication and heterogeneity in Parkinson disease genetic loci.
Sharma, Manu; Ioannidis, John P A; Aasly, Jan O; Annesi, Grazia; Brice, Alexis; Van Broeckhoven, Christine; Bertram, Lars; Bozi, Maria; Crosiers, David; Clarke, Carl; Facheris, Maurizio; Farrer, Matthew; Garraux, Gaetan; Gispert, Suzana; Auburger, Georg; Vilariño-Güell, Carles; Hadjigeorgiou, Georgios M; Hicks, Andrew A; Hattori, Nobutaka; Jeon, Beom; Lesage, Suzanne; Lill, Christina M; Lin, Juei-Jueng; Lynch, Timothy; Lichtner, Peter; Lang, Anthony E; Mok, Vincent; Jasinska-Myga, Barbara; Mellick, George D; Morrison, Karen E; Opala, Grzegorz; Pramstaller, Peter P; Pichler, Irene; Park, Sung Sup; Quattrone, Aldo; Rogaeva, Ekaterina; Ross, Owen A; Stefanis, Leonidas; Stockton, Joanne D; Satake, Wataru; Silburn, Peter A; Theuns, Jessie; Tan, Eng-King; Toda, Tatsushi; Tomiyama, Hiroyuki; Uitti, Ryan J; Wirdefeldt, Karin; Wszolek, Zbigniew; Xiromerisiou, Georgia; Yueh, Kuo-Chu; Zhao, Yi; Gasser, Thomas; Maraganore, Demetrius; Krüger, Rejko
2012-08-14
Eleven genetic loci have reached genome-wide significance in a recent meta-analysis of genome-wide association studies in Parkinson disease (PD) based on populations of Caucasian descent. The extent to which these genetic effects are consistent across different populations is unknown. Investigators from the Genetic Epidemiology of Parkinson's Disease Consortium were invited to participate in the study. A total of 11 SNPs were genotyped in 8,750 cases and 8,955 controls. Fixed as well as random effects models were used to provide the summary risk estimates for these variants. We evaluated between-study heterogeneity and heterogeneity between populations of different ancestry. In the overall analysis, single nucleotide polymorphisms (SNPs) in 9 loci showed significant associations with protective per-allele odds ratios of 0.78-0.87 (LAMP3, BST1, and MAPT) and susceptibility per-allele odds ratios of 1.14-1.43 (STK39, GAK, SNCA, LRRK2, SYT11, and HIP1R). For 5 of the 9 replicated SNPs there was nominally significant between-site heterogeneity in the effect sizes (I(2) estimates ranged from 39% to 48%). Subgroup analysis by ethnicity showed significantly stronger effects for the BST1 (rs11724635) in Asian vs Caucasian populations and similar effects for SNCA, LRRK2, LAMP3, HIP1R, and STK39 in Asian and Caucasian populations, while MAPT rs2942168 and SYT11 rs34372695 were monomorphic in the Asian population, highlighting the role of population-specific heterogeneity in PD. Our study allows insight to understand the distribution of newly identified genetic factors contributing to PD and shows that large-scale evaluation in diverse populations is important to understand the role of population-specific heterogeneity.
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Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.
2013-01-01
In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.
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Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India.
Chinniah, Rathika; Vijayan, Murali; Thirunavukkarasu, Manikandan; Mani, Dhivakar; Raju, Kamaraj; Ravi, Padma Malini; Sivanadham, Ramgopal; C, Kandeepan; N, Mahalakshmi; Karuppiah, Balakrishnan
2016-01-01
Seven human-specific Alu markers were studied in 574 unrelated individuals from 10 endogamous groups and 2 hill tribes of Tamil Nadu and Kerala states. DNA was isolated, amplified by PCR-SSP, and subjected to agarose gel electrophoresis, and genotypes were assigned for various Alu loci. Average heterozygosity among caste populations was in the range of 0.292-0.468. Among tribes, the average heterozygosity was higher for Paliyan (0.3759) than for Kani (0.2915). Frequency differences were prominent in all loci studied except Alu CD4. For Alu CD4, the frequency was 0.0363 in Yadavas, a traditional pastoral and herd maintaining population, and 0.2439 in Narikuravars, a nomadic gypsy population. The overall genetic difference (Gst) of 12 populations (castes and tribes) studied was 3.6%, which corresponds to the Gst values of 3.6% recorded earlier for Western Asian populations. Thus, our study confirms the genetic similarities between West Asian populations and South Indian castes and tribes and supported the large scale coastal migrations from Africa into India through West Asia. However, the average genetic difference (Gst) of Kani and Paliyan tribes with other South Indian tribes studied earlier was 8.3%. The average Gst of combined South and North Indian Tribes (CSNIT) was 9.5%. Neighbor joining tree constructed showed close proximity of Kani and Paliyan tribal groups to the other two South Indian tribes, Toda and Irula of Nilgiri hills studied earlier. Further, the analysis revealed the affinities among populations and confirmed the presence of North and South India specific lineages. Our findings have documented the highly diverse (micro differentiated) nature of South Indian tribes, predominantly due to isolation, than the endogamous population groups of South India. Thus, our study firmly established the genetic relationship of South Indian castes and tribes and supported the proposed large scale ancestral migrations from Africa, particularly into South India through West Asian corridor.
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Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India
Chinniah, Rathika; Vijayan, Murali; Thirunavukkarasu, Manikandan; Mani, Dhivakar; Raju, Kamaraj; Ravi, Padma Malini; Sivanadham, Ramgopal; C, Kandeepan; N, Mahalakshmi; Karuppiah, Balakrishnan
2016-01-01
Seven human-specific Alu markers were studied in 574 unrelated individuals from 10 endogamous groups and 2 hill tribes of Tamil Nadu and Kerala states. DNA was isolated, amplified by PCR-SSP, and subjected to agarose gel electrophoresis, and genotypes were assigned for various Alu loci. Average heterozygosity among caste populations was in the range of 0.292–0.468. Among tribes, the average heterozygosity was higher for Paliyan (0.3759) than for Kani (0.2915). Frequency differences were prominent in all loci studied except Alu CD4. For Alu CD4, the frequency was 0.0363 in Yadavas, a traditional pastoral and herd maintaining population, and 0.2439 in Narikuravars, a nomadic gypsy population. The overall genetic difference (Gst) of 12 populations (castes and tribes) studied was 3.6%, which corresponds to the Gst values of 3.6% recorded earlier for Western Asian populations. Thus, our study confirms the genetic similarities between West Asian populations and South Indian castes and tribes and supported the large scale coastal migrations from Africa into India through West Asia. However, the average genetic difference (Gst) of Kani and Paliyan tribes with other South Indian tribes studied earlier was 8.3%. The average Gst of combined South and North Indian Tribes (CSNIT) was 9.5%. Neighbor joining tree constructed showed close proximity of Kani and Paliyan tribal groups to the other two South Indian tribes, Toda and Irula of Nilgiri hills studied earlier. Further, the analysis revealed the affinities among populations and confirmed the presence of North and South India specific lineages. Our findings have documented the highly diverse (micro differentiated) nature of South Indian tribes, predominantly due to isolation, than the endogamous population groups of South India. Thus, our study firmly established the genetic relationship of South Indian castes and tribes and supported the proposed large scale ancestral migrations from Africa, particularly into South India through West Asian corridor. PMID:27315142
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Fant, Charles; Schlosser, C Adam; Gao, Xiang; Strzepek, Kenneth; Reilly, John
2016-01-01
The sustainability of future water resources is of paramount importance and is affected by many factors, including population, wealth and climate. Inherent in current methods to estimate these factors in the future is the uncertainty of their prediction. In this study, we integrate a large ensemble of scenarios--internally consistent across economics, emissions, climate, and population--to develop a risk portfolio of water stress over a large portion of Asia that includes China, India, and Mainland Southeast Asia in a future with unconstrained emissions. We isolate the effects of socioeconomic growth from the effects of climate change in order to identify the primary drivers of stress on water resources. We find that water needs related to socioeconomic changes, which are currently small, are likely to increase considerably in the future, often overshadowing the effect of climate change on levels of water stress. As a result, there is a high risk of severe water stress in densely populated watersheds by 2050, compared to recent history. There is strong evidence to suggest that, in the absence of autonomous adaptation or societal response, a much larger portion of the region's population will live in water-stressed regions in the near future. Tools and studies such as these can effectively investigate large-scale system sensitivities and can be useful in engaging and informing decision makers.
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Genetic rescue of an insular population of large mammals
Hogg, John T; Forbes, Stephen H; Steele, Brian M; Luikart, Gordon
2006-01-01
Natural populations worldwide are increasingly fragmented by habitat loss. Isolation at small population size is thought to reduce individual and population fitness via inbreeding depression. However, little is known about the time-scale over which adverse genetic effects may develop in natural populations or the number and types of traits likely to be affected. The benefits of restoring gene flow to isolates are therefore also largely unknown. In contrast, the potential costs of migration (e.g. disease spread) are readily apparent. Management for ecological connectivity has therefore been controversial and sometimes avoided. Using pedigree and life-history data collected during 25 years of study, we evaluated genetic decline and rescue in a population of bighorn sheep founded by 12 individuals in 1922 and isolated at an average size of 42 animals for 10–12 generations. Immigration was restored experimentally, beginning in 1985. We detected marked improvements in reproduction, survival and five fitness-related traits among descendants of the 15 recent migrants. Trait values were increased by 23–257% in maximally outbred individuals. This is the first demonstration, to our knowledge, of increased male and female fitness attributable to outbreeding realized in a fully competitive natural setting. Our findings suggest that genetic principles deserve broader recognition as practical management tools with near-term consequences for large-mammal conservation. PMID:16777743
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Fedy, B.C.; Doherty, K.E.
2011-01-01
Animal species across multiple taxa demonstrate multi-annual population cycles, which have long been of interest to ecologists. Correlated population cycles between species that do not share a predator-prey relationship are particularly intriguing and challenging to explain. We investigated annual population trends of greater sage-grouse (Centrocercus urophasianus) and cottontail rabbits (Sylvilagus sp.) across Wyoming to explore the possibility of correlations between unrelated species, over multiple cycles, very large spatial areas, and relatively southern latitudes in terms of cycling species. We analyzed sage-grouse lek counts and annual hunter harvest indices from 1982 to 2007. We show that greater sage-grouse, currently listed as warranted but precluded under the US Endangered Species Act, and cottontails have highly correlated cycles (r = 0. 77). We explore possible mechanistic hypotheses to explain the synchronous population cycles. Our research highlights the importance of control populations in both adaptive management and impact studies. Furthermore, we demonstrate the functional value of these indices (lek counts and hunter harvest) for tracking broad-scale fluctuations in the species. This level of highly correlated long-term cycling has not previously been documented between two non-related species, over a long time-series, very large spatial scale, and within more southern latitudes. ?? 2010 US Government.
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Burel, Julie G; Qian, Yu; Lindestam Arlehamn, Cecilia; Weiskopf, Daniela; Zapardiel-Gonzalo, Jose; Taplitz, Randy; Gilman, Robert H; Saito, Mayuko; de Silva, Aruna D; Vijayanand, Pandurangan; Scheuermann, Richard H; Sette, Alessandro; Peters, Bjoern
2017-02-15
In the context of large-scale human system immunology studies, controlling for technical and biological variability is crucial to ensure that experimental data support research conclusions. In this study, we report on a universal workflow to evaluate both technical and biological variation in multiparameter flow cytometry, applied to the development of a 10-color panel to identify all major cell populations and T cell subsets in cryopreserved PBMC. Replicate runs from a control donation and comparison of different gating strategies assessed the technical variability associated with each cell population and permitted the calculation of a quality control score. Applying our panel to a large collection of PBMC samples, we found that most cell populations showed low intraindividual variability over time. In contrast, certain subpopulations such as CD56 T cells and Temra CD4 T cells were associated with high interindividual variability. Age but not gender had a significant effect on the frequency of several populations, with a drastic decrease in naive T cells observed in older donors. Ethnicity also influenced a significant proportion of immune cell population frequencies, emphasizing the need to account for these covariates in immune profiling studies. We also exemplify the usefulness of our workflow by identifying a novel cell-subset signature of latent tuberculosis infection. Thus, our study provides a universal workflow to establish and evaluate any flow cytometry panel in systems immunology studies. Copyright © 2017 by The American Association of Immunologists, Inc.
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NASA Astrophysics Data System (ADS)
Iida, Taichi; Soga, Masashi; Koike, Shinsuke
2018-04-01
Dramatic increases in populations of large mammalian herbivores have become a major ecological issue, particularly in the northern hemisphere, due to their substantial impacts on both animal and plant communities through processes such as grazing, browsing, and trampling. However, little is known about the consequences of these population explosions on ecosystem functions. Here, we experimentally investigated how the population density of sika deer (Cervus nippon) in temperate deciduous forest areas in Japan affected the decomposition of mammal dung by dung beetles, which is a key process in forest ecosystems. We measured a range of environmental variables (e.g., vegetation cover, soil hardness) and the dung decomposition rate, measured as the amount of deer dung decomposed during one week, and sampled dung beetles at 16 study sites with three different deer densities (high/intermediate/low). We then used structural equation modeling to investigate the relationships between deer density, environmental variables, the biomass of dung beetles (classified into small or large species), and the dung decomposition rate. We found that the biomass of small species increased with increasing deer density, whereas that of large species was not related to deer density. Furthermore, the dung decomposition rate was positively related to the biomass of small species but unrelated to that of large species. Overall, our results showed that an increase in deer density affects the decomposition rate of mammal dung by changing the structure of dung beetle communities (i.e., increasing the number of small dung beetles). Such an understanding of how increases in large herbivore populations affect ecosystem functions is important for accurately evaluating the ecological consequences of their overabundance and ultimately managing their populations appropriately.
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Daniell, Nathan; Fraysse, François; Paul, Gunther
2012-01-01
Anthropometry has long been used for a range of ergonomic applications & product design. Although products are often designed for specific cohorts, anthropometric data are typically sourced from large scale surveys representative of the general population. Additionally, few data are available for emerging markets like China and India. This study measured 80 Chinese males that were representative of a specific cohort targeted for the design of a new product. Thirteen anthropometric measurements were recorded and compared to two large databases that represented a general population, a Chinese database and a Western database. Substantial differences were identified between the Chinese males measured in this study and both databases. The subjects were substantially taller, heavier and broader than subjects in the older Chinese database. However, they were still substantially smaller, lighter and thinner than Western males. Data from current Western anthropometric surveys are unlikely to accurately represent the target population for product designers and manufacturers in emerging markets like China.
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Spatial and temporal synchrony in reptile population dynamics in variable environments.
Greenville, Aaron C; Wardle, Glenda M; Nguyen, Vuong; Dickman, Chris R
2016-10-01
Resources are seldom distributed equally across space, but many species exhibit spatially synchronous population dynamics. Such synchrony suggests the operation of large-scale external drivers, such as rainfall or wildfire, or the influence of oasis sites that provide water, shelter, or other resources. However, testing the generality of these factors is not easy, especially in variable environments. Using a long-term dataset (13-22 years) from a large (8000 km(2)) study region in arid Central Australia, we tested firstly for regional synchrony in annual rainfall and the dynamics of six reptile species across nine widely separated sites. For species that showed synchronous spatial dynamics, we then used multivariate follow a multivariate auto-regressive state-space (MARSS) models to predict that regional rainfall would be positively associated with their populations. For asynchronous species, we used MARSS models to explore four other possible population structures: (1) populations were asynchronous, (2) differed between oasis and non-oasis sites, (3) differed between burnt and unburnt sites, or (4) differed between three sub-regions with different rainfall gradients. Only one species showed evidence of spatial population synchrony and our results provide little evidence that rainfall synchronizes reptile populations. The oasis or the wildfire hypotheses were the best-fitting models for the other five species. Thus, our six study species appear generally to be structured in space into one or two populations across the study region. Our findings suggest that for arid-dwelling reptile populations, spatial and temporal dynamics are structured by abiotic events, but individual responses to covariates at smaller spatial scales are complex and poorly understood.
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Kleindorfer, Dawn; Khoury, Jane; Moomaw, Charles J.; Alwell, Kathleen; Woo, Daniel; Flaherty, Matthew L.; Khatri, Pooja; Adeoye, Opeolu; Ferioli, Simona; Broderick, Joseph P.; Kissela, Brett M.
2010-01-01
Context While other studies (in largely white populations) have found that stroke incidence declined during the 1990s, we previously reported that stroke incidence in our population (18% of which was black) did not change during that decade and that incidence rates in blacks were significantly higher than in whites. We sought to update temporal trends in stroke incidence by adding new data obtained from our large, bi-racial population in 2005. Objective To examine temporal trends in stroke incidence and case fatality within a large, biracial population over time, by comparing stroke incidence rates from 1993/94, 1999, and 2005. Design, Setting, and Participants Within the Greater Cincinnati/Northern Kentucky population of 1.3 million, all strokes among area residents were ascertained at all local hospitals during 7/93-6/94 and calendar years 1999 and 2005. A sampling scheme was used to ascertain cases in the out-of-hospital setting. Only first-ever strokes were included in this analysis. Race-specific incidence rates, standardized to the 2000 U.S. Census population, and case-fatality rates were calculated. Results The number of physician-confirmed first-ever strokes in patients ≥20 years of age was 1,942 in 1993/94, 2,041 in 1999, and 1,921 in 2005. In all study periods, blacks had higher stroke incidence than whites, and case fatality rates were similar between races. In contrast to previous study periods, we found a significant decrease in overall stroke incidence in 2005. When stratified by race and stroke subtype, this change was driven by a decrease in ischemic stroke incidence among whites, while ischemic stroke incidence in blacks was unchanged. Hemorrhagic stroke incidence was unchanged in both races. Discussion For the first time, we report a significant decrease in stroke incidence within our population, which is consistent with other reports in the literature. This decrease was found only among whites, which suggests a worsening of the racial disparity in stroke incidence. PMID:20489177
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A call for tiger management using "reserves" of genetic diversity.
Bay, Rachael A; Ramakrishnan, Uma; Hadly, Elizabeth A
2014-01-01
Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.
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Ecology and population status of Northern Fulmars (Fulmarus glacialis) of the North Pacific
Hatch, Scott A.; Vermeer, Kees; Briggs, K.T.; Morgan, K.H.; Siegel-Causey, D.
1993-01-01
In the North Pacific, the breeding distribution of Northern Fulmars (Fulmarus glacialis) includes about equal numbers of very large colonies (50,000-500,000 individuals) and relatively small ones (5-5,000 individuals). The almost complete segregation of light and dark colour phases between adjacent colonies in the Bering Sea and Sea of Okhotsk suggests there is little gene flow among the major colonies. Annual productivity averaged 0.42 chicks per breeding pair in 10 years at one colony in the Gulf of Alaska; adult survival was 0.97 per year over five years at the same location. There is no clear indication of population change at either of two large colonies studied, but several small colonies in the western Aleutians and northern Gulf of Alaska have increased since the mid-1970s. Fulmars appear to have low vulnerability to oil pollution and drifting gill nets, but they are relatively heavy consumers of plastic debris. Introduced predators probably reduced fulmar populations in the past. Population monitoring is recommended for one or more of the large Pacific colonies and several of the smaller ones. Small colonies may provide early indications of changing population status.
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Pemberton, T J; Jakobsson, M; Conrad, D F; Coop, G; Wall, J D; Pritchard, J K; Patel, P I; Rosenberg, N A
2008-07-01
When performing association studies in populations that have not been the focus of large-scale investigations of haplotype variation, it is often helpful to rely on genomic databases in other populations for study design and analysis - such as in the selection of tag SNPs and in the imputation of missing genotypes. One way of improving the use of these databases is to rely on a mixture of database samples that is similar to the population of interest, rather than using the single most similar database sample. We demonstrate the effectiveness of the mixture approach in the application of African, European, and East Asian HapMap samples for tag SNP selection in populations from India, a genetically intermediate region underrepresented in genomic studies of haplotype variation.
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Coluccia, Emanuele; Gamboz, Nadia; Brandimonte, Maria A
2011-12-01
The present study aimed to provide normative data on a large sample of the elderly Italian population (N = 464; range of age = 49-94; range of education = 3-25) on both the word and the picture versions of a battery of free recall, cued recall, and recognition tests of memory. Results from multiple regression analyses showed that both age and education were significant predictors of performance. Therefore, norms were calculated taking into account these demographic variables. The availability of normative data based on a large sample will allow a more reliable use of the battery for clinical assessment in Italian-speaking dementia population.
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NASA Technical Reports Server (NTRS)
Williams, James G.
1992-01-01
Asteroid families are clusters of asteroids in proper element space which are thought to be fragments from former collisions. Studies of families promise to improve understanding of large collision events and a large event can open up the interior of a former parent body to view. While a variety of searches for families have found the same heavily populated families, and some searches have found the same families of lower population, there is much apparent disagreement between proposed families of lower population of different investigations. Indicators of reliability, factors compromising reliability, an illustration of the influence of different data samples, and a discussion of how several investigations perceived families in the same region of proper element space are given.
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Response of human populations to large-scale emergencies
NASA Astrophysics Data System (ADS)
Bagrow, James; Wang, Dashun; Barabási, Albert-László
2010-03-01
Until recently, little quantitative data regarding collective human behavior during dangerous events such as bombings and riots have been available, despite its importance for emergency management, safety and urban planning. Understanding how populations react to danger is critical for prediction, detection and intervention strategies. Using a large telecommunications dataset, we study for the first time the spatiotemporal, social and demographic response properties of people during several disasters, including a bombing, a city-wide power outage, and an earthquake. Call activity rapidly increases after an event and we find that, when faced with a truly life-threatening emergency, information rapidly propagates through a population's social network. Other events, such as sports games, do not exhibit this propagation.
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Large-scale evaluation of multimodal biometric authentication using state-of-the-art systems.
Snelick, Robert; Uludag, Umut; Mink, Alan; Indovina, Michael; Jain, Anil
2005-03-01
We examine the performance of multimodal biometric authentication systems using state-of-the-art Commercial Off-the-Shelf (COTS) fingerprint and face biometric systems on a population approaching 1,000 individuals. The majority of prior studies of multimodal biometrics have been limited to relatively low accuracy non-COTS systems and populations of a few hundred users. Our work is the first to demonstrate that multimodal fingerprint and face biometric systems can achieve significant accuracy gains over either biometric alone, even when using highly accurate COTS systems on a relatively large-scale population. In addition to examining well-known multimodal methods, we introduce new methods of normalization and fusion that further improve the accuracy.
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Ovaskainen, Otso; Smith, Alan D.; Osborne, Juliet L.; Reynolds, Don R.; Carreck, Norman L.; Martin, Andrew P.; Niitepõld, Kristjan; Hanski, Ilkka
2008-01-01
We used harmonic radar to track freely flying Glanville fritillary butterfly (Melitaea cinxia) females within an area of 30 ha. Butterflies originated from large and continuous populations in China and Estonia, and from newly established or old (> 5 years) small local populations in a highly fragmented landscape in Finland. Caterpillars were raised under common garden conditions and unmated females were tested soon after eclosion. The reconstructed flight paths for 66 individuals comprised a total distance of 51 km with high spatial resolution. Butterflies originating from large continuous populations and from old local populations in Finland exhibited similar movement behaviors, whereas butterflies originating from newly established local populations in the fragmented landscape in Finland moved significantly more than the others. There was no difference in the lengths of individual flight bouts, but the new-population females flew more frequently, resulting in longer daily movement tracks. The flight activity of all individuals was affected by environmental conditions, peaking at 19–23°C (depending on population type), in the early afternoon, and during calm weather. Butterflies from all population types showed a strong tendency to follow habitat edges between the open study area and the neighboring woodlands. PMID:19060191
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Hightower, Joseph E.; Pollock, Kenneth H.
2013-01-01
Striped bass Morone saxatilis in inland reservoirs play an important role ecologically and in supporting recreational fishing. To manage these populations, biologists need information about abundance and mortality. Abundance estimates can be used to assess the effectiveness of stocking programs that maintain most reservoir striped bass populations. Mortality estimates can indicate the relative impact of fishing versus natural mortality and the need for harvest regulation. The purpose of this chapter is to evaluate tagging studies as a way of obtaining information about abundance and mortality. These approaches can be grouped into three broad categories: tag recapture, tag return, and telemetry. Tag-recapture methods are typically used to estimate population size and other demographic parameters but are often difficult to apply in large systems. A fishing tournament can be an effective way of generating tagging or recapture effort in large systems, compared to using research sampling only. Tag-return methods that rely on angler harvest and catch and release can be used to estimate fishing (F) and natural (M) mortality rates and are a practical approach in large reservoirs. The key to success in tag-return studies is to build in auxiliary studies to estimate short-term tagging mortality, short- and longterm tag loss, reporting rate, and mortality associated with catch and release. F and M can also be estimated using telemetry tags. Advantages of this approach are that angler nonreporting does not bias estimates and fish with transmitters provide useful ecological data. Cost can be a disadvantage of telemetry studies; thus, combining telemetry tags with conventional tag returns in an integrated analysis is often the optimal approach. In summary, tagging methods can be a powerful tool for assessing the effectiveness of inland striped bass stocking programs and the relative impact of fishing versus natural mortality
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Miller, Joshua H.
2011-01-01
Natural accumulations of skeletal material (death assemblages) have the potential to provide historical data on species diversity and population structure for regions lacking decades of wildlife monitoring, thereby contributing valuable baseline data for conservation and management strategies. Previous studies of the ecological and temporal resolutions of death assemblages from terrestrial large-mammal communities, however, have largely focused on broad patterns of community composition in tropical settings. Here, I expand the environmental sampling of large-mammal death assemblages into a temperate biome and explore more demanding assessments of ecological fidelity by testing their capacity to record past population fluctuations of individual species in the well-studied ungulate community of Yellowstone National Park (Yellowstone). Despite dramatic ecological changes following the 1988 wildfires and 1995 wolf re-introduction, the Yellowstone death assemblage is highly faithful to the living community in species richness and community structure. These results agree with studies of tropical death assemblages and establish the broad capability of vertebrate remains to provide high-quality ecological data from disparate ecosystems and biomes. Importantly, the Yellowstone death assemblage also correctly identifies species that changed significantly in abundance over the last 20 to ∼80 years and the directions of those shifts (including local invasions and extinctions). The relative frequency of fresh versus weathered bones for individual species is also consistent with documented trends in living population sizes. Radiocarbon dating verifies the historical source of bones from Equus caballus (horse): a functionally extinct species. Bone surveys are a broadly valuable tool for obtaining population trends and baseline shifts over decadal-to-centennial timescales. PMID:21464921
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Tay, Alvin Kuowei; Mohsin, Mohammed; Rees, Susan; Steel, Zachary; Tam, Natalino; Soares, Zelia; Baker, Jessica; Silove, Derrick
2017-05-22
Post-traumatic stress disorder (PTSD) is the most widely assessed form of mental distress in cross-cultural studies conducted amongst populations exposed to mass conflict and displacement. Nevertheless, there have been longstanding concerns about the universality of PTSD as a diagnostic category when applied across cultures. One approach to examining this question is to assess whether the same factor structure can be identified in culturally diverse populations as has been described in populations of western societies. We examine this issue based on an analysis of the Harvard Trauma Questionnaire (HTQ) completed by a large community sample in conflict-affected Timor-Leste. Culturally adapted measures were applied to assess exposure to conflict-related traumatic events (TEs), ongoing adversities, symptoms of PTSD and psychological distress, and functional impairment amongst a large population sample (n = 2964, response rate: 82.4%) in post-conflict Timor-Leste. Confirmatory factor analyses of the ICD-10, ICD-11, DSM-IV, four-factor Emotional Numbing and five-factor Dysphoric-Arousal PTSD structures, found considerable support for all these models. Based on these classifications, concurrent validity was indicated by logistic regression analyses which showed that being a woman, trauma exposure, ongoing adversity, severe distress, and functional impairment were all associated with PTSD. Although symptom prevalence estimates varied widely based on different classifications, our study found a general agreement in PTSD assignments across contemporary diagnostic systems in a large conflict-affected population in Timor-Leste. Further studies are needed, however, to establish the construct and concurrent validity of PTSD in other cultures.
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Clarke, Kylea E; Rinderer, Thomas E; Franck, Pierre; Quezada-Euán, Javier G; Oldroyd, Benjamin P
2002-07-01
Until recently, African and European subspecies of the honeybee (Apis mellifera L.) had been geographically separated for around 10,000 years. However, human-assisted introductions have caused the mixing of large populations of African and European subspecies in South and Central America, permitting an unprecedented opportunity to study a large-scale hybridization event using molecular analyses. We obtained reference populations from Europe, Africa, and South America and used these to provide baseline information for a microsatellite and mitochondrial analysis of the process of Africanization of the bees of the Yucatan Peninsula, Mexico. The genetic structure of the Yucatecan population has changed dramatically over time. The pre-Africanized Yucatecan population (1985) comprised bees that were most similar to samples from southeastern Europe and northern and western Europe. Three years after the arrival of Africanized bees (1989), substantial paternal gene flow had occurred from feral Africanized drones into the resident European population, but maternal gene flow from the invading Africanized population into the local population was negligible. However by 1998, there was a radical shift with both African nuclear alleles (65%) and African-derived mitochondria (61%) dominating the genomes of domestic colonies. We suggest that although European mitochondria may eventually be driven to extinction in the feral population, stable introgression of European nuclear alleles has occurred.
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Valdez, Fernanda Pedone; Haag, Taiana; Azevedo, Fernando C C; Silveira, Leandro; Cavalcanti, Sandra M C; Salzano, Francisco M; Eizirik, Eduardo
2015-01-01
Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed 12 microsatellite loci to characterize genetic diversity and population structure of 52 jaguars sampled in 4 localities of the southern Pantanal, and compared them with prior studies of heavily fragmented populations of the Atlantic Forest. Although we observed some internal structure among the Pantanal localities, our results indicated that this area comprises a single population with high genetic variability. Moreover, our comparative analyses supported the hypothesis that the strong population structure observed in the Atlantic Forest derives from recent, anthropogenic fragmentation. We also observed significant but low levels of genetic differentiation between the Pantanal and Atlantic Forest populations, indicating recent connectivity between jaguars occurring in these biomes. Evidence for admixture between the Pantanal and a population on the western boundary of the Atlantic Forest corroborates the transitional nature of the latter area, where the jaguar population has already been extirpated. Our results can be used to understand jaguar population dynamics in a region that is less disturbed than the Atlantic forest, and to support the design of conservation strategies that maintain and restore natural connectivity among currently isolated areas. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Life-history and habitat features influence the within-river genetic structure of Atlantic salmon.
Vähä, Juha-Pekka; Erkinaro, Jaakko; Niemelä, Eero; Primmer, Craig R
2007-07-01
Defining populations and identifying ecological and life-history characteristics affecting genetic structure is important for understanding species biology and hence, for managing threatened or endangered species or populations. In this study, populations of the world's largest indigenous Atlantic salmon (Salmo salar) stock were first inferred using model-based clustering methods, following which life-history and habitat variables best predicting the genetic diversity of populations were identified. This study revealed that natal homing of Atlantic salmon within the Teno River system is accurate at least to the tributary level. Generally, defining populations by main tributaries was observed to be a reasonable approach in this large river system, whereas in the mainstem of the river, the number of inferred populations was fewer than the number of distinct sampling sites. Mainstem and headwater populations were genetically more diverse and less diverged, while each tributary fostered a distinct population with high genetic differentiation and lower genetic diversity. Population structure and variation in genetic diversity among populations were poorly explained by geographical distance. In contrast, age-structure, as estimated by the proportion of multisea-winter spawners, was the most predictive variable in explaining the variation in the genetic diversity of the populations. This observation, being in agreement with theoretical predictions, emphasizes the essence of large multisea-winter females in maintaining the genetic diversity of populations. In addition, the unique genetic diversity of populations, as estimated by private allele richness, was affected by the ease of accessibility of a site, with more difficult to access sites having lower unique genetic diversity. Our results show that despite this species' high capacity for migration, tributaries foster relatively closed populations with little gene flow which will be important to consider when developing management strategies for the system.
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Yu, Lin; Lu, Jianbo
2011-01-01
The Thousand-Island Lake region in Zhejiang Province, China is a highly fragmented landscape with a clear point-in-time of fragmentation as a result of flooding to form the reservoir. Islands in the artificial lake were surveyed to examine how population sex ratio of a dioecious plant specie Pistacia chinensis B. was affected by landscape fragmentation. A natural population on the mainland near the lake was also surveyed for comparison. Population size, sex ratio and diameter at breast height (DBH) of individuals were measured over 2 years. More than 1,500 individuals, distributed in 31 populations, were studied. Soil nitrogen in the different populations was measured to identify the relationship between sex ratio and micro-environmental conditions. In accordance with the results of many other reports on biased sex ratio in relation to environmental gradient, we found that poor soil nitrogen areas fostered male-biased populations. In addition, the degree of sex ratio bias increased with decreasing population size and population connectivity. The biased sex ratios were only found in younger individuals (less than 50 years old) in small populations, while a stable 1∶1 sex ratio was found in the large population on the mainland. We concluded that the effects of landscape fragmentation on the dioecious population sex ratio were mainly achieved in relation to changing soil nitrogen conditions in patches and pollen limitation within and among populations. Large populations could maintain a more suitable environment in terms of nutrient conditions and pollen flow, subsequently maintaining a stable sex ratio in dioecious plant populations. Both micro-environmental factors and spatial structure should be considered in fragmented landscape for the conservation of dioecious plant species.
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Clear: Composition of Likelihoods for Evolve and Resequence Experiments.
Iranmehr, Arya; Akbari, Ali; Schlötterer, Christian; Bafna, Vineet
2017-06-01
The advent of next generation sequencing technologies has made whole-genome and whole-population sampling possible, even for eukaryotes with large genomes. With this development, experimental evolution studies can be designed to observe molecular evolution "in action" via evolve-and-resequence (E&R) experiments. Among other applications, E&R studies can be used to locate the genes and variants responsible for genetic adaptation. Most existing literature on time-series data analysis often assumes large population size, accurate allele frequency estimates, or wide time spans. These assumptions do not hold in many E&R studies. In this article, we propose a method-composition of likelihoods for evolve-and-resequence experiments (Clear)-to identify signatures of selection in small population E&R experiments. Clear takes whole-genome sequences of pools of individuals as input, and properly addresses heterogeneous ascertainment bias resulting from uneven coverage. Clear also provides unbiased estimates of model parameters, including population size, selection strength, and dominance, while being computationally efficient. Extensive simulations show that Clear achieves higher power in detecting and localizing selection over a wide range of parameters, and is robust to variation of coverage. We applied the Clear statistic to multiple E&R experiments, including data from a study of adaptation of Drosophila melanogaster to alternating temperatures and a study of outcrossing yeast populations, and identified multiple regions under selection with genome-wide significance. Copyright © 2017 by the Genetics Society of America.
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MHC variability supports dog domestication from a large number of wolves: high diversity in Asia.
Niskanen, A K; Hagström, E; Lohi, H; Ruokonen, M; Esparza-Salas, R; Aspi, J; Savolainen, P
2013-01-01
The process of dog domestication is still somewhat unresolved. Earlier studies indicate that domestic dogs from all over the world have a common origin in Asia. So far, major histocompatibility complex (MHC) diversity has not been studied in detail in Asian dogs, although high levels of genetic diversity are expected at the domestication locality. We sequenced the second exon of the canine MHC gene DLA-DRB1 from 128 Asian dogs and compared our data with a previously published large data set of MHC alleles, mostly from European dogs. Our results show that Asian dogs have a higher MHC diversity than European dogs. We also estimated that there is only a small probability that new alleles have arisen by mutation since domestication. Based on the assumption that all of the currently known 102 DLA-DRB1 alleles come from the founding wolf population, we simulated the number of founding wolf individuals. Our simulations indicate an effective population size of at least 500 founding wolves, suggesting that the founding wolf population was large or that backcrossing has taken place.
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Cao, Ke; Zheng, Zhijun; Wang, Lirong; Liu, Xin; Zhu, Gengrui; Fang, Weichao; Cheng, Shifeng; Zeng, Peng; Chen, Changwen; Wang, Xinwei; Xie, Min; Zhong, Xiao; Wang, Xiaoli; Zhao, Pei; Bian, Chao; Zhu, Yinling; Zhang, Jiahui; Ma, Guosheng; Chen, Chengxuan; Li, Yanjun; Hao, Fengge; Li, Yong; Huang, Guodong; Li, Yuxiang; Li, Haiyan; Guo, Jian; Xu, Xun; Wang, Jun
2014-07-31
Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution. We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis. Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.
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MHC variability supports dog domestication from a large number of wolves: high diversity in Asia
Niskanen, A K; Hagström, E; Lohi, H; Ruokonen, M; Esparza-Salas, R; Aspi, J; Savolainen, P
2013-01-01
The process of dog domestication is still somewhat unresolved. Earlier studies indicate that domestic dogs from all over the world have a common origin in Asia. So far, major histocompatibility complex (MHC) diversity has not been studied in detail in Asian dogs, although high levels of genetic diversity are expected at the domestication locality. We sequenced the second exon of the canine MHC gene DLA–DRB1 from 128 Asian dogs and compared our data with a previously published large data set of MHC alleles, mostly from European dogs. Our results show that Asian dogs have a higher MHC diversity than European dogs. We also estimated that there is only a small probability that new alleles have arisen by mutation since domestication. Based on the assumption that all of the currently known 102 DLA–DRB1 alleles come from the founding wolf population, we simulated the number of founding wolf individuals. Our simulations indicate an effective population size of at least 500 founding wolves, suggesting that the founding wolf population was large or that backcrossing has taken place. PMID:23073392
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ERIC Educational Resources Information Center
Walker, Gabriela
2008-01-01
This manuscript briefly examines minority participation within the school population that is eligible for special education services--namely, African Americans in the United States and the Roma population in Romania. A large percentage of students from both minorities come to school unprepared to learn and they remain behind because of the…
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The Impact of Hearing Loss on Quality of Life in Older Adults
ERIC Educational Resources Information Center
Dalton, Dayna S.; Cruickshanks, Karen J.; Klein, Barbara E. K.; Klein, Ronald; Wiley, Terry L.; Nondahl, David M.
2003-01-01
Purpose: The authors investigate the impact of hearing loss on quality of life in a large population of older adults. Design and Methods: Data are from the 5-year follow-up Epidemiology of Hearing Loss Study, a population-based longitudinal study of age-related hearing impairment conducted in Beaver Dam, WI. Participants (N = 2,688) were 53-97…
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The Impact of Childhood Bullying among HIV-Positive Men: Psychosocial Correlates and Risk Factors
ERIC Educational Resources Information Center
Kamen, Charles; Bergstrom, Jessica; Vorasarun, Chaniga; Mardini, Mona; Patrick, Rudy; Lee, Susanne; Lazar, Rachael; Koopman, Cheryl; Gore-Felton, Cheryl
2013-01-01
Objectives: While some studies have examined the deleterious effects of childhood bullying on adults, no studies to date have focused on the effects of bullying on Persons Living with HIV (PLH), a particularly at-risk population. PLH experience higher rates of childhood and adulthood physical and sexual abuse than the population at large, and…
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A size-frequency study of large Martian craters
NASA Technical Reports Server (NTRS)
Woronow, A.
1975-01-01
The log normal frequency distribution law was used to analyze the crater population on the surface of Mars. Resulting data show possible evidence for the size frequency evolution of crater producing bodies. Some regions on Mars display excessive depletion of either large or small craters; the most likely causes of the depletion are considered. Apparently, eolian sedimentation has markedly altered the population of the small craters south of -30 deg latitude. The general effects of crater obliteration in the Southern Hemisphere appear to be confined to diameters of less than 20 km. A strong depletion of large craters in a large region just south of Deuteronilus Mensae, and in a small region centered at 35 deg latitude and 10 deg west longitude, may indicate locations of subsurface ice.
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Warfare and wildlife declines in Africa's protected areas.
Daskin, Joshua H; Pringle, Robert M
2018-01-18
Large-mammal populations are ecological linchpins, and their worldwide decline and extinction disrupts many ecosystem functions and services. Reversal of this trend will require an understanding of the determinants of population decline, to enable more accurate predictions of when and where collapses will occur and to guide the development of effective conservation and restoration policies. Many correlates of large-mammal declines are known, including low reproductive rates, overhunting, and habitat destruction. However, persistent uncertainty about the effects of one widespread factor-armed conflict-complicates conservation-planning and priority-setting efforts. Case studies have revealed that conflict can have either positive or negative local impacts on wildlife, but the direction and magnitude of its net effect over large spatiotemporal scales have not previously been quantified. Here we show that conflict frequency predicts the occurrence and severity of population declines among wild large herbivores in African protected areas from 1946 to 2010. Conflict was extensive during this period, occurring in 71% of protected areas, and conflict frequency was the single most important predictor of wildlife population trends among the variables that we analysed. Population trajectories were stable in peacetime, fell significantly below replacement with only slight increases in conflict frequency (one conflict-year per two-to-five decades), and were almost invariably negative in high-conflict sites, both in the full 65-year dataset and in an analysis restricted to recent decades (1989-2010). Yet total population collapse was infrequent, indicating that war-torn faunas can often recover. Human population density was also correlated (positively) with wildlife population trajectories in recent years; however, we found no significant effect, in either timespan, of species body mass, protected-area size, conflict intensity (human fatalities), drought frequency, presence of extractable mineral resources, or various metrics of development and governance. Our results suggest that sustained conservation activity in conflict zones-and rapid interventions following ceasefires-may help to save many at-risk populations and species.
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Massie, Danielle L.; Smith, Geoffrey; Bonvechio, Timothy F.; Bunch, Aaron J.; Lucchesi, David O.; Wagner, Tyler
2018-01-01
Quantifying spatial variability in fish growth and identifying large‐scale drivers of growth are fundamental to many conservation and management decisions. Although fish growth studies often focus on a single population, it is becoming increasingly clear that large‐scale studies are likely needed for addressing transboundary management needs. This is particularly true for species with high recreational value and for those with negative ecological consequences when introduced outside of their native range, such as the Flathead Catfish Pylodictis olivaris. This study quantified growth variability of the Flathead Catfish across a large portion of its contemporary range to determine whether growth differences existed between habitat types (i.e., reservoirs and rivers) and between native and introduced populations. Additionally, we investigated whether growth parameters varied as a function of latitude and time since introduction (for introduced populations). Length‐at‐age data from 26 populations across 11 states in the USA were modeled using a Bayesian hierarchical von Bertalanffy growth model. Population‐specific growth trajectories revealed large variation in Flathead Catfish growth and relatively high uncertainty in growth parameters for some populations. Relatively high uncertainty was also evident when comparing populations and when quantifying large‐scale patterns. Growth parameters (Brody growth coefficient [K] and theoretical maximum average length [L∞]) were not different (based on overlapping 90% credible intervals) between habitat types or between native and introduced populations. For populations within the introduced range of Flathead Catfish, latitude was negatively correlated with K. For native populations, we estimated an 85% probability that L∞ estimates were negatively correlated with latitude. Contrary to predictions, time since introduction was not correlated with growth parameters in introduced populations of Flathead Catfish. Results of this study suggest that Flathead Catfish growth patterns are likely shaped more strongly by finer‐scale processes (e.g., exploitation or prey abundances) as opposed to macro‐scale drivers.
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Wei, Binnian; Feng, June; Rehmani, Imran J; Miller, Sharyn; McGuffey, James E; Blount, Benjamin C; Wang, Lanqing
2014-09-25
Most sample preparation methods characteristically involve intensive and repetitive labor, which is inefficient when preparing large numbers of samples from population-scale studies. This study presents a robotic system designed to meet the sampling requirements for large population-scale studies. Using this robotic system, we developed and validated a method to simultaneously measure urinary anatabine, anabasine, nicotine and seven major nicotine metabolites: 4-Hydroxy-4-(3-pyridyl)butanoic acid, cotinine-N-oxide, nicotine-N-oxide, trans-3'-hydroxycotinine, norcotinine, cotinine and nornicotine. We analyzed robotically prepared samples using high-performance liquid chromatography (HPLC) coupled with triple quadrupole mass spectrometry in positive electrospray ionization mode using scheduled multiple reaction monitoring (sMRM) with a total runtime of 8.5 min. The optimized procedure was able to deliver linear analyte responses over a broad range of concentrations. Responses of urine-based calibrators delivered coefficients of determination (R(2)) of >0.995. Sample preparation recovery was generally higher than 80%. The robotic system was able to prepare four 96-well plate (384 urine samples) per day, and the overall method afforded an accuracy range of 92-115%, and an imprecision of <15.0% on average. The validation results demonstrate that the method is accurate, precise, sensitive, robust, and most significantly labor-saving for sample preparation, making it efficient and practical for routine measurements in large population-scale studies such as the National Health and Nutrition Examination Survey (NHANES) and the Population Assessment of Tobacco and Health (PATH) study. Published by Elsevier B.V.
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Learning Style Patterns among Special Needs Adult Students at King Saud University
ERIC Educational Resources Information Center
Alshuaibi, Abdulrahman
2017-01-01
Few studies of learning styles among adults with special needs exist worldwide. Even though there are large numbers of adults with special needs, this population in university education has been largely ignored in educational research. Therefore, this study aimed to gather and analyze learning styles of adult special needs students and to provide…
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ERIC Educational Resources Information Center
Soke, Gnakub N.; Rosenberg, Steven A.; Hamman, Richard F.; Fingerlin, Tasha; Robinson, Cordelia; Carpenter, Laura; Giarelli, Ellen; Lee, Li-Ching; Wiggins, Lisa D.; Durkin, Maureen S.; DiGuiseppi, Carolyn
2016-01-01
Self-injurious behaviors (SIB) have been reported in more than 30% of children with an autism spectrum disorder (ASD) in clinic-based studies. This study estimated the prevalence of SIB in a large population-based sample of children with ASD in the United States. A total of 8,065 children who met the surveillance case definition for ASD in the…
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Estimating avian population size using Bowden's estimator
Diefenbach, D.R.
2009-01-01
Avian researchers often uniquely mark birds, and multiple estimators could be used to estimate population size using individually identified birds. However, most estimators of population size require that all sightings of marked birds be uniquely identified, and many assume homogeneous detection probabilities. Bowden's estimator can incorporate sightings of marked birds that are not uniquely identified and relax assumptions required of other estimators. I used computer simulation to evaluate the performance of Bowden's estimator for situations likely to be encountered in bird studies. When the assumptions of the estimator were met, abundance and variance estimates and confidence-interval coverage were accurate. However, precision was poor for small population sizes (N < 50) unless a large percentage of the population was marked (>75%) and multiple (≥8) sighting surveys were conducted. If additional birds are marked after sighting surveys begin, it is important to initially mark a large proportion of the population (pm ≥ 0.5 if N ≤ 100 or pm > 0.1 if N ≥ 250) and minimize sightings in which birds are not uniquely identified; otherwise, most population estimates will be overestimated by >10%. Bowden's estimator can be useful for avian studies because birds can be resighted multiple times during a single survey, not all sightings of marked birds have to uniquely identify individuals, detection probabilities among birds can vary, and the complete study area does not have to be surveyed. I provide computer code for use with pilot data to design mark-resight surveys to meet desired precision for abundance estimates.
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Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms
2016-01-01
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance. Because of this relationship, many theories invoke a role for population size in the evolution of complexity. Such theories are difficult to test empirically because of the time required for the evolution of complexity in biological populations. Here, we used digital experimental evolution to test whether large or small asexual populations tend to evolve greater complexity. We find that both small and large—but not intermediate-sized—populations are favored to evolve larger genomes, which provides the opportunity for subsequent increases in phenotypic complexity. However, small and large populations followed different evolutionary paths towards these novel traits. Small populations evolved larger genomes by fixing slightly deleterious insertions, while large populations fixed rare beneficial insertions that increased genome size. These results demonstrate that genetic drift can lead to the evolution of complexity in small populations and that purifying selection is not powerful enough to prevent the evolution of complexity in large populations. PMID:27923053
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The limits of weak selection and large population size in evolutionary game theory.
Sample, Christine; Allen, Benjamin
2017-11-01
Evolutionary game theory is a mathematical approach to studying how social behaviors evolve. In many recent works, evolutionary competition between strategies is modeled as a stochastic process in a finite population. In this context, two limits are both mathematically convenient and biologically relevant: weak selection and large population size. These limits can be combined in different ways, leading to potentially different results. We consider two orderings: the [Formula: see text] limit, in which weak selection is applied before the large population limit, and the [Formula: see text] limit, in which the order is reversed. Formal mathematical definitions of the [Formula: see text] and [Formula: see text] limits are provided. Applying these definitions to the Moran process of evolutionary game theory, we obtain asymptotic expressions for fixation probability and conditions for success in these limits. We find that the asymptotic expressions for fixation probability, and the conditions for a strategy to be favored over a neutral mutation, are different in the [Formula: see text] and [Formula: see text] limits. However, the ordering of limits does not affect the conditions for one strategy to be favored over another.
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Veltsos, P; Gregson, E; Morrissey, B; Slate, J; Hoikkala, A; Butlin, R K; Ritchie, M G
2015-01-01
We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power. PMID:26198076
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Neville, H.M.; Dunham, J.B.; Peacock, M.M.
2006-01-01
Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective. ?? Springer 2006.
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Lounnas, M; Correa, A C; Vázquez, A A; Dia, A; Escobar, J S; Nicot, A; Arenas, J; Ayaqui, R; Dubois, M P; Gimenez, T; Gutiérrez, A; González-Ramírez, C; Noya, O; Prepelitchi, L; Uribe, N; Wisnivesky-Colli, C; Yong, M; David, P; Loker, E S; Jarne, P; Pointier, J P; Hurtrez-Boussès, S
2017-02-01
Population genetic studies are efficient for inferring the invasion history based on a comparison of native and invasive populations, especially when conducted at species scale. An expected outcome in invasive populations is variability loss, and this is especially true in self-fertilizing species. We here focus on the self-fertilizing Pseudosuccinea columella, an invasive hermaphroditic freshwater snail that has greatly expanded its geographic distribution and that acts as intermediate host of Fasciola hepatica, the causative agent of human and veterinary fasciolosis. We evaluated the distribution of genetic diversity at the largest geographic scale analysed to date in this species by surveying 80 populations collected during 16 years from 14 countries, using eight nuclear microsatellites and two mitochondrial genes. As expected, populations from North America, the putative origin area, were strongly structured by selfing and history and harboured much more genetic variability than invasive populations. We found high selfing rates (when it was possible to infer it), none-to-low genetic variability and strong population structure in most invasive populations. Strikingly, we found a unique genotype/haplotype in populations from eight invaded regions sampled all over the world. Moreover, snail populations resistant to infection by the parasite are genetically distinct from susceptible populations. Our results are compatible with repeated introductions in South America and flash worldwide invasion by this unique genotype/haplotype. Our study illustrates the population genetic consequences of biological invasion in a highly selfing species at very large geographic scale. We discuss how such a large-scale flash invasion may affect the spread of fasciolosis. © 2016 John Wiley & Sons Ltd.
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Selikoff, Irving J.
1976-01-01
Experiences in the past decade provide guidance in selecting priorities for investigation of health hazards in chemical industries. Pride of place should be given to the experience of large industrial populations, in part simply because large numbers of people are at risk and in part because such studies are more likely to give reliable answers. This recommendation has further strength when there is community exposure as well. Parenthetically, large populations provide opportunity to study multiple factor interaction; without this, toxic potential of a single agent may be obscured. Second, investigations should be mounted when there is reason for suspicion, as with particular chemical configurations, observed organ toxicity, animal carcinogenicity, unusual clinical experience (“signal” tumors). It may be added that when agents have already been used several decades, evaluation of human experience with them is now in order, if only to document absence of toxicity. The same recommendations hold for planned introduction of new agents or widened distribution of existing ones, until we have better information concerning validity of “pretesting” programs. Major advances have been made in epidemiological methods for these investigations. These now allow us to successfully focus on small defined groups as well as to manage large populations. PMID:1026418
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Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps.
Garud, Nandita R; Messer, Philipp W; Buzbas, Erkan O; Petrov, Dmitri A
2015-02-01
Adaptation from standing genetic variation or recurrent de novo mutation in large populations should commonly generate soft rather than hard selective sweeps. In contrast to a hard selective sweep, in which a single adaptive haplotype rises to high population frequency, in a soft selective sweep multiple adaptive haplotypes sweep through the population simultaneously, producing distinct patterns of genetic variation in the vicinity of the adaptive site. Current statistical methods were expressly designed to detect hard sweeps and most lack power to detect soft sweeps. This is particularly unfortunate for the study of adaptation in species such as Drosophila melanogaster, where all three confirmed cases of recent adaptation resulted in soft selective sweeps and where there is evidence that the effective population size relevant for recent and strong adaptation is large enough to generate soft sweeps even when adaptation requires mutation at a specific single site at a locus. Here, we develop a statistical test based on a measure of haplotype homozygosity (H12) that is capable of detecting both hard and soft sweeps with similar power. We use H12 to identify multiple genomic regions that have undergone recent and strong adaptation in a large population sample of fully sequenced Drosophila melanogaster strains from the Drosophila Genetic Reference Panel (DGRP). Visual inspection of the top 50 candidates reveals that in all cases multiple haplotypes are present at high frequencies, consistent with signatures of soft sweeps. We further develop a second haplotype homozygosity statistic (H2/H1) that, in combination with H12, is capable of differentiating hard from soft sweeps. Surprisingly, we find that the H12 and H2/H1 values for all top 50 peaks are much more easily generated by soft rather than hard sweeps. We discuss the implications of these results for the study of adaptation in Drosophila and in species with large census population sizes.
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Montero-Serra, Ignasi; Linares, Cristina; García, Marina; Pancaldi, Francesca; Frleta-Valić, Maša; Ledoux, Jean-Baptiste; Zuberer, Frederic; Merad, Djamel; Drap, Pierre; Garrabou, Joaquim
2015-01-01
Overexploitation is a major threat for the integrity of marine ecosystems. Understanding the ecological consequences of different extractive practices and the mechanisms underlying the recovery of populations is essential to ensure sustainable management plans. Precious corals are long-lived structural invertebrates, historically overfished, and their conservation is currently a worldwide concern. However, the processes underlying their recovery are poorly known. Here, we examined harvesting effects and recovery mechanisms of red coral Corallium rubrum by analyzing long-term photographic series taken on two populations that were harvested. We compared the relative importance of reproduction and re-growth as drivers of resilience. Harvesting heavily impacted coral populations causing large decreases in biomass and strong size-class distribution shifts towards populations dominated by small colonies. At the end of the study (after 4 and 7 years) only partial recovery was observed. The observed general pattern of low recruitment and high mortality of new recruits demonstrated limited effects of reproduction on population recovery. Adversely, low mortality of partially harvested adults and a large proportion of colonies showing new branches highlighted the importance of re-growth in the recovery process. The demographic projections obtained through stochastic models confirmed that the recovery rates of C. rubrum can be strongly modulated depending on harvesting procedures. Thus, leaving the basal section of the colonies when harvesting to avoid total mortality largely enhances the resilience of C. rubrum populations and quickens their recovery. On the other hand, the high survival of harvested colonies and the significant biomass reduction indicated that abundance may not be an adequate metric to assess the conservation status of clonal organisms because it can underestimate harvesting effects. This study highlights the unsustainability of current harvesting practices of C. rubrum and provides urgently needed data to improve management practices that are still largely based on untested assumptions. PMID:25706556
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Manek, Aditya K.; Ferrari, Maud C. O.; Pollock, Robyn J.; Vicente, Daniel; Weber, Lynn P.; Chivers, Douglas P.
2013-01-01
Many prey fishes possess large club cells in their epidermis. The role of these cells has garnered considerable attention from evolutionary ecologists. These cells likely form part of the innate immune system of fishes, however, they also have an alarm function, releasing chemical cues that serve to warn nearby conspecifics of danger. Experiments aimed at understanding the selection pressures leading to the evolution of these cells have been hampered by a surprisingly large intraspecific variation in epidermal club cell (ECC) investment. The goal of our current work was to explore the magnitude and nature of this variation in ECC investment. In a field survey, we documented large differences in ECC investment both within and between several populations of minnows. We then tested whether we could experimentally reduce variation in mean ECC number by raising fish under standard laboratory conditions for 4 weeks. Fish from different populations responded very differently to being held under standard laboratory conditions; some populations showed an increase in ECC investment while others remained unchanged. More importantly, we found some evidence that we could reduce within population variation in ECC investment through time, but could not reduce among-population variation in mean ECC investment. Given the large variation we observed in wild fish and our limited ability to converge mean cell number by holding the fish under standard conditions, we caution that future studies may be hard pressed to find subtle effects of various experimental manipulations; this will make elucidating the selection pressures leading to the evolution of the cells challenging. PMID:23469175
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Burel, Julie G.; Qian, Yu; Arlehamn, Cecilia Lindestam; Weiskopf, Daniela; Zapardiel-Gonzalo, Jose; Taplitz, Randy; Gilman, Robert H.; Saito, Mayuko; de Silva, Aruna D.; Vijayanand, Pandurangan; Scheuermann, Richard H.; Sette, Alessandro; Peters, Bjoern
2016-01-01
In the context of large-scale human system immunology studies, controlling for technical and biological variability is crucial to ensure that experimental data support research conclusions. Here, we report on a universal workflow to evaluate both technical and biological variation in multiparameter flow cytometry, applied to the development of a 10-color panel to identify all major cell populations and T cell subsets in cryopreserved PBMC. Replicate runs from a control donation and comparison of different gating strategies assessed technical variability associated with each cell population and permitted the calculation of a quality control score. Applying our panel to a large collection of PBMC samples, we found that most cell populations showed low intra-individual variability over time. In contrast, certain subpopulations such as CD56 T cells and Temra CD4 T cells were associated with high inter-individual variability. Age but not gender had a significant effect on the frequency of several populations, with a drastic decrease in naïve T cells observed in older donors. Ethnicity also influenced a significant proportion of immune cell population frequencies, emphasizing the need to account for these co-variates in immune profiling studies. Finally, we exemplify the usefulness of our workflow by identifying a novel cell-subset signature of latent tuberculosis infection. Thus, our study provides a universal workflow to establish and evaluate any flow cytometry panel in systems immunology studies. PMID:28069807
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ERIC Educational Resources Information Center
Lekhal, Ratib
2012-01-01
Associations between type and age of entry into Norwegian universally-accessible childcare and children's behavior problems at age 3 years were examined in this study. Data from 73,068 children in the large population-based, prospective Norwegian Mother and Child Cohort Study (MoBa) were used, and included information about childcare arrangements,…
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Unveiling adaptation using high-resolution lineage tracking
NASA Astrophysics Data System (ADS)
Blundell, Jamie; Levy, Sasha; Fisher, Daniel; Petrov, Dmitri; Sherlock, Gavin
2013-03-01
Human diseases such as cancer and microbial infections are adaptive processes inside the human body with enormous population sizes: between 106 -1012 cells. In spite of this our understanding of adaptation in large populations is limited. The key problem is the difficulty in identifying anything more than a handful of rare, large-effect beneficial mutations. The development and use of molecular barcodes allows us to uniquely tag hundreds of thousands of cells and enable us to track tens of thousands of adaptive mutations in large yeast populations. We use this system to test some of the key theories on which our understanding of adaptation in large populations is based. We (i) measure the fitness distribution in an evolving population at different times, (ii) identify when an appreciable fraction of clones in the population have at most a single adaptive mutation and isolate a large number of clones with independent single adaptive mutations, and (iii) use this clone collection to determine the distribution of fitness effects of single beneficial mutations.
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GWAS for detecting QTL associated with Columnaris Disease in two rainbow trout breeding populations
USDA-ARS?s Scientific Manuscript database
The purpose of this study was to prospect genomic regions that explain large portion of the additive genetic variance for resistance against Columnaris disease (CD) in rainbow trout. Two important aquaculture populations were investigated. The National Center for Cool and Cold Water Aquaculture (NCC...
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International Spotlight: Israel
ERIC Educational Resources Information Center
Glicksman, Allen; Litwin, Howard
2011-01-01
The State of Israel provides significant opportunities to study social processes that can enhance our understanding of the aging experience. It has high life expectancy and rapid growth of its older population. With an older cohort that is composed largely of former immigrants and includes a minority Arab population, Israel provides much diversity…
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Yurk, Brian P
2018-07-01
Animal movement behaviors vary spatially in response to environmental heterogeneity. An important problem in spatial ecology is to determine how large-scale population growth and dispersal patterns emerge within highly variable landscapes. We apply the method of homogenization to study the large-scale behavior of a reaction-diffusion-advection model of population growth and dispersal. Our model includes small-scale variation in the directed and random components of movement and growth rates, as well as large-scale drift. Using the homogenized model we derive simple approximate formulas for persistence conditions and asymptotic invasion speeds, which are interpreted in terms of residence index. The homogenization results show good agreement with numerical solutions for environments with a high degree of fragmentation, both with and without periodicity at the fast scale. The simplicity of the formulas, and their connection to residence index make them appealing for studying the large-scale effects of a variety of small-scale movement behaviors.
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Zubair, Niha; Graff, Mariaelisa; Luis Ambite, Jose; Bush, William S; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H; Absher, Devin; Assimes, Themistocles L; Bielinski, Suzette J; Bottinger, Erwin P; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H; Martin, Lisa W; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P; Robinson, Jennifer; Rotter, Jerome I; Ryckman, Kelli K; Schreiner, Pamela J; Stahl, Eli; Tao, Ran; Tsai, Michael Y; Waite, Lindsay L; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C; Loos, Ruth J F; Rich, Stephen S; Fornage, Myriam; North, Kari E; Kooperberg, Charles; Carty, Cara L
2016-12-15
Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Link, W.A.
2003-01-01
Heterogeneity in detection probabilities has long been recognized as problematic in mark-recapture studies, and numerous models developed to accommodate its effects. Individual heterogeneity is especially problematic, in that reasonable alternative models may predict essentially identical observations from populations of substantially different sizes. Thus even with very large samples, the analyst will not be able to distinguish among reasonable models of heterogeneity, even though these yield quite distinct inferences about population size. The problem is illustrated with models for closed and open populations.
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Hozé, C; Fritz, S; Phocas, F; Boichard, D; Ducrocq, V; Croiseau, P
2014-01-01
Single-breed genomic selection (GS) based on medium single nucleotide polymorphism (SNP) density (~50,000; 50K) is now routinely implemented in several large cattle breeds. However, building large enough reference populations remains a challenge for many medium or small breeds. The high-density BovineHD BeadChip (HD chip; Illumina Inc., San Diego, CA) containing 777,609 SNP developed in 2010 is characterized by short-distance linkage disequilibrium expected to be maintained across breeds. Therefore, combining reference populations can be envisioned. A population of 1,869 influential ancestors from 3 dairy breeds (Holstein, Montbéliarde, and Normande) was genotyped with the HD chip. Using this sample, 50K genotypes were imputed within breed to high-density genotypes, leading to a large HD reference population. This population was used to develop a multi-breed genomic evaluation. The goal of this paper was to investigate the gain of multi-breed genomic evaluation for a small breed. The advantage of using a large breed (Normande in the present study) to mimic a small breed is the large potential validation population to compare alternative genomic selection approaches more reliably. In the Normande breed, 3 training sets were defined with 1,597, 404, and 198 bulls, and a unique validation set included the 394 youngest bulls. For each training set, estimated breeding values (EBV) were computed using pedigree-based BLUP, single-breed BayesC, or multi-breed BayesC for which the reference population was formed by any of the Normande training data sets and 4,989 Holstein and 1,788 Montbéliarde bulls. Phenotypes were standardized by within-breed genetic standard deviation, the proportion of polygenic variance was set to 30%, and the estimated number of SNP with a nonzero effect was about 7,000. The 2 genomic selection (GS) approaches were performed using either the 50K or HD genotypes. The correlations between EBV and observed daughter yield deviations (DYD) were computed for 6 traits and using the different prediction approaches. Compared with pedigree-based BLUP, the average gain in accuracy with GS in small populations was 0.057 for the single-breed and 0.086 for multi-breed approach. This gain was up to 0.193 and 0.209, respectively, with the large reference population. Improvement of EBV prediction due to the multi-breed evaluation was higher for animals not closely related to the reference population. In the case of a breed with a small reference population size, the increase in correlation due to multi-breed GS was 0.141 for bulls without their sire in reference population compared with 0.016 for bulls with their sire in reference population. These results demonstrate that multi-breed GS can contribute to increase genomic evaluation accuracy in small breeds. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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Large Scale Flood Risk Analysis using a New Hyper-resolution Population Dataset
NASA Astrophysics Data System (ADS)
Smith, A.; Neal, J. C.; Bates, P. D.; Quinn, N.; Wing, O.
2017-12-01
Here we present the first national scale flood risk analyses, using high resolution Facebook Connectivity Lab population data and data from a hyper resolution flood hazard model. In recent years the field of large scale hydraulic modelling has been transformed by new remotely sensed datasets, improved process representation, highly efficient flow algorithms and increases in computational power. These developments have allowed flood risk analysis to be undertaken in previously unmodeled territories and from continental to global scales. Flood risk analyses are typically conducted via the integration of modelled water depths with an exposure dataset. Over large scales and in data poor areas, these exposure data typically take the form of a gridded population dataset, estimating population density using remotely sensed data and/or locally available census data. The local nature of flooding dictates that for robust flood risk analysis to be undertaken both hazard and exposure data should sufficiently resolve local scale features. Global flood frameworks are enabling flood hazard data to produced at 90m resolution, resulting in a mis-match with available population datasets which are typically more coarsely resolved. Moreover, these exposure data are typically focused on urban areas and struggle to represent rural populations. In this study we integrate a new population dataset with a global flood hazard model. The population dataset was produced by the Connectivity Lab at Facebook, providing gridded population data at 5m resolution, representing a resolution increase over previous countrywide data sets of multiple orders of magnitude. Flood risk analysis undertaken over a number of developing countries are presented, along with a comparison of flood risk analyses undertaken using pre-existing population datasets.
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Cryptic herbivores mediate the strength and form of ungulate impacts on a long-lived savanna tree.
Maclean, Janet E; Goheen, Jacob R; Doak, Daniel F; Palmer, Todd M; Young, Truman P
2011-08-01
Plant populations are regulated by a diverse array of herbivores that impose demographic filters throughout their life cycle. Few studies, however, simultaneously quantify the impacts of multiple herbivore guilds on the lifetime performance or population growth rate of plants. In African savannas, large ungulates (such as elephants) are widely regarded as important drivers of woody plant population dynamics, while the potential impacts of smaller, more cryptic herbivores (such as rodents) have largely been ignored. We combined a large-scale ungulate exclusion experiment with a five-year manipulation of rodent densities to quantify the impacts of three herbivore guilds (wild ungulates, domestic cattle, and rodents) on all life stages of a widespread savanna tree. We utilized demographic modeling to reveal the overall role of each guild in regulating tree population dynamics, and to elucidate the importance of different demographic hurdles in driving population growth under contrasting consumer communities. We found that wild ungulates dramatically reduced population growth, shifting the population trajectory from increase to decline, but that the mechanisms driving these effects were strongly mediated by rodents. The impact of wild ungulates on population growth was predominantly driven by their negative effect on tree reproduction when rodents were excluded, and on adult tree survival when rodents were present. By limiting seedling survival, rodents also reduced population growth; however, this effect was strongly dampened where wild ungulates were present. We suggest that these complex interactions between disparate consumer guilds can have important consequences for the population demography of long-lived species, and that the effects of a single consumer group are often likely to vary dramatically depending on the larger community in which interactions are embedded.
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Böndel, Katharina B; Lainer, Hilde; Nosenko, Tetyana; Mboup, Mamadou; Tellier, Aurélien; Stephan, Wolfgang
2015-11-01
After colonization population sizes may vary across the species range depending on environmental conditions and following colonizations. An interesting question is whether local adaptation occurs more frequently in large ancestral populations or in small derived populations. A higher number of new mutations and a lower effect of genetic drift should favor selection in large populations, whereas small derived populations may require an initial local adaptation event to facilitate the colonization of new habitats. Wild tomatoes are native to a broad range of different habitats characterized by variable abiotic conditions in South America, and represent an ideal system to study this interplay between demography and natural selection. Population genetic analyses and statistical inference of past demography were conducted on pooled-sequencing data from 30 genes (8,080 single nucleotide polymorphisms) from an extensive sampling of 23 Solanum chilense populations over Chile and Peru. We reveal first a north-south colonization associated with relaxed purifying selection in the south as shown by a decrease of genetic variation and an increasing proportion of nonsynonymous polymorphism from north to south, and population substructure with at least four genetic groups. Second, we uncover a dual picture of adaptation consisting of 1) a decreasing proportion of adaptive amino acid substitutions from north to south suggesting that adaptation is favored in large populations, whereas 2) signatures of local adaptation predominantly occur in the smaller populations from the marginal ranges in the south. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Lewis, Jesse S.; Farnsworth, Matthew L.; Burdett, Chris L.; Theobald, David M.; Gray, Miranda; Miller, Ryan S.
2017-01-01
Biotic and abiotic factors are increasingly acknowledged to synergistically shape broad-scale species distributions. However, the relative importance of biotic and abiotic factors in predicting species distributions is unclear. In particular, biotic factors, such as predation and vegetation, including those resulting from anthropogenic land-use change, are underrepresented in species distribution modeling, but could improve model predictions. Using generalized linear models and model selection techniques, we used 129 estimates of population density of wild pigs (Sus scrofa) from 5 continents to evaluate the relative importance, magnitude, and direction of biotic and abiotic factors in predicting population density of an invasive large mammal with a global distribution. Incorporating diverse biotic factors, including agriculture, vegetation cover, and large carnivore richness, into species distribution modeling substantially improved model fit and predictions. Abiotic factors, including precipitation and potential evapotranspiration, were also important predictors. The predictive map of population density revealed wide-ranging potential for an invasive large mammal to expand its distribution globally. This information can be used to proactively create conservation/management plans to control future invasions. Our study demonstrates that the ongoing paradigm shift, which recognizes that both biotic and abiotic factors shape species distributions across broad scales, can be advanced by incorporating diverse biotic factors. PMID:28276519
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Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto
2010-01-01
Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643
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Genetic and phylogenetic consequences of island biogeography.
Johnson, K P; Adler, F R; Cherry, J L
2000-04-01
Island biogeography theory predicts that the number of species on an island should increase with island size and decrease with island distance to the mainland. These predictions are generally well supported in comparative and experimental studies. These ecological, equilibrium predictions arise as a result of colonization and extinction processes. Because colonization and extinction are also important processes in evolution, we develop methods to test evolutionary predictions of island biogeography. We derive a population genetic model of island biogeography that incorporates island colonization, migration of individuals from the mainland, and extinction of island populations. The model provides a means of estimating the rates of migration and extinction from population genetic data. This model predicts that within an island population the distribution of genetic divergences with respect to the mainland source population should be bimodal, with much of the divergence dating to the colonization event. Across islands, this model predicts that populations on large islands should be on average more genetically divergent from mainland source populations than those on small islands. Likewise, populations on distant islands should be more divergent than those on close islands. Published observations of a larger proportion of endemic species on large and distant islands support these predictions.
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Identifying Multiple Populations in M71 using CN
NASA Astrophysics Data System (ADS)
Gerber, Jeffrey M.; Friel, Eileen D.; Vesperini, Enrico
2018-01-01
It is now well established that globular clusters (GCs) host multiple stellar populations characterized by differences in several light elements. While these populations have been found in nearly all GCs, we still lack an entirely successful model to explain their formation. A key constraint to these models is the detailed pattern of light element abundances seen among the populations; different techniques for identifying these populations probe different elements and do not always yield the same results. We study a large sample of stars in the GC M71 for light elements C and N, using the CN and CH band strength to identify multiple populations. Our measurements come from low-resolution spectroscopy obtained with the WIYN-3.5m telescope for ~150 stars from the tip of the red-giant branch down to the main-sequence turn-off. The large number of stars and broad spatial coverage of our sample (out to ~3.5 half-light radii) allows us to carry out a comprehensive characterization of the multiple populations in M71. We use a combination of the various spectroscopic and photometric indicators to draw a more complete picture of the properties of the populations and to investigate the consistency of classifications using different techniques.
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Alter, S. Elizabeth; Newsome, Seth D.; Palumbi, Stephen R.
2012-01-01
Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ∼5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size. PMID:22590499
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Kopelman, Naama M; Stone, Lewi; Wang, Chaolong; Gefel, Dov; Feldman, Marcus W; Hillel, Jossi; Rosenberg, Noah A
2009-12-08
Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations. We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations. These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent.
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2009-01-01
Background Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations. Results We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations. Conclusion These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent. PMID:19995433
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Blauw, Lisanne L; Boon, Mariëtte R; Rosendaal, Frits R; de Mutsert, Renée; Gast, Karin B; van Dijk, Ko Willems; Rensen, Patrick C N; Dekkers, Olaf M
2015-11-01
Animal studies and human studies in small selected populations have shown a positive association between nicotine smoking and resting energy expenditure (REE), but data in large cohorts are lacking. We aimed to investigate the association between smoking behavior and REE in a large, population-based study. Population-based cross-sectional study. In this cross-sectional analysis of baseline measurements from the Netherlands Epidemiology of Obesity (NEO) study (n=6673), we included participants with REE measurement by indirect calorimetry who were not using lipid or glucose lowering drugs (n=1189). We used linear regression analysis to examine the association of smoking status (never, former, occasional, current smoker) and smoking quantity (pack years) with REE per kilogram (kg) fat free mass (FFM) and with REE adjusted for FFM. Models were adjusted for age, sex, ethnicity, educational level, physical activity, energy intake and body mass index (BMI). Mean (standard deviation, SD) age was 55.2 (5.9) years and BMI was 26.3 (4.4) kg/m(2). 60% of the participants were women. Mean (SD) REE/FFM (kcal/day/kg FFM) was for male never smokers 25.1 (2.0), male current smokers 26.4 (2.8), female never smokers 28.9 (2.5) and female current smokers 30.1 (3.7). After adjustment, only current smokers had a higher REE/FFM (mean difference 1.28, 95% CI 0.64, 1.92), and a higher REE adjusted for FFM (mean difference 60.3 kcal/day, 95% CI 29.1, 91.5), compared with never smokers. There was no association between pack years and REE/FFM (mean difference -0.01, 95% CI -0.06, 0.04) or REE adjusted for FFM (mean difference 0.2, 95% CI -2.4, 2.8) in current smokers. Current smoking is associated with a higher resting energy expenditure compared with never smoking in a large population-based cohort. Copyright © 2015 Elsevier Inc. All rights reserved.
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Summer 2012 Colorado Wildfire Non-Profit Sector Case Study
2012-11-01
all- populations shelter accommodating individuals with Access and Functional Needs (AFN) and sheltering for companion animals. Penrose Equestrian...Center was established as the large animal shelter and was managed by the El Paso County CART. Both companion and large animals were accepted for...themselves as safe- www.redcross.org/safeandwell. Information on sheltering companion animals at multiple locations is distributed. Large Animal
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Ghoshal, Gourab; Muñuzuri, Alberto P; Pérez-Mercader, Juan
2016-01-12
Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.
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NASA Astrophysics Data System (ADS)
Ghoshal, Gourab; Muñuzuri, Alberto P.; Pérez-Mercader, Juan
2016-01-01
Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.
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James Grogan; R. Matthew Landis
2009-01-01
1. Current efforts to model population dynamics of high-value tropical timber species largely assume that individual growth history is unimportant to population dynamics, yet growth autocorrelation is known to adversely affect model predictions. In this study, we analyse a decade of annual census data from a natural population of big-leaf mahogany Swietenia macrophylla...
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Neurogenetic disorders in the Basque population.
Martí Massó, José Félix; Zarranz, Juan José; Otaegui, David; López de Munain, Adolfo
2015-01-01
In the molecular era, the study of neurogenetic disorders in relict populations provides an opportunity to discover new genes by linkage studies and to establish clearer genotype-phenotype correlations in large cohorts of individuals carrying the same mutation. The Basque people are one of the most ancient populations living in Europe and represent an excellent resource for this type of analysis in certain genetic conditions. Our objective was to describe neurogenetic disorders reported in the Basque population due to the presence of ancestral mutations or an accumulation of cases or both. We conducted a search in PubMed with the terms: Basque, neurogenetic disorders, genetic risk, and neurological disorders. We identified nine autosomal and two recessive disorders in the Basque population attributable to ancestral mutations (such as in PNRP, PARK8, FTDP-TDP43, LGMD2A, VCP, c9ORF72, and CMT4A), highly prevalent (DM1) or involving unique mutations (PARK1 or MAPT). Other genes were reported for their role as protective/risk factors in complex diseases such as multiple sclerosis, Alzheimer's disease, and Parkinson's disease. At the present time, when powerful sequencing techniques are identifying large numbers of genetic variants associated with unique phenotypes, the scrutiny of these findings in genetically homogeneous populations can help analyze genotype-phenotype correlations. © 2014 John Wiley & Sons Ltd/University College London.
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Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O’Connor, Timothy D.; Abecasis, Gonçalo R.; Wojcik, Genevieve L; Gignoux, Christopher R.; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E.; Bustamante, Carlos; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Qin, Zhaohui S.; Preethi Boorgula, Meher; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Ruczinski, Ingo; Scott, Alan F.; Taub, Margaret A.; Vergara, Candelaria; Levin, Albert M.; Padhukasahasram, Badri; Williams, L. Keoki; Dunston, Georgia M.; Faruque, Mezbah U.; Gietzen, Kimberly; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-Youn A.; Kumar, Rajesh; Schleimer, Robert; De La Vega, Francisco M.; Shringarpure, Suyash S.; Musharoff, Shaila; Burchard, Esteban G.; Eng, Celeste; Hernandez, Ryan D.; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Maul, Pissamai; Maul, Trevor; Watson, Harold; Ilma Araujo, Maria; Riccio Oliveira, Ricardo; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Francisco Herrera-Paz, Edwin; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Marina Vasquez, Olga; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria
2017-01-01
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry. PMID:28429804
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Data Mining Applied to Analysis of Contraceptive Methods Among College Students.
Simões, Priscyla Waleska; Cesconetto, Samuel; Dalló, Eduardo Daminelli; de Souza Pires, Maria Marlene; Comunello, Eros; Borges Tomaz, Felipe; Xavier, Eduardo Pícolo; da Rosa Brunel Alves, Pedro Antonio; Ceretta, Luciane Bisognin; Manenti, Sandra Aparecida
2017-01-01
The aim of this study was to use the Data Mining to analyze the profile of the use of contraceptive methods in a university population. We used a database about sexuality performed on a university population in southern Brazil. The results obtained by the generated rules are largely in line with the literature and epidemiology worldwide, showing significant points of vulnerability in the university population. Validation measures of the study, as such, accuracy, sensitivity, specificity, and area under the ROC curve were higher or at least similar as compared to recent studies using the same methodology.
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ERIC Educational Resources Information Center
Steel, Jennifer L.; Herlitz, Claes A.
2005-01-01
Objective: Several studies with small and ''high risk'' samples have demonstrated that a history of childhood or adolescent sexual abuse (CASA) is associated with sexual risk behaviors (SRBs). However, few studies with large random samples from the general population have specifically examined the relationship between CASA and SRBs with a…
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Intraspecific competition and density dependence of food consumption and growth in Arctic charr.
Amundsen, Per-Arne; Knudsen, Rune; Klemetsen, Anders
2007-01-01
1. Intraspecific competition for restricted food resources is considered to play a fundamental part in density dependence of somatic growth and other population characteristics, but studies simultaneously addressing the interrelationships between population density, food acquisition and somatic growth have been missing. 2. We explored the food consumption and individual growth rates of Arctic charr Salvelinus alpinus in a long-term survey following a large-scale density manipulation experiment in a subarctic lake. 3. Prior to the initiation of the experiment, the population density was high and the somatic growth rates low, revealing a severely overcrowded and stunted fish population. 4. During the 6-year period of stock depletion the population density of Arctic charr was reduced with about 75%, resulting in an almost twofold increase in food consumption rates and enhanced individual growth rates of the fish. 5. Over the decade following the density manipulation experiment, the population density gradually rose to intermediate levels, accompanied by corresponding reductions in food consumption and somatic growth rates. 6. The study revealed negative relationships with population density for both food consumption and individual growth rates, reflecting a strong positive correlation between quantitative food intake and somatic growth rates. 7. Both the growth and consumption rate relationships with population density were well described by negative power curves, suggesting that large density perturbations are necessary to induce improved feeding conditions and growth rates in stunted fish populations. 8. The findings demonstrate that quantitative food consumption represents the connective link between population density and individual growth rates, apparently being highly influenced by intraspecific competition for limited resources.
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Seroprevalence of Chlamydia trachomatis in Enugu, Nigeria.
Ikeme, A C; Ezegwui, H U; Ikeako, L C; Agbata, I; Agbata, E
2011-01-01
Chlamydia infections in women cause pelvic inflammatory disease, which often results in devastating consequences of infertility, ectopic pregnancy, or chronic pelvic pain. The infection is largely asymptomatic. To determine the seroprevalence of Chlamydia trachomatis in Enugu, South Eastern Nigeria. A population-based prospective study comprising female residents of Enugu, South Eastern Nigeria. Indirect solid phase enzyme immunoassay of Chlamydia antibodies was done using ImmunoComb C0. Trachomatis IgG Kit (Orgenics). The population comprised 136 female undergraduate students and 150 non-student women. The overall prevalence of C. trachomatis in the population studied was 29.4%. The percentage of subjects who admitted to be having multiple sexual partners was higher among the student population (71.2%) compared to those from the non-student population (28.8%). The highest percentage of seroprevalence was 28 (33.3%) in the age group of 20-24 years for the student population and 18 (21.4%) in the age group of 25-29 years for the non-student population. The highest seroprevalence of C. trachomatis antibodies (69.0%) in both populations was observed in females without any history of infection. Females that had pelvic inflammatory disease, sexually transmitted infection, and secondary infertility assayed for C. trachomatis had seroprevalence levels of 19%, 9.5%, and 2.4%, respectively. There was a positive correlation between positive Chlamydia assay and the type of subject population (student or non-student) with r2 value of 1.55 at P < 0.01. C. trachomatis infection is largely underdiagnosed and remains a silent disease in the apparently healthy population of Enugu, South eastern Nigeria.
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Seecharran, Tristan; Kalin-Manttari, Laura; Koskela, Katja; Nikkari, Simo; Dickins, Benjamin; Corander, Jukka; Skurnik, Mikael
2017-01-01
Yersinia pseudotuberculosis is a Gram-negative intestinal pathogen of humans and has been responsible for several nationwide gastrointestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic species of the genus Yersinia, Yersinia pestis and Yersinia enterocolitica allowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no purpose-designed large-scale global population genomic analysis of Y. pseudotuberculosis has been performed. Here we present analyses of the genomes of 134 strains of Y. pseudotuberculosis isolated from around the world, from multiple ecosystems since the 1960s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria. PMID:29177091
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On the use of star-shaped genealogies in inference of coalescence times.
Rosenberg, Noah A; Hirsh, Aaron E
2003-01-01
Genealogies from rapidly growing populations have approximate "star" shapes. We study the degree to which this approximation holds in the context of estimating the time to the most recent common ancestor (T(MRCA)) of a set of lineages. In an exponential growth scenario, we find that unless the product of population size (N) and growth rate (r) is at least approximately 10(5), the "pairwise comparison estimator" of T(MRCA) that derives from the star genealogy assumption has bias of 10-50%. Thus, the estimator is appropriate only for large populations that have grown very rapidly. The "tree-length estimator" of T(MRCA) is more biased than the pairwise comparison estimator, having low bias only for extremely large values of Nr. PMID:12930771
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HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.
Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; Rehm, Catherine; Greer, Sarah E; Lucey, Daniel L; Danley, Kristen; Alter, Harvey; Mellors, John W; Coffin, John M
2013-09-01
HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.
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de Thoisy, Benoit; Fayad, Ibrahim; Clément, Luc; Barrioz, Sébastien; Poirier, Eddy; Gond, Valéry
2016-01-01
Tropical forests with a low human population and absence of large-scale deforestation provide unique opportunities to study successful conservation strategies, which should be based on adequate monitoring tools. This study explored the conservation status of a large predator, the jaguar, considered an indicator of the maintenance of how well ecological processes are maintained. We implemented an original integrative approach, exploring successive ecosystem status proxies, from habitats and responses to threats of predators and their prey, to canopy structure and forest biomass. Niche modeling allowed identification of more suitable habitats, significantly related to canopy height and forest biomass. Capture/recapture methods showed that jaguar density was higher in habitats identified as more suitable by the niche model. Surveys of ungulates, large rodents and birds also showed higher density where jaguars were more abundant. Although jaguar density does not allow early detection of overall vertebrate community collapse, a decrease in the abundance of large terrestrial birds was noted as good first evidence of disturbance. The most promising tool comes from easily acquired LiDAR data and radar images: a decrease in canopy roughness was closely associated with the disturbance of forests and associated decreasing vertebrate biomass. This mixed approach, focusing on an apex predator, ecological modeling and remote-sensing information, not only helps detect early population declines in large mammals, but is also useful to discuss the relevance of large predators as indicators and the efficiency of conservation measures. It can also be easily extrapolated and adapted in a timely manner, since important open-source data are increasingly available and relevant for large-scale and real-time monitoring of biodiversity.
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de Thoisy, Benoit; Fayad, Ibrahim; Clément, Luc; Barrioz, Sébastien; Poirier, Eddy; Gond, Valéry
2016-01-01
Tropical forests with a low human population and absence of large-scale deforestation provide unique opportunities to study successful conservation strategies, which should be based on adequate monitoring tools. This study explored the conservation status of a large predator, the jaguar, considered an indicator of the maintenance of how well ecological processes are maintained. We implemented an original integrative approach, exploring successive ecosystem status proxies, from habitats and responses to threats of predators and their prey, to canopy structure and forest biomass. Niche modeling allowed identification of more suitable habitats, significantly related to canopy height and forest biomass. Capture/recapture methods showed that jaguar density was higher in habitats identified as more suitable by the niche model. Surveys of ungulates, large rodents and birds also showed higher density where jaguars were more abundant. Although jaguar density does not allow early detection of overall vertebrate community collapse, a decrease in the abundance of large terrestrial birds was noted as good first evidence of disturbance. The most promising tool comes from easily acquired LiDAR data and radar images: a decrease in canopy roughness was closely associated with the disturbance of forests and associated decreasing vertebrate biomass. This mixed approach, focusing on an apex predator, ecological modeling and remote-sensing information, not only helps detect early population declines in large mammals, but is also useful to discuss the relevance of large predators as indicators and the efficiency of conservation measures. It can also be easily extrapolated and adapted in a timely manner, since important open-source data are increasingly available and relevant for large-scale and real-time monitoring of biodiversity. PMID:27828993
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Song, Tian; Ding, Yan-wei; Sun, Yan; He, Yi-Ni; Qi, Dian-Jun; Wu, Ying; Wu, Bin; Lang, Lang; Yu, Kai; Zhao, Xin; Zhu, Liang-liang; Wang, Shuang; Yu, Xiao-Song
2015-09-19
Due to the rising standard of living environment and advances in public health and medical care in China, it has been a tendency in recent years that health-related quality of life (HRQoL) has been increasingly acknowledged in community health management. However, large-scale population-based study on evaluating HQRoL in northeast of China was not conducted. This article aims to investigate the HRQoL in community residents in Northeast China and explore the associated factors. Stratified multiple-stage sampling method was used in the cross-sectional survey to investigate HRQoL of community residents in northeast of China. Univariate analysis and multiple linear regressions were used to analyze the factors associated to HRQoL of the community residents. The results were confirmed that HRQoL in general population was well performed for the first time in northeast of China in a large scale population. Community residents had better mental health than physical health. The factors influencing HRQoL included gender, age, educational level, marital status, ethnic group, chronic disease status, having breakfast frequency weekly and sleep quality. However, drinking and smoking habits did not affect residents' HRQoL. In this study, the result of the large-scale survey was satisfactory in northeast of China, providing HRQoL status of community residents. Policies on specific health management in community public health would emphasize on lifestyle behaviors especially eating habits in order to improving HRQoL.
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A Ruby in the Rubbish: Beneficial Mutations, Deleterious Mutations and the Evolution of Sex
Peck, J. R.
1994-01-01
This study presents a mathematical model in which a single beneficial mutation arises in a very large population that is subject to frequent deleterious mutations. The results suggest that, if the population is sexual, then the deleterious mutations will have little effect on the ultimate fate of the beneficial mutation. However, if most offspring are produced asexually, then the probability that the beneficial mutation will be lost from the population may be greatly enhanced by the deleterious mutations. Thus, sexual populations may adapt much more quickly than populations where most reproduction is asexual. Some of the results were produced using computer simulation methods, and a technique was developed that allows treatment of arbitrarily large numbers of individuals in a reasonable amount of computer time. This technique may be of prove useful for the analysis of a wide variety of models, though there are some constraints on its applicability. For example, the technique requires that reproduction can be described by Poisson processes. PMID:8070669
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Ducrot, Arnaud; Giletti, Thomas
2014-09-01
In this work we study the asymptotic behaviour of the Kermack-McKendrick reaction-diffusion system in a periodic environment with non-diffusive susceptible population. This problem was proposed by Kallen et al. as a model for the spatial spread for epidemics, where it can be reasonable to assume that the susceptible population is motionless. For arbitrary dimensional space we prove that large classes of solutions of such a system have an asymptotic spreading speed in large time, and that the infected population has some pulse-like asymptotic shape. The analysis of the one-dimensional problem is more developed, as we are able to uncover a much more accurate description of the profile of solutions. Indeed, we will see that, for some initially compactly supported infected population, the profile of the solution converges to some pulsating travelling wave with minimal speed, that is to some entire solution moving at a constant positive speed and whose profile's shape is periodic in time.
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Population control methods in stochastic extinction and outbreak scenarios.
Segura, Juan; Hilker, Frank M; Franco, Daniel
2017-01-01
Adaptive limiter control (ALC) and adaptive threshold harvesting (ATH) are two related control methods that have been shown to stabilize fluctuating populations. Large variations in population abundance can threaten the constancy and the persistence stability of ecological populations, which may impede the success and efficiency of managing natural resources. Here, we consider population models that include biological mechanisms characteristic for causing extinctions on the one hand and pest outbreaks on the other hand. These models include Allee effects and the impact of natural enemies (as is typical of forest defoliating insects). We study the impacts of noise and different levels of biological parameters in three extinction and two outbreak scenarios. Our results show that ALC and ATH have an effect on extinction and outbreak risks only for sufficiently large control intensities. Moreover, there is a clear disparity between the two control methods: in the extinction scenarios, ALC can be effective and ATH can be counterproductive, whereas in the outbreak scenarios the situation is reversed, with ATH being effective and ALC being potentially counterproductive.
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ERIC Educational Resources Information Center
Sturges, Diana; Maurer, Trent W.; Cole, Oladipo
2009-01-01
This study investigated the effectiveness of role play in a large undergraduate science class. The targeted population consisted of 298 students enrolled in 2 sections of an undergraduate Human Anatomy and Physiology course taught by the same instructor. The section engaged in the role-play activity served as the study group, whereas the section…
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ERIC Educational Resources Information Center
Hallett, Victoria; Ronald, Angelica; Colvert, Emma; Ames, Catherine; Woodhouse, Emma; Lietz, Stephanie; Garnett, Tracy; Gillan, Nicola; Rijsdijk, Fruhling; Scahill, Lawrence; Bolton, Patrick; Happé, Francesca
2013-01-01
Background: Although many children with autism spectrum disorders (ASDs) experience difficulties with anxiety, the manifestation of these difficulties remains unresolved. The current study assessed anxiety in a large population-based twin sample, aged 10-15 years. Phenotypic analyses were used to explore anxiety symptoms in children with ASDs,…
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ERIC Educational Resources Information Center
Chiu, Pit Ho Patrio; Cheng, Shuk Han
2017-01-01
Recent studies on active learning classrooms (ACLs) have demonstrated their positive influence on student learning. However, most of the research evidence is derived from a few subject-specific courses or limited student enrolment. Empirical studies on this topic involving large student populations are rare. The present work involved a large-scale…
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Rajkumar, Revathi; Kashyap, V K
2004-08-19
A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations. Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe. The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them from the northern groups. Our study also indicates a heterogeneous origin for Lyngayat and Iyengar owing to their genetic proximity with southern populations and northern Brahmins. The high-ranking communities, in particular, Iyengar, Lyngayat, Vanniyar and northern Brahmins might have experienced genetic admixture from East Asian and European ethnic groups.
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Rajkumar, Revathi; Kashyap, VK
2004-01-01
Background A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations. Results Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe. Conclusion The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them from the northern groups. Our study also indicates a heterogeneous origin for Lyngayat and Iyengar owing to their genetic proximity with southern populations and northern Brahmins. The high-ranking communities, in particular, Iyengar, Lyngayat, Vanniyar and northern Brahmins might have experienced genetic admixture from East Asian and European ethnic groups. PMID:15317657
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Briggs-Gonzalez, Venetia; Bonefant, Christophe; Basille, Mathieu; Cherkiss, Michael S.; Beauchamp, Jeff; Mazzotti, Frank J.
2017-01-01
Successful species conservation is dependent on adequate estimates of population dynamics, but age-specific demographics are generally lacking for many long-lived iteroparous species such as large reptiles. Accurate demographic information allows estimation of population growth rate, as well as projection of future population sizes and quantitative analyses of fitness trade-offs involved in the evolution of life-history strategies.Here, a long-term capture–recapture study was conducted from 1978 to 2014 on the American crocodile (Crocodylus acutus) in southern Florida. Over the study period, 7,427 hatchlings were marked and 380 individuals were recaptured for as many as 25 years. We estimated survival to be strongly age dependent with hatchlings having the lowest survival rates (16%) but increasing to nearly 90% at adulthood based on mark–recapture models. More than 5% of the female population were predicted to be reproductive by age 8 years; the age-specific proportion of reproductive females steadily increased until age 18 when more than 95% of females were predicted to be reproductive. Population growth rate, estimated from a Leslie–Lefkovitch stage-class model, showed a positive annual growth rate of 4% over the study period.Using a prospective sensitivity analysis, we revealed that the adult stage, as expected, was the most critical stage for population growth rate; however, the survival of younger crocodiles before they became reproductive also had a surprisingly high elasticity. We found that variation in age-specific fecundity has very limited impact on population growth rate in American crocodiles.We used a comparative approach to show that the original life-history strategy of American crocodiles is actually shared by other large, long-lived reptiles: while adult survival rates always have a large impact on population growth, this decreases with declining increasing growth rates, in favour of a higher elasticity of the juvenile stage.Crocodiles, as a long-lived and highly fecund species, deviate from the usual association of life histories of “slow” species. Current management practices are focused on nests and hatchling survival; however, protection efforts that extend to juvenile crocodiles would be most effective for conservation of the species, especially in an ever-developing landscape.
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The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics.
Antunes, Agostinho; Troyer, Jennifer L; Roelke, Melody E; Pecon-Slattery, Jill; Packer, Craig; Winterbach, Christiaan; Winterbach, Hanlie; Hemson, Graham; Frank, Laurence; Stander, Philip; Siefert, Ludwig; Driciru, Margaret; Funston, Paul J; Alexander, Kathy A; Prager, Katherine C; Mills, Gus; Wildt, David; Bush, Mitch; O'Brien, Stephen J; Johnson, Warren E
2008-11-01
The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV(Ple)), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Phi(ST) = 0.92; nDNA F(ST) = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple) subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa ( approximately 324,000-169,000 years ago), which expanded during the Late Pleistocene ( approximately 100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple) variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.
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The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics
Antunes, Agostinho; Troyer, Jennifer L.; Roelke, Melody E.; Pecon-Slattery, Jill; Packer, Craig; Winterbach, Christiaan; Winterbach, Hanlie; Hemson, Graham; Frank, Laurence; Stander, Philip; Siefert, Ludwig; Driciru, Margaret; Funston, Paul J.; Alexander, Kathy A.; Prager, Katherine C.; Mills, Gus; Wildt, David; Bush, Mitch; O'Brien, Stephen J.; Johnson, Warren E.
2008-01-01
The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA ΦST = 0.92; nDNA F ST = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIVPle subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa (∼324,000–169,000 years ago), which expanded during the Late Pleistocene (∼100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition (∼14,000–7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIVPle variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently. PMID:18989457
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NASA Astrophysics Data System (ADS)
Jones, G. P.; Almany, G. R.; Russ, G. R.; Sale, P. F.; Steneck, R. S.; van Oppen, M. J. H.; Willis, B. L.
2009-06-01
The extent of larval dispersal on coral reefs has important implications for the persistence of coral reef metapopulations, their resilience and recovery from an increasing array of threats, and the success of protective measures. This article highlights a recent dramatic increase in research effort and a growing diversity of approaches to the study of larval retention within (self-recruitment) and dispersal among (connectivity) isolated coral reef populations. Historically, researchers were motivated by alternative hypotheses concerning the processes limiting populations and structuring coral reef assemblages, whereas the recent impetus has come largely from the need to incorporate dispersal information into the design of no-take marine protected area (MPA) networks. Although the majority of studies continue to rely on population genetic approaches to make inferences about dispersal, a wide range of techniques are now being employed, from small-scale larval tagging and paternity analyses, to large-scale biophysical circulation models. Multiple approaches are increasingly being applied to cross-validate and provide more realistic estimates of larval dispersal. The vast majority of empirical studies have focused on corals and fishes, where evidence for both extremely local scale patterns of self-recruitment and ecologically significant connectivity among reefs at scales of tens of kilometers (and in some cases hundreds of kilometers) is accumulating. Levels of larval retention and the spatial extent of connectivity in both corals and fishes appear to be largely independent of larval duration or reef size, but may be strongly influenced by geographic setting. It is argued that high levels of both self-recruitment and larval import can contribute to the resilience of reef populations and MPA networks, but these benefits will erode in degrading reef environments.
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Sensitive response of a model of symbiotic ecosystem to seasonal periodic drive
NASA Astrophysics Data System (ADS)
Rekker, A.; Lumi, N.; Mankin, R.
2014-11-01
A symbiotic ecosysytem (metapopulation) is studied by means of the stochastic Lotka-Volterra model with generalized Verhulst self-regulation. The effect of variable environment on the carrying capacities of populations is taken into account as an asymmetric dichotomous noise and as a deterministic periodic stimulus. In the framework of the mean-field theory an explicit self-consistency equation for the system in the long-time limit is presented. Also, expressions for the probability distribution and for the moments of the population size are found. In certain cases the mean population size exhibits large oscillations in time, even if the amplitude of the seasonal environmental drive is small. Particularly, it is shown that the occurrence of large oscillations of the mean population size can be controlled by noise parameters (such as amplitude and correlation time) and by the coupling strength of the symbiotic interaction between species.
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Extinction phase transitions in a model of ecological and evolutionary dynamics
NASA Astrophysics Data System (ADS)
Barghathi, Hatem; Tackkett, Skye; Vojta, Thomas
2017-07-01
We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental conditions, i.e., temporal disorder. Using large-scale Monte-Carlo simulations of up to 3 × 107 organisms and 105 generations, we find the extinction transition in time-independent environments to be in the well-known directed percolation universality class. In contrast, temporal disorder leads to a highly unusual extinction transition characterized by logarithmically slow population decay and enormous fluctuations even for large populations. The simulations provide strong evidence for this transition to be of exotic infinite-noise type, as recently predicted by a renormalization group theory. The transition is accompanied by temporal Griffiths phases featuring a power-law dependence of the life time on the population size.
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NASA Astrophysics Data System (ADS)
van der Marel, Nienke; Williams, Jonathan P.; Ansdell, M.; Manara, Carlo F.; Miotello, Anna; Tazzari, Marco; Testi, Leonardo; Hogerheijde, Michiel; Bruderer, Simon; van Terwisga, Sierk E.; van Dishoeck, Ewine F.
2018-02-01
Transition disks with large dust cavities around young stars are promising targets for studying planet formation. Previous studies have revealed the presence of gas cavities inside the dust cavities, hinting at recently formed, giant planets. However, many of these studies are biased toward the brightest disks in the nearby star-forming regions, and it is not possible to derive reliable statistics that can be compared with exoplanet populations. We present the analysis of 11 transition disks with large cavities (≥20 au radius) from a complete disk survey of the Lupus star-forming region, using ALMA Band 7 observations at 0.″3 (22–30 au radius) resolution of the 345 GHz continuum, 13CO and C18O 3–2 observations, and the spectral energy distribution of each source. Gas and dust surface density profiles are derived using the physical–chemical modeling code DALI. This is the first study of transition disks of large cavities within a complete disk survey within a star-forming region. The dust cavity sizes range from 20 to 90 au radius, and in three cases, a gas cavity is resolved as well. The deep drops in gas density and large dust cavity sizes are consistent with clearing by giant planets. The fraction of transition disks with large cavities in Lupus is ≳ 11 % , which is inconsistent with exoplanet population studies of giant planets at wide orbits. Furthermore, we present a hypothesis of an evolutionary path for large massive disks evolving into transition disks with large cavities.
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Stellar density distribution along the minor axis of the Large Magellanic Cloud
NASA Astrophysics Data System (ADS)
Piatti, Andrés E.
2018-02-01
We studied the spatial distribution of young and old stellar populations along the western half part of the minor axis of the Large Magellanic Cloud (LMC) using Washington MT1 photometry of selected fields, which span a deprojected distance range from the LMC bar centre out to ∼31.6 kpc. We found that both stellar populations share a mean LMC limiting radius of 8.9 ± 0.4 kpc; old populations are three times more dense than young populations at that LMC limit. When comparing this result with recent values for the LMC extension due to north, the old populations resulted significantly more elongated than the young ones. Bearing in mind previous claims that the elongation of the outermost LMC regions may be due to the tidal effects of the Milky Way (MW), our findings suggest that such a tidal interaction should not have taken place recently. The existence of young populations in the outermost western regions also supports previous results about ram pressure stripping effects of the LMC gaseous disc due to the motion of the LMC in the MW halo.
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Kalichman, Seth; Katner, Harold; Banas, Ellen; Kalichman, Moira
2017-07-01
AIDS stigmas delay HIV diagnosis, interfere with health care, and contribute to mental health problems among people living with HIV. While there are few studies of the geographical distribution of AIDS stigma, research suggests that AIDS stigmas are differentially experienced in rural and urban areas. We conducted computerized interviews with 696 men and women living with HIV in 113 different zip code areas that were classified as large-urban, small-urban, and rural areas in a southeast US state with high-HIV prevalence. Analyses conducted at the individual level (N = 696) accounting for clustering at the zip code level showed that internalized AIDS-related stigma (e.g., the sense of being inferior to others because of HIV) was experienced with greater magnitude in less densely populated communities. Multilevel models indicated that after adjusting for potential confounding factors, rural communities reported greater internalized AIDS-related stigma compared to large-urban areas and that small-urban areas indicated greater experiences of enacted stigma (e.g., discrimination) than large-urban areas. The associations between anticipated AIDS-related stigma (e.g., expecting discrimination) and population density at the community-level were not significant. Results suggest that people living in rural and small-urban settings experience greater AIDS-related internalized and enacted stigma than their counterparts living in large-urban centers. Research is needed to determine whether low-density population areas contribute to or are sought out by people who experienced greater AIDS-related stigma. Regardless of causal directions, interventions are needed to address AIDS-related stigma, especially among people in sparsely populated areas with limited resources.
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Field cage studies and progressive evaluation of genetically-engineered mosquitoes.
Facchinelli, Luca; Valerio, Laura; Ramsey, Janine M; Gould, Fred; Walsh, Rachael K; Bond, Guillermo; Robert, Michael A; Lloyd, Alun L; James, Anthony A; Alphey, Luke; Scott, Thomas W
2013-01-01
A genetically-engineered strain of the dengue mosquito vector Aedes aegypti, designated OX3604C, was evaluated in large outdoor cage trials for its potential to improve dengue prevention efforts by inducing population suppression. OX3604C is engineered with a repressible genetic construct that causes a female-specific flightless phenotype. Wild-type females that mate with homozygous OX3604C males will not produce reproductive female offspring. Weekly introductions of OX3604C males eliminated all three targeted Ae. aegypti populations after 10-20 weeks in a previous laboratory cage experiment. As part of the phased, progressive evaluation of this technology, we carried out an assessment in large outdoor field enclosures in dengue endemic southern Mexico. OX3604C males were introduced weekly into field cages containing stable target populations, initially at 10:1 ratios. Statistically significant target population decreases were detected in 4 of 5 treatment cages after 17 weeks, but none of the treatment populations were eliminated. Mating competitiveness experiments, carried out to explore the discrepancy between lab and field cage results revealed a maximum mating disadvantage of up 59.1% for OX3604C males, which accounted for a significant part of the 97% fitness cost predicted by a mathematical model to be necessary to produce the field cage results. Our results indicate that OX3604C may not be effective in large-scale releases. A strain with the same transgene that is not encumbered by a large mating disadvantage, however, could have improved prospects for dengue prevention. Insights from large outdoor cage experiments may provide an important part of the progressive, stepwise evaluation of genetically-engineered mosquitoes.
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Field Cage Studies and Progressive Evaluation of Genetically-Engineered Mosquitoes
Facchinelli, Luca; Valerio, Laura; Ramsey, Janine M.; Gould, Fred; Walsh, Rachael K.; Bond, Guillermo; Robert, Michael A.; Lloyd, Alun L.; James, Anthony A.; Alphey, Luke; Scott, Thomas W.
2013-01-01
Background A genetically-engineered strain of the dengue mosquito vector Aedes aegypti, designated OX3604C, was evaluated in large outdoor cage trials for its potential to improve dengue prevention efforts by inducing population suppression. OX3604C is engineered with a repressible genetic construct that causes a female-specific flightless phenotype. Wild-type females that mate with homozygous OX3604C males will not produce reproductive female offspring. Weekly introductions of OX3604C males eliminated all three targeted Ae. aegypti populations after 10–20 weeks in a previous laboratory cage experiment. As part of the phased, progressive evaluation of this technology, we carried out an assessment in large outdoor field enclosures in dengue endemic southern Mexico. Methodology/Principal Findings OX3604C males were introduced weekly into field cages containing stable target populations, initially at 10∶1 ratios. Statistically significant target population decreases were detected in 4 of 5 treatment cages after 17 weeks, but none of the treatment populations were eliminated. Mating competitiveness experiments, carried out to explore the discrepancy between lab and field cage results revealed a maximum mating disadvantage of up 59.1% for OX3604C males, which accounted for a significant part of the 97% fitness cost predicted by a mathematical model to be necessary to produce the field cage results. Conclusions/Significance Our results indicate that OX3604C may not be effective in large-scale releases. A strain with the same transgene that is not encumbered by a large mating disadvantage, however, could have improved prospects for dengue prevention. Insights from large outdoor cage experiments may provide an important part of the progressive, stepwise evaluation of genetically-engineered mosquitoes. PMID:23350003
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A sequential coalescent algorithm for chromosomal inversions
Peischl, S; Koch, E; Guerrero, R F; Kirkpatrick, M
2013-01-01
Chromosomal inversions are common in natural populations and are believed to be involved in many important evolutionary phenomena, including speciation, the evolution of sex chromosomes and local adaptation. While recent advances in sequencing and genotyping methods are leading to rapidly increasing amounts of genome-wide sequence data that reveal interesting patterns of genetic variation within inverted regions, efficient simulation methods to study these patterns are largely missing. In this work, we extend the sequential Markovian coalescent, an approximation to the coalescent with recombination, to include the effects of polymorphic inversions on patterns of recombination. Results show that our algorithm is fast, memory-efficient and accurate, making it feasible to simulate large inversions in large populations for the first time. The SMC algorithm enables studies of patterns of genetic variation (for example, linkage disequilibria) and tests of hypotheses (using simulation-based approaches) that were previously intractable. PMID:23632894
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NASA Astrophysics Data System (ADS)
Grange, Sophie; Owen-Smith, Norman; Gaillard, Jean-Michel; Druce, Dave J.; Moleón, Marcos; Mgobozi, Mandisa
2012-07-01
Large predators have been reintroduced to an increasing number of protected areas in South Africa. However, the conditions allowing both prey and predator populations to be sustained in enclosed areas are still unclear as there is a lack of understanding of the consequences of such reintroductions for ungulate population dynamics. Variation in lion numbers, two decades after their first release, offered a special opportunity to test the effects of predation pressure on the population dynamics of seven ungulate species in the 960 km2 Hluhluwe-iMfolozi Park (HiP), South Africa. We used two different approaches to examine predator-prey relationships: the population response of ungulates to predation pressure after accounting for possible confounding factors, and the pattern of ungulate adult mortality observed from carcass records. Rainfall patterns affected observed mortalities of several ungulate species in HiP. Although lion predation accounted for most ungulate mortality, it still had no detectable influence on ungulate population trends and mortality patterns, with one possible exception. This evidence suggests that the lion population had not yet attained the maximum abundance potentially supported by their ungulate prey; but following recent increases in lion numbers it will probably occur soon. It remains uncertain whether a quasi-stable balance will be reached between prey and predator populations, or whether favoured prey species will be depressed towards levels potentially generating oscillatory dynamics in this complex large mammal assemblage. We specifically recommend a continuous monitoring of predator and prey populations in HiP since lions are likely to show more impacts on their prey species in the next years.
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"I Am Here for a Reason": Minority Teachers Bridging Many Divides in Urban Education
ERIC Educational Resources Information Center
Magaldi, Danielle; Conway, Timothy; Trub, Leora
2018-01-01
Minority teachers are overwhelmingly employed in urban schools in underserved, low-income communities with large minority student populations. They receive little in the way of multicultural preparation, mentorship, and professional induction to meet the demands of teaching diverse student populations. This grounded theory study explores the…
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Climate-related genetic variation in drought-resistance of Douglas-fir ( Pseudotsuga menziesii )
Sheel Bansal; Constance A. Harrington; Peter J. Gould; J. Bradley St.Clair
2014-01-01
There is a general assumption that intraspecific populations originating from relatively arid climates will be better adapted to cope with the expected increase in drought from climate change. For ecologically and economically important species, more comprehensive, genecological studies that utilize large distributions of populations and direct measures of traits...
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ERIC Educational Resources Information Center
Laeger-Hagemeister, Mary A.
2011-01-01
Combining social capital theory and immigration history and theory a qualitative study was conducted using a variation of Critical Incident Technique to identify the motivations of individuals in rural communities who championed community responses to the influx of large immigrant populations. Twenty-eight individuals identified as key champions…
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Genetic variation of apolipoproteins, diet and other environmental interactions; an updated review.
Sotos-Prieto, Mercedes; Peñalvo, José Luis
2013-01-01
This paper summarizes the recent findings from studies investigating the potential environmental modulation of the genetic variation of apolipoprotein genes on metabolic traits. We reviewed nutrigenetic studies evaluating variations on apolipoproteins-related genes and its associated response to nutrients (mostly dietary fatty acids) or any other dietary or environmental component. Most revised research studied single nucleotide polymorphism (SNP) and specific nutrients through small intervention studies, and only few interactions have been replicated in large and independent populations (as in the case of -265T > C SNP in APOA2 gene). Although current knowledge shows that variations on apolipoprotein genes may contribute to the different response on metabolic traits due to dietary interventions, evidence is still scarce and results are inconsistent. Success in this area will require going beyond the limitations of current experimental designs and explore the hypotheses within large populations. Some of these limitations are being covered by the rapidly advance in high-throughput technologies and large scale-genome wide association studies. Copyright © AULA MEDICA EDICIONES 2013. Published by AULA MEDICA. All rights reserved.
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Zhang, Ge; Karns, Rebekah; Sun, Guangyun; Indugula, Subba Rao; Cheng, Hong; Havas-Augustin, Dubravka; Novokmet, Natalija; Rudan, Dusko; Durakovic, Zijad; Missoni, Sasa; Chakraborty, Ranajit; Rudan, Pavao; Deka, Ranjan
2011-01-01
Human height is a classical example of a polygenic quantitative trait. Recent large-scale genome-wide association studies (GWAS) have identified more than 200 height-associated loci, though these variants explain only 2∼10% of overall variability of normal height. The objective of this study was to investigate the variance explained by these loci in a relatively isolated population of European descent with limited admixture and homogeneous genetic background from the Adriatic coast of Croatia. In a sample of 1304 individuals from the island population of Hvar, Croatia, we performed genome-wide SNP typing and assessed the variance explained by genetic scores constructed from different panels of height-associated SNPs extracted from five published studies. The combined information of the 180 SNPs reported by Lango Allen el al. explained 7.94% of phenotypic variation in our sample. Genetic scores based on 20~50 SNPs reported by the remaining individual GWA studies explained 3~5% of height variance. These percentages of variance explained were within ranges comparable to the original studies and heterogeneity tests did not detect significant differences in effect size estimates between our study and the original reports, if the estimates were obtained from populations of European descent. We have evaluated the portability of height-associated loci and the overall fitting of estimated effect sizes reported in large cohorts to an isolated population. We found proportions of explained height variability were comparable to multiple reference GWAS in cohorts of European descent. These results indicate similar genetic architecture and comparable effect sizes of height loci among populations of European descent. © 2011 Zhang et al.
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Taylor, R T; Solis, M; Weathers, D B; Taylor, J W
1975-03-01
In a large-scale study in the Miragoane Valley of Haiti, designed to test the effects of aerial ultralow volume (ULV) malathion on epidemic Plasmodium falciparum malaria, spray operations resulted in an immediate and sharp decline in numbers of the vector, Anopheles albimanus. The adult population of this mosquito remained at less than 1% of previous levels until several weeks after a 50-day spray period (27 October-16 December 1972) during which six cycles were completed. The study area offered ideal conditions of wind, temperature, humidity, and mountain barriers. Mosquitoes in the area were highly susceptible to malathion. Results indicated that aerial ULV treatment with malathion can reduce A. albimanus populations rapidly and effectively when applications are made over an area as large as 20,000 acres. Preliminary results showed that effective control was not achieved in areas one-quarter that size; these areas were not sufficiently large, and infiltration of mosquitoes from adjacent untreated areas was possible.
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ERIC Educational Resources Information Center
Fleisch, Brahm; Taylor, Stephen; Schöer, Volker; Mabogoane, Thabo
2017-01-01
This article illustrates the value of large-scale impact evaluations with counterfactual components. It begins by exploring the limitations of small-scale impact studies, which do not allow reliable inference to a wider population or which do not use valid comparison groups. The paper then describes the design features of a recent large-scale…
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Zhang, X; Platt, R W; Cnattingius, S; Joseph, K S; Kramer, M S
2007-04-01
The objective of this study was to critically examine potential artifacts and biases underlying the use of 'customised' standards of birthweight for gestational age (GA). Population-based cohort study. Sweden. A total of 782,303 singletons > or =28 weeks of gestation born in 1992-2001 to Nordic mothers with complete data on birthweight; GA; and maternal age, parity, height, and pre-pregnancy weight. We compared perinatal mortality in four groups of infants based on the following classification of small for gestational age (SGA): non-SGA based on either population-based or customised standards (the reference group), SGA based on the population-based standard only, SGA based on the customised standard only, and SGA according to both standards. We used graphical methods to compare GA-specific birthweight cutoffs for SGA using the two standards and also used logistic regression to control for differences in GA and maternal pre-pregnancy body mass index (BMI) in the four groups. Perinatal mortality, including stillbirth and neonatal death. Customisation led to a large artifactual increase in the proportion of SGA infants born preterm. Adjustment for differences in GA and maternal BMI markedly reduced the excess risk among infants classified as SGA by customised standards only. The large increase in perinatal mortality risk among infants classified as SGA based on customised standards is largely an artifact due to inclusion of more preterm births.
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de Pesters, A; Coon, W G; Brunner, P; Gunduz, A; Ritaccio, A L; Brunet, N M; de Weerd, P; Roberts, M J; Oostenveld, R; Fries, P; Schalk, G
2016-07-01
Performing different tasks, such as generating motor movements or processing sensory input, requires the recruitment of specific networks of neuronal populations. Previous studies suggested that power variations in the alpha band (8-12Hz) may implement such recruitment of task-specific populations by increasing cortical excitability in task-related areas while inhibiting population-level cortical activity in task-unrelated areas (Klimesch et al., 2007; Jensen and Mazaheri, 2010). However, the precise temporal and spatial relationships between the modulatory function implemented by alpha oscillations and population-level cortical activity remained undefined. Furthermore, while several studies suggested that alpha power indexes task-related populations across large and spatially separated cortical areas, it was largely unclear whether alpha power also differentially indexes smaller networks of task-related neuronal populations. Here we addressed these questions by investigating the temporal and spatial relationships of electrocorticographic (ECoG) power modulations in the alpha band and in the broadband gamma range (70-170Hz, indexing population-level activity) during auditory and motor tasks in five human subjects and one macaque monkey. In line with previous research, our results confirm that broadband gamma power accurately tracks task-related behavior and that alpha power decreases in task-related areas. More importantly, they demonstrate that alpha power suppression lags population-level activity in auditory areas during the auditory task, but precedes it in motor areas during the motor task. This suppression of alpha power in task-related areas was accompanied by an increase in areas not related to the task. In addition, we show for the first time that these differential modulations of alpha power could be observed not only across widely distributed systems (e.g., motor vs. auditory system), but also within the auditory system. Specifically, alpha power was suppressed in the locations within the auditory system that most robustly responded to particular sound stimuli. Altogether, our results provide experimental evidence for a mechanism that preferentially recruits task-related neuronal populations by increasing cortical excitability in task-related cortical areas and decreasing cortical excitability in task-unrelated areas. This mechanism is implemented by variations in alpha power and is common to humans and the non-human primate under study. These results contribute to an increasingly refined understanding of the mechanisms underlying the selection of the specific neuronal populations required for task execution. Copyright © 2016 Elsevier Inc. All rights reserved.
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Construction and analysis of a giant gartersnake (Thamnophis gigas) population projection model
Rose, Jonathan P.; Ersan, Julia S. M.; Wylie, Glenn D.; Casazza, Michael L.; Halstead, Brian J.
2018-03-19
The giant gartersnake (Thamnophis gigas) is a state and federally threatened species precinctive to California. The range of the giant gartersnake has contracted in the last century because its wetland habitat has been drained for agriculture and development. As a result of this habitat alteration, giant gartersnakes now largely persist in and near rice agriculture in the Sacramento Valley, because the system of canals that conveys water for rice growing approximates historical wetland habitat. Many aspects of the demography of giant gartersnakes are unknown, including how individuals grow throughout their life, how size influences reproduction, and how survival varies over time and among populations. We studied giant gartersnakes throughout the Sacramento Valley of California from 1995 to 2016 using capture-mark-recapture to study the growth, reproduction, and survival of this threatened species. We then use these data to construct an Integral Projection Model, and analyze this demographic model to understand which vital rates contribute most to the growth rate of giant gartersnake populations. We find that giant gartersnakes exhibit indeterminate growth; growth slows as individuals’ age. Fecundity, probability of reproduction, and survival all increase with size, although survival may decline for the largest female giant gartersnakes. The population growth rate of giant gartersnakes is most influenced by the survival and growth of large adult females, and the size at which 1 year old recruits enter the population. Our results indicate that management actions benefitting these influential demographic parameters will have the greatest positive effect on giant gartersnake population growth rates, and therefore population persistence. This study informs the conservation and management of giant gartersnakes and their habitat, and illustrates the effectiveness of hierarchical Bayesian models for the study of rare and elusive species.
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Otwoma, Levy Michael; Kochzius, Marc
2016-01-01
The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean.
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Kochzius, Marc
2016-01-01
The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean. PMID:27798700
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Estimating trends in alligator populations from nightlight survey data
Fujisaki, Ikuko; Mazzotti, Frank J.; Dorazio, Robert M.; Rice, Kenneth G.; Cherkiss, Michael; Jeffery, Brian
2011-01-01
Nightlight surveys are commonly used to evaluate status and trends of crocodilian populations, but imperfect detection caused by survey- and location-specific factors makes it difficult to draw population inferences accurately from uncorrected data. We used a two-stage hierarchical model comprising population abundance and detection probability to examine recent abundance trends of American alligators (Alligator mississippiensis) in subareas of Everglades wetlands in Florida using nightlight survey data. During 2001–2008, there were declining trends in abundance of small and/or medium sized animals in a majority of subareas, whereas abundance of large sized animals had either demonstrated an increased or unclear trend. For small and large sized class animals, estimated detection probability declined as water depth increased. Detection probability of small animals was much lower than for larger size classes. The declining trend of smaller alligators may reflect a natural population response to the fluctuating environment of Everglades wetlands under modified hydrology. It may have negative implications for the future of alligator populations in this region, particularly if habitat conditions do not favor recruitment of offspring in the near term. Our study provides a foundation to improve inferences made from nightlight surveys of other crocodilian populations.
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Estimating trends in alligator populations from nightlight survey data
Fujisaki, Ikuko; Mazzotti, F.J.; Dorazio, R.M.; Rice, K.G.; Cherkiss, M.; Jeffery, B.
2011-01-01
Nightlight surveys are commonly used to evaluate status and trends of crocodilian populations, but imperfect detection caused by survey- and location-specific factors makes it difficult to draw population inferences accurately from uncorrected data. We used a two-stage hierarchical model comprising population abundance and detection probability to examine recent abundance trends of American alligators (Alligator mississippiensis) in subareas of Everglades wetlands in Florida using nightlight survey data. During 2001-2008, there were declining trends in abundance of small and/or medium sized animals in a majority of subareas, whereas abundance of large sized animals had either demonstrated an increased or unclear trend. For small and large sized class animals, estimated detection probability declined as water depth increased. Detection probability of small animals was much lower than for larger size classes. The declining trend of smaller alligators may reflect a natural population response to the fluctuating environment of Everglades wetlands under modified hydrology. It may have negative implications for the future of alligator populations in this region, particularly if habitat conditions do not favor recruitment of offspring in the near term. Our study provides a foundation to improve inferences made from nightlight surveys of other crocodilian populations. ?? 2011 US Government.
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Dewitt, James; Capistrant, Benjamin; Kohli, Nidhi; Mitteldorf, Darryl; Merengwa, Enyinnaya; West, William
2018-01-01
Background While deduplication and cross-validation protocols have been recommended for large Web-based studies, protocols for survey response validation of smaller studies have not been published. Objective This paper reports the challenges of survey validation inherent in a small Web-based health survey research. Methods The subject population was North American, gay and bisexual, prostate cancer survivors, who represent an under-researched, hidden, difficult-to-recruit, minority-within-a-minority population. In 2015-2016, advertising on a large Web-based cancer survivor support network, using email and social media, yielded 478 completed surveys. Results Our manual deduplication and cross-validation protocol identified 289 survey submissions (289/478, 60.4%) as likely spam, most stemming from advertising on social media. The basic components of this deduplication and validation protocol are detailed. An unexpected challenge encountered was invalid survey responses evolving across the study period. This necessitated the static detection protocol be augmented with a dynamic one. Conclusions Five recommendations for validation of Web-based samples, especially with smaller difficult-to-recruit populations, are detailed. PMID:29691203
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Effect of genotyped cows in the reference population on the genomic evaluation of Holstein cattle.
Uemoto, Y; Osawa, T; Saburi, J
2017-03-01
This study evaluated the dependence of reliability and prediction bias on the prediction method, the contribution of including animals (bulls or cows), and the genetic relatedness, when including genotyped cows in the progeny-tested bull reference population. We performed genomic evaluation using a Japanese Holstein population, and assessed the accuracy of genomic enhanced breeding value (GEBV) for three production traits and 13 linear conformation traits. A total of 4564 animals for production traits and 4172 animals for conformation traits were genotyped using Illumina BovineSNP50 array. Single- and multi-step methods were compared for predicting GEBV in genotyped bull-only and genotyped bull-cow reference populations. No large differences in realized reliability and regression coefficient were found between the two reference populations; however, a slight difference was found between the two methods for production traits. The accuracy of GEBV determined by single-step method increased slightly when genotyped cows were included in the bull reference population, but decreased slightly by multi-step method. A validation study was used to evaluate the accuracy of GEBV when 800 additional genotyped bulls (POPbull) or cows (POPcow) were included in the base reference population composed of 2000 genotyped bulls. The realized reliabilities of POPbull were higher than those of POPcow for all traits. For the gain of realized reliability over the base reference population, the average ratios of POPbull gain to POPcow gain for production traits and conformation traits were 2.6 and 7.2, respectively, and the ratios depended on heritabilities of the traits. For regression coefficient, no large differences were found between the results for POPbull and POPcow. Another validation study was performed to investigate the effect of genetic relatedness between cows and bulls in the reference and test populations. The effect of genetic relationship among bulls in the reference population was also assessed. The results showed that it is important to account for relatedness among bulls in the reference population. Our studies indicate that the prediction method, the contribution ratio of including animals, and genetic relatedness could affect the prediction accuracy in genomic evaluation of Holstein cattle, when including genotyped cows in the reference population.
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Kilburn, K H; Warshaw, R H; Thornton, J C; Thornton, K; Miller, A
1992-01-01
BACKGROUND: Published predicted values for total lung capacity and residual volume are often based on a small number of subjects and derive from different populations from predicted spirometric values. Equations from the only two large studies gave smaller predicted values for total lung capacity than the smaller studies. A large number of subjects have been studied from a population which has already provided predicted values for spirometry and transfer factor for carbon monoxide. METHODS: Total lung capacity was measured from standard posteroanterior and lateral chest radiographs and forced vital capacity by spirometry in a population sample of 771 subjects. Prediction equations were developed for total lung capacity (TLC), residual volume (RV) and RV/TLC in two groups--normal and total. Subjects with signs or symptoms of cardiopulmonary disease were combined with the normal subjects and equations for all subjects were also modelled. RESULTS: Prediction equations for TLC and RV in non-smoking normal men and women were square root transformations which included height and weight but not age. They included a coefficient for duration of smoking in current smokers. The predictive equation for RV/TLC included weight, age, age and duration of smoking for current smokers and ex-smokers of both sexes. For the total population the equations took the same form but the height coefficients and constants were slightly different. CONCLUSION: These population based prediction equations for TLC, RV and RV/TLC provide reference standards in a population that has provided reference standards for spirometry and single breath transfer factor for carbon monoxide. PMID:1412094
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Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate
Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.
2002-01-01
Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601
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Schuler, Hannes; Köppler, Kirsten; Daxböck-Horvath, Sabine; Rasool, Bilal; Krumböck, Susanne; Schwarz, Dietmar; Hoffmeister, Thomas S; Schlick-Steiner, Birgit C; Steiner, Florian M; Telschow, Arndt; Stauffer, Christian; Arthofer, Wolfgang; Riegler, Markus
2016-04-01
Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15-year-long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in Germany. Across most of Europe, populations consisted of either 100% singly (wCer1) infected individuals with haplotype HT1, or 100% doubly (wCer1&2) infected individuals with haplotype HT2, differentiated only by a single nucleotide polymorphism. In central Germany, singly infected populations were surrounded by transitional populations, consisting of both singly and doubly infected individuals, sandwiched between populations fixed for wCer1&2. Populations with fixed infection status showed perfect association of infection and mitochondria, suggesting a recent CI-driven selective sweep of wCer2 linked with HT2. Spatial analysis revealed a range expansion for wCer2 and a large transition zone in which wCer2 splashes appeared to coalesce into doubly infected populations. Unexpectedly, the transition zone contained a large proportion (22%) of wCer1&2 individuals with HT1, suggesting frequent intraspecific horizontal transmission. However, this horizontal transmission did not break the strict association between infection types and haplotypes in populations outside the transition zone, suggesting that this horizontally acquired Wolbachia infection may be transient. Our study provides new insights into the rarely studied Wolbachia invasion dynamics in field populations. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.
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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.
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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.
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The direct cost of epilepsy in the United States: A systematic review of estimates.
Begley, Charles E; Durgin, Tracy L
2015-09-01
To develop estimates of the direct cost of epilepsy in the United States for the general epilepsy population and sub-populations by systematically comparing similarities and differences in types of estimates and estimation methods from recently published studies. Papers published since 1995 were identified by systematic literature search. Information on types of estimates, study designs, data sources, types of epilepsy, and estimation methods was extracted from each study. Annual per person cost estimates from methodologically similar studies were identified, converted to 2013 U.S. dollars, and compared. From 4,104 publications discovered in the literature search, 21 were selected for review. Three were added that were published after the search. Eighteen were identified that reported estimates of average annual direct costs for the general epilepsy population in the United States. For general epilepsy populations (comprising all clinically defined subgroups), total direct healthcare costs per person ranged from $10,192 to $47,862 and epilepsy-specific costs ranged from $1,022 to $19,749. Four recent studies using claims data from large general populations yielded relatively similar epilepsy-specific annual cost estimates ranging from $8,412 to $11,354. Although more difficult to compare, studies examining direct cost differences for epilepsy sub-populations indicated a consistent pattern of markedly higher costs for those with uncontrolled or refractory epilepsy, and for those with comorbidities. This systematic review found that various approaches have been used to estimate the direct costs of epilepsy in the United States. However, recent studies using large claims databases and similar methods allow estimation of the direct cost burden of epilepsy for the general disease population, and show that it is greater for some patient subgroups. Additional research is needed to further understand the broader economic burden of epilepsy and how it varies across subpopulations. Wiley Periodicals, Inc. © 2015 International League Against Epilepsy.
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Dispersal and gene flow in the rare, parasitic Large Blue butterfly Maculinea arion.
Ugelvig, L V; Andersen, A; Boomsma, J J; Nash, D R
2012-07-01
Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼20km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10km. © 2012 Blackwell Publishing Ltd.
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Yagasaki, Hiroshi; Hamanoue, Satoshi; Oda, Tsukasa; Nakahata, Tatsutoshi; Asano, Shigetaka; Yamashita, Takayuki
2004-12-01
Fanconi anemia (FA) is a rare autosomal recessive disorder of hematopoiesis, with at least 11 complementation groups. FANCA, a gene for group A, accounts for the majority of FA patients. Previous studies of FANCA mutations revealed high allelic heterogeneity, frequent occurrence of large deletions, and interpopulation differences. However, systematic mutational analysis, including gene dosage assay to detect large deletions, has not been documented for Asian populations. A newly developed TaqMan quantitative PCR-based gene dosage assay, combined with sequencing of exons and cDNA fragments, allowed for detection of 48 mutant alleles of FANCA in 27 (77%) of 35 unrelated Japanese FA families with no detectable mutations in FANCC or FANCG. We identified 29 different mutations (21 nucleotide substitutions or small deletions/insertions and eight large deletions), at least 20 of which were novel. The FANCA mutational spectrum of the Japanese was different from that of other ethnic groups so far studied. This is the largest scale of mutation analysis of FANCA in the Japanese population. Characterization of these mutations provided new information regarding the mutagenesis mechanisms and structure-function relationship of FANCA. Specifically, our data suggest that diverse mechanisms including nonhomologous recombination as well as Alu-mediated homologous recombination are involved in the generation of large deletions in FANCA. Copyright 2004 Wiley-Liss, Inc.
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Hammond, Kenric W; Ben-Ari, Alon Y; Laundry, Ryan J; Boyko, Edward J; Samore, Matthew H
2015-12-01
Free text in electronic health records resists large-scale analysis. Text records facts of interest not found in encoded data, and text mining enables their retrieval and quantification. The U.S. Department of Veterans Affairs (VA) clinical data repository affords an opportunity to apply text-mining methodology to study clinical questions in large populations. To assess the feasibility of text mining, investigation of the relationship between exposure to adverse childhood experiences (ACEs) and recorded diagnoses was conducted among all VA-treated Gulf war veterans, utilizing all progress notes recorded from 2000-2011. Text processing extracted ACE exposures recorded among 44.7 million clinical notes belonging to 243,973 veterans. The relationship of ACE exposure to adult illnesses was analyzed using logistic regression. Bias considerations were assessed. ACE score was strongly associated with suicide attempts and serious mental disorders (ORs = 1.84 to 1.97), and less so with behaviorally mediated and somatic conditions (ORs = 1.02 to 1.36) per unit. Bias adjustments did not remove persistent associations between ACE score and most illnesses. Text mining to detect ACE exposure in a large population was feasible. Analysis of the relationship between ACE score and adult health conditions yielded patterns of association consistent with prior research. Copyright © 2015 International Society for Traumatic Stress Studies.
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Early signs of recovery of Acropora palmata in St. John, US Virgin Islands
Muller, E.M.; Rogers, Caroline S.; van Woesik, R.
2014-01-01
Since the 1980s, diseases have caused significant declines in the population of the threatened Caribbean coral Acropora palmata. Yet it is largely unknown whether the population densities have recovered from these declines and whether there have been any recent shifts in size-frequency distributions toward large colonies. It is also unknown whether colony size influences the risk of disease infection, the most common stressor affecting this species. To address these unknowns, we examined A. palmata colonies at ten sites around St. John, US Virgin Islands, in 2004 and 2010. The prevalence of white-pox disease was highly variable among sites, ranging from 0 to 53 %, and this disease preferentially targeted large colonies. We found that colony density did not significantly change over the 6-year period, although six out of ten sites showed higher densities through time. The size-frequency distributions of coral colonies at all sites were positively skewed in both 2004 and 2010, however, most sites showed a temporal shift toward more large-sized colonies. This increase in large-sized colonies occurred despite the presence of white-pox disease, a severe bleaching event, and several storms. This study provides evidence of slow recovery of the A. palmata population around St. John despite the persistence of several stressors.
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2014-01-01
Background Coronary heart disease and stroke are major contributors to preventable mortality. Evidence links work conditions to these diseases; however, occupational data are perceived to be difficult to collect for large population-based cohorts. We report methodological details and the feasibility of conducting an occupational ancillary study for a large U.S. prospective cohort being followed longitudinally for cardiovascular disease and stroke. Methods Current and historical occupational information were collected from active participants of the REasons for Geographic And Racial Differences in Stroke (REGARDS) Study. A survey was designed to gather quality occupational data among this national cohort of black and white men and women aged 45 years and older (enrolled 2003–2007). Trained staff conducted Computer-Assisted Telephone Interviews (CATI). After a brief pilot period, interviewers received additional training in the collection of narrative industry and occupation data before administering the survey to remaining cohort members. Trained coders used a computer-assisted coding system to assign U.S. Census codes for industry and occupation. All data were double coded; discrepant codes were independently resolved. Results Over a 2-year period, 17,648 participants provided consent and completed the occupational survey (87% response rate). A total of 20,427 jobs were assigned Census codes. Inter-rater reliability was 80% for industry and 74% for occupation. Less than 0.5% of the industry and occupation data were uncodable, compared with 12% during the pilot period. Concordance between the current and longest-held jobs was moderately high. The median time to collect employment status plus narrative and descriptive job information by CATI was 1.6 to 2.3 minutes per job. Median time to assign Census codes was 1.3 minutes per rater. Conclusions The feasibility of conducting high-quality occupational data collection and coding for a large heterogeneous population-based sample was demonstrated. We found that training for interview staff was important in ensuring that narrative responses for industry and occupation were adequately specified for coding. Estimates of survey administration time and coding from digital records provide an objective basis for planning future studies. The social and environmental conditions of work are important understudied risk factors that can be feasibly integrated into large population-based health studies. PMID:24512119
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MacDonald, Leslie A; Pulley, LeaVonne; Hein, Misty J; Howard, Virginia J
2014-02-10
Coronary heart disease and stroke are major contributors to preventable mortality. Evidence links work conditions to these diseases; however, occupational data are perceived to be difficult to collect for large population-based cohorts. We report methodological details and the feasibility of conducting an occupational ancillary study for a large U.S. prospective cohort being followed longitudinally for cardiovascular disease and stroke. Current and historical occupational information were collected from active participants of the REasons for Geographic And Racial Differences in Stroke (REGARDS) Study. A survey was designed to gather quality occupational data among this national cohort of black and white men and women aged 45 years and older (enrolled 2003-2007). Trained staff conducted Computer-Assisted Telephone Interviews (CATI). After a brief pilot period, interviewers received additional training in the collection of narrative industry and occupation data before administering the survey to remaining cohort members. Trained coders used a computer-assisted coding system to assign U.S. Census codes for industry and occupation. All data were double coded; discrepant codes were independently resolved. Over a 2-year period, 17,648 participants provided consent and completed the occupational survey (87% response rate). A total of 20,427 jobs were assigned Census codes. Inter-rater reliability was 80% for industry and 74% for occupation. Less than 0.5% of the industry and occupation data were uncodable, compared with 12% during the pilot period. Concordance between the current and longest-held jobs was moderately high. The median time to collect employment status plus narrative and descriptive job information by CATI was 1.6 to 2.3 minutes per job. Median time to assign Census codes was 1.3 minutes per rater. The feasibility of conducting high-quality occupational data collection and coding for a large heterogeneous population-based sample was demonstrated. We found that training for interview staff was important in ensuring that narrative responses for industry and occupation were adequately specified for coding. Estimates of survey administration time and coding from digital records provide an objective basis for planning future studies. The social and environmental conditions of work are important understudied risk factors that can be feasibly integrated into large population-based health studies.
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Molloy, Philip; Weeks, Karen
2018-01-01
The recent range expansion of human babesiosis in the northeastern United States, once found only in restricted coastal sites, is not well understood. This study sought to utilize a large number of samples to examine the population structure of the parasites on a fine scale to provide insights into the mode of emergence across the region. 228 B. microti samples collected in endemic northeastern U.S. sites were genotyped using published Variable number tandem repeat (VNTR) markers. The genetic diversity and population structure were analysed on a geographic scale using Phyloviz and TESS, programs that utilize two different methods to identify population membership without predefined population data. Three distinct populations were detected in northeastern US, each dominated by a single ancestral type. In contrast to the limited range of the Nantucket and Cape Cod populations, the mainland population dominated from New Jersey eastward to Boston. Ancestral populations of B. microti were sufficiently isolated to differentiate into distinct populations. Despite this, a single population was detected across a large geographic area of the northeast that historically had at least 3 distinct foci of transmission, central New Jersey, Long Island and southeastern Connecticut. We conclude that a single B. microti genotype has expanded across the northeastern U.S. The biological attributes associated with this parasite genotype that have contributed to such a selective sweep remain to be identified. PMID:29565993
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Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal
2015-01-01
HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.
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Public Health Crisis in War and Conflict - Health Security in Aggregate.
Quinn, John; Zelený, Tomáš; Subramaniam, Rammika; Bencko, Vladimír
2017-03-01
Public health status of populations is multifactorial and besides other factors it is linked to war and conflict. Public health crisis can erupt when states go to war or are invaded; health security may be reduced for affected populations. This study reviews in aggregate multiple indices of human security, human development and legitimacy of the state in order to describe a predictable global health portrait. Paradigm shift of large global powers to that non-state actors and proxies impact regional influence through scaled conflict and present major global health challenges for policy makers. Small scale conflict with large scale violence threatens health security for at-risk populations. The paper concludes that health security is directly proportional to state security. Copyright© by the National Institute of Public Health, Prague 2017
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Gichohi-Wainaina, Wanjiku N; Tanaka, Toshiko; Towers, G Wayne; Verhoef, Hans; Veenemans, Jacobien; Talsma, Elise F; Harryvan, Jan; Boekschoten, Mark V; Feskens, Edith J; Melse-Boonstra, Alida
2016-01-01
Large genome-wide association (GWA) studies of European ancestry individuals have identified multiple genetic variants influencing iron status. Studies on the generalizability of these associations to African ancestry populations have been limited. These studies are important given interethnic differences in iron status and the disproportionate burden of iron deficiency among African ancestry populations. We tested the associations of 20 previously identified iron status-associated single nucleotide polymorphisms (SNPs) in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans. In each study, we examined the associations present between 20 SNPs with ferritin and haemoglobin, adjusting for age, sex and CRP levels. In the meta analysis including all 4 African ancestry cohorts, we replicated previously reported associations with lowered haemoglobin concentrations for rs2413450 (β = -0.19, P = 0.02) and rs4820268 (β = -0.16, P = 0.04) in TMPRSS6. An association with increased ferritin concentrations was also confirmed for rs1867504 in TF (β = 1.04, P = <0.0001) in the meta analysis including the African cohorts only. In all meta analyses, we only replicated 4 of the 20 single nucleotide polymorphisms reported to be associated with iron status in large GWA studies of European ancestry individuals. While there is now evidence for the associations of a number of genetic variants with iron status in both European and African ancestry populations, the considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of iron status in ethnically diverse populations.
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Tanaka, Toshiko; Towers, G. Wayne; Verhoef, Hans; Veenemans, Jacobien; Talsma, Elise F.; Harryvan, Jan; Boekschoten, Mark V.; Feskens, Edith J.; Melse-Boonstra, Alida
2016-01-01
Background Large genome-wide association (GWA) studies of European ancestry individuals have identified multiple genetic variants influencing iron status. Studies on the generalizability of these associations to African ancestry populations have been limited. These studies are important given interethnic differences in iron status and the disproportionate burden of iron deficiency among African ancestry populations. Methods We tested the associations of 20 previously identified iron status-associated single nucleotide polymorphisms (SNPs) in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans. In each study, we examined the associations present between 20 SNPs with ferritin and haemoglobin, adjusting for age, sex and CRP levels. Results In the meta analysis including all 4 African ancestry cohorts, we replicated previously reported associations with lowered haemoglobin concentrations for rs2413450 (β = -0.19, P = 0.02) and rs4820268 (β = -0.16, P = 0.04) in TMPRSS6. An association with increased ferritin concentrations was also confirmed for rs1867504 in TF (β = 1.04, P = <0.0001) in the meta analysis including the African cohorts only. Conclusions In all meta analyses, we only replicated 4 of the 20 single nucleotide polymorphisms reported to be associated with iron status in large GWA studies of European ancestry individuals. While there is now evidence for the associations of a number of genetic variants with iron status in both European and African ancestry populations, the considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of iron status in ethnically diverse populations. PMID:27332551
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D'Cunha, Anitha; Pandit, Lekha; Malli, Chaithra
2017-06-01
Indian data have been largely missing from genome-wide databases that provide information on genetic variations in different populations. This hinders association studies for complex disorders in India. This study was aimed to determine whether the complex genetic structure and endogamy among Indians could potentially influence the design of case-control studies for autoimmune disorders in the south Indian population. A total of 12 single nucleotide variations (SNVs) related to genes associated with autoimmune disorders were genotyped in 370 healthy individuals belonging to six different caste groups in southern India. Allele frequencies were estimated; genetic divergence and phylogenetic relationship within the various caste groups and other HapMap populations were ascertained. Allele frequencies for all genotyped SNVs did not vary significantly among the different groups studied. Wright's FSTwas 0.001 per cent among study population and 0.38 per cent when compared with Gujarati in Houston (GIH) population on HapMap data. The analysis of molecular variance results showed a 97 per cent variation attributable to differences within the study population and <1 per cent variation due to differences between castes. Phylogenetic analysis showed a separation of Dravidian population from other HapMap populations and particularly from GIH population. Despite the complex genetic origins of the Indian population, our study indicated a low level of genetic differentiation among Dravidian language-speaking people of south India. Case-control studies of association among Dravidians of south India may not require stratification based on language and caste.
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Gubili, Chrysoula; Sims, David W.; Veríssimo, Ana; Domenici, Paolo; Ellis, Jim; Grigoriou, Panagiotis; Johnson, Andrew F.; McHugh, Matthew; Neat, Francis; Satta, Andrea; Scarcella, Giuseppe; Serra-Pereira, Bárbara; Soldo, Alen; Genner, Martin J.; Griffiths, Andrew M.
2014-01-01
Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species. PMID:26064555
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Complex Population Dynamics and the Coalescent Under Neutrality
Volz, Erik M.
2012-01-01
Estimates of the coalescent effective population size Ne can be poorly correlated with the true population size. The relationship between Ne and the population size is sensitive to the way in which birth and death rates vary over time. The problem of inference is exacerbated when the mechanisms underlying population dynamics are complex and depend on many parameters. In instances where nonparametric estimators of Ne such as the skyline struggle to reproduce the correct demographic history, model-based estimators that can draw on prior information about population size and growth rates may be more efficient. A coalescent model is developed for a large class of populations such that the demographic history is described by a deterministic nonlinear dynamical system of arbitrary dimension. This class of demographic model differs from those typically used in population genetics. Birth and death rates are not fixed, and no assumptions are made regarding the fraction of the population sampled. Furthermore, the population may be structured in such a way that gene copies reproduce both within and across demes. For this large class of models, it is shown how to derive the rate of coalescence, as well as the likelihood of a gene genealogy with heterochronous sampling and labeled taxa, and how to simulate a coalescent tree conditional on a complex demographic history. This theoretical framework encapsulates many of the models used by ecologists and epidemiologists and should facilitate the integration of population genetics with the study of mathematical population dynamics. PMID:22042576
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CANCER INCIDENCE IN THE AGRICULTURAL HEALTH STUDY
The Agricultural Health Study (AHS) was undertaken to ascertain the etiology of cancers observed to be elevated in agricultural populations. Methods: The AHS is a large prospective, cohort study of private applicators and commercial applicators licensed to apply restricted use ...
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Guevara Hidalgo, Esteban; Nemoto, Takahiro; Lecomte, Vivien
2017-06-01
Rare trajectories of stochastic systems are important to understand because of their potential impact. However, their properties are by definition difficult to sample directly. Population dynamics provides a numerical tool allowing their study, by means of simulating a large number of copies of the system, which are subjected to selection rules that favor the rare trajectories of interest. Such algorithms are plagued by finite simulation time and finite population size, effects that can render their use delicate. In this paper, we present a numerical approach which uses the finite-time and finite-size scalings of estimators of the large deviation functions associated to the distribution of rare trajectories. The method we propose allows one to extract the infinite-time and infinite-size limit of these estimators, which-as shown on the contact process-provides a significant improvement of the large deviation function estimators compared to the standard one.
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Neutral theory, microbial practice: challenges in bacterial population genetics.
Rocha, Eduardo P C
2018-04-19
Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of genetic exchanges, the population genetics of ill-defined populations, and the difficulty of untangling selection and demography in the light of the previous issues. Whilst studies in population genetics usually focus on single nucleotide polymorphism and allelic recombination, ignoring even small indels, a large fraction of genetic diversification in Bacteria results from horizontal gene transfer. Ignoring this fact defeats the purpose of population genetics: to characterize the genetic variation in populations and their adaptive effects. I'll argue that, following on Kimura's life work, one may need to develop new approaches to study microbes that reproduce asexually but are able to engage in gene exchanges with very distantly related organisms in a context where random sampling is often unachievable, populations are ill-defined, genetic linkage is strong, and random drift is rare.
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Insights into Modern Human Prehistory Using Ancient Genomes.
Yang, Melinda A; Fu, Qiaomei
2018-03-01
The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Epidemiology of infective endocarditis in a large Belgian non-referral hospital.
Poesen, K; Pottel, H; Colaert, J; De Niel, C
2014-06-01
Guidelines for diagnosis of infective endocarditis are largely based upon epidemiological studies in referral hospitals. Referral bias, however, might impair the validity of guidelines in non-referral hospitals. Recent studies in non-referral care centres on infective endocarditis are sparse. We conducted a retrospective epidemiological study on infective endocarditis in a large non-referral hospital in a Belgian city (Kortrijk). The medical record system was searched for all cases tagged with a putative diagnosis of infective endocarditis in the period 2003-2010. The cases that fulfilled the modified Duke criteria for probable or definite infective endocarditis were included. Compared to referral centres, an older population with infective endocarditis, and fewer predisposing cardiac factors and catheter-related infective endocarditis is seen in our population. Our patients have fewer prosthetic valve endocarditis as well as fewer staphylococcal endocarditis. Our patients undergo less surgery, although mortality rate seems to be highly comparable with referral centres, with nosocomial infective endocarditis as an independent predictor of mortality. The present study suggests that characteristics of infective endocarditis as well as associative factors might differ among non-referral hospitals and referral hospitals.
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L. Hao; G. Sun; Y. Liu; J. Wan; M. Qin; H. Qian; C. Liu; R. John; P. Fan; J. Chen
2015-01-01
Rice paddy fields provide important ecosystem services (e.g., food production, water retention, carbon sequestration) to a large population globally. However, these benefits are declining as a result of rapid environmental and socioeconomic transformations characterized by population growth, urbanization, and climate change in many Asian countries. This case study...
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Understanding Disabled Childhoods: What Can We Learn from Population-Based Studies?
ERIC Educational Resources Information Center
Emerson, Eric
2012-01-01
This article illustrates the potential value of undertaking secondary analyses of large-scale population-based survey data to better inform our understanding of disabled childhoods. It is argued that while such approaches can never address the lived experience of growing up with disability, they can provide valuable insights into the ways in which…
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Recent Patterns of Population Change in America's Urban Places.
ERIC Educational Resources Information Center
McCarthy, Kevin F.
Current U.S. settlement patterns have begun to exhibit a significant shift away from very large metropolitan centers toward more thinly settled peripheral areas. This new trend has been the subject of many recent studies which have considered data on the county level but have been unable to detect population movement within counties and among…
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Nesting ecology of Merriam's turkeys in the Black Hills, South Dakota
Mark A. Rumble; Robert A. Hodorff
1993-01-01
Merriamâs wild turkeys (Meleagris gallopavo merriami) were introduced to the Black Hills approximately 40 years ago, and recent population estimates show a large and stable population. Until now, few studies have evaluated nesting ecology of Merriamâs turkeys, and none occurred in predominantly pure ponderosa pine (Pinus ponderosa...
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A Shared Heritage: Afro-Latin@s and Black History
ERIC Educational Resources Information Center
Busey, Christopher L.; Cruz, Bárbara C.
2015-01-01
As the Latin@ population continues to grow in the United States, it is imperative that social studies teachers are aware of the rich history and sociocultural complexities of Latin@ identity. In particular, there is a large population of Latin@s of African descent throughout Latin America, the Caribbean, and North America. However, Afro-Latin@s…
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Roosting habitat of Merriam's turkeys in the Black Hills, South Dakota
Mark A. Rumble
1992-01-01
Lack of roost habitat (trees >40 cm diameter breast height [dbh] and >18 m2/ha basal area) can limit populations of Merriamâs turkeys (Meleagris gallopavo merriami). The Black Hills region has relatively large populations of Merriamâs turkeys, yet trees >40 cm dbh are uncommon. Consequently, I studied...
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USDA-ARS?s Scientific Manuscript database
The correct identification of the source population of an invasive species is a prerequisite for defining and testing different hypotheses concerning the environmental and evolutionary factors responsible for biological invasions. The native area of invasive species may be large, barely known and/or...
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Huang, Man; Wang, Dejun; Xu, Zhijun; Xu, Yongshan; Xu, Xiaoping; Ma, Yuefeng; Xia, Zheng
2015-09-01
Large-scale genome-wide association studies have identified TREM2 variants to be significantly associated with Alzheimer's disease (AD) in caucasian population. The goal of this systematic study and meta-analysis was to assess the association between Triggering receptor expressed on myeloid cells 2 (TREM2) variants and AD in East Asian population. In this study, literatures were searched in PubMed, MEDLINE, EMBASE, and the Cochrane library to screen citations from January 1990 to June 2014. Data analysis was done by using the Stata 12 software. Twelve studies were considered for analysis. A total of 13 535 patients with AD and 22 976 healthy controls were studied. The results showed that rs75932628 variant was significantly associated with AD in caucasian population (P < .001, odds ratio ¼ 3.17, 95% confidence interval 2.45-4.09). However, the association was not found in East Asian population. In our study, we found that TREM2 variant is likely not associated with AD in East Asian population.
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Rosenbaum, Howard C.; Pomilla, Cristina; Mendez, Martin; Leslie, Matthew S.; Best, Peter B.; Findlay, Ken P.; Minton, Gianna; Ersts, Peter J.; Collins, Timothy; Engel, Marcia H.; Bonatto, Sandro L.; Kotze, Deon P. G. H.; Meÿer, Mike; Barendse, Jaco; Thornton, Meredith; Razafindrakoto, Yvette; Ngouessono, Solange; Vely, Michel; Kiszka, Jeremy
2009-01-01
Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region. PMID:19812698
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Rosenbaum, Howard C; Pomilla, Cristina; Mendez, Martin; Leslie, Matthew S; Best, Peter B; Findlay, Ken P; Minton, Gianna; Ersts, Peter J; Collins, Timothy; Engel, Marcia H; Bonatto, Sandro L; Kotze, Deon P G H; Meÿer, Mike; Barendse, Jaco; Thornton, Meredith; Razafindrakoto, Yvette; Ngouessono, Solange; Vely, Michel; Kiszka, Jeremy
2009-10-08
Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.
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Wang, Xiaolong; Zhao, Wei; Li, Lin; You, Jian; Ni, Biao
2018-01-01
Four small oval populations and five large intensive populations of Rhododendron aureum growing at the alpine in Changbai Mountain (China) were studied in two types of habitat (in the tundra and in Betula ermanii forest). Identification and delimitation of genets were inferred from excavation in small populations and from amplified fragment length polymorphism (AFLP) markers by the standardized sampling design in large populations. Clonal architecture and clonal diversity were then estimated. For the four small populations, they were monoclonal, the spacer length (18.6 ± 5.6 in tundra, 29.7 ± 9.7 in Betula ermanii forest, P < 0.05) was shorter and branching intensity (136.7 ± 32.9 in tundra, 43.4 ± 12.3 in Betula ermanii forest, P < 0.05) was higher in the tundra than that in Betula ermanii forest. For the five large populations, they were composed of multiple genets with high level of clonal diversity (Simpson’s index D = 0.84, clonal richness R = 0.25, Fager's evenness E = 0.85); the spatial distribution of genets showed that the clonal growth strategy of R. aureum exhibits both guerilla and phalanx. Our results indicate that the clonal plasticity of R. aureum could enhance exploitation of resource heterogeneity and in turn greatly contribute to maintenance or improvement of fitness and the high clonal diversity of R. aureum increase the evolutionary rates to adapt the harsh alpine environment in Changbai Mountain. PMID:29746526
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Habel, J C; Mulwa, R K; Gassert, F; Rödder, D; Ulrich, W; Borghesio, L; Husemann, M; Lens, L
2014-01-01
The Eastern Afromontane cloud forests occur as geographically distinct mountain exclaves. The conditions of these forests range from large to small and from fairly intact to strongly degraded. For this study, we sampled individuals of the forest bird species, the Montane White-eye Zosterops poliogaster from 16 sites and four mountain archipelagos. We analysed 12 polymorphic microsatellites and three phenotypic traits, and calculated Species Distribution Models (SDMs) to project past distributions and predict potential future range shifts under a scenario of climate warming. We found well-supported genetic and morphologic clusters corresponding to the mountain ranges where populations were sampled, with 43% of all alleles being restricted to single mountains. Our data suggest that large-scale and long-term geographic isolation on mountain islands caused genetically and morphologically distinct population clusters in Z. poliogaster. However, major genetic and biometric splits were not correlated to the geographic distances among populations. This heterogeneous pattern can be explained by past climatic shifts, as highlighted by our SDM projections. Anthropogenically fragmented populations showed lower genetic diversity and a lower mean body mass, possibly in response to suboptimal habitat conditions. On the basis of these findings and the results from our SDM analysis we predict further loss of genotypic and phenotypic uniqueness in the wake of climate change, due to the contraction of the species' climatic niche and subsequent decline in population size. PMID:24713824
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Habel, J C; Mulwa, R K; Gassert, F; Rödder, D; Ulrich, W; Borghesio, L; Husemann, M; Lens, L
2014-09-01
The Eastern Afromontane cloud forests occur as geographically distinct mountain exclaves. The conditions of these forests range from large to small and from fairly intact to strongly degraded. For this study, we sampled individuals of the forest bird species, the Montane White-eye Zosterops poliogaster from 16 sites and four mountain archipelagos. We analysed 12 polymorphic microsatellites and three phenotypic traits, and calculated Species Distribution Models (SDMs) to project past distributions and predict potential future range shifts under a scenario of climate warming. We found well-supported genetic and morphologic clusters corresponding to the mountain ranges where populations were sampled, with 43% of all alleles being restricted to single mountains. Our data suggest that large-scale and long-term geographic isolation on mountain islands caused genetically and morphologically distinct population clusters in Z. poliogaster. However, major genetic and biometric splits were not correlated to the geographic distances among populations. This heterogeneous pattern can be explained by past climatic shifts, as highlighted by our SDM projections. Anthropogenically fragmented populations showed lower genetic diversity and a lower mean body mass, possibly in response to suboptimal habitat conditions. On the basis of these findings and the results from our SDM analysis we predict further loss of genotypic and phenotypic uniqueness in the wake of climate change, due to the contraction of the species' climatic niche and subsequent decline in population size.
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USDA-ARS?s Scientific Manuscript database
Our objective was to identify candidate QTL that had a large effect on seed weight using a selective population through GWAS and fixation index analysis. A selective population was previously used for the identification of QTL in linkage analysis of bi-parental RIL populations in plant species, but ...
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David Keith; H. Resit Akcakaya; Stuart H.M. Butchart; Ben Collen; Nicholas K. Dulvy; Elizabeth E. Holmes; Jeffrey A. Hutchings; Doug Keinath; Michael K. Schwartz; Andrew O. Shelton; Robin S. Waples
2015-01-01
Population trends play a large role in species risk assessments and conservation planning, and species are often considered threatened if their recent rate of decline meets certain thresholds, regardless how large the population is. But how reliable an indicator of extinction risk is a single estimate of population trend? Given the integral role this decline-...
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Targeted enrichment strategies for next-generation plant biology
Richard Cronn; Brian J. Knaus; Aaron Liston; Peter J. Maughan; Matthew Parks; John V. Syring; Joshua Udall
2012-01-01
The dramatic advances offered by modem DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation sequencing platforms. Factors like large genome...
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Development and validation of a low-density SNP panel related to prolificacy in sheep
USDA-ARS?s Scientific Manuscript database
High-density SNP panels (e.g., 50,000 and 600,000 markers) have been used in exploratory population genetic studies with commercial and minor breeds of sheep. However, routine genetic diversity evaluations of large numbers of samples with large panels are in general cost-prohibitive for gene banks. ...
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Wiederholt, Ruscena; Fernandez-Duque, Eduardo; Diefenbach, Duane R.; Rudran, Rasanayagam
2010-01-01
Overexploitation of wildlife populations occurs across the humid tropics and is a significant threat to the long-term survival of large-bodied primates. To investigate the impacts of hunting on primates and ways to mitigate them, we developed a spatially explicit, individual-based model for a landscape that included hunted and un-hunted areas. We used the large-bodied neotropical red howler monkey (Alouatta seniculus) as our case study species because its life history characteristics make it vulnerable to hunting. We modeled the influence of different rates of harvest and proportions of landscape dedicated to un-hunted reserves on population persistence, population size, social dynamics, and hunting yields of red howler monkeys. In most scenarios, the un-hunted populations maintained a constant density regardless of hunting pressure elsewhere, and allowed the overall population to persist. Therefore, the overall population was quite resilient to extinction; only in scenarios without any un-hunted areas did the population go extinct. However, the total and hunted populations did experience large declines over 100 years under moderate and high hunting pressure. In addition, when reserve area decreased, population losses and losses per unit area increased disproportionately. Furthermore, hunting disrupted the social structure of troops. The number of male turnovers and infanticides increased in hunted populations, while birth rates decreased and exacerbated population losses due to hunting. Finally, our results indicated that when more than 55% of the landscape was harvested at high (30%) rates, hunting yields, as measured by kilograms of biomass, were less than those obtained from moderate harvest rates. Additionally, hunting yields, expressed as the number of individuals hunted/year/km2, increased in proximity to un-hunted areas, and suggested that dispersal from un-hunted areas may have contributed to hunting sustainability. These results indicate that un-hunted areas serve to enhance hunting yields, population size, and population persistence in hunted landscapes. Therefore, spatial regulation of hunting via a reserve system may be an effective management strategy for sustainable hunting, and we recommend it because it may also be more feasible to implement than harvest quotas or restrictions on season length.
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Software engineering the mixed model for genome-wide association studies on large samples.
Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J
2009-11-01
Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.
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Straile, Dietmar; Adrian, Rita; Schindler, Daniel E.
2012-01-01
Spring phenologies are advancing in many ecosystems associated with climate warming causing unpredictable changes in ecosystem functioning. Here we establish a phenological model for Daphnia, an aquatic keystone herbivore based on decadal data on water temperatures and the timing of Daphnia population maxima from Lake Constance, a large European lake. We tested this model with long-term time-series data from two lakes (Müggelsee, Germany; Lake Washington, USA), and with observations from a diverse set of 49 lakes/sites distributed widely across the Northern Hemisphere (NH). The model successfully captured the observed temporal variation of Daphnia phenology in the two case study sites (r2 = 0.25 and 0.39 for Müggelsee and Lake Washington, respectively) and large-scale spatial variation in the NH (R2 = 0.57). These results suggest that Daphnia phenology follows a uniform temperature dependency in NH lakes. Our approach – based on temperature phenologies – has large potential to study and predict phenologies of animal and plant populations across large latitudinal gradients in other ecosystems. PMID:23071520
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Ratkiewicz, Mirosław; Matosiuk, Maciej; Saveljev, Alexander P; Sidorovich, Vadim; Ozolins, Janis; Männil, Peep; Balciauskas, Linas; Kojola, Ilpo; Okarma, Henryk; Kowalczyk, Rafał; Schmidt, Krzysztof
2014-01-01
Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers) was found in lynx from Norway and Białowieża Primeval Forest (BPF), which coincided with a recent demographic bottleneck (Norway) or high habitat fragmentation (BPF). The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum) on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus) in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and microsatellite population divergence patterns with climatic and ecological factors may suggest separate selective pressures acting on males and females in this solitary carnivore.
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Chopan, Mustafa
2017-01-01
The evidence base for the health effects of spice consumption is insufficient, with only one large population-based study and no reports from Europe or North America. Our objective was to analyze the association between consumption of hot red chili peppers and mortality, using a population-based prospective cohort from the National Health and Nutritional Examination Survey (NHANES) III, a representative sample of US noninstitutionalized adults, in which participants were surveyed from 1988 to 1994. The frequency of hot red chili pepper consumption was measured in 16,179 participants at least 18 years of age. Total and cause-specific mortality were the main outcome measures. During 273,877 person-years of follow-up (median 18.9 years), a total of 4,946 deaths were observed. Total mortality for participants who consumed hot red chili peppers was 21.6% compared to 33.6% for those who did not (absolute risk reduction of 12%; relative risk of 0.64). Adjusted for demographic, lifestyle, and clinical characteristics, the hazard ratio was 0.87 (P = 0.01; 95% Confidence Interval 0.77, 0.97). Consumption of hot red chili peppers was associated with a 13% reduction in the instantaneous hazard of death. Similar, but statistically nonsignificant trends were seen for deaths from vascular disease, but not from other causes. In this large population-based prospective study, the consumption of hot red chili pepper was associated with reduced mortality. Hot red chili peppers may be a beneficial component of the diet. PMID:28068423
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The dynamics of zooxanthellae populations: A long-term study in the field
Fagoonee; Wilson; Hassell; Turner
1999-02-05
Coral bleaching characterized by the expulsion of symbiotic algae (zooxanthellae) is an increasing problem worldwide. Global warming has been implicated as one cause, but the phenomenon cannot be fully comprehended without an understanding of the variability of zooxanthellae populations in field conditions. Results from a 6-year field study are presented, providing evidence of density regulation but also of large variability in the zooxanthellae population with regular episodes of very low densities. These bleaching events are likely to be part of a constant variability in zooxanthellae density caused by environmental fluctuations superimposed on a strong seasonal cycle in abundance.
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Wood, Jacquelyn L A; Yates, Matthew C; Fraser, Dylan J
2016-06-01
It is widely thought that small populations should have less additive genetic variance and respond less efficiently to natural selection than large populations. Across taxa, we meta-analytically quantified the relationship between adult census population size (N) and additive genetic variance (proxy: h (2)) and found no reduction in h (2) with decreasing N; surveyed populations ranged from four to one million individuals (1735 h (2) estimates, 146 populations, 83 species). In terms of adaptation, ecological conditions may systematically differ between populations of varying N; the magnitude of selection these populations experience may therefore also differ. We thus also meta-analytically tested whether selection changes with N and found little evidence for systematic differences in the strength, direction or form of selection with N across different trait types and taxa (7344 selection estimates, 172 populations, 80 species). Collectively, our results (i) indirectly suggest that genetic drift neither overwhelms selection more in small than in large natural populations, nor weakens adaptive potential/h (2) in small populations, and (ii) imply that natural populations of varying sizes experience a variety of environmental conditions, without consistently differing habitat quality at small N. However, we caution that the data are currently insufficient to determine whether some small populations may retain adaptive potential definitively. Further study is required into (i) selection and genetic variation in completely isolated populations of known N, under-represented taxonomic groups, and nongeneralist species, (ii) adaptive potential using multidimensional approaches and (iii) the nature of selective pressures for specific traits.
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Avian movements and wetland connectivity in landscape conservation
Haig, Susan M.; Mehlman, D.W.; Oring, L.W.
1998-01-01
The current conservation crisis calls for research and management to be carried out on a long-term, multi-species basis at large spatial scales. Unfortunately, scientists, managers, and agencies often are stymied in their effort to conduct these large-scale studies because of a lack of appropriate technology, methodology, and funding. This issue is of particular concern in wetland conservation, for which the standard landscape approach may include consideration of a large tract of land but fail to incorporate the suite of wetland sites frequently used by highly mobile organisms such as waterbirds (e.g., shorebirds, wading birds, waterfowl). Typically, these species have population dynamics that require use of multiple wetlands, but this aspect of their life history has often been ignored in planning for their conservation. We outline theoretical, empirical, modeling, and planning problems associated with this issue and suggest solutions to some current obstacles. These solutions represent a tradeoff between typical in-depth single-species studies and more generic multi-species studies. They include studying within- and among-season movements of waterbirds on a spatial scale appropriate to both widely dispersing and more stationary species; multi-species censuses at multiple sites; further development and use of technology such as satellite transmitters and population-specific molecular markers; development of spatially explicit population models that consider within-season movements of waterbirds; and recognition from funding agencies that landscape-level issues cannot adequately be addressed without support for these types of studies.
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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.
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SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.
Amigo, Jorge; Salas, Antonio; Phillips, Christopher; Carracedo, Angel
2008-10-10
In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 x 10(9) genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested. In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.
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Yuan, Jun–hui; Cheng, Fang–Yun; Zhou, Shi–Liang
2012-01-01
Background Tree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers. Methodology/Principal Findings Twenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (FST value of 0.302). Moderate genetic diversity at the population level (HS of 0.516) and high population diversity at the species level (HT of 0.749) were detected. Significant excess homozygosity (FIS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier's maximum-difference algorithm. Conclusions/Significance Our data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of this species and for improving the genetic basis for breeding its cultivars. PMID:22523566
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A High Resolution View of Galactic Centers: Arp 220 and M31
NASA Astrophysics Data System (ADS)
Lockhart, Kelly E.
The centers of galaxy are small in size and yet incredibly complex. They play host to supermassive black holes and nuclear star clusters (NSCs) and are subject to large gas inows, nuclear starbursts, and active galactic nuclear (AGN) activity. They can also be the launching site for large-scale galactic outows. However, though these systems are quite important to galactic evolution, observations are quite difficult due to their small size. Using high spatial resolution narrowband imaging with HST/WFC3 of Arp 220, a latestage galaxy merger, I discover an ionized gas bubble feature ( r = 600 pc) just off the nucleus. The bubble is aligned with both the western nucleus and with the large-scale galactic outflow. Using energetics arguments, I link the bubble with a young, obscured AGN or with an intense nuclear starburst. Given its alignment along the large-scale outflow axis, I argue that the bubble presents evidence for a link between the galactic center and the large-scale outflow. I also present new observations of the NSC in M31, the closest large spiral galaxy to our own. Using the OSIRIS near-infrared integral field spectrograph (IFS) on Keck, I map the kinematics of the old stellar population in the eccentric disk of the NSC. I compare the observations to models to derive a precession speed of the disk of 0+/-5 km s-1 pc-1 , and hence confirm that winds from the old stellar population may be the source of gas needed to form the young stellar population in the NSC. Studies of galactic centers are dependent on high spatial resolution observations. In particular, IFSs are ideal instruments for these studies as they provide two-dimensional spectroscopy of the field of view, enabling 2D kinematic studies. I report on work to characterize and improve the data reduction pipeline of the OSIRIS IFS, and discuss implications for future generations of IFS instrumentation.
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Antrobus, T.J.; Guilfoyle, M.P.; Barrow, W.C.; Hamel, P.B.; Wakeley, J.S.
2000-01-01
Neotropical migrants are birds that breed in North America and winter primarily in Central and South America. Long-term population studies of birds in the Eastern United States indicated declines of some forest-dwelling birds, many of which winter in the Neotropics (Peterjohn and others 1995). These declines were attributed to loss of wintering and breeding habitat due to deforestation and fragmentation, respectively. Many species of Nearctic migrants--birds that breed in the northern regions of North America and winter in the Southern United States--are also experiencing population declines. Because large areas of undistrubed, older, bottomland hardwood forests oftern contain large numbers of habitat specialists, including forest-interior neotropical migrants and wintering Nearctic migrants, these forests may be critical in maintaining avian diversity. This study had two primary objectivs: (1) to create a baseline data set that can be used as a standard against which other bottomland hardwood forests can be compared, and (2) to establish long-term monitoring stations during both breeding and wintering seasons to discern population trends of avian species using bottomland hardwood forests.
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Chromosome surveys of human populations: between epidemiology and anthropology.
de Chadarevian, Soraya
2014-09-01
It is commonly held that after 1945 human genetics turned medical and focussed on the individual rather than on the study of human populations that had become discredited. However, a closer look at the research practices at the time quickly reveals that human population studies, using old and new tools, prospered in this period. The essay focuses on the rise of chromosome analysis as a new tool for the study of human populations. It reviews a broad array of population studies ranging from newborn screening programmes to studies of isolated or 'primitive' people. Throughout, it highlights the continuing role of concerns and opportunities raised by the propagation of atomic energy for civilian and military uses, the collection of large data bases and computers, and the role of international organisations like the World Health Organisation and the International Biological Programme in shaping research agendas and carving out a space for human heredity in the postwar era. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Rosenblatt, Adam E.; Nifong, James C.; Heithaus, Michael R.; Mazzotti, Frank J.; Cherkiss, Michael S.; Jeffery, Brian M.; Elsey, Ruth M.; Decker, Rachel A.; Silliman, Brian R.; Guillette, Louis J.; Lowers, Russell H.; Larson, Justin C.
2015-01-01
Individual niche specialization (INS) is increasingly recognized as an important component of ecological and evolutionary dynamics. However, most studies that have investigated INS have focused on the effects of niche width and inter- and intraspecific competition on INS in small-bodied species for short time periods, with less attention paid to INS in large-bodied reptilian predators and the effects of available prey types on INS. We investigated the prevalence, causes, and consequences of INS in foraging behaviors across different populations of American alligators (Alligator mississippiensis), the dominant aquatic apex predator across the southeast US, using stomach contents and stable isotopes. Gut contents revealed that, over the short term, although alligator populations occupied wide ranges of the INS spectrum, general patterns were apparent. Alligator populations inhabiting lakes exhibited lower INS than coastal populations, likely driven by variation in habitat type and available prey types. Stable isotopes revealed that over longer time spans alligators exhibited remarkably consistent use of variable mixtures of carbon pools (e.g., marine and freshwater food webs). We conclude that INS in large-bodied reptilian predator populations is likely affected by variation in available prey types and habitat heterogeneity, and that INS should be incorporated into management strategies to efficiently meet intended goals. Also, ecological models, which typically do not consider behavioral variability, should include INS to increase model realism and applicability.
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Rosenblatt, Adam E; Nifong, James C; Heithaus, Michael R; Mazzotti, Frank J; Cherkiss, Michael S; Jeffery, Brian M; Elsey, Ruth M; Decker, Rachel A; Silliman, Brian R; Guillette, Louis J; Lowers, Russell H; Larson, Justin C
2015-05-01
Individual niche specialization (INS) is increasingly recognized as an important component of ecological and evolutionary dynamics. However, most studies that have investigated INS have focused on the effects of niche width and inter- and intraspecific competition on INS in small-bodied species for short time periods, with less attention paid to INS in large-bodied reptilian predators and the effects of available prey types on INS. We investigated the prevalence, causes, and consequences of INS in foraging behaviors across different populations of American alligators (Alligator mississippiensis), the dominant aquatic apex predator across the southeast US, using stomach contents and stable isotopes. Gut contents revealed that, over the short term, although alligator populations occupied wide ranges of the INS spectrum, general patterns were apparent. Alligator populations inhabiting lakes exhibited lower INS than coastal populations, likely driven by variation in habitat type and available prey types. Stable isotopes revealed that over longer time spans alligators exhibited remarkably consistent use of variable mixtures of carbon pools (e.g., marine and freshwater food webs). We conclude that INS in large-bodied reptilian predator populations is likely affected by variation in available prey types and habitat heterogeneity, and that INS should be incorporated into management strategies to efficiently meet intended goals. Also, ecological models, which typically do not consider behavioral variability, should include INS to increase model realism and applicability.
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Murray, J D; McKay, G M; Sharman, G B
1979-06-01
The greater glider, currently but incorrectly known as Schoinobates volans, is widely distributed in forested regions in eastern Australia. All animals studied from six different localities had 20 autosomes but there were four chromosomally distinct populations. At Royal National Park, N.S.W., all female greater gliders studied had 22 chromosomes including two large submetacentric X chromosomes with subterminal secondary constrictions in their longer arms. This form of X chromosome occurred also at Bondo State Forest, Myall Lakes and Coff's Harbour, N.S.W., and at Eidsvold, Qld. At Coomooboolaroo, Qld, the X chromosome was also a large submetacentric but a secondary constriction occurred in the shorter arm. Two chromosomally distinct types apparently occur in Royal National Park, one with XY males as in all other populations, and one with XY1Y2 males. Y or Y1, but not Y2, chromosomes were eliminated from the bone marrow in all populations but were present in spermatogonia, primary spermatocytes and cultured fibroblasts. Animals from Bondo State Forest had three or more acrocentric or metacentric supernumerary chromosomes.
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Scandinavian epidemiological research in gastroenterology and hepatology.
Björnsson, Einar S; Ekbom, Anders
2015-06-01
In the last decades, a large number of epidemiological studies in gastroenterology and hepatology have originated from the Scandinavian countries. With the help of large health databases, with good validity and other registries related to patient outcomes, researchers from the Scandinavian countries have been able to make some very important contributions to the field. These countries, Sweden, Norway, Finland, Denmark and Iceland, have all universal access to health care and have shown to be ideal for epidemiological research. Population-based studies have been frequent and follow-up studies have been able to describe the temporal trends and changes in phenotypes. Our ability in Scandinavia to follow up defined groups of patients over time has been crucial to learn the natural history of many gastrointestinal and liver diseases and often in a population-based setting. Patient-related outcomes measures will probably gain increasing importance in the future, but Scandinavian gastroenterologists and surgeons are likely to have a better infrastructure for such endeavors compared to most other populations. Thus, there is a bright future for international competitive research within the field of gastrointestinal and liver diseases in Scandinavia.
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Rawlence, Nicolas J; Collins, Catherine J; Anderson, Christian N K; Maxwell, Justin J; Smith, Ian W G; Robertson, Bruce C; Knapp, Michael; Horsburgh, Katherine Ann; Stanton, Jo-Ann L; Scofield, R Paul; Tennyson, Alan J D; Matisoo-Smith, Elizabeth A; Waters, Jonathan M
2016-08-01
While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450-1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to overhunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline. © 2016 John Wiley & Sons Ltd.
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The value of cows in reference populations for genomic selection of new functional traits.
Buch, L H; Kargo, M; Berg, P; Lassen, J; Sørensen, A C
2012-06-01
Today, almost all reference populations consist of progeny tested bulls. However, older progeny tested bulls do not have reliable estimated breeding values (EBV) for new traits. Thus, to be able to select for these new traits, it is necessary to build a reference population. We used a deterministic prediction model to test the hypothesis that the value of cows in reference populations depends on the availability of phenotypic records. To test the hypothesis, we investigated different strategies of building a reference population for a new functional trait over a 10-year period. The trait was either recorded on a large scale (30 000 cows per year) or on a small scale (2000 cows per year). For large-scale recording, we compared four scenarios where the reference population consisted of 30 sires; 30 sires and 170 test bulls; 30 sires and 2000 cows; or 30 sires, 2000 cows and 170 test bulls in the first year with measurements of the new functional trait. In addition to varying the make-up of the reference population, we also varied the heritability of the trait (h2 = 0.05 v. 0.15). The results showed that a reference population of test bulls, cows and sires results in the highest accuracy of the direct genomic values (DGV) for a new functional trait, regardless of its heritability. For small-scale recording, we compared two scenarios where the reference population consisted of the 2000 cows with phenotypic records or the 30 sires of these cows in the first year with measurements of the new functional trait. The results showed that a reference population of cows results in the highest accuracy of the DGV whether the heritability is 0.05 or 0.15, because variation is lost when phenotypic data on cows are summarized in EBV of their sires. The main conclusions from this study are: (i) the fewer phenotypic records, the larger effect of including cows in the reference population; (ii) for small-scale recording, the accuracy of the DGV will continue to increase for several years, whereas the increases in the accuracy of the DGV quickly decrease with large-scale recording; (iii) it is possible to achieve accuracies of the DGV that enable selection for new functional traits recorded on a large scale within 3 years from commencement of recording; and (iv) a higher heritability benefits a reference population of cows more than a reference population of bulls.
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Charlesworth, Brian; Charlesworth, Deborah; Coyne, Jerry A; Langley, Charles H
2016-08-01
The 1966 GENETICS papers by John Hubby and Richard Lewontin were a landmark in the study of genome-wide levels of variability. They used the technique of gel electrophoresis of enzymes and proteins to study variation in natural populations of Drosophila pseudoobscura, at a set of loci that had been chosen purely for technical convenience, without prior knowledge of their levels of variability. Together with the independent study of human populations by Harry Harris, this seminal study provided the first relatively unbiased picture of the extent of genetic variability in protein sequences within populations, revealing that many genes had surprisingly high levels of diversity. These papers stimulated a large research program that found similarly high electrophoretic variability in many different species and led to statistical tools for interpreting the data in terms of population genetics processes such as genetic drift, balancing and purifying selection, and the effects of selection on linked variants. The current use of whole-genome sequences in studies of variation is the direct descendant of this pioneering work. Copyright © 2016 by the Genetics Society of America.
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Demographics of Investigators Involved in OSSA-Funded Research
NASA Technical Reports Server (NTRS)
Stern, S. Alan; Konkel, Ronald; Habegger, Jay; Byerly, Radford, Jr.
1991-01-01
The birth of the U.S. civil space program and the subsequent, dramatic growth in the ranks of the space science research population occurred in the 1950s and 1960s'. The large, post- Sputnik/ Apollo buildup in space program manpower is now approximately one career-lifetime in the past. It is therefore natural to anticipate that a large fraction of the space program engineers, scientists, and managers who pioneered the early exploration of space are approaching retirement. Such a "retirement wave" bodes both a loss of manpower and, more fundamentally, a loss of experience from the civil-space manpower base. Such losses could play a critical role constraining in NASA's ability to expand or maintain its technical capabilities. If this indeed applies to the NASA space science research population, then the potential for problems is exacerbated by the anticipated growth in flight rates, data volume, and data-set diversity which will accompany the planned expansion in the OSSA science effort during the 1990s and 2000s. The purpose of this study was to describe the OSSA PI/Co-I population and to determine the degree to which the OSSA space science investigator population faces a retirement wave, and to estimate the future population of PIs in the 1990-2010 era. To conduct such a study, we investigated the present demographics of the PI and Co-1 population contained in the NASA/OSSA Announcement of Opportunity (AO) mailing list. PIs represent the "leadership" class of the OSSA scientific researcher population, and Co-Is represent one important, oncoming component of the "replacement" generation. Using the PI population data, we then make projection estimates of the future PI population from 1991 through 2010, under various NASA growth/PI demand scenarios.
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Population Genetics of the Aquatic Fungus Tetracladium marchalianum over Space and Time
Anderson, Jennifer L.; Shearer, Carol A.
2011-01-01
Aquatic hyphomycete fungi are fundamental mediators of energy flow and nutrient spiraling in rivers. These microscopic fungi are primarily dispersed in river currents, undergo substantial annual fluctuations in abundance, and reproduce either predominantly or exclusively asexually. These aspects of aquatic hyphomycete biology are expected to influence levels and distributions of genetic diversity over both spatial and temporal scales. In this study, we investigated the spatiotemporal distribution of genotypic diversity in the representative aquatic hyphomycete Tetracladium marchalianum. We sampled populations of this fungus from seven sites, three sites each in two rivers in Illinois, USA, and one site in a Wisconsin river, USA, and repeatedly sampled one population over two years to track population genetic parameters through two seasonal cycles. The resulting fungal isolates (N = 391) were genotyped at eight polymorphic microsatellite loci. In spite of seasonal reductions in the abundance of this species, genotypic diversity was consistently very high and allele frequencies remarkably stable over time. Likewise, genotypic diversity was very high at all sites. Genetic differentiation was only observed between the most distant rivers (∼450 km). Clear evidence that T. marchalianum reproduces sexually in nature was not observed. Additionally, we used phylogenetic analysis of partial β-tubulin gene sequences to confirm that the fungal isolates studied here represent a single species. These results suggest that populations of T. marchalianum may be very large and highly connected at local scales. We speculate that large population sizes and colonization of alternate substrates in both terrestrial and aquatic environments may effectively buffer the aquatic populations from in-stream population fluctuations and facilitate stability in allele frequencies over time. These data also suggest that overland dispersal is more important for structuring populations of T. marchalianum over geographic scales than expected. PMID:21264239
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Turner, Thomas L.; Stewart, Andrew D.; Fields, Andrew T.; Rice, William R.; Tarone, Aaron M.
2011-01-01
Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size. PMID:21437274
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Projected effects of climate and development on California wildfire emissions through 2100.
Hurteau, Matthew D; Westerling, Anthony L; Wiedinmyer, Christine; Bryant, Benjamin P
2014-02-18
Changing climatic conditions are influencing large wildfire frequency, a globally widespread disturbance that affects both human and natural systems. Understanding how climate change, population growth, and development patterns will affect the area burned by and emissions from wildfires and how populations will in turn be exposed to emissions is critical for climate change adaptation and mitigation planning. We quantified the effects of a range of population growth and development patterns in California on emission projections from large wildfires under six future climate scenarios. Here we show that end-of-century wildfire emissions are projected to increase by 19-101% (median increase 56%) above the baseline period (1961-1990) in California for a medium-high temperature scenario, with the largest emissions increases concentrated in northern California. In contrast to other measures of wildfire impacts previously studied (e.g., structural loss), projected population growth and development patterns are unlikely to substantially influence the amount of projected statewide wildfire emissions. However, increases in wildfire emissions due to climate change may have detrimental impacts on air quality and, combined with a growing population, may result in increased population exposure to unhealthy air pollutants.
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PICALM gene rs3851179 polymorphism contributes to Alzheimer's disease in an Asian population.
Liu, Guiyou; Zhang, Shuyan; Cai, Zhiyou; Ma, Guoda; Zhang, Liangcai; Jiang, Yongshuai; Feng, Rennan; Liao, Mingzhi; Chen, Zugen; Zhao, Bin; Li, Keshen
2013-06-01
PICALM gene rs3851179 polymorphism was reported to an Alzheimer's disease (AD) susceptibility locus in a Caucasian population. However, recent studies reported consistent and inconsistent results in an Asian population. Four studies indicated no association between rs3851179 and AD in a Chinese population and one study reported weak association in a Japanese population. We consider that the failure to replicate the significant association between rs3851179 and AD may be caused by at least two reasons. The first reason may be the genetic heterogeneity in AD among different populations, and the second may be the relatively small sample size compared with large-scale GWAS in Caucasian ancestry. In order to confirm this view, in this research, we first evaluated the genetic heterogeneity of rs3851179 polymorphism in Caucasian and Asian populations. We then investigated rs3851179 polymorphism in an Asian population by a pooled analysis method and a meta-analysis method. We did not observe significant genetic heterogeneity of rs3851179 in the Caucasian and Asian populations. Our results indicate that rs3851179 polymorphism is significantly associated with AD in the Asian population by both pooled analysis and meta-analysis methods. We believe that our findings will be very useful for future genetic studies in AD.
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Pharmacokinetics of Antibiotics in Sub-Saharan African Patient Populations: A Systematic Review.
Bos, Jeannet C; van Hest, Reinier M; Prins, Jan M
2017-08-01
In sub-Saharan Africa (SSA), severe febrile illness accounts for a large majority of medical admissions. SSA patients may also suffer from cachexia and organ dysfunction resulting from tuberculosis, hepatitis B, and hypertension. It is hard to tell how these conditions influence the pharmacokinetics (PK) of antibiotics in this population. The aim of this systematic review was to summarize antibiotic PK data of SSA adult patient populations to clarify whether inappropriate drug concentrations that may also lead to antimicrobial resistance are likely to occur. An electronic search was conducted in Ovid MEDLINE, Embase, and the African Index Medicus collecting studies from 1946 to May 2016. Reviewers independently selected studies reporting outcome data on volume of distribution (V), clearance, and half-life. Relevant information was abstracted and quality assessed. Twelve studies were selected, addressing 6 antibiotic classes. There were 6 studies on fluoroquinolones and 1 on β-lactam antibiotics. Nine out of 12 originated from South Africa and 6 of those dealt with intensive care unit (ICU) populations. The quality of most studies was low. Studies on amikacin, teicoplanin, and ertapenem (n = 4) displayed a pattern of a large V with low drug concentrations. Fluoroquinolone PK changes were less prominent and more diverse whereas the probability of pharmacodynamic target attainment was low for the treatment of tuberculosis in South Africa. Interindividual variability of V was high for 10/12 studies. Antibiotic PK data of SSA adult patient populations are scarce, but disease-induced inappropriate drug concentrations do occur. Data from non-ICU, severely ill patients, and β-lactam data are particularly lacking, whereas β-lactam antibiotics are commonly used, and typically vulnerable to disease-induced PK changes. Studies investigating the PK and pharmacodynamics of β-lactam antibiotics in severely ill, adult SSA patient populations are needed to improve local antibiotic dosing strategies.
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Agricultural landscapes: Can they support healthy bird populations as well as farm products?
Peterjohn, B.G.
2003-01-01
At the beginning of the twentieth century, prospects for bird populations occupying farmlands were promising. Agricultural expansion and the resulting deforestation produced wholesale changes to the landscape of eastern North America (Trautman 1977, Zeranski and Baptist 1990, Nicholson 1997). Regional avifaunas were transformed as Horned Larks (Eremophila alpestris), Dickcissels (Spiza americana), and other farmland birds undertook range expansions (Hurley and Franks 1976, Askins 1999). Those farmland birds became conspicuous, frequently in numbers that are hard to imagine today (Trautman 1940).One hundred years later, many of those once plentiful species experienced dramatic population declines (Askins 1993, Peterjohn and Sauer 1999). Those trends were evident for many decades, although pre-1965 trends were largely based on anecdotal accounts and were frequently attributed to changing regional landscapes due to urban expansion, farm abandonment resulting in increased forest cover, and the more intensive use of remaining agricultural fields (Trautman 1940, Herkert 1991, Askins 2000). However, numerous specific factors were implicated in local declines of individual species (Kantrud 1981, Bollinger et al. 1990, Lymn and Temple 1991, Bowen and Kruse 1993, Herkert 1994, Houston and Schmutz 1999, Blackwell and Dolbeer 2001).Understanding factors responsible for population changes can be approached at various geographic scales. Local studies identify specific factors influencing small populations, but the applicability of those results across broad geographic areas is often uncertain. Studies conducted at large geographic scales identify broad patterns of change, but those patterns frequently involve interrelated factors that may be only loosely related to the actual causes of population change. However, correlations between broad patterns of changes in bird populations and land-use characteristics provide a basis for directing future studies conducted at smaller geographic scales.
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Bender, Anne Mette; Kawachi, Ichiro; Jørgensen, Torben; Pisinger, Charlotta
2015-01-01
We sought to examine whether neighborhood deprivation is associated with participation in a large population-based health check. Such analyses will help answer the question whether health checks, which are designed to meet the needs of residents in deprived neighborhoods, may increase participation and prove to be more effective in preventing disease. In Europe, no study has previously looked at the association between neighborhood deprivation and participation in a population-based health check. The study population comprised 12,768 persons invited for a health check including screening for ischemic heart disease and lifestyle counseling. The study population was randomly drawn from a population of 179,097 persons living in 73 neighborhoods in Denmark. Data on neighborhood deprivation (percentage with basic education, with low income and not in work) and individual socioeconomic position were retrieved from national administrative registers. Multilevel regression analyses with log links and binary distributions were conducted to obtain relative risks, intraclass correlation coefficients and proportional change in variance. Large differences between neighborhoods existed in both deprivation levels and neighborhood health check participation rate (mean 53%; range 35-84%). In multilevel analyses adjusted for age and sex, higher levels of all three indicators of neighborhood deprivation and a deprivation score were associated with lower participation in a dose-response fashion. Persons living in the most deprived neighborhoods had up to 37% decreased probability of participating compared to those living in the least deprived neighborhoods. Inclusion of individual socioeconomic position in the model attenuated the neighborhood deprivation coefficients, but all except for income deprivation remained statistically significant. Neighborhood deprivation was associated with participation in a population-based health check in a dose-response manner, in which increasing neighborhood deprivation was associated with decreasing participation. This suggests the need to develop preventive health checks tailored to deprived neighborhoods.
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Roos, Johannes Lodewikus; Pretorius, Herman Walter; Karayiorgou, Maria
2009-01-01
The clinical characteristics of an Afrikaner founder population sample recruited for a schizophrenia genetic study are described. Comparisons on several clinical characteristics between this sample and a U.S. sample of schizophrenia patients show that generalization of findings in a founder population to the population at large is applicable. The assessment of the frequency of the 22q11 deletion in Afrikaner schizophrenia patients is approximately 2%, similar to findings in a U.S. sample. Results of analysis of early non-psychotic deviant behavior in subjects under the age of 10 years in the Afrikaner population broadly replicated findings in a U.S. sample. Approximately half of male schizophrenia patients and a quarter of female patients in the Afrikaner schizophrenia database used or abused cannabis. Male users of cannabis with severe early deviant behavior had the lowest mean age of criteria onset, namely 18.4 years. These findings confirm previous findings, indicating that early deviance is linked to later outcome of disease. The clinical characteristics and premorbid variables in 12 childhood-onset Afrikaner schizophrenia patients thus far recruited in this study compare favorably with what is known about childhood-onset schizophrenia in a U.S. sample. The prevalence of co-morbid OCD/OCS in this Afrikaner schizophrenia founder sample was 13.2% which is in keeping with that of co-morbid OCD in schizophrenia, estimated at 12.2% by the U.S. National Institute of Mental Health. These findings confirm that the clinical characteristics of a schizophrenia sample drawn from the Afrikaner founder population can be generalized to the schizophrenia population at large when compared to findings reported in the literature.
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Atzmon, Gil; Hao, Li; Pe'er, Itsik; Velez, Christopher; Pearlman, Alexander; Palamara, Pier Francesco; Morrow, Bernice; Friedman, Eitan; Oddoux, Carole; Burns, Edward; Ostrer, Harry
2010-06-11
For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.
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Atzmon, Gil; Hao, Li; Pe'er, Itsik; Velez, Christopher; Pearlman, Alexander; Palamara, Pier Francesco; Morrow, Bernice; Friedman, Eitan; Oddoux, Carole; Burns, Edward; Ostrer, Harry
2010-01-01
For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads. PMID:20560205
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Fant, Charles; Schlosser, C. Adam; Gao, Xiang; Strzepek, Kenneth; Reilly, John
2016-01-01
The sustainability of future water resources is of paramount importance and is affected by many factors, including population, wealth and climate. Inherent in current methods to estimate these factors in the future is the uncertainty of their prediction. In this study, we integrate a large ensemble of scenarios—internally consistent across economics, emissions, climate, and population—to develop a risk portfolio of water stress over a large portion of Asia that includes China, India, and Mainland Southeast Asia in a future with unconstrained emissions. We isolate the effects of socioeconomic growth from the effects of climate change in order to identify the primary drivers of stress on water resources. We find that water needs related to socioeconomic changes, which are currently small, are likely to increase considerably in the future, often overshadowing the effect of climate change on levels of water stress. As a result, there is a high risk of severe water stress in densely populated watersheds by 2050, compared to recent history. There is strong evidence to suggest that, in the absence of autonomous adaptation or societal response, a much larger portion of the region’s population will live in water-stressed regions in the near future. Tools and studies such as these can effectively investigate large-scale system sensitivities and can be useful in engaging and informing decision makers. PMID:27028871
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De Groot, G. A.; During, H. J.; Ansell, S. W.; Schneider, H.; Bremer, P.; Wubs, E. R. J.; Maas, J. W.; Korpelainen, H.; Erkens, R. H. J.
2012-01-01
Background and Aims Populations established by long-distance colonization are expected to show low levels of genetic variation per population, but strong genetic differentiation among populations. Whether isolated populations indeed show this genetic signature of isolation depends on the amount and diversity of diaspores arriving by long-distance dispersal, and time since colonization. For ferns, however, reliable estimates of long-distance dispersal rates remain largely unknown, and previous studies on fern population genetics often sampled older or non-isolated populations. Young populations in recent, disjunct habitats form a useful study system to improve our understanding of the genetic impact of long-distance dispersal. Methods Microsatellite markers were used to analyse the amount and distribution of genetic diversity in young populations of four widespread calcicole ferns (Asplenium scolopendrium, diploid; Asplenium trichomanes subsp. quadrivalens, tetraploid; Polystichum setiferum, diploid; and Polystichum aculeatum, tetraploid), which are rare in The Netherlands but established multiple populations in a forest (the Kuinderbos) on recently reclaimed Dutch polder land following long-distance dispersal. Reference samples from populations throughout Europe were used to assess how much of the existing variation was already present in the Kuinderbos. Key Results A large part of the Dutch and European genetic diversity in all four species was already found in the Kuinderbos. This diversity was strongly partitioned among populations. Most populations showed low genetic variation and high inbreeding coefficients, and were assigned to single, unique gene pools in cluster analyses. Evidence for interpopulational gene flow was low, except for the most abundant species. Conclusions The results show that all four species, diploids as well as polyploids, were capable of frequent long-distance colonization via single-spore establishment. This indicates that even isolated habitats receive dense and diverse spore rains, including genotypes capable of self-fertilization. Limited gene flow may conserve the genetic signature of multiple long-distance colonization events for several decades. PMID:22323427
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Tourism in Austria: biodiversity, environmental sustainability, and growth issues.
Malik, Muhammad Asad Saleem; Shah, Syed Asim; Zaman, Khalid
2016-12-01
This study examined the long-run and causal relationships between international tourism, biodiversity loss, environmental sustainability, and specific growth factors under the premises of sustainable tourism in Austria, by using a consistent time series data from 1975 to 2015. The results reveal that inbound tourism, per capita income, and population density affected the potential habitat area while population density largely affected the food production in a country. Inbound tourism and population density both deteriorate the environmental quality in a form of increasing carbon dioxide (CO 2 ) emissions and fossil fuel energy consumption while per capita income reduces the fossil fuel energy consumption. Food exports increase per capita income, while food imports and population density both decrease economic growth. Inbound tourism and economic growth advance population density while forest area and food exports decrease the population density. The study supports growth-led tourism and growth-led food production in a country.
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Low incidence of inbreeding in a long-lived primate population isolated for 75 years.
Widdig, Anja; Muniz, Laura; Minkner, Mirjam; Barth, Yvonne; Bley, Stefanie; Ruiz-Lambides, Angelina; Junge, Olaf; Mundry, Roger; Kulik, Lars
2017-01-01
When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients ( F ) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate. When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.
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Fedy, B.C.; Aldridge, Cameron L.
2011-01-01
Long-term population monitoring is the cornerstone of animal conservation and management. The accuracy and precision of models developed using monitoring data can be influenced by the protocols guiding data collection. The greater sage-grouse (Centrocercus urophasianus) is a species of concern that has been monitored over decades, primarily, by counting the number of males that attend lek (breeding) sites. These lek count data have been used to assess long-term population trends and for multiple mechanistic studies. However, some studies have questioned the efficacy of lek counts to accurately identify population trends. In response, monitoring protocols were changed to have a goal of counting lek sites multiple times within a season. We assessed the influence of this change in monitoring protocols on model accuracy and precision applying generalized additive models to describe trends over time. We found that at large spatial scales including >50 leks, the absence of repeated counts within a year did not significantly alter population trend estimates or interpretation. Increasing sample size decreased the model confidence intervals. We developed a population trend model for Wyoming greater sage-grouse from 1965 to 2008, identifying significant changes in the population indices and capturing the cyclic nature of this species. Most sage-grouse declines in Wyoming occurred between 1965 and the 1990s and lek count numbers generally increased from the mid-1990s to 2008. Our results validate the combination of monitoring data collected under different protocols in past and future studies-provided those studies are addressing large-scale questions. We suggest that a larger sample of individual leks is preferable to multiple counts of a smaller sample of leks. ?? 2011 The Wildlife Society.
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Crandall, Eric D.; Liggins, Libby; Bongaerts, Pim; Treml, Eric A.
2016-01-01
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations. PMID:29491947
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Riginos, Cynthia; Crandall, Eric D; Liggins, Libby; Bongaerts, Pim; Treml, Eric A
2016-12-01
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.
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NCI Cohort Consortium Membership
The NCI Cohort Consortium membership is international and includes investigators responsible for more than 40 high-quality cohorts who are studying large and diverse populations in more than 15 different countries.
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ERIC Educational Resources Information Center
Quesen, Sarah
2016-01-01
When studying differential item functioning (DIF) with students with disabilities (SWD) focal groups typically suffer from small sample size, whereas the reference group population is usually large. This makes it possible for a researcher to select a sample from the reference population to be similar to the focal group on the ability scale. Doing…
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James Grogan; R. Matthew Landis; Christopher M. Free; Mark D. Schulze; Marco Lentini; Mark S. Ashton
2014-01-01
Summary 1. The impacts of selective harvesting in tropical forests on population recovery and future timber yields by high-value species remain largely unknown for lack of demographic data spanning all phases of life history, from seed to senescence. In this study, we use an individual- based model parameterized using 15 years of annual census data to simulate...
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ERIC Educational Resources Information Center
Dewinter, J.; De Graaf, H.; Begeer, S.
2017-01-01
This study compared sexual orientation and romantic relationship experience in a large sample of adolescents and adults with autism spectrum disorder (ASD) (n = 675) and general population peers (n = 8064). Gender identity was explored in the ASD group in relation to assigned gender at birth. Compared to general population peers, more people with…
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Martin P. Schilling; Paul G. Wolf; Aaron M. Duffy; Hardeep S. Rai; Carol A. Rowe; Bryce A. Richardson; Karen E. Mock
2014-01-01
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-...
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Small mammal populations after a wildfire in northeast Minnesota.
Richard R. Buech; Karl Siderits; Robert E. Radtke; Howard L. Sheldon; Donald Elsing
1977-01-01
Small mammals were studied shortly after a large wildfire in northeast Minnesota. An average of only 16 as many small mammals were in three forest communities that had burned than were in comparable unburned areas. The greatest reduction was for the red-backed vole. An analysis of population attributes suggests that deer mice immigrated to the burned area. Small...
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Further Validation of a U.S. Adult Social Self-Efficacy Inventory in Chinese Populations
ERIC Educational Resources Information Center
Fan, Jinyan; Meng, Hui; Zhao, Bihua; Patel, Trishna
2012-01-01
The authors report further validity evidence for the Chinese version of a U.S. adult social self-efficacy inventory, the "Perceived Social Self-Efficacy" (PSSE) scale in Chinese populations. Study 1 participants were 323 new graduate students enrolled at a large university in an east coast city of the People's Republic of China. Differential item…
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Elucidating the genetic architecture of reproductive ageing in the Japanese population.
Horikoshi, Momoko; Day, Felix R; Akiyama, Masato; Hirata, Makoto; Kamatani, Yoichiro; Matsuda, Koichi; Ishigaki, Kazuyoshi; Kanai, Masahiro; Wright, Hollis; Toro, Carlos A; Ojeda, Sergio R; Lomniczi, Alejandro; Kubo, Michiaki; Ong, Ken K; Perry, John R B
2018-05-17
Population studies elucidating the genetic architecture of reproductive ageing have been largely limited to European ancestries, restricting the generalizability of the findings and overlooking possible key genes poorly captured by common European genetic variation. Here, we report 26 loci (all P < 5 × 10 -8 ) for reproductive ageing, i.e. puberty timing or age at menopause, in a non-European population (up to 67,029 women of Japanese ancestry). Highlighted genes for menopause include GNRH1, which supports a primary, rather than passive, role for hypothalamic-pituitary GnRH signalling in the timing of menopause. For puberty timing, we demonstrate an aetiological role for receptor-like protein tyrosine phosphatases by combining evidence across population genetics and pre- and peri-pubertal changes in hypothalamic gene expression in rodent and primate models. Furthermore, our findings demonstrate widespread differences in allele frequencies and effect estimates between Japanese and European associated variants, highlighting the benefits and challenges of large-scale trans-ethnic approaches.
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Fitzgerald, Timothy L; Lea, C S; Brinkley, Jason; Zervos, Emmanuel E
2014-01-01
Conflicting data exists regarding the influence of population density on colorectal cancer (CRC) outcomes; to better understand this, the present study evaluated outcomes along an urban-rural continuum. Colorectal patients aged ≥40 years from 1992 to 2002 were identified in the SEER (Surveillance, Epidemiology, and End Results) Registries of the National Cancer Institute in the USA. A total of 176 011 patients were identified, with median age 71; most lived in populous counties and were white (90%). Patients from large metropolitan counties were more often African-American, and those in rural counties were more likely to be white and have low socioeconomic status (SES). Patients from large metropolitan (>1 million) and rural counties were more likely to have metastatic disease and decreased survival compared to smaller metropolitan counties (<1 million). Late stage of presentation and diminished survival were also associated with African-American race, male sex and lower SES. Metropolitan counties with populations <1 million had superior CRC outcomes, in part secondary to race and SES.
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Williams, Samuel M.; Otway, Nicholas M.; Nielsen, Einar E.; Maher, Safia L.; Bennett, Mike B.; Ovenden, Jennifer R.
2017-01-01
Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14, p < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier. PMID:28791159
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Holmes, Bonnie J; Williams, Samuel M; Otway, Nicholas M; Nielsen, Einar E; Maher, Safia L; Bennett, Mike B; Ovenden, Jennifer R
2017-07-01
Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark ( Galeocerdo cuvier ) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring ( F ST > 0.14, p < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier .
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Multi-ethnic genome-wide association study identifies novel locus for type 2 diabetes susceptibility
Cook, James P; Morris, Andrew P
2016-01-01
Genome-wide association studies (GWAS) have traditionally been undertaken in homogeneous populations from the same ancestry group. However, with the increasing availability of GWAS in large-scale multi-ethnic cohorts, we have evaluated a framework for detecting association of genetic variants with complex traits, allowing for population structure, and developed a powerful test of heterogeneity in allelic effects between ancestry groups. We have applied the methodology to identify and characterise loci associated with susceptibility to type 2 diabetes (T2D) using GWAS data from the Resource for Genetic Epidemiology on Adult Health and Aging, a large multi-ethnic population-based cohort, created for investigating the genetic and environmental basis of age-related diseases. We identified a novel locus for T2D susceptibility at genome-wide significance (P<5 × 10−8) that maps to TOMM40-APOE, a region previously implicated in lipid metabolism and Alzheimer's disease. We have also confirmed previous reports that single-nucleotide polymorphisms at the TCF7L2 locus demonstrate the greatest extent of heterogeneity in allelic effects between ethnic groups, with the lowest risk observed in populations of East Asian ancestry. PMID:27189021
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ASTEROSEISMIC CLASSIFICATION OF STELLAR POPULATIONS AMONG 13,000 RED GIANTS OBSERVED BY KEPLER
DOE Office of Scientific and Technical Information (OSTI.GOV)
Stello, Dennis; Bedding, Timothy R.; Benomar, Othman
2013-03-10
Of the more than 150,000 targets followed by the Kepler Mission, about 10% were selected as red giants. Due to their high scientific value, in particular for Galaxy population studies and stellar structure and evolution, their Kepler light curves were made public in late 2011. More than 13,000 (over 85%) of these stars show intrinsic flux variability caused by solar-like oscillations making them ideal for large-scale asteroseismic investigations. We automatically extracted individual frequencies and measured the period spacings of the dipole modes in nearly every red giant. These measurements naturally classify the stars into various populations, such as the redmore » giant branch, the low-mass (M/M{sub Sun} {approx}< 1.8) helium-core-burning red clump, and the higher-mass (M/M{sub Sun} {approx}> 1.8) secondary clump. The period spacings also reveal that a large fraction of the stars show rotationally induced frequency splittings. This sample of stars will undoubtedly provide an extremely valuable source for studying the stellar population in the direction of the Kepler field, in particular when combined with complementary spectroscopic surveys.« less
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Population equations for degree-heterogenous neural networks
NASA Astrophysics Data System (ADS)
Kähne, M.; Sokolov, I. M.; Rüdiger, S.
2017-11-01
We develop a statistical framework for studying recurrent networks with broad distributions of the number of synaptic links per neuron. We treat each group of neurons with equal input degree as one population and derive a system of equations determining the population-averaged firing rates. The derivation rests on an assumption of a large number of neurons and, additionally, an assumption of a large number of synapses per neuron. For the case of binary neurons, analytical solutions can be constructed, which correspond to steps in the activity versus degree space. We apply this theory to networks with degree-correlated topology and show that complex, multi-stable regimes can result for increasing correlations. Our work is motivated by the recent finding of subnetworks of highly active neurons and the fact that these neurons tend to be connected to each other with higher probability.
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Koch, Raphael; Demant, Martin; Aung, Thiha; Diering, Nina; Cicholas, Anna; Chapuy, Bjoern; Wenzel, Dirk; Lahmann, Marlen; Güntsch, Annemarie; Kiecke, Christina; Becker, Sabrina; Hupfeld, Timo; Venkataramani, Vivek; Ziepert, Marita; Opitz, Lennart; Klapper, Wolfram; Trümper, Lorenz; Wulf, Gerald G
2014-04-03
Tumors are composed of phenotypically heterogeneous cell populations. The nongenomic mechanisms underlying transitions and interactions between cell populations are largely unknown. Here, we show that diffuse large B-cell lymphomas possess a self-organized infrastructure comprising side population (SP) and non-SP cells, where transitions between clonogenic states are modulated by exosome-mediated Wnt signaling. DNA methylation modulated SP-non-SP transitions and was correlated with the reciprocal expressions of Wnt signaling pathway agonist Wnt3a in SP cells and the antagonist secreted frizzled-related protein 4 in non-SP cells. Lymphoma SP cells exhibited autonomous clonogenicity and exported Wnt3a via exosomes to neighboring cells, thus modulating population equilibrium in the tumor.
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Laupland, Kevin B; Church, Deirdre L
2005-01-01
Background Giardia lamblia (intestinalis) and Cryptosporidium parvum are the two most important intestinal parasites infecting North Americans but there is a paucity of active population-based surveillance data from Canada. This study determined the incidence of and demographic risk factors for developing Giardia sp. and Cryptosporidium sp. infections in a general Canadian population. Methods Population-based laboratory surveillance was conducted among all residents of the Calgary Health Region (CHR; population ≅ 1 million) during May 1, 1999 and April 30, 2002. Results Giardia sp. infection occurred at a rate of 19.6 per 100,000 populations per year. Although the yearly incidence was stable, a significant seasonal variation was observed with a peak in late summer to early fall. Males were at higher risk for development of this infection as compared to females (21.2 vs. 17.9 per 100,000/yr; relative risk (RR) 1.19; 95% confidence interval (CI), 1.00–1.40, p = 0.047), and there was a significant decrease in risk associated with an increasing age. Cryptosporidium sp. infection occurred at an overall rate of 6.0 per 100,000 populations per year although a large outbreak of Cryptosporidium sp. infections occurred in the second half of the summer of 2001. During August and September of 2001, the incidence of cryptosporidiosis was 55.1 per 100,000 per year as compared to 3.1 per 100,000 per year for the remainder of the surveillance period (p < 0.0001). Cryptosporidiosis was largely a disease of children with an incidence of 17.8 per 100,000 per year occurring among those aged < 20 years of age compared to 1.25 per 100,000 per year for adults ≥ 20 years of age (RR 14.19; 95% CI, 9.77–21.11; p < 0.0001). Conclusion This study provides important information on the occurrence and demographic risk groups for acquisition of giardiasis and cryptosporidiosis in a non-selected Canadian population. PMID:16168061
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Nabi, Hermann; Bochud, Murielle; Glaus, Jennifer; Lasserre, Aurélie M; Waeber, Gérard; Vollenweider, Peter; Preisig, Martin
2013-10-01
Studies on the association between homocysteine levels and depression have shown conflicting results. To examine the association between serum total homocysteine (tHcy) levels and major depressive disorder (MDD) in a large community sample with an extended age range. A total of 3392 men and women aged 35-66 years participating in the CoLaus study and its psychiatric arm (PsyCoLaus) were included in the analyses. High tHcy measured from fasting blood samples was defined as a concentration ≥15μmol/L. MDD was assessed using the semi-structured Diagnostic Interview for Genetics Studies. In multivariate analyses, elevated tHcy levels were associated with greater odds of meeting the diagnostic criteria for lifetime MDD among men (OR=1.71; 95% CI, 1.18-2.50). This was particularly the case for remitted MDD. Among women, there was no significant association between tHcy levels and MDD and the association tended to be in the opposite direction (OR=0.61; 95% CI, 0.34-1.08). In this large population-based study, elevated tHcy concentrations are associated with lifetime MDD and particularly with remitted MDD among men. Copyright © 2013 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Austermann, Jason Edward
One of the primary drivers in the development of large format millimeter detector arrays is the study of sub-millimeter galaxies (SMGs) - a population of very luminous high-redshift dust-obscured starbursts that are widely believed to be the dominant contributor to the Far-Infrared Background (FIB). The characterization of such a population requires the ability to map large patches of the (sub-)millimeter sky to high sensitivity within a feasible amount of time. I present this dissertation on the design, integration, and characterization of the 144-pixel AzTEC millimeter-wave camera and its application to the study of the sub-millimeter galaxy population. In particular, I present an unprecedented characterization of the "blank-field" (fields with no known mass bias) SMG number counts by mapping over 0.5 deg^2 to 1.1mm depths of ~1mJy - a previously unattained depth on these scales. This survey provides the tightest SMG number counts available, particularly for the brightest and rarest SMGs that require large survey areas for a significant number of detections. These counts are compared to the predictions of various models of the evolving mm/sub-mm source population, providing important constraints for the ongoing refinement of semi-analytic and hydrodynamical models of galaxy formation. I also present the results of an AzTEC 0.15 deg^2 survey of the COSMOS field, which uncovers a significant over-density of bright SMGs that are spatially correlated to foreground mass structures, presumably as a result of gravitational lensing. Finally, I compare the results of the available SMG surveys completed to date and explore the effects of cosmic variance on the interpretation of individual surveys.
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SNPs and Haplotypes in Native American Populations
Kidd, Judith R.; Friedlaender, Françoise; Pakstis, Andrew J.; Furtado, Manohar; Fang, Rixun; Wang, Xudong; Nievergelt, Caroline M.; Kidd, Kenneth K.
2013-01-01
Autosomal DNA polymorphisms can provide new information and understanding of both the origins of and relationships among modern Native American populations. At the same time that autosomal markers can be highly informative, they are also susceptible to ascertainment biases in the selection of the markers to use. Identifying markers that can be used for ancestry inference among Native American populations can be considered separate from identifying markers to further the quest for history. In the current study we are using data on nine Native American populations to compare the results based on a large haplotype-based dataset with relatively small independent sets of SNPs. We are interested in what types of limited datasets an individual laboratory might be able to collect are best for addressing two different questions of interest. First, how well can we differentiate the Native American populations and/or infer ancestry by assigning an individual to her population(s) of origin? Second, how well can we infer the historical/evolutionary relationships among Native American populations and their Eurasian origins. We conclude that only a large comprehensive dataset involving multiple autosomal markers on multiple populations will be able to answer both questions; different small sets of markers are able to answer only one or the other of these questions. Using our largest dataset we see a general increasing distance from Old World populations from North to South in the New World except for an unexplained close relationship between our Maya and Quechua samples. PMID:21913176
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English Teaching and the Economic Development of Colombia.
ERIC Educational Resources Information Center
Stansfield, Charles W.
To supply the large number of workers qualified for complex jobs, a demand created by the growing needs of a rapidly growing population, Colombia must make provisions for an expanded system of higher education. This can be accomplished by sending students abroad to study at the university level. The large number of students coming to the United…
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Mesoscopic fluctuations of the population of a qubit in a strong alternating field
NASA Astrophysics Data System (ADS)
Denisenko, M. V.; Satanin, A. M.
2016-12-01
Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau-Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of the population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.
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Mooney, H A
1980-01-01
Plants of the widely distributed species Heliotropium curassavicum L. have a large photosynthetic acclimation potential to temperature. There are, however, some differences among the acclimation potentials of populations occupying dissimilar thermal regimes. Plants of populations originating from a cool maritime climate have a greater acclimation potential than plants of populations originating from a desert habitat, which is characterized by large seasonal changes in temperature.
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Impact of biology knowledge on the conservation and management of large pelagic sharks.
Yokoi, Hiroki; Ijima, Hirotaka; Ohshimo, Seiji; Yokawa, Kotaro
2017-09-06
Population growth rate, which depends on several biological parameters, is valuable information for the conservation and management of pelagic sharks, such as blue and shortfin mako sharks. However, reported biological parameters for estimating the population growth rates of these sharks differ by sex and display large variability. To estimate the appropriate population growth rate and clarify relationships between growth rate and relevant biological parameters, we developed a two-sex age-structured matrix population model and estimated the population growth rate using combinations of biological parameters. We addressed elasticity analysis and clarified the population growth rate sensitivity. For the blue shark, the estimated median population growth rate was 0.384 with a range of minimum and maximum values of 0.195-0.533, whereas those values of the shortfin mako shark were 0.102 and 0.007-0.318, respectively. The maturity age of male sharks had the largest impact for blue sharks, whereas that of female sharks had the largest impact for shortfin mako sharks. Hypotheses for the survival process of sharks also had a large impact on the population growth rate estimation. Both shark maturity age and survival rate were based on ageing validation data, indicating the importance of validating the quality of these data for the conservation and management of large pelagic sharks.
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Estimation of population size using open capture-recapture models
McDonald, T.L.; Amstrup, Steven C.
2001-01-01
One of the most important needs for wildlife managers is an accurate estimate of population size. Yet, for many species, including most marine species and large mammals, accurate and precise estimation of numbers is one of the most difficult of all research challenges. Open-population capture-recapture models have proven useful in many situations to estimate survival probabilities but typically have not been used to estimate population size. We show that open-population models can be used to estimate population size by developing a Horvitz-Thompson-type estimate of population size and an estimator of its variance. Our population size estimate keys on the probability of capture at each trap occasion and therefore is quite general and can be made a function of external covariates measured during the study. Here we define the estimator and investigate its bias, variance, and variance estimator via computer simulation. Computer simulations make extensive use of real data taken from a study of polar bears (Ursus maritimus) in the Beaufort Sea. The population size estimator is shown to be useful because it was negligibly biased in all situations studied. The variance estimator is shown to be useful in all situations, but caution is warranted in cases of extreme capture heterogeneity.
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Micro RNAs from DNA Viruses are Found Widely in Plasma in a Large Observational Human Population.
Koupenova, Milka; Mick, Eric; Corkrey, Heather A; Huan, Tianxiao; Clancy, Lauren; Shah, Ravi; Benjamin, Emelia J; Levy, Daniel; Kurt-Jones, Evelyn A; Tanriverdi, Kahraman; Freedman, Jane E
2018-04-23
Viral infections associate with disease risk and select families of viruses encode miRNAs that control an efficient viral cycle. The association of viral miRNA expression with disease in a large human population has not been previously explored. We sequenced plasma RNA from 40 participants of the Framingham Heart Study (FHS, Offspring Cohort, Visit 8) and identified 3 viral miRNAs from 3 different human Herpesviridae. These miRNAs were mostly related to viral latency and have not been previously detected in human plasma. Viral miRNA expression was then screened in the plasma of 2763 participants of the remaining cohort utilizing high-throughput RT-qPCR. All 3 viral miRNAs associated with combinations of inflammatory or prothrombotic circulating biomarkers (sTNFRII, IL-6, sICAM1, OPG, P-selectin) but did not associate with hypertension, coronary heart disease or cancer. Using a large observational population, we demonstrate that the presence of select viral miRNAs in the human circulation associate with inflammatory biomarkers and possibly immune response, but fail to associate with overt disease. This study greatly extends smaller singular observations of viral miRNAs in the human circulation and suggests that select viral miRNAs, such as those for latency, may not impact disease manifestation.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fant, Charles; Schlosser, C. Adam; Gao, Xiang
The sustainability of future water resources is of paramount importance and is affected by many factors, including population, wealth and climate. Inherent in current methods to estimate these factors in the future is the uncertainty of their prediction. In this study, we integrate a large ensemble of scenarios—internally consistent across economics, emissions, climate, and population—to develop a risk portfolio of water stress over a large portion of Asia that includes China, India, and Mainland Southeast Asia in a future with unconstrained emissions. We isolate the effects of socioeconomic growth from the effects of climate change in order to identify themore » primary drivers of stress on water resources. We find that water needs related to socioeconomic changes, which are currently small, are likely to increase considerably in the future, often overshadowing the effect of climate change on levels of water stress. As a result, there is a high risk of severe water stress in densely populated watersheds by 2050, compared to recent history. There is strong evidence to suggest that, in the absence of autonomous adaptation or societal response, a much larger portion of the region’s population will live in water-stressed regions in the near future. Lastly, tools and studies such as these can effectively investigate large-scale system sensitivities and can be useful in engaging and informing decision makers.« less
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Dental Fear and Avoidance in Treatment Seekers at a Large, Urban Dental Clinic.
Heyman, Richard E; Slep, Amy M Smith; White-Ajmani, Mandi; Bulling, Lisanne; Zickgraf, Hana F; Franklin, Martin E; Wolff, Mark S
2016-01-01
The prevalence and correlates of dental fear have been studied in representative population studies, but not in patients presenting for dental treatment. We hypothesized that dental fear among patients presenting at a large, urban college of dentistry would be similar to that of the population (e.g. 11% high dental fear, 17% to 35% moderate or higher fear) and that fear would be associated with avoidance of routine dental care, increased use of urgent dental care and poor oral health. Participants were 1070 consecutive patients at a large, urban dental care center. All patients completed a clinical interview, including demographics, medical history, dental history and presenting concerns, and behavioral health history. Patients were also asked to rate their dental anxiety/fear on a 1 (none) to 10 (high) scale. Over 20% of patients reported elevated anxiety/fear, of which 12.30% reported moderate and 8.75% high fear. Severity of dental anxiety/fear was strongly related to the likelihood of avoiding dental services in the past and related to myriad presenting problems. As hypothesized, the prevalence of moderate or higher fear in dental patients was considerable and closely matched that found in general population surveys. Thus, the 'dental home' is an ideal location to treat clinically significant dental anxiety/fear.
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Inferring microevolution from museum collections and resampling: lessons learned from Cepaea.
Ożgo, Małgorzata; Liew, Thor-Seng; Webster, Nicole B; Schilthuizen, Menno
2017-01-01
Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.
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Bhaskar, Anand; Wang, Y X Rachel; Song, Yun S
2015-02-01
With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal that is difficult to pick up with small sample sizes. Lastly, we use our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing data set of tens of thousands of individuals assayed at a few hundred genic regions. © 2015 Bhaskar et al.; Published by Cold Spring Harbor Laboratory Press.
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VISIT-TS: A multimedia tool for population studies on tic disorders.
Vachon, M Jonathan; Striley, Catherine W; Gordon, Mollie R; Schroeder, Miriam L; Bihun, Emily C; Koller, Jonathan M; Black, Kevin J
2016-01-01
Population-based assessment of Tourette syndrome (TS) and other tic disorders produces a paradox. On one hand, ideally diagnosis of tic disorders requires expert observation. In fact, diagnostic criteria for TS explicitly require expert assessment of tics for a definite diagnosis. On the other hand, large-scale population surveys with expert assessment of every subject are impracticable. True, several published studies have successfully used expert assessment to find tic prevalence in a representative population (e.g. all students in a school district). However, extending these studies to larger populations is daunting. We created a multimedia tool to demonstrate tics to a lay audience, discuss their defining and common attributes, and address features that differentiate tics from other movements and vocalizations. A first version was modified to improve clarity and to include a more diverse group in terms of age and ethnicity. The result is a tool intended for epidemiological research. It may also provide additional benefits, such as more representative minority recruitment for other TS studies and increased community awareness of TS.
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Linkages between large-scale climate patterns and the dynamics of Alaskan caribou populations
Kyle Joly; David R. Klein; David L. Verbyla; T. Scott Rupp; F. Stuart Chapin
2011-01-01
Recent research has linked climate warming to global declines in caribou and reindeer (both Rangifer tarandus) populations. We hypothesize large-scale climate patterns are a contributing factor explaining why these declines are not universal. To test our hypothesis for such relationships among Alaska caribou herds, we calculated the population growth...
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The Genetics of Mexico Recapitulates Native American Substructure and Affects Biomedical Traits
Moreno-Estrada, Andrés; Gignoux, Christopher R.; Fernández-López, Juan Carlos; Zakharia, Fouad; Sikora, Martin; Contreras, Alejandra V.; Acuña-Alonzo, Victor; Sandoval, Karla; Eng, Celeste; Romero-Hidalgo, Sandra; Ortiz-Tello, Patricia; Robles, Victoria; Kenny, Eimear E.; Nuño-Arana, Ismael; Barquera-Lozano, Rodrigo; Macín-Pérez, Gastón; Granados-Arriola, Julio; Huntsman, Scott; Galanter, Joshua M.; Via, Marc; Ford, Jean G.; Chapela, Rocío; Rodriguez-Cintron, William; Rodríguez-Santana, Jose R.; Romieu, Isabelle; Sienra-Monge, Juan José; Navarro, Blanca del Rio; London, Stephanie J.; Ruiz-Linares, Andrés; Garcia-Herrera, Rodrigo; Estrada, Karol; Hidalgo-Miranda, Alfredo; Jimenez-Sanchez, Gerardo; Carnevale, Alessandra; Soberón, Xavier; Canizales-Quinteros, Samuel; Rangel-Villalobos, Héctor; Silva-Zolezzi, Irma; Burchard, Esteban Gonzalez; Bustamante, Carlos D.
2014-01-01
Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1,000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between sub-continental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide. PMID:24926019
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Paquet, Victor; Joseph, Caroline; D'Souza, Clive
2012-01-01
Anthropometric studies typically require a large number of individuals that are selected in a manner so that demographic characteristics that impact body size and function are proportionally representative of a user population. This sampling approach does not allow for an efficient characterization of the distribution of body sizes and functions of sub-groups within a population and the demographic characteristics of user populations can often change with time, limiting the application of the anthropometric data in design. The objective of this study is to demonstrate how demographically representative user populations can be developed from samples that are not proportionally representative in order to improve the application of anthropometric data in design. An engineering anthropometry problem of door width and clear floor space width is used to illustrate the value of the approach.
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Barri, Fernando
2018-01-01
Guanacos (Lama guanicoe) are large ungulates that have been valued by human populations in South America since the Late Pleistocene. Even though they were very abundant until the end of the 19th century (before the high deforestation rate of the last decades), guanacos have nearly disappeared in the Gran Chaco ecoregion, with relicts and isolated populations surviving in some areas, such as the shrubland area near the saline depressions of Córdoba province, Argentina. In this report, we present the first data from a locally endangered guanaco wild population, through the study of skeletal remains recovered in La Providencia ranch. Our results showed that most of the elements belonged to adults aged between 36 and 96 months; sex evaluation showed similar numbers of males and females. Statistical analysis of the body size of modern samples from Córdoba demonstrated that guanacos from the Chaco had large dimensions and presented lower size variability than the modern and archaeological specimens in our database. Moreover, they exhibited dimensions similar to those of modern guanacos from Patagonia and San Juan, and to archaeological specimens from Ongamira and Cerro Colorado, although further genetic studies are needed to corroborate a possible phylogenetic relationship. Finally, we used archaeozoological techniques to provide a first characterization of a relict guanaco population from the Chaco ecoregion, demonstrating its value to the study of modern skeletal remains and species conservation biology. PMID:29641579
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Mullins, Jacinta; McDevitt, Allan D; Kowalczyk, Rafał; Ruczyńska, Iwona; Górny, Marcin; Wójcik, Jan M
2014-01-01
The red fox ( Vulpes vulpes ) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002-2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.
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Cystic fibrosis carrier screening in a North American population.
Zvereff, Val V; Faruki, Hawazin; Edwards, Marcia; Friedman, Kenneth J
2014-07-01
The aim of this study was to compare the mutation frequency distribution for a 32-mutation panel and a 69-mutation panel used for cystic fibrosis carrier screening. Further aims of the study were to examine the race-specific detection rates provided by both panels and to assess the performance of extended panels in large-scale, population-based cystic fibrosis carrier screening. Although genetic screening for the most common CFTR mutations allows detection of nearly 90% of cystic fibrosis carriers, the large number of other mutations, and their distribution within different ethnic groups, limits the utility of general population screening. Patients referred for cystic fibrosis screening from January 2005 through December 2010 were tested using either a 32-mutation panel (n = 1,601,308 individuals) or a 69-mutation panel (n = 109,830). The carrier frequencies observed for the 69-mutation panel study population (1/36) and Caucasian (1/27) and African-American individuals (1/79) agree well with published cystic fibrosis carrier frequencies; however, a higher carrier frequency was observed for Hispanic-American individuals (1/48) using the 69-mutation panel as compared with the 32-mutation panel (1/69). The 69-mutation panel detected ~20% more mutations than the 32-mutation panel for both African-American and Hispanic-American individuals. Expanded panels using race-specific variants can improve cystic fibrosis carrier detection rates within specific populations. However, it is important that the pathogenicity and the relative frequency of these variants are confirmed.
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Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra)
Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A
2012-01-01
Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (FST range: 0.06–0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts. PMID:22086081
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Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra).
Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A
2012-04-01
Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (F(ST) range: 0.06-0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts.
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Thomas, Elaine
2005-01-01
This article is the second in a series of three that will give health care professionals (HCPs) a sound introduction to medical statistics (Thomas, 2004). The objective of research is to find out about the population at large. However, it is generally not possible to study the whole of the population and research questions are addressed in an appropriate study sample. The next crucial step is then to use the information from the sample of individuals to make statements about the wider population of like individuals. This procedure of drawing conclusions about the population, based on study data, is known as inferential statistics. The findings from the study give us the best estimate of what is true for the relevant population, given the sample is representative of the population. It is important to consider how accurate this best estimate is, based on a single sample, when compared to the unknown population figure. Any difference between the observed sample result and the population characteristic is termed the sampling error. This article will cover the two main forms of statistical inference (hypothesis tests and estimation) along with issues that need to be addressed when considering the implications of the study results. Copyright (c) 2005 Whurr Publishers Ltd.
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NASA Astrophysics Data System (ADS)
Allstadt, A. J.; Gorzo, J.; Bateman, B. L.; Heglund, P. J.; Pidgeon, A. M.; Thogmartin, W.; Vavrus, S. J.; Radeloff, V.
2016-12-01
Often, fewer birds are often observed in an area experiencing extreme weather, as local populations tend to leave an area (via out-migration or concentration in refugia) or experience a change in population size (via mortality or reduced fecundity). Further, weather patterns are often coherent over large areas so unsuitable weather may threaten large portions of an entire species range simultaneously. However, beyond a few iconic irruptive species, rarely have studies applied both the necessary scale and sensitivity required to assess avian population responses over entire species range. Here, we examined the effects of pre-breeding season weather on the distribution and abundances of 103 North American bird species from the late 1966-2010 using observed abundance records from the Breeding Bird Survey. We compared abundances with measures of drought and temperature over each species' range, and with three atmospheric teleconnections that describe large-scale circulation patterns influencing conditions on the ground. More than 90% of the species responded to at least one of our five weather variables. Grassland bird species tended to be most responsive to weather conditions and forest birds the least, though we found relations among all habitat types. For most species, the response was movement rather than large effects on the overall population size. Maps of these responses indicate that concentration and out-migration are both common strategies for coping with challenging weather conditions across a species range. The dynamic distribution of many bird species makes clear the need to account for temporal variability in conservation planning, as areas that are less important for a species' breeding success in most years may be very important in years with abnormal weather conditions.
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Spatial variation in senescence rates in a bird metapopulation.
Holand, H; Kvalnes, T; Gamelon, M; Tufto, J; Jensen, H; Pärn, H; Ringsby, T H; Sæther, B-E
2016-07-01
Investigating factors which affect the decline in survival with age, i.e. actuarial senescence, is important in order to understand how demographic rates vary in wild populations. Although the evidence for the occurrence of actuarial senescence in wild populations is growing, very few studies have compared actuarial senescence rates between wild populations of the same species. We used data from a long-time study of demography of house sparrows (Passer domesticus) to investigate differences in rates of actuarial senescence between habitats and sub-populations. We also investigated whether rates of actuarial senescence differed between males and females. We found that rates of actuarial senescence showed large spatial variation. We also found that the onset of actuarial senescence varied between sub-populations. However, these differences were not significantly explained by a general difference in habitat type. We also found no significant difference in actuarial senescence rates between males and females. This study shows that senescence rates in natural populations may vary significantly between sub-populations and that failing to account for such differences may give a biased estimate of senescence rates of a species.
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Adiabatic theory for the population distribution in the evolutionary minority game
NASA Astrophysics Data System (ADS)
Chen, Kan; Wang, Bing-Hong; Yuan, Baosheng
2004-02-01
We study the evolutionary minority game (EMG) using a statistical mechanics approach. We derive a theory for the steady-state population distribution of the agents. The theory is based on an “adiabatic approximation” in which short time fluctuations in the population distribution are integrated out to obtain an effective equation governing the steady-state distribution. We discover the mechanism for the transition from segregation (into opposing groups) to clustering (towards cautious behaviors). The transition is determined by two generic factors: the market impact (of the agents’ own actions) and the short time market inefficiency (arbitrage opportunities) due to fluctuations in the numbers of agents using opposite strategies. A large market impact favors “extreme” players who choose fixed opposite strategies, while large market inefficiency favors cautious players. The transition depends on the number of agents (N) and the effective rate of strategy switching. When N is small, the market impact is relatively large; this favors the extreme behaviors. Frequent strategy switching, on the other hand, leads to a clustering of the cautious agents.
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Dynamical Origin and Terrestrial Impact Flux of Large Near-Earth Asteroids
NASA Astrophysics Data System (ADS)
Nesvorný, David; Roig, Fernando
2018-01-01
Dynamical models of the asteroid delivery from the main belt suggest that the current impact flux of diameter D> 10 km asteroids on the Earth is ≃0.5–1 Gyr‑1. Studies of the Near-Earth Asteroid (NEA) population find a much higher flux, with ≃ 7 D> 10 km asteroid impacts per Gyr. Here we show that this problem is rooted in the application of impact probability of small NEAs (≃1.5 Gyr‑1 per object), whose population is well characterized, to large NEAs. In reality, large NEAs evolve from the main belt by different escape routes, have a different orbital distribution, and lower impact probabilities (0.8 ± 0.3 Gyr‑1 per object) than small NEAs. In addition, we find that the current population of two D> 10 km NEAs (Ganymed and Eros) is a slight fluctuation over the long-term average of 1.1+/- 0.5 D> 10 km NEAs in a steady state. These results have important implications for our understanding of the occurrence of the K/T-scale impacts on the terrestrial worlds.
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Heerman, Lisa; DeAngelis, Donald L.; Borcherding, Jost
2017-01-01
Usually, the origin of a within-cohort bimodal size distribution is assumed to be caused by initial size differences or by one discrete period of accelerated growth for one part of the population. The aim of this study was to determine if more continuous pathways exist allowing shifts from the small to the large fraction within a bimodal age-cohort. Therefore, a Eurasian perch population, which had already developed a bimodal size-distribution and had differential resource use of the two size-cohorts, was examined. Results revealed that formation of a bimodal size-distribution can be a continuous process. Perch from the small size-cohort were able to grow into the large size-cohort by feeding on macroinvertebrates not used by their conspecifics. The diet shifts were accompanied by morphological shape changes. Intra-specific competition seemed to trigger the development towards an increasing number of large individuals. A stage-structured matrix model confirmed these assumptions. The fact that bimodality can be a continuous process is important to consider for the understanding of ecological processes and links within ecosystems.
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DeAngelis, Donald L.; Borcherding, Jost
2017-01-01
Usually, the origin of a within-cohort bimodal size distribution is assumed to be caused by initial size differences or by one discrete period of accelerated growth for one part of the population. The aim of this study was to determine if more continuous pathways exist allowing shifts from the small to the large fraction within a bimodal age-cohort. Therefore, a Eurasian perch population, which had already developed a bimodal size-distribution and had differential resource use of the two size-cohorts, was examined. Results revealed that formation of a bimodal size-distribution can be a continuous process. Perch from the small size-cohort were able to grow into the large size-cohort by feeding on macroinvertebrates not used by their conspecifics. The diet shifts were accompanied by morphological shape changes. Intra-specific competition seemed to trigger the development towards an increasing number of large individuals. A stage-structured matrix model confirmed these assumptions. The fact that bimodality can be a continuous process is important to consider for the understanding of ecological processes and links within ecosystems. PMID:28650963
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Natural disasters and population mobility in Bangladesh.
Gray, Clark L; Mueller, Valerie
2012-04-17
The consequences of environmental change for human migration have gained increasing attention in the context of climate change and recent large-scale natural disasters, but as yet relatively few large-scale and quantitative studies have addressed this issue. We investigate the consequences of climate-related natural disasters for long-term population mobility in rural Bangladesh, a region particularly vulnerable to environmental change, using longitudinal survey data from 1,700 households spanning a 15-y period. Multivariate event history models are used to estimate the effects of flooding and crop failures on local population mobility and long-distance migration while controlling for a large set of potential confounders at various scales. The results indicate that flooding has modest effects on mobility that are most visible at moderate intensities and for women and the poor. However, crop failures unrelated to flooding have strong effects on mobility in which households that are not directly affected but live in severely affected areas are the most likely to move. These results point toward an alternate paradigm of disaster-induced mobility that recognizes the significant barriers to migration for vulnerable households as well their substantial local adaptive capacity.
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Zierath, Sharon; Hughes, Angela M.; Fretwell, Neale; Dibley, Mark
2017-01-01
Background A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom PanelTM test. Results From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare. Conclusions The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner’s rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs. PMID:29166669
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Zierath, Sharon; Hughes, Angela M; Fretwell, Neale; Dibley, Mark; Ekenstedt, Kari J
2017-01-01
A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom PanelTM test. From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare. The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner's rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs.
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Male mating strategy and the introgression of a growth hormone transgene.
Valosaari, Kata-Riina; Aikio, Sami; Kaitala, Veijo
2008-11-01
Escaped transgenic organisms (GMO's) may threaten the populations of their wild relatives if able to hybridize with each other. The introgression of a growth enhancement transgene into a wild Atlantic salmon population may be affected by the transgene's effects not only on fitness parameters, but also on mating behaviour. Large anadromous GMO males are most preferred in mating, but a transgene can also give the large sneakers a reproductive advantage over the smaller wild individuals. With a simulation model, we studied whether the increase in the proportion and mating success of sneakers in transgenic and hybrid genotypes could facilitate the introgression of a transgene into wild population after the release of GMOs. The model combines population dynamics and Mendelian inheritance of a transgenic trait. We found that the introgression of the transgene is strongly affected by the greater mating preference of large GMO males. Furthermore, the difference in reproductive success between the anadromous versus sneaker strategy defines how much GMO's have to be preferred to be able to invade. These results emphasize the importance of detailed knowledge of reproductive systems and the effect of a transgene on the phenotype and behaviour of GMOs when assessing the consequences of their release or escape to the wild.
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Autosomal recessive disorders among Arabs: an overview from Kuwait.
Teebi, A S
1994-01-01
Kuwait has a cosmopolitan population of 1.7 million, mostly Arabs. This population is a mosaic of large and small minorities representing most Arab communities. In general, Kuwait's population is characterized by a rapid rate of growth, large family size, high rates of consanguineous marriages within the Arab communities with low frequency of intermarriage between them, and the presence of genetic isolates and semi-isolates in some extended families and Bedouin tribes. Genetic services have been available in Kuwait for over a decade. During this time it has become clear that Arabs have a high frequency of genetic disorders, and in particular autosomal recessive traits. Their pattern is unique and some disorders are relatively common. Examples are Bardet-Biedl and Meckel syndromes, phenylketonuria, and familial Mediterranean fever. A relatively large number of new syndromes and variants have been delineated in Kuwait's population, many being the result of homozygosity for autosomal recessive genes that occurred because of inbreeding. Some of these syndromes have subsequently been found in other parts of the world, negating the concept of the private syndrome. This paper provides an overview of autosomal recessive disorders among the Arabs in Kuwait from a personal perspective and published studies, and highlights the need for genetic services in Arab countries with the goal of prevention and treatment of genetic disorders. PMID:8014972
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Eble, Jeff A.; Rocha, Luiz A.; Craig, Matthew T.; Bowen, Brian W.
2014-01-01
Recent reports of localized larval recruitment in predominately small-range fishes are countered by studies that show high genetic connectivity across large oceanic distances. This discrepancy may result from the different timescales over which genetic and demographic processes operate or rather may indicate regular long-distance dispersal in some species. Here, we contribute an analysis of mtDNA cytochrome b diversity in the widely distributed Brown Surgeonfish (Acanthurus nigrofuscus; N = 560), which revealed significant genetic structure only at the extremes of the range (ΦCT = 0.452; P < .001). Collections from Hawaii to the Eastern Indian Ocean comprise one large, undifferentiated population. This pattern of limited genetic subdivision across reefs of the central Indo-Pacific has been observed in a number of large-range reef fishes. Conversely, small-range fishes are often deeply structured over the same area. These findings demonstrate population connectivity differences among species at biogeographic and evolutionary timescales, which likely translates into differences in dispersal ability at ecological and demographic timescales. While interspecific differences in population connectivity complicate the design of management strategies, the integration of multiscale connectivity patterns into marine resource planning will help ensure long-term ecosystem stability by preserving functionally diverse communities. PMID:25505914
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Male mating strategy and the introgression of a growth hormone transgene
Valosaari, Kata-Riina; Aikio, Sami; Kaitala, Veijo
2008-01-01
Escaped transgenic organisms (GMO's) may threaten the populations of their wild relatives if able to hybridize with each other. The introgression of a growth enhancement transgene into a wild Atlantic salmon population may be affected by the transgene's effects not only on fitness parameters, but also on mating behaviour. Large anadromous GMO males are most preferred in mating, but a transgene can also give the large sneakers a reproductive advantage over the smaller wild individuals. With a simulation model, we studied whether the increase in the proportion and mating success of sneakers in transgenic and hybrid genotypes could facilitate the introgression of a transgene into wild population after the release of GMOs. The model combines population dynamics and Mendelian inheritance of a transgenic trait. We found that the introgression of the transgene is strongly affected by the greater mating preference of large GMO males. Furthermore, the difference in reproductive success between the anadromous versus sneaker strategy defines how much GMO's have to be preferred to be able to invade. These results emphasize the importance of detailed knowledge of reproductive systems and the effect of a transgene on the phenotype and behaviour of GMOs when assessing the consequences of their release or escape to the wild. PMID:25567801
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Persson, Lennart; Elliott, J Malcolm
2013-05-01
The theory of cannibal dynamics predicts a link between population dynamics and individual life history. In particular, increased individual growth has, in both modeling and empirical studies, been shown to result from a destabilization of population dynamics. We used data from a long-term study of the dynamics of two leech (Erpobdella octoculata) populations to test the hypothesis that maximum size should be higher in a cycling population; one of the study populations exhibited a delayed feedback cycle while the other population showed no sign of cyclicity. A hump-shaped relationship between individual mass of 1-year-old leeches and offspring density the previous year was present in both populations. As predicted from the theory, the maximum mass of individuals was much larger in the fluctuating population. In contrast to predictions, the higher growth rate was not related to energy extraction from cannibalism. Instead, the higher individual mass is suggested to be due to increased availability of resources due to a niche widening with increased individual body mass. The larger individual mass in the fluctuating population was related to a stronger correlation between the densities of 1-year-old individuals and 2-year-old individuals the following year in this population. Although cannibalism was the major mechanism regulating population dynamics, its importance was negligible in terms of providing cannibalizing individuals with energy subsequently increasing their fecundity. Instead, the study identifies a need for theoretical and empirical studies on the largely unstudied interplay between ontogenetic niche shifts and cannibalistic population dynamics.
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Niedhammer, Isabelle; David, Simone; Degioanni, Stephanie; Drummond, Anne; Philip, Pierre; Acquarone, D; Aicardi, F; André-Mazeaud, P; Arsento, M; Astier, R; Baille, H; Bajon-Thery, F; Barre, E; Basire, C; Battu, J L; Baudry, S; Beatini, C; Beaud'huin, N; Becker, C; Bellezza, D; Beque, C; Bernstein, O; Beyssier, C; Blanc-Cascio, F; Blanchet, N; Blondel, C; Boisselot, R; Bordes-Dupuy, G; Borrelly, N; Bouhnik, D; Boulanger, M F; Boulard, J; Borreau, P; Bourret, D; Boustière, A M; Breton, C; Bugeon, G; Buono-Michel, M; Canonne, J F; Capella, D; Cavin-Rey, M; Cervoni, C; Charreton, D; Charrier, D; Chauvin, M A; Chazal, B; Cougnot, C; Cuvelier, G; Dalivoust, G; Daumas, R; Debaille, A; De Bretteville, L; Delaforge, G; Delchambre, A; Domeny, L; Donati, Y; Ducord-Chapelet, J; Duran, C; Durand-Bruguerolle, D; Fabre, D; Faivre, A; Falleri, R; Ferrando, G; Ferrari-Galano, J; Flutet, M; Fouché, J P; Fournier, F; Freyder, E; Galy, M; Garcia, A; Gazazian, G; Gérard, C; Girard, F; Giuge, M; Goyer, C; Gravier, C; Guyomard, A; Hacquin, M C; Halimi, E; Ibagnes, T; Icart, P; Jacquin, M C; Jaubert, B; Joret, J P; Julien, J P; Kacel, M; Kesmedjian, E; Lacroix, P; Lafon-Borelli, M; Lallai, S; Laudicina, J; Leclercq, X; Ledieu, S; Leroy, J; Leroyer, L; Loesche, F; Londi, D; Longueville, J M; Lotte, M C; Louvain, S; Lozé, M; Maculet-Simon, M; Magallon, G; Marcelot, V; Mareel, M C; Martin, P; Masse, A M; Méric, M; Milliet, C; Mokhtari, R; Monville, A M; Muller, B; Obadia, G; Pelser, M; Peres, L; Perez, E; Peyron, M; Peyronnin, F; Postel, S; Presseq, P; Pyronnet, E; Quinsat, C; Raulot-Lapointe, H; Rigaud, P; Robert, F; Robert, O; Roger, K; Roussel, A; Roux, J P; Rubini-Remigy, D; Sabate, N; Saccomano-Pertus, C; Salengro, B; Salengro-Trouillez, P; Samson, E; Sendra-Gille, L; Seyrig, C; Stoll, G; Tarpinian, N; Tavernier, M; Tempesta, S; Terracol, H; Torresani, F; Triglia, M F; Vandomme, V; Vieillard, F; Vilmot, K; Vital, N
2009-09-01
The purpose of this study was to explore the associations between workplace bullying, the characteristics of workplace bullying, and sleep disturbances in a large sample of employees of the French working population. Workplace bullying, evaluated using the validated instrument developed by Leymann, and sleep disturbances, as well as covariates, were measured using a self-administered questionnaire. Covariates included age, marital status, presence of children, education, occupation, working hours, night work, physical and chemical exposures at work, self-reported health, and depressive symptoms. Statistical analysis was performed using logistic regression analysis and was carried out separately for men and women. General working population. The study population consisted of a random sample of 3132 men and 4562 women of the working population in the southeast of France. Workplace bullying was strongly associated with sleep disturbances. Past exposure to bullying also increased the risk for this outcome. The more frequent the exposure to bullying, the higher the risk of experiencing sleep disturbances. Observing someone else being bullied in the workplace was also associated with the outcome. Adjustment for covariates did not modify the results. Additional adjustment for self-reported health and depressive symptoms diminished the magnitude of the associations that remained significant. The prevalence of workplace bullying (around 10%) was found to be high in this study as well was the impact of this major job-related stressor on sleep disturbances. Although no conclusion about causality could be drawn from this cross-sectional study, the findings suggest that the contribution of workplace bullying to the burden of sleep disturbances may be substantial.
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Dmitriew, Caitlin; Blanckenhorn, Wolf U
2012-01-01
The black scavenger fly Sepsis punctum exhibits striking among-population variation in the direction and magnitude of sexual size dimorphism, modification to the male forelimb and pre-copulatory behaviour. In some populations, male-biased sexual size dimorphism is observed; in other, less dimorphic, populations males court prior to mating. Such variation in reproductive traits is of interest to evolutionary biologists because it has the potential to limit gene flow among populations, contributing to speciation. Here, we investigate whether large male body size and modified forefemur are associated with higher male mating success within populations, whether these traits are associated with higher mating success among populations, and if these traits carry viability costs that could constrain their response to sexual selection. Flies from five distinct populations were reared at high or low food, generating high and low quality males. The expression of body size, forelimb morphology and courtship rate were each greater at high food, but high food males experienced higher mating success or reduced latency to first copulation in only one of the populations. Among populations, overall mating success increased with the degree of male-bias in overall body size and forelimb modification, suggesting that these traits have evolved as a means of increasing male mating rate. The increased mating success observed in large-male populations raises the question of why variation in magnitude of dimorphism persists among populations. One reason may be that costs of producing a large size constrain the evolution of ever-larger males. We found no evidence that juvenile mortality under food stress was greater for large-male populations, but development time was considerably longer and may represent an important constraint in an ephemeral and competitive growth environment.
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2008-01-01
Background Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome. Results A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. Conclusion Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background. PMID:18312628
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NASA Astrophysics Data System (ADS)
Ma, Zhanshan (Sam)
In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three categories of population dynamics models: deterministic modeling with Logistic chaos map as an example, stochastic modeling with spatial distribution patterns as an example, as well as survival analysis and extended evolutionary game theory (EEGT) modeling. Sample experiment results with Genetic algorithms (GA) are presented to demonstrate the applications of these models. The proposed EC population dynamics approach also makes survival selection largely unnecessary or much simplified since the individuals are naturally selected (controlled) by the mathematical models for EC population dynamics.
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Interstellar gamma-ray emission from cosmic rays in star-forming galaxies
NASA Astrophysics Data System (ADS)
Martin, P.
2014-04-01
Context. Fermi/LAT observations of star-forming galaxies in the ~0.1-100 GeV range have made possible a first population study. Evidence was found for a correlation between γ-ray luminosity and tracers of the star formation activity. Studying galactic cosmic rays (CRs) in various global conditions can yield information about their origin and transport in the interstellar medium (ISM). Aims: This work addresses the question of the scaling laws that can be expected for the interstellar γ-ray emission as a function of global galactic properties, with the goal of establishing whether the current experimental data in the GeV range can be constraining. Methods: I developed a 2D model for the non-thermal emissions from steady-state CR populations interacting with the ISM in star-forming galaxies. Most CR-related parameters were taken from Milky Way studies, and a large number of galaxies were then simulated with sizes from 4 to 40 kpc, several gas distributions, and star formation rates (SFRs) covering six orders of magnitude. Results: The evolution of the γ-ray luminosity over the 100 keV-100 TeV range is presented, with emphasis on the contribution of the different emission processes and particle populations, and on the transition between transport regimes. The model can reproduce the normalisation and trend inferred from the Fermi/LAT population study over most of the SFR range. This is obtained with a plain diffusion scheme, a single diffusion coefficient, and the assumption that CRs experience large-scale volume-averaged interstellar conditions. There is, however, no universal relation between high-energy γ-ray luminosity and star formation activity, as illustrated by the scatter introduced by different galactic global properties and the downturn in γ-ray emission at the low end. Conclusions: The current Fermi/LAT population study does not call for major modifications of the transport scheme for CRs in the Milky Way when extrapolated to other systems, probably because the uncertainties are still too large. Additional constraints may be expected from doubling the Fermi/LAT exposure time and later from observing at TeV energies with the Cherenkov Telescope Array.
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Evolutionary dynamics of social dilemmas in structured heterogeneous populations.
Santos, F C; Pacheco, J M; Lenaerts, Tom
2006-02-28
Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations.
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NASA Astrophysics Data System (ADS)
Guevara Hidalgo, Esteban; Nemoto, Takahiro; Lecomte, Vivien
Rare trajectories of stochastic systems are important to understand because of their potential impact. However, their properties are by definition difficult to sample directly. Population dynamics provide a numerical tool allowing their study, by means of simulating a large number of copies of the system, which are subjected to a selection rule that favors the rare trajectories of interest. However, such algorithms are plagued by finite simulation time- and finite population size- effects that can render their use delicate. Using the continuous-time cloning algorithm, we analyze the finite-time and finite-size scalings of estimators of the large deviation functions associated to the distribution of the rare trajectories. We use these scalings in order to propose a numerical approach which allows to extract the infinite-time and infinite-size limit of these estimators.
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NASA Astrophysics Data System (ADS)
Wagner-Kaiser, R.; Mackey, Dougal; Sarajedini, Ata; Cohen, Roger E.; Geisler, Doug; Yang, Soung-Chul; Grocholski, Aaron J.; Cummings, Jeffrey D.
2018-03-01
We leverage new high-quality data from Hubble Space Telescope program GO-14164 to explore the variation in horizontal branch morphology among globular clusters in the Large Magellanic Cloud (LMC). Our new observations lead to photometry with a precision commensurate with that available for the Galactic globular cluster population. Our analysis indicates that, once metallicity is accounted for, clusters in the LMC largely share similar horizontal branch morphologies regardless of their location within the system. Furthermore, the LMC clusters possess, on average, slightly redder morphologies than most of the inner halo Galactic population; we find, instead, that their characteristics tend to be more similar to those exhibited by clusters in the outer Galactic halo. Our results are consistent with previous studies, showing a correlation between horizontal branch morphology and age.
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Research progress of plant population genomics based on high-throughput sequencing.
Wang, Yun-sheng
2016-08-01
Population genomics, a new paradigm for population genetics, combine the concepts and techniques of genomics with the theoretical system of population genetics and improve our understanding of microevolution through identification of site-specific effect and genome-wide effects using genome-wide polymorphic sites genotypeing. With the appearance and improvement of the next generation high-throughput sequencing technology, the numbers of plant species with complete genome sequences increased rapidly and large scale resequencing has also been carried out in recent years. Parallel sequencing has also been done in some plant species without complete genome sequences. These studies have greatly promoted the development of population genomics and deepened our understanding of the genetic diversity, level of linking disequilibium, selection effect, demographical history and molecular mechanism of complex traits of relevant plant population at a genomic level. In this review, I briely introduced the concept and research methods of population genomics and summarized the research progress of plant population genomics based on high-throughput sequencing. I also discussed the prospect as well as existing problems of plant population genomics in order to provide references for related studies.
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A Markov chain model for studying suicide dynamics: an illustration of the Rose theorem
2014-01-01
Background High-risk strategies would only have a modest effect on suicide prevention within a population. It is best to incorporate both high-risk and population-based strategies to prevent suicide. This study aims to compare the effectiveness of suicide prevention between high-risk and population-based strategies. Methods A Markov chain illness and death model is proposed to determine suicide dynamic in a population and examine its effectiveness for reducing the number of suicides by modifying certain parameters of the model. Assuming a population with replacement, the suicide risk of the population was estimated by determining the final state of the Markov model. Results The model shows that targeting the whole population for suicide prevention is more effective than reducing risk in the high-risk tail of the distribution of psychological distress (i.e. the mentally ill). Conclusions The results of this model reinforce the essence of the Rose theorem that lowering the suicidal risk in the population at large may be more effective than reducing the high risk in a small population. PMID:24948330
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Larsen, Christina Viskum Lytken; Curtis, Tine; Bjerregaard, Peter
2013-12-01
An increase in social pathologies is a key feature in indigenous populations undergoing transition. The Greenland Inuit are a large indigenous population constituting a majority in their own country, which makes it possible to investigate differences within the population. This led us to study gambling behavior and problem gambling among Greenland Inuit in relation to the ongoing social transition and traumatic events during childhood. A large representative cross-sectional study was conducted among Greenland Inuit (n = 2,189). Data was collected among adults (18+) in 9 towns and 13 villages in Greenland from 2005 to 2010. Problem gambling, gambling behavior and traumatic childhood events were measured through a self-administered questionnaire. The lie/bet screen was used to identify past year and lifetime problem gambling. Social transition was measured as place of residence and a combination of residence, education and occupation. The lifetime prevalence of problem gambling was 16 % among men and 10 % among women (p < 0.0001); and higher in towns (19 %) compared to the capital of Nuuk (11 %) and in villages (12 %) (men only, p = 0.020). Lifetime problem gambling was associated with social transition (p = 0.023), alcohol problems in childhood home (p = 0.001/p = 0.002) and sexual abuse in childhood (women only, p = 0.030). A comparably high prevalence of lifetime problem gambling among Greenland Inuit adds problem gambling to the list of social pathologies in Greenland. A significant association between lifetime problem gambling, social transition and traumatic childhood events suggests people caught between tradition and modern ways of life are more vulnerable to gambling problems.
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Spatial effects in discrete generation population models.
Carrillo, C; Fife, P
2005-02-01
A framework is developed for constructing a large class of discrete generation, continuous space models of evolving single species populations and finding their bifurcating patterned spatial distributions. Our models involve, in separate stages, the spatial redistribution (through movement laws) and local regulation of the population; and the fundamental properties of these events in a homogeneous environment are found. Emphasis is placed on the interaction of migrating individuals with the existing population through conspecific attraction (or repulsion), as well as on random dispersion. The nature of the competition of these two effects in a linearized scenario is clarified. The bifurcation of stationary spatially patterned population distributions is studied, with special attention given to the role played by that competition.
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Percolation threshold determines the optimal population density for public cooperation
NASA Astrophysics Data System (ADS)
Wang, Zhen; Szolnoki, Attila; Perc, Matjaž
2012-03-01
While worldwide census data provide statistical evidence that firmly link the population density with several indicators of social welfare, the precise mechanisms underlying these observations are largely unknown. Here we study the impact of population density on the evolution of public cooperation in structured populations and find that the optimal density is uniquely related to the percolation threshold of the host graph irrespective of its topological details. We explain our observations by showing that spatial reciprocity peaks in the vicinity of the percolation threshold, when the emergence of a giant cooperative cluster is hindered neither by vacancy nor by invading defectors, thus discovering an intuitive yet universal law that links the population density with social prosperity.
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Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands
Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien
2016-01-01
The remote estimation of a region’s population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach. PMID:27254151
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Utilization of Large Data Sets in Maternal Health in Finland: A Case for Global Health Research.
Lamminpää, Reeta; Gissler, Mika; Vehviläinen-Julkunen, Katri
In recent years, the use of large data sets, such as electronic health records, has increased. These large data sets are often referred to as "Big Data," which have various definitions. The purpose of this article was to summarize and review the utilization, strengths, and challenges of register data, which means a written record containing regular entries of items or details, and Big Data, especially in maternal nursing, using 4 examples of studies from the Finnish Medical Birth Register data and relate these to other international databases and data sets. Using large health register data is crucial when studying and understanding outcomes of maternity care. This type of data enables comparisons on a population level and can be utilized in research related to maternal health, with important issues and implications for future research and clinical practice. Although there are challenges connected with register data and Big Data, these large data sets offer the opportunity for timely insight into population-based information on relevant research topics in maternal health. Nurse researchers need to understand the possibilities and limitations of using existing register data in maternity research. Maternal child nurse researchers can be leaders of the movement to utilize Big Data to improve global maternal health.
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Calculating expected DNA remnants from ancient founding events in human population genetics
Stacey, Andrew; Sheffield, Nathan C; Crandall, Keith A
2008-01-01
Background Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters. Conclusion The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible. PMID:18928554
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Tang, Shiming; Zhang, Yimeng; Li, Zhihao; Li, Ming; Liu, Fang; Jiang, Hongfei; Lee, Tai Sing
2018-04-26
One general principle of sensory information processing is that the brain must optimize efficiency by reducing the number of neurons that process the same information. The sparseness of the sensory representations in a population of neurons reflects the efficiency of the neural code. Here, we employ large-scale two-photon calcium imaging to examine the responses of a large population of neurons within the superficial layers of area V1 with single-cell resolution, while simultaneously presenting a large set of natural visual stimuli, to provide the first direct measure of the population sparseness in awake primates. The results show that only 0.5% of neurons respond strongly to any given natural image - indicating a ten-fold increase in the inferred sparseness over previous measurements. These population activities are nevertheless necessary and sufficient to discriminate visual stimuli with high accuracy, suggesting that the neural code in the primary visual cortex is both super-sparse and highly efficient. © 2018, Tang et al.
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Valdivia, Abel; Cox, Courtney E.; Silbiger, Nyssa J.; Bruno, John F.
2017-01-01
Invasive lionfish are assumed to significantly affect Caribbean reef fish communities. However, evidence of lionfish effects on native reef fishes is based on uncontrolled observational studies or small-scale, unrepresentative experiments, with findings ranging from no effect to large effects on prey density and richness. Moreover, whether lionfish affect populations and communities of native reef fishes at larger, management-relevant scales is unknown. The purpose of this study was to assess the effects of lionfish on coral reef prey fish communities in a natural complex reef system. We quantified lionfish and the density, richness, and composition of native prey fishes (0–10 cm total length) at sixteen reefs along ∼250 km of the Belize Barrier Reef from 2009 to 2013. Lionfish invaded our study sites during this four-year longitudinal study, thus our sampling included fish community structure before and after our sites were invaded, i.e., we employed a modified BACI design. We found no evidence that lionfish measurably affected the density, richness, or composition of prey fishes. It is possible that higher lionfish densities are necessary to detect an effect of lionfish on prey populations at this relatively large spatial scale. Alternatively, negative effects of lionfish on prey could be small, essentially undetectable, and ecologically insignificant at our study sites. Other factors that influence the dynamics of reef fish populations including reef complexity, resource availability, recruitment, predation, and fishing could swamp any effects of lionfish on prey populations. PMID:28560093
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Hackerott, Serena; Valdivia, Abel; Cox, Courtney E; Silbiger, Nyssa J; Bruno, John F
2017-01-01
Invasive lionfish are assumed to significantly affect Caribbean reef fish communities. However, evidence of lionfish effects on native reef fishes is based on uncontrolled observational studies or small-scale, unrepresentative experiments, with findings ranging from no effect to large effects on prey density and richness. Moreover, whether lionfish affect populations and communities of native reef fishes at larger, management-relevant scales is unknown. The purpose of this study was to assess the effects of lionfish on coral reef prey fish communities in a natural complex reef system. We quantified lionfish and the density, richness, and composition of native prey fishes (0-10 cm total length) at sixteen reefs along ∼250 km of the Belize Barrier Reef from 2009 to 2013. Lionfish invaded our study sites during this four-year longitudinal study, thus our sampling included fish community structure before and after our sites were invaded, i.e., we employed a modified BACI design. We found no evidence that lionfish measurably affected the density, richness, or composition of prey fishes. It is possible that higher lionfish densities are necessary to detect an effect of lionfish on prey populations at this relatively large spatial scale. Alternatively, negative effects of lionfish on prey could be small, essentially undetectable, and ecologically insignificant at our study sites. Other factors that influence the dynamics of reef fish populations including reef complexity, resource availability, recruitment, predation, and fishing could swamp any effects of lionfish on prey populations.
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Stavrakos, S-K; Ahmed-Kristensen, S; Goldman, T
2016-09-01
Designers at the conceptual phase of products such as headphones, stress the importance of comfort, e.g. executing comfort studies and the need for a reliable user panel. This paper proposes a methodology to issue a reliable user panel to represent large populations and validates the proposed framework to predict comfort factors, such as physical fit. Data of 200 heads was analyzed by forming clusters, 9 archetypal people were identified out of a 200 people's ear database. The archetypes were validated by comparing the archetypes' responses on physical fit against those of 20 participants interacting with 6 headsets. This paper suggests a new method of selecting representative user samples for prototype testing compared to costly and time consuming methods which relied on the analysis of human geometry of large populations. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Study of selected phenotype switching strategies in time varying environment
NASA Astrophysics Data System (ADS)
Horvath, Denis; Brutovsky, Branislav
2016-03-01
Population heterogeneity plays an important role across many research, as well as the real-world, problems. The population heterogeneity relates to the ability of a population to cope with an environment change (or uncertainty) preventing its extinction. However, this ability is not always desirable as can be exemplified by an intratumor heterogeneity which positively correlates with the development of resistance to therapy. Causation of population heterogeneity is therefore in biology and medicine an intensively studied topic. In this paper the evolution of a specific strategy of population diversification, the phenotype switching, is studied at a conceptual level. The presented simulation model studies evolution of a large population of asexual organisms in a time-varying environment represented by a stochastic Markov process. Each organism disposes with a stochastic or nonlinear deterministic switching strategy realized by discrete-time models with evolvable parameters. We demonstrate that under rapidly varying exogenous conditions organisms operate in the vicinity of the bet-hedging strategy, while the deterministic patterns become relevant as the environmental variations are less frequent. Statistical characterization of the steady state regimes of the populations is done using the Hellinger and Kullback-Leibler functional distances and the Hamming distance.
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Al-Mamun, Hawlader Abdullah; Clark, Samuel A; Kwan, Paul; Gondro, Cedric
2015-11-24
Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N e ), heterozygosity, fixation index (F ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r (2) and D'), N e , heterozygosity, F ST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N e than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F ST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep.
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Gender equality in university sportspeople's drinking.
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.
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ERIC Educational Resources Information Center
Friedrichs, Bettina; Igl, Wilmar; Larsson, Henrik; Larsson, Jan-Olov
2012-01-01
Objective: To explore the associations of subtypes of adult ADHD with other psychiatric problems, stressful life events, and sex differences. Method: Odds ratios were calculated using information from 17,899 participants from a population-based survey of adult twins born in Sweden between 1959 and 1985. Results: Symptoms of attention deficit…
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Landscape-level effects of forest management on bird species in the Ozarks of southeastern Missouri
Richard L. Clawson; John Faaborg; Wendy K. Gram; Paul A. Porneluzi
2002-01-01
This study was designed as an experiment to test how bird populations in an extensively forested landscape respond to small (group and single-tree selection) and large (clearcut) openings. Our objectives are to test the landscape-level effects of even-aged and uneven-aged forest management relative to no-harvest management on population density and reproductive success...
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Clostridium difficile in the Military Population
2016-08-05
association between race and infection . This is similar to the Buchner and associates case- control study; which noted an increase in occurrence of C...sustained within a hospital , additional persons infected with C. difficile are needed10. Acute appendicitis ranking first among diagnoses for hospitalized ...Buchner AM, Sonnenberg A. Epidemiology of Clostridium difficile infection in a large population of hospitalized US military veterans. Dig Dis Sci
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ERIC Educational Resources Information Center
Borders, Tyrone F.; Aday, Lu Ann; Xu, Ke Tom
2004-01-01
As elderly people become a larger proportion of the rural population, it is important to identify those at risk for poor health. Predictors of health-related quality of life can be useful in designing interventions. Purpose: One objective of the present study was to profile the health-related quality of life of community-dwelling, elderly people…
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Silva, Luís; Elias, Rui B; Moura, Mónica; Meimberg, Harald; Dias, Eduardo
2011-12-01
The Azorean endemic gymnosperm Juniperus brevifolia (Seub.) Antoine is a top priority species for conservation in Macaronesia, based on its ecological significance in natural plant communities. To evaluate genetic variability and differentiation among J. brevifolia populations from the Azorean archipelago, we studied 15 ISSR and 15 RAPD markers in 178 individuals from 18 populations. The average number of polymorphic bands per population was 65 for both ISSR and RAPD. The majority of genetic variability was found within populations and among populations within islands, and this partitioning of variability was confirmed by AMOVA. The large majority of population pairwise F(ST) values were above 0.3 and below 0.6. The degree of population genetic differentiation in J. brevifolia was relatively high compared with other species, including Juniperus spp. The genetic differentiation among populations suggests that provenance should be considered when formulating augmentation or reintroduction strategies.
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Brennan, Angela K.; Cross, Paul C.; Higgs, Megan D.; Edwards, W. Henry; Scurlock, Brandon M.; Creel, Scott
2014-01-01
Understanding how animal density is related to pathogen transmission is important to develop effective disease control strategies, but requires measuring density at a scale relevant to transmission. However, this is not straightforward or well-studied among large mammals with group sizes that range several orders of magnitude or aggregation patterns that vary across space and time. To address this issue, we examined spatial variation in elk (Cervus canadensis) aggregation patterns and brucellosis across 10 regions in the Greater Yellowstone Area where previous studies suggest the disease may be increasing. We hypothesized that rates of increasing brucellosis would be better related to the frequency of large groups than mean group size or population density, but we examined whether other measures of density would also explain rising seroprevalence. To do this, we measured wintering elk density and group size across multiple spatial and temporal scales from monthly aerial surveys. We used Bayesian hierarchical models and 20 years of serologic data to estimate rates of increase in brucellosis within the 10 regions, and to examine the linear relationships between these estimated rates of increase and multiple measures of aggregation. Brucellosis seroprevalence increased over time in eight regions (one region showed an estimated increase from 0.015 in 1991 to 0.26 in 2011), and these rates of increase were positively related to all measures of aggregation. The relationships were weaker when the analysis was restricted to areas where brucellosis was present for at least two years, potentially because aggregation was related to disease-establishment within a population. Our findings suggest that (1) group size did not explain brucellosis increases any better than population density and (2) some elk populations may have high densities with small groups or lower densities with large groups, but brucellosis is likely to increase in either scenario. In this case, any one control method such as reducing population density or group size may not be sufficient to reduce transmission. This study highlights the importance of examining the density-transmission relationship at multiple scales and across populations before broadly applying disease control strategies.
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The Rise of Concussions in the Adolescent Population.
Zhang, Alan L; Sing, David C; Rugg, Caitlin M; Feeley, Brian T; Senter, Carlin
2016-08-01
Concussion injuries have been highlighted to the American public through media and research. While recent studies have shown increased traumatic brain injuries (TBIs) diagnosed in emergency departments across the United States, no studies have evaluated trends in concussion diagnoses across the general US population in various age groups. To evaluate the current incidence and trends in concussions diagnosed across varying age groups and health care settings in a large cross-sectional population. Descriptive epidemiological study. Administrative health records of 8,828,248 members of a large private-payer insurance group in the United States were queried. Patients diagnosed with concussion from years 2007 through 2014 were stratified by year of diagnosis, age group, sex, classification of concussion, and health care setting of diagnosis (eg, emergency department vs physician's office). Chi-square testing was used for statistical analysis. From a cohort of 8,828,248 patients, 43,884 patients were diagnosed with a concussion. Of these patients, 55% were male and over 32% were in the adolescent age group (10-19 years old). The highest incidence of concussion was seen in patients aged 15 to 19 years (16.5/1000 patients), followed by those aged 10 to 14 years (10.5/1000 patients), 20 to 24 years (5.2/1000 patients), and 5 to 9 years (3.5/1000 patients). Overall, there was a 60% increase in concussion incidence from 2007 to 2014. The largest increases were in the 10- to 14-year (143%) and 15- to 19-year (87%) age groups. Based on International Classification of Disease-9th Revision classification, 29% of concussions were associated with some form of loss of consciousness. Finally, 56% of concussions were diagnosed in the emergency department and 29% in a physician's office, with the remainder in urgent care clinics or inpatient settings. The incidence of concussion diagnosed in the general US population is increasing, driven largely by a substantial rise in the adolescent age group. The youth population should be prioritized for ongoing work in concussion education, diagnosis, treatment, and prevention. The rise of concussions in the adolescent age group across the general population is concerning, and clinical efforts to prevent these injuries are needed.
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Spreadsheet Simulation of the Law of Large Numbers
ERIC Educational Resources Information Center
Boger, George
2005-01-01
If larger and larger samples are successively drawn from a population and a running average calculated after each sample has been drawn, the sequence of averages will converge to the mean, [mu], of the population. This remarkable fact, known as the law of large numbers, holds true if samples are drawn from a population of discrete or continuous…
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Purcell, Shaun ; Neale, Benjamin ; Todd-Brown, Kathe ; Thomas, Lori ; Ferreira, Manuel A. R. ; Bender, David ; Maller, Julian ; Sklar, Pamela ; de Bakker, Paul I. W. ; Daly, Mark J. ; Sham, Pak C.
2007-01-01
Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis. PMID:17701901
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NASA Astrophysics Data System (ADS)
Wang, Xubo; Li, Qi; Yu, Hong; Kong, Lingfeng
2016-12-01
Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding programs in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8-20.6, and a mean expected heterozygosity of 0.902-0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a relatively large number of broodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided important information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.
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Tschanz, Joann T; Treiber, Katherine; Norton, Maria C; Welsh-Bohmer, Kathleen A; Toone, Leslie; Zandi, Peter P; Szekely, Christine A; Lyketsos, Constantine; Breitner, John C S
2005-01-01
There are several population-based studies of aging, memory, and dementia being conducted worldwide. Of these, the Cache County Study on Memory, Health and Aging is noteworthy for its large number of "oldest-old" members. This study, which has been following an initial cohort of 5,092 seniors since 1995, has reported among its major findings the role of the Apolipoprotein E gene on modifying the risk for Alzheimer's disease (AD) in males and females and identifying pharmacologic compounds that may act to reduce AD risk. This article summarizes the major findings of the Cache County study to date, describes ongoing investigations, and reports preliminary analyses on the outcome of the oldest-old in this population, the subgroup of participants who were over age 84 at the study's inception.
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High-levels of microplastic pollution in a large, remote, mountain lake.
Free, Christopher M; Jensen, Olaf P; Mason, Sherri A; Eriksen, Marcus; Williamson, Nicholas J; Boldgiv, Bazartseren
2014-08-15
Despite the large and growing literature on microplastics in the ocean, little information exists on microplastics in freshwater systems. This study is the first to evaluate the abundance, distribution, and composition of pelagic microplastic pollution in a large, remote, mountain lake. We quantified pelagic microplastics and shoreline anthropogenic debris in Lake Hovsgol, Mongolia. With an average microplastic density of 20,264 particles km(-2), Lake Hovsgol is more heavily polluted with microplastics than the more developed Lakes Huron and Superior in the Laurentian Great Lakes. Fragments and films were the most abundant microplastic types; no plastic microbeads and few pellets were observed. Household plastics dominated the shoreline debris and were comprised largely of plastic bottles, fishing gear, and bags. Microplastic density decreased with distance from the southwestern shore, the most populated and accessible section of the park, and was distributed by the prevailing winds. These results demonstrate that without proper waste management, low-density populations can heavily pollute freshwater systems with consumer plastics. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Impacts of Noise Barriers on Near-Road Air Quality
Numerous health studies show an increase in adverse health effects for populations near large roadways. A study was designed to assess traffic emission impacts on air quality near a heavily traveled highway. The portion of highway studied included a section of open field and a se...
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Carter, Marissa J; Fife, Caroline E; Walker, David; Thomson, Brett
2009-07-01
To determine the percentage of individuals that would be excluded from wound care randomized controlled trials (RCTs) as a surrogate for applicability to general populations. A representative sample of wound-care RCTs was selected from the literature in the past 10 years. Exclusion criteria from the trials were evaluated, and prevalence values for each excluded condition were obtained from a large wound-care population, as well as from the literature. The percentage of patients excluded on this basis was calculated. Seventeen RCTs testing "high-technology" wound-care products were evaluated. : Patients in the trials were treated for ulcers (venous, diabetic foot, and pressure ulcers). A percentage of patients in the study population were excluded for each RCT. More than 50% of the study population would have been excluded in 15 of the 17 RCTs. When less clinically relevant exclusion criteria were removed, 14 of 17 RCTs would still have excluded between 25% and 50% of the study population. The results raise serious questions regarding the applicability of these RCTs to wound-care populations.
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Population activity structure of excitatory and inhibitory neurons
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
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ERIC Educational Resources Information Center
Marshall, Althea T.
2010-01-01
Purpose: The purpose of this investigation was to examine the impact of Chromosome 4p- syndrome on the communication and expressive language phenotype of a large cross-cultural population of children, adolescents, and adults. Method: A large-scale survey study was conducted and a descriptive research design was used to analyze quantitative and…
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Determining potential wildlife benefits from wildfire in Arizona ponderosa pine forests
Philip O. Lowe; Peter F. Ffolliott; John H. Dieterich; David R. Patton
1978-01-01
Large wildfires are frequently destructive to the timber resource, but wildlife may not be so adversely affected. A study of selected species of wildlife (deer, elk, rodents, and birds) that were present on large burned areas, 1, 3, 7, and 20 years old, indicated population fluctuations and habitat changes that are, for the most part, predictable, and can be expressed...
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ERIC Educational Resources Information Center
Nichols, Joe D.; White, Janet J.; Price, Margret
2006-01-01
This study was designed to examine the epistemological beliefs about the nature of knowledge, views of intelligence and motivational perceptions. Two samples were drawn from two large urban high schools in the Southwest portion of the United States with large Hispanic/Latino student populations while a third was drawn from a majority Anglo student…
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ERIC Educational Resources Information Center
Johnson, Carla C.; Bolshakova, Virginia L. J.; Waldron, Tammy
2016-01-01
This study examined the ability of Transformative Professional Development (TPD) to transform science teacher quality and associated impact on science achievement, including particular focus on English Language Learners (ELL). TPD was implemented in a large, low-performing, urban district in the southwest with predominantly Latino ELL populations.…
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Flea (Siphonaptera) species richness in the Great Basin Desert and island biogeography theory.
Bossard, Robert L
2014-06-01
Numbers of flea (Siphonaptera) species (flea species richness) on individual mammals should be higher on large mammals, mammals with dense populations, and mammals with large geographic ranges, if mammals are islands for fleas. I tested the first two predictions with regressions of H. J. Egoscue's trapping data on flea species richness collected from individual mammals against mammal size and population density from the literature. Mammal size and population density did not correlate with flea species richness. Mammal geographic range did, in earlier studies. The intermediate-sized (31 g), moderately dense (0.004 individuals/m(2)) Peromyscus truei (Shufeldt) had the highest richness with eight flea species on one individual. Overall, island biogeography theory does not describe the distribution of flea species on mammals in the Great Basin Desert, based on H. J. Egoscue's collections. Alternatively, epidemiological or metapopulation theories may explain flea species richness. © 2014 The Society for Vector Ecology.
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Decomposing the effect of crime on population changes.
Foote, Andrew
2015-04-01
This article estimates the effect of crime on migration rates for counties in U.S. metropolitan areas and makes three contributions to the literature. First, I use administrative data on migration flows between counties, which gives me more precise estimates of population changes than data used in previous studies. Second, I am able to decompose net population changes into gross migration flows in order to identify how individuals respond to crime rate changes. Finally, I include county-level trends so that my identification comes from shocks away from the trend. I find effects that are one-fiftieth the size of the most prominent estimate in the literature; and although the long-run effects are somewhat larger, they are still only approximately one-twentieth as large. I also find that responses to crime rates differ by subgroups, and that increases in crime cause white households to leave the county, with effects almost 10 times as large as for black households.
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Rhythmic behavior in a two-population mean-field Ising model
NASA Astrophysics Data System (ADS)
Collet, Francesca; Formentin, Marco; Tovazzi, Daniele
2016-10-01
Many real systems composed of a large number of interacting components, as, for instance, neural networks, may exhibit collective periodic behavior even though single components have no natural tendency to behave periodically. Macroscopic oscillations are indeed one of the most common self-organized behavior observed in living systems. In the present paper we study some dynamical features of a two-population generalization of the mean-field Ising model with the scope of investigating simple mechanisms capable to generate rhythms in large groups of interacting individuals. We show that the system may undergo a transition from a disordered phase, where the magnetization of each population fluctuates closely around zero, to a phase in which they both display a macroscopic regular rhythm. In particular, there exists a region in the parameter space where having two groups of spins with inter- and intrapopulation interactions of different strengths suffices for the emergence of a robust periodic behavior.
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Equilibrium Strategy and Population-Size Effects in Lowest Unique Bid Auctions
NASA Astrophysics Data System (ADS)
Pigolotti, Simone; Bernhardsson, Sebastian; Juul, Jeppe; Galster, Gorm; Vivo, Pierpaolo
2012-02-01
In lowest unique bid auctions, N players bid for an item. The winner is whoever places the lowest bid, provided that it is also unique. We use a grand canonical approach to derive an analytical expression for the equilibrium distribution of strategies. We then study the properties of the solution as a function of the mean number of players, and compare them with a large data set of internet auctions. The theory agrees with the data with striking accuracy for small population-size N, while for larger N a qualitatively different distribution is observed. We interpret this result as the emergence of two different regimes, one in which adaptation is feasible and one in which it is not. Our results question the actual possibility of a large population to adapt and find the optimal strategy when participating in a collective game.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, Sen; Zhang, Wei; Lian, Jianming
This paper studies a multi-stage pricing problem for a large population of thermostatically controlled loads. The problem is formulated as a reverse Stackelberg game that involves a mean field game in the hierarchy of decision making. In particular, in the higher level, a coordinator needs to design a pricing function to motivate individual agents to maximize the social welfare. In the lower level, the individual utility maximization problem of each agent forms a mean field game coupled through the pricing function that depends on the average of the population control/state. We derive the solution to the reverse Stackelberg game bymore » connecting it to a team problem and the competitive equilibrium, and we show that this solution corresponds to the optimal mean field control that maximizes the social welfare. Realistic simulations are presented to validate the proposed methods.« less
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An adaptive two-stage sequential design for sampling rare and clustered populations
Brown, J.A.; Salehi, M.M.; Moradi, M.; Bell, G.; Smith, D.R.
2008-01-01
How to design an efficient large-area survey continues to be an interesting question for ecologists. In sampling large areas, as is common in environmental studies, adaptive sampling can be efficient because it ensures survey effort is targeted to subareas of high interest. In two-stage sampling, higher density primary sample units are usually of more interest than lower density primary units when populations are rare and clustered. Two-stage sequential sampling has been suggested as a method for allocating second stage sample effort among primary units. Here, we suggest a modification: adaptive two-stage sequential sampling. In this method, the adaptive part of the allocation process means the design is more flexible in how much extra effort can be directed to higher-abundance primary units. We discuss how best to design an adaptive two-stage sequential sample. ?? 2008 The Society of Population Ecology and Springer.
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Macfarlane, Gary J; Beasley, Marcus; Smith, Blair H; Jones, Gareth T; Macfarlane, Tatiana V
2015-01-01
Introduction: Biobank-type studies are typically large but have very low participation rates. It has been suggested that these studies may provide biased estimates of prevalence but are likely to provide valid estimates of association. We test these hypotheses using data collected on pain in a large Biobank study in the United Kingdom. Methods: UK Biobank recruited 503,325 persons aged 40–69 years (participation rate 5.5%). Participants completed questionnaires, including pain, lifestyle and environment factors. As a comparison, we used both a large population study of pain (MUSICIAN: n = 8847, aged: 40–69 years) conducted 2008–2009 and the National Child Development study (NCDS) which recruited all persons in Great Britain born during one week of 1958 and followed them up at age 44 years (n = 9377). Results: ‘Any pain’ (UK Biobank 61.0%; MUSICIAN 63.9%), chronic pain (42.9%, 52.2%) and site-specific musculoskeletal pain (back 26.2%, 29.7%; shoulder/neck 23.3%, 25.3%) were generally similar in UK Biobank and MUSICIAN. The prevalence of chronic pain and most regional musculoskeletal pains in UK Biobank were all within 2% of that in NCDS. Conclusion: UK Biobank has provided estimates of the prevalence of pain which are similar to those from previous large-scale studies, although a formal comparison of the estimates cannot be made. It has also confirmed known associations with the reporting of pain. Despite its very low participation rate, such a study provides the opportunity to investigate novel exposure–pain relationships and investigate rarer exposures and characteristics to further our knowledge of the epidemiology of pain. PMID:26526341
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Kraker, Jessica; Viswanathan, Shiv Kumar; Knöll, Ralph; Sadayappan, Sakthivel
2016-01-01
The South Asian population, numbered at 1.8 billion, is estimated to comprise around 20% of the global population and 1% of the American population, and has one of the highest rates of cardiovascular disease. While South Asians show increased classical risk factors for developing heart failure, the role of population-specific genetic risk factors has not yet been examined for this group. Hypertrophic cardiomyopathy (HCM) is one of the major cardiac genetic disorders among South Asians, leading to contractile dysfunction, heart failure, and sudden cardiac death. This disease displays autosomal dominant inheritance, and it is associated with a large number of variants in both sarcomeric and non-sarcomeric proteins. The South Asians, a population with large ethnic diversity, potentially carries region-specific polymorphisms. There is high variability in disease penetrance and phenotypic expression of variants associated with HCM. Thus, extensive studies are required to decipher pathogenicity and the physiological mechanisms of these variants, as well as the contribution of modifier genes and environmental factors to disease phenotypes. Conducting genotype-phenotype correlation studies will lead to improved understanding of HCM and, consequently, improved treatment options for this high-risk population. The objective of this review is to report the history of cardiovascular disease and HCM in South Asians, present previously published pathogenic variants, and introduce current efforts to study HCM using induced pluripotent stem cell-derived cardiomyocytes, next-generation sequencing, and gene editing technologies. The authors ultimately hope that this review will stimulate further research, drive novel discoveries, and contribute to the development of personalized medicine with the aim of expanding therapeutic strategies for HCM. PMID:27840609
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Trends in Global Gender Inequality (Forthcoming, Social Forces).
Dorius, Shawn F; Firebaugh, Glenn
2010-07-01
This study investigates trends in gender inequality for the world as a whole. Using data encompassing a large majority of the world's population, we examine world trends over recent decades for key indicators of gender inequality in education, mortality, political representation, and economic activity. We find that gender inequality is declining in virtually all major domains, that the decline is occurring across diverse religious and cultural traditions, and that population growth is slowing the decline because populations are growing faster in countries where there is the greatest gender inequality.
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Trends in Global Gender Inequality (Forthcoming, Social Forces)
Dorius, Shawn F.; Firebaugh, Glenn
2011-01-01
This study investigates trends in gender inequality for the world as a whole. Using data encompassing a large majority of the world’s population, we examine world trends over recent decades for key indicators of gender inequality in education, mortality, political representation, and economic activity. We find that gender inequality is declining in virtually all major domains, that the decline is occurring across diverse religious and cultural traditions, and that population growth is slowing the decline because populations are growing faster in countries where there is the greatest gender inequality. PMID:21643494
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Spontaneous emergence of cataclysmic networks in spatially extended systems
NASA Astrophysics Data System (ADS)
Manrubia, Susanna C.; Poyatos, Juan F.; Pérez-Mercader, Juan
2002-11-01
A system of interacting chemical species able to catalyse each others' production is studied. We consider a two-dimensional surface where single molecules attach, diffuse, catalytically interact, and decay. The population of species molecules and the network of interactions among them are dynamical entities. After a short transient time, robust catalytic cycles emerge and a "stationary" state of high diversity and large population numbers settles down. Population dynamics and physical space select among possible graphs of catalytic interactions. The organization of the system is robust: parasitic invaders are short-lived, their populations are kept at low levels, and are unable to sweep away the emerging catalytic cycles.
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Air pollution exposure: Who is at high risk?
NASA Astrophysics Data System (ADS)
Peled, Ronit
2011-04-01
This article reviews the sub-population groups who are at high risk and first to be harmed by air pollution coming from anthropogenic combustions. Epidemiological studies from the last few decades contributed to the understanding of the different levels of susceptibility to air pollution. Older people and young infants, people who suffer from allergies, pulmonary and heart diseases, pregnant women and newborn babies, and deprived populations that suffer from low socio-economic status have all been described as populations at risk. A better understanding of the role of air pollution on large as well as specific populations' health, will promote a better protection policy.
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Population Studies of Intact Vitamin D Binding Protein by Affinity Capture ESI-TOF-MS
Borges, Chad R.; Jarvis, Jason W.; Oran, Paul E.; Rogers, Stephen P.; Nelson, Randall W.
2008-01-01
Blood plasma proteins with molecular weights greater than approximately 30 kDa are refractory to comprehensive, high-throughput qualitative characterization of microheterogeneity across human populations. Analytical techniques for obtaining high mass resolution for targeted, intact protein characterization and, separately, high sample throughput exist, but efficient means of coupling these assay characteristics remain rather limited. This article discusses the impetus for analyzing intact proteins in a targeted manner across populations and describes the methodology required to couple mass spectrometric immunoassay with electrospray ionization mass spectrometry for the purpose of qualitatively characterizing a prototypical large plasma protein, vitamin D binding protein, across populations. PMID:19137103
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Mesoscopic fluctuations of the population of a qubit in a strong alternating field
DOE Office of Scientific and Technical Information (OSTI.GOV)
Denisenko, M. V., E-mail: mar.denisenko@gmail.com; Satanin, A. M.
Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau–Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of themore » population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.« less
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Young, Katherine
2014-09-30
database.) In fiscal year 2015, NREL is working with universities to populate additional case studies on OpenEI. The goal is to provide a large enough dataset to start conducting analyses of exploration programs to identify correlations between successful exploration plans for areas with similar geologic occurrence models.
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Zedrosser, Andreas; Pelletier, Fanie; Bischof, Richard; Festa-Bianchet, Marco; Swenson, Jon E
2013-01-01
In iteroparous mammals, conditions experienced early in life may have long-lasting effects on lifetime reproductive success. Human-induced mortality is also an important demographic factor in many populations of large mammals and may influence lifetime reproductive success. Here, we explore the effects of early development, population density, and human hunting on survival and lifetime reproductive success in brown bear (Ursus arctos) females, using a 25-year database of individually marked bears in two populations in Sweden. Survival of yearlings to 2 years was not affected by population density or body mass. Yearlings that remained with their mother had higher survival than independent yearlings, partly because regulations prohibit the harvest of bears in family groups. Although mass as a yearling did not affect juvenile survival, it was positively associated with measures of lifetime reproductive success and individual fitness. The majority of adult female brown bear mortality (72%) in our study was due to human causes, mainly hunting, and many females were killed before they reproduced. Therefore, factors allowing females to survive several hunting seasons had a strong positive effect on lifetime reproductive success. We suggest that, in many hunted populations of large mammals, sport harvest is an important influence on both population dynamics and life histories.
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NASA Astrophysics Data System (ADS)
Bertola, L. D.; Jongbloed, H.; van der Gaag, K. J.; de Knijff, P.; Yamaguchi, N.; Hooghiemstra, H.; Bauer, H.; Henschel, P.; White, P. A.; Driscoll, C. A.; Tende, T.; Ottosson, U.; Saidu, Y.; Vrieling, K.; de Iongh, H. H.
2016-08-01
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.
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Bertola, L D; Jongbloed, H; van der Gaag, K J; de Knijff, P; Yamaguchi, N; Hooghiemstra, H; Bauer, H; Henschel, P; White, P A; Driscoll, C A; Tende, T; Ottosson, U; Saidu, Y; Vrieling, K; de Iongh, H H
2016-08-04
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.
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Bertola, L. D.; Jongbloed, H.; van der Gaag, K. J.; de Knijff, P.; Yamaguchi, N.; Hooghiemstra, H.; Bauer, H.; Henschel, P.; White, P. A.; Driscoll, C. A.; Tende, T.; Ottosson, U.; Saidu, Y.; Vrieling, K.; de Iongh, H. H.
2016-01-01
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion. PMID:27488946
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Meisner, Joshua K.; Price, Richard J.
2010-01-01
Arterial occlusive disease (AOD) is the leading cause of morbidity and mortality through the developed world, which creates a significant need for effective therapies to halt disease progression. Despite success of animal and small-scale human therapeutic arteriogenesis studies, this promising concept for treating AOD has yielded largely disappointing results in large-scale clinical trials. One reason for this lack of successful translation is that endogenous arteriogenesis is highly dependent on a poorly understood sequence of events and interactions between bone marrow derived cells (BMCs) and vascular cells, which makes designing effective therapies difficult. We contend that the process follows a complex, ordered sequence of events with multiple, specific BMC populations recruited at specific times and locations. Here we present the evidence suggesting roles for multiple BMC populations from neutrophils and mast cells to progenitor cells and propose how and where these cell populations fit within the sequence of events during arteriogenesis. Disruptions in these various BMC populations can impair the arteriogenesis process in patterns that characterize specific patient populations. We propose that an improved understanding of how arteriogenesis functions as a system can reveal individual BMC populations and functions that can be targeted for overcoming particular impairments in collateral vessel development. PMID:21044213
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Seagrass Herbivory Levels Sustain Site-Fidelity in a Remnant Dugong Population.
D'Souza, Elrika; Patankar, Vardhan; Arthur, Rohan; Marbà, Núria; Alcoverro, Teresa
2015-01-01
Herds of dugong, a largely tropical marine megaherbivore, are known to undertake long-distance movements, sequentially overgrazing seagrass meadows in their path. Given their drastic declines in many regions, it is unclear whether at lower densities, their grazing is less intense, reducing their need to travel between meadows. We studied the effect of the feeding behaviour of a small dugong population in the Andaman and Nicobar archipelago, India to understand how small isolated populations graze seagrasses. In the seven years of our observation, all recorded dugongs travelled either solitarily or in pairs, and their use of seagrasses was limited to 8 meadows, some of which were persistently grazed. These meadows were relatively large, contiguous and dominated by short-lived seagrasses species. Dugongs consumed approximately 15% of meadow primary production, but there was a large variation (3-40% of total meadow production) in consumption patterns between meadows. The impact of herbivory was relatively high, with shoot densities c. 50% higher inside herbivore exclosures than in areas exposed to repeated grazing. Our results indicate that dugongs in the study area repeatedly graze the same meadows probably because the proportion of primary production consumed reduces shoot density to levels that are still above values that can trigger meadow abandonment. This ability of seagrasses to cope perhaps explains the long-term site fidelity shown by individual dugongs in these meadows. The fact that seagrass meadows in the archipelago are able to support dugong foraging requirements allows us to clearly identify locations where this remnant population persists, and where urgent management efforts can be directed.
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Seagrass Herbivory Levels Sustain Site-Fidelity in a Remnant Dugong Population
Patankar, Vardhan; Marbà, Núria
2015-01-01
Herds of dugong, a largely tropical marine megaherbivore, are known to undertake long-distance movements, sequentially overgrazing seagrass meadows in their path. Given their drastic declines in many regions, it is unclear whether at lower densities, their grazing is less intense, reducing their need to travel between meadows. We studied the effect of the feeding behaviour of a small dugong population in the Andaman and Nicobar archipelago, India to understand how small isolated populations graze seagrasses. In the seven years of our observation, all recorded dugongs travelled either solitarily or in pairs, and their use of seagrasses was limited to 8 meadows, some of which were persistently grazed. These meadows were relatively large, contiguous and dominated by short-lived seagrasses species. Dugongs consumed approximately 15% of meadow primary production, but there was a large variation (3–40% of total meadow production) in consumption patterns between meadows. The impact of herbivory was relatively high, with shoot densities c. 50% higher inside herbivore exclosures than in areas exposed to repeated grazing. Our results indicate that dugongs in the study area repeatedly graze the same meadows probably because the proportion of primary production consumed reduces shoot density to levels that are still above values that can trigger meadow abandonment. This ability of seagrasses to cope perhaps explains the long-term site fidelity shown by individual dugongs in these meadows. The fact that seagrass meadows in the archipelago are able to support dugong foraging requirements allows us to clearly identify locations where this remnant population persists, and where urgent management efforts can be directed. PMID:26492558
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Li, X; Yang, S; Dong, K; Tang, Z; Li, K; Fan, B; Wang, Z; Liu, B
2017-10-01
Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5-56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study. © 2017 Stichting International Foundation for Animal Genetics.
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Jamie Marie Marranca,; Amy Welsh,; Roseman, Edward F.
2015-01-01
Lake sturgeon (Acipenser fulvescens) have experienced significant habitat loss, resulting in reduced population sizes. Three artificial reefs were built in the Huron-Erie corridor in the Great Lakes to replace lost spawning habitat. Genetic data were collected to determine the source and numbers of adult lake sturgeon spawning on the reefs and to determine if the founder effect resulted in reduced genetic diversity. DNA was extracted from larval tail clips and 12 microsatellite loci were amplified. Larval genotypes were then compared to 22 previously studied spawning lake sturgeon populations in the Great Lakes to determine the source of the parental population. The effective number of breeders (Nb) was calculated for each reef cohort. The larval genotypes were then compared to the source population to determine if there were any losses in genetic diversity that are indicative of the founder effect. The St. Clair and Detroit River adult populations were found to be the source parental population for the larvae collected on all three artificial reefs. There were large numbers of contributing adults relative to the number of sampled larvae. There was no significant difference between levels of genetic diversity in the source population and larval samples from the artificial reefs; however, there is some evidence for a genetic bottleneck in the reef populations likely due to the founder effect. Habitat restoration in the Huron-Erie corridor is likely resulting in increased habitat for the large lake sturgeon population in the system and in maintenance of the population's genetic diversity.
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Integrated methods for teaching population health.
Sistrom, Maria Gilson; Zeigen, Laura; Jones, Melissa; Durham, Korana Fiol; Boudrot, Thomas
2011-01-01
The Institute of Medicine recommends reforms to public health education to better prepare the public health workforce. This study addresses the application of two of the recommended reforms in the population health nursing curriculum at one university: use of an ecological model and distance learning methods. Using interdisciplinary faculty, integrated teaching and learning methods, and a multimedia curriculum, this study examined the following question: can distance learning be designed to support learning goals and outcomes specific to an ecological approach and population health concepts in general? Course content was evaluated using students' perception of practice utility and understanding of population health concepts. Integrated teaching methods were evaluated using a scale as well as comparison to other student distance learning experiences within the university. Findings demonstrated that both the ecological model and distance learning methods were successfully used to teach population health to a large nursing student cohort. 2011, SLACK Incorporated.
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Geremia, Chris; Miller, Michael W.; Hoeting, Jennifer A.; Antolin, Michael F.; Hobbs, N. Thompson
2015-01-01
Epidemics of chronic wasting disease (CWD) of North American Cervidae have potential to harm ecosystems and economies. We studied a migratory population of mule deer (Odocoileus hemionus) affected by CWD for at least three decades using a Bayesian framework to integrate matrix population and disease models with long-term monitoring data and detailed process-level studies. We hypothesized CWD prevalence would be stable or increase between two observation periods during the late 1990s and after 2010, with higher CWD prevalence making deer population decline more likely. The weight of evidence suggested a reduction in the CWD outbreak over time, perhaps in response to intervening harvest-mediated population reductions. Disease effects on deer population growth under current conditions were subtle with a 72% chance that CWD depressed population growth. With CWD, we forecasted a growth rate near one and largely stable deer population. Disease effects appear to be moderated by timing of infection, prolonged disease course, and locally variable infection. Long-term outcomes will depend heavily on whether current conditions hold and high prevalence remains a localized phenomenon. PMID:26509806
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Jessop, Tim S.; Smissen, Peter; Scheelings, Franciscus; Dempster, Tim
2012-01-01
Humans are increasingly subsidizing and altering natural food webs via changes to nutrient cycling and productivity. Where human trophic subsidies are concentrated and persistent within natural environments, their consumption could have complex consequences for wild animals through altering habitat preferences, phenotypes and fitness attributes that influence population dynamics. Human trophic subsidies conceptually create both costs and benefits for animals that receive increased calorific and altered nutritional inputs. Here, we evaluated the effects of a common terrestrial human trophic subsidies, human food refuse, on population and phenotypic (comprising morphological and physiological health indices) parameters of a large predatory lizard (∼2 m length), the lace monitor (Varanus varius), in southern Australia by comparison with individuals not receiving human trophic subsidies. At human trophic subsidies sites, lizards were significantly more abundant and their sex ratio highly male biased compared to control sites in natural forest. Human trophic subsidies recipient lizards were significantly longer, heavier and in much greater body condition. Blood parasites were significantly lower in human trophic subsidies lizards. Collectively, our results imply that human trophic subsidized sites were especially attractive to adult male lace monitors and had large phenotypic effects. However, we cannot rule out that the male-biased aggregations of large monitors at human trophic subsidized sites could lead to reductions in reproductive fitness, through mate competition and offspring survival, and through greater exposure of eggs and juveniles to predation. These possibilities could have negative population consequences. Aggregations of these large predators may also have flow on effects to surrounding food web dynamics through elevated predation levels. Given that flux of energy and nutrients into food webs is central to the regulation of populations and their communities, we advocate further studies of human trophic subsidies be undertaken to evaluate the potentially large ecological implications of this significant human environmental alteration. PMID:22509271
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Estoup, Arnaud; Jarne, Philippe; Cornuet, Jean-Marie
2002-09-01
Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.
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Concerted evolution at the population level: pupfish HindIII satellite DNA sequences.
Elder, J F; Turner, B J
1994-01-01
The canonical monomers (approximately 170 bp) of an abundant (1.9 x 10(6) copies per diploid genome) satellite DNA sequence family in the genome of Cyprinodon variegatus, a "pupfish" that ranges along the Atlantic coast from Cape Cod to central Mexico, are divergent in base sequence in 10 of 12 samples collected from natural populations. The divergence involves substitutions, deletions, and insertions, is marked in scope (mean pairwise sequence similarity = 61.6%; range = 35-95.9%), is largely confined to the 3' half of the monomer, and is not correlated with the distance among collecting sites. Repetitive cloning and direct genomic sequencing experiments failed to detect intrapopulation and intraindividual variation, suggesting high levels of sequence homogeneity within populations. The satellite sequence has therefore undergone "concerted evolution," at the level of the local population. Concerted evolution has previously almost always been discussed in terms of the divergence of species or higher taxa; its intraspecific occurrence apparently has not been reported previously. The generality of the observation is difficult to evaluate, for although satellite DNAs from a large number of organisms have been studied in detail, there appear to be little or no other data on their sequence variation in natural populations. The relationship (if any) between concerted, population level, satellite DNA divergence and the extent of gene flow/genetic isolation among conspecific natural populations remains to be established. Images PMID:8302879
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Wu, H; Baynes, R E; Leavens, T; Tell, L A; Riviere, J E
2013-06-01
The objective of this study was to develop a population pharmacokinetic (PK) model and predict tissue residues and the withdrawal interval (WDI) of flunixin in cattle. Data were pooled from published PK studies in which flunixin was administered through various dosage regimens to diverse populations of cattle. A set of liver data used to establish the regulatory label withdrawal time (WDT) also were used in this study. Compartmental models with first-order absorption and elimination were fitted to plasma and liver concentrations by a population PK modeling approach. Monte Carlo simulations were performed with the population mean and variabilities of PK parameters to predict liver concentrations of flunixin. The PK of flunixin was described best by a 3-compartment model with an extra liver compartment. The WDI estimated in this study with liver data only was the same as the label WDT. However, a longer WDI was estimated when both plasma and liver data were included in the population PK model. This study questions the use of small groups of healthy animals to determine WDTs for drugs intended for administration to large diverse populations. This may warrant a reevaluation of the current procedure for establishing WDT to prevent violative residues of flunixin. © 2012 Blackwell Publishing Ltd.
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Genetics Home Reference: thiopurine S-methyltransferase deficiency
... activity: a large, prospective population study. Pharmacogenomics. 2008 Mar;9(3):303-9. doi: 10.2217/14622416. ... genotype and thiopurine dosing. Clin Pharmacol Ther. 2011 Mar;89(3):387-91. doi: 10.1038/clpt. ...
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The biophysical basis and clinical applications of rheoencephalography.
DOT National Transportation Integrated Search
1967-05-01
A method for screening large populations for asymptomatic but potentially incapacitating cerebrovascular disease has obvious application in aviation medicine. Rheoencephalography (REG), a simple, rapid and innocuous method of studying the cranial cir...
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Harada, Sei; Hirayama, Akiyoshi; Chan, Queenie; Kurihara, Ayako; Fukai, Kota; Iida, Miho; Kato, Suzuka; Sugiyama, Daisuke; Kuwabara, Kazuyo; Takeuchi, Ayano; Akiyama, Miki; Okamura, Tomonori; Ebbels, Timothy M D; Elliott, Paul; Tomita, Masaru; Sato, Asako; Suzuki, Chizuru; Sugimoto, Masahiro; Soga, Tomoyoshi; Takebayashi, Toru
2018-01-01
Cohort studies with metabolomics data are becoming more widespread, however, large-scale studies involving 10,000s of participants are still limited, especially in Asian populations. Therefore, we started the Tsuruoka Metabolomics Cohort Study enrolling 11,002 community-dwelling adults in Japan, and using capillary electrophoresis-mass spectrometry (CE-MS) and liquid chromatography-mass spectrometry. The CE-MS method is highly amenable to absolute quantification of polar metabolites, however, its reliability for large-scale measurement is unclear. The aim of this study is to examine reproducibility and validity of large-scale CE-MS measurements. In addition, the study presents absolute concentrations of polar metabolites in human plasma, which can be used in future as reference ranges in a Japanese population. Metabolomic profiling of 8,413 fasting plasma samples were completed using CE-MS, and 94 polar metabolites were structurally identified and quantified. Quality control (QC) samples were injected every ten samples and assessed throughout the analysis. Inter- and intra-batch coefficients of variation of QC and participant samples, and technical intraclass correlation coefficients were estimated. Passing-Bablok regression of plasma concentrations by CE-MS on serum concentrations by standard clinical chemistry assays was conducted for creatinine and uric acid. In QC samples, coefficient of variation was less than 20% for 64 metabolites, and less than 30% for 80 metabolites out of the 94 metabolites. Inter-batch coefficient of variation was less than 20% for 81 metabolites. Estimated technical intraclass correlation coefficient was above 0.75 for 67 metabolites. The slope of Passing-Bablok regression was estimated as 0.97 (95% confidence interval: 0.95, 0.98) for creatinine and 0.95 (0.92, 0.96) for uric acid. Compared to published data from other large cohort measurement platforms, reproducibility of metabolites common to the platforms was similar to or better than in the other studies. These results show that our CE-MS platform is suitable for conducting large-scale epidemiological studies.
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Familial aggregation of age-related macular degeneration in the Utah population.
Luo, Ling; Harmon, Jennifer; Yang, Xian; Chen, Haoyu; Patel, Shrena; Mineau, Geraldine; Yang, Zhenglin; Constantine, Ryan; Buehler, Jeanette; Kaminoh, Yuuki; Ma, Xiang; Wong, Tien Y; Zhang, Maonian; Zhang, Kang
2008-02-01
We examined familial aggregation and risk of age-related macular degeneration in the Utah population using a population-based case-control study. Over one million unique patient records were searched within the University of Utah Health Sciences Center and the Utah Population Database (UPDB), identifying 4764 patients with AMD. Specialized kinship analysis software was used to test for familial aggregation of disease, estimate the magnitude of familial risks, and identify families at high risk for disease. The population-attributable risk (PAR) for AMD was calculated to be 0.34. Recurrence risks in relatives indicate increased relative risks in siblings (2.95), first cousins (1.29), second cousins (1.13), and parents (5.66) of affected cases. There were 16 extended large families with AMD identified for potential use in genetic studies. Each family had five or more living affected members. The familial aggregation of AMD shown in this study exemplifies the merit of the UPDB and supports recent research demonstrating significant genetic contribution to disease development and progression.
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Hakenberg, Jörg; Cheng, Wei-Yi; Thomas, Philippe; Wang, Ying-Chih; Uzilov, Andrew V; Chen, Rong
2016-01-08
Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort helps gain insights into polymorphic and disease-associated variants, a joint perspective can be more powerful in identifying polymorphisms, rare variants, disease-associations, genetic burden, somatic variants, and disease mechanisms. We have set up a Reference Variant Store (RVS) containing variants observed in a number of large-scale sequencing efforts, such as 1000 Genomes, ExAC, Scripps Wellderly, UK10K; various genotyping studies; and disease association databases. RVS holds extensive annotations pertaining to affected genes, functional impacts, disease associations, and population frequencies. RVS currently stores 400 million distinct variants observed in more than 80,000 human samples. RVS facilitates cross-study analysis to discover novel genetic risk factors, gene-disease associations, potential disease mechanisms, and actionable variants. Due to its large reference populations, RVS can also be employed for variant filtration and gene prioritization. A web interface to public datasets and annotations in RVS is available at https://rvs.u.hpc.mssm.edu/.
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WFIRST: Resolving the Milky Way Galaxy
NASA Astrophysics Data System (ADS)
Kalirai, Jason; Conroy, Charlie; Dressler, Alan; Geha, Marla; Levesque, Emily; Lu, Jessica; Tumlinson, Jason
2018-01-01
WFIRST will yield a transformative impact in measuring and characterizing resolved stellar populations in the Milky Way. The proximity and level of detail that such populations need to be studied at directly map to all three pillars of WFIRST capabilities - sensitivity from a 2.4 meter space based telescope, resolution from 0.1" pixels, and large 0.3 degree field of view from multiple detectors. In this poster, we describe the activities of the WFIRST Science Investigation Team (SIT), "Resolving the Milky Way with WFIRST". Notional programs guiding our analysis include targeting sightlines to establish the first well-resolved large scale maps of the Galactic bulge aand central region, pockets of star formation in the disk, benchmark star clusters, and halo substructure and ultra faint dwarf satellites. As an output of this study, our team is building optimized strategies and tools to maximize stellar population science with WFIRST. This will include: new grids of IR-optimized stellar evolution and synthetic spectroscopic models; pipelines and algorithms for optimal data reduction at the WFIRST sensitivity and pixel scale; wide field simulations of Milky Way environments including new astrometric studies; and strategies and automated algorithms to find substructure and dwarf galaxies in the Milky Way through the WFIRST High Latitude Survey.
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Mandák, Bohumil; Hadincová, Věroslava; Mahelka, Václav; Wildová, Radka
2013-01-01
Background North American Pinus strobus is a highly invasive tree species in Central Europe. Using ten polymorphic microsatellite loci we compared various aspects of the large-scale genetic diversity of individuals from 30 sites in the native distribution range with those from 30 sites in the European adventive distribution range. To investigate the ascertained pattern of genetic diversity of this intercontinental comparison further, we surveyed fine-scale genetic diversity patterns and changes over time within four highly invasive populations in the adventive range. Results Our data show that at the large scale the genetic diversity found within the relatively small adventive range in Central Europe, surprisingly, equals the diversity found within the sampled area in the native range, which is about thirty times larger. Bayesian assignment grouped individuals into two genetic clusters separating North American native populations from the European, non-native populations, without any strong genetic structure shown over either range. In the case of the fine scale, our comparison of genetic diversity parameters among the localities and age classes yielded no evidence of genetic diversity increase over time. We found that SGS differed across age classes within the populations under study. Old trees in general completely lacked any SGS, which increased over time and reached its maximum in the sapling stage. Conclusions Based on (1) the absence of difference in genetic diversity between the native and adventive ranges, together with the lack of structure in the native range, and (2) the lack of any evidence of any temporal increase in genetic diversity at four highly invasive populations in the adventive range, we conclude that population amalgamation probably first happened in the native range, prior to introduction. In such case, there would have been no need for multiple introductions from previously isolated populations, but only several introductions from genetically diverse populations. PMID:23874648
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Bustillo, Jorge L; Diaz, Jose D; Pacheco, Idarmes C; Gritz, David C
2015-03-01
Serological studies indicate that rates of ocular toxoplasmosis (OT) vary geographically, with higher rates in tropical regions. Little is known about population-based rates of active OT. We aimed to describe the epidemiology of OT in Central Cuba. This large-population, cross-sectional cohort study used a prospective database at a large regional referral centre in Central Cuba. The patient database was searched for all patients who presented with OT during the 12-month study period from 1 April 2011 to 31 March 2012. Inclusion criteria were the clinical diagnosis of OT, characterised by focal retinochoroidal inflammation and a response to therapy as expected. Gender-stratified and age-stratified study population data from the 2012 Cuban Census were used to calculate incidence rates and prevalence ratios. Among 279 identified patients with OT, 158 presented with active OT. Of these, 122 new-onset and 36 prior-onset cases were confirmed. Based on the total population in the Sancti Spiritus province (466,106 persons), the overall incidence of active OT was 26.2 per 100,000 person-years (95% CI 21.7 to 31.3) with an annual prevalence ratio of 33.9 per 100,000 persons (95% CI 28.8 to 39.6). The incidence of active OT was lowest in the oldest age group and highest in patients aged 25-44 years (4.5 and 42.1 per 100,000 person-years, respectively). This first report describing population-based rates of OT in the Cuban population highlights the importance of patient age as a likely risk factor for OT. Disease rates were found to be highest in females and young to middle-aged adults. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
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Fant, Charles; Schlosser, C. Adam; Gao, Xiang; ...
2016-03-30
The sustainability of future water resources is of paramount importance and is affected by many factors, including population, wealth and climate. Inherent in current methods to estimate these factors in the future is the uncertainty of their prediction. In this study, we integrate a large ensemble of scenarios—internally consistent across economics, emissions, climate, and population—to develop a risk portfolio of water stress over a large portion of Asia that includes China, India, and Mainland Southeast Asia in a future with unconstrained emissions. We isolate the effects of socioeconomic growth from the effects of climate change in order to identify themore » primary drivers of stress on water resources. We find that water needs related to socioeconomic changes, which are currently small, are likely to increase considerably in the future, often overshadowing the effect of climate change on levels of water stress. As a result, there is a high risk of severe water stress in densely populated watersheds by 2050, compared to recent history. There is strong evidence to suggest that, in the absence of autonomous adaptation or societal response, a much larger portion of the region’s population will live in water-stressed regions in the near future. Lastly, tools and studies such as these can effectively investigate large-scale system sensitivities and can be useful in engaging and informing decision makers.« less
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Solano, Angela Rosaria; Cardoso, Florencia Cecilia; Romano, Vanesa; Perazzo, Florencia; Bas, Carlos; Recondo, Gonzalo; Santillan, Francisco Bernardo; Gonzalez, Eduardo; Abalo, Eduardo; Viniegra, María; Michel, José Davalos; Nuñez, Lina María; Noblia, Cristina Maria; Mc Lean, Ignacio; Canton, Enrique Diaz; Chacon, Reinaldo Daniel; Cortese, Gustavo; Varela, Eduardo Beccar; Greco, Martín; Barrientos, María Laura; Avila, Silvia Adela; Vuotto, Hector Daniel; Lorusso, Antonio; Podesta, Ernesto Jorge; Mando, Oscar Gaspar
2017-09-01
BRCA1/2 mutations in Latin America are scarcely documented and in serious need of knowledge about the spectrum of BRCA pathogenic variants, information which may alter clinical practice and subsequently improve patient outcome. In addition, the search for data on testing policies in different regions constitutes a fundamental strength for the present study, which analyzes BRCA1/2 gene sequences and large rearrangements in 940 probands with familial and/or personal history of breast/ovary cancer (BOC). In non-mutated DNA samples, Multiplex Ligation-dependent Probe Amplification assays (MLPA) were used for the analysis of large rearrangements. Our studies detected 179 deleterious mutations out of 940 (19.04%) probands, including 5 large rearrangements and 22 novel mutations. The recurrent mutations accounted for 15.08% of the total and only 2.87% of the probands analyzed, very different from a Hispanic panel previously described. a) this first comprehensive description of the spectrum in BRCA1/2 sheds light on the low frequency of recurrent mutations; b) this information is key in clinical practice to select adequate sequencing studies in our population, subsequently improve patient outcome and prevent damage associated to false normal reports resulting from the use of invalid population panels; c) panels of mutations from other populations should be cautiously validated before imported, even those of apparently similar origin, a concept to be considered beyond significance in Argentina.
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Solano, Angela Rosaria; Cardoso, Florencia Cecilia; Romano, Vanesa; Perazzo, Florencia; Bas, Carlos; Recondo, Gonzalo; Santillan, Francisco Bernardo; Gonzalez, Eduardo; Abalo, Eduardo; Viniegra, María; Michel, José Davalos; Nuñez, Lina María; Noblia, Cristina Maria; Mc Lean, Ignacio; Canton, Enrique Diaz; Chacon, Reinaldo Daniel; Cortese, Gustavo; Varela, Eduardo Beccar; Greco, Martín; Barrientos, María Laura; Avila, Silvia Adela; Vuotto, Hector Daniel; Lorusso, Antonio; Podesta, Ernesto Jorge; Mando, Oscar Gaspar
2017-01-01
BRCA1/2 mutations in Latin America are scarcely documented and in serious need of knowledge about the spectrum of BRCA pathogenic variants, information which may alter clinical practice and subsequently improve patient outcome. In addition, the search for data on testing policies in different regions constitutes a fundamental strength for the present study, which analyzes BRCA1/2 gene sequences and large rearrangements in 940 probands with familial and/or personal history of breast/ovary cancer (BOC). In non-mutated DNA samples, Multiplex Ligation-dependent Probe Amplification assays (MLPA) were used for the analysis of large rearrangements. Our studies detected 179 deleterious mutations out of 940 (19.04%) probands, including 5 large rearrangements and 22 novel mutations. The recurrent mutations accounted for 15.08% of the total and only 2.87% of the probands analyzed, very different from a Hispanic panel previously described. In conclusion: a) this first comprehensive description of the spectrum in BRCA1/2 sheds light on the low frequency of recurrent mutations; b) this information is key in clinical practice to select adequate sequencing studies in our population, subsequently improve patient outcome and prevent damage associated to false normal reports resulting from the use of invalid population panels; c) panels of mutations from other populations should be cautiously validated before imported, even those of apparently similar origin, a concept to be considered beyond significance in Argentina. PMID:28947987
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Munim, Shama; Maheen, Humaira
2012-11-01
To determine the association between gestation weight gain (GWG) and adverse pregnancy outcome in a Pakistani population. Analytical study. The Aga Khan University, Karachi, from February 2003 to 2007. This study used secondary data of 4,735 women from a large cohort study on fetal growth. Pre-pregnancy BMI was categorized according to the recommendations from the institute of medicine (IOM, 2009) and gestation weight gain (GWG) was noted. Chi-square test was used to find the association of GWG and pre-pregnancy BMI with low birth weight (LBW), preterm delivery, large for gestational age (LGA), and caesarean section. Logistic regression analysis was performed to control for confounders like age, parity, working status and ethnicity. The prevalence of LBW decreased with increasing BMI. GWG of the population was noted as 8.5 kg. LBW was observed to have an inverse relationship with GWG. Women below the age of 19 were twice more likely to have LBW than above 35 years of age. Weight gain above the recommended range were twice more likely to have large for dates.Overweight women were 1.5 times more likely to deliver preterm whereas obese women were 1.4 times more likely to undergo caesarean section than women with normal BMI. The optimal weight gain was estimated to be 8.5 kg to prevent low birth weight in our population. Obese women are more likely to have LGA, caesarean sections and pre-term deliveries.
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The prevalence of compulsive buying: a meta-analysis.
Maraz, Aniko; Griffiths, Mark D; Demetrovics, Zsolt
2016-03-01
To estimate the pooled prevalence of compulsive buying behaviour (CBB) in different populations and to determine the effect of age, gender, location and screening instrument on the reported heterogeneity in estimates of CBB and whether publication bias could be identified. Three databases were searched (Medline, PsychInfo, Web of Science) using the terms 'compulsive buying', 'pathological buying' and 'compulsive shopping' to estimate the pooled prevalence of CBB in different populations. Forty studies reporting 49 prevalence estimates from 16 countries were located (n = 32,000). To conduct the meta-analysis, data from non-clinical studies regarding mean age and gender proportion, geographical study location and screening instrument used to assess CBB were extracted by multiple independent observers and evaluated using a random-effects model. Four a priori subgroups were analysed using pooled estimation (Cohen's Q) and covariate testing (moderator and meta-regression analysis). The CBB pooled prevalence of adult representative studies was 4.9% (3.4-6.9%, eight estimates, 10,102 participants), although estimates were higher among university students: 8.3% (5.9-11.5%, 19 estimates, 14,947 participants) in adult non-representative samples: 12.3% (7.6-19.1%, 11 estimates, 3929 participants) and in shopping-specific samples: 16.2% (8.8-27.8%, 11 estimates, 4686 participants). Being young and female were associated with increased tendency, but not location (United States versus non-United States). Meta-regression revealed large heterogeneity within subgroups, due mainly to diverse measures and time-frames (current versus life-time) used to assess CBB. A pooled estimate of compulsive buying behaviour in the populations studied is approximately 5%, but there is large variation between samples accounted for largely by use of different time-frames and measures. © 2016 Society for the Study of Addiction.
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Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops.
Linde, Celeste C; Smith, Leon M; Peakall, Rod
2016-05-12
The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens. The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common. Pathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains.
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Adolescents'"Meaning" of Leisure.
ERIC Educational Resources Information Center
Callaway, Rolland
A study examined the attitudes of high school students toward various leisure activities. The study population consisted of 85 students attending a large, desegregated midwestern high school. Study participants were asked to rate each of 18 activities with respect to the following four sets of adjectives on a four-point scale: good/bad,…
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Inferring population structure and demographic history using Y-STR data from worldwide populations.
Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui
2015-02-01
The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies.
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Tropical warming and the dynamics of endangered primates.
Wiederholt, Ruscena; Post, Eric
2010-04-23
Many primate species are severely threatened, but little is known about the effects of global warming and the associated intensification of El Niño events on primate populations. Here, we document the influences of the El Niño southern oscillation (ENSO) and hemispheric climatic variability on the population dynamics of four genera of ateline (neotropical, large-bodied) primates. All ateline genera experienced either an immediate or a lagged negative effect of El Niño events. ENSO events were also found to influence primate resource levels through neotropical arboreal phenology. Furthermore, frugivorous primates showed a high degree of interspecific population synchrony over large scales across Central and South America attributable to the recent trends in large-scale climate. These results highlight the role of large-scale climatic variation and trends in ateline primate population dynamics, and emphasize that global warming could pose additional threats to the persistence of multiple species of endangered primates.
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Large-scale climatic anomalies affect marine predator foraging behaviour and demography.
Bost, Charles A; Cotté, Cedric; Terray, Pascal; Barbraud, Christophe; Bon, Cécile; Delord, Karine; Gimenez, Olivier; Handrich, Yves; Naito, Yasuhiko; Guinet, Christophe; Weimerskirch, Henri
2015-10-27
Determining the links between the behavioural and population responses of wild species to environmental variations is critical for understanding the impact of climate variability on ecosystems. Using long-term data sets, we show how large-scale climatic anomalies in the Southern Hemisphere affect the foraging behaviour and population dynamics of a key marine predator, the king penguin. When large-scale subtropical dipole events occur simultaneously in both subtropical Southern Indian and Atlantic Oceans, they generate tropical anomalies that shift the foraging zone southward. Consequently the distances that penguins foraged from the colony and their feeding depths increased and the population size decreased. This represents an example of a robust and fast impact of large-scale climatic anomalies affecting a marine predator through changes in its at-sea behaviour and demography, despite lack of information on prey availability. Our results highlight a possible behavioural mechanism through which climate variability may affect population processes.
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Large-scale climatic anomalies affect marine predator foraging behaviour and demography
NASA Astrophysics Data System (ADS)
Bost, Charles A.; Cotté, Cedric; Terray, Pascal; Barbraud, Christophe; Bon, Cécile; Delord, Karine; Gimenez, Olivier; Handrich, Yves; Naito, Yasuhiko; Guinet, Christophe; Weimerskirch, Henri
2015-10-01
Determining the links between the behavioural and population responses of wild species to environmental variations is critical for understanding the impact of climate variability on ecosystems. Using long-term data sets, we show how large-scale climatic anomalies in the Southern Hemisphere affect the foraging behaviour and population dynamics of a key marine predator, the king penguin. When large-scale subtropical dipole events occur simultaneously in both subtropical Southern Indian and Atlantic Oceans, they generate tropical anomalies that shift the foraging zone southward. Consequently the distances that penguins foraged from the colony and their feeding depths increased and the population size decreased. This represents an example of a robust and fast impact of large-scale climatic anomalies affecting a marine predator through changes in its at-sea behaviour and demography, despite lack of information on prey availability. Our results highlight a possible behavioural mechanism through which climate variability may affect population processes.
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Xu, Man K; Morin, Alexandre J S; Marsh, Herbert W; Richards, Marcus; Jones, Peter B
2016-08-01
The factorial structure of the Parental Bonding Instrument (PBI) has been frequently studied in diverse samples but no study has examined its psychometric properties from large, population-based samples. In particular, important questions have not been addressed such as the measurement invariance properties across parental and offspring gender. We evaluated the PBI based on responses from a large, representative population-based sample, using an exploratory structural equation modeling method appropriate for categorical data. Analysis revealed a three-factor structure representing "care," "overprotection," and "autonomy" parenting styles. In terms of psychometric measurement validity, our results supported the complete invariance of the PBI ratings across sons and daughters for their mothers and fathers. The PBI ratings were also robust in relation to personality and mental health status. In terms of predictive value, paternal care showed a protective effect on mental health at age 43 in sons. The PBI is a sound instrument for capturing perceived parenting styles, and is predictive of mental health in middle adulthood. © The Author(s) 2016.
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Mcdonald, P. Sean; Essington, Timothy E.; Davis, Jonathan P.; Galloway, Aaron W.E.; Stevick, Bethany C.; Jensen, Gregory C.; VanBlaricom, Glenn R.; Armstrong, David A.
2015-01-01
Marine bivalves are important ecosystem constituents and frequently support valuable fisheries. In many nearshore areas, human disturbance—including declining habitat and water quality—can affect the distribution and abundance of bivalve populations, and complicate ecosystem and fishery management assessments. Infaunal bivalves, in particular, are frequently cryptic and difficult to detect; thus, assessing potential impacts on their populations requires suitable, scalable methods for estimating abundance and distribution. In this study, population size of a common benthic bivalve (the geoduck Panopea generosa) is estimated with a Bayesian habitat-based model fit to scuba and tethered camera data in Hood Canal, a fjord basin in Washington state. Densities declined more than two orders of magnitude along a north—south gradient, concomitant with patterns of deepwater dissolved oxygen, and intensity and duration of seasonal hypoxia. Across the basin, geoducks were most abundant in loose, unconsolidated, sand substrate. The current study demonstrates the utility of using scuba, tethered video, and habitat models to estimate the abundance and distribution of a large infaunal bivalve at a regional (385-km2) scale.
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Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system
Bian, Yingnan; Zhang, Suhua; Zhou, Wei; Zhao, Qi; Siqintuya; Zhu, Ruxin; Wang, Zheng; Gao, Yuzhen; Hong, Jie; Lu, Daru; Li, Chengtao
2016-01-01
The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population. PMID:26842947
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Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system.
Bian, Yingnan; Zhang, Suhua; Zhou, Wei; Zhao, Qi; Siqintuya; Zhu, Ruxin; Wang, Zheng; Gao, Yuzhen; Hong, Jie; Lu, Daru; Li, Chengtao
2016-02-04
The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population.
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Urbanization and the problem of restricting the growth of very large cities.
Bialkovskaia, V; Novikov, V
1983-10-01
This article discusses the problem of preventing the excessive growth of very large cities to the detriment of the development of smaller urban settlements in the USSR. The increase in size of the urban population throughout the entire USSR is mainly connected with the increase in the number of city dwellers. In 1960 and 1970 the number of largest cities in the USSR increased, along with a share of the nation's population living in these large cities. The low natural increase in population of very large cities creates a high demand for labor power which must come from the population of other cities. In 1970-1980, Moscow, one of the largest millionaire cities, had the lowest population growth rate of all major USSR cities (113.7%). The growth of Moscow and other very large cities in the last few years has been due to the mechanical increase in population and the increase in area. The analysis of Moscow's pattern of population growth over time focuses on changes in the level of availability of social and everyday services. The prewar period is characterized by a reserve of labor resources, the highest growth in industry and science, but a low overall population dynamic in the city. In the postwar period there was a significant decline in the annual increase of all indicators; this was a period of strong social development of the city. The period between 1966 and 1980 shows a further slowdown in the growth rate of city forming branches by an accelerated development of municipal service branches. The demand for measures to restrict the growth of very large Soviet cities depends on: 1) the reorientation of the development of the economic base, 2) the restructuring of their economy, and 3) the siting of various types of production of goods and services. Developing the specialization of the urban economy consists of planned development of the production of goods and services based on the use of available resources.
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Population delineation of polar bears using satellite collar data
Bethke, R.; Taylor, Mitchell K.; Amstrup, Steven C.; Messier, François
1996-01-01
To produce reliable estimates of the size or vital rates of a given population, it is important that the boundaries of the population under study are clearly defined. This is particularly critical for large, migratory animals where levels of sustainable harvest are based on these estimates, and where small errors may have serious long-term consequences for the population. Once populations are delineated, rates of exchange between adjacent populations can be determined and accounted/corrected for when calculating abundance (e.g., based on mark-recapture data). Using satellite radio-collar locations for polar bears in the western Canadian Arctic, we illustrate one approach to delineating wildlife populations that integrates cluster analysis methods for determining group membership with home range plotting procedures to define spatial utilization. This approach is flexible with respect to the specific procedures used and provides an objective and quantitative basis for defining population boundaries.
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Siragusa, Enrico; Haiminen, Niina; Utro, Filippo; Parida, Laxmi
2017-10-09
Computer simulations can be used to study population genetic methods, models and parameters, as well as to predict potential outcomes. For example, in plant populations, predicting the outcome of breeding operations can be studied using simulations. In-silico construction of populations with pre-specified characteristics is an important task in breeding optimization and other population genetic studies. We present two linear time Simulation using Best-fit Algorithms (SimBA) for two classes of problems where each co-fits two distributions: SimBA-LD fits linkage disequilibrium and minimum allele frequency distributions, while SimBA-hap fits founder-haplotype and polyploid allele dosage distributions. An incremental gap-filling version of previously introduced SimBA-LD is here demonstrated to accurately fit the target distributions, allowing efficient large scale simulations. SimBA-hap accuracy and efficiency is demonstrated by simulating tetraploid populations with varying numbers of founder haplotypes, we evaluate both a linear time greedy algoritm and an optimal solution based on mixed-integer programming. SimBA is available on http://researcher.watson.ibm.com/project/5669.
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Chen, Zongliang; Wang, Baobao; Dong, Xiaomei; Liu, Han; Ren, Longhui; Chen, Jian; Hauck, Andrew; Song, Weibin; Lai, Jinsheng
2014-06-04
Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations. A set of 708 F2 progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method. We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.
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Davis, Amy J.; Hooten, Mevin B.; Phillips, Michael L.; Doherty, Paul F.
2014-01-01
Evaluation of population dynamics for rare and declining species is often limited to data that are sparse and/or of poor quality. Frequently, the best data available for rare bird species are based on large-scale, population count data. These data are commonly based on sampling methods that lack consistent sampling effort, do not account for detectability, and are complicated by observer bias. For some species, short-term studies of demographic rates have been conducted as well, but the data from such studies are typically analyzed separately. To utilize the strengths and minimize the weaknesses of these two data types, we developed a novel Bayesian integrated model that links population count data and population demographic data through population growth rate (λ) for Gunnison sage-grouse (Centrocercus minimus). The long-term population index data available for Gunnison sage-grouse are annual (years 1953–2012) male lek counts. An intensive demographic study was also conducted from years 2005 to 2010. We were able to reduce the variability in expected population growth rates across time, while correcting for potential small sample size bias in the demographic data. We found the population of Gunnison sage-grouse to be variable and slightly declining over the past 16 years.
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Rosenberg, Noah A; Mahajan, Saurabh; Gonzalez-Quevedo, Catalina; Blum, Michael G B; Nino-Rosales, Laura; Ninis, Vasiliki; Das, Parimal; Hegde, Madhuri; Molinari, Laura; Zapata, Gladys; Weber, James L; Belmont, John W; Patel, Pragna I
2006-12-01
Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States-sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.
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Renal Denervation for Treatment of Hypertension: a Second Start and New Challenges.
Persu, Alexandre; Kjeldsen, Sverre; Staessen, Jan A; Azizi, Michel
2016-01-01
Following the publication of the randomized controlled but open-label trial Symplicity HTN-2, catheter-based renal sympathetic denervation was proposed as a novel treatment for drug-resistant hypertension. Thousands of procedures were routinely performed in Europe, Australia and Asia, and many observational studies were published. A sudden shift from overoptimistic views to radical scepticism occurred later, when the large US randomized sham-controlled trial Symplicity HTN-3 failed to meet its primary blood pressure lowering efficacy endpoint. Experts are divided on the reasons accounting for the large discrepancy between the results of initial studies and those of Symplicity HTN-3. Indeed, the blood pressure lowering effect associated with renal denervation was overestimated in initial trials due to various patient and physician-related biases, whereas it could have been underestimated in Symplicity HTN-3, which was well designed but not rigorously executed. Still, there is a large consensus on the need to further study catheter-based renal denervation in more controlled conditions, with particular emphasis on identification of predictors of blood pressure response. US and European experts have recently issued very similar recommendations on design of upcoming trials, procedural aspects, drug treatment, patient population and inclusion-exclusion criteria. Application of these new standards may represent a second chance for renal denervation to demonstrate--or not--its efficacy and safety in various patient populations. With its highly standardized treatment regimen, the French trial DENERHTN paved the way for this new approach and may inspire upcoming studies testing novel renal denervation systems in different populations.
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Insights into DDT Resistance from the Drosophila melanogaster Genetic Reference Panel
Schmidt, Joshua M.; Battlay, Paul; Gledhill-Smith, Rebecca S.; Good, Robert T.; Lumb, Chris; Fournier-Level, Alexandre; Robin, Charles
2017-01-01
Insecticide resistance is considered a classic model of microevolution, where a strong selective agent is applied to a large natural population, resulting in a change in frequency of alleles that confer resistance. While many insecticide resistance variants have been characterized at the gene level, they are typically single genes of large effect identified in highly resistant pest species. In contrast, multiple variants have been implicated in DDT resistance in Drosophila melanogaster; however, only the Cyp6g1 locus has previously been shown to be relevant to field populations. Here we use genome-wide association studies (GWAS) to identify DDT-associated polygenes and use selective sweep analyses to assess their adaptive significance. We identify and verify two candidate DDT resistance loci. A largely uncharacterized gene, CG10737, has a function in muscles that ameliorates the effects of DDT, while a putative detoxifying P450, Cyp6w1, shows compelling evidence of positive selection. PMID:28935691
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The Occupational Aspirations and Expectations of College Students Majoring in Jazz Studies
ERIC Educational Resources Information Center
Devroop, Karendra
2012-01-01
This study was designed to investigate the occupational aspirations and occupational expectations of college students majoring in jazz studies in the United States. Participants included the population of jazz studies majors (N = 211) at a large mid-southern university known for its prestigious and internationally recognized jazz program. A…
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Karen E. Bagne; Deborah M. Finch
2009-01-01
Avian populations were monitored using point counts from 2002 to 2007, two years before and four years after a 2800 ha fuel reduction project. The study area was within a ponderosa pine forest near Santa Fe, New Mexico, USA. Adjacent unthinned areas were also monitored as a reference for population variation related to other factors. For individual bird species...
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ERIC Educational Resources Information Center
Plotnikoff, Ronald C.; Lippke, Sonia; Reinbold-Matthews, Melissa; Courneya, Kerry S.; Karunamuni, Nandini; Sigal, Ronald J.; Birkett, Nicholas
2007-01-01
This study was designed to test the validity of a transtheoretical model's physical activity (PA) stage measure with intention and different intensities of behavior in a large population-based sample of adults living with diabetes (Type 1 diabetes, n = 697; Type 2 diabetes, n = 1,614) and examine different age groups. The overall…
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Lichtenstein, James L. L.; Wright, Colin M; McEwen, Brendan; Pinter-Wollman, Noa; Pruitt, Jonathan N.
2018-01-01
Individual animals differ consistently in their behaviour, thus impacting a wide variety of ecological outcomes. Recent advances in animal personality research have established the ecological importance of the multidimensional behavioural volume occupied by individuals and by multispecies communities. Here, we examine the degree to which the multidimensional behavioural volume of a group predicts the outcome of both intra- and interspecific interactions. In particular, we test the hypothesis that a population of conspecifics will experience low intraspecific competition when the population occupies a large volume in behavioural space. We further hypothesize that populations of interacting species will exhibit greater interspecific competition when one or both species occupy large volumes in behavioural space. We evaluate these hypotheses by studying groups of katydids (Scudderia nymphs) and froghoppers (Philaenus spumarius), which compete for food and space on their shared host plant, Solidago canadensis. We found that individuals in single-species groups of katydids positioned themselves closer to one another, suggesting reduced competition, when groups occupied a large behavioural volume. When both species were placed together, we found that the survival of froghoppers was greatest when both froghoppers and katydids occupied a small volume in behavioural space, particularly at high froghopper densities. These results suggest that groups that occupy large behavioural volumes can have low intraspecific competition but high interspecific competition. Thus, behavioural hypervolumes appear to have ecological consequences at both the level of the population and the community and may help to predict the intensity of competition both within and across species. PMID:29681647
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The functional spectrum of low-frequency coding variation.
Marth, Gabor T; Yu, Fuli; Indap, Amit R; Garimella, Kiran; Gravel, Simon; Leong, Wen Fung; Tyler-Smith, Chris; Bainbridge, Matthew; Blackwell, Tom; Zheng-Bradley, Xiangqun; Chen, Yuan; Challis, Danny; Clarke, Laura; Ball, Edward V; Cibulskis, Kristian; Cooper, David N; Fulton, Bob; Hartl, Chris; Koboldt, Dan; Muzny, Donna; Smith, Richard; Sougnez, Carrie; Stewart, Chip; Ward, Alistair; Yu, Jin; Xue, Yali; Altshuler, David; Bustamante, Carlos D; Clark, Andrew G; Daly, Mark; DePristo, Mark; Flicek, Paul; Gabriel, Stacey; Mardis, Elaine; Palotie, Aarno; Gibbs, Richard
2011-09-14
Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.
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Cigarette Smoking and the Risk of Barrett's Esophagus
Kubo, Ai; Levin, T.R.; Block, Gladys; Rumore, Gregory; Quesenberry, Charles P.; Buffler, Patricia; Corley, Douglas A.
2008-01-01
Introduction We examined the association between smoking and the risk of Barrett's esophagus (BE), a metaplastic precursor to esophageal adenocarcinoma. Methods We conducted a case-control study within the Kaiser Permanente Northern California population. Patients with a new diagnosis of BE (n=320) were matched to persons with gastroesophageal reflux disease (GERD) (n=316) and to population controls (n=317). Information was collected using validated questionnaires from direct in-person interviews and electronic databases. Analyses used multivariate unconditional logistic regression that controlled for age, gender, race and education. Results Ever smoking status, smoking intensity (pack-years), and smoking cessation were not associated with the risk of BE. Stratified analyses suggested that ever smoking may be associated with an increased risk of BE among some groups (compared to population controls): persons with long-segment Barrett's esophagus (odds ratio [OR]=1.72, 95% confidence interval [CI] 1.12-2.63); subjects without GERD symptoms (OR=3.98, 95% CI 1.58-10.0); obese subjects (OR=3.38, 95%CI 1.46-7.82); and persons with a large abdominal circumference (OR=3.02, 95%CI (1.18-2.75)). Conclusion Smoking was not a strong or consistent risk factor for BE in a large community-based study, although associations may be present in some population subgroups. PMID:18853262
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Gething, Peter W; Patil, Anand P; Hay, Simon I
2010-04-01
Risk maps estimating the spatial distribution of infectious diseases are required to guide public health policy from local to global scales. The advent of model-based geostatistics (MBG) has allowed these maps to be generated in a formal statistical framework, providing robust metrics of map uncertainty that enhances their utility for decision-makers. In many settings, decision-makers require spatially aggregated measures over large regions such as the mean prevalence within a country or administrative region, or national populations living under different levels of risk. Existing MBG mapping approaches provide suitable metrics of local uncertainty--the fidelity of predictions at each mapped pixel--but have not been adapted for measuring uncertainty over large areas, due largely to a series of fundamental computational constraints. Here the authors present a new efficient approximating algorithm that can generate for the first time the necessary joint simulation of prevalence values across the very large prediction spaces needed for global scale mapping. This new approach is implemented in conjunction with an established model for P. falciparum allowing robust estimates of mean prevalence at any specified level of spatial aggregation. The model is used to provide estimates of national populations at risk under three policy-relevant prevalence thresholds, along with accompanying model-based measures of uncertainty. By overcoming previously unchallenged computational barriers, this study illustrates how MBG approaches, already at the forefront of infectious disease mapping, can be extended to provide large-scale aggregate measures appropriate for decision-makers.
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Probabilistic models for neural populations that naturally capture global coupling and criticality
2017-01-01
Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality. PMID:28926564
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Population-expression models of immune response
NASA Astrophysics Data System (ADS)
Stromberg, Sean P.; Antia, Rustom; Nemenman, Ilya
2013-06-01
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenotype to an effector phenotype which controls the pathogen, and subsequently to a memory phenotype that is maintained and responsible for long-term protection. The expansion and the differentiation have been considered largely independently. Changes in cell populations are typically described using ecologically based ordinary differential equation models. In contrast, differentiation of single cells is studied within systems biology and is frequently modeled by considering changes in gene and protein expression in individual cells. Recent advances in experimental systems biology make available for the first time data to allow the coupling of population and high dimensional expression data of immune cells during infections. Here we describe and develop population-expression models which integrate these two processes into systems biology on the multicellular level. When translated into mathematical equations, these models result in non-conservative, non-local advection-diffusion equations. We describe situations where the population-expression approach can make correct inference from data while previous modeling approaches based on common simplifying assumptions would fail. We also explore how model reduction techniques can be used to build population-expression models, minimizing the complexity of the model while keeping the essential features of the system. While we consider problems in immunology in this paper, we expect population-expression models to be more broadly applicable.
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Chakrabarti, Priyadarshini; Sarkar, Sagartirtha; Basu, Parthiba
2018-05-01
Pesticides have been reported to be one of the major drivers in the global pollinator losses. The large-scale decline in honey bees, an important pollinator group, has resulted in comprehensive studies on honey bee colonies. Lack of information on native wild pollinators has paved the way for this study, which highlights the underlying evolutionary changes occurring in the wild honey bee populations exposed to pesticides along an agricultural intensification landscape. The study reports an increased genetic diversity in native Apis cerana Fabricius (Hymenoptera: Apidae) populations continually exposed to pesticide stress. An increased heterozygosity, evidenced by a higher electrophoretic banding pattern, was observed in the pesticide-exposed populations for two isozymes involved with xenobiotic metabolism-esterase and glucose-6-phosphate dehydrogenase. Differential banding patterns also revealed a higher percentage of polymorphic loci, number of polymorphic bands, Nei's genetic distance, etc. observed in these populations in the Randomly Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) experiments using three random decamer primers. Higher heterozygosity, being indicative of a more resistant population, implies population survival within the threshold pesticide stress. This study reports such changes for the first time in native wild Indian honey bee populations exposed to pesticides and has far-reaching implications on the population adaptability under pesticide stress.
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Kim, Hyunmi; Thurman, David J; Durgin, Tracy; Faught, Edward; Helmers, Sandra
2016-05-01
This study aims to determine prevalence and incidence of epilepsy in the US pediatric population. We analyzed commercial claims and Medicaid insurance claims data between 2008 and 2012. Over 8 million continuously enrolled lives aged 0 to 19 years were included. Our definition of a prevalent case of epilepsy was based on International Classification of Diseases-coded diagnoses of epilepsy or seizures and evidence of prescribed antiepileptic drugs. Incident cases were identified in subjects continuously enrolled for ≥2 years of which the first 2 years had no indication of epilepsy or seizures. The overall prevalence estimate for 2012 was 6.8 per 1,000 children. The overall incidence estimate for 2012 was 104 per 100,000 pediatric population. This study provides estimates of the prevalence and incidence of epilepsy in the US pediatric population, using large claims datasets from multiple US population sectors. The findings appear reasonably representative of the US-insured pediatric population. © The Author(s) 2015.
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Unique disease heritage of the Dutch-German Mennonite population.
Orton, Noelle C; Innes, A Micheil; Chudley, Albert E; Bech-Hansen, N Torben
2008-04-15
The Dutch-German Mennonites are a religious isolate with foundational roots in the 16th century. A tradition of endogamy, large families, detailed genealogical records, and a unique disease history all contribute to making this a valuable population for genetic studies. Such studies in the Dutch-German Mennonite population have already contributed to the identification of the causative genes in several conditions such as the incomplete form of X-linked congenital stationary night blindness (CSNB2; previously iCSNB) and hypophosphatasia (HOPS), as well as the discovery of founder mutations within established disease genes (MYBPC1, CYP17alpha). The Dutch-German Mennonite population provides a strong resource for gene discovery and could lead to the identification of additional disease genes with relevance to the general population. In addition, further research developments should enhance delivery of clinical genetic services to this unique community. In the current review we discuss 31 genetic conditions, including 17 with identified gene mutations, within the Dutch-German Mennonite population. Copyright 2008 Wiley-Liss, Inc.
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CD30 expression in follicular lymphoma.
Gardner, L J; Polski, J M; Evans, H L; Perkins, S L; Dunphy, C H
2001-08-01
CD30(+) anaplastic large cell lymphomas were originally described as being of T-cell, null cell, and B-cell origin. CD30, however, is not a specific marker of anaplastic large cell lymphoma and has been found to be expressed in reactive as well as neoplastic populations as a probable activation marker. In addition, CD30(+) cells have also been described in both diffuse large B-cell and follicular lymphomas (FLs), resembling the pattern seen in reactive tonsils and lymph nodes. We report an index case of FL with CD30 expression, which on initial touch preparations and flow cytometric immunophenotyping revealed a prominent population of CD30(+) cells with marked cellular pleomorphism (anaplasia) in a background of typical FL. Immunohistochemistry of the paraffin section for CD30 in our index case confirmed unequivocal CD30(+) pleomorphic cells in the malignant nodules in occasional clusters. This case prompted a study of additional cases of FL for pattern of immunoreactivity with CD30 on paraffin sections. Twenty-two additional cases of FL (grades 1-3) were retrieved for CD30 immunoperoxidase staining as in the index case. This study demonstrated 32% of the additional cases of FL had definitive CD30(+), large, pleomorphic malignant cells by paraffin immunohistochemistry. In 2 cases (9%), the pattern of immunoreactivity with CD30 showed clustering and variable staining of large cells, as our index case. This study underscores the morphologic and immunophenotypic spectrum of FL that includes CD30 staining and cellular pleomorphism.
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Chiu, Han-Mo; Chen, Sam Li-Sheng; Yen, Amy Ming-Fang; Chiu, Sherry Yueh-Hsia; Fann, Jean Ching-Yuan; Lee, Yi-Chia; Pan, Shin-Liang; Wu, Ming-Shiang; Liao, Chao-Sheng; Chen, Hsiu-Hsi; Koong, Shin-Lan; Chiou, Shu-Ti
2015-09-15
The effectiveness of fecal immunochemical testing (FIT) in reducing colorectal cancer (CRC) mortality has not yet been fully assessed in a large, population-based service screening program. A prospective cohort study of the follow-up of approximately 5 million Taiwanese from 2004 to 2009 was conducted to compare CRC mortality for an exposed (screened) group and an unexposed (unscreened) group in a population-based CRC screening service targeting community residents of Taiwan who were 50 to 69 years old. Given clinical capacity, this nationwide screening program was first rolled out in 2004. In all, 1,160,895 eligible subjects who were 50 to 69 years old (ie, 21.4% of the 5,417,699 subjects of the underlying population) participated in the biennial nationwide screening program by 2009. The actual effectiveness in reducing CRC mortality attributed to the FIT screening was 62% (relative rate for the screened group vs the unscreened group, 0.38; 95% confidence interval, 0.35-0.42) with a maximum follow-up of 6 years. The 21.4% coverage of the population receiving FIT led to a significant 10% reduction in CRC mortality (relative rate, 0.90; 95% confidence interval, 0.84-0.95) after adjustments for a self-selection bias. This large, prospective Taiwanese cohort undergoing population-based FIT screening for CRC had the statistical power to demonstrate a significant CRC mortality reduction, although the follow-up time was short. Although such findings are informative for health decision makers, continued follow-up of this large cohort will be required to estimate the long-term impact of FIT screening if the covered population is expanded. © 2015 American Cancer Society.
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Hossack, Blake R.; Adams, Michael J.; Pearl, Christopher A.; Pilliod, David S.; Corn, P. Stephen; , KRISTINE W. WILSON; , EVELYN L. BULL; , KRISTIN LOHR; , DEBRA PATLA; , JASON JONES
2013-01-01
Despite the high profile of amphibian declines and the increasing threat of drought and fragmentation to aquatic ecosystems, few studies have examined long-term rates of change for a single species across a large geographic area. We analyzed growth in annual egg-mass counts of the Columbia spotted frog (Rana luteiventris) across the northwestern United States, an area encompassing 3 genetic clades. On the basis of data collected by multiple partners from 98 water bodies between 1991 and 2011, we used state-space and linear-regression models to measure effects of patch characteristics, frequency of summer drought, and wetland restoration on population growth. Abundance increased in the 2 clades with greatest decline history, but declined where populations are considered most secure. Population growth was negatively associated with temporary hydroperiods and landscape modification (measured by the human footprint index), but was similar in modified and natural water bodies. The effect of drought was mediated by the size of the water body: populations in large water bodies maintained positive growth despite drought, whereas drought magnified declines in small water bodies. Rapid growth in restored wetlands in areas of historical population declines provided strong evidence of successful management. Our results highlight the importance of maintaining large areas of habitat and underscore the greater vulnerability of small areas of habitat to environmental stochasticity. Similar long-term growth rates in modified and natural water bodies and rapid, positive responses to restoration suggest pond construction and other forms of management can effectively increase population growth. These tools are likely to become increasingly important to mitigate effects of increased drought expected from global climate change.
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Tele-electrocardiography in the epidemiological 'Study of Health in Pomerania' (SHIP).
Alte, Dietrich; Völzke, Henry; Robinson, Daniel M; Kleine, Volker; Grabe, Hans Jörgen; John, Ulrich; Felix, Stephan B
2006-01-01
We have evaluated a portable electrocardiogram (ECG) card in the large population-based epidemiological 'Study of Health in Pomerania' (SHIP). In all, 7008 men and women (20-79 years) were randomly selected from population registries and 4310 subjects participated. Participants used an ECG card for four weeks and recorded two ECGs daily. The participants were also encouraged to record additional ECGs in the case of symptomatic arrhythmias, chest pain or dizziness. The ECGs were sent via telephone. Acrobat (.pdf) files arrived at the study centre via email. Arrhythmias were analysed by visual ECG inspection. Seventy-one per cent of the participants sent at least 80% of the requested ECGs for four weeks. There were few problems (about 70) in the total of 38,162 ECGs transmitted. Overall, 94% of all ECGs were rated as 'good'. Physicians required about 1.5 h to read approximately 100 ECGs daily. The functionality and ergonomics of ECG cards appear to be sufficiently developed for large-scale use in epidemiological studies.
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Contributions of vital rates to growth of a protected population of American black bears
Mitchell, M.S.; Pacifici, L.B.; Grand, J.B.; Powell, R.A.
2009-01-01
Analyses of large, long-lived animals suggest that adult survival generally has the potential to contribute more than reproduction to population growth rate (??), but because survival varies little, high variability in reproduction can have a greater influence. This pattern has been documented for several species of large mammals, but few studies have evaluated such contributions of vital rates to ?? for American black bears (Ursus americanus). We used variance-based perturbation analyses (life table response experiments, LTRE) and analytical sensitivity and elasticity analyses to examine the actual and potential contributions of variation of vital rates to variation in growth rate (??) of a population of black bears inhabiting the Pisgah Bear Sanctuary in the southern Appalachian Mountains of North Carolina, using a 22-year dataset. We found that recruitment varied more than other vital rates; LTRE analyses conducted over several time intervals thus indicated that recruitment generally contributed at least as much as juvenile and adult survival to observed variation in ??, even though the latter 2 vital rates had the greater potential to affect ??. Our findings are consistent with predictions from studies on polar bears (U. maritimus) and grizzly bears (U. arctos), but contrast with the few existing studies on black bears in ways that suggest levels of protection from human-caused mortality might explain whether adult survival or recruitment contribute most to variation in ?? for this species. We hypothesize that ?? is most strongly influenced by recruitment in protected populations where adult survival is relatively high and constant, whereas adult survival will most influence ?? for unprotected populations. ?? 2009 International Association for Bear Research and Management.
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Pembleton, Luke W; Inch, Courtney; Baillie, Rebecca C; Drayton, Michelle C; Thakur, Preeti; Ogaji, Yvonne O; Spangenberg, German C; Forster, John W; Daetwyler, Hans D; Cogan, Noel O I
2018-06-02
Exploitation of data from a ryegrass breeding program has enabled rapid development and implementation of genomic selection for sward-based biomass yield with a twofold-to-threefold increase in genetic gain. Genomic selection, which uses genome-wide sequence polymorphism data and quantitative genetics techniques to predict plant performance, has large potential for the improvement in pasture plants. Major factors influencing the accuracy of genomic selection include the size of reference populations, trait heritability values and the genetic diversity of breeding populations. Global diversity of the important forage species perennial ryegrass is high and so would require a large reference population in order to achieve moderate accuracies of genomic selection. However, diversity of germplasm within a breeding program is likely to be lower. In addition, de novo construction and characterisation of reference populations are a logistically complex process. Consequently, historical phenotypic records for seasonal biomass yield and heading date over a 18-year period within a commercial perennial ryegrass breeding program have been accessed, and target populations have been characterised with a high-density transcriptome-based genotyping-by-sequencing assay. Ability to predict observed phenotypic performance in each successive year was assessed by using all synthetic populations from previous years as a reference population. Moderate and high accuracies were achieved for the two traits, respectively, consistent with broad-sense heritability values. The present study represents the first demonstration and validation of genomic selection for seasonal biomass yield within a diverse commercial breeding program across multiple years. These results, supported by previous simulation studies, demonstrate the ability to predict sward-based phenotypic performance early in the process of individual plant selection, so shortening the breeding cycle, increasing the rate of genetic gain and allowing rapid adoption in ryegrass improvement programs.
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Xu, Shuhua; Jin, Li
2008-01-01
Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (FST > 0.25, mean FST = 0.43) but small frequency differences (7999 AIMs validated) within both populations (FST < 0.05, mean FST < 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations. PMID:18760393
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Dietary patterns and colorectal cancer: results from a Canadian population-based study.
Chen, Zhi; Wang, Peizhong Peter; Woodrow, Jennifer; Zhu, Yun; Roebothan, Barbara; Mclaughlin, John R; Parfrey, Patrick S
2015-01-15
The relationship between major dietary patterns and colorectal cancer (CRC) in other populations largely remains consistent across studies. The objective of the present study is to assess if dietary patterns are associated with the risk of CRC in the population of Newfoundland and Labrador (NL). Data from a population based case-control study in the province of NL were analyzed, including 506 CRC patients (306 men and 200 women) and 673 controls (400 men and 273 women), aged 20-74 years. Dietary habits were assessed by a 169-item food frequency questionnaire (FFQ). Logistic regression analyses were performed to investigate the association between dietary patterns and the CRC risk. Three major dietary patterns were derived using factor analysis, namely a Meat-diet pattern, a Plant-based diet pattern and a Sugary-diet pattern. In combination the three dietary patterns explained 74% of the total variance in food intake. Results suggest that the Meat-diet and the Sugary-diet increased the risk of CRC with corresponding odds ratios (ORs) of 1.84 (95% CI: 1.19-2.86) and 2.26 (95% CI: 1.39-3.66) for people in the highest intake quintile compared to those in the lowest. Whereas plant-based diet pattern decreases the risk of CRC with a corresponding OR of 0.55 (95% CI: 0.35-0.87). Even though odds ratios (ORs) were not always statistically significant, largely similar associations across three cancer sites were found: the proximal colon, the distal colon, and the rectum. The finding that Meat-diet/Sugary-diet patterns increased and Plant-based diet pattern decreased the risk of CRC would guide the promotion of healthy eating for primary prevention of CRC in this population.
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Chia, Nicholas H; Leyden, James M; Newbury, Jonathan; Jannes, Jim; Kleinig, Timothy J
2016-05-01
Endovascular thrombectomy (ET) is standard-of-care for ischemic stroke patients with large vessel occlusion, but estimates of potentially eligible patients from population-based studies have not been published. Such data are urgently needed to rationally plan hyperacute services. Retrospective analysis determined the incidence of ET-eligible ischemic strokes in a comprehensive population-based stroke study (Adelaide, Australia 2009-2010). Stroke patients were stratified via a prespecified eligibility algorithm derived from recent ET trials comprising stroke subtype, pathogenesis, severity, premorbid modified Rankin Score, presentation delay, large vessel occlusion, and target mismatch penumbra. Recognizing centers may interpret recent ET trials either loosely or rigidly; 2 eligibility algorithms were applied: restrictive (key criteria modified Rankin Scale score 0-1, presentation delay <3.5 hours, and target mismatch penumbra) and permissive (modified Rankin Scale score 0-3 and presentation delay <5 hours). In a population of 148 027 people, 318 strokes occurred in the 1-year study period (crude attack rate 215 [192-240] per 100 000 person-years). The number of ischemic strokes eligible by restrictive criteria was 17/258 (7%; 95% confidence intervals 4%-10%) and by permissive criteria, an additional 16 were identified, total 33/258 (13%; 95% confidence intervals 9%-18%). Two of 17 patients (and 6/33 permissive patients) had thrombolysis contraindications. Using the restrictive algorithm, there were 11 (95% confidence intervals 4-18) potential ET cases per 100 000 person-years or 22 (95% confidence intervals 13-31) using the permissive algorithm. In this cohort, ≈7% of ischemic strokes were potentially eligible for ET (13% with permissive criteria). In similar populations, the permissive criteria predict that ≤22 strokes per 100 000 person-years may be eligible for ET. © 2016 American Heart Association, Inc.
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Liu, Xiaoming; Fu, Yun-Xin; Maxwell, Taylor J.; Boerwinkle, Eric
2010-01-01
It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood of the observed SNP configurations to infer population mutation rate θ = 4Neμ, population exponential growth rate R, and error rate ɛ, simultaneously. Using simulation, we show the combined effects of the parameters, θ, n, ɛ, and R on the accuracy of parameter estimation. We compared our maximum composite likelihood estimator (MCLE) of θ with other θ estimators that take into account the error. The results show the MCLE performs well when the sample size is large or the error rate is high. Using parametric bootstrap, composite likelihood can also be used as a statistic for testing the model goodness-of-fit of the observed DNA sequences. The MCLE method is applied to sequence data on the ANGPTL4 gene in 1832 African American and 1045 European American individuals. PMID:19952140
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Molecular hyperdiversity and evolution in very large populations.
Cutter, Asher D; Jovelin, Richard; Dey, Alivia
2013-04-01
The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements. © 2013 Blackwell Publishing Ltd.
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Stallings, Christopher D
2009-01-01
Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations. Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human population density increases, presence of large-bodied fishes declines, and fish communities become dominated by a few smaller-bodied species. Complete disappearance of several large-bodied fishes indicates ecological and local extinctions have occurred in some densely populated areas. These findings fill a fundamentally important gap in our knowledge of the ecosystem effects of artisanal fisheries in developing nations, and provide support for multiple approaches to data collection where they are commonly unavailable.
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Stallings, Christopher D.
2009-01-01
Background Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations. Methodology/Principal Findings Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human population density increases, presence of large-bodied fishes declines, and fish communities become dominated by a few smaller-bodied species. Conclusions/Significance Complete disappearance of several large-bodied fishes indicates ecological and local extinctions have occurred in some densely populated areas. These findings fill a fundamentally important gap in our knowledge of the ecosystem effects of artisanal fisheries in developing nations, and provide support for multiple approaches to data collection where they are commonly unavailable. PMID:19421312
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Spheroidal Populated Star Systems
NASA Astrophysics Data System (ADS)
Angeletti, Lucio; Giannone, Pietro
2008-10-01
Globular clusters and low-ellipticity early-type galaxies can be treated as systems populated by a large number of stars and whose structures can be schematized as spherically symmetric. Their studies profit from the synthesis of stellar populations. The computation of synthetic models makes use of various contributions from star evolution and stellar dynamics. In the first sections of the paper we present a short review of our results on the occurrence of galactic winds in star systems ranging from globular clusters to elliptical galaxies, and the dynamical evolution of a typical massive globular cluster. In the subsequent sections we describe our approach to the problem of the stellar populations in elliptical galaxies. The projected radial behaviours of spectro-photometric indices for a sample of eleven galaxies are compared with preliminary model results. The best agreement between observation and theory shows that our galaxies share a certain degree of heterogeneity. The gas energy dissipation varies from moderate to large, the metal yield ranges from solar to significantly oversolar, the dispersion of velocities is isotropic in most of the cases and anisotropic in the remaining instances.
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1982-05-01
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