Colony mapping: A new technique for monitoring crevice-nesting seabirds

USGS Publications Warehouse

Renner, H.M.; Renner, M.; Reynolds, J.H.; Harping, A.M.A.; Jones, I.L.; Irons, D.B.; Byrd, G.V.

2006-01-01

Monitoring populations of auklets and other crevice-nesting seabirds remains problematic, although numerous methods have been attempted since the mid-1960s. Anecdotal evidence suggests several large auklet colonies have recently decreased in both abundance and extent, concurrently with vegetation encroachment and succession. Quantifying changes in the geographical extent of auklet colonies may be a useful alternative to monitoring population size directly. We propose a standardized method for colony mapping using a randomized systematic grid survey with two components: a simple presence/absence survey and an auklet evidence density survey. A quantitative auklet evidence density index was derived from the frequency of droppings and feathers. This new method was used to map the colony on St. George Island in the southeastern Bering Sea and results were compared to previous colony mapping efforts. Auklet presence was detected in 62 of 201 grid cells (each grid cell = 2500 m2) by sampling a randomly placed 16 m2 plot in each cell; estimated colony area = 155 000 m2. The auklet evidence density index varied by two orders of magnitude across the colony and was strongly correlated with means of replicated counts of birds socializing on the colony surface. Quantitatively mapping all large auklet colonies is logistically feasible using this method and would provide an important baseline for monitoring colony status. Regularly monitoring select colonies using this method may be the best means of detecting changes in distribution and population size of crevice-nesting seabirds. ?? The Cooper Ornithological Society 2006.

Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.

PubMed

Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu; Scheuermann, Richard H

2016-01-01

Flow cytometry (FCM) is a fluorescence-based single-cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap-FR, a novel method for cell population mapping across FCM samples. FlowMap-FR is based on the Friedman-Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap-FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap-FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap-FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap-FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap-FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback-Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL-distance in distinguishing equivalent from nonequivalent cell populations. FlowMap-FR was also employed as a distance metric to match cell populations delineated by manual gating across 30 FCM samples from a benchmark FlowCAP data set. An F-measure of 0.88 was obtained, indicating high precision and recall of the FR-based population matching results. FlowMap-FR has been implemented as a standalone R/Bioconductor package so that it can be easily incorporated into current FCM data analytical workflows. © The Authors. Published by Wiley Periodicals, Inc. on behalf of ISAC.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

PubMed

Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah

2015-09-03

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

Estimating the Population Size of Female Sex Worker Population in Tehran, Iran: Application of Direct Capture-Recapture Method.

PubMed

Karami, Manoochehr; Khazaei, Salman; Poorolajal, Jalal; Soltanian, Alireza; Sajadipoor, Mansour

2017-08-01

There is no reliable estimate of the size of female sex workers (FSWs). This study aimed to estimate the size of FSWs in south of Tehran, Iran in 2016 using direct capture-recapture method. In the capture phase, the hangouts of FSWs were mapped as their meeting places. FSWs who agreed to participate in the study tagged with a T-shirt. The recapture phase was implemented at the same places tagging FSWs with a blue bracelet. The total estimated size of FSWs was 690 (95% CI 633, 747). About 89.43% of FSWs experienced sexual intercourse prior to age 20. The prevalence of human immunodeficiency virus infection among FSWs was 4.60%. The estimated population size of FSWs was much more than our expectation. This issue must be the focus of special attention for planning prevention strategies. However, alternative estimates require to estimating the number FSWs, reliably.

Comparing different stimulus configurations for population receptive field mapping in human fMRI

PubMed Central

Alvarez, Ivan; de Haas, Benjamin; Clark, Chris A.; Rees, Geraint; Schwarzkopf, D. Samuel

2015-01-01

Population receptive field (pRF) mapping is a widely used approach to measuring aggregate human visual receptive field properties by recording non-invasive signals using functional MRI. Despite growing interest, no study to date has systematically investigated the effects of different stimulus configurations on pRF estimates from human visual cortex. Here we compared the effects of three different stimulus configurations on a model-based approach to pRF estimation: size-invariant bars and eccentricity-scaled bars defined in Cartesian coordinates and traveling along the cardinal axes, and a novel simultaneous “wedge and ring” stimulus defined in polar coordinates, systematically covering polar and eccentricity axes. We found that the presence or absence of eccentricity scaling had a significant effect on goodness of fit and pRF size estimates. Further, variability in pRF size estimates was directly influenced by stimulus configuration, particularly for higher visual areas including V5/MT+. Finally, we compared eccentricity estimation between phase-encoded and model-based pRF approaches. We observed a tendency for more peripheral eccentricity estimates using phase-encoded methods, independent of stimulus size. We conclude that both eccentricity scaling and polar rather than Cartesian stimulus configuration are important considerations for optimal experimental design in pRF mapping. While all stimulus configurations produce adequate estimates, simultaneous wedge and ring stimulation produced higher fit reliability, with a significant advantage in reduced acquisition time. PMID:25750620

Spatially associated clump populations in Rosette from CO and dust maps

NASA Astrophysics Data System (ADS)

Veltchev, Todor V.; Ossenkopf-Okada, Volker; Stanchev, Orlin; Schneider, Nicola; Donkov, Sava; Klessen, Ralf S.

2018-04-01

Spatial association of clumps from different tracers turns out to be a valuable tool to determine the physical properties of molecular clouds. It provides a reliable estimate for the X-factors, serves to trace the density of clumps seen in column densities only, and allows one to measure the velocity dispersion of clumps identified in dust emission. We study the spatial association between clump populations, extracted by use of the GAUSSCLUMPS technique from 12CO (1-0), 13CO (1-0) line maps and Herschel dust-emission maps of the star-forming region Rosette, and analyse their physical properties. All CO clumps that overlap with another CO or dust counterpart are found to be gravitationally bound and located in the massive star-forming filaments of the molecular cloud. They obey a single mass-size relation M_cl∝ R_cl^γ with γ ≃ 3 (implying constant mean density) and display virtually no velocity-size relation. We interpret their population as low-density structures formed through compression by converging flows and still not evolved under the influence of self-gravity. The high-mass parts of their clump mass functions are fitted by a power law dN_cl/d log M_cl∝ M_cl^{Γ } and display a nearly Salpeter slope Γ ˜ -1.3. On the other hand, clumps extracted from the dust-emission map exhibit a shallower mass-size relation with γ = 2.5 and mass functions with very steep slopes Γ ˜ -2.3 even if associated with CO clumps. They trace density peaks of the associated CO clumps at scales of a few tenths of pc where no single density scaling law should be expected.

From innervation density to tactile acuity: 1. Spatial representation.

PubMed

Brown, Paul B; Koerber, H Richard; Millecchia, Ronald

2004-06-11

We tested the hypothesis that the population receptive field representation (a superposition of the excitatory receptive field areas of cells responding to a tactile stimulus) provides spatial information sufficient to mediate one measure of static tactile acuity. In psychophysical tests, two-point discrimination thresholds on the hindlimbs of adult cats varied as a function of stimulus location and orientation, as they do in humans. A statistical model of the excitatory low threshold mechanoreceptive fields of spinocervical, postsynaptic dorsal column and spinothalamic tract neurons was used to simulate the population receptive field representations in this neural population of the one- and two-point stimuli used in the psychophysical experiments. The simulated and observed thresholds were highly correlated. Simulated and observed thresholds' relations to physiological and anatomical variables such as stimulus location and orientation, receptive field size and shape, map scale, and innervation density were strikingly similar. Simulated and observed threshold variations with receptive field size and map scale obeyed simple relationships predicted by the signal detection model, and were statistically indistinguishable from each other. The population receptive field representation therefore contains information sufficient for this discrimination.

Using a programmatic mapping approach to plan for HIV prevention and harm reduction interventions for people who inject drugs in three South African cities.

PubMed

Scheibe, Andrew; Shelly, Shaun; Lambert, Andrew; Schneider, Andrea; Basson, Rudolf; Medeiros, Nelson; Padayachee, Kalvanya; Savva, Helen; Hausler, Harry

2017-06-07

Stigma, criminalisation and a lack of data on drug use contribute to the "invisibility" of people who inject drugs (PWID) and make HIV prevention and treatment service delivery challenging. We aimed to confirm locations where PWID congregate in Cape Town, eThekwini and Tshwane (South Africa) and to estimate PWID population sizes within selected electoral wards in these areas to inform South Africa's first multi-site HIV prevention project for PWID. Field workers (including PWID peers) interviewed community informants to identify suspected injecting locations in selected electoral wards in each city and then visited these locations and interviewed PWID. Interviews were used to gather information about the accessibility of sterile injecting equipment, location coordinates and movement patterns. We used the Delphi method to obtain final population size estimates for the mapped wards based on estimates from wisdom of the crowd methods, the literature and programmatic data. Between January and April 2015, we mapped 45 wards. Tshwane teams interviewed 39 PWID in 12 wards, resulting in an estimated number of accessible PWID ranging from 568 to 1431. In eThekwini, teams interviewed 40 PWID in 15 wards with an estimated number of accessible PWID ranging from 184 to 350. The Cape Town team interviewed 61 PWID in 18 wards with an estimated number of accessible PWID ranging between 398 and 503. Sterile needles were only available at one location. Almost all needles were bought from pharmacies. Between 80 and 86% of PWID frequented more than one location per day. PWID who reported movement visited a median of three locations a day. Programmatic mapping led by PWID peers can be used effectively to identify and reach PWID and build relationships where access to HIV prevention commodities for PWID is limited. PWID reported limited access to sterile injecting equipment, highlighting an important HIV prevention need. Programmatic mapping data show that outreach programmes should be flexible and account for the mobile nature of PWID populations. The PWID population size estimates can be used to develop service delivery targets and as baseline measures.

Using Satellite Imagery to Assess Large-Scale Habitat Characteristics of Adirondack Park, New York, USA

NASA Astrophysics Data System (ADS)

McClain, Bobbi J.; Porter, William F.

2000-11-01

Satellite imagery is a useful tool for large-scale habitat analysis; however, its limitations need to be tested. We tested these limitations by varying the methods of a habitat evaluation for white-tailed deer ( Odocoileus virginianus) in the Adirondack Park, New York, USA, utilizing harvest data to create and validate the assessment models. We used two classified images, one with a large minimum mapping unit but high accuracy and one with no minimum mapping unit but slightly lower accuracy, to test the sensitivity of the evaluation to these differences. We tested the utility of two methods of assessment, habitat suitability index modeling, and pattern recognition modeling. We varied the scale at which the models were applied by using five separate sizes of analysis windows. Results showed that the presence of a large minimum mapping unit eliminates important details of the habitat. Window size is relatively unimportant if the data are averaged to a large resolution (i.e., township), but if the data are used at the smaller resolution, then the window size is an important consideration. In the Adirondacks, the proportion of hardwood and softwood in an area is most important to the spatial dynamics of deer populations. The low occurrence of open area in all parts of the park either limits the effect of this cover type on the population or limits our ability to detect the effect. The arrangement and interspersion of cover types were not significant to deer populations.

Large Impact Features on Saturn's Middle-sized Icy Satellites: Global Image Mosaics and Topography

NASA Technical Reports Server (NTRS)

Schenk, P. M.; Moore, J. M.; McKinnon, W. B.

2003-01-01

With the approach of Cassini to the Saturn system, attention naturally focuses on the planet, its rings and Titan, but the Saturn system is also populated by a number of smaller satellites. The seven middle-sized icy satellites, along with those of Uranus, (between 400 and 1500 km wide) are distinctly different geophysically and geologically from their much larger Galilean-class brethren [e.g., 1]. Topographic mapping of these bodies is a critical part of understanding their geologic evolution. Here we describe our recent efforts to map the topography of these satellites using Voyager data.

QTL mapping of flowering time, fruit size and number in populations involving andromonoecious true lemon cucumber

USDA-ARS?s Scientific Manuscript database

Andromonoecious sex expression in cucumber is controlled by the m locus, which encodes the 1-aminocyclopropane-1 –carboxylic acid synthase (ACS) in the ethylene biosynthesis pathway. This gene seems to have pleotropic effects on fruit size and number, but the genetic basis is unknown. The True Lemon...

Mapping of the stochastic Lotka-Volterra model to models of population genetics and game theory

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2017-08-01

The relationship between the M -species stochastic Lotka-Volterra competition (SLVC) model and the M -allele Moran model of population genetics is explored via timescale separation arguments. When selection for species is weak and the population size is large but finite, precise conditions are determined for the stochastic dynamics of the SLVC model to be mappable to the neutral Moran model, the Moran model with frequency-independent selection, and the Moran model with frequency-dependent selection (equivalently a game-theoretic formulation of the Moran model). We demonstrate how these mappings can be used to calculate extinction probabilities and the times until a species' extinction in the SLVC model.

Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

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.

The Genetic Basis of Natural Variation in Kernel Size and Related Traits Using a Four-Way Cross Population in Maize.

PubMed

Chen, Jiafa; Zhang, Luyan; Liu, Songtao; Li, Zhimin; Huang, Rongrong; Li, Yongming; Cheng, Hongliang; Li, Xiantang; Zhou, Bo; Wu, Suowei; Chen, Wei; Wu, Jianyu; Ding, Junqiang

2016-01-01

Kernel size is an important component of grain yield in maize breeding programs. To extend the understanding on the genetic basis of kernel size traits (i.e., kernel length, kernel width and kernel thickness), we developed a set of four-way cross mapping population derived from four maize inbred lines with varied kernel sizes. In the present study, we investigated the genetic basis of natural variation in seed size and other components of maize yield (e.g., hundred kernel weight, number of rows per ear, number of kernels per row). In total, ten QTL affecting kernel size were identified, three of which (two for kernel length and one for kernel width) had stable expression in other components of maize yield. The possible genetic mechanism behind the trade-off of kernel size and yield components was discussed.

The Genetic Basis of Natural Variation in Kernel Size and Related Traits Using a Four-Way Cross Population in Maize

PubMed Central

Liu, Songtao; Li, Zhimin; Huang, Rongrong; Li, Yongming; Cheng, Hongliang; Li, Xiantang; Zhou, Bo; Wu, Suowei; Chen, Wei; Wu, Jianyu; Ding, Junqiang

2016-01-01

Kernel size is an important component of grain yield in maize breeding programs. To extend the understanding on the genetic basis of kernel size traits (i.e., kernel length, kernel width and kernel thickness), we developed a set of four-way cross mapping population derived from four maize inbred lines with varied kernel sizes. In the present study, we investigated the genetic basis of natural variation in seed size and other components of maize yield (e.g., hundred kernel weight, number of rows per ear, number of kernels per row). In total, ten QTL affecting kernel size were identified, three of which (two for kernel length and one for kernel width) had stable expression in other components of maize yield. The possible genetic mechanism behind the trade-off of kernel size and yield components was discussed. PMID:27070143

A map of copy number variations in Chinese populations.

PubMed

Lou, Haiyi; Li, Shilin; Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies.

A Map of Copy Number Variations in Chinese Populations

PubMed Central

Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies. PMID:22087296

Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

PubMed Central

2012-01-01

Background Quantitative trait loci (QTL) detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i.e. designs with low power. Practical recommendations for experimental designs for QTL detection in outbred populations are given on the basis of this bias quantification. Furthermore, an original algorithm is proposed to adjust the location of a QTL, obtained with interval mapping, which co located with a marker. Conclusions Therefore, one should be attentive when one QTL is mapped at the location of one marker, especially under low power conditions. PMID:22520935

Dissection of genetic factors underlying wheat kernel shape and size in an elite x nonadapted cross using a high density SNP linkage map

USDA-ARS?s Scientific Manuscript database

Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414...

The genetic architecture of UV floral patterning in sunflower.

PubMed

Moyers, Brook T; Owens, Gregory L; Baute, Gregory J; Rieseberg, Loren H

2017-07-01

The patterning of floral ultraviolet (UV) pigmentation varies both intra- and interspecifically in sunflowers and many other plant species, impacts pollinator attraction, and can be critical to reproductive success and crop yields. However, the genetic basis for variation in UV patterning is largely unknown. This study examines the genetic architecture for proportional and absolute size of the UV bullseye in Helianthus argophyllus , a close relative of the domesticated sunflower. A camera modified to capture UV light (320-380 nm) was used to phenotype floral UV patterning in an F 2 mapping population, then quantitative trait loci (QTL) were identified using genotyping-by-sequencing and linkage mapping. The ability of these QTL to predict the UV patterning of natural population individuals was also assessed. Proportional UV pigmentation is additively controlled by six moderate effect QTL that are predictive of this phenotype in natural populations. In contrast, UV bullseye size is controlled by a single large effect QTL that also controls flowerhead size and co-localizes with a major flowering time QTL in Helianthus . The co-localization of the UV bullseye size QTL, flowerhead size QTL and a previously known flowering time QTL may indicate a single highly pleiotropic locus or several closely linked loci, which could inhibit UV bullseye size from responding to selection without change in correlated characters. The genetic architecture of proportional UV pigmentation is relatively simple and different from that of UV bullseye size, and so should be able to respond to natural or artificial selection independently. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Extensive genome-wide autozygosity in the population isolates of Daghestan.

PubMed

Karafet, Tatiana M; Bulayeva, Kazima B; Bulayev, Oleg A; Gurgenova, Farida; Omarova, Jamilia; Yepiskoposyan, Levon; Savina, Olga V; Veeramah, Krishna R; Hammer, Michael F

2015-10-01

Isolated populations are valuable resources for mapping disease genes, as inbreeding increases genome-wide homozygosity and enhances the ability to map disease alleles on a genetically uniform background within a relatively homogenous environment. The populations of Daghestan are thought to have resided in the Caucasus Mountains for hundreds of generations and are characterized by a high prevalence of certain complex diseases. To explore the extent to which their unique population history led to increased levels of inbreeding, we genotyped >550 000 autosomal single-nucleotide polymorphisms (SNPs) in a set of 14 population isolates speaking Nakh-Daghestanian (ND) languages. The ND-speaking populations showed greatly elevated coefficients of inbreeding, very high numbers and long lengths of Runs of Homozygosity, and elevated linkage disequilibrium compared with surrounding groups from the Caucasus, the Near East, Europe, Central and South Asia. These results are consistent with the hypothesis that most ND-speaking groups descend from a common ancestral population that fragmented into a series of genetic isolates in the Daghestanian highlands. They have subsequently maintained a long-term small effective population size as a result of constant inbreeding and very low levels of gene flow. Given these findings, Daghestanian population isolates are likely to be useful for mapping genes associated with complex diseases.

The population in China’s earthquake-prone areas has increased by over 32 million along with rapid urbanization

NASA Astrophysics Data System (ADS)

He, Chunyang; Huang, Qingxu; Dou, Yinyin; Tu, Wei; Liu, Jifu

2016-07-01

Accurate assessments of the population exposed to seismic hazard are crucial in seismic risk mapping. Recent rapid urbanization in China has resulted in substantial changes in the size and structure of the population exposed to seismic hazard. Using the latest population census data and seismic maps, this work investigated spatiotemporal changes in the exposure of the population in the most seismically hazardous areas (MSHAs) in China from 1990 to 2010. In the context of rapid urbanization and massive rural-to-urban migration, nearly one-tenth of the Chinese population in 2010 lived in MSHAs. From 1990 to 2010, the MSHA population increased by 32.53 million at a significantly higher rate of change (33.6%) than the national average rate (17.7%). The elderly population in MSHAs increased by 81.4%, which is much higher than the group’s national growth rate of 58.9%. Greater attention should be paid to the demographic changes in earthquake-prone areas in China.

Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

PubMed Central

Vipin, Cina Ann; Luckett, David J.; Harper, John D.I.; Ash, Gavin J.; Kilian, Andrzej; Ellwood, Simon R.; Phan, Huyen T.T.; Raman, Harsh

2013-01-01

We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F8 recombinant inbred line population derived from Kiev Mutant/P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies. PMID:24273424

Radio morphology and parent population of X-ray selected BL Lacertae objects

NASA Technical Reports Server (NTRS)

Laurent-Muehleisen, S. A.; Kollgaard, R. I.; Moellenbrock, G. A.; Feigelson, E. D.

1993-01-01

High-dynamic range (typically 1700:1) radio maps of 15 X-ray BL Lac (XBL) objects from the HEAO-1 Large Area Sky Survey are presented. Morphological characteristics of these sources are compared with Fanaroff-Riley (FR) class I radio galaxies in the context of unified schemes, with reference to one-sided kiloparsec-scale emission. Evidence that cluster membership of XBLs is significantly higher than previously thought is also presented. It is shown that the extended radio powers, X-ray emission, core-to-lobe ratios, and linear sizes of the radio selected BL Lac (RBL) and XBL populations are consistent with an FR I radio galaxy parent population. A source list and VLA observing log and map parameters are provided.

Crater-based dating of geological units on Mars: methods and application for the new global geological map

USGS Publications Warehouse

Platz, Thomas; Michael, Gregory; Tanaka, Kenneth L.; Skinner, James A.; Fortezzo, Corey M.

2013-01-01

The new, post-Viking generation of Mars orbital imaging and topographical data provide significant higher-resolution details of surface morphologies, which induced a new effort to photo-geologically map the surface of Mars at 1:20,000,000 scale. Although from unit superposition relations a relative stratigraphical framework can be compiled, it was the ambition of this mapping project to provide absolute unit age constraints through crater statistics. In this study, the crater counting method is described in detail, starting with the selection of image data, type locations (both from the mapper’s and crater counter’s perspectives) and the identification of impact craters. We describe the criteria used to validate and analyse measured crater populations, and to derive and interpret crater model ages. We provide examples of how geological information about the unit’s resurfacing history can be retrieved from crater size–frequency distributions. Three cases illustrate short-, intermediate, and long-term resurfacing histories. In addition, we introduce an interpretation-independent visualisation of the crater resurfacing history that uses the reduction of the crater population in a given size range relative to the expected population given the observed crater density at larger sizes. From a set of potential type locations, 48 areas from 22 globally mapped units were deemed suitable for crater counting. Because resurfacing ages were derived from crater statistics, these secondary ages were used to define the unit age rather than the base age. Using the methods described herein, we modelled ages that are consistent with the interpreted stratigraphy. Our derived model ages allow age assignments to be included in unit names. We discuss the limitations of using the crater dating technique for global-scale geological mapping. Finally, we present recommendations for the documentation and presentation of crater statistics in publications.

Spatiotemporal distribution of Holocene populations in North America

PubMed Central

Chaput, Michelle A.; Kriesche, Björn; Betts, Matthew; Martindale, Andrew; Kulik, Rafal; Schmidt, Volker; Gajewski, Konrad

2015-01-01

As the Cordilleran and Laurentide Ice Sheets retreated, North America was colonized by human populations; however, the spatial patterns of subsequent population growth are unclear. Temporal frequency distributions of aggregated radiocarbon (14C) dates are used as a proxy of population size and can be used to track this expansion. The Canadian Archaeological Radiocarbon Database contains more than 35,000 14C dates and is used in this study to map the spatiotemporal demographic changes of Holocene populations in North America at a continental scale for the past 13,000 y. We use the kernel method, which converts the spatial distribution of 14C dates into estimates of population density at 500-y intervals. The resulting maps reveal temporally distinct, dynamic patterns associated with paleodemographic trends that correspond well to genetic, archaeological, and ethnohistoric evidence of human occupation. These results have implications for hypothesizing and testing migration routes into and across North America as well as the relative influence of North American populations on the evolution of the North American ecosystem. PMID:26351683

Gender differences of the morphology of the distal femur and proximal tibia in a Korean population.

PubMed

Lim, Hong-Chul; Bae, Ji-Hoon; Yoon, Ji-Yeol; Kim, Seung-Ju; Kim, Jae-Gyoon; Lee, Jae-Moon

2013-01-01

We conducted this study to determine whether the sizes of distal femurs and proximal tibiae in Korean men and women are different, and to assess suitability of the sizes of prostheses currently used in Korea. We performed morphological analysis of proximal tibia and distal femur on 115 patients (56 male, 59 female) using MRI to investigate a gender difference. Tibial mediolateral dimension (tMAP), tibial medial anteroposterior dimension (tMAP), tibial lateral anteroposterior dimension (tLAP) femoral mediolateral dimension (fML), femoral medial anteroposterior dimension (fMAP), and femoral lateral anteroposterior dimension (fLAP) were measured. The ratio of tMAP and tLAP to tML (plateau aspect ratio, tAP/tML×100%), and that of fMAP and fLAP to fML (condylar aspect ratio, fAP/fML×100%) were calculated. The measurements were compared with the similar dimensions of four total knee implants currently used. The tML and tAP lengths showed a significant gender difference (P<0.05). The plateau aspect ratio (tMAP/tML) revealed a significant difference between male (0.74±0.05) and female (0.68±0.04, P<0.05). For morphotype of distal femur, males were found to have significantly large values (P<0.05) in the parameters, except for fLAP. With regards to the ratio of the ML width to the AP length, the women showed a narrower ML width than the men. Both genders were distributed within the range of the dimensions of the prostheses currently used prostheses. Korean population revealed that women have smaller dimensions than male counterparts. In both genders, a relatively small size of prostheses matches distal femur and proximal tibia better among the implants currently used in Korea. Copyright © 2012 Elsevier B.V. All rights reserved.

Participatory mapping of sex trade and enumeration of sex workers using capture-recapture methodology in Diego-Suarez, Madagascar.

PubMed

Kruse, Natalie; Behets, Frieda M-T F; Vaovola, Georgine; Burkhardt, Gillian; Barivelo, Texina; Amida, X; Dallabetta, Gina

2003-08-01

Capture-recapture methodology has been employed to estimate the size of hidden or difficult-to-reach human populations such as sex workers, homeless persons, and intravenous drug users. This study took place in the context of efforts to improve the quality of curative and preventive services for sexually transmitted infections offered to sex workers in Diego-Suarez, Madagascar in partnership with sex workers. The goal of this study was to better understand sex-trading practices, map out sex work sites, and estimate the size of a mobile sex-worker population in Diego-Suarez, Madagascar using methods that can be reproduced in other resource-poor settings. Forty sex workers were trained to function as field researchers. Key informants in designated neighborhoods were identified and interviewed. Basic maps of sex-trade sites were designed by hand. The number of sex workers in Diego-Suarez was estimated using capture-recapture methodology. An educational brochure was used to "capture" sex workers during a first phase, and "recapture" 2 weeks later. Most sex trade was street based and mobile. Capture-recapture methods estimated a total of 2684 sex workers (95% CI: 2588-2780) in Diego-Suarez, or approximately 12% of the 15- to 49-year-old female population in the city. Geographic mapping and capture-recapture proved to be low-cost and relatively easy to use techniques for counting a hard-to-reach population, such as female street-based sex workers. Sex workers can be capable fieldworkers, and their active participation in research concerning sex work should be considered whenever possible. A high proportion of women of reproductive age were found to engage in sex work, indicating that there is an urgent need to scale up sexually transmitted infection and HIV prevention activities targeting sex workers, their sexual partners, and the general population.

A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery

PubMed Central

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

Surface-material maps of Viking landing sites on Mars

NASA Technical Reports Server (NTRS)

Moore, H. J.; Keller, J. M.

1991-01-01

Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations.

PubMed Central

McKeigue, P M

1997-01-01

Where recent admixture has occurred between two populations that have different disease rates for genetic reasons, family-based association studies can be used to map the genes underlying these differences, if the ancestry of the alleles at each locus examined can be assigned to one of the two founding populations. This article explores the statistical power and design requirements of this approach. Markers suitable for assigning the ancestry of genomic regions could be defined by grouping alleles at closely spaced microsatellite loci into haplotypes, or generated by representational difference analysis. For a given relative risk between populations, the sample size required to detect a disease locus that accounts for this relative risk by linkage-disequilibrium mapping in an admixed population is not critically dependent on assumptions about genotype penetrances or allele frequencies. Using the transmission-disequilibrium test to search the genome for a locus that accounts for a relative risk of between 2 and 3 in a high-risk population, compared with a low-risk population, generally requires between 150 and 800 case-parent pairs of mixed descent. The optimal strategy is to conduct an initial study using markers spaced at < or = 10 cM with cases from the second and third generations of mixed descent, and then to map the disease loci more accurately in a subsequent study of a population with a longer history of admixture. This approach has greater statistical power than allele-sharing designs and has obvious applications to the genetics of hypertension, non-insulin-dependent diabetes, and obesity. PMID:8981962

Spatiotemporal analysis and mapping of oral cancer risk in changhua county (taiwan): an application of generalized bayesian maximum entropy method.

PubMed

Yu, Hwa-Lung; Chiang, Chi-Ting; Lin, Shu-De; Chang, Tsun-Kuo

2010-02-01

Incidence rate of oral cancer in Changhua County is the highest among the 23 counties of Taiwan during 2001. However, in health data analysis, crude or adjusted incidence rates of a rare event (e.g., cancer) for small populations often exhibit high variances and are, thus, less reliable. We proposed a generalized Bayesian Maximum Entropy (GBME) analysis of spatiotemporal disease mapping under conditions of considerable data uncertainty. GBME was used to study the oral cancer population incidence in Changhua County (Taiwan). Methodologically, GBME is based on an epistematics principles framework and generates spatiotemporal estimates of oral cancer incidence rates. In a way, it accounts for the multi-sourced uncertainty of rates, including small population effects, and the composite space-time dependence of rare events in terms of an extended Poisson-based semivariogram. The results showed that GBME analysis alleviates the noises of oral cancer data from population size effect. Comparing to the raw incidence data, the maps of GBME-estimated results can identify high risk oral cancer regions in Changhua County, where the prevalence of betel quid chewing and cigarette smoking is relatively higher than the rest of the areas. GBME method is a valuable tool for spatiotemporal disease mapping under conditions of uncertainty. 2010 Elsevier Inc. All rights reserved.

The Global Contribution of Secondary Craters on the Icy Satellites

NASA Astrophysics Data System (ADS)

Hoogenboom, T.; Johnson, K. E.; Schenk, P.

2014-12-01

At present, surface ages of bodies in the Outer Solar System are determined only from crater size-frequency distributions (a method dependent on an understanding of the projectile populations responsible for impact craters in these planetary systems). To derive accurate ages using impact craters, the impactor population must be understood. Impact craters in the Outer Solar System can be primary, secondary or sesquinary. The contribution of secondary craters to the overall population has recently become a "topic of interest." Our objective is to better understand the contribution of dispersed secondary craters to the small crater populations, and ultimately that of small comets to the projectile flux on icy satellites in general. We measure the diameters of obvious secondary craters (determined by e.g. irregular crater shape, small size, clustering) formed by all primary craters on Ganymede for which we have sufficiently high resolution data to map secondary craters. Primary craters mapped range from approximately 40 km to 210 km. Image resolution ranges from 45 to 440 m/pixel. Bright terrain on Ganymede is our primary focus. These resurfaced terrains have relatively low crater densities and serve as a basis for characterizing secondary populations as a function of primary size on an icy body for the first time. Although focusing on Ganymede, we also investigate secondary crater size, frequency, distribution, and formation, as well as secondary crater chain formation on icy satellites throughout the Saturnian and Jovian systems principally Rhea. We compare our results to similar studies of secondary cratering on the Moon and Mercury. Using Galileo and Voyager data, we have identified approximately 3,400 secondary craters on Ganymede. In some cases, we measured crater density as a function of distance from a primary crater. Because of the limitations of the Galileo data, it is necessary to extrapolate from small data sets to the global population of secondary craters. Nonetheless, we confirm that secondary craters on Ganymede have narrow size-frequency distributions and that they correlate with primary crater diameter. From these data we will evaluate the contribution of secondary craters over a range of crater diameters.

The Relationship between Mono-abundance and Mono-age Stellar Populations in the Milky Way Disk

NASA Astrophysics Data System (ADS)

Minchev, I.; Steinmetz, M.; Chiappini, C.; Martig, M.; Anders, F.; Matijevic, G.; de Jong, R. S.

2017-01-01

Studying the Milky Way disk structure using stars in narrow bins of [Fe/H] and [α/Fe] has recently been proposed as a powerful method to understand the Galactic thick and thin disk formation. It has been assumed so far that these mono-abundance populations (MAPs) are also coeval, or mono-age, populations. Here we study this relationship for a Milky Way chemodynamical model and show that equivalence between MAPs and mono-age populations exists only for the high-[α/Fe] tail, where the chemical evolution curves of different Galactic radii are far apart. At lower [α/Fe]-values an MAP is composed of stars with a range in ages, even for small observational uncertainties and a small MAP bin size. Due to the disk inside-out formation, for these MAPs younger stars are typically located at larger radii, which results in negative radial age gradients that can be as large as 2 Gyr kpc-1. Positive radial age gradients can result for MAPs at the lowest [α/Fe] and highest [Fe/H] end. Such variations with age prevent the simple interpretation of observations for which accurate ages are not available. Studying the variation with radius of the stellar surface density and scale height in our model, we find good agreement to recent analyses of the APOGEE red-clump (RC) sample when 1-4 Gyr old stars dominate (as expected for the RC). Our results suggest that the APOGEE data are consistent with a Milky Way model for which mono-age populations flare for all ages. We propose observational tests for the validity of our predictions and argue that using accurate age measurements, such as from asteroseismology, is crucial for putting constraints on Galactic formation and evolution.

Structural Variation Shapes the Landscape of Recombination in Mouse

PubMed Central

Morgan, Andrew P.; Gatti, Daniel M.; Najarian, Maya L.; Keane, Thomas M.; Galante, Raymond J.; Pack, Allan I.; Mott, Richard; Churchill, Gary A.; de Villena, Fernando Pardo-Manuel

2017-01-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from 6886 DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as 26% of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or 12% of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. PMID:28592499

Structural Variation Shapes the Landscape of Recombination in Mouse.

PubMed

Morgan, Andrew P; Gatti, Daniel M; Najarian, Maya L; Keane, Thomas M; Galante, Raymond J; Pack, Allan I; Mott, Richard; Churchill, Gary A; de Villena, Fernando Pardo-Manuel

2017-06-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from [Formula: see text] DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as [Formula: see text] of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or [Formula: see text] of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. Copyright © 2017 by the Genetics Society of America.

The impact of sample size on the reproducibility of voxel-based lesion-deficit mappings.

PubMed

Lorca-Puls, Diego L; Gajardo-Vidal, Andrea; White, Jitrachote; Seghier, Mohamed L; Leff, Alexander P; Green, David W; Crinion, Jenny T; Ludersdorfer, Philipp; Hope, Thomas M H; Bowman, Howard; Price, Cathy J

2018-07-01

This study investigated how sample size affects the reproducibility of findings from univariate voxel-based lesion-deficit analyses (e.g., voxel-based lesion-symptom mapping and voxel-based morphometry). Our effect of interest was the strength of the mapping between brain damage and speech articulation difficulties, as measured in terms of the proportion of variance explained. First, we identified a region of interest by searching on a voxel-by-voxel basis for brain areas where greater lesion load was associated with poorer speech articulation using a large sample of 360 right-handed English-speaking stroke survivors. We then randomly drew thousands of bootstrap samples from this data set that included either 30, 60, 90, 120, 180, or 360 patients. For each resample, we recorded effect size estimates and p values after conducting exactly the same lesion-deficit analysis within the previously identified region of interest and holding all procedures constant. The results show (1) how often small effect sizes in a heterogeneous population fail to be detected; (2) how effect size and its statistical significance varies with sample size; (3) how low-powered studies (due to small sample sizes) can greatly over-estimate as well as under-estimate effect sizes; and (4) how large sample sizes (N ≥ 90) can yield highly significant p values even when effect sizes are so small that they become trivial in practical terms. The implications of these findings for interpreting the results from univariate voxel-based lesion-deficit analyses are discussed. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

HapZipper: sharing HapMap populations just got easier.

PubMed

Chanda, Pritam; Elhaik, Eran; Bader, Joel S

2012-11-01

The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techniques is becoming an integral part of data production and analysis. The HapMap project is one of the largest public resources of human single-nucleotide polymorphisms (SNPs), characterizing over 3 million SNPs genotyped in over 1000 individuals. The standard format and biological properties of HapMap data suggest that a dedicated genetic compression method can outperform generic compression tools. We propose a compression methodology for genetic data by introducing HapZipper, a lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma. We demonstrate the usefulness of HapZipper by compressing HapMap 3 populations to <5% of their original sizes. HapZipper is freely downloadable from https://bitbucket.org/pchanda/hapzipper/downloads/HapZipper.tar.bz2.

North America Today: A Reproducible Atlas. 1995 Revised Edition.

ERIC Educational Resources Information Center

1995

This book contains illustrative maps, tables and graphs depicting North America's: size; population; resources; commodities; trade; languages; religions; cities; environment; food and agriculture; schooling; jobs; energy; industry, demographic statistics; women; aspects of government; and territorial disputes. Sections of the book include: (1)…

Natural Selection in the Great Apes

PubMed Central

Cagan, Alexander; Theunert, Christoph; Laayouni, Hafid; Santpere, Gabriel; Pybus, Marc; Casals, Ferran; Prüfer, Kay; Navarro, Arcadi; Marques-Bonet, Tomas; Bertranpetit, Jaume; Andrés, Aida M.

2016-01-01

Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size. Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments. Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species. We also identify loci with evidence of positive selection across several lineages. Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes. Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context. The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurl.com/nf8qmzh. PMID:27795229

Linkage mapping and molecular diversity at the flower sex locus in wild and cultivated grapevine reveal a prominent SSR haplotype in hermaphrodite plants.

PubMed

Battilana, Juri; Lorenzi, Silvia; Moreira, Flavia M; Moreno-Sanz, Paula; Failla, Osvaldo; Emanuelli, Francesco; Grando, M Stella

2013-07-01

Cultivars used for wine and table grape have self-fertile hermaphrodite flowers whereas wild European vines and American and Asian species are dioecious, having either male or female flowers. Consistent with previous studies, the flower sex trait was mapped as a single major locus on chromosome 2 based on a pure Vitis vinifera population segregating for hermaphrodite and female progeny, and a hybrid population producing all three flower sex types. The sex locus was placed between the same SSR and SNP markers on both genetic maps, although abnormal segregation hampered to fine map the genomic region. From a total of 55 possible haplotypes inferred for three SSR markers around the sex locus, in a population of 132 V. sylvestris accessions and 171 V. vinifera cultivars, one of them accounted for 66 % of the hermaphrodite individuals and may be the result of domestication. Specific size variants of the VVIB23 microsatellite sequence within the 3'-UTR of a putative YABBY1 gene were found to be statistically significantly associated with the sex alleles M, H and f; these markers can provide assistance in defining the status of wild grapevine germplasm.

The Population Genomics of Repeated Evolution in the Blind Cavefish Astyanax mexicanus

PubMed Central

Bradic, Martina; Teotónio, Henrique; Borowsky, Richard L.

2013-01-01

Distinct populations of Astyanax mexicanus cavefish offer striking examples of repeatable convergence or parallelism in their independent evolutions from surface to cave phenotypes. However, the extent to which the repeatability of evolution occurred at the genetic level remains poorly understood. To address this, we first characterized the genetic diversity of 518 single-nucleotide polymorphisms (SNPs), obtained through RAD tag sequencing and distributed throughout the genome, in seven cave and three groups of surface populations. The cave populations represented two distinct lineages (old and new). Thirty-one SNPs were significantly differentiated between surface and old cave populations, two SNPs were differentiated between surface and new cave populations, and 44 SNPs were significantly differentiated in both old and new cave populations. In addition, we determined whether these SNPs map to the same locations of previously described quantitative trait loci (QTL) between surface and cave populations. A total of 25 differentiated SNPs co-map with several QTL, such as one containing a fibroblast growth factor gene (Fgf8) involved in eye development and lens size. Further, the identity of many SNPs that co-mapped with QTL was the same in independently derived cave populations. These conclusions were further confirmed by haplotype analyses of SNPs within QTL regions. Our findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment. PMID:23927992

Genetic dissection and validation of candidate genes for flag leaf size in rice (Oryza sativa L.).

PubMed

Tang, Xinxin; Gong, Rong; Sun, Wenqiang; Zhang, Chaopu; Yu, Sibin

2018-04-01

Two major loci with functional candidate genes were identified and validated affecting flag leaf size, which offer desirable genes to improve leaf architecture and photosynthetic capacity in rice. Leaf size is a major determinant of plant architecture and yield potential in crops. However, the genetic and molecular mechanisms regulating leaf size remain largely elusive. In this study, quantitative trait loci (QTLs) for flag leaf length and flag leaf width in rice were detected with high-density single nucleotide polymorphism genotyping of a chromosomal segment substitution line (CSSL) population, in which each line carries one or a few chromosomal segments from the japonica cultivar Nipponbare in a common background of the indica variety Zhenshan 97. In total, 14 QTLs for flag leaf length and nine QTLs for flag leaf width were identified in the CSSL population. Among them, qFW4-2 for flag leaf width was mapped to a 37-kb interval, with the most likely candidate gene being the previously characterized NAL1. Another major QTL for both flag leaf width and length was delimited by substitution mapping to a small region of 13.5 kb that contains a single gene, Ghd7.1. Mutants of Ghd7.1 generated using CRISPR/CAS9 approach showed reduced leaf size. Allelic variation analyses also validated Ghd7.1 as a functional candidate gene for leaf size, photosynthetic capacity and other yield-related traits. These results provide useful genetic information for the improvement of leaf size and yield in rice breeding programs.

Explosive genetic evidence for explosive human population growth

PubMed Central

Gao, Feng; Keinan, Alon

2016-01-01

The advent of next-generation sequencing technology has allowed the collection of vast amounts of genetic variation data. A recurring discovery from studying larger and larger samples of individuals had been the extreme, previously unexpected, excess of very rare genetic variants, which has been shown to be mostly due to the recent explosive growth of human populations. Here, we review recent literature that inferred recent changes in population size in different human populations and with different methodologies, with many pointing to recent explosive growth, especially in European populations for which more data has been available. We also review the state-of-the-art methods and software for the inference of historical population size changes that lead to these discoveries. Finally, we discuss the implications of recent population growth on personalized genomics, on purifying selection in the non-equilibrium state it entails and, as a consequence, on the genetic architecture underlying complex disease and the performance of mapping methods in discovering rare variants that contribute to complex disease risk. PMID:27710906

Increase of Elderly Population in the Rainstorm Hazard Areas of China.

PubMed

Liang, Pujun; Xu, Wei; Ma, Yunjia; Zhao, Xiujuan; Qin, Lianjie

2017-08-26

In light of global warming, increased extreme precipitation events have enlarged the population exposed to floods to some extent. Extreme precipitation risk assessments are of great significance in China and allow for the response to climate change and mitigation of risks to the population. China is one of the countries most influenced by climate change and has unique national population conditions. The influence of extreme precipitation depends on the degree of exposure and vulnerability of the population. Accurate assessments of the population exposed to rising rainstorm trends are crucial to mapping extreme precipitation risks. Studying the population exposed to rainstorm hazard areas (RSHA) at the microscale is extremely urgent, due to the local characteristics of extreme precipitation events and regional diversity of the population. The spatial distribution of population density was mapped based on the national population census data from China in 1990, 2000 and 2010. RSHA were also identified using precipitation data from 1975-2015 in China, and the rainstorm tendency values were mapped using GIS in this paper. The spatial characteristics of the rainstorm tendencies were then analyzed. Finally, changes in the population in the RSHA are discussed. The results show that the extreme precipitation trends are increasing in southeastern China. From 1990 to 2010, the population in RSHA increased by 110 million, at a rate of 14.6%. The elderly in the region increased by 38 million at a rate of 86.4%. Studying the size of the population exposed to rainstorm hazards at the county scale can provide scientific evidence for developing disaster prevention and mitigation strategies from the bottom up.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes.

PubMed

Mok, Calvin A; Au, Vinci; Thompson, Owen A; Edgley, Mark L; Gevirtzman, Louis; Yochem, John; Lowry, Joshua; Memar, Nadin; Wallenfang, Matthew R; Rasoloson, Dominique; Bowerman, Bruce; Schnabel, Ralf; Seydoux, Geraldine; Moerman, Donald G; Waterston, Robert H

2017-10-01

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C . elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2 We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures. Copyright © 2017 by the Genetics Society of America.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes

PubMed Central

Mok, Calvin A.; Au, Vinci; Thompson, Owen A.; Edgley, Mark L.; Gevirtzman, Louis; Yochem, John; Lowry, Joshua; Memar, Nadin; Wallenfang, Matthew R.; Rasoloson, Dominique; Bowerman, Bruce; Schnabel, Ralf; Seydoux, Geraldine; Moerman, Donald G.; Waterston, Robert H.

2017-01-01

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2. We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures. PMID:28827289

The genetics of rhizosheath size in a multiparent mapping population of wheat.

PubMed

Delhaize, Emmanuel; Rathjen, Tina M; Cavanagh, Colin R

2015-08-01

Rhizosheaths comprise soil that adheres to plant roots and, in some species, are indicative of root hair length. In this study, the genetics of rhizosheath size in wheat was investigated by screening the progeny of multiparent advanced generation intercrosses (MAGIC). Two MAGIC populations were screened for rhizosheath size using a high throughput method. One MAGIC population was developed from intercrosses between four parents (4-way) and the other from intercrosses between eight parents (8-way). Transgressive segregation for rhizosheath size was observed in both the 4-way and 8-way MAGIC populations. A quantitative trait loci (QTL) analysis of the 4-way population identified six major loci located on chromosomes 2B, 4D, 5A, 5B, 6A, and 7A together accounting for 42% of the variation in rhizosheath size. Rhizosheath size was strongly correlated with root hair length and was robust across different soil types in the absence of chemical constraints. Rhizosheath size in the MAGIC populations was a reliable surrogate for root hair length and, therefore, the QTL identified probably control root hair elongation. Members of the basic helix-loop-helix family of transcription factors have previously been identified to regulate root hair length in Arabidopsis and rice. Since several wheat members of the basic helix-loop-helix family of genes are located within or near the QTL, these genes are candidates for controlling the long root hair trait. The QTL for rhizosheath size identified in this study provides the opportunity to implement marker-assisted selection to increase root hair length for improved phosphate acquisition in wheat. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays).

PubMed

Wang, Baobao; Liu, Han; Liu, Zhipeng; Dong, Xiaomei; Guo, Jinjie; Li, Wei; Chen, Jing; Gao, Chi; Zhu, Yanbin; Zheng, Xinmei; Chen, Zongliang; Chen, Jian; Song, Weibin; Hauck, Andrew; Lai, Jinsheng

2018-01-18

Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

Fast and Accurate Construction of Ultra-Dense Consensus Genetic Maps Using Evolution Strategy Optimization

PubMed Central

Mester, David; Ronin, Yefim; Schnable, Patrick; Aluru, Srinivas; Korol, Abraham

2015-01-01

Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time. PMID:25867943

The Middle East Today: An Atlas of Reproducible Pages. Revised Edition.

ERIC Educational Resources Information Center

World Eagle, Inc., Wellesley, MA.

This book contains blank outline maps of the continent/region, tables and graphics depicting the size, population, resources and water, commodities , trade, cities, languages, religions, industry, energy, food and agriculture, demographic statistics, aspects of the national economies, and aspects of the national governments of the Middle East.…

Mapping by admixture linkage disequilibrium in human populations: Limits and guidelines

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

Stephens, J.C.; Briscoe, D.; O`Brien, S.J.

1994-10-01

Certain human hereditary conditions, notably those with low penetrance and those which require an environmental event such as infectious disease exposure, are difficult to localize in pedigree analysis, because of uncertainty in the phenotype of an affected patient`s relatives. An approach to locating these genes in human cohort studies would be to use association analysis, which depends on linkage disequilibrium of flanking polymorphic DNA markers. In theory, a high degree of linkage disequilibrium between genes separated by 10-20 cM will be generated and persist in populations that have a history of recent (3-20 generations ago) admixture between genetically differentiated racialmore » groups, such as has occurred in African Americans and Hispanic populations. We have conducted analytic and computer simulations to quantify the effect of genetic, genomic, and population parameters that affect the amount and ascertainment of linkage disequilibrium in populations with a history of genetic admixture. Our goal is to thoroughly explore the ranges of all relevant parameters or factors (e.g., sample size and degree of genetic differentiation between populations) that may be involved in gene localization studies, in hopes of prescribing guidelines for an efficient mapping strategy. The results provide reasonable limits on sample size (200-300 patients), marker number (200-300 in 20-cM intervals), and allele differentiation (loci with allele frequency difference of {ge}.3 between admixed parent populations) to produce an efficient approach (>95% ascertainment) for locating genes not easily tracked in human pedigrees. 321 refs., 8 figs., 7 tabs.« less

Targeted Recombinant Progeny: a design for ultra-high resolution mapping of Quantitative Trait Loci in crosses between inbred or pure lines.

PubMed

Heifetz, Eliyahu M; Soller, Morris

2015-07-07

High-resolution mapping of the loci (QTN) responsible for genetic variation in quantitative traits is essential for positional cloning of candidate genes, and for effective marker assisted selection. The confidence interval (QTL) flanking the point estimate of QTN-location is proportional to the number of individuals in the mapping population carrying chromosomes recombinant in the given interval. Consequently, many designs for high resolution QTN mapping are based on increasing the proportion of recombinants in the mapping population. The "Targeted Recombinant Progeny" (TRP) design is a new design for high resolution mapping of a target QTN in crosses between pure, or inbred lines. It is a three-generation procedure generating a large number of recombinant individuals within a QTL previously shown to contain a QTN. This is achieved by having individuals that carry chromosomes recombinant across the target QTL interval as parents of a large mapping population; most of whom will therefore carry recombinant chromosomes targeted to the given QTL. The TRP design is particularly useful for high resolution mapping of QTN that differentiate inbred or pure lines, and hence are not amenable to high resolution mapping by genome-wide association tests. In the absence of residual polygenic variation, population sizes required for achieving given mapping resolution by the TRP-F2 design relative to a standard F2 design ranged from 0.289 for a QTN with standardized allele substitution effect = 0.2, mapped to an initial QTL of 0.2 Morgan to 0.041 for equivalent QTN mapped to an initial QTL of 0.02 M. In the presence of residual polygenic variation, the relative effectiveness of the TRP design ranges from 1.068 to 0.151 for the same initial QTL intervals and QTN effect. Thus even in the presence of polygenic variation, the TRP can still provide major savings. Simulation showed that mapping by TRP should be based on 30-50 markers spanning the initial interval; and on at least 50 or more G2 families representing this number of recombination points,. The TRP design can be an effective procedure for achieving high and ultra-high mapping resolution of a target QTN previously mapped to a known confidence interval (QTL).

Rock magnetic properties estimated from coercivity - blocking temperature diagram: application to recent volcanic rocks

NASA Astrophysics Data System (ADS)

Terada, T.; Sato, M.; Mochizuki, N.; Yamamoto, Y.; Tsunakawa, H.

2013-12-01

Magnetic properties of ferromagnetic minerals generally depend on their chemical composition, crystal structure, size, and shape. In the usual paleomagnetic study, we use a bulk sample which is the assemblage of magnetic minerals showing broad distributions of various magnetic properties. Microscopic and Curie-point observations of the bulk sample enable us to identify the constituent magnetic minerals, while other measurements, for example, stepwise thermal and/or alternating field demagnetizations (ThD, AFD) make it possible to estimate size, shape and domain state of the constituent magnetic grains. However, estimation based on stepwise demagnetizations has a limitation that magnetic grains with the same coercivity Hc (or blocking temperature Tb) can be identified as the single population even though they could have different size and shape. Dunlop and West (1969) carried out mapping of grain size and coercivity (Hc) using pTRM. However, it is considered that their mapping method is basically applicable to natural rocks containing only SD grains, since the grain sizes are estimated on the basis of the single domain theory (Neel, 1949). In addition, it is impossible to check thermal alteration due to laboratory heating in their experiment. In the present study we propose a new experimental method which makes it possible to estimate distribution of size and shape of magnetic minerals in a bulk sample. The present method is composed of simple procedures: (1) imparting ARM to a bulk sample, (2) ThD at a certain temperature, (3) stepwise AFD on the remaining ARM, (4) repeating the steps (1) ~ (3) with ThD at elevating temperatures up to the Curie temperature of the sample. After completion of the whole procedures, ARM spectra are calculated and mapped on the HC-Tb plane (hereafter called HC-Tb diagram). We analyze the Hc-Tb diagrams as follows: (1) For uniaxial SD populations, theoretical curve for a certain grain size (or shape anisotropy) is drawn on the Hc-Tb diagram. The curves are calculated using the single domain theory, since coercivity and blocking temperature of uniaxial SD grains can be expressed as a function of size and shape. (2) Boundary between SD and MD grains are calculated and drawn on the Hc-Tb diagram according to the theory by Butler and Banerjee (1975). (3) Theoretical predictions by (1) and (2) are compared with the obtained ARM spectra to estimate quantitive distribution of size, shape and domain state of magnetic grains in the sample. This mapping method has been applied to three samples: Hawaiian basaltic lava extruded in 1995, Ueno basaltic lava formed during Matsuyama chron, and Oshima basaltic lava extruded in 1986. We will discuss physical states of magnetic grains (size, shape, domain state, etc.) and their possible origins.

Satellite-aided evaluation of population exposure to air pollution

USGS Publications Warehouse

Todd, William J.; George, Anthony J.; Bryant, Nevin A.

1979-01-01

The Clean Air Act Amendments of 1977 set schedules for states to implement regional, spatial assessments of air quality impacts. Accordingly, the U.S. Environmental Protection Agency recently published guidelines for quantifying population exposure to adverse air quality impact by using air quality and population data by census tracts. Our research complements the EPA guidelines in that it demonstrates the ability to determine population exposure to air pollution through computer processing that utilizes Landsat satellite-derived land use information. Three variables-a 1985 estimate of total suspended particulates for 2-km2 grid cells, Landsat-derived residential land cover data for 0.45-ha cells, and population totals for census tracts-were spatially registered and cross-tabulated to produce tabular and map products illustrating relative air quality exposure for residential population by 2-km2 cells. It would cost $20,000 to replicate our analysis for an area similar in size to the 4000-km2 Portland area. Once completed, the spatially fine, computer-compatible air quality and population data are amenable to the timely and efficient generation of population-at-risk tabular and map information on a continuous or periodic basis.

A Picea abies Linkage Map Based on SNP Markers Identifies QTLs for Four Aspects of Resistance to Heterobasidion parviporum Infection

PubMed Central

Lind, Mårten; Källman, Thomas; Chen, Jun; Ma, Xiao-Fei; Bousquet, Jean; Morgante, Michele; Zaina, Giusi; Karlsson, Bo; Elfstrand, Malin; Lascoux, Martin; Stenlid, Jan

2014-01-01

A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor. PMID:25036209

Mapping of neuron soma size as an effective approach to delineate differences between neural populations.

PubMed

Lingley, Alexander J; Bowdridge, Joshua C; Farivar, Reza; Duffy, Kevin R

2018-04-30

A single histological marker applied to a slice of tissue often reveals myriad cytoarchitectonic characteristics that can obscure differences between neuron populations targeted for study. Isolation and measurement of a single feature from the tissue is possible through a variety of approaches, however, visualizing the data numerically or through graphs alone can preclude being able to identify important features and effects that are not obvious from direct observation of the tissue. We demonstrate an efficient, effective, and robust approach to quantify and visualize cytoarchitectural features in histologically prepared brain sections. We demonstrate that this approach is able to reveal small differences between populations of neurons that might otherwise have gone undiscovered. We used stereological methods to record the cross-sectional soma area and in situ position of neurons within sections of the cat, monkey, and human visual system. The two-dimensional coordinate of every measured cell was used to produce a scatter plot that recapitulated the natural spatial distribution of cells, and each point in the plot was color-coded according to its respective soma area. The final graphic display was a multi-dimensional map of neuron soma size that revealed subtle differences across neuron aggregations, permitted delineation of regional boundaries, and identified small differences between populations of neurons modified by a period of sensory deprivation. This approach to collecting and displaying cytoarchitectonic data is simple, efficient, and provides a means of investigating small differences between neuron populations. Copyright © 2018. Published by Elsevier B.V.

Using Genealogical Mapping and Genetic Neighborhood Sizes to Quantify Dispersal Distances in the Neotropical Passerine, the Black-Capped Vireo

PubMed Central

Athrey, Giridhar; Lance, Richard F.; Leberg, Paul L.

2015-01-01

Dispersal is a key demographic process, ultimately responsible for genetic connectivity among populations. Despite its importance, quantifying dispersal within and between populations has proven difficult for many taxa. Even in passerines, which are among the most intensely studied, individual movement and its relation to gene flow remains poorly understood. In this study we used two parallel genetic approaches to quantify natal dispersal distances in a Neotropical migratory passerine, the black-capped vireo. First, we employed a strategy of sampling evenly across the landscape coupled with parentage assignment to map the genealogical relationships of individuals across the landscape, and estimate dispersal distances; next, we calculated Wright’s neighborhood size to estimate gene dispersal distances. We found that a high percentage of captured individuals were assigned at short distances within the natal population, and males were assigned to the natal population more often than females, confirming sex-biased dispersal. Parentage-based dispersal estimates averaged 2400m, whereas gene dispersal estimates indicated dispersal distances ranging from 1600–4200 m. Our study was successful in quantifying natal dispersal distances, linking individual movement to gene dispersal distances, while also providing a detailed look into the dispersal biology of Neotropical passerines. The high-resolution information was obtained with much reduced effort (sampling only 20% of breeding population) compared to mark-resight approaches, demonstrating the potential applicability of parentage-based approaches for quantifying dispersal in other vagile passerine species. PMID:26461257

Disease limits populations: plague and black-tailed prairie dogs

USGS Publications Warehouse

Cully, Jack F.; Johnson, T.; Collinge, S.K.; Ray, C.

2010-01-01

Plague is an exotic vector-borne disease caused by the bacterium Yersinia pestis that causes mortality rates approaching 100% in black-tailed prairie dogs (Cynomys ludovicianus). We mapped the perimeter of the active portions of black-tailed prairie dog colonies annually between 1999 and 2005 at four prairie dog colony complexes in areas with a history of plague, as well as at two complexes that were located outside the distribution of plague at the time of mapping and had therefore never been affected by the disease. We hypothesized that the presence of plague would significantly reduce overall black-tailed prairie dog colony area, reduce the sizes of colonies on these landscapes, and increase nearest-neighbor distances between colonies. Within the region historically affected by plague, individual colonies were smaller, nearest-neighbor distances were greater, and the proportion of potential habitat occupied by active prairie dog colonies was smaller than at plague-free sites. Populations that endured plague were composed of fewer large colonies (>100 ha) than populations that were historically plague free. We suggest that these differences among sites in colony size and isolation may slow recolonization after extirpation. At the same time, greater intercolony distances may also reduce intercolony transmission of pathogens. Reduced transmission among smaller and more distant colonies may ultimately enhance long-term prairie dog population persistence in areas where plague is present.

Disease limits populations: plague and black-tailed prairie dogs.

PubMed

Cully, Jack F; Johnson, Tammi L; Collinge, Sharon K; Ray, Chris

2010-01-01

Plague is an exotic vector-borne disease caused by the bacterium Yersinia pestis that causes mortality rates approaching 100% in black-tailed prairie dogs (Cynomys ludovicianus). We mapped the perimeter of the active portions of black-tailed prairie dog colonies annually between 1999 and 2005 at four prairie dog colony complexes in areas with a history of plague, as well as at two complexes that were located outside the distribution of plague at the time of mapping and had therefore never been affected by the disease. We hypothesized that the presence of plague would significantly reduce overall black-tailed prairie dog colony area, reduce the sizes of colonies on these landscapes, and increase nearest-neighbor distances between colonies. Within the region historically affected by plague, individual colonies were smaller, nearest-neighbor distances were greater, and the proportion of potential habitat occupied by active prairie dog colonies was smaller than at plague-free sites. Populations that endured plague were composed of fewer large colonies (>100 ha) than populations that were historically plague free. We suggest that these differences among sites in colony size and isolation may slow recolonization after extirpation. At the same time, greater intercolony distances may also reduce intercolony transmission of pathogens. Reduced transmission among smaller and more distant colonies may ultimately enhance long-term prairie dog population persistence in areas where plague is present.

Disease Limits Populations: Plague and Black-Tailed Prairie Dogs

PubMed Central

Johnson, Tammi L.; Collinge, Sharon K.; Ray, Chris

2010-01-01

Abstract Plague is an exotic vector-borne disease caused by the bacterium Yersinia pestis that causes mortality rates approaching 100% in black-tailed prairie dogs (Cynomys ludovicianus). We mapped the perimeter of the active portions of black-tailed prairie dog colonies annually between 1999 and 2005 at four prairie dog colony complexes in areas with a history of plague, as well as at two complexes that were located outside the distribution of plague at the time of mapping and had therefore never been affected by the disease. We hypothesized that the presence of plague would significantly reduce overall black-tailed prairie dog colony area, reduce the sizes of colonies on these landscapes, and increase nearest-neighbor distances between colonies. Within the region historically affected by plague, individual colonies were smaller, nearest-neighbor distances were greater, and the proportion of potential habitat occupied by active prairie dog colonies was smaller than at plague-free sites. Populations that endured plague were composed of fewer large colonies (>100 ha) than populations that were historically plague free. We suggest that these differences among sites in colony size and isolation may slow recolonization after extirpation. At the same time, greater intercolony distances may also reduce intercolony transmission of pathogens. Reduced transmission among smaller and more distant colonies may ultimately enhance long-term prairie dog population persistence in areas where plague is present. PMID:20158327

Semi-automated Approach to Mapping Sub-hectare Agricultural Fields using Very High Resolution Data in a High-Performance Computing Environment

NASA Astrophysics Data System (ADS)

Wooten, M.; Neigh, C. S. R.; Carroll, M.; McCarty, J. L.

2017-12-01

In areas susceptible to drought such as sub-Saharan Africa, Crop Area (CA) and agricultural mapping have become increasingly important as strain on natural ecosystems increases. In Ethiopia alone, the population has grown four-fold in the last 70 years, and rapidly growing human populations bring added stress to ecosystems as more wildlands are converted to pastures and subsistence agriculture. Monitoring change in agriculture is one of the more essential goals of famine early warning systems. However, due to the sub-hectare size of rainfed agricultural fields in regions such as Tigray, Ethiopia, moderate resolution satellite imagery is insufficient at capturing these smallholder farms. Thanks to the increasing density of observations and ease of access to very high resolution (VHR) data, we have developed a generalized method for mapping CA with VHR data and have used this to generate wall-to-wall CA map for the entire Tigray region and samples in Myanmar, Senegal, and Vietnam. Here we present the methodology and early results as well as potential future applications.

Stochastic Evolution Dynamic of the Rock-Scissors-Paper Game Based on a Quasi Birth and Death Process

NASA Astrophysics Data System (ADS)

Yu, Qian; Fang, Debin; Zhang, Xiaoling; Jin, Chen; Ren, Qiyu

2016-06-01

Stochasticity plays an important role in the evolutionary dynamic of cyclic dominance within a finite population. To investigate the stochastic evolution process of the behaviour of bounded rational individuals, we model the Rock-Scissors-Paper (RSP) game as a finite, state dependent Quasi Birth and Death (QBD) process. We assume that bounded rational players can adjust their strategies by imitating the successful strategy according to the payoffs of the last round of the game, and then analyse the limiting distribution of the QBD process for the game stochastic evolutionary dynamic. The numerical experiments results are exhibited as pseudo colour ternary heat maps. Comparisons of these diagrams shows that the convergence property of long run equilibrium of the RSP game in populations depends on population size and the parameter of the payoff matrix and noise factor. The long run equilibrium is asymptotically stable, neutrally stable and unstable respectively according to the normalised parameters in the payoff matrix. Moreover, the results show that the distribution probability becomes more concentrated with a larger population size. This indicates that increasing the population size also increases the convergence speed of the stochastic evolution process while simultaneously reducing the influence of the noise factor.

Stochastic Evolution Dynamic of the Rock-Scissors-Paper Game Based on a Quasi Birth and Death Process.

PubMed

Yu, Qian; Fang, Debin; Zhang, Xiaoling; Jin, Chen; Ren, Qiyu

2016-06-27

Stochasticity plays an important role in the evolutionary dynamic of cyclic dominance within a finite population. To investigate the stochastic evolution process of the behaviour of bounded rational individuals, we model the Rock-Scissors-Paper (RSP) game as a finite, state dependent Quasi Birth and Death (QBD) process. We assume that bounded rational players can adjust their strategies by imitating the successful strategy according to the payoffs of the last round of the game, and then analyse the limiting distribution of the QBD process for the game stochastic evolutionary dynamic. The numerical experiments results are exhibited as pseudo colour ternary heat maps. Comparisons of these diagrams shows that the convergence property of long run equilibrium of the RSP game in populations depends on population size and the parameter of the payoff matrix and noise factor. The long run equilibrium is asymptotically stable, neutrally stable and unstable respectively according to the normalised parameters in the payoff matrix. Moreover, the results show that the distribution probability becomes more concentrated with a larger population size. This indicates that increasing the population size also increases the convergence speed of the stochastic evolution process while simultaneously reducing the influence of the noise factor.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

PubMed

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

2018-01-01

Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations

PubMed Central

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert

2018-01-01

Background Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. Materials and methods A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39). Results The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. Conclusion This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data. PMID:29351563

The United States Today: An Atlas of Reproducible Pages.

ERIC Educational Resources Information Center

World Eagle, Inc., Wellesley, MA.

Black and white maps, graphs and tables that may be reproduced are presented in this volume focusing on the United States. Some of the features of the United States depicted are: size, population, agriculture and resources, manufactures, trade, citizenship, employment, income, poverty, the federal budget, energy, health, education, crime, and the…

The genetic and developmental basis of an exaggerated craniofacial trait in East African cichlids.

PubMed

Concannon, Moira R; Albertson, R Craig

2015-12-01

The evolution of an exaggerated trait can lead to a novel morphology that allows organisms to exploit new niches. The molecular bases of such phenotypes can reveal insights into the evolution of unique traits. Here, we investigate a rare morphological innovation in modern haplochromine cichlids, a flap of fibrous tissue that causes a pronounced projection of the snout, which is limited to a single genus (Labeotropheus) of Lake Malawi cichlids. We compare flap size in our focal species L. fuelleborni (LF) to homologous landmarks in other closely related cichlid species that show a range of ecological overlap with LF, and demonstrate that variation in flap size is discontinuous among Malawi cichlid species. We demonstrate further that flap development in LF begins at early juvenile stages, and scales allometrically with body size. We then used an F2 hybrid mapping population, derived via crossing LF to a close ecological competitor that lacks this trait, Tropheops "red cheek" (TRC), to identify quantitative trait loci (QTL) that underlie flap development. In all, we identified four loci associated with variation in flap size, and for each the LF allele contributed to a larger flap. We next cross-referenced our QTL map with population genomic data, comparing natural populations of LF and TRC, to identify divergent polymorphisms within each QTL interval. Candidate genes for flap development are discussed. Together, these data indicate a relatively simple and tractable genetic basis for this morphological innovation, which is consistent with its apparently sudden and saltatory evolutionary history. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 662-670, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Is the Cortical Deficit in Amblyopia Due to Reduced Cortical Magnification, Loss of Neural Resolution, or Neural Disorganization?

PubMed

Clavagnier, Simon; Dumoulin, Serge O; Hess, Robert F

2015-11-04

The neural basis of amblyopia is a matter of debate. The following possibilities have been suggested: loss of foveal cells, reduced cortical magnification, loss of spatial resolution of foveal cells, and topographical disarray in the cellular map. To resolve this we undertook a population receptive field (pRF) functional magnetic resonance imaging analysis in the central field in humans with moderate-to-severe amblyopia. We measured the relationship between averaged pRF size and retinal eccentricity in retinotopic visual areas. Results showed that cortical magnification is normal in the foveal field of strabismic amblyopes. However, the pRF sizes are enlarged for the amblyopic eye. We speculate that the pRF enlargement reflects loss of cellular resolution or an increased cellular positional disarray within the representation of the amblyopic eye. The neural basis of amblyopia, a visual deficit affecting 3% of the human population, remains a matter of debate. We undertook the first population receptive field functional magnetic resonance imaging analysis in participants with amblyopia and compared the projections from the amblyopic and fellow normal eye in the visual cortex. The projection from the amblyopic eye was found to have a normal cortical magnification factor, enlarged population receptive field sizes, and topographic disorganization in all early visual areas. This is consistent with an explanation of amblyopia as an immature system with a normal complement of cells whose spatial resolution is reduced and whose topographical map is disordered. This bears upon a number of competing theories for the psychophysical defect and affects future treatment therapies. Copyright © 2015 the authors 0270-6474/15/3514740-16$15.00/0.

Critical fluctuations near the pitchfork bifurcations of period-doubling maps

NASA Astrophysics Data System (ADS)

Noble, Andrew; Karimeddiny, Saba; Hastings, Alan; Machta, Jonathan

2015-03-01

Period-doubling maps, such as the logistic map, have been a subject of intense study in both physics and biology. The period-doubling route to chaos proceeds through a sequence of supercritical pitchfork bifurcations. Here, motivated by applications to population ecology, we investigate the asymptotic behavior of period-doubling bifurcations subject to environmental or demographic noise. We demonstrate, analytically, that fluctuations in the vicinity of each noisy pitchfork bifurcation are described by finite-size mean-field theory. Our results establish an exact correspondence between the bifurcations of far-from-equilibrium systems and the mean-field critical phenomena of equilibrium systems. This material is based upon work supported by the National Science Foundation under INSPIRE Grant No. 1344187.

The Diversity Outbred Mouse Population

PubMed Central

Churchill, Gary A.; Gatti, Daniel M.; Munger, Steven C.; Svenson, Karen L.

2012-01-01

The Diversity Outbred (DO) population is a heterogeneous stock derived from the same eight founder strains as the Collaborative Cross (CC) inbred strains. Genetically heterogeneous DO mice display a broad range of phenotypes. Natural levels of heterozygosity provide genetic buffering and, as a result, DO mice are robust and breed well. Genetic mapping analysis in the DO presents new challenges and opportunities. Specialized algorithms are required to reconstruct haplotypes from high-density SNP array data. The eight founder haplotypes can be combined into 36 possible diplotypes, which must be accommodated in QTL mapping analysis. Population structure of the DO must be taken into account here. Estimated allele effects of 8 founder haplotypes provide information that is not available in two-parent crosses and can dramatically reduce the number of candidate loci. Allele effects can also distinguish chance co-location of QTL from pleiotropy – which provides a basis for establishing causality in expression QTL studies. We recommended sample sizes of 200 to 800 mice for QTL mapping studies, larger than for traditional crosses. The CC inbred strains provide a resource for independent validation of DO mapping results. Genetic heterogeneity of the DO can provide a powerful advantage in our ability to generalize conclusions to other genetically diverse populations. Genetic diversity can also help to avoid the pitfall of identifying an idiosyncratic reaction that occurs only in a limited genetic context. Informatics tools and data resources associated with the CC, the DO, and their founder strains are developing rapidly. We anticipate a flood of new results to follow as our community begins to adopt and utilize these new genetic resource populations. PMID:22892839

Assessing genome-wide copy number variation in the Han Chinese population.

PubMed

Lu, Jianqi; Lou, Haiyi; Fu, Ruiqing; Lu, Dongsheng; Zhang, Feng; Wu, Zhendong; Zhang, Xi; Li, Changhua; Fang, Baijun; Pu, Fangfang; Wei, Jingning; Wei, Qian; Zhang, Chao; Wang, Xiaoji; Lu, Yan; Yan, Shi; Yang, Yajun; Jin, Li; Xu, Shuhua

2017-10-01

Copy number variation (CNV) is a valuable source of genetic diversity in the human genome and a well-recognised cause of various genetic diseases. However, CNVs have been considerably under-represented in population-based studies, particularly the Han Chinese which is the largest ethnic group in the world. To build a representative CNV map for the Han Chinese population. We conducted a genome-wide CNV study involving 451 male Han Chinese samples from 11 geographical regions encompassing 28 dialect groups, representing a less-biased panel compared with the currently available data. We detected CNVs by using 4.2M NimbleGen comparative genomic hybridisation array and whole-genome deep sequencing of 51 samples to optimise the filtering conditions in CNV discovery. A comprehensive Han Chinese CNV map was built based on a set of high-quality variants (positive predictive value >0.8, with sizes ranging from 369 bp to 4.16 Mb and a median of 5907 bp). The map consists of 4012 CNV regions (CNVRs), and more than half are novel to the 30 East Asian CNV Project and the 1000 Genomes Project Phase 3. We further identified 81 CNVRs specific to regional groups, which was indicative of the subpopulation structure within the Han Chinese population. Our data are complementary to public data sources, and the CNV map may facilitate in the identification of pathogenic CNVs and further biomedical research studies involving the Han Chinese population. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Population Size, Growth, and Environmental Justice Near Oil and Gas Wells in Colorado.

PubMed

McKenzie, Lisa M; Allshouse, William B; Burke, Troy; Blair, Benjamin D; Adgate, John L

2016-11-01

We evaluated population size and factors influencing environmental justice near oil and gas (O&G) wells. We mapped nearest O&G well to residential properties to evaluate population size, temporal relationships between housing and O&G development, and 2012 housing market value distributions in three major Colorado O&G basins. We reviewed land use, building, real estate, and state O&G regulations to evaluate distributive and participatory justice. We found that by 2012 at least 378,000 Coloradans lived within 1 mile of an active O&G well, and this population was growing at a faster rate than the overall population. In the Denver Julesburg and San Juan basins, which experienced substantial O&G development prior to 2000, we observed a larger proportion of lower value homes within 500 feet of an O&G well and that most O&G wells predated houses. In the Piceance Basin, which had not experienced substantial prior O&G development, we observed a larger proportion of high value homes within 500 feet of an O&G well and that most houses predated O&G wells. We observed economic, rural, participatory, and/or distributive injustices that could contribute to health risk vulnerabilities in populations near O&G wells. We encourage policy makers to consider measures to reduce these injustices.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

PubMed

N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

2017-01-01

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms

PubMed Central

N’Diaye, Amidou; Haile, Jemanesh K.; Fowler, D. Brian; Ammar, Karim; Pozniak, Curtis J.

2017-01-01

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called ‘large p, small n’ problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly. PMID:28878789

Transitive Relational Mappings in Three- and Four-Year-Olds: The Analogy of Goldilocks and the Three Bears.

ERIC Educational Resources Information Center

Goswami, Usha

1995-01-01

In three experiments, three- and four-year olds were asked to map relative size from one array of objects to another, map relative size to relative proportion, and map relative size to a variety of perceptual dimensions. Children were able to make relational mappings based on size when spatial positions and concrete representations of size of…

Interspecific and intraspecific variation in seed size and germination requirements of Sarracenia (Sarraceniaceae).

PubMed

Ellison, A M

2001-03-01

Seed size and germination requirements of eight (of nine) Sarracenia species, and 13 populations of S. purpurea were studied. All species except for S. purpurea are restricted to the southeastern United States, whereas S. purpurea ranges across Canada, southward along the eastern United States into Maryland and Virginia (S. purpurea ssp. purpurea), and from New Jersey southward into northern Florida and the coast of the Gulf of Mexico (S. purpurea ssp. venosa). I tested the hypotheses that dormancy-breaking requirements vary predictably among species across a latitudinal gradient. I also sought to determine whether seed size and germination requirements were useful characters for resolving systematic and phylogenetic questions within this genus. Seed size varied significantly among species, but variability in seed size within S. purpurea exceeded the variability in seed size observed across all eight species studied. Seeds of all species are morphophysiologically dormant upon dispersal. Length of required cool, moist pretreatment varied among species, and germination in higher latitude populations is enhanced with longer pretreatment. In contrast, variability in germination requirements of subspecies, varieties, and populations of the geographically wide-ranging S. purpurea was not related clearly to geographic location (latitude or elevation). Germination requirements do not map onto a proposed phylogeny of Sarracenia, but observed differences in germination requirements of S. purpurea ssp. venosa var. burkii relative to other populations of S. purpurea support the recent proposal to elevate this variety to species status.

ComVisMD - compact visualization of multidimensional data: experimenting with cricket players data

NASA Astrophysics Data System (ADS)

Dandin, Shridhar B.; Ducassé, Mireille

2018-03-01

Database information is multidimensional and often displayed in tabular format (row/column display). Presented in aggregated form, multidimensional data can be used to analyze the records or objects. Online Analytical database Processing (OLAP) proposes mechanisms to display multidimensional data in aggregated forms. A choropleth map is a thematic map in which areas are colored in proportion to the measurement of a statistical variable being displayed, such as population density. They are used mostly for compact graphical representation of geographical information. We propose a system, ComVisMD inspired by choropleth map and the OLAP cube to visualize multidimensional data in a compact way. ComVisMD displays multidimensional data like OLAP Cube, where we are mapping an attribute a (first dimension, e.g. year started playing cricket) in vertical direction, object coloring based on b (second dimension, e.g. batting average), mapping varying-size circles based on attribute c (third dimension, e.g. highest score), mapping numbers based on attribute d (fourth dimension, e.g. matches played). We illustrate our approach on cricket players data, namely on two tables Country and Player. They have a large number of rows and columns: 246 rows and 17 columns for players of one country. ComVisMD’s visualization reduces the size of the tabular display by a factor of about 4, allowing users to grasp more information at a time than the bare table display.

Characterizing fishing effort and spatial extent of coastal fisheries.

PubMed

Stewart, Kelly R; Lewison, Rebecca L; Dunn, Daniel C; Bjorkland, Rhema H; Kelez, Shaleyla; Halpin, Patrick N; Crowder, Larry B

2010-12-29

Biodiverse coastal zones are often areas of intense fishing pressure due to the high relative density of fishing capacity in these nearshore regions. Although overcapacity is one of the central challenges to fisheries sustainability in coastal zones, accurate estimates of fishing pressure in coastal zones are limited, hampering the assessment of the direct and collateral impacts (e.g., habitat degradation, bycatch) of fishing. We compiled a comprehensive database of fishing effort metrics and the corresponding spatial limits of fisheries and used a spatial analysis program (FEET) to map fishing effort density (measured as boat-meters per km²) in the coastal zones of six ocean regions. We also considered the utility of a number of socioeconomic variables as indicators of fishing pressure at the national level; fishing density increased as a function of population size and decreased as a function of coastline length. Our mapping exercise points to intra and interregional 'hotspots' of coastal fishing pressure. The significant and intuitive relationships we found between fishing density and population size and coastline length may help with coarse regional characterizations of fishing pressure. However, spatially-delimited fishing effort data are needed to accurately map fishing hotspots, i.e., areas of intense fishing activity. We suggest that estimates of fishing effort, not just target catch or yield, serve as a necessary measure of fishing activity, which is a key link to evaluating sustainability and environmental impacts of coastal fisheries.

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

PubMed Central

2014-01-01

Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species. PMID:24581176

Genetic mapping of QTL for the sizes of eight consecutive leaves below the tassel in maize (Zea mays L.).

PubMed

Yang, Cong; Tang, Dengguo; Qu, Jingtao; Zhang, Ling; Zhang, Lei; Chen, Zhengjie; Liu, Jian

2016-11-01

A set of RIL population was used to detect QTL associated with the sizes of eight consecutive leaves, across different environments, and ten QTL clusters were identified as main QTLs. One of the important parameters of the maize leaf architecture that affects light penetration into the canopy, leaf size, has long attracted breeders' attention for optimizing the plant type of maize and for maximizing the grain yield (GY). In this study, we used 253 RIL lines derived from a cross between B73 and SICAU1212 to investigate the leaf widths (LWs), leaf lengths (LLs), and leaf areas (LAs) of eight consecutive leaves of maize below the tassel and GY across different environments and to identify quantitative traits loci (QTLs) controlling the above-mentioned traits, using inclusive interval mapping for single-environment analysis plus a mixed-model-based composite interval mapping for joint analysis. A total of 171 and 159 putative QTLs were detected through these two mapping methods, respectively. Single-environment mapping revealed that 39 stable QTLs explained more than 10 % of the phenotypic variance, and 35 of the 39 QTLs were also detected by joint analysis. In addition, joint analysis showed that nine of the 159 QTLs exhibited significant QTL × environment interaction and 15 significant epistatic interactions were identified. Approximately 47.17 % of the QTLs for leaf architectural traits in joint analysis were concentrated in ten main chromosomal regions, namely, bins 1.07, 2.02, 3.06, 4.09, 5.01, 5.02, 5.03-5.04, 5.07, 6.07, and 8.05. This study should provide a basis for further fine-mapping of these main genetic regions and improvement of maize leaf architecture.

Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues.

PubMed

Ku, Taeyun; Swaney, Justin; Park, Jeong-Yoon; Albanese, Alexandre; Murray, Evan; Cho, Jae Hun; Park, Young-Gyun; Mangena, Vamsi; Chen, Jiapei; Chung, Kwanghun

2016-09-01

The biology of multicellular organisms is coordinated across multiple size scales, from the subnanoscale of molecules to the macroscale, tissue-wide interconnectivity of cell populations. Here we introduce a method for super-resolution imaging of the multiscale organization of intact tissues. The method, called magnified analysis of the proteome (MAP), linearly expands entire organs fourfold while preserving their overall architecture and three-dimensional proteome organization. MAP is based on the observation that preventing crosslinking within and between endogenous proteins during hydrogel-tissue hybridization allows for natural expansion upon protein denaturation and dissociation. The expanded tissue preserves its protein content, its fine subcellular details, and its organ-scale intercellular connectivity. We use off-the-shelf antibodies for multiple rounds of immunolabeling and imaging of a tissue's magnified proteome, and our experiments demonstrate a success rate of 82% (100/122 antibodies tested). We show that specimen size can be reversibly modulated to image both inter-regional connections and fine synaptic architectures in the mouse brain.

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.

PubMed

Dukić, Marinela; Berner, Daniel; Roesti, Marius; Haag, Christoph R; Ebert, Dieter

2016-10-13

Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.

A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

PubMed Central

2011-01-01

Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development. PMID:22103327

How size matters: exploring the association between quality of mental health services and catchment area size.

PubMed

Ala-Nikkola, Taina; Sadeniemi, Minna; Kaila, Minna; Saarni, Samuli; Kontio, Raija; Pirkola, Sami; Joffe, Grigori; Oranta, Olli; Wahlbeck, Kristian

2016-08-12

The diversity of mental health and substance abuse services (MHS) available to service users is seen as an indicator of the quality of the service system. In most countries MHS are provided by a mix of public, private and third sector providers. In Finland, officially, the municipalities are responsible for organizing the services needed, but the real extent and roles of private and third sector service providers are not known. Our previous study showed that the catchment area population size was strongly associated with diversity of mental health services. It is not known whether this was due to some types of services or some provider types being more sensitive to the size effect than others. The aim of this study was to investigate the association between area population size and diversity of mental health services, i.e. which types of services and which service providers' contributions are sensitive to population size. To map and classify services, we used the ESMS-R. The diversity of services was defined as the count of main types of care. Providers were classified as public, private or third sectors. The diversity of outpatient, residential and voluntary services correlated positively with catchment area population size. The strongest positive correlation between the size of population and services available was found in third sector activities followed by public providers, but no correlation was found for diversity of private services. The third sector and public corporations each provided 44 % of the service units. Third sector providers produced all self-help services and most of the day care services. Third sector and private companies provided a significant part (59 %) of the residential care service units. Significant positive correlations were found between size of catchment area population and diversity of residential, outpatient and voluntary services, indicating that these services concentrate on areas with larger population bases. The third sector seems to significantly complement the public sector in providing different services. Thus the third sector be needs to be functionally integrated with other MHS services to achieve a diversified and integrated service system.

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.

PubMed

Muchero, Wellington; Guo, Jianjun; DiFazio, Stephen P; Chen, Jin-Gui; Ranjan, Priya; Slavov, Gancho T; Gunter, Lee E; Jawdy, Sara; Bryan, Anthony C; Sykes, Robert; Ziebell, Angela; Klápště, Jaroslav; Porth, Ilga; Skyba, Oleksandr; Unda, Faride; El-Kassaby, Yousry A; Douglas, Carl J; Mansfield, Shawn D; Martin, Joel; Schackwitz, Wendy; Evans, Luke M; Czarnecki, Olaf; Tuskan, Gerald A

2015-01-23

QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here, multiyear and multienvironment evaluation of cell wall phenotypes was conducted in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree and two partially overlapping populations of unrelated P. trichocarpa genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. QTL mapping was conducted using a high-density genetic map with 3,568 SNP markers. As a fine-mapping approach, chromosome-wide association mapping targeting a QTL hot-spot on linkage group XIV was performed in the two P. trichocarpa populations. Both populations were genotyped using the 34 K Populus Infinium SNP array and whole-genome resequencing of one of the populations facilitated marker-saturation of candidate intervals for gene identification. Five QTLs ranging in size from 0.6 to 1.8 Mb were mapped on linkage group XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6-carbon sugars using the mapping pedigree. Six candidate loci exhibiting significant associations with phenotypes were identified within QTL intervals. These associations were reproducible across multiple environments, two independent genotyping platforms, and different plant growth stages. cDNA sequencing for allelic variants of three of the six loci identified polymorphisms leading to variable length poly glutamine (PolyQ) stretch in a transcription factor annotated as an ANGUSTIFOLIA C-terminus Binding Protein (CtBP) and premature stop codons in a KANADI transcription factor as well as a protein kinase. Results from protoplast transient expression assays suggested that each of the polymorphisms conferred allelic differences in the activation of cellulose, hemicelluloses, and lignin pathway marker genes. This study illustrates the utility of complementary QTL and association mapping as tools for gene discovery with no a priori candidate gene selection. This proof of concept in a perennial organism opens up opportunities for discovery of novel genetic determinants of economically important but complex traits in plants.

Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

PubMed

Manrubia, Susanna; Cuesta, José A

2017-04-01

An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

Graptemys pulchra Baur 1893: Alabama Map Turtle

USGS Publications Warehouse

Lovich, Jeffrey E.; Godwin, James C.; McCoy, C.J.; Rhodin, A. G. J.; Pritchard, P. C. H.; van Dijk, P. P.; Saumure, Raymond A.; Buhlmann, K.A.; Iverson, J.B.; Mittermeier, R.A.

2014-01-01

The Alabama Map Turtle, Graptemys pulchra (Family Emydidae), is a moderately large riverine species endemic to the Mobile Bay drainage system of Alabama, Georgia, and Mississippi. Sexual size dimorphism is pronounced, with adult females (carapace length [CL] to 273 mm) attaining more than twice the size of adult males (CL to 117 mm). The species is an inhabitant of relatively large, swift creeks and rivers, often with wide sandbars. Stream sections open to the sun and with abundant basking sites in the form of logs and brush are preferred. Six to seven clutches of 4–7 eggs are laid each year on river sandbars. Although the species is locally abundant, populations are threatened by habitat destruction, declines in their prey base, commercial collection, and vandalism. It is listed as a Species of Special Concern in Alabama.

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

PubMed Central

Vij, Shubha; Kuhl, Heiner; Kuznetsova, Inna S.; Komissarov, Aleksey; Yurchenko, Andrey A.; Van Heusden, Peter; Singh, Siddharth; Thevasagayam, Natascha M.; Prakki, Sai Rama Sridatta; Purushothaman, Kathiresan; Saju, Jolly M.; Jiang, Junhui; Mbandi, Stanley Kimbung; Jonas, Mario; Hin Yan Tong, Amy; Mwangi, Sarah; Lau, Doreen; Ngoh, Si Yan; Liew, Woei Chang; Shen, Xueyan; Hon, Lawrence S.; Drake, James P.; Boitano, Matthew; Hall, Richard; Chin, Chen-Shan; Lachumanan, Ramkumar; Korlach, Jonas; Trifonov, Vladimir; Kabilov, Marsel; Tupikin, Alexey; Green, Darrell; Moxon, Simon; Garvin, Tyler; Sedlazeck, Fritz J.; Vurture, Gregory W.; Gopalapillai, Gopikrishna; Kumar Katneni, Vinaya; Noble, Tansyn H.; Scaria, Vinod; Sivasubbu, Sridhar; Jerry, Dean R.; O'Brien, Stephen J.; Schatz, Michael C.; Dalmay, Tamás; Turner, Stephen W.; Lok, Si; Christoffels, Alan; Orbán, László

2016-01-01

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics. PMID:27082250

A fast least-squares algorithm for population inference

PubMed Central

2013-01-01

Background Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual’s genotype can be modeled as a probabilistic function of ancestral population memberships, Q, and the allele frequencies in those populations, P. The parameters, P and Q, of this binomial likelihood model can be inferred using slow sampling methods such as Markov Chain Monte Carlo methods or faster gradient based approaches such as sequential quadratic programming. This paper proposes a least-squares simplification of the binomial likelihood model motivated by a Euclidean interpretation of the genotype feature space. This results in a faster algorithm that easily incorporates the degree of admixture within the sample of individuals and improves estimates without requiring trial-and-error tuning. Results We show that the expected value of the least-squares solution across all possible genotype datasets is equal to the true solution when part of the problem has been solved, and that the variance of the solution approaches zero as its size increases. The Least-squares algorithm performs nearly as well as Admixture for these theoretical scenarios. We compare least-squares, Admixture, and FRAPPE for a variety of problem sizes and difficulties. For particularly hard problems with a large number of populations, small number of samples, or greater degree of admixture, least-squares performs better than the other methods. On simulated mixtures of real population allele frequencies from the HapMap project, Admixture estimates sparsely mixed individuals better than Least-squares. The least-squares approach, however, performs within 1.5% of the Admixture error. On individual genotypes from the HapMap project, Admixture and least-squares perform qualitatively similarly and within 1.2% of each other. Significantly, the least-squares approach nearly always converges 1.5- to 6-times faster. Conclusions The computational advantage of the least-squares approach along with its good estimation performance warrants further research, especially for very large datasets. As problem sizes increase, the difference in estimation performance between all algorithms decreases. In addition, when prior information is known, the least-squares approach easily incorporates the expected degree of admixture to improve the estimate. PMID:23343408

A fast least-squares algorithm for population inference.

PubMed

Parry, R Mitchell; Wang, May D

2013-01-23

Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual's genotype can be modeled as a probabilistic function of ancestral population memberships, Q, and the allele frequencies in those populations, P. The parameters, P and Q, of this binomial likelihood model can be inferred using slow sampling methods such as Markov Chain Monte Carlo methods or faster gradient based approaches such as sequential quadratic programming. This paper proposes a least-squares simplification of the binomial likelihood model motivated by a Euclidean interpretation of the genotype feature space. This results in a faster algorithm that easily incorporates the degree of admixture within the sample of individuals and improves estimates without requiring trial-and-error tuning. We show that the expected value of the least-squares solution across all possible genotype datasets is equal to the true solution when part of the problem has been solved, and that the variance of the solution approaches zero as its size increases. The Least-squares algorithm performs nearly as well as Admixture for these theoretical scenarios. We compare least-squares, Admixture, and FRAPPE for a variety of problem sizes and difficulties. For particularly hard problems with a large number of populations, small number of samples, or greater degree of admixture, least-squares performs better than the other methods. On simulated mixtures of real population allele frequencies from the HapMap project, Admixture estimates sparsely mixed individuals better than Least-squares. The least-squares approach, however, performs within 1.5% of the Admixture error. On individual genotypes from the HapMap project, Admixture and least-squares perform qualitatively similarly and within 1.2% of each other. Significantly, the least-squares approach nearly always converges 1.5- to 6-times faster. The computational advantage of the least-squares approach along with its good estimation performance warrants further research, especially for very large datasets. As problem sizes increase, the difference in estimation performance between all algorithms decreases. In addition, when prior information is known, the least-squares approach easily incorporates the expected degree of admixture to improve the estimate.

Bamboo-Dominated Forests of the Southwest Amazon: Detection, Spatial Extent, Life Cycle Length and Flowering Waves

PubMed Central

de Carvalho, Anelena L.; Nelson, Bruce W.; Bianchini, Milton C.; Plagnol, Daniela; Kuplich, Tatiana M.; Daly, Douglas C.

2013-01-01

We map the extent, infer the life-cycle length and describe spatial and temporal patterns of flowering of sarmentose bamboos (Guadua spp) in upland forests of the southwest Amazon. We first examine the spectra and the spectral separation of forests with different bamboo life stages. False-color composites from orbital sensors going back to 1975 are capable of distinguishing life stages. These woody bamboos flower produce massive quantities of seeds and then die. Life stage is synchronized, forming a single cohort within each population. Bamboo dominates at least 161,500 km2 of forest, coincident with an area of recent or ongoing tectonic uplift, rapid mechanical erosion and poorly drained soils rich in exchangeable cations. Each bamboo population is confined to a single spatially continuous patch or to a core patch with small outliers. Using spatial congruence between pairs of mature-stage maps from different years, we estimate an average life cycle of 27–28 y. It is now possible to predict exactly where and approximately when new bamboo mortality events will occur. We also map 74 bamboo populations that flowered between 2001 and 2008 over the entire domain of bamboo-dominated forest. Population size averaged 330 km2. Flowering events of these populations are temporally and/or spatially separated, restricting or preventing gene exchange. Nonetheless, adjacent populations flower closer in time than expected by chance, forming flowering waves. This may be a consequence of allochronic divergence from fewer ancestral populations and suggests a long history of widespread bamboo in the southwest Amazon. PMID:23359438

Mapping copy number variation by population-scale genome sequencing.

PubMed

Mills, Ryan E; Walter, Klaudia; Stewart, Chip; Handsaker, Robert E; Chen, Ken; Alkan, Can; Abyzov, Alexej; Yoon, Seungtai Chris; Ye, Kai; Cheetham, R Keira; Chinwalla, Asif; Conrad, Donald F; Fu, Yutao; Grubert, Fabian; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Iakoucheva, Lilia M; Iqbal, Zamin; Kang, Shuli; Kidd, Jeffrey M; Konkel, Miriam K; Korn, Joshua; Khurana, Ekta; Kural, Deniz; Lam, Hugo Y K; Leng, Jing; Li, Ruiqiang; Li, Yingrui; Lin, Chang-Yun; Luo, Ruibang; Mu, Xinmeng Jasmine; Nemesh, James; Peckham, Heather E; Rausch, Tobias; Scally, Aylwyn; Shi, Xinghua; Stromberg, Michael P; Stütz, Adrian M; Urban, Alexander Eckehart; Walker, Jerilyn A; Wu, Jiantao; Zhang, Yujun; Zhang, Zhengdong D; Batzer, Mark A; Ding, Li; Marth, Gabor T; McVean, Gil; Sebat, Jonathan; Snyder, Michael; Wang, Jun; Ye, Kenny; Eichler, Evan E; Gerstein, Mark B; Hurles, Matthew E; Lee, Charles; McCarroll, Steven A; Korbel, Jan O

2011-02-03

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

Cortical connective field estimates from resting state fMRI activity.

PubMed

Gravel, Nicolás; Harvey, Ben; Nordhjem, Barbara; Haak, Koen V; Dumoulin, Serge O; Renken, Remco; Curčić-Blake, Branislava; Cornelissen, Frans W

2014-01-01

One way to study connectivity in visual cortical areas is by examining spontaneous neural activity. In the absence of visual input, such activity remains shaped by the underlying neural architecture and, presumably, may still reflect visuotopic organization. Here, we applied population connective field (CF) modeling to estimate the spatial profile of functional connectivity in the early visual cortex during resting state functional magnetic resonance imaging (RS-fMRI). This model-based analysis estimates the spatial integration between blood-oxygen level dependent (BOLD) signals in distinct cortical visual field maps using fMRI. Just as population receptive field (pRF) mapping predicts the collective neural activity in a voxel as a function of response selectivity to stimulus position in visual space, CF modeling predicts the activity of voxels in one visual area as a function of the aggregate activity in voxels in another visual area. In combination with pRF mapping, CF locations on the cortical surface can be interpreted in visual space, thus enabling reconstruction of visuotopic maps from resting state data. We demonstrate that V1 ➤ V2 and V1 ➤ V3 CF maps estimated from resting state fMRI data show visuotopic organization. Therefore, we conclude that-despite some variability in CF estimates between RS scans-neural properties such as CF maps and CF size can be derived from resting state data.

Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil.

PubMed

Royaert, Stefan; Jansen, Johannes; da Silva, Daniela Viana; de Jesus Branco, Samuel Martins; Livingstone, Donald S; Mustiga, Guiliana; Marelli, Jean-Philippe; Araújo, Ioná Santos; Corrêa, Ronan Xavier; Motamayor, Juan Carlos

2016-02-11

Witches' broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. We developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant 'TSH 1188' and the tolerant 'CCN 51' at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone 'SCAVINA 6'. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between 'CCN 51' and 'TSH 1188'. We combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the 'CCN 51' parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material.

Persistence versus extinction for a class of discrete-time structured population models.

PubMed

Jin, Wen; Smith, Hal L; Thieme, Horst R

2016-03-01

We provide sharp conditions distinguishing persistence and extinction for a class of discrete-time dynamical systems on the positive cone of an ordered Banach space generated by a map which is the sum of a positive linear contraction A and a nonlinear perturbation G that is compact and differentiable at zero in the direction of the cone. Such maps arise as year-to-year projections of population age, stage, or size-structure distributions in population biology where typically A has to do with survival and individual development and G captures the effects of reproduction. The threshold distinguishing persistence and extinction is the principal eigenvalue of (II−A)(−1)G'(0) provided by the Krein-Rutman Theorem, and persistence is described in terms of associated eigenfunctionals. Our results significantly extend earlier persistence results of the last two authors which required more restrictive conditions on G. They are illustrated by application of the results to a plant model with a seed bank.

Who Are the Okinawans? Ancestry, Genome Diversity, and Implications for the Genetic Study of Human Longevity From a Geographically Isolated Population

PubMed Central

Hsueh, Wen-Chi; He, Qimei; Willcox, D. Craig; Nievergelt, Caroline M.; Donlon, Timothy A.; Kwok, Pui-Yan; Suzuki, Makoto; Willcox, Bradley J.

2014-01-01

Isolated populations have advantages for genetic studies of longevity from decreased haplotype diversity and long-range linkage disequilibrium. This permits smaller sample sizes without loss of power, among other utilities. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome—more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λs) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans. PMID:24444611

Statistical Physics of Population Genetics in the Low Population Size Limit

NASA Astrophysics Data System (ADS)

Atwal, Gurinder

The understanding of evolutionary processes lends itself naturally to theory and computation, and the entire field of population genetics has benefited greatly from the influx of methods from applied mathematics for decades. However, in spite of all this effort, there are a number of key dynamical models of evolution that have resisted analytical treatment. In addition, modern DNA sequencing technologies have magnified the amount of genetic data available, revealing an excess of rare genetic variants in human genomes, challenging the predictions of conventional theory. Here I will show that methods from statistical physics can be used to model the distribution of genetic variants, incorporating selection and spatial degrees of freedom. In particular, a functional path-integral formulation of the Wright-Fisher process maps exactly to the dynamics of a particle in an effective potential, beyond the mean field approximation. In the small population size limit, the dynamics are dominated by instanton-like solutions which determine the probability of fixation in short timescales. These results are directly relevant for understanding the unusual genetic variant distribution at moving frontiers of populations.

Genetic and QTL analysis of resistance to Xiphinema index in a grapevine cross.

PubMed

Xu, K; Riaz, S; Roncoroni, N C; Jin, Y; Hu, R; Zhou, R; Walker, M A

2008-01-01

Resistance to the dagger nematode Xiphinema index has been an important objective in grape rootstock breeding programs. This nematode not only causes severe feeding damage to the root system, but it also vectors grapevine fanleaf virus (GFLV), the causal agent of fanleaf degeneration and one of the most severe viral diseases of grape. The established screening procedures for dagger nematode resistance are time consuming and can produce inconsistent results. A fast and reliable greenhouse-based system for screening resistance to X. index that is suitable for genetic studies and capable of evaluating breeding populations is needed. In this report, the dynamics of nematode numbers, gall formation, and root weight loss were investigated using a variety of soil mixes and pot sizes over a 52-week period. Results indicated that the number of galls formed was correlated with the size of the nematode population and with the degree of root weight loss. After inoculation with 100 nematodes, gall formation could be reliably evaluated in 4-8 weeks in most plant growth conditions and results were obtained 6 months more rapidly than past evaluation methods. This modified X. index resistance screening method was successfully applied to 185 of the 188 F(1) progeny from a cross of D8909-15 x F8909-17 (the 9621 population), which segregates for a form of X. index resistance originally derived from Vitis arizonica. Quantitative trait loci (QTL) analysis was carried out on both parental genetic maps of 255 markers using MapQTL 4.0. Results revealed that X. index resistance is controlled by a major QTL, designated Xiphinema index Resistance 1 (XiR1), near marker VMC5a10 on chromosome 19. The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population.

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

PubMed Central

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

2014-01-01

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

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

PubMed Central

Wenzl, Peter; Li, Haobing; Carling, Jason; Zhou, Meixue; Raman, Harsh; Paul, Edie; Hearnden, Phillippa; Maier, Christina; Xia, Ling; Caig, Vanessa; Ovesná, Jaroslava; Cakir, Mehmet; Poulsen, David; Wang, Junping; Raman, Rosy; Smith, Kevin P; Muehlbauer, Gary J; Chalmers, Ken J; Kleinhofs, Andris; Huttner, Eric; Kilian, Andrzej

2006-01-01

Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations. PMID:16904008

Characterizing Fishing Effort and Spatial Extent of Coastal Fisheries

PubMed Central

Stewart, Kelly R.; Lewison, Rebecca L.; Dunn, Daniel C.; Bjorkland, Rhema H.; Kelez, Shaleyla; Halpin, Patrick N.; Crowder, Larry B.

2010-01-01

Biodiverse coastal zones are often areas of intense fishing pressure due to the high relative density of fishing capacity in these nearshore regions. Although overcapacity is one of the central challenges to fisheries sustainability in coastal zones, accurate estimates of fishing pressure in coastal zones are limited, hampering the assessment of the direct and collateral impacts (e.g., habitat degradation, bycatch) of fishing. We compiled a comprehensive database of fishing effort metrics and the corresponding spatial limits of fisheries and used a spatial analysis program (FEET) to map fishing effort density (measured as boat-meters per km2) in the coastal zones of six ocean regions. We also considered the utility of a number of socioeconomic variables as indicators of fishing pressure at the national level; fishing density increased as a function of population size and decreased as a function of coastline length. Our mapping exercise points to intra and interregional ‘hotspots’ of coastal fishing pressure. The significant and intuitive relationships we found between fishing density and population size and coastline length may help with coarse regional characterizations of fishing pressure. However, spatially-delimited fishing effort data are needed to accurately map fishing hotspots, i.e., areas of intense fishing activity. We suggest that estimates of fishing effort, not just target catch or yield, serve as a necessary measure of fishing activity, which is a key link to evaluating sustainability and environmental impacts of coastal fisheries. PMID:21206903

NASA's New Orbital Debris Engineering Model, ORDEM2010

NASA Technical Reports Server (NTRS)

Krisko, Paula H.

2010-01-01

This paper describes the functionality and use of ORDEM2010, which replaces ORDEM2000, as the NASA Orbital Debris Program Office (ODPO) debris engineering model. Like its predecessor, ORDEM2010 serves the ODPO mission of providing spacecraft designers/operators and debris observers with a publicly available model to calculate orbital debris flux by current-state-of-knowledge methods. The key advance in ORDEM2010 is the input file structure of the yearly debris populations from 1995-2035 of sizes 10 micron - 1 m. These files include debris from low-Earth orbits (LEO) through geosynchronous orbits (GEO). Stable orbital elements (i.e., those that do not randomize on a sub-year timescale) are included in the files as are debris size, debris number, material density, random error and population error. Material density is implemented from ground-test data into the NASA breakup model and assigned to debris fragments accordingly. The random and population errors are due to machine error and uncertainties in debris sizes. These high-fidelity population files call for a much higher-level model analysis than what was possible with the populations of ORDEM2000. Population analysis in the ORDEM2010 model consists of mapping matrices that convert the debris population elements to debris fluxes. One output mode results in a spacecraft encompassing 3-D igloo of debris flux, compartmentalized by debris size, velocity, pitch, and yaw with respect to spacecraft ram direction. The second output mode provides debris flux through an Earth-based telescope/radar beam from LEO through GEO. This paper compares the new ORDEM2010 with ORDEM2000 in terms of processes and results with examples of specific orbits.

Common determinants of body size and eye size in chickens from an advanced intercross line.

PubMed

Prashar, Ankush; Hocking, Paul M; Erichsen, Jonathan T; Fan, Qiao; Saw, Seang Mei; Guggenheim, Jeremy A

2009-06-15

Myopia development is characterised by an increased axial eye length. Therefore, identifying factors that influence eye size may provide new insights into the aetiology of myopia. In humans, axial length is positively correlated to height and weight, and in mice, eye weight is positively correlated with body weight. The purpose of this study was to examine the relationship between eye size and body size in chickens from a genetic cross in which alleles with major effects on eye and body size were segregating. Chickens from a cross between a layer line (small body size and eye size) and a broiler line (large body and eye size) were interbred for 10 generations so that alleles for eye and body size would have the chance to segregate independently. At 3 weeks of age, 510 chicks were assessed using in vivo high resolution A-scan ultrasonography and keratometry. Equatorial eye diameter and eye weight were measured after enucleation. The variations in eye size parameters that could be explained by body weight (BW), body length (BL), head width (HW) and sex were examined using multiple linear regression. It was found that BW, BL and HW and sex together predicted 51-56% of the variation in eye weight, axial length, corneal radius, and equatorial eye diameter. By contrast, the same variables predicted only 22% of the variation in lens thickness. After adjusting for sex, the three body size parameters predicted 45-49% of the variation in eye weight, axial length, corneal radius, and eye diameter, but only 0.4% of the variation in lens thickness. In conclusion, about half of the variation in eye size in the chickens of this broiler-layer advanced intercross line is likely to be determined by pleiotropic genes that also influence body size. Thus, mapping the quantitative trait loci (QTL) that determine body size may be useful in understanding the genetic determination of eye size (a logical inference of this result is that the 20 or more genetic variants that have recently been shown to influence human height may also be found to influence axial eye length). Furthermore, adjusting for body size will be essential in mapping pure eye size QTL in this chicken population, and may also have value in mapping eye size QTL in humans.

Introduction and Testing of a Monitoring and Colony-Mapping Method for Waterbird Populations That Uses High-Speed and Ultra-Detailed Aerial Remote Sensing

PubMed Central

Bakó, Gábor; Tolnai, Márton; Takács, Ádám

2014-01-01

Remote sensing is a method that collects data of the Earth's surface without causing disturbances. Thus, it is worthwhile to use remote sensing methods to survey endangered ecosystems, as the studied species will behave naturally while undisturbed. The latest passive optical remote sensing solutions permit surveys from long distances. State-of-the-art highly sensitive sensor systems allow high spatial resolution image acquisition at high altitudes and at high flying speeds, even in low-visibility conditions. As the aerial imagery captured by an airplane covers the entire study area, all the animals present in that area can be recorded. A population assessment is conducted by visual interpretations of an ortho image map. The basic objective of this study is to determine whether small- and medium-sized bird species are recognizable in the ortho images by using high spatial resolution aerial cameras. The spatial resolution needed for identifying the bird species in the ortho image map was studied. The survey was adjusted to determine the number of birds in a colony at a given time. PMID:25046012

Hierarchical nuclear and cytoplasmic genetic architectures for plant growth and defense within Arabidopsis.

PubMed

Joseph, Bindu; Corwin, Jason A; Züst, Tobias; Li, Baohua; Iravani, Majid; Schaepman-Strub, Gabriela; Turnbull, Lindsay A; Kliebenstein, Daniel J

2013-06-01

To understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth rates. This population contains genetic variation in both the nuclear and cytoplasmic genomes, allowing us to separate their contributions. The cytoplasmic genome regulated a significant variance in growth but not defense, which was due to cytonuclear epistasis. Furthermore, growth adhered to an infinitesimal model of genetic architecture, while defense metabolism was more of a moderate-effect model. We found a lack of concordance between quantitative trait loci (QTL) regulating defense and those regulating growth. Given the published evidence proving the link between glucosinolates and growth, this is likely a false negative result caused by the limited population size. This size limitation creates an inability to test the entire potential genetic landscape possible between these two parents. We uncovered a significant effect of glucosinolates on growth once we accounted for allelic differences in growth QTLs. Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis.

Hierarchical Nuclear and Cytoplasmic Genetic Architectures for Plant Growth and Defense within Arabidopsis[C][W

PubMed Central

Joseph, Bindu; Corwin, Jason A.; Züst, Tobias; Li, Baohua; Iravani, Majid; Schaepman-Strub, Gabriela; Turnbull, Lindsay A.; Kliebenstein, Daniel J.

2013-01-01

To understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth rates. This population contains genetic variation in both the nuclear and cytoplasmic genomes, allowing us to separate their contributions. The cytoplasmic genome regulated a significant variance in growth but not defense, which was due to cytonuclear epistasis. Furthermore, growth adhered to an infinitesimal model of genetic architecture, while defense metabolism was more of a moderate-effect model. We found a lack of concordance between quantitative trait loci (QTL) regulating defense and those regulating growth. Given the published evidence proving the link between glucosinolates and growth, this is likely a false negative result caused by the limited population size. This size limitation creates an inability to test the entire potential genetic landscape possible between these two parents. We uncovered a significant effect of glucosinolates on growth once we accounted for allelic differences in growth QTLs. Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis. PMID:23749847

Effect of reaction-step-size noise on the switching dynamics of stochastic populations

NASA Astrophysics Data System (ADS)

Be'er, Shay; Heller-Algazi, Metar; Assaf, Michael

2016-05-01

In genetic circuits, when the messenger RNA lifetime is short compared to the cell cycle, proteins are produced in geometrically distributed bursts, which greatly affects the cellular switching dynamics between different metastable phenotypic states. Motivated by this scenario, we study a general problem of switching or escape in stochastic populations, where influx of particles occurs in groups or bursts, sampled from an arbitrary distribution. The fact that the step size of the influx reaction is a priori unknown and, in general, may fluctuate in time with a given correlation time and statistics, introduces an additional nondemographic reaction-step-size noise into the system. Employing the probability-generating function technique in conjunction with Hamiltonian formulation, we are able to map the problem in the leading order onto solving a stationary Hamilton-Jacobi equation. We show that compared to the "usual case" of single-step influx, bursty influx exponentially decreases the population's mean escape time from its long-lived metastable state. In particular, close to bifurcation we find a simple analytical expression for the mean escape time which solely depends on the mean and variance of the burst-size distribution. Our results are demonstrated on several realistic distributions and compare well with numerical Monte Carlo simulations.

Genetic Mapping of Fixed Phenotypes: Disease Frequency as a Breed Characteristic

PubMed Central

Jones, Paul; Martin, Alan; Ostrander, Elaine A.; Lark, Karl G.

2009-01-01

Traits that have been stringently selected to conform to specific criteria in a closed population are phenotypic stereotypes. In dogs, Canis familiaris, such stereotypes have been produced by breeding for conformation, performance (behaviors), etc. We measured phenotypes on a representative sample to establish breed stereotypes. DNA samples from 147 dog breeds were used to characterize single nucleotide polymorphism allele frequencies for association mapping of breed stereotypes. We identified significant size loci (quantitative trait loci [QTLs]), implicating candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Behavioral loci for herding, pointing, and boldness implicated candidate genes appropriate to behavior (e.g., MC2R, DRD1, and PCDH9). Significant loci for longevity, a breed characteristic inversely correlated with breed size, were identified. The power of this approach to identify loci regulating the incidence of specific polygenic diseases is demonstrated by the association of a specific IGF1 haplotype with hip dysplasia, patella luxation, and pacreatitis. PMID:19321632

Genetic mapping of fixed phenotypes: disease frequency as a breed characteristic.

PubMed

Chase, Kevin; Jones, Paul; Martin, Alan; Ostrander, Elaine A; Lark, Karl G

2009-01-01

Traits that have been stringently selected to conform to specific criteria in a closed population are phenotypic stereotypes. In dogs, Canis familiaris, such stereotypes have been produced by breeding for conformation, performance (behaviors), etc. We measured phenotypes on a representative sample to establish breed stereotypes. DNA samples from 147 dog breeds were used to characterize single nucleotide polymorphism allele frequencies for association mapping of breed stereotypes. We identified significant size loci (quantitative trait loci [QTLs]), implicating candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Behavioral loci for herding, pointing, and boldness implicated candidate genes appropriate to behavior (e.g., MC2R, DRD1, and PCDH9). Significant loci for longevity, a breed characteristic inversely correlated with breed size, were identified. The power of this approach to identify loci regulating the incidence of specific polygenic diseases is demonstrated by the association of a specific IGF1 haplotype with hip dysplasia, patella luxation, and pancreatitis.

Impact of cell size on inventory and mapping errors in a cellular geographic information system

NASA Technical Reports Server (NTRS)

Wehde, M. E. (Principal Investigator)

1979-01-01

The author has identified the following significant results. The effect of grid position was found insignificant for maps but highly significant for isolated mapping units. A modelable relationship between mapping error and cell size was observed for the map segment analyzed. Map data structure was also analyzed with an interboundary distance distribution approach. Map data structure and the impact of cell size on that structure were observed. The existence of a model allowing prediction of mapping error based on map structure was hypothesized and two generations of models were tested under simplifying assumptions.

Voltage and pace-capture mapping of linear ablation lesions overestimates chronic ablation gap size.

PubMed

O'Neill, Louisa; Harrison, James; Chubb, Henry; Whitaker, John; Mukherjee, Rahul K; Bloch, Lars Ølgaard; Andersen, Niels Peter; Dam, Høgni; Jensen, Henrik K; Niederer, Steven; Wright, Matthew; O'Neill, Mark; Williams, Steven E

2018-04-26

Conducting gaps in lesion sets are a major reason for failure of ablation procedures. Voltage mapping and pace-capture have been proposed for intra-procedural identification of gaps. We aimed to compare gap size measured acutely and chronically post-ablation to macroscopic gap size in a porcine model. Intercaval linear ablation was performed in eight Göttingen minipigs with a deliberate gap of ∼5 mm left in the ablation line. Gap size was measured by interpolating ablation contact force values between ablation tags and thresholding at a low force cut-off of 5 g. Bipolar voltage mapping and pace-capture mapping along the length of the line were performed immediately, and at 2 months, post-ablation. Animals were euthanized and gap sizes were measured macroscopically. Voltage thresholds to define scar were determined by receiver operating characteristic analysis as <0.56 mV (acutely) and <0.62 mV (chronically). Taking the macroscopic gap size as gold standard, error in gap measurements were determined for voltage, pace-capture, and ablation contact force maps. All modalities overestimated chronic gap size, by 1.4 ± 2.0 mm (ablation contact force map), 5.1 ± 3.4 mm (pace-capture), and 9.5 ± 3.8 mm (voltage mapping). Error on ablation contact force map gap measurements were significantly less than for voltage mapping (P = 0.003, Tukey's multiple comparisons test). Chronically, voltage mapping and pace-capture mapping overestimated macroscopic gap size by 11.9 ± 3.7 and 9.8 ± 3.5 mm, respectively. Bipolar voltage and pace-capture mapping overestimate the size of chronic gap formation in linear ablation lesions. The most accurate estimation of chronic gap size was achieved by analysis of catheter-myocardium contact force during ablation.

Genetic mapping of resistance to Fusarium oxysporum f. sp. tulipae in tulip.

PubMed

Tang, Nan; van der Lee, Theo; Shahin, Arwa; Holdinga, Maarten; Bijman, Paul; Caser, Matteo; Visser, Richard G F; van Tuyl, Jaap M; Arens, Paul

Fusarium oxysporum is a major problem in the production of tulip bulbs. Breeding for resistant cultivars through a conventional approach is a slow process due to the long life cycle of tulip. Until now, marker-assisted selection (MAS) has been hampered by the large genome size and the absence of a genetic map. This study is aimed at construction of the first genetic map for tulip and at the identification of loci associated with resistance to F. oxysporum . A cross-pollinated population of 125 individuals segregating for Fusarium resistance was obtained from Tulipa gesneriana "Kees Nelis" and T. fosteriana "Cantata." Fusarium resistance of the mapping population was evaluated through a soil infection test in two consecutive years, and a spot inoculation test in which a green fluorescent protein tagged Fusarium strain was used for inoculation. The genetic maps have been constructed for the parents separately. The genetic map of "Kees Nelis" comprised 342 markers on 27 linkage groups covering 1707 cM, while the map of "Cantata" comprised 300 markers on 21 linkage groups covering 1201 cM. Median distance between markers was 3.9 cM for "Kees Nelis" and 3.1 cM for "Cantata." Six putative quantitative trait loci (QTLs) for Fusarium resistance were identified, derived from both parents. QTL2, QTL3, and QTL6 were significant in all disease tests. For the flanking markers of the QTLs, phenotypic means of the two allelic groups, segregating from a parent for such a marker, were significantly different. These markers will be useful for the development of MAS in tulip breeding.

A survey of publicly funded aged psychiatry services in Australia and New Zealand.

PubMed

O'Connor, Daniel; Melding, Pamela

2006-04-01

To map the size and distribution of publicly funded aged psychiatry (psychogeriatric) services in Australia and New Zealand in 2003. Services were tracked exhaustively through personal, professional and academic contacts, electronic searches and word-of-mouth. Directors or managers of services were asked to complete a brief questionnaire concerning their locality, services, staff profile and patient contacts. Services varied widely with respect to their numbers, size and community outreach. Victoria was the only Australian state to provide specialist, multidisciplinary aged psychiatry teams with community, acute inpatient and residential arms in all its major cities. New South Wales, the state with the largest aged population, performed relatively poorly on most indicators. New Zealand performed relatively well despite its small size and widely dispersed population. Publicly funded aged mental health services are effective and reach frail, multiply disabled old people who cannot access private psychiatrists and are often overlooked by services for younger adults. At the time of our survey, such services were distributed in Australia in a highly inequitable fashion.

Models for loosely linked gene duplicates suggest lengthy persistence of both copies.

PubMed

O'Hely, Martin; Wockner, Leesa

2007-06-21

Consider the appearance of a duplicate copy of a gene at a locus linked loosely, if at all, to the locus at which the gene is usually found. If all copies of the gene are subject to non-functionalizing mutations, then two fates are possible: loss of functional copies at the duplicate locus (loss of duplicate expression), or loss of functional copies at the original locus (map change). This paper proposes a simple model to address the probability of map change, the time taken for a map change and/or loss of duplicate expression, and considers where in the spectrum between loss of duplicate expression and map change such a duplicate complex is likely to be found. The findings are: the probability of map change is always half the reciprocal of the population size N, the time for a map change to occur is order NlogN generations, and that there is a marked tendency for duplicates to remain near equi-frequency with the gene at the original locus for a large portion of that time. This is in excellent agreement with simulations.

Size Matters — Determinants of Modern, Community-Oriented Mental Health Services

PubMed Central

Ala-Nikkola, Taina; Pirkola, Sami; Kontio, Raija; Joffe, Grigori; Pankakoski, Maiju; Malin, Maili; Sadeniemi, Minna; Kaila, Minna; Wahlbeck, Kristian

2014-01-01

Governances, structures and contents of mental health services are being reformed across countries. There is a need for data to support those changes. The aim of this study was to explore the quality, i.e., diversity and community orientation, and quantity, i.e., personnel resources, of mental health and substance abuse services (MHS) and evaluate correlation between population needs and quality and quantity of MHS. The European Service Mapping Schedule—Revised (ESMS-R) was used to classify mental health and substance abuse services in southern Finland. Municipal-level aggregate data, local data on unemployment rate, length of education, age of retirement, proportion of single households, alcohol sales and a composite mental health index were used as indicators of population mental health needs. Population size correlated strongly with service diversity, explaining 84% of the variance. Personnel resources did not associate with diversity or community orientation. The indicators of mental health services need did not have the expected association with quality and quantity of services. In terms of service organization, the results may support larger population bases, at least 150,000 adult inhabitants, when aiming for higher diversity. PMID:25153471

The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum)

PubMed Central

Milano, Elizabeth R.; Lowry, David B.; Juenger, Thomas E.

2016-01-01

The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within plant species. However, we know surprisingly little about the genetic mechanisms underlying the locally adapted traits involved in ecotype formation. The genetic architecture underlying locally adapted traits dictates how an organism will respond to environmental selection pressures, and has major implications for evolutionary ecology, conservation, and crop breeding. To understand the genetic architecture underlying the divergence of switchgrass (Panicum virgatum) ecotypes, we constructed a genetic mapping population through a four-way outbred cross between two northern upland and two southern lowland accessions. Trait segregation in this mapping population was largely consistent with multiple independent loci controlling the suite of traits that characterizes ecotype divergence. We assembled a joint linkage map using ddRADseq, and mapped quantitative trait loci (QTL) for traits that are divergent between ecotypes, including flowering time, plant size, physiological processes, and disease resistance. Overall, we found that most QTL had small to intermediate effects. While we identified colocalizing QTL for multiple traits, we did not find any large-effect QTL that clearly controlled multiple traits through pleiotropy or tight physical linkage. These results indicate that ecologically important traits in switchgrass have a complex genetic basis, and that similar loci may underlie divergence across the geographic range of the ecotypes. PMID:27613751

Transethnic differences in GWAS signals: A simulation study.

PubMed

Zanetti, Daniela; Weale, Michael E

2018-05-07

Genome-wide association studies (GWASs) have allowed researchers to identify thousands of single nucleotide polymorphisms (SNPs) and other variants associated with particular complex traits. Previous studies have reported differences in the strength and even the direction of GWAS signals across different populations. These differences could be due to a combination of (1) lack of power, (2) allele frequency differences, (3) linkage disequilibrium (LD) differences, and (4) true differences in causal variant effect sizes. To determine whether properties (1)-(3) on their own might be sufficient to explain the patterns previously noted in strong GWAS signals, we simulated case-control data of European, Asian and African ancestry, applying realistic allele frequencies and LD from 1000 Genomes data but enforcing equal causal effect sizes across populations. Much of the observed differences in strong GWAS signals could indeed be accounted for by allele frequency and LD differences, enhanced by the Euro-centric SNP bias and lower SNP coverage found in older GWAS panels. While we cannot rule out a role for true transethnic effect size differences, our results suggest that strong causal effects may be largely shared among human populations, motivating the use of transethnic data for fine-mapping. © 2018 John Wiley & Sons Ltd/University College London.

Radiative lifetimes of zincblende CdSe/CdS quantum dots

DOE PAGES

Gong, Ke; Martin, James E.; Shea-Rohwer, Lauren E.; ...

2015-01-02

Recent synthetic advances have made available very monodisperse zincblende CdSe/CdS quantum dots having near-unity photoluminescence quantum yields. Because of the absence of nonradiative decay pathways, accurate values of the radiative lifetimes can be obtained from time-resolved PL measurements. Radiative lifetimes can also be obtained from the Einstein relations, using the static absorption spectra and the relative thermal populations in the angular momentum sublevels. We found that one of the inputs into these calculations is the shell thickness, and it is useful to be able to determine shell thickness from spectroscopic measurements. We use an empirically corrected effective mass model tomore » produce a “map” of exciton wavelength as a function of core size and shell thickness. These calculations use an elastic continuum model and the known lattice and elastic constants to include the effect of lattice strain on the band gap energy. The map is in agreement with the known CdSe sizing curve and with the shell thicknesses of zincblende core/shell particles obtained from TEM images. Furthermore, if selenium–sulfur diffusion is included and lattice strain is omitted from the calculation then the resulting map is appropriate for wurtzite CdSe/CdS quantum dots synthesized at high temperatures, and this map is very similar to one previously reported (J. Am. Chem. Soc. 2009, 131, 14299). Radiative lifetimes determined from time-resolved measurements are compared to values obtained from the Einstein relations, and found to be in excellent agreement. For a specific core size (2.64 nm diameter, in the present case), radiative lifetimes are found to decrease with increasing shell thickness. Thus, this is similar to the size dependence of one-component CdSe quantum dots and in contrast to the size dependence in type-II quantum dots.« less

Census-independent population mapping in northern Nigeria

DOE PAGES

Weber, Eric M.; Seaman, Vincent Y.; Stewart, Robert N.; ...

2017-10-21

Although remote sensing has long been used to aid in the estimation of population, it has usually been in the context of spatial disaggregation of national census data, with the census counts serving both as observational data for specifying models and as constraints on model outputs. Here we present a framework for estimating populations from the bottom up, entirely independently of national census data, a critical need in areas without recent and reliable census data. To make observations of population density, we replace national census data with a microcensus, in which we enumerate population for a sample of small areasmore » within the states of Kano and Kaduna in northern Nigeria. Using supervised texture-based classifiers with very high resolution satellite imagery, we produce a binary map of human settlement at 8-meter resolution across the two states and then a more refined classification consisting of 7 residential types and 1 non-residential type. Using the residential types and a model linking them to the population density observations, we produce population estimates across the two states in a gridded raster format, at approximately 90-meter resolution. We also demonstrate a simulation framework for capturing uncertainty and presenting estimates as prediction intervals for any region of interest of any size and composition within the study region. As a result, used in concert with previously published demographic estimates, our population estimates allowed for predictions of the population under 5 in ten administrative wards that fit strongly with reference data collected during polio vaccination campaigns.« less

Census-independent population mapping in northern Nigeria

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

Weber, Eric M.; Seaman, Vincent Y.; Stewart, Robert N.

Although remote sensing has long been used to aid in the estimation of population, it has usually been in the context of spatial disaggregation of national census data, with the census counts serving both as observational data for specifying models and as constraints on model outputs. Here we present a framework for estimating populations from the bottom up, entirely independently of national census data, a critical need in areas without recent and reliable census data. To make observations of population density, we replace national census data with a microcensus, in which we enumerate population for a sample of small areasmore » within the states of Kano and Kaduna in northern Nigeria. Using supervised texture-based classifiers with very high resolution satellite imagery, we produce a binary map of human settlement at 8-meter resolution across the two states and then a more refined classification consisting of 7 residential types and 1 non-residential type. Using the residential types and a model linking them to the population density observations, we produce population estimates across the two states in a gridded raster format, at approximately 90-meter resolution. We also demonstrate a simulation framework for capturing uncertainty and presenting estimates as prediction intervals for any region of interest of any size and composition within the study region. As a result, used in concert with previously published demographic estimates, our population estimates allowed for predictions of the population under 5 in ten administrative wards that fit strongly with reference data collected during polio vaccination campaigns.« less

A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.

PubMed Central

Davis, G L; McMullen, M D; Baysdorfer, C; Musket, T; Grant, D; Staebell, M; Xu, G; Polacco, M; Koster, L; Melia-Hancock, S; Houchins, K; Chao, S; Coe, E H

1999-01-01

We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits. PMID:10388831

Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic

USGS Publications Warehouse

Sillett, Scott T.; Chandler, Richard B.; Royle, J. Andrew; Kéry, Marc; Morrison, Scott A.

2012-01-01

Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural disasters and to habitat alteration related to climate change. Our results demonstrate that hierarchical distance-sampling models hold promise for estimating population size and spatial density variation at large scales. Our statistical methods have been incorporated into the R package unmarked to facilitate their use by animal ecologists, and we provide annotated code in the Supplement.

Estimating the number of male sex workers with the capture-recapture technique in Nigeria.

PubMed

Adebajo, Sylvia B; Eluwa, George I; Tocco, Jack U; Ahonsi, Babatunde A; Abiodun, Lolade Y; Anene, Oliver A; Akpona, Dennis O; Karlyn, Andrew S; Kellerman, Scott

2013-12-01

Estimating the size of populations most affected by HIV such as men who have sex with men (MSM) though crucial for structuring responses to the epidemic presents significant challenges, especially in a developing society. Using capture-recapture methodology, the size of MSM-SW in Nigeria was estimated in three major cities (Lagos, Kano and Port Harcourt) between July and December 2009. Following interviews with key informants, locations and times when MSM-SW were available to male clients were mapped and designated as "hotspots". Counts were conducted on two consecutive weekends. Population estimates were computed using a standardized Lincoln formula. Fifty-six hotspots were identified in Kano, 38 in Lagos and 42 in Port Harcourt. On a given weekend night, Port Harcourt had the largest estimated population of MSM sex workers, 723 (95% CI: 594-892) followed by Lagos state with 620 (95%CI: 517-724) and Kano state with 353 (95%CI: 332-373). This study documents a large population of MSM-SW in 3 Nigerian cities where higher HIV prevalence among MSM compared to the general population has been documented. Research and programming are needed to better understand and address the health vulnerabilities that MSM-SW and their clients face.

A comparison of turtle sampling methods in a small lake in Standing Stone State Park, Overton County, Tennessee

USGS Publications Warehouse

Weber, A.; Layzer, James B.

2011-01-01

We used basking traps and hoop nets to sample turtles in Standing Stone Lake at 2-week intervals from May to November 2006. In alternate weeks, we conducted visual basking surveys. We collected and observed four species of turtles: spiny softshell (Apalone spinifera), northern map turtle (Graptemys geographica), pond slider (Trachernys scripta), and snapping turtle (Chelydra serpentina). Relative abundances varied greatly among sampling methods. To varying degrees, all methods were species selective. Population estimates from mark and recaptures of three species, basking counts, and hoop net catches indicated that pond sliders were the most abundant species, but northern map turtles were 8× more abundant than pond sliders in basking trap catches. We saw relatively few snapping turtles basking even though population estimates indicated they were the second most abundant species. Populations of all species were dominated by adult individuals. Sex ratios of three species differed significantly from 1:1. Visual surveys were the most efficient method for determining the presence of species, but capture methods were necessary to obtain size and sex data.

The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera.

PubMed

Sargent, D J; Rys, A; Nier, S; Simpson, D W; Tobutt, K R

2007-01-01

We have developed 46 primer pairs from exon sequences flanking polymorphic introns of 23 Fragaria gene sequences and one Malus sequence deposited in the EMBL database. Sequencing of a set of the PCR products amplified with the novel primer pairs in diploid Fragaria showed the products to be homologous to the sequences from which the primers were originally designed. By scoring the segregation of the 24 genes in two diploid Fragaria progenies FV x FN (F. vesca x F. nubicola F(2)) and 815 x 903BC (F. vesca x F. viridis BC(1)) 29 genetic loci at discrete positions on the seven linkage groups previously characterised could be mapped, bringing to 35 the total number of known function genes mapped in Fragaria. Twenty primer pairs, representing 14 genes, amplified a product of the expected size in both Malus and Prunus. To demonstrate the applicability of these gene-specific loci to comparative mapping in Rosaceae, five markers that displayed clear polymorphism between the parents of a Malus and a Prunus mapping population were selected. The markers were then scored and mapped in at least one of the two additional progenies.

Mapping Agricultural Fields in Sub-Saharan Africa with a Computer Vision Approach

NASA Astrophysics Data System (ADS)

Debats, S. R.; Luo, D.; Estes, L. D.; Fuchs, T.; Caylor, K. K.

2014-12-01

Sub-Saharan Africa is an important focus for food security research, because it is experiencing unprecedented population growth, agricultural activities are largely dominated by smallholder production, and the region is already home to 25% of the world's undernourished. One of the greatest challenges to monitoring and improving food security in this region is obtaining an accurate accounting of the spatial distribution of agriculture. Households are the primary units of agricultural production in smallholder communities and typically rely on small fields of less than 2 hectares. Field sizes are directly related to household crop productivity, management choices, and adoption of new technologies. As population and agriculture expand, it becomes increasingly important to understand both the distribution of field sizes as well as how agricultural communities are spatially embedded in the landscape. In addition, household surveys, a common tool for tracking agricultural productivity in Sub-Saharan Africa, would greatly benefit from spatially explicit accounting of fields. Current gridded land cover data sets do not provide information on individual agricultural fields or the distribution of field sizes. Therefore, we employ cutting edge approaches from the field of computer vision to map fields across Sub-Saharan Africa, including semantic segmentation, discriminative classifiers, and automatic feature selection. Our approach aims to not only improve the binary classification accuracy of cropland, but also to isolate distinct fields, thereby capturing crucial information on size and geometry. Our research focuses on the development of descriptive features across scales to increase the accuracy and geographic range of our computer vision algorithm. Relevant data sets include high-resolution remote sensing imagery and Landsat (30-m) multi-spectral imagery. Training data for field boundaries is derived from hand-digitized data sets as well as crowdsourcing.

Prospects of Fine-Mapping Trait-Associated Genomic Regions by Using Summary Statistics from Genome-wide Association Studies.

PubMed

Benner, Christian; Havulinna, Aki S; Järvelin, Marjo-Riitta; Salomaa, Veikko; Ripatti, Samuli; Pirinen, Matti

2017-10-05

During the past few years, various novel statistical methods have been developed for fine-mapping with the use of summary statistics from genome-wide association studies (GWASs). Although these approaches require information about the linkage disequilibrium (LD) between variants, there has not been a comprehensive evaluation of how estimation of the LD structure from reference genotype panels performs in comparison with that from the original individual-level GWAS data. Using population genotype data from Finland and the UK Biobank, we show here that a reference panel of 1,000 individuals from the target population is adequate for a GWAS cohort of up to 10,000 individuals, whereas smaller panels, such as those from the 1000 Genomes Project, should be avoided. We also show, both theoretically and empirically, that the size of the reference panel needs to scale with the GWAS sample size; this has important consequences for the application of these methods in ongoing GWAS meta-analyses and large biobank studies. We conclude by providing software tools and by recommending practices for sharing LD information to more efficiently exploit summary statistics in genetics research. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Medical Geography: a Promising Field of Application for Geostatistics.

PubMed

Goovaerts, P

2009-01-01

The analysis of health data and putative covariates, such as environmental, socio-economic, behavioral or demographic factors, is a promising application for geostatistics. It presents, however, several methodological challenges that arise from the fact that data are typically aggregated over irregular spatial supports and consist of a numerator and a denominator (i.e. population size). This paper presents an overview of recent developments in the field of health geostatistics, with an emphasis on three main steps in the analysis of areal health data: estimation of the underlying disease risk, detection of areas with significantly higher risk, and analysis of relationships with putative risk factors. The analysis is illustrated using age-adjusted cervix cancer mortality rates recorded over the 1970-1994 period for 118 counties of four states in the Western USA. Poisson kriging allows the filtering of noisy mortality rates computed from small population sizes, enhancing the correlation with two putative explanatory variables: percentage of habitants living below the federally defined poverty line, and percentage of Hispanic females. Area-to-point kriging formulation creates continuous maps of mortality risk, reducing the visual bias associated with the interpretation of choropleth maps. Stochastic simulation is used to generate realizations of cancer mortality maps, which allows one to quantify numerically how the uncertainty about the spatial distribution of health outcomes translates into uncertainty about the location of clusters of high values or the correlation with covariates. Last, geographically-weighted regression highlights the non-stationarity in the explanatory power of covariates: the higher mortality values along the coast are better explained by the two covariates than the lower risk recorded in Utah.

Assortative mating and fragmentation within dog breeds.

PubMed

Björnerfeldt, Susanne; Hailer, Frank; Nord, Maria; Vilà, Carles

2008-01-28

There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds.

Assortative mating and fragmentation within dog breeds

PubMed Central

2008-01-01

Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds. PMID:18226210

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.

PubMed

Puritz, Jonathan B; Hollenbeck, Christopher M; Gold, John R

2014-01-01

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

PubMed Central

Hollenbeck, Christopher M.; Gold, John R.

2014-01-01

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com. PMID:24949246

Molecular Population Genetics of the Alcohol Dehydrogenase Gene Region of DROSOPHILA MELANOGASTER

PubMed Central

Aquadro, Charles F.; Desse, Susan F.; Bland, Molly M.; Langley, Charles H.; Laurie-Ahlberg, Cathy C.

1986-01-01

Variation in the DNA restriction map of a 13-kb region of chromosome II including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21–200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5' to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L) t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations. PMID:3026893

The mutation-drift balance in spatially structured populations.

PubMed

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

2016-08-07

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

The Cluster Population of UGC 2885

NASA Astrophysics Data System (ADS)

Holwerda, Benne

2017-08-01

UGC 2885 was discoverd to be the most extended disk galaxy [250 kpc diameter] by Vera Rubin in the 1980's. We ask for HST observations of UGC 2885 as it is close enough to resolve the GC population with HST but it is a substantially more extended disk than any studied before. LCDM galaxy assembly implies that the GC population comes from small accreted systems and the disk -and the clusters associated with it- predominantly from gas accretion (matching angular momentum to the disk). Several scaling relations between the GC population and parent galaxy have been observed but these differ for disk and spheroidal (massive) galaxies.We propose to observe this galaxy with HST in 4 point WFC3 mosaic with coordinated ACS parallels to probe both the disk and outer halo component of the GC population. GC populations have been studied extensively using HST color mosaics of local disk galaxies and these can serve as comparison samples. How UGC 2885 cluster populations relate to its stellar and halo mass, luminosity and with radius will reveal the formation history of extra-ordinary disk.Our goals are twofold: our science goal is to map the luminosity, (some) size, and color distributions of the stellar and globular clusters in and around this disk. In absolute terms, we expect to find many GC but the relative relation of the GC population to this galaxy's mass (stellar and halo) and size will shed light on its formation history; similar to a group or cluster central elliptical or to a field galaxy (albeit one with a disk 10x the Milky Way's size)? Our secondary motive is to make an HST tribute image to the late Vera Rubin.

Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus)

EPA Pesticide Factsheets

Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.This dataset is associated with the following publication:Waits , E., J. Martinson , B. Rinner, S. Morris, D. Proestou, D. Champlin , and D. Nacci. Genetic linkage map and comparative genome analysis for the estuarine Atlanti

Illicit Drug Users in the Tanzanian Hinterland: Population Size Estimation Through Key Informant-Driven Hot Spot Mapping.

PubMed

Ndayongeje, Joel; Msami, Amani; Laurent, Yovin Ivo; Mwankemwa, Syangu; Makumbuli, Moza; Ngonyani, Alois M; Tiberio, Jenny; Welty, Susie; Said, Christen; Morris, Meghan D; McFarland, Willi

2018-02-12

We mapped hot spots and estimated the numbers of people who use drugs (PWUD) and who inject drugs (PWID) in 12 regions of Tanzania. Primary (ie, current and past PWUD) and secondary (eg, police, service providers) key informants identified potential hot spots, which we visited to verify and count the number of PWUD and PWID present. Adjustments to counts and extrapolation to regional estimates were done by local experts through iterative rounds of discussion. Drug use, specifically cocaine and heroin, occurred in all regions. Tanga had the largest numbers of PWUD and PWID (5190 and 540, respectively), followed by Mwanza (3300 and 300, respectively). Findings highlight the need to strengthen awareness of drug use and develop prevention and harm reduction programs with broader reach in Tanzania. This exercise provides a foundation for understanding the extent and locations of drug use, a baseline for future size estimations, and a sampling frame for future research.

Geographic variation in sexual behavior can explain geospatial heterogeneity in the severity of the HIV epidemic in Malawi.

PubMed

Palk, Laurence; Blower, Sally

2018-02-09

In sub-Saharan Africa, where ~ 25 million individuals are infected with HIV and transmission is predominantly heterosexual, there is substantial geographic variation in the severity of epidemics. This variation has yet to be explained. Here, we propose that it is due to geographic variation in the size of the high-risk group (HRG): the group with a high number of sex partners. We test our hypothesis by conducting a geospatial analysis of data from Malawi, where ~ 13% of women and ~ 8% of men are infected with HIV. We used georeferenced HIV testing and behavioral data from ~ 14,000 participants of a nationally representative population-level survey: the 2010 Malawi Demographic and Health Survey (MDHS). We constructed gender-stratified epidemic surface prevalence (ESP) maps by spatially smoothing and interpolating the HIV testing data. We used the behavioral data to construct gender-stratified risk maps that reveal geographic variation in the size of the HRG. We tested our hypothesis by fitting gender-stratified spatial error regression (SER) models to the MDHS data. The ESP maps show considerable geographic variation in prevalence: 1-29% (women), 1-20% (men). Risk maps reveal substantial geographic variation in the size of the HRG: 0-40% (women), 16-58% (men). Prevalence and the size of the HRG are highest in urban centers. However, the majority of HIV-infected individuals (~75% of women, ~ 80% of men) live in rural areas, as does most of the HRG (~ 80% of women, ~ 85% of men). We identify a significant (P < 0.001) geospatial relationship linking the size of the HRG with prevalence: the greater the size, the higher the prevalence. SER models show HIV prevalence in women is expected to exceed the national average in districts where > 20% of women are in the HRG. Most importantly, the SER models show that geographic variation in the size of the HRG can explain a substantial proportion (73% for women, 67% for men) of the geographic variation in epidemic severity. Taken together, our results provide substantial support for our hypothesis. They provide a potential mechanistic explanation for the geographic variation in the severity of the HIV epidemic in Malawi and, potentially, in other countries in sub-Saharan Africa.

Partitioning of pyroclasts between ballistic transport and a convective plume: Kīlauea volcano, 19 March 2008

NASA Astrophysics Data System (ADS)

Houghton, B. F.; Swanson, D. A.; Biass, S.; Fagents, S. A.; Orr, T. R.

2017-05-01

We describe the discrete ballistic and wind-advected products of a small, but exceptionally well-characterized, explosive eruption of wall-rock-derived pyroclasts from Kīlauea volcano on 19 March 2008 and, for the first time, integrate the size distribution of the two subpopulations to reconstruct the true size distribution of a population of pyroclasts as it exited from the vent. Based on thinning and fining relationships, the wind-advected fraction had a mass of 6.1 × 105 kg and a thickness half distance of 110 m, placing it at the bottom end of the magnitude and intensity spectra of pyroclastic falls. The ballistic population was mapped, in the field and by using structure-from-motion techniques, to a diameter of > 10-20 cm over an area of 0.1 km2, with an estimated mass of 1 × 105 kg. Initial ejection velocities of 50-80 m/s were estimated from inversion of isopleths. The total grain size distribution was estimated by using a mass partitioning of 98% of wind-advected material and 2% of ballistics, resulting in median and sorting values of -1.7ϕ and 3.1ϕ. It is markedly broader than those calculated for the products of magmatic explosive eruptions, because the grain size of 19 March 2008 clast population is unrelated to a volcanic fragmentation event and instead was "inherited" from a population of talus clasts that temporary blocked the vent prior to the eruption. Despite a conspicuous near-field presence, the ballistic subpopulation has only a minor influence on the grain size distribution because of its rapid thinning and fining away from source.

Mapping global cropland and field size.

PubMed

Fritz, Steffen; See, Linda; McCallum, Ian; You, Liangzhi; Bun, Andriy; Moltchanova, Elena; Duerauer, Martina; Albrecht, Fransizka; Schill, Christian; Perger, Christoph; Havlik, Petr; Mosnier, Aline; Thornton, Philip; Wood-Sichra, Ulrike; Herrero, Mario; Becker-Reshef, Inbal; Justice, Chris; Hansen, Matthew; Gong, Peng; Abdel Aziz, Sheta; Cipriani, Anna; Cumani, Renato; Cecchi, Giuliano; Conchedda, Giulia; Ferreira, Stefanus; Gomez, Adriana; Haffani, Myriam; Kayitakire, Francois; Malanding, Jaiteh; Mueller, Rick; Newby, Terence; Nonguierma, Andre; Olusegun, Adeaga; Ortner, Simone; Rajak, D Ram; Rocha, Jansle; Schepaschenko, Dmitry; Schepaschenko, Maria; Terekhov, Alexey; Tiangwa, Alex; Vancutsem, Christelle; Vintrou, Elodie; Wenbin, Wu; van der Velde, Marijn; Dunwoody, Antonia; Kraxner, Florian; Obersteiner, Michael

2015-05-01

A new 1 km global IIASA-IFPRI cropland percentage map for the baseline year 2005 has been developed which integrates a number of individual cropland maps at global to regional to national scales. The individual map products include existing global land cover maps such as GlobCover 2005 and MODIS v.5, regional maps such as AFRICOVER and national maps from mapping agencies and other organizations. The different products are ranked at the national level using crowdsourced data from Geo-Wiki to create a map that reflects the likelihood of cropland. Calibration with national and subnational crop statistics was then undertaken to distribute the cropland within each country and subnational unit. The new IIASA-IFPRI cropland product has been validated using very high-resolution satellite imagery via Geo-Wiki and has an overall accuracy of 82.4%. It has also been compared with the EarthStat cropland product and shows a lower root mean square error on an independent data set collected from Geo-Wiki. The first ever global field size map was produced at the same resolution as the IIASA-IFPRI cropland map based on interpolation of field size data collected via a Geo-Wiki crowdsourcing campaign. A validation exercise of the global field size map revealed satisfactory agreement with control data, particularly given the relatively modest size of the field size data set used to create the map. Both are critical inputs to global agricultural monitoring in the frame of GEOGLAM and will serve the global land modelling and integrated assessment community, in particular for improving land use models that require baseline cropland information. These products are freely available for downloading from the http://cropland.geo-wiki.org website. © 2015 John Wiley & Sons Ltd.

Detecting negative selection on recurrent mutations using gene genealogy

PubMed Central

2013-01-01

Background Whether or not a mutant allele in a population is under selection is an important issue in population genetics, and various neutrality tests have been invented so far to detect selection. However, detection of negative selection has been notoriously difficult, partly because negatively selected alleles are usually rare in the population and have little impact on either population dynamics or the shape of the gene genealogy. Recently, through studies of genetic disorders and genome-wide analyses, many structural variations were shown to occur recurrently in the population. Such “recurrent mutations” might be revealed as deleterious by exploiting the signal of negative selection in the gene genealogy enhanced by their recurrence. Results Motivated by the above idea, we devised two new test statistics. One is the total number of mutants at a recurrently mutating locus among sampled sequences, which is tested conditionally on the number of forward mutations mapped on the sequence genealogy. The other is the size of the most common class of identical-by-descent mutants in the sample, again tested conditionally on the number of forward mutations mapped on the sequence genealogy. To examine the performance of these two tests, we simulated recurrently mutated loci each flanked by sites with neutral single nucleotide polymorphisms (SNPs), with no recombination. Using neutral recurrent mutations as null models, we attempted to detect deleterious recurrent mutations. Our analyses demonstrated high powers of our new tests under constant population size, as well as their moderate power to detect selection in expanding populations. We also devised a new maximum parsimony algorithm that, given the states of the sampled sequences at a recurrently mutating locus and an incompletely resolved genealogy, enumerates mutation histories with a minimum number of mutations while partially resolving genealogical relationships when necessary. Conclusions With their considerably high powers to detect negative selection, our new neutrality tests may open new venues for dealing with the population genetics of recurrent mutations as well as help identifying some types of genetic disorders that may have escaped identification by currently existing methods. PMID:23651527

Stratigraphy, Sequence, and Crater Populations of Lunar Impact Basins from Lunar Orbiter Laser Altimeter (LOLA) Data: Implications for the Late Heavy Bombardment

NASA Technical Reports Server (NTRS)

Fassett, C. I.; Head, J. W.; Kadish, S. J.; Mazarico, E.; Neumann, G. A.; Smith, D. E.; Zuber, M. T.

2012-01-01

New measurements of the topography of the Moon from the Lunar Orbiter Laser Altimeter (LOLA)[1] provide an excellent base-map for analyzing the large crater population (D.20 km)of the lunar surface [2, 3]. We have recently used this data to calculate crater size-frequency distributions (CSFD) for 30 lunar impact basins, which have implications for their stratigraphy and sequence. These data provide an avenue for assessing the timing of the transitions between distinct crater populations characteristic of ancient and young lunar terrains, which has been linked to the late heavy bombardment (LHB). We also use LOLA data to re-examine relative stratigraphic relationships between key lunar basins.

Comparing the efficiency of digital and conventional soil mapping to predict soil types in a semi-arid region in Iran

NASA Astrophysics Data System (ADS)

Zeraatpisheh, Mojtaba; Ayoubi, Shamsollah; Jafari, Azam; Finke, Peter

2017-05-01

The efficiency of different digital and conventional soil mapping approaches to produce categorical maps of soil types is determined by cost, sample size, accuracy and the selected taxonomic level. The efficiency of digital and conventional soil mapping approaches was examined in the semi-arid region of Borujen, central Iran. This research aimed to (i) compare two digital soil mapping approaches including Multinomial logistic regression and random forest, with the conventional soil mapping approach at four soil taxonomic levels (order, suborder, great group and subgroup levels), (ii) validate the predicted soil maps by the same validation data set to determine the best method for producing the soil maps, and (iii) select the best soil taxonomic level by different approaches at three sample sizes (100, 80, and 60 point observations), in two scenarios with and without a geomorphology map as a spatial covariate. In most predicted maps, using both digital soil mapping approaches, the best results were obtained using the combination of terrain attributes and the geomorphology map, although differences between the scenarios with and without the geomorphology map were not significant. Employing the geomorphology map increased map purity and the Kappa index, and led to a decrease in the 'noisiness' of soil maps. Multinomial logistic regression had better performance at higher taxonomic levels (order and suborder levels); however, random forest showed better performance at lower taxonomic levels (great group and subgroup levels). Multinomial logistic regression was less sensitive than random forest to a decrease in the number of training observations. The conventional soil mapping method produced a map with larger minimum polygon size because of traditional cartographic criteria used to make the geological map 1:100,000 (on which the conventional soil mapping map was largely based). Likewise, conventional soil mapping map had also a larger average polygon size that resulted in a lower level of detail. Multinomial logistic regression at the order level (map purity of 0.80), random forest at the suborder (map purity of 0.72) and great group level (map purity of 0.60), and conventional soil mapping at the subgroup level (map purity of 0.48) produced the most accurate maps in the study area. The multinomial logistic regression method was identified as the most effective approach based on a combined index of map purity, map information content, and map production cost. The combined index also showed that smaller sample size led to a preference for the order level, while a larger sample size led to a preference for the great group level.

Mapping Prevalence and Incidence of Coral Disease in reef-building corals at two Natural Reserves of the Southwest Puerto Rico

NASA Astrophysics Data System (ADS)

Sanchez Viruet, I.; Irizarry-Soto, E.; Ruiz-Valentín, I.

2016-02-01

Coral diseases seems to be the main cause of coral reef decline in the Caribbean. Before the bleaching event of 2005, coral reefs in Puerto Rico were dominated by the reef-building taxa: Orbicella annularis, Porites astreoides, Montastrea cavernosa, Agaricia agaracites and Colpophyllia natans. After the event, live-coral cover significantly declined and more than 90% of the scleractinian corals in the U.S. Virgin Islands and Puerto Rico showed signals of thermal stressors. The prevalence of coral diseases in five reef-building coral (Orbicella annularis, Orbicella franksi, Orbicella faveolata, Porites porites and Pseudiploria strigosa) species was assessed by tagging, photographing, and mapping all diseased and healthy colonies within 10 permanent 40m2 band transects at each inshore and mid-shelf reefs of Belvedere and Punta Guaniquilla Natural Reserves using a random stratified sampling method. Maximum and perpendicular diameter was used to assess coral size using Coral Point Count with Excel Extension. Corals were classified into three size class populations (class I: 0-50cm, class II: 50-100cm and class III: >100 cm). Data was used to develop a GIS-based map containing coral species, size and disease presence. Preliminary results of the inshore area showed a higher disease prevalence in Belvedere natural reserve and for P. strigosa (17.1%) and O. annularis (9.3%). Frequency distribution analysis showed a dominance of O. faveolata at Punta Guaniquilla and Belvedere (127 and 88 individuals respectively). Size class I dominates the distribution of each species within the natural reserves with a higher disease prevalence. Future work include continue prevalence surveys of the outer reef shelf on both natural reserves, monitoring and GIS-based mapping of incidence and resilience through time. This study will help in the assessment of the status of the coral reef of the southwest insular platform.

Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy

PubMed Central

Xu, Shuhua; Huang, Wei; Qian, Ji; Jin, Li

2008-01-01

The Uyghur (UIG) population, settled in Xinjiang, China, is a population presenting a typical admixture of Eastern and Western anthropometric traits. We dissected its genomic structure at population level, individual level, and chromosome level by using 20,177 SNPs spanning nearly the entire chromosome 21. Our results showed that UIG was formed by two-way admixture, with 60% European ancestry and 40% East Asian ancestry. Overall linkage disequilibrium (LD) in UIG was similar to that in its parental populations represented in East Asia and Europe with regard to common alleles, and UIG manifested elevation of LD only within 500 kb and at a level of 0.1 < r2 < 0.8 when ancestry-informative markers (AIMs) were used. The size of chromosomal segments that were derived from East Asian and European ancestries averaged 2.4 cM and 4.1 cM, respectively. Both the magnitude of LD and fragmentary ancestral chromosome segments indicated a long history of Uyghur. Under the assumption of a hybrid isolation (HI) model, we estimated that the admixture event of UIG occurred about 126 [107∼146] generations ago, or 2520 [2140∼2920] years ago assuming 20 years per generation. In spite of the long history and short LD of Uyghur compared with recent admixture populations such as the African-American population, we suggest that mapping by admixture LD (MALD) is still applicable in the Uyghur population but ∼10-fold AIMs are necessary for a whole-genome scan. PMID:18355773

The Role of Local Ancestry Adjustment in Association Studies Using Admixed Populations

PubMed Central

Zhang, Jianqi; Stram, Daniel O.

2016-01-01

Association analysis using admixed populations imposes challenges and opportunities for disease mapping. By developing some explicit results for the variance of an allele of interest conditional on either local or global ancestry and by simulation of recently admixed genomes we evaluate power and false-positive rates under a variety of scenarios concerning linkage disequilibrium (LD) and the presence of unmeasured variants. Pairwise LD patterns were compared between admixed and nonadmixed populations using the HapMap phase 3 data. Based on the above, we showed that as follows: For causal variants with similar effect size in all populations, power is generally higher in a study using admixed population than using nonadmixed population, especially for highly differentiated SNPs. This gain of power is achieved with adjustment of global ancestry, which completely removes any cross-chromosome inflation of type I error rates, and addresses much of the intrachromosome inflation.If reliably estimated, adjusting for local ancestry precisely recovers the localization that could have been achieved in a stratified analysis of source populations. Improved localization is most evident for highly differentiated SNPs; however, the advantage of higher power is lost on exactly the same differentiated SNPs.In the real admixed populations such as African Americans and Latinos, the expansion of LD is not as dramatic as in our simulation.While adjustment for global ancestry is required prior to announcing a novel association seen in an admixed population, local ancestry adjustment may best be regarded as a localization tool not strictly required for discovery purposes. PMID:25043967

Earthquake hazard and risk assessment based on Unified Scaling Law for Earthquakes: Greater Caucasus and Crimea

NASA Astrophysics Data System (ADS)

Kossobokov, Vladimir G.; Nekrasova, Anastasia K.

2018-05-01

We continue applying the general concept of seismic risk analysis in a number of seismic regions worldwide by constructing regional seismic hazard maps based on morphostructural analysis, pattern recognition, and the Unified Scaling Law for Earthquakes (USLE), which generalizes the Gutenberg-Richter relationship making use of naturally fractal distribution of earthquake sources of different size in a seismic region. The USLE stands for an empirical relationship log10 N(M, L) = A + B·(5 - M) + C·log10 L, where N(M, L) is the expected annual number of earthquakes of a certain magnitude M within a seismically prone area of linear dimension L. We use parameters A, B, and C of USLE to estimate, first, the expected maximum magnitude in a time interval at seismically prone nodes of the morphostructural scheme of the region under study, then map the corresponding expected ground shaking parameters (e.g., peak ground acceleration, PGA, or macro-seismic intensity). After a rigorous verification against the available seismic evidences in the past (usually, the observed instrumental PGA or the historically reported macro-seismic intensity), such a seismic hazard map is used to generate maps of specific earthquake risks for population, cities, and infrastructures (e.g., those based on census of population, buildings inventory). The methodology of seismic hazard and risk assessment is illustrated by application to the territory of Greater Caucasus and Crimea.

Effects of simulated daily precipitation patterns on annual plant populations depend on life stage and climatic region.

PubMed

Köchy, Martin

2008-03-27

To improve the understanding of consequences of climate change for annual plant communities, I used a detailed, grid-based model that simulates the effect of daily rainfall variability on individual plants in five climatic regions on a gradient from 100 to 800 mm mean annual precipitation (MAP). The model explicitly considers moisture storage in the soil. I manipulated daily rainfall variability by changing the daily mean rain (DMR, rain volume on rainy days averaged across years for each day of the year) by +/- 20%. At the same time I adjusted intervals appropriately between rainy days for keeping the mean annual volume constant. In factorial combination with changing DMR I also changed MAP by +/- 20%. Increasing MAP generally increased water availability, establishment, and peak shoot biomass. Increasing DMR increased the time that water was continuously available to plants in the upper 15 to 30 cm of the soil (longest wet period, LWP). The effect of DMR diminished with increasing humidity of the climate. An interaction between water availability and density-dependent germination increased the establishment of seedlings in the arid region, but in the more humid regions the establishment of seedlings decreased with increasing DMR. As plants matured, competition among individuals and their productivity increased, but the size of these effects decreased with the humidity of the regions. Therefore, peak shoot biomass generally increased with increasing DMR but the effect size diminished from the semiarid to the mesic Mediterranean region. Increasing DMR reduced via LWP the annual variability of biomass in the semiarid and dry Mediterranean regions. More rainstorms (greater DMR) increased the recharge of soil water reservoirs in more arid sites with consequences for germination, establishment, productivity, and population persistence. The order of magnitudes of DMR and MAP overlapped partially so that their combined effect is important for projections of climate change effects on annual vegetation.

A second-order orientation-contrast stimulus for population-receptive-field-based retinotopic mapping.

PubMed

Yildirim, Funda; Carvalho, Joana; Cornelissen, Frans W

2018-01-01

Visual field or retinotopic mapping is one of the most frequently used paradigms in fMRI. It uses activity evoked by position-varying high luminance contrast visual patterns presented throughout the visual field for determining the spatial organization of cortical visual areas. While the advantage of using high luminance contrast is that it tends to drive a wide range of neural populations - thus resulting in high signal-to-noise BOLD responses - this may also be a limitation, especially for approaches that attempt to squeeze more information out of the BOLD response, such as population receptive field (pRF) mapping. In that case, more selective stimulation of a subset of neurons - despite reduced signals - could result in better characterization of pRF properties. Here, we used a second-order stimulus based on local differences in orientation texture - to which we refer as orientation contrast - to perform retinotopic mapping. Participants in our experiment viewed arrays of Gabor patches composed of a foreground (a bar) and a background. These could only be distinguished on the basis of a difference in patch orientation. In our analyses, we compare the pRF properties obtained using this new orientation contrast-based retinotopy (OCR) to those obtained using classic luminance contrast-based retinotopy (LCR). Specifically, in higher order cortical visual areas such as LO, our novel approach resulted in non-trivial reductions in estimated population receptive field size of around 30%. A set of control experiments confirms that the most plausible cause for this reduction is that OCR mainly drives neurons sensitive to orientation contrast. We discuss how OCR - by limiting receptive field scatter and reducing BOLD displacement - may result in more accurate pRF localization as well. Estimation of neuronal properties is crucial for interpreting cortical function. Therefore, we conclude that using our approach, it is possible to selectively target particular neuronal populations, opening the way to use pRF modeling to dissect the response properties of more clearly-defined neuronal populations in different visual areas. Copyright © 2017 Elsevier Inc. All rights reserved.

Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat

PubMed Central

Liu, Guozheng; Zhao, Yusheng; Gowda, Manje; Longin, C. Friedrich H.; Reif, Jochen C.; Mette, Michael F.

2016-01-01

Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L.) and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs), but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population. PMID:27383841

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

PubMed Central

Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

2014-01-01

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information. PMID:25914583

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench).

PubMed

Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

2014-12-01

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information.

Mapped Plot Patch Size Estimates

Treesearch

Paul C. Van Deusen

2005-01-01

This paper demonstrates that the mapped plot design is relatively easy to analyze and describes existing formulas for mean and variance estimators. New methods are developed for using mapped plots to estimate average patch size of condition classes. The patch size estimators require assumptions about the shape of the condition class, limiting their utility. They may...

Maternal choline supplementation improves spatial mapping and increases basal forebrain cholinergic neuron number and size in aged Ts65Dn mice.

PubMed

Ash, Jessica A; Velazquez, Ramon; Kelley, Christy M; Powers, Brian E; Ginsberg, Stephen D; Mufson, Elliott J; Strupp, Barbara J

2014-10-01

Down syndrome (DS) is marked by intellectual disability (ID) and early-onset of Alzheimer's disease (AD) neuropathology, including basal forebrain cholinergic neuron (BFCN) degeneration. The present study tested the hypothesis that maternal choline supplementation (MCS) improves spatial mapping and protects against BFCN degeneration in the Ts65Dn mouse model of DS and AD. During pregnancy and lactation, dams were assigned to either a choline sufficient (1.1g/kg choline chloride) or choline supplemented (5.0g/kg choline chloride) diet. Between 13 and 17months of age, offspring were tested in the radial arm water maze (RAWM) to examine spatial mapping followed by unbiased quantitative morphometry of BFCNs. Spatial mapping was significantly impaired in unsupplemented Ts65Dn mice relative to normal disomic (2N) littermates. Additionally, a significantly lower number and density of medial septum (MS) hippocampal projection BFCNs was also found in unsupplemented Ts65Dn mice. Notably, MCS significantly improved spatial mapping and increased number, density, and size of MS BFCNs in Ts65Dn offspring. Moreover, the density and number of MS BFCNs correlated significantly with spatial memory proficiency, providing support for a functional relationship between these behavioral and morphometric effects of MCS for trisomic offspring. Thus, increasing maternal choline intake during pregnancy may represent a safe and effective treatment approach for expectant mothers carrying a DS fetus, as well as a possible means of BFCN neuroprotection during aging for the population at large. Copyright © 2014 Elsevier Inc. All rights reserved.

Efficiency gain of marker-assisted backcrossing by sequentially increasing marker densities over generations.

PubMed

Prigge, Vanessa; Melchinger, Albrecht E; Dhillon, Baldev S; Frisch, Matthias

2009-06-01

Expenses for marker assays are the major costs in marker-assisted backcrossing programs for the transfer of target genes from a donor into the genetic background of a recipient genotype. Our objectives were to (1) investigate the effect of employing sequentially increasing marker densities over backcross generations on the recurrent parent genome (RPG) recovery and the number of marker data points (MDP) required, and (2) determine optimum designs for attaining RPG thresholds of 93-98% with a minimum number of MDP. We simulated the introgression of one dominant target gene for genome models of sugar beet (Beta vulgaris L.) and maize (Zea mays L.) with varying marker distances of 5-80 cM and population sizes of 30-250 plants across BC(1) to BC(3) generations. Employing less dense maps in early backcross generations resulted in savings of over 50% in the number of required MDP compared with using a constant set of markers and was accompanied only by small reductions in the attained RPG values. The optimum designs were characterized by increasing marker densities and increasing population sizes in advanced generations for both genome models. We conclude that increasing simultaneously the marker density and the population size from early to advanced backcross generations results in gene introgression with a minimum number of required MDP.

High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.

PubMed

Bartholomé, Jérôme; Mandrou, Eric; Mabiala, André; Jenkins, Jerry; Nabihoudine, Ibouniyamine; Klopp, Christophe; Schmutz, Jeremy; Plomion, Christophe; Gion, Jean-Marc

2015-06-01

Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome. © 2014 CIRAD. New Phytologist © 2014 New Phytologist Trust.

Medical Geography: a Promising Field of Application for Geostatistics

PubMed Central

Goovaerts, P.

2008-01-01

The analysis of health data and putative covariates, such as environmental, socio-economic, behavioral or demographic factors, is a promising application for geostatistics. It presents, however, several methodological challenges that arise from the fact that data are typically aggregated over irregular spatial supports and consist of a numerator and a denominator (i.e. population size). This paper presents an overview of recent developments in the field of health geostatistics, with an emphasis on three main steps in the analysis of areal health data: estimation of the underlying disease risk, detection of areas with significantly higher risk, and analysis of relationships with putative risk factors. The analysis is illustrated using age-adjusted cervix cancer mortality rates recorded over the 1970–1994 period for 118 counties of four states in the Western USA. Poisson kriging allows the filtering of noisy mortality rates computed from small population sizes, enhancing the correlation with two putative explanatory variables: percentage of habitants living below the federally defined poverty line, and percentage of Hispanic females. Area-to-point kriging formulation creates continuous maps of mortality risk, reducing the visual bias associated with the interpretation of choropleth maps. Stochastic simulation is used to generate realizations of cancer mortality maps, which allows one to quantify numerically how the uncertainty about the spatial distribution of health outcomes translates into uncertainty about the location of clusters of high values or the correlation with covariates. Last, geographically-weighted regression highlights the non-stationarity in the explanatory power of covariates: the higher mortality values along the coast are better explained by the two covariates than the lower risk recorded in Utah. PMID:19412347

A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence.

PubMed

Grattapaglia, Dario; Mamani, Eva M C; Silva-Junior, Orzenil B; Faria, Danielle A

2015-03-01

Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite-only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination-based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8-Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome-wide population genetics and comparative mapping in Eucalyptus. © 2014 John Wiley & Sons Ltd.

EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

PubMed Central

2010-01-01

Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species. PMID:20712870

A Statistical Analysis of Corona Topography: New Insights into Corona Formation and Evolution

NASA Technical Reports Server (NTRS)

Stofan, E. R.; Glaze, L. S.; Smrekar, S. E.; Baloga, S. M.

2003-01-01

Extensive mapping of the surface of Venus and continued analysis of Magellan data have allowed a more comprehensive survey of coronae to be conducted. Our updated corona database contains 514 features, an increase from the 326 coronae of the previous survey. We include a new set of 106 Type 2 or stealth coronae, which have a topographic rather than a fracture annulus. The large increase in the number of coronae over the 1992 survey results from several factors, including the use of the full Magellan data set and the addition of features identified as part of the systematic geologic mapping of Venus. Parameters of the population that we have analyzed to date include size and topography.

PhyloGeoViz: a web-based program that visualizes genetic data on maps.

PubMed

Tsai, Yi-Hsin E

2011-05-01

The first step of many population genetic studies is the simple visualization of allele frequencies on a landscape. This basic data exploration can be challenging without proprietary software, and the manual plotting of data is cumbersome and unfeasible at large sample sizes. I present an open source, web-based program that plots any kind of frequency or count data as pie charts in Google Maps (Google Inc., Mountain View, CA). Pie polygons are then exportable to Google Earth (Google Inc.), a free Geographic Information Systems platform. Import of genetic data into Google Earth allows phylogeographers access to a wealth of spatial information layers integral to forming hypotheses and understanding patterns in the data. © 2010 Blackwell Publishing Ltd.

Population resizing on fitness improvement genetic algorithm to optimize promotion visit route based on android and google maps API

NASA Astrophysics Data System (ADS)

Listyorini, Tri; Muzid, Syafiul

2017-06-01

The promotion team of Muria Kudus University (UMK) has done annual promotion visit to several senior high schools in Indonesia. The visits were done to numbers of schools in Kudus, Jepara, Demak, Rembang and Purwodadi. To simplify the visit, each visit round is limited to 15 (fifteen) schools. However, the team frequently faces some obstacles during the visit, particularly in determining the route that they should take toward the targeted school. It is due to the long distance or the difficult route to reach the targeted school that leads to elongated travel duration and inefficient fuel cost. To solve these problems, the development of a certain application using heuristic genetic algorithm method based on the dynamic of population size or Population Resizing on Fitness lmprovement Genetic Algorithm (PRoFIGA), was done. This android-based application was developed to make the visit easier and to determine a shorter route for the team, hence, the visiting period will be effective and efficient. The result of this research was an android-based application to determine the shortest route by combining heuristic method and Google Maps Application Programming lnterface (API) that display the route options for the team.

Genetic Architecture of Local Adaptation in Lunar and Diurnal Emergence Times of the Marine Midge Clunio marinus (Chironomidae, Diptera)

PubMed Central

Kaiser, Tobias S.; Heckel, David G.

2012-01-01

Circadian rhythms pre-adapt the physiology of most organisms to predictable daily changes in the environment. Some marine organisms also show endogenous circalunar rhythms. The genetic basis of the circalunar clock and its interaction with the circadian clock is unknown. Both clocks can be studied in the marine midge Clunio marinus (Chironomidae, Diptera), as different populations have different local adaptations in their lunar and diurnal rhythms of adult emergence, which can be analyzed by crossing experiments. We investigated the genetic basis of population variation in clock properties by constructing the first genetic linkage map for this species, and performing quantitative trait locus (QTL) analysis on variation in both lunar and diurnal timing. The genome has a genetic length of 167–193 centimorgans based on a linkage map using 344 markers, and a physical size of 95–140 megabases estimated by flow cytometry. Mapping the sex determining locus shows that females are the heterogametic sex, unlike most other Chironomidae. We identified two QTL each for lunar emergence time and diurnal emergence time. The distribution of QTL confirms a previously hypothesized genetic basis to a correlation of lunar and diurnal emergence times in natural populations. Mapping of clock genes and light receptors identified ciliary opsin 2 (cOps2) as a candidate to be involved in both lunar and diurnal timing; cryptochrome 1 (cry1) as a candidate gene for lunar timing; and two timeless (tim2, tim3) genes as candidate genes for diurnal timing. This QTL analysis of lunar rhythmicity, the first in any species, provides a unique entree into the molecular analysis of the lunar clock. PMID:22384150

Genetic architecture of local adaptation in lunar and diurnal emergence times of the marine midge Clunio marinus (Chironomidae, Diptera).

PubMed

Kaiser, Tobias S; Heckel, David G

2012-01-01

Circadian rhythms pre-adapt the physiology of most organisms to predictable daily changes in the environment. Some marine organisms also show endogenous circalunar rhythms. The genetic basis of the circalunar clock and its interaction with the circadian clock is unknown. Both clocks can be studied in the marine midge Clunio marinus (Chironomidae, Diptera), as different populations have different local adaptations in their lunar and diurnal rhythms of adult emergence, which can be analyzed by crossing experiments. We investigated the genetic basis of population variation in clock properties by constructing the first genetic linkage map for this species, and performing quantitative trait locus (QTL) analysis on variation in both lunar and diurnal timing. The genome has a genetic length of 167-193 centimorgans based on a linkage map using 344 markers, and a physical size of 95-140 megabases estimated by flow cytometry. Mapping the sex determining locus shows that females are the heterogametic sex, unlike most other Chironomidae. We identified two QTL each for lunar emergence time and diurnal emergence time. The distribution of QTL confirms a previously hypothesized genetic basis to a correlation of lunar and diurnal emergence times in natural populations. Mapping of clock genes and light receptors identified ciliary opsin 2 (cOps2) as a candidate to be involved in both lunar and diurnal timing; cryptochrome 1 (cry1) as a candidate gene for lunar timing; and two timeless (tim2, tim3) genes as candidate genes for diurnal timing. This QTL analysis of lunar rhythmicity, the first in any species, provides a unique entree into the molecular analysis of the lunar clock.

Fifteen years of quantitative trait loci studies in fish: challenges and future directions.

PubMed

Ashton, David T; Ritchie, Peter A; Wellenreuther, Maren

2017-03-01

Understanding the genetic basis of phenotypic variation is a major challenge in biology. Here, we systematically evaluate 146 quantitative trait loci (QTL) studies on teleost fish over the last 15 years to investigate (i) temporal trends and (ii) factors affecting QTL detection and fine-mapping. The number of fish QTL studies per year increased over the review period and identified a cumulative number of 3632 putative QTLs. Most studies used linkage-based mapping approaches and were conducted on nonmodel species with limited genomic resources. A gradual and moderate increase in the size of the mapping population and a sharp increase in marker density from 2011 onwards were observed; however, the number of QTLs and variance explained by QTLs changed only minimally over the review period. Based on these findings, we discuss the causative factors and outline how larger sample sizes, phenomics, comparative genomics, epigenetics and software development could improve both the quantity and quality of QTLs in future genotype-phenotype studies. Given that the technical limitations on DNA sequencing have mostly been overcome in recent years, a renewed focus on these and other study design factors will likely lead to significant improvements in QTL studies in the future. © 2016 John Wiley & Sons Ltd.

Bathymetric and sediment facies maps for China Bend and Marcus Flats, Franklin D. Roosevelt Lake, Washington, 2008 and 2009

USGS Publications Warehouse

Weakland, Rhonda J.; Fosness, Ryan L.; Williams, Marshall L.; Barton, Gary J.

2011-01-01

The U.S. Geological Survey (USGS) created bathymetric and sediment facies maps for portions of two reaches of Lake Roosevelt in support of an interdisciplinary study of white sturgeon (Acipenser transmontanus) and their habitat areas within Franklin D. Roosevelt Lake, Washington. In October 2008, scientists from the USGS used a boat-mounted multibeam echo sounder (MBES) to describe bathymetric data to characterize surface relief at China Bend and Marcus Flats, between Northport and Kettle Falls, Washington. In March 2009, an underwater video camera was used to view and record sediment facies that were then characterized by sediment type, grain size, and areas of sand deposition. Smelter slag has been identified as having the characteristics of sand-sized black particles; the two non-invasive surveys attempted to identify areas containing black-colored particulate matter that may be elements and minerals, organic material, or slag. The white sturgeon population in Lake Roosevelt is threatened by the failure of natural recruitment, resulting in a native population that consists primarily of aging fish and that is gradually declining as fish die and are not replaced by nonhatchery reared juvenile fish. These fish spawn and rear in the riverine and upper reservoir reaches where smelter slag is present in the sediment of the river lake bed. Effects of slag on the white sturgeon population in Lake Roosevelt are largely unknown. Two recent studies demonstrated that copper and other metals are mobilized from slag in aqueous environments with concentrations of copper and zinc in bed sediments reaching levels of 10,000 and 30,000 mg/kg due to the presence of smelter slag. Copper was found to be highly toxic to 30-day-old white sturgeon with 96-h LC50 concentrations ranging from 3 to 5 (u or mu)g copper per liter. Older juvenile and adult sturgeons commonly ingest substantial amounts of sediment while foraging. Future study efforts in Lake Roosevelt should include sampling of bottom material to confirm the presence or absence of slag material indicated on the map. In addition, follow-up acoustic work to determine stream velocities at varying discharges, in conjunction with sediment mapping, would be helpful to more accurately identify areas of scour and areas of sediment deposition where slag deposits may accumulate within the Marcus Flats and China Bend reaches. MBES mapping could also be used to determine changes in bed elevation and sedimentation in the study reaches and could help evaluate annual deposition and provide estimates on fine-sediment thickness.

Expading fluvial remote sensing to the riverscape: Mapping depth and grain size on the Merced River, California

NASA Astrophysics Data System (ADS)

Richardson, Ryan T.

This study builds upon recent research in the field of fluvial remote sensing by applying techniques for mapping physical attributes of rivers. Depth, velocity, and grain size are primary controls on the types of habitat present in fluvial ecosystems. This thesis focuses on expanding fluvial remote sensing to larger spatial extents and sub-meter resolutions, which will increase our ability to capture the spatial heterogeneity of habitat at a resolution relevant to individual salmonids and an extent relevant to species. This thesis consists of two chapters, one focusing on expanding the spatial extent over which depth can be mapped using Optimal Band Ratio Analysis (OBRA) and the other developing general relations for mapping grain size from three-dimensional topographic point clouds. The two chapters are independent but connected by the overarching goal of providing scientists and managers more useful tools for quantifying the amount and quality of salmonid habitat via remote sensing. The OBRA chapter highlights the true power of remote sensing to map depths from hyperspectral images as a central component of watershed scale analysis, while also acknowledging the great challenges involved with increasing spatial extent. The grain size mapping chapter establishes the first general relations for mapping grain size from roughness using point clouds. These relations will significantly reduce the time needed in the field by eliminating the need for independent measurements of grain size for calibrating the roughness-grain size relationship and thus making grain size mapping with SFM more cost effective for river restoration and monitoring. More data from future studies are needed to refine these relations and establish their validity and generality. In conclusion, this study adds to the rapidly growing field of fluvial remote sensing and could facilitate river research and restoration.

Map Projections and the Visual Detective: How to Tell if a Map Is Equal-Area, Conformal, or Neither

ERIC Educational Resources Information Center

Olson, Judy M.

2006-01-01

The ability to see whether a map is equal-area, conformal, or neither is useful for looking intelligently at large-area maps. For example, only if a map is equal-area can reliable judgments of relative size be made. If a map is equal-area, latitude-longitude cells are equal in size between a given pair of parallels, the cells between a given pair…

Fine-Scale Map of Encyclopedia of DNA Elements Regions in the Korean Population

PubMed Central

Yoo, Yeon-Kyeong; Ke, Xiayi; Hong, Sungwoo; Jang, Hye-Yoon; Park, Kyunghee; Kim, Sook; Ahn, TaeJin; Lee, Yeun-Du; Song, Okryeol; Rho, Na-Young; Lee, Moon Sue; Lee, Yeon-Su; Kim, Jaeheup; Kim, Young J.; Yang, Jun-Mo; Song, Kyuyoung; Kimm, Kyuchan; Weir, Bruce; Cardon, Lon R.; Lee, Jong-Eun; Hwang, Jung-Joo

2006-01-01

The International HapMap Project aims to generate detailed human genome variation maps by densely genotyping single-nucleotide polymorphisms (SNPs) in CEPH, Chinese, Japanese, and Yoruba samples. This will undoubtedly become an important facility for genetic studies of diseases and complex traits in the four populations. To address how the genetic information contained in such variation maps is transferable to other populations, the Korean government, industries, and academics have launched the Korean HapMap project to genotype high-density Encyclopedia of DNA Elements (ENCODE) regions in 90 Korean individuals. Here we show that the LD pattern, block structure, haplotype diversity, and recombination rate are highly concordant between Korean and the two HapMap Asian samples, particularly Japanese. The availability of information from both Chinese and Japanese samples helps to predict more accurately the possible performance of HapMap markers in Korean disease-gene studies. Tagging SNPs selected from the two HapMap Asian maps, especially the Japanese map, were shown to be very effective for Korean samples. These results demonstrate that the HapMap variation maps are robust in related populations and will serve as an important resource for the studies of the Korean population in particular. PMID:16702437

The Cellular Automata for modelling of spreading of lava flow on the earth surface

NASA Astrophysics Data System (ADS)

Jarna, A.

2012-12-01

Volcanic risk assessment is a very important scientific, political and economic issue in densely populated areas close to active volcanoes. Development of effective tools for early prediction of a potential volcanic hazard and management of crises are paramount. However, to this date volcanic hazard maps represent the most appropriate way to illustrate the geographical area that can potentially be affected by a volcanic event. Volcanic hazard maps are usually produced by mapping out old volcanic deposits, however dynamic lava flow simulation gaining popularity and can give crucial information to corroborate other methodologies. The methodology which is used here for the generation of volcanic hazard maps is based on numerical simulation of eruptive processes by the principle of Cellular Automata (CA). The python script is integrated into ArcToolbox in ArcMap (ESRI) and the user can select several input and output parameters which influence surface morphology, size and shape of the flow, flow thickness, flow velocity and length of lava flows. Once the input parameters are selected, the software computes and generates hazard maps on the fly. The results can be exported to Google Maps (.klm format) to visualize the results of the computation. For validation of the simulation code are used data from a real lava flow. Comparison of the simulation results with real lava flows mapped out from satellite images will be presented.

Differential receptive field organizations give rise to nearly identical neural correlations across three parallel sensory maps in weakly electric fish

PubMed Central

2017-01-01

Understanding how neural populations encode sensory information thereby leading to perception and behavior (i.e., the neural code) remains an important problem in neuroscience. When investigating the neural code, one must take into account the fact that neural activities are not independent but are actually correlated with one another. Such correlations are seen ubiquitously and have a strong impact on neural coding. Here we investigated how differences in the antagonistic center-surround receptive field (RF) organization across three parallel sensory maps influence correlations between the activities of electrosensory pyramidal neurons. Using a model based on known anatomical differences in receptive field center size and overlap, we initially predicted large differences in correlated activity across the maps. However, in vivo electrophysiological recordings showed that, contrary to modeling predictions, electrosensory pyramidal neurons across all three segments displayed nearly identical correlations. To explain this surprising result, we incorporated the effects of RF surround in our model. By systematically varying both the RF surround gain and size relative to that of the RF center, we found that multiple RF structures gave rise to similar levels of correlation. In particular, incorporating known physiological differences in RF structure between the three maps in our model gave rise to similar levels of correlation. Our results show that RF center overlap alone does not determine correlations which has important implications for understanding how RF structure influences correlated neural activity. PMID:28863136

Oscillatory Critical Amplitudes in Hierarchical Models and the Harris Function of Branching Processes

NASA Astrophysics Data System (ADS)

Costin, Ovidiu; Giacomin, Giambattista

2013-02-01

Oscillatory critical amplitudes have been repeatedly observed in hierarchical models and, in the cases that have been taken into consideration, these oscillations are so small to be hardly detectable. Hierarchical models are tightly related to iteration of maps and, in fact, very similar phenomena have been repeatedly reported in many fields of mathematics, like combinatorial evaluations and discrete branching processes. It is precisely in the context of branching processes with bounded off-spring that T. Harris, in 1948, first set forth the possibility that the logarithm of the moment generating function of the rescaled population size, in the super-critical regime, does not grow near infinity as a power, but it has an oscillatory prefactor (the Harris function). These oscillations have been observed numerically only much later and, while the origin is clearly tied to the discrete character of the iteration, the amplitude size is not so well understood. The purpose of this note is to reconsider the issue for hierarchical models and in what is arguably the most elementary setting—the pinning model—that actually just boils down to iteration of polynomial maps (and, notably, quadratic maps). In this note we show that the oscillatory critical amplitude for pinning models and the Harris function coincide. Moreover we make explicit the link between these oscillatory functions and the geometry of the Julia set of the map, making thus rigorous and quantitative some ideas set forth in Derrida et al. (Commun. Math. Phys. 94:115-132, 1984).

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map.

PubMed

Kumar, Ajay; Mantovani, E E; Seetan, R; Soltani, A; Echeverry-Solarte, M; Jain, S; Simsek, S; Doehlert, D; Alamri, M S; Elias, E M; Kianian, S F; Mergoum, M

2016-03-01

Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414566), was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP) markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL) and width (KW) are genetically independent, while a large number (∼59%) of the quantitative trait loci (QTL) for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A) and (7A) genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools. Copyright © 2016 Crop Science Society of America.

Changes in population and agricultural land in conterminous United States counties, 1790 to 1997

USGS Publications Warehouse

Waisanen, Pamela J.; Bliss, Norman B.

2002-01-01

We have developed a data set of changes in population and agricultural land for the conterminous United States at the county level, resulting in more spatial detail than in previously available compilations. The purpose was to provide data on the timing of land conversion as an input to dynamic models of the carbon cycle, although a wide variety of applications exist for the physical, biological, and social sciences. The spatial data represent the appropriate county boundaries for each census year between 1790 and 1997, and the census attributes are attached to the appropriate spatial region. The resulting time series and maps show the history of population (1790-1990) and the history of agricultural development (1850-1997). The patterns of agricultural development reflect the influences of climate, soil productivity, increases in population size, variations in the general economy, and technological changes in the energy, transportation, and agricultural sectors.

Cooperation Dilemma in Finite Populations under Fluctuating Environments

NASA Astrophysics Data System (ADS)

Assaf, Michael; Mobilia, Mauro; Roberts, Elijah

2013-12-01

We present a novel approach allowing the study of rare events like fixation under fluctuating environments, modeled as extrinsic noise, in evolutionary processes characterized by the dominance of one species. Our treatment consists of mapping the system onto an auxiliary model, exhibiting metastable species coexistence, that can be analyzed semiclassically. This approach enables us to study the interplay between extrinsic and demographic noise on the statistics of interest. We illustrate our theory by considering the paradigmatic prisoner’s dilemma game, whose evolution is described by the probability that cooperators fixate the population and replace all defectors. We analytically and numerically demonstrate that extrinsic noise may drastically enhance the cooperation fixation probability and even change its functional dependence on the population size. These results, which generalize earlier works in population genetics, indicate that extrinsic noise may help sustain and promote a much higher level of cooperation than static settings.

Comparing power and precision of within-breed and multibreed genome-wide association studies of production traits using whole-genome sequence data for 5 French and Danish dairy cattle breeds.

PubMed

van den Berg, Irene; Boichard, Didier; Lund, Mogens Sandø

2016-11-01

The objective of this study was to compare mapping precision and power of within-breed and multibreed genome-wide association studies (GWAS) and to compare the results obtained by the multibreed GWAS with 3 meta-analysis methods. The multibreed GWAS was expected to improve mapping precision compared with a within-breed GWAS because linkage disequilibrium is conserved over shorter distances across breeds than within breeds. The multibreed GWAS was also expected to increase detection power for quantitative trait loci (QTL) segregating across breeds. GWAS were performed for production traits in dairy cattle, using imputed full genome sequences of 16,031 bulls, originating from 6 French and Danish dairy cattle populations. Our results show that a multibreed GWAS can be a valuable tool for the detection and fine mapping of quantitative trait loci. The number of QTL detected with the multibreed GWAS was larger than the number detected by the within-breed GWAS, indicating an increase in power, especially when the 2 Holstein populations were combined. The largest number of QTL was detected when all populations were combined. The analysis combining all breeds was, however, dominated by Holstein, and QTL segregating in other breeds but not in Holstein were sometimes overshadowed by larger QTL segregating in Holstein. Therefore, the GWAS combining all breeds except Holstein was useful to detect such peaks. Combining all breeds except Holstein resulted in smaller QTL intervals on average, but this outcome was not the case when the Holstein populations were included in the analysis. Although no decrease in the average QTL size was observed, mapping precision did improve for several QTL. Out of 3 different multibreed meta-analysis methods, the weighted z-scores model resulted in the most similar results to the full multibreed GWAS and can be useful as an alternative to a full multibreed GWAS. Differences between the multibreed GWAS and the meta-analyses were larger when different breeds were combined than when the 2 Holstein populations were combined. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar).

PubMed

Tsai, Hsin Yuan; Hamilton, Alastair; Guy, Derrick R; Tinch, Alan E; Bishop, Stephen C; Houston, Ross D

2015-05-19

Performance and quality traits such as harvest weight, fillet weight and flesh color are of economic importance to the Atlantic salmon aquaculture industry. The genetic factors underlying these traits are of scientific and commercial interest. However, such traits are typically polygenic in nature, with the number and size of QTL likely to vary between studies and populations. The aim of this study was to investigate the genetic basis of several growth and fillet traits measured at harvest in a large farmed salmon population by using SNP markers. Due to the marked heterochiasmy in salmonids, an efficient two-stage mapping approach was applied whereby QTL were detected using a sire-based linkage analysis, a sparse SNP marker map and exploiting low rates of recombination, while a subsequent dam-based analysis focused on the significant chromosomes with a denser map to confirm QTL and estimate their position. The harvest traits all showed significant heritability, ranging from 0.05 for fillet yield up to 0.53 for the weight traits. In the sire-based analysis, 1695 offspring with trait records and their 20 sires were successfully genotyped for the SNPs on the sparse map. Chromosomes 13, 18, 19 and 20 were shown to harbor genome-wide significant QTL affecting several growth-related traits. The QTL on chr. 13, 18 and 20 were detected in the dam-based analysis using 512 offspring from 10 dams and explained approximately 6-7 % of the within-family variation in these traits. We have detected several QTL affecting economically important complex traits in a commercial salmon population. Overall, the results suggest that the traits are relatively polygenic and that QTL tend to be pleiotropic (affecting the weight of several components of the harvested fish). Comparison of QTL regions across studies suggests that harvest trait QTL tend to be relatively population-specific. Therefore, the application of marker or genomic selection for improvement in these traits is likely to be most effective when the discovery population is closely related to the selection candidates (e.g. within-family genomic selection).

Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

PubMed

Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

2015-01-01

Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

Mapping Challenging Mutations by Whole-Genome Sequencing

PubMed Central

Smith, Harold E.; Fabritius, Amy S.; Jaramillo-Lambert, Aimee; Golden, Andy

2016-01-01

Whole-genome sequencing provides a rapid and powerful method for identifying mutations on a global scale, and has spurred a renewed enthusiasm for classical genetic screens in model organisms. The most commonly characterized category of mutation consists of monogenic, recessive traits, due to their genetic tractability. Therefore, most of the mapping methods for mutation identification by whole-genome sequencing are directed toward alleles that fulfill those criteria (i.e., single-gene, homozygous variants). However, such approaches are not entirely suitable for the characterization of a variety of more challenging mutations, such as dominant and semidominant alleles or multigenic traits. Therefore, we have developed strategies for the identification of those classes of mutations, using polymorphism mapping in Caenorhabditis elegans as our model for validation. We also report an alternative approach for mutation identification from traditional recombinant crosses, and a solution to the technical challenge of sequencing sterile or terminally arrested strains where population size is limiting. The methods described herein extend the applicability of whole-genome sequencing to a broader spectrum of mutations, including classes that are difficult to map by traditional means. PMID:26945029

Craters of the Pluto-Charon system

NASA Astrophysics Data System (ADS)

Robbins, Stuart J.; Singer, Kelsi N.; Bray, Veronica J.; Schenk, Paul; Lauer, Tod R.; Weaver, Harold A.; Runyon, Kirby; McKinnon, William B.; Beyer, Ross A.; Porter, Simon; White, Oliver L.; Hofgartner, Jason D.; Zangari, Amanda M.; Moore, Jeffrey M.; Young, Leslie A.; Spencer, John R.; Binzel, Richard P.; Buie, Marc W.; Buratti, Bonnie J.; Cheng, Andrew F.; Grundy, William M.; Linscott, Ivan R.; Reitsema, Harold J.; Reuter, Dennis C.; Showalter, Mark R.; Tyler, G. Len; Olkin, Catherine B.; Ennico, Kimberly S.; Stern, S. Alan; New Horizons Lorri, Mvic Instrument Teams

2017-05-01

NASA's New Horizons flyby mission of the Pluto-Charon binary system and its four moons provided humanity with its first spacecraft-based look at a large Kuiper Belt Object beyond Triton. Excluding this system, multiple Kuiper Belt Objects (KBOs) have been observed for only 20 years from Earth, and the KBO size distribution is unconstrained except among the largest objects. Because small KBOs will remain beyond the capabilities of ground-based observatories for the foreseeable future, one of the best ways to constrain the small KBO population is to examine the craters they have made on the Pluto-Charon system. The first step to understanding the crater population is to map it. In this work, we describe the steps undertaken to produce a robust crater database of impact features on Pluto, Charon, and their two largest moons, Nix and Hydra. These include an examination of different types of images and image processing, and we present an analysis of variability among the crater mapping team, where crater diameters were found to average ± 10% uncertainty across all sizes measured (∼0.5-300 km). We also present a few basic analyses of the crater databases, finding that Pluto's craters' differential size-frequency distribution across the encounter hemisphere has a power-law slope of approximately -3.1 ± 0.1 over diameters D ≈ 15-200 km, and Charon's has a slope of -3.0 ± 0.2 over diameters D ≈ 10-120 km; it is significantly shallower on both bodies at smaller diameters. We also better quantify evidence of resurfacing evidenced by Pluto's craters in contrast with Charon's. With this work, we are also releasing our database of potential and probable impact craters: 5287 on Pluto, 2287 on Charon, 35 on Nix, and 6 on Hydra.

Craters of the Pluto-Charon System

NASA Technical Reports Server (NTRS)

Robbins, Stuart J.; Singer, Kelsi N.; Bray, Veronica J.; Schenk, Paul; Lauer, Todd R.; Weaver, Harold A.; Runyon, Kirby; Mckinnon, William B.; Beyer, Ross A.; Porter, Simon;

Tipping news in information accumulation system

NASA Astrophysics Data System (ADS)

Shin, J. K.

2010-05-01

As a continuous opinion dynamics model, the information accumulation system (IAS) includes three basic mechanisms of the news, the inheritance and the diffusion as contributing to the information accumulation process of a system. A system is composed of agents who diffuse information through internal interaction, while each of them has incomplete memory or inheritance rate. The news comes from external sources of information, such as mass media. Previously the model IAS was studied only for the small news problems. In this study, a tipping news problem is considered. A key question of the problem is: what is the minimum strength of advertisement that can tip the minority opinion to a majority one? Dynamics of the IAS is briefly revisited with a special interest on nonlinear behavior of the model. In particular, it is shown that a discrete map of the IAS for a single color problem can be transformed into a logistic map, from which the dynamics of the IAS can be better understood. To show the applicability of the IAS model, the result is applied to explain the concept of the critical population size, which claims that there is a minimum population size for a social knowledge system to be continuously inherited without being lost. And critical size of the tipping news is found analytically in terms of IAS parameters. Some of the key results from the present study are compared in detail with the results from the Brownian particle model, which is believed to be the most similar model to the IAS. The concept of tipping news is used to show that a traditional society can tip at an exceptionally low inter-community exposure. Finally, the result was applied to the language competition problem.

Earthquake Hazard and Risk Assessment based on Unified Scaling Law for Earthquakes: Altai-Sayan Region

NASA Astrophysics Data System (ADS)

Kossobokov, V. G.; Nekrasova, A.

2017-12-01

We continue applying the general concept of seismic risk analysis in a number of seismic regions worldwide by constructing regional seismic hazard maps based on morphostructural analysis, pattern recognition, and the Unified Scaling Law for Earthquakes, USLE, which generalizes the Gutenberg-Richter relationship making use of naturally fractal distribution of earthquake sources of different size in a seismic region. The USLE stands for an empirical relationship log10N(M, L) = A + B·(5 - M) + C·log10L, where N(M, L) is the expected annual number of earthquakes of a certain magnitude M within an seismically prone area of linear dimension L. We use parameters A, B, and C of USLE to estimate, first, the expected maximum credible magnitude in a time interval at seismically prone nodes of the morphostructural scheme of the region under study, then map the corresponding expected ground shaking parameters (e.g. peak ground acceleration, PGA, or macro-seismic intensity etc.). After a rigorous testing against the available seismic evidences in the past (usually, the observed instrumental PGA or the historically reported macro-seismic intensity), such a seismic hazard map is used to generate maps of specific earthquake risks for population, cities, and infrastructures (e.g., those based on census of population, buildings inventory, etc.). This, USLE based, methodology of seismic hazard and risks assessment is applied to the territory of Altai-Sayan Region, of Russia. The study supported by the Russian Science Foundation Grant No. 15-17-30020.

Evaluation of algorithms used to order markers on genetic maps.

PubMed

Mollinari, M; Margarido, G R A; Vencovsky, R; Garcia, A A F

2009-12-01

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.

QTL mapping of root traits in phosphorus-deficient soils reveals important genomic regions for improving NDVI and grain yield in barley.

PubMed

Gong, Xue; McDonald, Glenn

2017-09-01

Major QTLs for root rhizosheath size are not correlated with grain yield or yield response to phosphorus. Important QTLs were found to improve phosphorus efficiency. Root traits are important for phosphorus (P) acquisition, but they are often difficult to characterize and their breeding values are seldom assessed under field conditions. This has shed doubts on using seedling-based criteria of root traits to select and breed for P efficiency. Eight root traits were assessed under controlled conditions in a barley doubled-haploid population in soils differing in P levels. The population was also phenotyped for grain yield, normalized difference vegetation index (NDVI), grain P uptake and P utilization efficiency at maturity (PutE GY ) under field conditions. Several quantitative traits loci (QTLs) from the root screening and the field trials were co-incident. QTLs for root rhizosheath size and root diameter explained the highest phenotypic variation in comparison to QTLs for other root traits. Shared QTLs were found between root diameter and grain yield, and total root length and PutE GY . A common major QTL for rhizosheath size and NDVI was mapped to the HvMATE gene marker on chromosome 4H. Collocations between major QTLs for NDVI and grain yield were detected on chromosomes 6H and 7H. When results from BIP and MET were combined, QTLs detected for grain yield were also those QTLs found for NDVI. QTLs qGY5H, qGY6H and qGY7Hb on 7H were robust QTLs in improving P efficiency. A selection of multiple loci may be needed to optimize the breeding outcomes due to the QTL x Environment interaction. We suggest that rhizosheath size alone is not a reliable trait to predict P efficiency or grain yield.

Development of Public Immortal Mapping Populations, Molecular Markers and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

USDA-ARS?s Scientific Manuscript database

In this study we describe public immortal mapping populations of self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea. We propose that these resources are valuable reference tools for the Brassica community. The B. rapa population consists of 150 recombinant...

Visual motion transforms visual space representations similarly throughout the human visual hierarchy.

PubMed

Harvey, Ben M; Dumoulin, Serge O

2016-02-15

Several studies demonstrate that visual stimulus motion affects neural receptive fields and fMRI response amplitudes. Here we unite results of these two approaches and extend them by examining the effects of visual motion on neural position preferences throughout the hierarchy of human visual field maps. We measured population receptive field (pRF) properties using high-field fMRI (7T), characterizing position preferences simultaneously over large regions of the visual cortex. We measured pRFs properties using sine wave gratings in stationary apertures, moving at various speeds in either the direction of pRF measurement or the orthogonal direction. We find direction- and speed-dependent changes in pRF preferred position and size in all visual field maps examined, including V1, V3A, and the MT+ map TO1. These effects on pRF properties increase up the hierarchy of visual field maps. However, both within and between visual field maps the extent of pRF changes was approximately proportional to pRF size. This suggests that visual motion transforms the representation of visual space similarly throughout the visual hierarchy. Visual motion can also produce an illusory displacement of perceived stimulus position. We demonstrate perceptual displacements using the same stimulus configuration. In contrast to effects on pRF properties, perceptual displacements show only weak effects of motion speed, with far larger speed-independent effects. We describe a model where low-level mechanisms could underlie the observed effects on neural position preferences. We conclude that visual motion induces similar transformations of visuo-spatial representations throughout the visual hierarchy, which may arise through low-level mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

PubMed Central

Kijas, James W.; Lenstra, Johannes A.; Hayes, Ben; Boitard, Simon; Porto Neto, Laercio R.; San Cristobal, Magali; Servin, Bertrand; McCulloch, Russell; Whan, Vicki; Gietzen, Kimberly; Paiva, Samuel; Barendse, William; Ciani, Elena; Raadsma, Herman; McEwan, John; Dalrymple, Brian

2012-01-01

Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species. PMID:22346734

Population weighted raster maps can communicate findings of social audits: examples from three continents.

PubMed

Mitchell, Steven; Cockcroft, Anne; Andersson, Neil

2011-12-21

Maps can portray trends, patterns, and spatial differences that might be overlooked in tabular data and are now widely used in health research. Little has been reported about the process of using maps to communicate epidemiological findings. Population weighted raster maps show colour changes over the study area. Similar to the rasters of barometric pressure in a weather map, data are the health occurrence--a peak on the map represents a higher value of the indicator in question. The population relevance of each sentinel site, as determined in the stratified last stage random sample, combines with geography (inverse-distance weighting) to provide a population-weighted extension of each colour. This transforms the map to show population space rather than simply geographic space. Maps allowed discussion of strategies to reduce violence against women in a context of political sensitivity about quoting summary indicator figures. Time-series maps showed planners how experiences of health services had deteriorated despite a reform programme; where in a country HIV risk behaviours were improving; and how knowledge of an economic development programme quickly fell off across a region. Change maps highlighted where indicators were improving and where they were deteriorating. Maps of potential impact of interventions, based on multivariate modelling, displayed how partial and full implementation of programmes could improve outcomes across a country. Scale depends on context. To support local planning, district maps or local government authority maps of health indicators were more useful than national maps; but multinational maps of outcomes were more useful for regional institutions. Mapping was useful to illustrate in which districts enrolment in religious schools--a rare occurrence--was more prevalent. Population weighted raster maps can present social audit findings in an accessible and compelling way, increasing the use of evidence by planners with limited numeracy skills or little time to look at evidence. Maps complement epidemiological analysis, but they are not a substitute. Much less do they substitute for rigorous epidemiological designs, like randomised controlled trials.

Linkage map of the honey bee, Apis mellifera, based on RAPD markers

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

Hunt, G.J.; Page, R.E. Jr.

A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkagemore » groups. We estimate the total genome size to be {approximately}3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species. 71 refs., 6 figs., 1 tab.« less

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

PubMed

Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

2014-12-01

Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

High resolution hybrid optical and acoustic sea floor maps (Invited)

NASA Astrophysics Data System (ADS)

Roman, C.; Inglis, G.

2013-12-01

This abstract presents a method for creating hybrid optical and acoustic sea floor reconstructions at centimeter scale grid resolutions with robotic vehicles. Multibeam sonar and stereo vision are two common sensing modalities with complementary strengths that are well suited for data fusion. We have recently developed an automated two stage pipeline to create such maps. The steps can be broken down as navigation refinement and map construction. During navigation refinement a graph-based optimization algorithm is used to align 3D point clouds created with both the multibeam sonar and stereo cameras. The process combats the typical growth in navigation error that has a detrimental affect on map fidelity and typically introduces artifacts at small grid sizes. During this process we are able to automatically register local point clouds created by each sensor to themselves and to each other where they overlap in a survey pattern. The process also estimates the sensor offsets, such as heading, pitch and roll, that describe how each sensor is mounted to the vehicle. The end results of the navigation step is a refined vehicle trajectory that ensures the points clouds from each sensor are consistently aligned, and the individual sensor offsets. In the mapping step, grid cells in the map are selectively populated by choosing data points from each sensor in an automated manner. The selection process is designed to pick points that preserve the best characteristics of each sensor and honor some specific map quality criteria to reduce outliers and ghosting. In general, the algorithm selects dense 3D stereo points in areas of high texture and point density. In areas where the stereo vision is poor, such as in a scene with low contrast or texture, multibeam sonar points are inserted in the map. This process is automated and results in a hybrid map populated with data from both sensors. Additional cross modality checks are made to reject outliers in a robust manner. The final hybrid map retains the strengths of both sensors and shows improvement over the single modality maps and a naively assembled multi-modal map where all the data points are included and averaged. Results will be presented from marine geological and archaeological applications using a 1350 kHz BlueView multibeam sonar and 1.3 megapixel digital still cameras.

Phenotypic assessments of peanut nested association mapping (NAM) populations

USDA-ARS?s Scientific Manuscript database

Nested association mapping (NAM) is a valuable innovation and multi-parental mapping population strategy in peanut genetics which increases the power to map quantitative trait loci and assists in extending the gene pool of elite peanut lines. In the peanut research community, two structured mapping ...

Chronic hepatitis C and individuals with a history of injecting drugs in Spain: population assessment, challenges for successful treatment.

PubMed

Roncero, Carlos; Littlewood, Richard; Vega, Pablo; Martinez-Raga, Jose; Torrens, Marta

2017-06-01

In Spain, there is a need to improve chronic hepatitis C care among people who inject drugs (PWID). Injecting drug use is an important risk behaviour for hepatitis C virus (HCV) infection. Review of 28 sources of the relevant published literature mapped the size of the addiction-HCV population in Spain. Experts in opioid use disorder (OUD) treatment in Spain completed a consensus to define the population size, HCV prevalence and access or barriers to hepatitis C treatment for PWID populations. In Spain, over 300 000 individuals have a lifetime history of injecting drugs. Currently, 150 000 individuals in Spain have OUD; many have injected drugs. Each year, 80 000 individuals engage with treatment services for OUD. A proportion of this group continues to inject drugs. There is a high HCV prevalence in PWID - estimates of 60-80% in Spain. Uptake of hepatitis C therapy in PWID in Spain is limited; barriers include awareness of treatment pathways, advocacy for regular screening and effective joint care. There is an urgent need to address barriers to effective hepatitis C care for PWID in Spain. Practical and specific strategies including peer-led solutions, patient buddy systems and joint working models at the local level can make important short-term differences.

Allee’s dynamics and bifurcation structures in von Bertalanffy’s population size functions

NASA Astrophysics Data System (ADS)

Leonel Rocha, J.; Taha, Abdel-Kaddous; Fournier-Prunaret, D.

2018-03-01

The interest and the relevance of the study of the population dynamics and the extinction phenomenon are our main motivation to investigate the induction of Allee Effect in von Bertalanffy’s population size functions. The adjustment or correction factor of rational type introduced allows us to analyze simultaneously strong and weak Allee’s functions and functions with no Allee effect, whose classification is dependent on the stability of the fixed point x = 0. This classification is founded on the concepts of strong and weak Allee’s effects to the population growth rates associated. The transition from strong Allee effect to no Allee effect, passing through the weak Allee effect, is verified with the evolution of the rarefaction critical density or Allee’s limit. The existence of cusp points on a fold bifurcation curve is related to this phenomenon of transition on Allee’s dynamics. Moreover, the “foliated” structure of the parameter plane considered is also explained, with respect to the evolution of the Allee limit. The bifurcation analysis is based on the configurations of fold and flip bifurcation curves. The chaotic semistability and the nonadmissibility bifurcation curves are proposed to this family of 1D maps, which allow us to define and characterize the corresponding Allee effect region.

A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

PubMed Central

2010-01-01

Background The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L.) has and continues to be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR) markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank. Results Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers) were polymorphic in these populations, respectively, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome maps), representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers, respectively. These distorted loci tended to cluster on LG1, LG3, LG4 and LG5. There were only 15 EST-SSR markers mapped due to low polymorphism. By comparison, there were potential synteny, collinear order of some markers and conservation of collinear linkage groups among the maps and with the AA genome but not fully conservative. Conclusion A composite linkage map was constructed from three individual mapping populations with 175 SSR markers in 22 composite linkage groups. This composite genetic linkage map is among the first "true" tetraploid peanut maps produced. This map also consists of 47 SSRs that have been used in the published AA genome maps, and could be used in comparative mapping studies. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts. All 1044 primer pairs are provided as additional files and the three RIL populations will be made available to public upon request for quantitative trait loci (QTL) analysis and linkage map improvement. PMID:20105299

Genetics of Rapid and Extreme Size Evolution in Island Mice

PubMed Central

Gray, Melissa M.; Parmenter, Michelle D.; Hogan, Caley A.; Ford, Irene; Cuthbert, Richard J.; Ryan, Peter G.; Broman, Karl W.; Payseur, Bret A.

2015-01-01

Organisms on islands provide a revealing window into the process of adaptation. Populations that colonize islands often evolve substantial differences in body size from their mainland relatives. Although the ecological drivers of this phenomenon have received considerable attention, its genetic basis remains poorly understood. We use house mice (subspecies: Mus musculus domesticus) from remote Gough Island to provide a genetic portrait of rapid and extreme size evolution. In just a few hundred generations, Gough Island mice evolved the largest body size among wild house mice from around the world. Through comparisons with a smaller-bodied wild-derived strain from the same subspecies (WSB/EiJ), we demonstrate that Gough Island mice achieve their exceptional body weight primarily by growing faster during the 6 weeks after birth. We use genetic mapping in large F2 intercrosses between Gough Island mice and WSB/EiJ to identify 19 quantitative trait loci (QTL) responsible for the evolution of 16-week weight trajectories: 8 QTL for body weight and 11 QTL for growth rate. QTL exhibit modest effects that are mostly additive. We conclude that body size evolution on islands can be genetically complex, even when substantial size changes occur rapidly. In comparisons to published studies of laboratory strains of mice that were artificially selected for divergent body sizes, we discover that the overall genetic profile of size evolution in nature and in the laboratory is similar, but many contributing loci are distinct. Our results underscore the power of genetically characterizing the entire growth trajectory in wild populations and lay the foundation necessary for identifying the mutations responsible for extreme body size evolution in nature. PMID:26199233

Genetics of Rapid and Extreme Size Evolution in Island Mice.

PubMed

Gray, Melissa M; Parmenter, Michelle D; Hogan, Caley A; Ford, Irene; Cuthbert, Richard J; Ryan, Peter G; Broman, Karl W; Payseur, Bret A

2015-09-01

Organisms on islands provide a revealing window into the process of adaptation. Populations that colonize islands often evolve substantial differences in body size from their mainland relatives. Although the ecological drivers of this phenomenon have received considerable attention, its genetic basis remains poorly understood. We use house mice (subspecies: Mus musculus domesticus) from remote Gough Island to provide a genetic portrait of rapid and extreme size evolution. In just a few hundred generations, Gough Island mice evolved the largest body size among wild house mice from around the world. Through comparisons with a smaller-bodied wild-derived strain from the same subspecies (WSB/EiJ), we demonstrate that Gough Island mice achieve their exceptional body weight primarily by growing faster during the 6 weeks after birth. We use genetic mapping in large F(2) intercrosses between Gough Island mice and WSB/EiJ to identify 19 quantitative trait loci (QTL) responsible for the evolution of 16-week weight trajectories: 8 QTL for body weight and 11 QTL for growth rate. QTL exhibit modest effects that are mostly additive. We conclude that body size evolution on islands can be genetically complex, even when substantial size changes occur rapidly. In comparisons to published studies of laboratory strains of mice that were artificially selected for divergent body sizes, we discover that the overall genetic profile of size evolution in nature and in the laboratory is similar, but many contributing loci are distinct. Our results underscore the power of genetically characterizing the entire growth trajectory in wild populations and lay the foundation necessary for identifying the mutations responsible for extreme body size evolution in nature. Copyright © 2015 by the Genetics Society of America.

Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example.

PubMed

Liu, Yanyan; Xiong, Sican; Sun, Wei; Zou, Fei

2018-02-02

Multiparent populations (MPP) have become popular resources for complex trait mapping because of their wider allelic diversity and larger population size compared with traditional two-way recombinant inbred (RI) strains. In mice, the collaborative cross (CC) is one of the most popular MPP and is derived from eight genetically diverse inbred founder strains. The strategy of generating RI intercrosses (RIX) from MPP in general and from the CC in particular can produce a large number of completely reproducible heterozygote genomes that better represent the (outbred) human population. Since both maternal and paternal haplotypes of each RIX are readily available, RIX is a powerful resource for studying both standing genetic and epigenetic variations of complex traits, in particular, the parent-of-origin (PoO) effects, which are important contributors to many complex traits. Furthermore, most complex traits are affected by >1 genes, where multiple quantitative trait locus mapping could be more advantageous. In this paper, for MPP-RIX data but taking CC-RIX as a working example, we propose a general Bayesian variable selection procedure to simultaneously search for multiple genes with founder allelic effects and PoO effects. The proposed model respects the complex relationship among RIX samples, and the performance of the proposed method is examined by extensive simulations. Copyright © 2018 Liu et al.

SU-G-IeP1-12: Size Selective Arterial Cerebral Blood Volume Mapping Using Multiple Inversion Time Arterial Spin Labeling

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

Jung, Y; Johnston, M; Whitlow, C

Purpose: To demonstrate the feasibility of a novel method for size specific arterial cerebral blood volume (aCBV) mapping using pseudo-continuous arterial spin labeling (PCASL), with multiple TI. Methods: Multiple PCASL images were obtained from a subject with TI of [300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000] ms. Each TI pair was averaged six times. Two scans were performed: one without a flow crusher gradient and the other with a crusher gradient (10cm/s in three directions) to remove signals from large arteries. Scan times were 5min. without a crusher gradient and 5.5 min withmore » a crusher gradient. Non-linear fitting algorithm finds the minimum mean squared solution of per-voxel based aCBV, cerebral blood flow, and arterial transit time, and fits the data into a hemodynamic model that represents superposition of blood volume and flow components within a single voxel. Results: aCBV maps with a crusher gradient represent signals from medium and small sized arteries, while those without a crusher gradient represent signals from all sized arteries, indicating that flow crusher gradients can be effectively employed to achieve size-specific aCBV mapping. Regardless of flow crusher, the CBF and ATT maps are very similar in appearance. Conclusion: Quantitative size selective blood volume mapping controlled by a flow crusher is feasible without additional information because the ASL quantification process doesn’t require an arterial input function measured from a large artery. The size specific blood volume mapping is not interfered by sSignals from large arteries do not interfere with size specific aCBV mapping in the applications of interest in for applications in which only medium or small arteries are of interest.« less

Space-time models for a panzootic in bats, with a focus on the endangered Indiana bat

USGS Publications Warehouse

Thogmartin, Wayne E.; King, R. Andrew; Szymanski, Jennifer A.; Pruitt, Lori

2012-01-01

Knowledge of current trends of quickly spreading infectious wildlife diseases is vital to efficient and effective management. We developed space-time mixed-effects logistic regressions to characterize a disease, white-nose syndrome (WNS), quickly spreading among endangered Indiana bats (Myotis sodalis) in eastern North America. Our goal was to calculate and map the risk probability faced by uninfected colonies of hibernating Indiana bats. Model covariates included annual distance from and direction to nearest sources of infection, geolocational information, size of the Indiana bat populations within each wintering population, and total annual size of populations known or suspected to be affected by WNS. We considered temporal, spatial, and spatiotemporal formulae through the use of random effects for year, complex (a collection of interacting hibernacula), and yearxcomplex. Since first documented in 2006, WNS has spread across much of the range of the Indiana bat. No sizeable wintering population now occurs outside of the migrational distance of an infected source. Annual rates of newly affected wintering Indiana bat populations between winter 2007 to 2008 and 2010 to 2011 were 4, 6, 8, and 12%; this rate increased each year at a rate of 3%. If this increasing rate of newly affected populations continues, all wintering populations may be affected by 2016. Our models indicated the probability of a wintering population exhibiting infection was a linear function of proximity to affected Indiana bat populations and size of the at-risk population. Geographic location was also important, suggesting broad-scale influences. For every 50-km increase in distance from a WNS-affected population, risk of disease declined by 6% (95% CI=5.2-5.7%); for every increase of 1,000 Indiana bats, there was an 8% (95% CI = 1-21%) increase in disease risk. The increasing rate of infection seems to be associated with the movement of this disease into the core of the Indiana bat range. Our spatially explicit estimates of disease risk may aid managers in prioritizing surveillance and management for wintering populations of Indiana bats and help understand the risk faced by other hibernating bat species.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India—An application of small area estimation techniques

PubMed Central

Aditya, Kaustav; Sud, U. C.

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011–12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable. PMID:29879202

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India-An application of small area estimation techniques.

PubMed

Chandra, Hukum; Aditya, Kaustav; Sud, U C

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011-12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable.

Mapping Air Population

NASA Astrophysics Data System (ADS)

Peterson, Michael P.; Hunt, Paul; Weiß, Konrad

2018-05-01

"Air population" refers to the total number of people flying above the earth at any point in time. The total number of passengers can then be estimated by multiplying the number of seats for each aircraft by the current seat occupancy rate. Using this method, the estimated air population is determined by state for the airspace over the United States. In the interactive, real-time mapping system, maps are provided to show total air population, the density of air population (air population / area of state), and the ratio of air population to ground population.

Availability and Quality of Size Estimations of Female Sex Workers, Men Who Have Sex with Men, People Who Inject Drugs and Transgender Women in Low- and Middle-Income Countries

PubMed Central

Sabin, Keith; Zhao, Jinkou; Garcia Calleja, Jesus Maria; Sheng, Yaou; Arias Garcia, Sonia; Reinisch, Annette; Komatsu, Ryuichi

2016-01-01

Objective To assess the availability and quality of population size estimations of female sex workers (FSW), men who have sex with men (MSM), people who inject drug (PWID) and transgender women. Methods Size estimation data since 2010 were retrieved from global reporting databases, Global Fund grant application documents, and the peer-reviewed and grey literature. Overall quality and availability were assessed against a defined set of criteria, including estimation methods, geographic coverage, and extrapolation approaches. Estimates were compositely categorized into ‘nationally adequate’, ‘nationally inadequate but locally adequate’, ‘documented but inadequate methods’, ‘undocumented or untimely’ and ‘no data.’ Findings Of 140 countries assessed, 41 did not report any estimates since 2010. Among 99 countries with at least one estimate, 38 were categorized as having nationally adequate estimates and 30 as having nationally inadequate but locally adequate estimates. Multiplier, capture-recapture, census and enumeration, and programmatic mapping were the most commonly used methods. Most countries relied on only one estimate for a given population while about half of all reports included national estimates. A variety of approaches were applied to extrapolate from sites-level numbers to national estimates in two-thirds of countries. Conclusions Size estimates for FSW, MSM, PWID and transgender women are increasingly available but quality varies widely. The different approaches present challenges for data use in design, implementation and evaluation of programs for these populations in half of the countries assessed. Guidance should be further developed to recommend: a) applying multiple estimation methods; b) estimating size for a minimum number of sites; and, c) documenting extrapolation approaches. PMID:27163256

Accounting for rate instability and spatial patterns in the boundary analysis of cancer mortality maps

PubMed Central

Goovaerts, Pierre

2006-01-01

Boundary analysis of cancer maps may highlight areas where causative exposures change through geographic space, the presence of local populations with distinct cancer incidences, or the impact of different cancer control methods. Too often, such analysis ignores the spatial pattern of incidence or mortality rates and overlooks the fact that rates computed from sparsely populated geographic entities can be very unreliable. This paper proposes a new methodology that accounts for the uncertainty and spatial correlation of rate data in the detection of significant edges between adjacent entities or polygons. Poisson kriging is first used to estimate the risk value and the associated standard error within each polygon, accounting for the population size and the risk semivariogram computed from raw rates. The boundary statistic is then defined as half the absolute difference between kriged risks. Its reference distribution, under the null hypothesis of no boundary, is derived through the generation of multiple realizations of the spatial distribution of cancer risk values. This paper presents three types of neutral models generated using methods of increasing complexity: the common random shuffle of estimated risk values, a spatial re-ordering of these risks, or p-field simulation that accounts for the population size within each polygon. The approach is illustrated using age-adjusted pancreatic cancer mortality rates for white females in 295 US counties of the Northeast (1970–1994). Simulation studies demonstrate that Poisson kriging yields more accurate estimates of the cancer risk and how its value changes between polygons (i.e. boundary statistic), relatively to the use of raw rates or local empirical Bayes smoother. When used in conjunction with spatial neutral models generated by p-field simulation, the boundary analysis based on Poisson kriging estimates minimizes the proportion of type I errors (i.e. edges wrongly declared significant) while the frequency of these errors is predicted well by the p-value of the statistical test. PMID:19023455

Nanotechnology Approaches to Studying Epigenetic Changes in Cancer

NASA Astrophysics Data System (ADS)

Riehn, Robert

2011-03-01

Placing polyelectrolytes into confined geometries has a profound effect on their molecular configuration. For instance, placing long DNA molecules into channels with a cross-section of about 100 nm 2 stretches them out to about 70% of their contour length. We are using this effect to map epigenetic changes on single DNA and chromatin strands. This mapping on single molecules becomes central in the study of the heterogeneity of cell population in cancer, since rapid change of epigenetic makeup, propagated through rare cancer stem cells, is a hallmark of its progression. We demonstrate the basic building blocks for the single-molecule epigenetic analysis of genomic sized DNA. In particular, we have achieved the mapping of methylated regions in DNA with heterogeneous 5-methyl cytosine modification using a specific fluorescent marker. We further show that chromatin with an intact histone structure can be stretched similar to DNA, and that the epigenetic state of histone tails can be detected using fluorescent antibodies.

Neighborhood size of training data influences soil map disaggregation

USDA-ARS?s Scientific Manuscript database

Soil class mapping relies on the ability of sample locations to represent portions of the landscape with similar soil types; however, most digital soil mapping (DSM) approaches intersect sample locations with one raster pixel per covariate layer regardless of pixel size. This approach does not take ...

A population 'consensus', partial linkage map of Picea abies Karst. based on RAPD markers

Treesearch

G. Bucci; Thomas L. Kubisiak; W.L. Nance; P. Menozzi

1997-01-01

The authors built a "consensus" partial linkage map based on RAPD markers using 48 sibships of eight megagametophytes each from a natural population of Norway spruce. A RAPD linkage map for a single individual from the same population had previously been constructed. Using 30 random decamers that had yielded 83 RAPD markers in the single-tree map, eight...

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers.

PubMed

de Miguel, Marina; de Maria, Nuria; Guevara, M Angeles; Diaz, Luis; Sáez-Laguna, Enrique; Sánchez-Gómez, David; Chancerel, Emilie; Aranda, Ismael; Collada, Carmen; Plomion, Christophe; Cabezas, José-Antonio; Cervera, María-Teresa

2012-10-04

Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

PubMed Central

2012-01-01

Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest. PMID:23036012

Toward standardized mapping for left atrial analysis and cardiac ablation guidance

NASA Astrophysics Data System (ADS)

Rettmann, M. E.; Holmes, D. R.; Linte, C. A.; Packer, D. L.; Robb, R. A.

2014-03-01

In catheter-based cardiac ablation, the pulmonary vein ostia are important landmarks for guiding the ablation procedure, and for this reason, have been the focus of many studies quantifying their size, structure, and variability. Analysis of pulmonary vein structure, however, has been limited by the lack of a standardized reference space for population based studies. Standardized maps are important tools for characterizing anatomic variability across subjects with the goal of separating normal inter-subject variability from abnormal variability associated with disease. In this work, we describe a novel technique for computing flat maps of left atrial anatomy in a standardized space. A flat map of left atrial anatomy is created by casting a single ray through the volume and systematically rotating the camera viewpoint to obtain the entire field of view. The technique is validated by assessing preservation of relative surface areas and distances between the original 3D geometry and the flat map geometry. The proposed methodology is demonstrated on 10 subjects which are subsequently combined to form a probabilistic map of anatomic location for each of the pulmonary vein ostia and the boundary of the left atrial appendage. The probabilistic map demonstrates that the location of the inferior ostia have higher variability than the superior ostia and the variability of the left atrial appendage is similar to the superior pulmonary veins. This technique could also have potential application in mapping electrophysiology data, radio-frequency ablation burns, or treatment planning in cardiac ablation therapy.

Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases

PubMed Central

Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T.; Morgan, Alex A.; Moreno-Estrada, Andres; Nilsen, Geoffrey B.; Ruau, David; Lincoln, Stephen E.; Bustamante, Carlos D.; Butte, Atul J.

2012-01-01

Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations. PMID:22511877

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

PubMed Central

Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S.; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C.L.L.; Singh, Sube; Jain, Mukesh; Tyagi, Akhilesh K.; Parida, Swarup K.

2013-01-01

We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5′ untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication. PMID:23633531

Myocardial infarction size and location: a comparative study of epicardial isopotential mapping, thallium-201 scintigraphy, electrocardiography and vectorcardiography

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

Toyama, S.; Suzuki, K.; Takahashi, T.

1987-07-01

Based on epicardial isopotential mapping (the Ep Map), which was calculated from body surface isopotential mapping (the Body Map) with Yamashita's method, using the finite element technique, we predicted the location and size of the abnormal depolarized area (the infarcted area) in 19 clinical cases of anterior and 18 cases of inferoposterior infarction. The prediction was done using Toyama's diagnostic method, previously reported. The accuracy of the prediction by the Ep Map was assessed by comparing it with findings from thallium-201 scintigraphy (SCG), electrocardiography (ECG) and vectorcardiography (VCG). In all cases of anterior infarction, the location of the abnormal depolarizedmore » areas determined on the Ep Map, which was localized at the anterior wall along the anterior intraventricular septum, agreed with the location of the abnormal findings obtained by SCG, ECG and VCG. For all inferoposterior infarction cases, the abnormal depolarized areas were localized at the posterior wall and the location also coincided with that of the abnormal findings obtained by SCG, ECG and VCG. Furthermore, we ranked and ordered the size of the abnormal depolarized areas, which were predicted by the Ep Map for both anterior and inferoposterior infarction cases. In the cases of anterior infarction, the order of the size of the abnormal depolarized area by the Ep Map was correlated to the size of the abnormal findings by SCG, as well as to the results from Selvester's QRS scoring system in ECG and to the angle of the maximum QRS vector in the horizontal plane in VCG.« less

Comparison of RAPD Linkage Maps Constructed For a Single Longleaf Pine From Both Haploid and Diploid Mapping Populations

Treesearch

Thomas L. Kubisiak; C.Dana Nelson; W.L. Name; M. Stine

1996-01-01

Considerable concern has been voiced regarding the reproducibility/transferability of RAPD markers across different genetic backgrounds in genetic mapping experiments. Therefore, separate gametic subsets (mapping populations) were used to construct individual random amplified polymorphic DNA (RAPD) linkage maps for a single longleaf pine (Pinus palustris...

Human population, urban settlement patterns and their impact on Plasmodium falciparum malaria endemicity.

PubMed

Tatem, Andrew J; Guerra, Carlos A; Kabaria, Caroline W; Noor, Abdisalan M; Hay, Simon I

2008-10-27

The efficient allocation of financial resources for malaria control and the optimal distribution of appropriate interventions require accurate information on the geographic distribution of malaria risk and of the human populations it affects. Low population densities in rural areas and high population densities in urban areas can influence malaria transmission substantially. Here, the Malaria Atlas Project (MAP) global database of Plasmodium falciparum parasite rate (PfPR) surveys, medical intelligence and contemporary population surfaces are utilized to explore these relationships and other issues involved in combining malaria risk maps with those of human population distribution in order to define populations at risk more accurately. First, an existing population surface was examined to determine if it was sufficiently detailed to be used reliably as a mask to identify areas of very low and very high population density as malaria free regions. Second, the potential of international travel and health guidelines (ITHGs) for identifying malaria free cities was examined. Third, the differences in PfPR values between surveys conducted in author-defined rural and urban areas were examined. Fourth, the ability of various global urban extent maps to reliably discriminate these author-based classifications of urban and rural in the PfPR database was investigated. Finally, the urban map that most accurately replicated the author-based classifications was analysed to examine the effects of urban classifications on PfPR values across the entire MAP database. Masks of zero population density excluded many non-zero PfPR surveys, indicating that the population surface was not detailed enough to define areas of zero transmission resulting from low population densities. In contrast, the ITHGs enabled the identification and mapping of 53 malaria free urban areas within endemic countries. Comparison of PfPR survey results showed significant differences between author-defined 'urban' and 'rural' designations in Africa, but not for the remainder of the malaria endemic world. The Global Rural Urban Mapping Project (GRUMP) urban extent mask proved most accurate for mapping these author-defined rural and urban locations, and further sub-divisions of urban extents into urban and peri-urban classes enabled the effects of high population densities on malaria transmission to be mapped and quantified. The availability of detailed, contemporary census and urban extent data for the construction of coherent and accurate global spatial population databases is often poor. These known sources of uncertainty in population surfaces and urban maps have the potential to be incorporated into future malaria burden estimates. Currently, insufficient spatial information exists globally to identify areas accurately where population density is low enough to impact upon transmission. Medical intelligence does however exist to reliably identify malaria free cities. Moreover, in Africa, urban areas that have a significant effect on malaria transmission can be mapped.

Using known map category marginal frequencies to improve estimates of thematic map accuracy

NASA Technical Reports Server (NTRS)

Card, D. H.

1982-01-01

By means of two simple sampling plans suggested in the accuracy-assessment literature, it is shown how one can use knowledge of map-category relative sizes to improve estimates of various probabilities. The fact that maximum likelihood estimates of cell probabilities for the simple random sampling and map category-stratified sampling were identical has permitted a unified treatment of the contingency-table analysis. A rigorous analysis of the effect of sampling independently within map categories is made possible by results for the stratified case. It is noted that such matters as optimal sample size selection for the achievement of a desired level of precision in various estimators are irrelevant, since the estimators derived are valid irrespective of how sample sizes are chosen.

Size and spatial distribution of stray dog population in the University of São Paulo campus, Brazil.

PubMed

Dias, Ricardo Augusto; Guilloux, Aline Gil Alves; Borba, Mauro Riegert; Guarnieri, Maria Cristina de Lourdes; Prist, Ricardo; Ferreira, Fernando; Amaku, Marcos; Neto, José Soares Ferreira; Stevenson, Mark

2013-06-01

A longitudinal study was carried out to describe the size and spatial distribution of the stray dog population in the University of São Paulo campus, Brazil from November 2010 to November 2011. The campus is located within the urban area of São Paulo, the largest city of Brazil, with a population over 11 million. The 4.2 km(2) that comprise the university grounds are walled, with 10 access gates, allowing stray dogs to move in and out freely. Over 100,000 people and 50,000 vehicles circulate in the campus daily. Five observations were made during the study period, using a mark-resight method. The same route was performed in all observations, being traveled twice on each observation day. Observed animals were photographed and the sight coordinates were obtained using a GPS device. The estimated size of the stray dog population varied from 32 (CI 95% 23-56) to 56 (CI 95% 45-77) individuals. Differences between in- and outward dog movements influenced dog population estimates. Overlapping home ranges of docile dogs were observed in areas where most people circulate. An elusive group was observed close to a protected rain forest area and the estimated home range for this group did not overlap with the home ranges for other dogs within the campus. A kernel density map showed that higher densities of stray dog sighting is associated with large organic matter generators, such as university restaurants. We conclude that the preferred source of food of the stray dogs on the University of São Paulo campus was leftover food deliberately offered by restaurant users. The population was stable during the study period and the constant source of food was the main reason to retain this population within the campus. Copyright © 2012 Elsevier B.V. All rights reserved.

Mapping of disease-associated variants in admixed populations

PubMed Central

2011-01-01

Recent developments in high-throughput genotyping and whole-genome sequencing will enhance the identification of disease loci in admixed populations. We discuss how a more refined estimation of ancestry benefits both admixture mapping and association mapping, making disease loci identification in admixed populations more powerful. High-throughput genotyping and sequencing will enable refined estimation of ancestry, thus enhancing disease loci identification in admixed populations PMID:21635713

Towards the Development and Validation of a Global Field Size and Irrigation Map using Crowdsourcing, Mobile Apps and Google Earth Engine in support of GEOGLAM

NASA Astrophysics Data System (ADS)

Fritz, S.; Nordling, J.; See, L. M.; McCallum, I.; Perger, C.; Becker-Reshef, I.; Mucher, S.; Bydekerke, L.; Havlik, P.; Kraxner, F.; Obersteiner, M.

2014-12-01

The International Institute for Applied Systems Analysis (IIASA) has developed a global cropland extent map, which supports the monitoring and assessment activities of GEOGLAM (Group on Earth Observations Global Agricultural Monitoring Initiative). Through the European-funded SIGMA (Stimulating Innovation for Global Monitoring of Agriculture and its Impact on the Environment in support of GEOGLAM) project, IIASA is continuing to support GEOGLAM by providing cropland projections in the future and modelling environmental impacts on agriculture under various scenarios. In addition, IIASA is focusing on two specific elements within SIGMA: the development of a global field size and irrigation map; and mobile app development for in-situ data collection and validation of remotely-sensed products. Cropland field size is a very useful indicator for agricultural monitoring yet the information we have at a global scale is currently very limited. IIASA has already created a global map of field size at a 1 km resolution using crowdsourced data from Geo-Wiki as a first approximation. Using automatic classification of Landsat imagery and algorithms contained within Google Earth Engine, initial experimentation has shown that circular fields and landscape structures can easily be extracted. Not only will this contribute to improving the global map of field size, it can also be used to create a global map that contains a large proportion of the world's irrigated areas, which will be another useful contribution to GEOGLAM. The field size map will also be used to stratify and develop a global crop map in SIGMA. Mobile app development in support of in-situ data collection is another area where IIASA is currently working. An Android app has been built using the Open Data Toolkit (ODK) and extended further with spatial mapping capabilities called GeoODK. The app allows users to collect data on different crop types and delineate fields on the ground, which can be used to validate the field size map. The app can also cache map data so that high resolution satellite imagery and reference data from the users can be viewed in the field without the need for an internet connection. This app will be used for calibration and validation of the data products in SIGMA, e.g. data collection at JECAM (Joint Experiment of Crop Assessment and Monitoring) sites.

The Lunar Rock Size Frequency Distribution from Diviner Infrared Measurements

NASA Astrophysics Data System (ADS)

Elder, C. M.; Hayne, P. O.; Piqueux, S.; Bandfield, J.; Williams, J. P.; Ghent, R. R.; Paige, D. A.

2016-12-01

Knowledge of the rock size frequency distribution on a planetary body is important for understanding its geologic history and for selecting landing sites. The rock size frequency distribution can be estimated by counting rocks in high resolution images, but most bodies in the solar system have limited areas with adequate coverage. We propose an alternative method to derive and map rock size frequency distributions using multispectral thermal infrared data acquired at multiple times during the night. We demonstrate this new technique for the Moon using data from the Lunar Reconnaissance Orbiter (LRO) Diviner radiometer in conjunction with three dimensional thermal modeling, leveraging the differential cooling rates of different rock sizes. We assume an exponential rock size frequency distribution, which has been shown to yield a good fit to rock populations in various locations on the Moon, Mars, and Earth [2, 3] and solve for the best radiance fits as a function of local time and wavelength. This method presents several advantages: 1) unlike other thermally derived rock abundance techniques, it is sensitive to rocks smaller than the diurnal skin depth; 2) it does not result in apparent decrease in rock abundance at night; and 3) it can be validated using images taken at the lunar surface. This method yields both the fraction of the surface covered in rocks of all sizes and the exponential factor, which defines the rate of drop-off in the exponential function at large rock sizes. We will present maps of both these parameters for the Moon, and provide a geological interpretation. In particular, this method reveals rocks in the lunar highlands that are smaller than previous thermal methods could detect. [1] Bandfield J. L. et al. (2011) JGR, 116, E00H02. [2] Golombek and Rapp (1997) JGR, 102, E2, 4117-4129. [3] Cintala, M.J. and K.M. McBride (1995) NASA Technical Memorandum 104804.

Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.).

PubMed

Ma, Yu; Coyne, Clarice J; Grusak, Michael A; Mazourek, Michael; Cheng, Peng; Main, Dorrie; McGee, Rebecca J

2017-02-13

Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea seeds requires the development of genome-wide tools. The objectives of this research were to develop these tools by: identifying genome-wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS); constructing a high-density linkage map and comparative maps with other legumes, and identifying quantitative trait loci (QTL) for levels of boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc in the seed, as well as for seed weight. In this study, 1609 high quality SNPs were found to be polymorphic between 'Kiflica' and 'Aragorn', two parents of an F 6 -derived recombinant inbred line (RIL) population. Mapping 1683 markers including 75 previously published markers and 1608 SNPs developed from the present study generated a linkage map of size 1310.1 cM. Comparative mapping with other legumes demonstrated that the highest level of synteny was observed between pea and the genome of Medicago truncatula. QTL analysis of the RIL population across two locations revealed at least one QTL for each of the mineral nutrient traits. In total, 46 seed mineral concentration QTLs, 37 seed mineral content QTLs, and 6 seed weight QTLs were discovered. The QTLs explained from 2.4% to 43.3% of the phenotypic variance. The genome-wide SNPs and the genetic linkage map developed in this study permitted QTL identification for pea seed mineral nutrients that will serve as important resources to enable marker-assisted selection (MAS) for nutritional quality traits in pea breeding programs.

The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum)

DOE PAGES

Milano, E. R.; Lowry, D. B.; Juenger, T. E.

2016-09-09

The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within plant species. However, we know surprisingly little about the genetic mechanisms underlying the locally adapted traits involved in ecotype formation. The genetic architecture underlying locally adapted traits dictates how an organism will respond to environmental selection pressures, and has major implications for evolutionary ecology, conservation, and crop breeding. To understand the genetic architecture underlying the divergence of switchgrass (Panicum virgatum) ecotypes, we constructed a genetic mapping population through a four-way outbred cross between two northern upland and two southern lowland accessions. Trait segregation in this mappingmore » population was largely consistent with multiple independent loci controlling the suite of traits that characterizes ecotype divergence. We assembled a joint linkage map using ddRADseq, and mapped quantitative trait loci (QTL) for traits that are divergent between ecotypes, including flowering time, plant size, physiological processes, and disease resistance. Overall, we found that most QTL had small to intermediate effects. While we identified colocalizing QTL for multiple traits, we did not find any large-effect QTL that clearly controlled multiple traits through pleiotropy or tight physical linkage. These results indicate that ecologically important traits in switchgrass have a complex genetic basis, and that similar loci may underlie divergence across the geographic range of the ecotypes.« less

The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum)

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

Milano, E. R.; Lowry, D. B.; Juenger, T. E.

The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within plant species. However, we know surprisingly little about the genetic mechanisms underlying the locally adapted traits involved in ecotype formation. The genetic architecture underlying locally adapted traits dictates how an organism will respond to environmental selection pressures, and has major implications for evolutionary ecology, conservation, and crop breeding. To understand the genetic architecture underlying the divergence of switchgrass (Panicum virgatum) ecotypes, we constructed a genetic mapping population through a four-way outbred cross between two northern upland and two southern lowland accessions. Trait segregation in this mappingmore » population was largely consistent with multiple independent loci controlling the suite of traits that characterizes ecotype divergence. We assembled a joint linkage map using ddRADseq, and mapped quantitative trait loci (QTL) for traits that are divergent between ecotypes, including flowering time, plant size, physiological processes, and disease resistance. Overall, we found that most QTL had small to intermediate effects. While we identified colocalizing QTL for multiple traits, we did not find any large-effect QTL that clearly controlled multiple traits through pleiotropy or tight physical linkage. These results indicate that ecologically important traits in switchgrass have a complex genetic basis, and that similar loci may underlie divergence across the geographic range of the ecotypes.« less

Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping.

PubMed

Frickenhaus, Stephan; Kannan, Srinivasaraghavan; Zacharias, Martin

2009-02-01

A direct conformational clustering and mapping approach for peptide conformations based on backbone dihedral angles has been developed and applied to compare conformational sampling of Met-enkephalin using two molecular dynamics (MD) methods. Efficient clustering in dihedrals has been achieved by evaluating all combinations resulting from independent clustering of each dihedral angle distribution, thus resolving all conformational substates. In contrast, Cartesian clustering was unable to accurately distinguish between all substates. Projection of clusters on dihedral principal component (PCA) subspaces did not result in efficient separation of highly populated clusters. However, representation in a nonlinear metric by Sammon mapping was able to separate well the 48 highest populated clusters in just two dimensions. In addition, this approach also allowed us to visualize the transition frequencies between clusters efficiently. Significantly, higher transition frequencies between more distinct conformational substates were found for a recently developed biasing-potential replica exchange MD simulation method allowing faster sampling of possible substates compared to conventional MD simulations. Although the number of theoretically possible clusters grows exponentially with peptide length, in practice, the number of clusters is only limited by the sampling size (typically much smaller), and therefore the method is well suited also for large systems. The approach could be useful to rapidly and accurately evaluate conformational sampling during MD simulations, to compare different sampling strategies and eventually to detect kinetic bottlenecks in folding pathways.

High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

PubMed Central

Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

2013-01-01

Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

Early-life exposures and Johne's disease risk in zoo ruminants.

PubMed

Burgess, Tristan L; Witte, Carmel L; Rideout, Bruce A

2018-01-01

Johne's disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic, progressive bacterial enteritis of ruminants that can cause serious losses in both livestock and exotic species. Infection risk in exotic ruminants is associated with maternal infection status, but the effect of other herdmates on risk of infection has not been reported, to our knowledge. We conducted a retrospective cohort study to evaluate the association between MAP infection status and early-life contact with infected herdmates. The study population included 3,234 individuals representing 128 species at San Diego Zoo Global facilities between 1991 and 2010. Animal movement, health, and pathology records were used to trace enclosure-sharing contacts between members of the study population and any MAP-infected animal. Contact-days were counted by age of the reference animal and the number of unique infected individuals contacted. Herdmate infection status was stratified by stage of infection (180 d prior to diagnosis), age, and whether relevant lesions were found at autopsy. Having an infected herdmate was a strong risk factor for infection (OR = 4.4; 95% CI: 1.9-10.3), and each method of defining herdmate infection status showed significant differences in infection risk. The best predictor was number of contact-days within the first week of life, with a 2-fold increase in risk associated with each doubling in the number of contact-days (OR = 2.1; 95% CI: 1.1-4.0). We conclude that early contact with infected animals is an important predictor of MAP infection risk, although the effect size is smaller than that previously described for maternal infection status.

A Global Picture of the Gamma-Ricker Map: A Flexible Discrete-Time Model with Factors of Positive and Negative Density Dependence.

PubMed

Liz, Eduardo

2018-02-01

The gamma-Ricker model is one of the more flexible and general discrete-time population models. It is defined on the basis of the Ricker model, introducing an additional parameter [Formula: see text]. For some values of this parameter ([Formula: see text], population is overcompensatory, and the introduction of an additional parameter gives more flexibility to fit the stock-recruitment curve to field data. For other parameter values ([Formula: see text]), the gamma-Ricker model represents populations whose per-capita growth rate combines both negative density dependence and positive density dependence. The former can lead to overcompensation and dynamic instability, and the latter can lead to a strong Allee effect. We study the impact of the cooperation factor in the dynamics and provide rigorous conditions under which increasing the Allee effect strength stabilizes or destabilizes population dynamics, promotes or prevents population extinction, and increases or decreases population size. Our theoretical results also include new global stability criteria and a description of the possible bifurcations.

A sugar pine consensus map: Comparative mapping between the Pinus subgenus Pinus and the subgenus Strobus

Treesearch

Kathleen D. Jermstad; Andrew J. Eckert; Bohun B. Kinloch; Dean A. Davis; Deems C. Burton; Annette D. Mix; Jill L. Wegrzyn; David B. Neale

2011-01-01

We have constructed a consensus genetic linkage map for sugar pine using three mapping populations that segregate for resistance to white pine blister rust, a disease caused by the fungal pathogen Cronartium ribicola. The major gene of resistance, Cr1, was mapped in two of the populations and included in the consensus map, which contains 400 markers organized into 19...

Registration of a rice gene mapping population of Lemont X Jasmine 85 recombinant inbred lines

USDA-ARS?s Scientific Manuscript database

A mapping population developed from a cross of rice (Oryza sativa L.) tropical japonica cultivar ‘Lemont’ and indica cultivar ‘Jasmine 85’ was developed to facilitate genetic studies for important agronomic traits. The indica- and japonica-based rice recombinant inbred line (RIL) mapping population ...

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

USGS Publications Warehouse

Sleeter, Rachel; Gould, Michael

2007-01-01

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

Nanoparticles that do not adhere to mucus provide uniform and long-lasting drug delivery to airways following inhalation

PubMed Central

Schneider, Craig S.; Xu, Qingguo; Boylan, Nicholas J.; Chisholm, Jane; Tang, Benjamin C.; Schuster, Benjamin S.; Henning, Andreas; Ensign, Laura M.; Lee, Ethan; Adstamongkonkul, Pichet; Simons, Brian W.; Wang, Sho-Yu S.; Gong, Xiaoqun; Yu, Tao; Boyle, Michael P.; Suk, Jung Soo; Hanes, Justin

2017-01-01

Mucoadhesive particles (MAP) have been widely explored for pulmonary drug delivery because of their perceived benefits in improving particle residence in the lungs. However, retention of particles adhesively trapped in airway mucus may be limited by physiologic mucus clearance mechanisms. In contrast, particles that avoid mucoadhesion and have diameters smaller than mucus mesh spacings rapidly penetrate mucus layers [mucus-penetrating particles (MPP)], which we hypothesized would provide prolonged lung retention compared to MAP. We compared in vivo behaviors of variously sized, polystyrene-based MAP and MPP in the lungs following inhalation. MAP, regardless of particle size, were aggregated and poorly distributed throughout the airways, leading to rapid clearance from the lungs. Conversely, MPP as large as 300 nm exhibited uniform distribution and markedly enhanced retention compared to size-matched MAP. On the basis of these findings, we formulated biodegradable MPP (b-MPP) with an average diameter of <300 nm and examined their behavior following inhalation relative to similarly sized biodegradable MAP (b-MAP). Although b-MPP diffused rapidly through human airway mucus ex vivo, b-MAP did not. Rapid b-MPP movements in mucus ex vivo correlated to a more uniform distribution within the airways and enhanced lung retention time as compared to b-MAP. Furthermore, inhalation of b-MPP loaded with dexamethasone sodium phosphate (DP) significantly reduced inflammation in a mouse model of acute lung inflammation compared to both carrier-free DP and DP-loaded MAP. These studies provide a careful head-to-head comparison of MAP versus MPP following inhalation and challenge a long-standing dogma that favored the use of MAP for pulmonary drug delivery. PMID:28435870

Generation of a Saturated Genetic Recombination Map for Avocado (Persea americana)

USDA-ARS?s Scientific Manuscript database

Two large mapping populations of avocado consisting of 1582 trees were genotyped with 5050 SNP markers from transcribed genes using an Illumina Infinium SNP chip. A Florida mapping population consisted of 527 progeny from 'Tonnage' x 'Simmonds' and 249 from 'Simmonds' x 'Tonnage'. A California map...

Hemisphere-Dependent Attentional Modulation of Human Parietal Visual Field Representations

PubMed Central

Silver, Michael A.

2015-01-01

Posterior parietal cortex contains several areas defined by topographically organized maps of the contralateral visual field. However, recent studies suggest that ipsilateral stimuli can elicit larger responses in the right than left hemisphere within these areas, depending on task demands. Here we determined the effects of spatial attention on the set of visual field locations (the population receptive field [pRF]) that evoked a response for each voxel in human topographic parietal cortex. A two-dimensional Gaussian was used to model the pRF in each voxel, and we measured the effects of attention on not only the center (preferred visual field location) but also the size (visual field extent) of the pRF. In both hemispheres, larger pRFs were associated with attending to the mapping stimulus compared with attending to a central fixation point. In the left hemisphere, attending to the stimulus also resulted in more peripheral preferred locations of contralateral representations, compared with attending fixation. These effects of attention on both pRF size and preferred location preserved contralateral representations in the left hemisphere. In contrast, attentional modulation of pRF size but not preferred location significantly increased representation of the ipsilateral (right) visual hemifield in right parietal cortex. Thus, attention effects in topographic parietal cortex exhibit hemispheric asymmetries similar to those seen in hemispatial neglect. Our findings suggest potential mechanisms underlying the behavioral deficits associated with this disorder. PMID:25589746

Bayesian population receptive field modelling.

PubMed

Zeidman, Peter; Silson, Edward Harry; Schwarzkopf, Dietrich Samuel; Baker, Chris Ian; Penny, Will

2017-09-08

We introduce a probabilistic (Bayesian) framework and associated software toolbox for mapping population receptive fields (pRFs) based on fMRI data. This generic approach is intended to work with stimuli of any dimension and is demonstrated and validated in the context of 2D retinotopic mapping. The framework enables the experimenter to specify generative (encoding) models of fMRI timeseries, in which experimental stimuli enter a pRF model of neural activity, which in turns drives a nonlinear model of neurovascular coupling and Blood Oxygenation Level Dependent (BOLD) response. The neuronal and haemodynamic parameters are estimated together on a voxel-by-voxel or region-of-interest basis using a Bayesian estimation algorithm (variational Laplace). This offers several novel contributions to receptive field modelling. The variance/covariance of parameters are estimated, enabling receptive fields to be plotted while properly representing uncertainty about pRF size and location. Variability in the haemodynamic response across the brain is accounted for. Furthermore, the framework introduces formal hypothesis testing to pRF analysis, enabling competing models to be evaluated based on their log model evidence (approximated by the variational free energy), which represents the optimal tradeoff between accuracy and complexity. Using simulations and empirical data, we found that parameters typically used to represent pRF size and neuronal scaling are strongly correlated, which is taken into account by the Bayesian methods we describe when making inferences. We used the framework to compare the evidence for six variants of pRF model using 7 T functional MRI data and we found a circular Difference of Gaussians (DoG) model to be the best explanation for our data overall. We hope this framework will prove useful for mapping stimulus spaces with any number of dimensions onto the anatomy of the brain. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson.

PubMed

Thomson, M J; Tai, T H; McClung, A M; Lai, X-H; Hinga, M E; Lobos, K B; Xu, Y; Martinez, C P; McCouch, S R

2003-08-01

An advanced backcross population between an accession of Oryza rufipogon (IRGC 105491) and the U.S. cultivar Jefferson (Oryza sativa ssp. japonica) was developed to identify quantitative trait loci (QTLs) for yield, yield components and morphological traits. The genetic linkage map generated for this population consisted of 153 SSR and RFLP markers with an average interval size of 10.3 cM. Thirteen traits were examined, nine of which were measured in multiple environments. Seventy-six QTLs above an experiment-wise significance threshold of P<0.01 (corresponding to an interval mapping LOD>3.6 or a composite interval mapping LOD>3.9) were identified. For the traits measured in multiple environments, 47% of the QTLs were detected in at least two environments. The O. rufipogon allele was favorable for 53% of the yield and yield component QTLs, including loci for yield, grains per panicle, panicle length, and grain weight. Morphological traits related to the domestication process and/or weedy characteristics, including plant height, shattering, tiller type and awns, were found clustered on chromosomes 1 and 4. Comparisons to previous studies involving wild x cultivated crosses revealed O. rufipogon alleles with stable effects in multiple genetic backgrounds and environments, several of which have not been detected in studies between Oryza sativa cultivars, indicating potentially novel alleles from O. rufipogon. Some O. rufipogon-derived QTLs, however, were in similar regions as previously reported QTLs from Oryza sativa cultivars, providing evidence for conservation of these QTLs across the Oryza genus. In addition, several QTLs for grain weight, plant height, and flowering time were localized to putative homeologous regions in maize where QTLs for these traits have been previously reported, supporting the hypothesis of functional conservation of QTLs across the grasses.

Relationship between pure Schistosoma haematobium infection in Upper Egypt and irrigation systems. Part 1: methods of study.

PubMed

Hammam, H M; Allam, F A; Hassanein, F; El-Garby, M T

1975-01-01

Four villages in Assiut Governorate were studied. They were matched for availability and time of introduction of medical services, the size of population and the socioeconomic status. One village had a basin system of irrigation. The other three villages had perennial irrigation introduced at different dates. A sketch map of each village was made showing the location of every house and the irrigation channels. Total coverage was intended in Gezirat El-Maabda (with basin irrigation) and Nazza Karar (with perennial irrigation-recently introduced). In El-Ghorayeb and Garf Sarhan (with older systems of perennial irrigation) systematic random samples were studied. The Study included a full, double check clinical examination of urine and stools samples and a social study. Data about educational level and activities that bring the individual in contact with canal water were recorded. Tables showing the age and sex distribution of the total population and the population studied in each village are presented and show validity of the samples taken from the population.

A method to separate and quantify the effects of indentation size, residual stress and plastic damage when mapping properties using instrumented indentation

NASA Astrophysics Data System (ADS)

Hou, X. D.; Jennett, N. M.

2017-11-01

Instrumented indentation is a convenient and increasingly rapid method of high resolution mapping of surface properties. There is, however, significant untapped potential for the quantification of these properties, which is only possible by solving a number of serious issues that affect the absolute values for mechanical properties obtained from small indentations. The three most pressing currently are the quantification of: the indentation size effect (ISE), residual stress, and pile-up and sink-in—which is itself affected by residual stress and ISE. Hardness based indentation mapping is unable to distinguish these effects. We describe a procedure that uses an elastic modulus as an internal reference and combines the information available from an indentation modulus map, a hardness map, and a determination of the ISE coefficient (using self-similar geometry indentation) to correct for the effects of stress, pile up and the indentation size effect, to leave a quantified map of plastic damage and grain refinement hardening in a surface. This procedure is used to map the residual stress in a cross-section of the machined surface of a previously stress free metal. The effect of surface grinding is compared to milling and is shown to cause different amounts of work hardening, increase in residual stress, and surface grain size reduction. The potential use of this procedure for mapping coatings in cross-section is discussed.

Controllable self-assembly of mesoporous hydroxyapatite.

PubMed

Chen, Jingdi; Wang, Zihao; Wen, Zhenliang; Yang, Shen; Wang, Jianhua; Zhang, Qiqing

2015-03-01

In this paper, mesoporous hydroxyapatite (HAp) of controllable pore size was tailored with the template of a biodegradable mono-alkyl phosphate (MAP) via a simple route by hydrothermal treatment. A serial study of the various experimental parameters on pore size of HAp was investigated. The additive amount of MAP and hydrothermal temperature were important factors for the pore structure and pore size. Powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and nitrogen adsorption-desorption (BET, BJH) were used to characterize the structure and composition of the HAp samples. Both XRD and BJH results indicated that regular mesoporous HAp nanoparticles (with a mean pore size of 3.5nm) were successfully produced. As shown in transmission electron microscopy (TEM), orderly uniform pore structure appeared in the HAp particles. Because of the special structure of the MAP and the interaction between ionized MAP and other ions in solution, the product presents uniform mesoporous structure with well-defined pore size. Copyright © 2015 Elsevier B.V. All rights reserved.

Creating a literature database of low-calorie sweeteners and health studies: evidence mapping.

PubMed

Wang, Ding Ding; Shams-White, Marissa; Bright, Oliver John M; Parrott, J Scott; Chung, Mei

2016-01-05

Evidence mapping is an emerging tool used to systematically identify, organize and summarize the quantity and focus of scientific evidence on a broad topic, but there are currently no methodological standards. Using the topic of low-calorie sweeteners (LCS) and selected health outcomes, we describe the process of creating an evidence-map database and demonstrate several example descriptive analyses using this database. The process of creating an evidence-map database is described in detail. The steps include: developing a comprehensive literature search strategy, establishing study eligibility criteria and a systematic study selection process, extracting data, developing outcome groups with input from expert stakeholders and tabulating data using descriptive analyses. The database was uploaded onto SRDR™ (Systematic Review Data Repository), an open public data repository. Our final LCS evidence-map database included 225 studies, of which 208 were interventional studies and 17 were cohort studies. An example bubble plot was produced to display the evidence-map data and visualize research gaps according to four parameters: comparison types, population baseline health status, outcome groups, and study sample size. This plot indicated a lack of studies assessing appetite and dietary intake related outcomes using LCS with a sugar intake comparison in people with diabetes. Evidence mapping is an important tool for the contextualization of in-depth systematic reviews within broader literature and identifies gaps in the evidence base, which can be used to inform future research. An open evidence-map database has the potential to promote knowledge translation from nutrition science to policy.

Palaeogeographic reconstruction of sandstones using weighted mean grain-size maps, with examples from the Karoo Basin (South Africa) and the Sydney Basin (Australia)

NASA Astrophysics Data System (ADS)

le Roux, J. P.

1992-12-01

Although sandstone grain-size maps can be a powerful means of reconstructing ancient depositional environments, they have rarely been used in the past. In this paper, two case studies are presented to illustrate the potential of this technique where other, more conventional methods may not be applicable. In the first case, a braided to anastomosing river system in the Triassic Molteno Formation of the South African Karoo Basin is examined. The weighted mean grain-size map clearly portrays the distribution of channels and islands and compares very well with other methods of reconstruction. The second case study examines an offshore shoal in the Permian Nowra Sandstone of the Sydney Basin in Australia. Here the grain-size map shows a north-northeasterly trend parallel to the orientation of the shoal, with a zone of coarsest grains displaced to the east of the shoal crest. This probably reflects the location of the breaker zone. As grain size is an important factor controlling the porosity and permeability of sediments, these maps can provide very useful information when exploring for epigenetic, stratabound ore deposits such as uranium, or planning production wells for oil and gas.

A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control.

PubMed

Devoghalaere, Fanny; Doucen, Thomas; Guitton, Baptiste; Keeling, Jeannette; Payne, Wendy; Ling, Toby John; Ross, John James; Hallett, Ian Charles; Gunaseelan, Kularajathevan; Dayatilake, G A; Diak, Robert; Breen, Ken C; Tustin, D Stuart; Costes, Evelyne; Chagné, David; Schaffer, Robert James; David, Karine Myriam

2012-01-13

Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.

A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control

PubMed Central

2012-01-01

Background Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. Results High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. Conclusions The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point. PMID:22243694

Construction of adhesion maps for contacts between a sphere and a half-space: Considering size effects of the sphere.

PubMed

Zhang, Yuyan; Wang, Xiaoli; Li, Hanqing; Yang, Weixu

2015-11-15

Previous adhesion maps, such as the JG (Johnson-Greenwood) and YCG (Yao-Ciavarella-Gao) maps, are used to guide the selection of Bradley, DMT, M-D, JKR and Hertz models. However, when the size of the contact sphere decreases to the small scale, the applicability of JG and YCG maps is limited because the assumptions regarding the contact region profile, interaction between contact bodies and sphere shape in the classical models constituting these two maps are no longer valid. To avoid this limitation, in this paper, a new numerical model considering size effects of the sphere is established first and then introduced into the new adhesion maps together with the YGG (Yao-Guduru-Gao) model and Hertz model. Regimes of these models in the new map under a certain sphere radius are demarcated by the criteria related to the relative force differences and the ratio of contact radius to sphere radius. In addition, the approaches at pull-off, jump-in and jump-out for different Tabor parameters and sphere radii are provided in the new maps. Finally, to make the new maps more feasible, the numerical results of approaches, force and contact radius involved in the maps are formularized by using the piecewise fitting. Copyright © 2015 Elsevier Inc. All rights reserved.

Distribution, Statistics, and Resurfacing of Large Impact Basins on Mercury

NASA Technical Reports Server (NTRS)

Fassett, Caleb I.; Head, James W.; Baker, David M. H.; Chapman, Clark R.; Murchie, Scott L.; Neumann, Gregory A.; Oberst, Juergen; Prockter, Louise M.; Smith, David E.; Solomon, Sean C.;

Historical habitat connectivity affects current genetic structure in a grassland species.

PubMed

Münzbergová, Z; Cousins, S A O; Herben, T; Plačková, I; Mildén, M; Ehrlén, J

2013-01-01

Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co-dominant markers to estimate genetic diversity and deviation from Hardy-Weinberg equilibrium in 31 populations distributed within a 5 km(2) agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

Mapping asthma-associated variants in admixed populations

PubMed Central

Mersha, Tesfaye B.

2015-01-01

Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease–associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders. PMID:26483834

The Global Trachoma Mapping Project: Methodology of a 34-Country Population-Based Study

PubMed Central

Solomon, Anthony W.; Pavluck, Alexandre L.; Courtright, Paul; Aboe, Agatha; Adamu, Liknaw; Alemayehu, Wondu; Alemu, Menbere; Alexander, Neal D. E.; Kello, Amir Bedri; Bero, Berhanu; Brooker, Simon J.; Chu, Brian K.; Dejene, Michael; Emerson, Paul M.; Flueckiger, Rebecca M.; Gadisa, Solomon; Gass, Katherine; Gebre, Teshome; Habtamu, Zelalem; Harvey, Erik; Haslam, Dominic; King, Jonathan D.; Mesurier, Richard Le; Lewallen, Susan; Lietman, Thomas M.; MacArthur, Chad; Mariotti, Silvio P.; Massey, Anna; Mathieu, Els; Mekasha, Addis; Millar, Tom; Mpyet, Caleb; Muñoz, Beatriz E.; Ngondi, Jeremiah; Ogden, Stephanie; Pearce, Joseph; Sarah, Virginia; Sisay, Alemayehu; Smith, Jennifer L.; Taylor, Hugh R.; Thomson, Jo; West, Sheila K.; Willis, Rebecca; Bush, Simon; Haddad, Danny; Foster, Allen

2015-01-01

ABSTRACT Purpose: To complete the baseline trachoma map worldwide by conducting population-based surveys in an estimated 1238 suspected endemic districts of 34 countries. Methods: A series of national and sub-national projects owned, managed and staffed by ministries of health, conduct house-to-house cluster random sample surveys in evaluation units, which generally correspond to “health district” size: populations of 100,000–250,000 people. In each evaluation unit, we invite all residents aged 1 year and older from h households in each of c clusters to be examined for clinical signs of trachoma, where h is the number of households that can be seen by 1 team in 1 day, and the product h × c is calculated to facilitate recruitment of 1019 children aged 1–9 years. In addition to individual-level demographic and clinical data, household-level water, sanitation and hygiene data are entered into the purpose-built LINKS application on Android smartphones, transmitted to the Cloud, and cleaned, analyzed and ministry-of-health-approved via a secure web-based portal. The main outcome measures are the evaluation unit-level prevalence of follicular trachoma in children aged 1–9 years, prevalence of trachomatous trichiasis in adults aged 15 + years, percentage of households using safe methods for disposal of human feces, and percentage of households with proximate access to water for personal hygiene purposes. Results: In the first year of fieldwork, 347 field teams commenced work in 21 projects in 7 countries. Conclusion: With an approach that is innovative in design and scale, we aim to complete baseline mapping of trachoma throughout the world in 2015. PMID:26158580

Using GIS Mapping to Target Public Health Interventions: Examining Birth Outcomes Across GIS Techniques.

PubMed

MacQuillan, E L; Curtis, A B; Baker, K M; Paul, R; Back, Y O

2017-08-01

With advances in spatial analysis techniques, there has been a trend in recent public health research to assess the contribution of area-level factors to health disparity for a number of outcomes, including births. Although it is widely accepted that health disparity is best addressed by targeted, evidence-based and data-driven community efforts, and despite national and local focus in the U.S. to reduce infant mortality and improve maternal-child health, there is little work exploring how choice of scale and specific GIS visualization technique may alter the perception of analyses focused on health disparity in birth outcomes. Retrospective cohort study. Spatial analysis of individual-level vital records data for low birthweight and preterm births born to black women from 2007 to 2012 in one mid-sized Midwest city using different geographic information systems (GIS) visualization techniques [geocoded address records were aggregated at two levels of scale and additionally mapped using kernel density estimation (KDE)]. GIS analyses in this study support our hypothesis that choice of geographic scale (neighborhood or census tract) for aggregated birth data can alter programmatic decision-making. Results indicate that the relative merits of aggregated visualization or the use of KDE technique depend on the scale of intervention. The KDE map proved useful in targeting specific areas for interventions in cities with smaller populations and larger census tracts, where they allow for greater specificity in identifying intervention areas. When public health programmers seek to inform intervention placement in highly populated areas, however, aggregated data at the census tract level may be preferred, since it requires lower investments in terms of time and cartographic skill and, unlike neighborhood, census tracts are standardized in that they become smaller as the population density of an area increases.

Statistical power calculations for mixed pharmacokinetic study designs using a population approach.

PubMed

Kloprogge, Frank; Simpson, Julie A; Day, Nicholas P J; White, Nicholas J; Tarning, Joel

2014-09-01

Simultaneous modelling of dense and sparse pharmacokinetic data is possible with a population approach. To determine the number of individuals required to detect the effect of a covariate, simulation-based power calculation methodologies can be employed. The Monte Carlo Mapped Power method (a simulation-based power calculation methodology using the likelihood ratio test) was extended in the current study to perform sample size calculations for mixed pharmacokinetic studies (i.e. both sparse and dense data collection). A workflow guiding an easy and straightforward pharmacokinetic study design, considering also the cost-effectiveness of alternative study designs, was used in this analysis. Initially, data were simulated for a hypothetical drug and then for the anti-malarial drug, dihydroartemisinin. Two datasets (sampling design A: dense; sampling design B: sparse) were simulated using a pharmacokinetic model that included a binary covariate effect and subsequently re-estimated using (1) the same model and (2) a model not including the covariate effect in NONMEM 7.2. Power calculations were performed for varying numbers of patients with sampling designs A and B. Study designs with statistical power >80% were selected and further evaluated for cost-effectiveness. The simulation studies of the hypothetical drug and the anti-malarial drug dihydroartemisinin demonstrated that the simulation-based power calculation methodology, based on the Monte Carlo Mapped Power method, can be utilised to evaluate and determine the sample size of mixed (part sparsely and part densely sampled) study designs. The developed method can contribute to the design of robust and efficient pharmacokinetic studies.

Increased genomic prediction accuracy in wheat breeding using a large Australian panel.

PubMed

Norman, Adam; Taylor, Julian; Tanaka, Emi; Telfer, Paul; Edwards, James; Martinant, Jean-Pierre; Kuchel, Haydn

2017-12-01

Genomic prediction accuracy within a large panel was found to be substantially higher than that previously observed in smaller populations, and also higher than QTL-based prediction. In recent years, genomic selection for wheat breeding has been widely studied, but this has typically been restricted to population sizes under 1000 individuals. To assess its efficacy in germplasm representative of commercial breeding programmes, we used a panel of 10,375 Australian wheat breeding lines to investigate the accuracy of genomic prediction for grain yield, physical grain quality and other physiological traits. To achieve this, the complete panel was phenotyped in a dedicated field trial and genotyped using a custom Axiom TM Affymetrix SNP array. A high-quality consensus map was also constructed, allowing the linkage disequilibrium present in the germplasm to be investigated. Using the complete SNP array, genomic prediction accuracies were found to be substantially higher than those previously observed in smaller populations and also more accurate compared to prediction approaches using a finite number of selected quantitative trait loci. Multi-trait genetic correlations were also assessed at an additive and residual genetic level, identifying a negative genetic correlation between grain yield and protein as well as a positive genetic correlation between grain size and test weight.

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep.

PubMed

Kominakis, A; Hager-Theodorides, A L; Saridaki, A; Antonakos, G; Tsiamis, G

2017-10-01

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals' genomic relationships. The Wright's fixation F ST index was also employed to assess herds' genetic homogeneity and to indirectly estimate past migration rates. The Wright's fixation F IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r 2 and |D'| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed's formation was as high as 549, was then reduced to 463 in 1981 (end of the breed's formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals' genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.

Effect of rosemary essential oil and modified-atmosphere packaging (MAP) on meat quality and survival of pathogens in poultry fillets

PubMed Central

Kahraman, Tolga; Issa, Ghassan; Bingol, Enver Baris; Kahraman, Beren Basaran; Dumen, Emek

2015-01-01

The effect of rosemary (Rosmarinus officinalis L.) essential oil (REO) and modified-atmosphere packaging (MAP) on the survival of certain pathogens (Salmonella Typhimurium and Listeria monocytogenes) in poultry fillets and on their meat quality during 7 days of refrigerated storage were investigated. Because REO at 0.05% and 0.1% had weak antibacterial activity and REO at 0.3%, 0.5% and 1.0% imparted unacceptable organoleptic properties, only REO at 0.2% was used to treat the poultry meat. The results showed that adding 0.2% REO to poultry fillets did not reduce the size of the population of S. Typhimurium and L. monocytogenes. However, REO treatment significantly decreased the L* (lightness) value and increased the a* (redness) value of stored fillets, and adding REO in combination with MAP reduced the level of lipid oxidation. In conclusion, in a suitable combination, REO can be applied to improve the quality of meat, but further studies should be conducted to determine the appropriate commercial level for different meat products. PMID:26273279

Mapping of Soil-Ecological Conditions of a Medium-Size Industrial City (Birobidzhan City, Jewish Autonomous Oblast, FarEast of Russia as an Example)

NASA Astrophysics Data System (ADS)

Kalmanova, V. B.; Matiushkina, L. A.

2018-01-01

The authors analyze soil relations with other elements of the city ecosystem (the position in the landscape, soil-forming rocks and lithology, vegetation and its state) to develop the legend and map of soils in the City of Birobidzhan (scale 1:25 000). The focus of study is the morphological structure of urban soils with different degree of disturbance of these relations under the impact of technical effects, economic and recreational activities of the city population. The soil cover structure is composed of four large ecological groups of soils: natural untransformed, natural with a disturbed surface, anthropogenic soils and technogenic surface formations. Using cartometry of the mapped soil contours the authors created the scheme of soil-ecological city zoning, which in a general way depicts the state of soil ecological functions in the city as well as identified zones of soils with preserved, partially and fully distured ecological functions and zones of local geochemical anomalies at the initial formation stage (environmental risk zones).

Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms

PubMed Central

Horikoshi, Momoko; Pasquali, Lorenzo; Wiltshire, Steven; Huyghe, Jeroen R.; Mahajan, Anubha; Asimit, Jennifer L.; Ferreira, Teresa; Locke, Adam E.; Robertson, Neil R.; Wang, Xu; Sim, Xueling; Fujita, Hayato; Hara, Kazuo; Young, Robin; Zhang, Weihua; Choi, Sungkyoung; Chen, Han; Kaur, Ismeet; Takeuchi, Fumihiko; Fontanillas, Pierre; Thuillier, Dorothée; Yengo, Loic; Below, Jennifer E.; Tam, Claudia H.T.; Wu, Ying; Abecasis, Gonçalo; Altshuler, David; Bell, Graeme I.; Blangero, John; Burtt, Noél P.; Duggirala, Ravindranath; Florez, Jose C.; Hanis, Craig L.; Seielstad, Mark; Atzmon, Gil; Chan, Juliana C.N.; Ma, Ronald C.W.; Froguel, Philippe; Wilson, James G.; Bharadwaj, Dwaipayan; Dupuis, Josee; Meigs, James B.; Cho, Yoon Shin; Park, Taesung; Kooner, Jaspal S.; Chambers, John C.; Saleheen, Danish; Kadowaki, Takashi; Tai, E. Shyong; Mohlke, Karen L.; Cox, Nancy J.; Ferrer, Jorge; Zeggini, Eleftheria; Kato, Norihiro; Teo, Yik Ying; Boehnke, Michael; McCarthy, Mark I.; Morris, Andrew P.

2016-01-01

To gain insight into potential regulatory mechanisms through which the effects of variants at four established type 2 diabetes (T2D) susceptibility loci (CDKAL1, CDKN2A-B, IGF2BP2 and KCNQ1) are mediated, we undertook transancestral fine-mapping in 22 086 cases and 42 539 controls of East Asian, European, South Asian, African American and Mexican American descent. Through high-density imputation and conditional analyses, we identified seven distinct association signals at these four loci, each with allelic effects on T2D susceptibility that were homogenous across ancestry groups. By leveraging differences in the structure of linkage disequilibrium between diverse populations, and increased sample size, we localised the variants most likely to drive each distinct association signal. We demonstrated that integration of these genetic fine-mapping data with genomic annotation can highlight potential causal regulatory elements in T2D-relevant tissues. These analyses provide insight into the mechanisms through which T2D association signals are mediated, and suggest future routes to understanding the biology of specific disease susceptibility loci. PMID:26911676

Identifying grain-size dependent errors on global forest area estimates and carbon studies

Treesearch

Daolan Zheng; Linda S. Heath; Mark J. Ducey

2008-01-01

Satellite-derived coarse-resolution data are typically used for conducting global analyses. But the forest areas estimated from coarse-resolution maps (e.g., 1 km) inevitably differ from a corresponding fine-resolution map (such as a 30-m map) that would be closer to ground truth. A better understanding of changes in grain size on area estimation will improve our...

Influence of lidar, Landsat imagery, disturbance history, plot location accuracy, and plot size on accuracy of imputation maps of forest composition and structure

Treesearch

Harold S.J. Zald; Janet L. Ohmann; Heather M. Roberts; Matthew J. Gregory; Emilie B. Henderson; Robert J. McGaughey; Justin Braaten

2014-01-01

This study investigated how lidar-derived vegetation indices, disturbance history from Landsat time series (LTS) imagery, plot location accuracy, and plot size influenced accuracy of statistical spatial models (nearest-neighbor imputation maps) of forest vegetation composition and structure. Nearest-neighbor (NN) imputation maps were developed for 539,000 ha in the...

De novo assembly and phasing of a Korean human genome.

PubMed

Seo, Jeong-Sun; Rhie, Arang; Kim, Junsoo; Lee, Sangjin; Sohn, Min-Hwan; Kim, Chang-Uk; Hastie, Alex; Cao, Han; Yun, Ji-Young; Kim, Jihye; Kuk, Junho; Park, Gun Hwa; Kim, Juhyeok; Ryu, Hanna; Kim, Jongbum; Roh, Mira; Baek, Jeonghun; Hunkapiller, Michael W; Korlach, Jonas; Shin, Jong-Yeon; Kim, Changhoon

2016-10-13

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

The identification of QTL controlling ergot sclerotia size in hexaploid wheat implicates a role for the Rht dwarfing alleles.

PubMed

Gordon, Anna; Basler, Ryan; Bansept-Basler, Pauline; Fanstone, Vicky; Harinarayan, Lakshmi; Grant, Paul K; Birchmore, Richard; Bayles, Rosemary A; Boyd, Lesley A; O'Sullivan, Donal M

2015-12-01

Four QTL conferring resistance to ergot were identified in the UK winter wheat varieties 'Robigus' and 'Solstice'. Two QTL co-located with semi-dwarfing alleles at the Rht loci Rht - 1B and Rht - 1D implicating a role of these DELLA proteins in infection success of Claviceps purpurea. The fungal pathogen Claviceps purpurea infects ovaries of a broad range of temperate grasses and cereals, including hexaploid wheat, causing a disease commonly known as ergot. Sclerotia produced in place of seed carry a cocktail of harmful alkaloid compounds that result in a range of symptoms in humans and animals, causing ergotism. Following a field assessment of C. purpurea infection in winter wheat, two varieties 'Robigus' and 'Solstice' were selected which consistently produced the largest differential effect on ergot sclerotia weights. They were crossed to produce a doubled haploid mapping population, and a marker map, consisting of 714 genetic loci and a total length of 2895 cM was produced. Four ergot reducing QTL were identified using both sclerotia weight and size as phenotypic parameters; QCp.niab.2A and QCp.niab.4B being detected in the wheat variety 'Robigus', and QCp.niab.6A and QCp.niab.4D in the variety 'Solstice'. The ergot resistance QTL QCp.niab.4B and QCp.niab.4D peaks mapped to the same markers as the known reduced height (Rht) loci on chromosomes 4B and 4D, Rht-B1 and Rht-D1, respectively. In both cases, the reduction in sclerotia weight and size was associated with the semi-dwarfing alleles, Rht-B1b from 'Robigus' and Rht-D1b from 'Solstice'. Two-dimensional, two-QTL scans identified significant additive interactions between QTL QCp.niab.4B and QCp.niab.4D, and between QCp.niab.2A and QCp.niab.4B when looking at sclerotia size, but not between QCp.niab.2A and QCp.niab.4D. The two plant height QTL, QPh.niab.4B and QPh.niab.4D, which mapped to the same locations as QCp.niab.4B and QCp.niab.4D, also displayed significant genetic interactions.

Automated grain mapping using wide angle convergent beam electron diffraction in transmission electron microscope for nanomaterials.

PubMed

Kumar, Vineet

2011-12-01

The grain size statistics, commonly derived from the grain map of a material sample, are important microstructure characteristics that greatly influence its properties. The grain map for nanomaterials is usually obtained manually by visual inspection of the transmission electron microscope (TEM) micrographs because automated methods do not perform satisfactorily. While the visual inspection method provides reliable results, it is a labor intensive process and is often prone to human errors. In this article, an automated grain mapping method is developed using TEM diffraction patterns. The presented method uses wide angle convergent beam diffraction in the TEM. The automated technique was applied on a platinum thin film sample to obtain the grain map and subsequently derive grain size statistics from it. The grain size statistics obtained with the automated method were found in good agreement with the visual inspection method.

3-dimensional examination of the adult mouse subventricular zone reveals lineage-specific microdomains.

PubMed

Azim, Kasum; Fiorelli, Roberto; Zweifel, Stefan; Hurtado-Chong, Anahi; Yoshikawa, Kazuaki; Slomianka, Lutz; Raineteau, Olivier

2012-01-01

Recent studies suggest that the subventricular zone (SVZ) of the lateral ventricle is populated by heterogeneous populations of stem and progenitor cells that, depending on their exact location, are biased to acquire specific neuronal fates. This newly described heterogeneity of SVZ stem and progenitor cells underlines the necessity to develop methods for the accurate quantification of SVZ stem and progenitor subpopulations. In this study, we provide 3-dimensional topographical maps of slow cycling "stem" cells and progenitors based on their unique cell cycle properties. These maps revealed that both cell populations are present throughout the lateral ventricle wall as well as in discrete regions of the dorsal wall. Immunodetection of transcription factors expressed in defined progenitor populations further reveals that divergent lineages have clear regional enrichments in the rostro-caudal as well as in the dorso-ventral span of the lateral ventricle. Thus, progenitors expressing Tbr2 and Dlx2 were confined to dorsal and dorso-lateral regions of the lateral ventricle, respectively, while Mash1+ progenitors were more homogeneously distributed. All cell populations were enriched in the rostral-most region of the lateral ventricle. This diversity and uneven distribution greatly impede the accurate quantification of SVZ progenitor populations. This is illustrated by measuring the coefficient of error of estimates obtained by using increasing section sampling interval. Based on our empirical data, we provide such estimates for all progenitor populations investigated in this study. These can be used in future studies as guidelines to judge if the precision obtained with a sampling scheme is sufficient to detect statistically significant differences between experimental groups if a biological effect is present. Altogether, our study underlines the need to consider the SVZ of the lateral ventricle as a complex 3D structure and define methods to accurately assess neural stem cells or progenitor diversity and population sizes in physiological or experimental paradigms.

In search of causal variants: refining disease association signals using cross-population contrasts.

PubMed

Saccone, Nancy L; Saccone, Scott F; Goate, Alison M; Grucza, Richard A; Hinrichs, Anthony L; Rice, John P; Bierut, Laura J

2008-08-29

Genome-wide association (GWA) using large numbers of single nucleotide polymorphisms (SNPs) is now a powerful, state-of-the-art approach to mapping human disease genes. When a GWA study detects association between a SNP and the disease, this signal usually represents association with a set of several highly correlated SNPs in strong linkage disequilibrium. The challenge we address is to distinguish among these correlated loci to highlight potential functional variants and prioritize them for follow-up. We implemented a systematic method for testing association across diverse population samples having differing histories and LD patterns, using a logistic regression framework. The hypothesis is that important underlying biological mechanisms are shared across human populations, and we can filter correlated variants by testing for heterogeneity of genetic effects in different population samples. This approach formalizes the descriptive comparison of p-values that has typified similar cross-population fine-mapping studies to date. We applied this method to correlated SNPs in the cholinergic nicotinic receptor gene cluster CHRNA5-CHRNA3-CHRNB4, in a case-control study of cocaine dependence composed of 504 European-American and 583 African-American samples. Of the 10 SNPs genotyped in the r2 > or = 0.8 bin for rs16969968, three demonstrated significant cross-population heterogeneity and are filtered from priority follow-up; the remaining SNPs include rs16969968 (heterogeneity p = 0.75). Though the power to filter out rs16969968 is reduced due to the difference in allele frequency in the two groups, the results nevertheless focus attention on a smaller group of SNPs that includes the non-synonymous SNP rs16969968, which retains a similar effect size (odds ratio) across both population samples. Filtering out SNPs that demonstrate cross-population heterogeneity enriches for variants more likely to be important and causative. Our approach provides an important and effective tool to help interpret results from the many GWA studies now underway.

Spatial Tuning Shifts Increase the Discriminability and Fidelity of Population Codes in Visual Cortex

PubMed Central

2017-01-01

Selective visual attention enables organisms to enhance the representation of behaviorally relevant stimuli by altering the encoding properties of single receptive fields (RFs). Yet we know little about how the attentional modulations of single RFs contribute to the encoding of an entire visual scene. Addressing this issue requires (1) measuring a group of RFs that tile a continuous portion of visual space, (2) constructing a population-level measurement of spatial representations based on these RFs, and (3) linking how different types of RF attentional modulations change the population-level representation. To accomplish these aims, we used fMRI to characterize the responses of thousands of voxels in retinotopically organized human cortex. First, we found that the response modulations of voxel RFs (vRFs) depend on the spatial relationship between the RF center and the visual location of the attended target. Second, we used two analyses to assess the spatial encoding quality of a population of voxels. We found that attention increased fine spatial discriminability and representational fidelity near the attended target. Third, we linked these findings by manipulating the observed vRF attentional modulations and recomputing our measures of the fidelity of population codes. Surprisingly, we discovered that attentional enhancements of population-level representations largely depend on position shifts of vRFs, rather than changes in size or gain. Our data suggest that position shifts of single RFs are a principal mechanism by which attention enhances population-level representations in visual cortex. SIGNIFICANCE STATEMENT Although changes in the gain and size of RFs have dominated our view of how attention modulates visual information codes, such hypotheses have largely relied on the extrapolation of single-cell responses to population responses. Here we use fMRI to relate changes in single voxel receptive fields (vRFs) to changes in population-level representations. We find that vRF position shifts contribute more to population-level enhancements of visual information than changes in vRF size or gain. This finding suggests that position shifts are a principal mechanism by which spatial attention enhances population codes for relevant visual information. This poses challenges for labeled line theories of information processing, suggesting that downstream regions likely rely on distributed inputs rather than single neuron-to-neuron mappings. PMID:28242794

The scaling of human interactions with city size

PubMed Central

Schläpfer, Markus; Bettencourt, Luís M. A.; Grauwin, Sébastian; Raschke, Mathias; Claxton, Rob; Smoreda, Zbigniew; West, Geoffrey B.; Ratti, Carlo

2014-01-01

The size of cities is known to play a fundamental role in social and economic life. Yet, its relation to the structure of the underlying network of human interactions has not been investigated empirically in detail. In this paper, we map society-wide communication networks to the urban areas of two European countries. We show that both the total number of contacts and the total communication activity grow superlinearly with city population size, according to well-defined scaling relations and resulting from a multiplicative increase that affects most citizens. Perhaps surprisingly, however, the probability that an individual's contacts are also connected with each other remains largely unaffected. These empirical results predict a systematic and scale-invariant acceleration of interaction-based spreading phenomena as cities get bigger, which is numerically confirmed by applying epidemiological models to the studied networks. Our findings should provide a microscopic basis towards understanding the superlinear increase of different socioeconomic quantities with city size, that applies to almost all urban systems and includes, for instance, the creation of new inventions or the prevalence of certain contagious diseases. PMID:24990287

How integrated are neurology and palliative care services? Results of a multicentre mapping exercise.

PubMed

van Vliet, Liesbeth M; Gao, Wei; DiFrancesco, Daniel; Crosby, Vincent; Wilcock, Andrew; Byrne, Anthony; Al-Chalabi, Ammar; Chaudhuri, K Ray; Evans, Catherine; Silber, Eli; Young, Carolyn; Malik, Farida; Quibell, Rachel; Higginson, Irene J

2016-05-10

Patients affected by progressive long-term neurological conditions might benefit from specialist palliative care involvement. However, little is known on how neurology and specialist palliative care services interact. This study aimed to map the current level of connections and integration between these services. The mapping exercise was conducted in eight centres with neurology and palliative care services in the United Kingdom. The data were provided by the respective neurology and specialist palliative care teams. Questions focused on: i) catchment and population served; ii) service provision and staffing; iii) integration and relationships. Centres varied in size of catchment areas (39-5,840 square miles) and population served (142,000-3,500,000). Neurology and specialist palliative care were often not co-terminus. Service provisions for neurology and specialist palliative care were also varied. For example, neurology services varied in the number and type of provided clinics and palliative care services in the settings they work in. Integration was most developed in Motor Neuron Disease (MND), e.g., joint meetings were often held, followed by Parkinsonism (made up of Parkinson's Disease (PD), Multiple-System Atrophy (MSA) and Progressive Supranuclear Palsy (PSP), with integration being more developed for MSA and PSP) and least in Multiple Sclerosis (MS), e.g., most sites had no formal links. The number of neurology patients per annum receiving specialist palliative care reflected these differences in integration (range: 9-88 MND, 3-25 Parkinsonism, and 0-5 MS). This mapping exercise showed heterogeneity in service provision and integration between neurology and specialist palliative care services, which varied not only between sites but also between diseases. This highlights the need and opportunities for improved models of integration, which should be rigorously tested for effectiveness.

High-Resolution Maps of Mouse Reference Populations

PubMed Central

Simecek, Petr; Forejt, Jiri; Williams, Robert W.; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E.; Bennett, Beth; Deschepper, Christian F.; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A.

2017-01-01

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. PMID:28839117

High-Resolution Maps of Mouse Reference Populations.

PubMed

Simecek, Petr; Forejt, Jiri; Williams, Robert W; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E; Bennett, Beth; Deschepper, Christian F; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A

2017-10-05

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. Copyright © 2017 Simecek et al.

Recapitulation of genome-wide association studies on pulse pressure and mean arterial pressure in the Korean population.

PubMed

Hong, Kyung-Won; Min, Haesook; Heo, Byeong-Mun; Joo, Seong Eun; Kim, Sung Soo; Kim, Yeonjung

2012-06-01

Increased pulse pressure (PP) and decreased mean arterial pressure (MAP) are strong prognostic predictors of adverse cardiovascular events. Recently, the International Consortium for Blood Pressure Genome-Wide Association Studies (ICBP-GWAS) reported eight loci that influenced PP and MAP. The ICBP-GWAS examined 51 cohorts--comprising 122 671 individuals of European ancestry--and identified eight SNPs: five that governed PP and three that controlled MAP. Six of these loci were novel. To replicate these newly identified loci and examine genetic architecture of PP and MAP between European and Asian populations, we conducted a meta-analysis of the eight SNPs combining data from ICBP and general population-based Korean cohorts. Two SNPs (rs13002573 (FIGN) and rs871606 (CHIC2)) for PP and two SNPs (rs1446468 (FIGN) and rs319690 (MAP4)) for MAP were replicated in Koreans. Although our GWAS only found moderate association, we believe that the findings promote us to propose that a similar genetic architecture governs PP and MAP in Asians and Europeans. However, further studies will be needed to confirm the possibility using other Asian population.

Dynamic population mapping using mobile phone data.

PubMed

Deville, Pierre; Linard, Catherine; Martin, Samuel; Gilbert, Marius; Stevens, Forrest R; Gaughan, Andrea E; Blondel, Vincent D; Tatem, Andrew J

2014-11-11

During the past few decades, technologies such as remote sensing, geographical information systems, and global positioning systems have transformed the way the distribution of human population is studied and modeled in space and time. However, the mapping of populations remains constrained by the logistics of censuses and surveys. Consequently, spatially detailed changes across scales of days, weeks, or months, or even year to year, are difficult to assess and limit the application of human population maps in situations in which timely information is required, such as disasters, conflicts, or epidemics. Mobile phones (MPs) now have an extremely high penetration rate across the globe, and analyzing the spatiotemporal distribution of MP calls geolocated to the tower level may overcome many limitations of census-based approaches, provided that the use of MP data is properly assessed and calibrated. Using datasets of more than 1 billion MP call records from Portugal and France, we show how spatially and temporarily explicit estimations of population densities can be produced at national scales, and how these estimates compare with outputs produced using alternative human population mapping methods. We also demonstrate how maps of human population changes can be produced over multiple timescales while preserving the anonymity of MP users. With similar data being collected every day by MP network providers across the world, the prospect of being able to map contemporary and changing human population distributions over relatively short intervals exists, paving the way for new applications and a near real-time understanding of patterns and processes in human geography.

Dynamic population mapping using mobile phone data

PubMed Central

Deville, Pierre; Martin, Samuel; Gilbert, Marius; Stevens, Forrest R.; Gaughan, Andrea E.; Blondel, Vincent D.; Tatem, Andrew J.

2014-01-01

During the past few decades, technologies such as remote sensing, geographical information systems, and global positioning systems have transformed the way the distribution of human population is studied and modeled in space and time. However, the mapping of populations remains constrained by the logistics of censuses and surveys. Consequently, spatially detailed changes across scales of days, weeks, or months, or even year to year, are difficult to assess and limit the application of human population maps in situations in which timely information is required, such as disasters, conflicts, or epidemics. Mobile phones (MPs) now have an extremely high penetration rate across the globe, and analyzing the spatiotemporal distribution of MP calls geolocated to the tower level may overcome many limitations of census-based approaches, provided that the use of MP data is properly assessed and calibrated. Using datasets of more than 1 billion MP call records from Portugal and France, we show how spatially and temporarily explicit estimations of population densities can be produced at national scales, and how these estimates compare with outputs produced using alternative human population mapping methods. We also demonstrate how maps of human population changes can be produced over multiple timescales while preserving the anonymity of MP users. With similar data being collected every day by MP network providers across the world, the prospect of being able to map contemporary and changing human population distributions over relatively short intervals exists, paving the way for new applications and a near real-time understanding of patterns and processes in human geography. PMID:25349388

Mapping populations at risk: improving spatial demographic data for infectious disease modeling and metric derivation

PubMed Central

2012-01-01

The use of Global Positioning Systems (GPS) and Geographical Information Systems (GIS) in disease surveys and reporting is becoming increasingly routine, enabling a better understanding of spatial epidemiology and the improvement of surveillance and control strategies. In turn, the greater availability of spatially referenced epidemiological data is driving the rapid expansion of disease mapping and spatial modeling methods, which are becoming increasingly detailed and sophisticated, with rigorous handling of uncertainties. This expansion has, however, not been matched by advancements in the development of spatial datasets of human population distribution that accompany disease maps or spatial models. Where risks are heterogeneous across population groups or space or dependent on transmission between individuals, spatial data on human population distributions and demographic structures are required to estimate infectious disease risks, burdens, and dynamics. The disease impact in terms of morbidity, mortality, and speed of spread varies substantially with demographic profiles, so that identifying the most exposed or affected populations becomes a key aspect of planning and targeting interventions. Subnational breakdowns of population counts by age and sex are routinely collected during national censuses and maintained in finer detail within microcensus data. Moreover, demographic and health surveys continue to collect representative and contemporary samples from clusters of communities in low-income countries where census data may be less detailed and not collected regularly. Together, these freely available datasets form a rich resource for quantifying and understanding the spatial variations in the sizes and distributions of those most at risk of disease in low income regions, yet at present, they remain unconnected data scattered across national statistical offices and websites. In this paper we discuss the deficiencies of existing spatial population datasets and their limitations on epidemiological analyses. We review sources of detailed, contemporary, freely available and relevant spatial demographic data focusing on low income regions where such data are often sparse and highlight the value of incorporating these through a set of examples of their application in disease studies. Moreover, the importance of acknowledging, measuring, and accounting for uncertainty in spatial demographic datasets is outlined. Finally, a strategy for building an open-access database of spatial demographic data that is tailored to epidemiological applications is put forward. PMID:22591595

Quantification of both the area-at-risk and acute myocardial infarct size in ST-segment elevation myocardial infarction using T1-mapping.

PubMed

Bulluck, Heerajnarain; Hammond-Haley, Matthew; Fontana, Marianna; Knight, Daniel S; Sirker, Alex; Herrey, Anna S; Manisty, Charlotte; Kellman, Peter; Moon, James C; Hausenloy, Derek J

2017-08-01

A comprehensive cardiovascular magnetic resonance (CMR) in reperfused ST-segment myocardial infarction (STEMI) patients can be challenging to perform and can be time-consuming. We aimed to investigate whether native T1-mapping can accurately delineate the edema-based area-at-risk (AAR) and post-contrast T1-mapping and synthetic late gadolinium (LGE) images can quantify MI size at 1.5 T. Conventional LGE imaging and T2-mapping could then be omitted, thereby shortening the scan duration. Twenty-eight STEMI patients underwent a CMR scan at 1.5 T, 3 ± 1 days following primary percutaneous coronary intervention. The AAR was quantified using both native T1 and T2-mapping. MI size was quantified using conventional LGE, post-contrast T1-mapping and synthetic magnitude-reconstructed inversion recovery (MagIR) LGE and synthetic phase-sensitive inversion recovery (PSIR) LGE, derived from the post-contrast T1 maps. Native T1-mapping performed as well as T2-mapping in delineating the AAR (41.6 ± 11.9% of the left ventricle [% LV] versus 41.7 ± 12.2% LV, P = 0.72; R 2 0.97; ICC 0.986 (0.969-0.993); bias -0.1 ± 4.2% LV). There were excellent correlation and inter-method agreement with no bias, between MI size by conventional LGE, synthetic MagIR LGE (bias 0.2 ± 2.2%LV, P = 0.35), synthetic PSIR LGE (bias 0.4 ± 2.2% LV, P = 0.060) and post-contrast T1-mapping (bias 0.3 ± 1.8% LV, P = 0.10). The mean scan duration was 58 ± 4 min. Not performing T2 mapping (6 ± 1 min) and conventional LGE (10 ± 1 min) would shorten the CMR study by 15-20 min. T1-mapping can accurately quantify both the edema-based AAR (using native T1 maps) and acute MI size (using post-contrast T1 maps) in STEMI patients without major cardiovascular risk factors. This approach would shorten the duration of a comprehensive CMR study without significantly compromising on data acquisition and would obviate the need to perform T2 maps and LGE imaging.

Integrating population dynamics into mapping human exposure to seismic hazard

NASA Astrophysics Data System (ADS)

Freire, S.; Aubrecht, C.

2012-11-01

Disaster risk is not fully characterized without taking into account vulnerability and population exposure. Assessment of earthquake risk in urban areas would benefit from considering the variation of population distribution at more detailed spatial and temporal scales, and from a more explicit integration of this improved demographic data with existing seismic hazard maps. In the present work, "intelligent" dasymetric mapping is used to model population dynamics at high spatial resolution in order to benefit the analysis of spatio-temporal exposure to earthquake hazard in a metropolitan area. These night- and daytime-specific population densities are then classified and combined with seismic intensity levels to derive new spatially-explicit four-class-composite maps of human exposure. The presented approach enables a more thorough assessment of population exposure to earthquake hazard. Results show that there are significantly more people potentially at risk in the daytime period, demonstrating the shifting nature of population exposure in the daily cycle and the need to move beyond conventional residence-based demographic data sources to improve risk analyses. The proposed fine-scale maps of human exposure to seismic intensity are mainly aimed at benefiting visualization and communication of earthquake risk, but can be valuable in all phases of the disaster management process where knowledge of population densities is relevant for decision-making.

Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps

PubMed Central

Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J.; Hunt, Sarah; Deloukas, Panos; Bentley, David R.; Morton, Newton E.

2004-01-01

Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences. PMID:15604137

Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.

PubMed

Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R; Morton, Newton E

2004-12-28

Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.

Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility.

PubMed

Nashef, A; Qabaja, R; Salaymeh, Y; Botzman, M; Munz, M; Dommisch, H; Krone, B; Hoffmann, P; Wellmann, J; Laudes, M; Berger, K; Kocher, T; Loos, B; van der Velde, N; Uitterlinden, A G; de Groot, L C P G M; Franke, A; Offenbacher, S; Lieb, W; Divaris, K; Mott, R; Gat-Viks, I; Wiess, E; Schaefer, A; Iraqi, F A; Haddad, Y H

2018-05-01

Periodontitis is one of the most common inflammatory human diseases with a strong genetic component. Due to the limited sample size of available periodontitis cohorts and the underlying trait heterogeneity, genome-wide association studies (GWASs) of chronic periodontitis (CP) have largely been unsuccessful in identifying common susceptibility factors. A combination of quantitative trait loci (QTL) mapping in mice with association studies in humans has the potential to discover novel risk loci. To this end, we assessed alveolar bone loss in response to experimental periodontal infection in 25 lines (286 mice) from the Collaborative Cross (CC) mouse population using micro-computed tomography (µCT) analysis. The orthologous human chromosomal regions of the significant QTL were analyzed for association using imputed genotype data (OmniExpress BeadChip arrays) derived from case-control samples of aggressive periodontitis (AgP; 896 cases, 7,104 controls) and chronic periodontitis (CP; 2,746 cases, 1,864 controls) of northwest European and European American descent, respectively. In the mouse genome, QTL mapping revealed 2 significant loci (-log P = 5.3; false discovery rate = 0.06) on chromosomes 1 ( Perio3) and 14 ( Perio4). The mapping resolution ranged from ~1.5 to 3 Mb. Perio3 overlaps with a previously reported QTL associated with residual bone volume in F2 cross and includes the murine gene Ccdc121. Its human orthologue showed previously a nominal significant association with CP in humans. Use of variation data from the genomes of the CC founder strains further refined the QTL and suggested 7 candidate genes ( CAPN8, DUSP23, PCDH17, SNORA17, PCDH9, LECT1, and LECT2). We found no evidence of association of these candidates with the human orthologues. In conclusion, the CC populations enabled mapping of confined QTL that confer susceptibility to alveolar bone loss in mice and larger human phenotype-genotype samples and additional expression data from gingival tissues are likely required to identify true positive signals.

Wild boar mapping using population-density statistics: From polygons to high resolution raster maps.

PubMed

Pittiglio, Claudia; Khomenko, Sergei; Beltran-Alcrudo, Daniel

2018-01-01

The wild boar is an important crop raider as well as a reservoir and agent of spread of swine diseases. Due to increasing densities and expanding ranges worldwide, the related economic losses in livestock and agricultural sectors are significant and on the rise. Its management and control would strongly benefit from accurate and detailed spatial information on species distribution and abundance, which are often available only for small areas. Data are commonly available at aggregated administrative units with little or no information about the distribution of the species within the unit. In this paper, a four-step geostatistical downscaling approach is presented and used to disaggregate wild boar population density statistics from administrative units of different shape and size (polygons) to 5 km resolution raster maps by incorporating auxiliary fine scale environmental variables. 1) First a stratification method was used to define homogeneous bioclimatic regions for the analysis; 2) Under a geostatistical framework, the wild boar densities at administrative units, i.e. subnational areas, were decomposed into trend and residual components for each bioclimatic region. Quantitative relationships between wild boar data and environmental variables were estimated through multiple regression and used to derive trend components at 5 km spatial resolution. Next, the residual components (i.e., the differences between the trend components and the original wild boar data at administrative units) were downscaled at 5 km resolution using area-to-point kriging. The trend and residual components obtained at 5 km resolution were finally added to generate fine scale wild boar estimates for each bioclimatic region. 3) These maps were then mosaicked to produce a final output map of predicted wild boar densities across most of Eurasia. 4) Model accuracy was assessed at each different step using input as well as independent data. We discuss advantages and limits of the method and its potential application in animal health.

Wild boar mapping using population-density statistics: From polygons to high resolution raster maps

PubMed Central

Pittiglio, Claudia; Khomenko, Sergei

2018-01-01

The wild boar is an important crop raider as well as a reservoir and agent of spread of swine diseases. Due to increasing densities and expanding ranges worldwide, the related economic losses in livestock and agricultural sectors are significant and on the rise. Its management and control would strongly benefit from accurate and detailed spatial information on species distribution and abundance, which are often available only for small areas. Data are commonly available at aggregated administrative units with little or no information about the distribution of the species within the unit. In this paper, a four-step geostatistical downscaling approach is presented and used to disaggregate wild boar population density statistics from administrative units of different shape and size (polygons) to 5 km resolution raster maps by incorporating auxiliary fine scale environmental variables. 1) First a stratification method was used to define homogeneous bioclimatic regions for the analysis; 2) Under a geostatistical framework, the wild boar densities at administrative units, i.e. subnational areas, were decomposed into trend and residual components for each bioclimatic region. Quantitative relationships between wild boar data and environmental variables were estimated through multiple regression and used to derive trend components at 5 km spatial resolution. Next, the residual components (i.e., the differences between the trend components and the original wild boar data at administrative units) were downscaled at 5 km resolution using area-to-point kriging. The trend and residual components obtained at 5 km resolution were finally added to generate fine scale wild boar estimates for each bioclimatic region. 3) These maps were then mosaicked to produce a final output map of predicted wild boar densities across most of Eurasia. 4) Model accuracy was assessed at each different step using input as well as independent data. We discuss advantages and limits of the method and its potential application in animal health. PMID:29768413

POSTERIOR PREDICTIVE MODEL CHECKS FOR DISEASE MAPPING MODELS. (R827257)

EPA Science Inventory

Disease incidence or disease mortality rates for small areas are often displayed on maps. Maps of raw rates, disease counts divided by the total population at risk, have been criticized as unreliable due to non-constant variance associated with heterogeneity in base population si...

Comparative hi-density intraspecific linkage mapping using three elite populations from common parents

USDA-ARS?s Scientific Manuscript database

High-density linkage maps are fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, e.g., Upland cotton (Gossypium hirsutum L., 2n=52). Using 3 full-sib intra-specific mapping populations fr...

Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity

PubMed Central

Athanasiadis, Georgios; Cheng, Jade Y.; Vilhjálmsson, Bjarni J.; Jørgensen, Frank G.; Als, Thomas D.; Le Hellard, Stephanie; Espeseth, Thomas; Sullivan, Patrick F.; Hultman, Christina M.; Kjærgaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas

2016-01-01

Denmark has played a substantial role in the history of Northern Europe. Through a nationwide scientific outreach initiative, we collected genetic and anthropometrical data from ∼800 high school students and used them to elucidate the genetic makeup of the Danish population, as well as to assess polygenic predictions of phenotypic traits in adolescents. We observed remarkable homogeneity across different geographic regions, although we could still detect weak signals of genetic structure reflecting the history of the country. Denmark presented genomic affinity with primarily neighboring countries with overall resemblance of decreasing weight from Britain, Sweden, Norway, Germany, and France. A Polish admixture signal was detected in Zealand and Funen, and our date estimates coincided with historical evidence of Wend settlements in the south of Denmark. We also observed considerably diverse demographic histories among Scandinavian countries, with Denmark having the smallest current effective population size compared to Norway and Sweden. Finally, we found that polygenic prediction of self-reported adolescent height in the population was remarkably accurate (R2 = 0.639 ± 0.015). The high homogeneity of the Danish population could render population structure a lesser concern for the upcoming large-scale gene-mapping studies in the country. PMID:27535931

Borehole sampling of fracture populations - compensating for borehole sampling bias in crystalline bedrock aquifers, Mirror Lake, Grafton County, New Hampshire

USGS Publications Warehouse

McDonald, G.D.; Paillet, Frederick L.; Barton, C.C.; Johnson, C.D.

1997-01-01

The clustering of orientations of hydraulically conductive fractures in bedrock at the Mirror Lake, New Hampshire fractured rock study site was investigated by comparing the orientations of fracture populations in two subvertical borehole arrays with those mapped on four adjacent subvertical roadcuts. In the boreholes and the roadcuts, the orientation of fracture populations appears very similar after borehole data are compensated for undersampling of steeply dipping fractures. Compensated borehole and pavement fracture data indicate a northeast-striking population of fractures with varying dips concentrated near that of the local foliation in the adjacent rock. The data show no correlation between fracture density (fractures/linear meter) and distance from lithologic contacts in both the boreholes and the roadcuts. The population of water-producing borehole fractures is too small (28 out of 610 fractures) to yield meaningful orientation comparisons. However, the orientation of large aperture fractures (which contains all the producing fractures) contains two or three subsidiary clusters in orientation frequency that are not evident in stereographic projections of the entire population containing all aperture sizes. Further, these subsidiary orientation clusters do not coincide with the dominant (subhorizontal and subvertical) regional fracture orientations.

Geologic map of the Sunnymead 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Matti, Jonathan C.

2001-01-01

a. This Readme; includes in Appendix I, data contained in sun_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

PubMed Central

De La Vega, Francisco M.; Isaac, Hadar; Collins, Andrew; Scafe, Charles R.; Halldórsson, Bjarni V.; Su, Xiaoping; Lippert, Ross A.; Wang, Yu; Laig-Webster, Marion; Koehler, Ryan T.; Ziegle, Janet S.; Wogan, Lewis T.; Stevens, Junko F.; Leinen, Kyle M.; Olson, Sheri J.; Guegler, Karl J.; You, Xiaoqing; Xu, Lily H.; Hemken, Heinz G.; Kalush, Francis; Itakura, Mitsuo; Zheng, Yi; de Thé, Guy; O'Brien, Stephen J.; Clark, Andrew G.; Istrail, Sorin; Hunkapiller, Michael W.; Spier, Eugene G.; Gilbert, Dennis A.

2005-01-01

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies. PMID:15781572

Utilizing individual fish biomass and relative abundance models to map environmental niche associations of adult and juvenile targeted fishes.

PubMed

Galaiduk, Ronen; Radford, Ben T; Harvey, Euan S

2018-06-21

Many fishes undergo ontogenetic habitat shifts to meet their energy and resource needs as they grow. Habitat resource partitioning and patterns of habitat connectivity between conspecific fishes at different life-history stages is a significant knowledge gap. Species distribution models were used to examine patterns in the relative abundance, individual biomass estimates and environmental niche associations of different life stages of three iconic West Australian fishes. Continuous predictive maps describing the spatial distribution of abundance and individual biomass of the study species were created as well predictive hotspot maps that identify possible areas for aggregation of individuals of similar life stages of multiple species (i.e. spawning grounds, fisheries refugia or nursery areas). The models and maps indicate that processes driving the abundance patterns could be different from the body size associated demographic processes throughout an individual's life cycle. Incorporating life-history in the spatially explicit management plans can ensure that critical habitat of the vulnerable stages (e.g. juvenile fish, spawning stock) is included within proposed protected areas and can enhance connectivity between various functional areas (e.g. nursery areas and adult populations) which, in turn, can improve the abundance of targeted species as well as other fish species relying on healthy ecosystem functioning.

A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda

PubMed Central

Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Muñoz, Patricio; Martínez-García, Pedro J.; Neale, David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Echt, Craig S.

2015-01-01

A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii. PMID:26068575

Efficient transformation of an auditory population code in a small sensory system.

PubMed

Clemens, Jan; Kutzki, Olaf; Ronacher, Bernhard; Schreiber, Susanne; Wohlgemuth, Sandra

2011-08-16

Optimal coding principles are implemented in many large sensory systems. They include the systematic transformation of external stimuli into a sparse and decorrelated neuronal representation, enabling a flexible readout of stimulus properties. Are these principles also applicable to size-constrained systems, which have to rely on a limited number of neurons and may only have to fulfill specific and restricted tasks? We studied this question in an insect system--the early auditory pathway of grasshoppers. Grasshoppers use genetically fixed songs to recognize mates. The first steps of neural processing of songs take place in a small three-layer feed-forward network comprising only a few dozen neurons. We analyzed the transformation of the neural code within this network. Indeed, grasshoppers create a decorrelated and sparse representation, in accordance with optimal coding theory. Whereas the neuronal input layer is best read out as a summed population, a labeled-line population code for temporal features of the song is established after only two processing steps. At this stage, information about song identity is maximal for a population decoder that preserves neuronal identity. We conclude that optimal coding principles do apply to the early auditory system of the grasshopper, despite its size constraints. The inputs, however, are not encoded in a systematic, map-like fashion as in many larger sensory systems. Already at its periphery, part of the grasshopper auditory system seems to focus on behaviorally relevant features, and is in this property more reminiscent of higher sensory areas in vertebrates.

Highly polygenic variation in environmental perception determines dauer larvae formation in growing populations of Caenorhabditis elegans.

PubMed

Green, James W M; Stastna, Jana J; Orbidans, Helen E; Harvey, Simon C

2014-01-01

Determining how complex traits are genetically controlled is a requirement if we are to predict how they evolve and how they might respond to selection. This requires understanding how distinct, and often more simple, life history traits interact and change in response to environmental conditions. In order to begin addressing such issues, we have been analyzing the formation of the developmentally arrested dauer larvae of Caenorhabditis elegans under different conditions. We find that 18 of 22 previously identified quantitative trait loci (QTLs) affecting dauer larvae formation in growing populations, assayed by determining the number of dauer larvae present at food patch exhaustion, can be recovered under various environmental conditions. We also show that food patch size affects both the ability to detect QTLs and estimates of effect size, and demonstrate that an allele of nath-10 affects dauer larvae formation in growing populations. To investigate the component traits that affect dauer larvae formation in growing populations we map, using the same introgression lines, QTLs that affect dauer larvae formation in response to defined amounts of pheromone. This identifies 36 QTLs, again demonstrating the highly polygenic nature of the genetic variation underlying dauer larvae formation. These data indicate that QTLs affecting the number of dauer larvae at food exhaustion in growing populations of C. elegans are highly reproducible, and that nearly all can be explained by variation affecting dauer larvae formation in response to defined amounts of pheromone. This suggests that most variation in dauer larvae formation in growing populations is a consequence of variation in the perception of the food and pheromone environment (i.e. chemosensory variation) and in the integration of these cues.

Selecting the optimum plot size for a California design-based stream and wetland mapping program.

PubMed

Lackey, Leila G; Stein, Eric D

2014-04-01

Accurate estimates of the extent and distribution of wetlands and streams are the foundation of wetland monitoring, management, restoration, and regulatory programs. Traditionally, these estimates have relied on comprehensive mapping. However, this approach is prohibitively resource-intensive over large areas, making it both impractical and statistically unreliable. Probabilistic (design-based) approaches to evaluating status and trends provide a more cost-effective alternative because, compared with comprehensive mapping, overall extent is inferred from mapping a statistically representative, randomly selected subset of the target area. In this type of design, the size of sample plots has a significant impact on program costs and on statistical precision and accuracy; however, no consensus exists on the appropriate plot size for remote monitoring of stream and wetland extent. This study utilized simulated sampling to assess the performance of four plot sizes (1, 4, 9, and 16 km(2)) for three geographic regions of California. Simulation results showed smaller plot sizes (1 and 4 km(2)) were most efficient for achieving desired levels of statistical accuracy and precision. However, larger plot sizes were more likely to contain rare and spatially limited wetland subtypes. Balancing these considerations led to selection of 4 km(2) for the California status and trends program.

Predictive Modeling and Mapping of Fish Distributions in Small Streams of the Canadian Rocky Mountain Foothills

NASA Astrophysics Data System (ADS)

McCleary, R. J.; Hassan, M. A.

2006-12-01

An automated procedure was developed to model spatial fish distributions within small streams in the Foothills of Alberta. Native fish populations and their habitats are susceptible to impacts arising from both industrial forestry and rapid development of petroleum resources in the region. Knowledge of fish distributions and the effects of industrial activities on their habitats is required to help conserve native fish populations. Resource selection function (RSF) models were used to explain presence/absence of fish in small streams. Target species were bull trout, rainbow trout and non-native brook trout. Using GIS, the drainage network was divided into reaches with uniform slope and drainage area and then polygons for each reach were created. Predictor variables described stream size, stream energy, climate and land-use. We identified a set of candidate models and selected the best model using a standard Akaike Information Criteria approach. The best models were validated with two external data sets. Drainage area and basin slope parameters were included in all best models. This finding emphasizes the importance of controlling for the energy dimension at the basin scale in investigations into the effects of land-use on aquatic resources in this transitional landscape between the mountains and plains. The best model for bull trout indicated a relation between the presence of artificial migration barriers in downstream areas and the extirpation of the species from headwater reaches. We produced reach-scale maps by species and summarized this information within all small catchments across the 12,000 km2 study area. These maps had included three categories based on predicted probability of capture for individual reaches. The high probability category had a 78 percent accuracy for correctly predicting both fish present and fish not-present reaches. Basin scale maps highlight specific watersheds likely to support both native bull trout and invasive brook trout, while reach-scale maps indicate specific reaches where interactions between these two species are likely to occur. With regional calibration, this automated modeling and mapping procedure could apply in headwater catchments throughout the Rocky Mountain Foothills and other areas where sporadic waterfalls or other natural migration barriers are not an important feature limiting fish distribution.

Estimating landscape carrying capacity through maximum clique analysis

USGS Publications Warehouse

Donovan, Therese; Warrington, Greg; Schwenk, W. Scott; Dinitz, Jeffrey H.

2012-01-01

Habitat suitability (HS) maps are widely used tools in wildlife science and establish a link between wildlife populations and landscape pattern. Although HS maps spatially depict the distribution of optimal resources for a species, they do not reveal the population size a landscape is capable of supporting--information that is often crucial for decision makers and managers. We used a new approach, "maximum clique analysis," to demonstrate how HS maps for territorial species can be used to estimate the carrying capacity, N(k), of a given landscape. We estimated the N(k) of Ovenbirds (Seiurus aurocapillus) and bobcats (Lynx rufus) in an 1153-km2 study area in Vermont, USA. These two species were selected to highlight different approaches in building an HS map as well as computational challenges that can arise in a maximum clique analysis. We derived 30-m2 HS maps for each species via occupancy modeling (Ovenbird) and by resource utilization modeling (bobcats). For each species, we then identified all pixel locations on the map (points) that had sufficient resources in the surrounding area to maintain a home range (termed a "pseudo-home range"). These locations were converted to a mathematical graph, where any two points were linked if two pseudo-home ranges could exist on the landscape without violating territory boundaries. We used the program Cliquer to find the maximum clique of each graph. The resulting estimates of N(k) = 236 Ovenbirds and N(k) = 42 female bobcats were sensitive to different assumptions and model inputs. Estimates of N(k) via alternative, ad hoc methods were 1.4 to > 30 times greater than the maximum clique estimate, suggesting that the alternative results may be upwardly biased. The maximum clique analysis was computationally intensive but could handle problems with < 1500 total pseudo-home ranges (points). Given present computational constraints, it is best suited for species that occur in clustered distributions (where the problem can be broken into several, smaller problems), or for species with large home ranges relative to grid scale where resampling the points to a coarser resolution can reduce the problem to manageable proportions.

Strong fluctuations in aboveground population size do not limit genetic diversity in populations of an endangered biennial species.

PubMed

Münzbergová, Zuzana; Šurinová, Maria; Husáková, Iveta; Brabec, Jiří

2018-04-26

Assessing genetic diversity within populations of rare species and understanding its determinants are crucial for effective species protection. While a lot is known about the relationships between genetic diversity, fitness, and current population size, very few studies explored the effects of past population size. Knowledge of past population size may, however, improve our ability to predict future population fates. We studied Gentianella praecox subsp. bohemica, a biennial species with extensive seed bank. We tested the effect of current, past minimal and maximal population size, and harmonic mean of population sizes within the last 15 years on genetic diversity and fitness. Maximum population size over the last 15 years was the best predictor of expected heterozygosity of the populations and was significantly related to current population size and management. Plant fitness was significantly related to current as well as maximum population size and expected heterozygosity. The results suggested that information on past population size may improve our understanding of contemporary genetic diversity across populations. They demonstrated that despite the strong fluctuations in population size, large reductions in population size do not result in immediate loss of genetic diversity and reduction of fitness within the populations. This is likely due to the seed bank of the species serving as reservoir of the genetic diversity of the populations. From a conservation point of view, this suggests that the restoration of small populations of short-lived species with permanent seed bank is possible as these populations may still be genetically diverse.

Attention modulates spatial priority maps in the human occipital, parietal and frontal cortices

PubMed Central

Sprague, Thomas C.; Serences, John T.

2014-01-01

Computational theories propose that attention modulates the topographical landscape of spatial ‘priority’ maps in regions of visual cortex so that the location of an important object is associated with higher activation levels. While single-unit recording studies have demonstrated attention-related increases in the gain of neural responses and changes in the size of spatial receptive fields, the net effect of these modulations on the topography of region-level priority maps has not been investigated. Here, we used fMRI and a multivariate encoding model to reconstruct spatial representations of attended and ignored stimuli using activation patterns across entire visual areas. These reconstructed spatial representations reveal the influence of attention on the amplitude and size of stimulus representations within putative priority maps across the visual hierarchy. Our results suggest that attention increases the amplitude of stimulus representations in these spatial maps, particularly in higher visual areas, but does not substantively change their size. PMID:24212672

Spatio-temporal earthquake risk assessment for the Lisbon Metropolitan Area - A contribution to improving standard methods of population exposure and vulnerability analysis

NASA Astrophysics Data System (ADS)

Freire, Sérgio; Aubrecht, Christoph

2010-05-01

The recent 7.0 M earthquake that caused severe damage and destruction in parts of Haiti struck close to 5 PM (local time), at a moment when many people were not in their residences, instead being in their workplaces, schools, or churches. Community vulnerability assessment to seismic hazard relying solely on the location and density of resident-based census population, as is commonly the case, would grossly misrepresent the real situation. In particular in the context of global (climate) change, risk analysis is a research field increasingly gaining in importance whereas risk is usually defined as a function of hazard probability and vulnerability. Assessment and mapping of human vulnerability has however generally been lagging behind hazard analysis efforts. Central to the concept of vulnerability is the issue of human exposure. Analysis of exposure is often spatially tied to administrative units or reference objects such as buildings, spanning scales from the regional level to local studies for small areas. Due to human activities and mobility, the spatial distribution of population is time-dependent, especially in metropolitan areas. Accurately estimating population exposure is a key component of catastrophe loss modeling, one element of effective risk analysis and emergency management. Therefore, accounting for the spatio-temporal dynamics of human vulnerability correlates with recent recommendations to improve vulnerability analyses. Earthquakes are the prototype for a major disaster, being low-probability, rapid-onset, high-consequence events. Lisbon, Portugal, is subject to a high risk of earthquake, which can strike at any day and time, as confirmed by modern history (e.g. December 2009). The recently-approved Special Emergency and Civil Protection Plan (PEERS) is based on a Seismic Intensity map, and only contemplates resident population from the census as proxy for human exposure. In the present work we map and analyze the spatio-temporal distribution of population in the daily cycle to re-assess exposure to earthquake hazard in the Lisbon Metropolitan Area, home to almost three million people. New high-resolution (50 m grids) daytime and nighttime population distribution maps are developed using dasymetric mapping. The modeling approach uses areal interpolation to combine best-available census data and statistics with land use and land cover data. Mobility statistics are considered for mapping daytime distribution, and empirical parameters used for interpolation are obtained from a previous effort in high resolution population mapping of part of the study area. Finally, the population distribution maps are combined with the Seismic Hazard Intensity map to: (1) quantify and compare human exposure to seismic intensity levels in the daytime and nighttime periods, and (2) derive nighttime and daytime overall Earthquake Risk maps. This novel approach yields previously unavailable spatio-temporal population distribution information for the study area, enabling refined and more accurate earthquake risk mapping and assessment. Additionally, such population exposure datasets can be combined with different hazard maps to improve spatio-temporal assessment and risk mapping for any type of hazard, natural or man-made. We believe this improved characterization of vulnerability and risk can benefit all phases of the disaster management process where human exposure has to be considered, namely in emergency planning, risk mitigation, preparedness, and response to an event.

Magma volumes and storage in the middle crust

NASA Astrophysics Data System (ADS)

Memeti, V.; Barnes, C. G.; Paterson, S. R.

2015-12-01

Quantifying magma volumes in magma plumbing systems is mostly done through geophysical means or based on volcanic eruptions. Detailed studies of plutons, however, are useful in revealing depths and evolving volumes of stored magmas over variable lifetimes of magma systems. Knowledge of the location, volume, and longevity of stored magma is critical for understanding where in the crust magmas attain their chemical signature, how these systems physically behave and how source, storage levels, and volcanoes are connected. Detailed field mapping, combined with single mineral geochemistry and geochronology of plutons, allow estimates of size and longevity of melt-interconnected magma batches that existed during the construction of magma storage sites. The Tuolumne intrusive complex (TIC) recorded a 10 myr magmatic history. Detailed maps of the major units in different parts of the TIC indicate overall smaller scale (cm- to <1 km) compositional variation in the oldest, outer Kuna Crest unit and mainly larger scale (>10 km) changes in the younger Half Dome and Cathedral Peak units. Mineral-scale trace element data from hornblende of granodiorites to gabbros from the Kuna Crest lobe show distinct hornblende compositions and zoning patterns. Mixed hornblende populations occur only at the transition to the main TIC. This compositional heterogeneity in the first 1-2 myr points to low volume magmatism resulting in smaller, discrete and not chemically interacting magma bodies. Trace element and Sr- and Pb-isotope data from growth zones of K-feldspar phenocrysts from the two younger granodiorites indicate complex mineral zoning, but general isotopic overlap, suggesting in-situ, inter-unit mixing and fractionation. This is supported by hybrid zones between units, mixing of zircon, hornblende, and K-feldspar populations and late leucogranites. Thus, magma body sizes increased later resulting in overall more homogeneous, but complexly mixing magma mushes that fractionated locally.

Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses

PubMed Central

Zhang, S; Meng, L; Wang, J; Zhang, L

2017-01-01

Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population. PMID:28722705

Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses.

PubMed

Zhang, S; Meng, L; Wang, J; Zhang, L

2017-10-01

Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population.

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.

PubMed

Liu, Jimmy Z; van Sommeren, Suzanne; Huang, Hailiang; Ng, Siew C; Alberts, Rudi; Takahashi, Atsushi; Ripke, Stephan; Lee, James C; Jostins, Luke; Shah, Tejas; Abedian, Shifteh; Cheon, Jae Hee; Cho, Judy; Dayani, Naser E; Franke, Lude; Fuyuno, Yuta; Hart, Ailsa; Juyal, Ramesh C; Juyal, Garima; Kim, Won Ho; Morris, Andrew P; Poustchi, Hossein; Newman, William G; Midha, Vandana; Orchard, Timothy R; Vahedi, Homayon; Sood, Ajit; Sung, Joseph Y; Malekzadeh, Reza; Westra, Harm-Jan; Yamazaki, Keiko; Yang, Suk-Kyun; Barrett, Jeffrey C; Alizadeh, Behrooz Z; Parkes, Miles; Bk, Thelma; Daly, Mark J; Kubo, Michiaki; Anderson, Carl A; Weersma, Rinse K

2015-09-01

Ulcerative colitis and Crohn's disease are the two main forms of inflammatory bowel disease (IBD). Here we report the first trans-ancestry association study of IBD, with genome-wide or Immunochip genotype data from an extended cohort of 86,640 European individuals and Immunochip data from 9,846 individuals of East Asian, Indian or Iranian descent. We implicate 38 loci in IBD risk for the first time. For the majority of the IBD risk loci, the direction and magnitude of effect are consistent in European and non-European cohorts. Nevertheless, we observe genetic heterogeneity between divergent populations at several established risk loci driven by differences in allele frequency (NOD2) or effect size (TNFSF15 and ATG16L1) or a combination of these factors (IL23R and IRGM). Our results provide biological insights into the pathogenesis of IBD and demonstrate the usefulness of trans-ancestry association studies for mapping loci associated with complex diseases and understanding genetic architecture across diverse populations.

Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale

PubMed Central

Zackrisson, Martin; Hallin, Johan; Ottosson, Lars-Göran; Dahl, Peter; Fernandez-Parada, Esteban; Ländström, Erik; Fernandez-Ricaud, Luciano; Kaferle, Petra; Skyman, Andreas; Stenberg, Simon; Omholt, Stig; Petrovič, Uroš; Warringer, Jonas; Blomberg, Anders

2016-01-01

The capacity to map traits over large cohorts of individuals—phenomics—lags far behind the explosive development in genomics. For microbes, the estimation of growth is the key phenotype because of its link to fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved growth phenotypes at an unprecedented scale. Advancements were achieved through the introduction of transmissive scanning hardware and software technology, frequent acquisition of exact colony population size measurements, extraction of population growth rates from growth curves, and removal of spatial bias by reference-surface normalization. Our prototype arrangement automatically records and analyzes close to 100,000 growth curves in parallel. We demonstrate the power of the approach by extending and nuancing the known salt-defense biology in baker’s yeast. The introduced framework represents a major advance in microbial phenomics by providing high-quality data for extensive cohorts of individuals and generating well-populated and standardized phenomics databases PMID:27371952

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

PubMed Central

Huang, Hailiang; Ng, Siew C; Alberts, Rudi; Takahashi, Atsushi; Ripke, Stephan; Lee, James C; Jostins, Luke; Shah, Tejas; Abedian, Shifteh; Cheon, Jae Hee; Cho, Judy; Dayani, Naser E; Franke, Lude; Fuyuno, Yuta; Hart, Ailsa; Juyal, Ramesh C; Juyal, Garima; Kim, Won Ho; Morris, Andrew P; Poustchi, Hossein; Newman, William G; Midha, Vandana; Orchard, Timothy R; Vahedi, Homayon; Sood, Ajit; Sung, Joseph Y; Malekzadeh, Reza; Westra, Harm-Jan; Yamazaki, Keiko; Yang, Suk-Kyun; Barrett, Jeffrey C; Alizadeh, Behrooz Z; Parkes, Miles; BK, Thelma; Daly, Mark J; Kubo, Michiaki; Anderson, Carl A; Weersma, Rinse K

2016-01-01

Ulcerative colitis and Crohn’s disease are the two main forms of inflammatory bowel disease (IBD). Here, we report the first trans-ethnic association study of IBD, with genome-wide or Immunochip genotype data from an extended cohort of 86,640 European individuals and Immunochip data from 9,846 individuals of East-Asian, Indian or Iranian descent. We implicate 38 loci in IBD risk for the first time. For the majority of IBD risk loci, the direction and magnitude of effect is consistent in European and non-European cohorts. Nevertheless, we observe genetic heterogeneity between divergent populations at several established risk loci driven by a combination of differences in allele frequencies (NOD2), effect sizes (TNFSF15, ATG16L1) or a combination of both (IL23R, IRGM). Our results provide biological insights into the pathogenesis of IBD, and demonstrate the utility of trans-ethnic association studies for mapping complex disease loci and understanding genetic architecture across diverse populations. PMID:26192919

Evolutionary rescue in vertebrates: evidence, applications and uncertainty

PubMed Central

Vander Wal, E.; Garant, D.; Festa-Bianchet, M.; Pelletier, F.

2013-01-01

The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations. PMID:23209171

Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population.

PubMed

Ding, Junqiang; Zhang, Luyan; Chen, Jiafa; Li, Xiantang; Li, Yongming; Cheng, Hongliang; Huang, Rongrong; Zhou, Bo; Li, Zhimin; Wang, Jiankang; Wu, Jianyu

2015-01-01

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.

Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population

PubMed Central

Li, Xiantang; Li, Yongming; Cheng, Hongliang; Huang, Rongrong; Zhou, Bo; Li, Zhimin; Wang, Jiankang; Wu, Jianyu

2015-01-01

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize. PMID:26509792

Maternal choline supplementation improves spatial mapping and increases basal forebrain cholinergic neuron number and size in aged Ts65Dn mice

PubMed Central

Ash, Jessica A.; Velazquez, Ramon; Kelley, Christy M.; Powers, Brian E.; Ginsberg, Stephen D.; Mufson, Elliott J.; Strupp, Barbara J.

2014-01-01

Down syndrome (DS) is marked by intellectual disability (ID) and early-onset of Alzheimer’s disease (AD) neuropathology, including basal forebrain cholinergic neuron (BFCN) degeneration. The present study tested the hypothesis that maternal choline supplementation (MCS) lessens hippocampal dysfunction and protects against BFCN degeneration in the Ts65Dn mouse model of DS and AD. During pregnancy and lactation, dams were assigned to either a choline sufficient (1.1 g/kg choline chloride) or choline supplemented (5.0 g/kg choline chloride) diet. Between 13 and 17 months of age, offspring were tested in the radial arm water maze (RAWM) to examine spatial learning and memory followed by unbiased quantitative morphometry of BFCNs. Spatial mapping was significantly impaired in unsupplemented Ts65Dn mice relative to normal disomic (2N) littermates. Additionally, a significantly lower number and density of medial septum (MS) hippocampal projection BFCNs was also found in unsupplemented Ts65Dn mice. Notably, MCS significantly improved spatial mapping and increased number, density, and size of MS BFCNs in Ts65Dn offspring. Moreover, the density and number of MS BFCNs correlated significantly with spatial memory proficiency, providing powerful support for a functional relationship between these behavioral and morphometric effects of MCS for the trisomic offspring. Thus, increasing maternal choline intake during pregnancy may represent a safe and effective treatment approach for expectant mothers carrying a DS fetus, as well as a possible means of BFCN neuroprotection during aging for the population at large. PMID:24932939

Geologic map of the Riverside East 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Cox, Brett F.

2001-01-01

a. This Readme; includes in Appendix I, data contained in rse_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Corona North 7.5' quadrangle, Riverside and San Bernardino counties, California

USGS Publications Warehouse

Morton, Douglas M.; Gray, C.H.; Bovard, Kelly R.; Dawson, Michael

2002-01-01

a. This Readme; includes in Appendix I, data contained in crn_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced precise 1:24,000- scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Corona South 7.5' quadrangle, Riverside and Orange counties, California

USGS Publications Warehouse

Gray, C.H.; Morton, Douglas M.; Weber, F. Harold; Digital preparation by Bovard, Kelly R.; O'Brien, Timothy

2002-01-01

a. A Readme file; includes in Appendix I, data contained in crs_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Lake Mathews 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Weber, F. Harold

2001-01-01

a. This Readme; includes in Appendix I, data contained in lkm_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Miscellaneous Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous.Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand.In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Steele Peak 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; digital preparation by Alvarez, Rachel M.; Diep, Van M.

2001-01-01

a. This Readme; includes in Appendix I, data contained in stp_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Riverside West 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Cox, Brett F.

2001-01-01

a. This Readme; includes in Appendix I, data contained in rsw_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f.Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Improving alpine-region spectral unmixing with optimal-fit snow endmembers

NASA Technical Reports Server (NTRS)

Painter, Thomas H.; Roberts, Dar A.; Green, Robert O.; Dozier, Jeff

1995-01-01

Surface albedo and snow-covered-area (SCA) are crucial inputs to the hydrologic and climatologic modeling of alpine and seasonally snow-covered areas. Because the spectral albedo and thermal regime of pure snow depend on grain size, areal distribution of snow grain size is required. Remote sensing has been shown to be an effective (and necessary) means of deriving maps of grain size distribution and snow-covered-area. Developed here is a technique whereby maps of grain size distribution improve estimates of SCA from spectral mixture analysis with AVIRIS data.

Global rates of habitat loss and implications for amphibian conservation

USGS Publications Warehouse

Gallant, Alisa L.; Klaver, R.W.; Casper, G.S.; Lannoo, M.J.

2007-01-01

A large number of factors are known to affect amphibian population viability, but most authors agree that the principal causes of amphibian declines are habitat loss, alteration, and fragmentation. We provide a global assessment of land use dynamics in the context of amphibian distributions. We accomplished this by compiling global maps of amphibian species richness and recent rates of change in land cover, land use, and human population growth. The amphibian map was developed using a combination of published literature and digital databases. We used an ecoregion framework to help interpret species distributions across environmental, rather than political, boundaries. We mapped rates of land cover and use change with statistics from the World Resources Institute, refined with a global digital dataset on land cover derived from satellite data. Temporal maps of human population were developed from the World Resources Institute database and other published sources. Our resultant map of amphibian species richness illustrates that amphibians are distributed in an uneven pattern around the globe, preferring terrestrial and freshwater habitats in ecoregions that are warm and moist. Spatiotemporal patterns of human population show that, prior to the 20th century, population growth and spread was slower, most extensive in the temperate ecoregions, and largely exclusive of major regions of high amphibian richness. Since the beginning of the 20th century, human population growth has been exponential and has occurred largely in the subtropical and tropical ecoregions favored by amphibians. Population growth has been accompanied by broad-scale changes in land cover and land use, typically in support of agriculture. We merged information on land cover, land use, and human population growth to generate a composite map showing the rates at which humans have been changing the world. When compared with the map of amphibian species richness, we found that many of the regions of the earth supporting the richest assemblages of amphibians are currently undergoing the highest rates of landscape modification.

Enumeration of sex workers in the central business district of Nairobi, Kenya.

PubMed

Kimani, Joshua; McKinnon, Lyle R; Wachihi, Charles; Kusimba, Judith; Gakii, Gloria; Birir, Sarah; Muthui, Mercy; Kariri, Anthony; Muriuki, Festus K; Muraguri, Nicholas; Musyoki, Helgar; Ball, T Blake; Kaul, Rupert; Gelmon, Lawrence

2013-01-01

Accurate program planning for populations most at risk for HIV/STI acquisition requires knowledge of the size and location where these populations can best be reached. To obtain this information for sex workers operating at 137 hotspots in the central business district (CBD) in Nairobi, Kenya, we utilized a combined mapping and capture-recapture enumeration exercise. The majority of identified hotspots in this study were bars. Based on this exercise, we estimate that 6,904 male and female sex workers (95% confidence intervals, 6690 and 7118) were working nightly in the Nairobi CBD in April 2009. Wide ranges of captures per spot were obtained, suggesting that relatively few hot spots (18%) contain a relatively high proportion of the area's sex workers (65%). We provide geographic data including relatively short distances from hotspots to our dedicated sex worker outreach program in the CBD (mean<1 km), and clustering of hotspots within a relatively small area. Given the size covered and areas where sex work is likely taking place in Nairobi, the estimate is several times lower than what would be obtained if the entire metropolitan area was enumerated. These results have important practical and policy implications for enhancing HIV/STI prevention efforts.

The genetic architecture of maize height.

PubMed

Peiffer, Jason A; Romay, Maria C; Gore, Michael A; Flint-Garcia, Sherry A; Zhang, Zhiwu; Millard, Mark J; Gardner, Candice A C; McMullen, Michael D; Holland, James B; Bradbury, Peter J; Buckler, Edward S

2014-04-01

Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pedigree or estimates of the genomic identity-by-state among related plants, height is also accurately predictable. But, mapping alleles explaining natural variation in maize height remains a formidable challenge. To address this challenge, we measured the plant height, ear height, flowering time, and node counts of plants grown in >64,500 plots across 13 environments. These plots contained >7300 inbreds representing most publically available maize inbreds in the United States and families of the maize Nested Association Mapping (NAM) panel. Joint-linkage mapping of quantitative trait loci (QTL), fine mapping in near isogenic lines (NILs), genome-wide association studies (GWAS), and genomic best linear unbiased prediction (GBLUP) were performed. The heritability of maize height was estimated to be >90%. Mapping NAM family-nested QTL revealed the largest explained 2.1 ± 0.9% of height variation. The effects of two tropical alleles at this QTL were independently validated by fine mapping in NIL families. Several significant associations found by GWAS colocalized with established height loci, including brassinosteroid-deficient dwarf1, dwarf plant1, and semi-dwarf2. GBLUP explained >80% of height variation in the panels and outperformed bootstrap aggregation of family-nested QTL models in evaluations of prediction accuracy. These results revealed maize height was under strong genetic control and had a highly polygenic genetic architecture. They also showed that multiple models of genetic architecture differing in polygenicity and effect sizes can plausibly explain a population's variation in maize height, but they may vary in predictive efficacy.

High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.

PubMed

Brown, Allan F; Yousef, Gad G; Chebrolu, Kranthi K; Byrd, Robert W; Everhart, Koyt W; Thomas, Aswathy; Reid, Robert W; Parkin, Isobel A P; Sharpe, Andrew G; Oliver, Rebekah; Guzman, Ivette; Jackson, Eric W

2014-09-01

A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.).

PubMed

Jiang, Congcong; Shi, Jiaqin; Li, Ruiyuan; Long, Yan; Wang, Hao; Li, Dianrong; Zhao, Jianyi; Meng, Jinling

2014-04-01

This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations. Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F2 population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

USDA-ARS?s Scientific Manuscript database

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collectio...

Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits

PubMed Central

Zembrzycki, Andreas; Chou, Shen-Ju; Ashery-Padan, Ruth; Stoykova, Anastassia; O’Leary, Dennis D.M.

2013-01-01

Summary Primary somatosensory cortex (S1) contains a complete body map that mirrors subcortical maps developed by peripheral sensory input projecting to sensory hindbrain, thalamus, then S1. Peripheral changes during development alter these maps through ‘bottom-up’ plasticity. Unknown is how S1 size influences map organization and if an altered S1 map feedbacks to affect subcortical maps. We show in mice that S1 is significantly reduced by cortex-specific deletion of Pax6, resulting in a reduced body map and loss of body representations by exclusion of later-differentiating sensory thalamocortical input. An initially normal sensory thalamus was re-patterned to match the aberrant S1 map by apoptotic deletion of thalamic neurons representing body parts with axons excluded from S1. Deleted representations were rescued by altering competition between thalamocortical axons by sensory deprivation or increasing S1. Thus, S1 size determined resolution and completeness of body maps and engaged ‘top-down’ plasticity that re-patterned sensory thalamus to match S1. PMID:23831966

LOD score exclusion analyses for candidate genes using random population samples.

PubMed

Deng, H W; Li, J; Recker, R R

2001-05-01

While extensive analyses have been conducted to test for, no formal analyses have been conducted to test against, the importance of candidate genes with random population samples. We develop a LOD score approach for exclusion analyses of candidate genes with random population samples. Under this approach, specific genetic effects and inheritance models at candidate genes can be analysed and if a LOD score is < or = - 2.0, the locus can be excluded from having an effect larger than that specified. Computer simulations show that, with sample sizes often employed in association studies, this approach has high power to exclude a gene from having moderate genetic effects. In contrast to regular association analyses, population admixture will not affect the robustness of our analyses; in fact, it renders our analyses more conservative and thus any significant exclusion result is robust. Our exclusion analysis complements association analysis for candidate genes in random population samples and is parallel to the exclusion mapping analyses that may be conducted in linkage analyses with pedigrees or relative pairs. The usefulness of the approach is demonstrated by an application to test the importance of vitamin D receptor and estrogen receptor genes underlying the differential risk to osteoporotic fractures.

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation.

PubMed

Stephan, Wolfgang

2016-01-01

In the past 15 years, numerous methods have been developed to detect selective sweeps underlying adaptations. These methods are based on relatively simple population genetic models, including one or two loci at which positive directional selection occurs, and one or two marker loci at which the impact of selection on linked neutral variation is quantified. Information about the phenotype under selection is not included in these models (except for fitness). In contrast, in the quantitative genetic models of adaptation, selection acts on one or more phenotypic traits, such that a genotype-phenotype map is required to bridge the gap to population genetics theory. Here I describe the range of population genetic models from selective sweeps in a panmictic population of constant size to evolutionary traffic when simultaneous sweeps at multiple loci interfere, and I also consider the case of polygenic selection characterized by subtle allele frequency shifts at many loci. Furthermore, I present an overview of the statistical tests that have been proposed based on these population genetics models to detect evidence for positive selection in the genome. © 2015 John Wiley & Sons Ltd.

Social network analysis of the genetic structure of Pacific islanders.

PubMed

Terrell, John Edward

2010-05-01

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

Spread of an Inactive Form of Caspase-12 in Humans Is Due to Recent Positive Selection

PubMed Central

Xue, Yali ; Daly, Allan ; Yngvadottir, Bryndis ; Liu, Mengning ; Coop, Graham ; Kim, Yuseob ; Sabeti, Pardis ; Chen, Yuan ; Stalker, Jim ; Huckle, Elizabeth ; Burton, John ; Leonard, Steven ; Rogers, Jane ; Tyler-Smith, Chris 

2006-01-01

The human caspase-12 gene is polymorphic for the presence or absence of a stop codon, which results in the occurrence of both active (ancestral) and inactive (derived) forms of the gene in the population. It has been shown elsewhere that carriers of the inactive gene are more resistant to severe sepsis. We have now investigated whether the inactive form has spread because of neutral drift or positive selection. We determined its distribution in a worldwide sample of 52 populations and resequenced the gene in 77 individuals from the HapMap Yoruba, Han Chinese, and European populations. There is strong evidence of positive selection from low diversity, skewed allele-frequency spectra, and the predominance of a single haplotype. We suggest that the inactive form of the gene arose in Africa ∼100–500 thousand years ago (KYA) and was initially neutral or almost neutral but that positive selection beginning ∼60–100 KYA drove it to near fixation. We further propose that its selective advantage was sepsis resistance in populations that experienced more infectious diseases as population sizes and densities increased. PMID:16532395

Identification of milling and baking quality QTL in multiple soft wheat mapping populations.

PubMed

Cabrera, Antonio; Guttieri, Mary; Smith, Nathan; Souza, Edward; Sturbaum, Anne; Hua, Duc; Griffey, Carl; Barnett, Marla; Murphy, Paul; Ohm, Herb; Uphaus, Jim; Sorrells, Mark; Heffner, Elliot; Brown-Guedira, Gina; Van Sanford, David; Sneller, Clay

2015-11-01

Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.

Current status of Mycobacterium avium subspecies paratuberculosis infection in animals & humans in India: What needs to be done?

PubMed

Singh, Ajay Vir; Chauhan, Devendra Singh; Singh, Shoor Vir; Kumar, Vijay; Singh, Abhinendra; Yadav, Anjali; Yadav, Virendra Singh

2016-11-01

Mycobacterium avium subspecies paratuberculosis (MAP) has emerged as a major health problem for domestic livestock and human beings. Reduced per animal productivity of domestic livestock seriously impacts the economics of dairy farming globally. High to very high bioload of MAP in domestic livestock and also in the human population has been reported from north India. Presence of live MAP bacilli in commercial supplies of raw and pasteurized milk and milk products indicates its public health significance. MAP is not inactivated during pasteurization, therefore, entering into human food chain daily. Recovery of MAP from patients with inflammatory bowel disease or Crohn's disease and animal healthcare workers suffering with chronic gastrointestinal problems indicate a close association of MAP with a number of chronic and other diseases affecting human health. Higher bioload of MAP in the animals increases the risk of exposure to the human population with MAP. This review summarizes the current status of MAP infection in animals as well as in human beings and also highlights the prospects of effective management and control of disease in animals to reduce the risk of exposure to human population.

Success and failure in replication of genotype-phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations?

PubMed

Schielzeth, Holger; Rios Villamil, Alejandro; Burri, Reto

2018-03-25

Recent developments in sequencing technologies have facilitated genomewide mapping of phenotypic variation in natural populations. Such mapping efforts face a number of challenges potentially leading to low reproducibility. However, reproducible research forms the basis of scientific progress. We here discuss the options for replication and the reasons for potential nonreproducibility. We then review the evidence for reproducible quantitative trait loci (QTL) with a focus on natural animal populations. Existing case studies of replication fall into three categories: (i) traits that have been mapped to major effect loci (including chromosomal inversion and supergenes) by independent research teams; (ii) QTL fine-mapped in discovery populations; and (iii) attempts to replicate QTL across multiple populations. Major effect loci, in particular those associated with inversions, have been successfully replicated in several cases within and across populations. Beyond such major effect variants, replication has been more successful within than across populations, suggesting that QTL discovered in natural populations may often be population-specific. This suggests that biological causes (differences in linkage patterns, allele frequencies or context-dependencies of QTL) contribute to nonreproducibility. Evidence from other fields, notably animal breeding and QTL mapping in humans, suggests that a significant fraction of QTL is indeed reproducible in direction and magnitude at least within populations. However, there is also a large number of QTL that cannot be easily reproduced. We put forward that more studies should explicitly address the causes and context-dependencies of QTL signals, in particular to disentangle linkage differences, allele frequency differences and gene-by-environment interactions as biological causes of nonreproducibility of QTL, especially between populations. © 2018 John Wiley & Sons Ltd.

US Topo: topographic maps for the nation

USGS Publications Warehouse

Carswell, William J.

2013-01-01

US Topo is the next generation of topographic maps from the U.S. Geological Survey (USGS). Arranged in the familiar 7.5-minute quadrangle format, digital US Topo maps are designed to look and feel (and perform) like the traditional paper topographic maps for which the USGS is so well known. In contrast to paper-based maps, US Topo maps provide modern technical advantages that support faster, wider public distribution and enable basic, on-screen geographic analysis for all users. The US Topo quadrangle map has been redesigned so that map elements are visually distinguishable with the imagery turned on and off, while keeping the file size as small as possible. The US Topo map redesign includes improvements to various display factors, including symbol definitions (color, line thickness, line symbology, area fills), layer order, and annotation fonts. New features for 2013 include the following: a raster shaded relief layer, military boundaries, cemeteries and post offices, and a US Topo cartographic symbols legend as an attachment. US Topo quadrangle maps are available free on the Web. Each map quadrangle is constructed in GeoPDF® format using key layers of geographic data (orthoimagery, roads, geographic names, topographic contours, and hydrographic features) from The National Map databases. US Topo quadrangle maps can be printed from personal computers or plotters as complete, full-sized, maps or in customized sections, in a user-desired specific format. Paper copies of the maps can also be purchased from the USGS Store. Download links and a users guide are featured on the US Topo Web site. US Topo users can turn geographic data layers on and off as needed; they can zoom in and out to highlight specific features or see a broader area. File size for each digital 7.5-minute quadrangle, about 30 megabytes. Associated electronic tools for geographic analysis are available free for download. The US Topo provides the Nation with a topographic product that users can quickly incorporate into decisionmaking, operational or recreational activities.

A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

PubMed Central

2011-01-01

Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species. PMID:21492453

High resolution population distribution maps for Southeast Asia in 2010 and 2015.

PubMed

Gaughan, Andrea E; Stevens, Forrest R; Linard, Catherine; Jia, Peng; Tatem, Andrew J

2013-01-01

Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.

High Resolution Population Distribution Maps for Southeast Asia in 2010 and 2015

PubMed Central

Gaughan, Andrea E.; Stevens, Forrest R.; Linard, Catherine; Jia, Peng; Tatem, Andrew J.

2013-01-01

Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org. PMID:23418469

Activities and preliminary results of nearshore benthic habitat mapping in southern California, 1998

USGS Publications Warehouse

Cochrane, Guy R.; Lafferty, Kevin D.

2000-01-01

The nearshore benthic habitat of the Santa Barbara coast and Channel Islands supports a diversity of marine life that are commercially, recreationally, and intrinsically valuable. Some of these resources are known to be endangered including a variety of rockfish and the White Abalone. State and National agencies have been mandated to preserve and enhance these resources and require detailed habitat characterization in order to do so. This project will characterize and map the benthic habitat in areas that have been selected because they have been set aside as National Sanctuaries or State Preserves, or are areas of ongoing or planned fish population studies. Various management strategies are being developed to protect marine resources in the Santa Barbara Channel Islands Region. One approach under investigation is to implement no-take marine reserves (Agardy, T., 1997; Bohnsack, 1998; Roberts, 1997). One small reserve presently exists on Anacapa Island and there is a growing momentum to add additional reserves to form a reserve network (Lafferty et al., 2000). Reserves may provide relatively pristine marine communities in a wild state for study and appreciation. In addition, they may buffer some species from over-fishing. A key feature of marine reserve design is to protect a representation of the existing habitats in a region (Roberts, 1997). Unfortunately, the distribution of habitats is not well known in this area since the underwater equivalent of soils and vegetation maps that are widely available for terrestrial systems do not yet exist. Managers need habitat maps to help determine the most appropriate boundaries for reserves in a network in order to meet various criteria and goals (such as habitat representation, reserve size, habitat heterogeneity, reserve spacing, inclusion of sensitive habitats, etc.). Another use for habitat mapping is to better understand the distribution of those habitats that are particularly important to fished species or sensitive species. Combining habitat mapping with ongoing studies of egg and larval fish counts by the National Marine Fisheries Service (Russell Vetter), rockfish population studies by the California Department of Fish and Game (Dave VenTresca), and white abalone (Kevin Lafferty and others, USGS) will extend the ability to predict the distribution of these species and identify areas with appropriate habitat that might be suitable for restoration. Additional uses for habitat mapping include managing visitor use, kelp distribution, and archeological resources.

Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms.

PubMed

Horikoshi, Momoko; Pasquali, Lorenzo; Wiltshire, Steven; Huyghe, Jeroen R; Mahajan, Anubha; Asimit, Jennifer L; Ferreira, Teresa; Locke, Adam E; Robertson, Neil R; Wang, Xu; Sim, Xueling; Fujita, Hayato; Hara, Kazuo; Young, Robin; Zhang, Weihua; Choi, Sungkyoung; Chen, Han; Kaur, Ismeet; Takeuchi, Fumihiko; Fontanillas, Pierre; Thuillier, Dorothée; Yengo, Loic; Below, Jennifer E; Tam, Claudia H T; Wu, Ying; Abecasis, Gonçalo; Altshuler, David; Bell, Graeme I; Blangero, John; Burtt, Noél P; Duggirala, Ravindranath; Florez, Jose C; Hanis, Craig L; Seielstad, Mark; Atzmon, Gil; Chan, Juliana C N; Ma, Ronald C W; Froguel, Philippe; Wilson, James G; Bharadwaj, Dwaipayan; Dupuis, Josee; Meigs, James B; Cho, Yoon Shin; Park, Taesung; Kooner, Jaspal S; Chambers, John C; Saleheen, Danish; Kadowaki, Takashi; Tai, E Shyong; Mohlke, Karen L; Cox, Nancy J; Ferrer, Jorge; Zeggini, Eleftheria; Kato, Norihiro; Teo, Yik Ying; Boehnke, Michael; McCarthy, Mark I; Morris, Andrew P

2016-05-15

To gain insight into potential regulatory mechanisms through which the effects of variants at four established type 2 diabetes (T2D) susceptibility loci (CDKAL1, CDKN2A-B, IGF2BP2 and KCNQ1) are mediated, we undertook transancestral fine-mapping in 22 086 cases and 42 539 controls of East Asian, European, South Asian, African American and Mexican American descent. Through high-density imputation and conditional analyses, we identified seven distinct association signals at these four loci, each with allelic effects on T2D susceptibility that were homogenous across ancestry groups. By leveraging differences in the structure of linkage disequilibrium between diverse populations, and increased sample size, we localised the variants most likely to drive each distinct association signal. We demonstrated that integration of these genetic fine-mapping data with genomic annotation can highlight potential causal regulatory elements in T2D-relevant tissues. These analyses provide insight into the mechanisms through which T2D association signals are mediated, and suggest future routes to understanding the biology of specific disease susceptibility loci. © The Author 2016. Published by Oxford University Press.

Use of geostatistics to determine the spatial distribution and infestation rate of leaf-cutting ant nests (Hymenoptera: Formicidae) in eucalyptus plantations.

PubMed

Lasmar, O; Zanetti, R; dos Santos, A; Fernandes, B V

2012-08-01

One of the fundamental steps in pest sampling is the assessment of the population distribution in the field. Several studies have investigated the distribution and appropriate sampling methods for leaf-cutting ants; however, more reliable methods are still required, such as those that use geostatistics. The objective of this study was to determine the spatial distribution and infestation rate of leaf-cutting ant nests in eucalyptus plantations by using geostatistics. The study was carried out in 2008 in two eucalyptus stands in Paraopeba, Minas Gerais, Brazil. All of the nests in the studied area were located and used for the generation of GIS maps, and the spatial pattern of distribution was determined considering the number and size of nests. Each analysis and map was made using the R statistics program and the geoR package. The nest spatial distribution in a savanna area of Minas Gerais was clustered to a certain extent. The models generated allowed the production of kriging maps of areas infested with leaf-cutting ants, where chemical intervention would be necessary, reducing the control costs, impact on humans, and the environment.

Uncertainty in Population Estimates for Endangered Animals and Improving the Recovery Process

PubMed Central

Haines, Aaron M.; Zak, Matthew; Hammond, Katie; Scott, J. Michael; Goble, Dale D.; Rachlow, Janet L.

2013-01-01

Simple Summary The objective of our study was to evaluate the mention of uncertainty (i.e., variance) associated with population size estimates within U.S. recovery plans for endangered animals. To do this we reviewed all finalized recovery plans for listed terrestrial vertebrate species. We found that more recent recovery plans reported more estimates of population size and uncertainty. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty. We recommend that updated recovery plans combine uncertainty of population size estimates with a minimum detectable difference to aid in successful recovery. Abstract United States recovery plans contain biological information for a species listed under the Endangered Species Act and specify recovery criteria to provide basis for species recovery. The objective of our study was to evaluate whether recovery plans provide uncertainty (e.g., variance) with estimates of population size. We reviewed all finalized recovery plans for listed terrestrial vertebrate species to record the following data: (1) if a current population size was given, (2) if a measure of uncertainty or variance was associated with current estimates of population size and (3) if population size was stipulated for recovery. We found that 59% of completed recovery plans specified a current population size, 14.5% specified a variance for the current population size estimate and 43% specified population size as a recovery criterion. More recent recovery plans reported more estimates of current population size, uncertainty and population size as a recovery criterion. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty compared to reptiles and amphibians. We suggest the use of calculating minimum detectable differences to improve confidence when delisting endangered animals and we identified incentives for individuals to get involved in recovery planning to improve access to quantitative data. PMID:26479531

US Topo Product Standard

USGS Publications Warehouse

Cooley, Michael J.; Davis, Larry R.; Fishburn, Kristin A.; Lestinsky, Helmut; Moore, Laurence R.

2011-01-01

A full-size style sheet template in PDF that defines the placement of map elements, marginalia, and font sizes and styles accompanies this standard. The GeoPDF US Topo maps are fashioned to conform to this style sheet so that a user can print out a map at the 1:24,000-scale using the dimensions of the traditional standard 7.5-minute quadrangle. Symbology and type specifications for feature content are published separately. In addition, the GeoPDF design allows for custom printing, so that a user may zoom in and out, turn layers on and off, and view or print any combination of layers or any map portion at any desired scale.

Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing

PubMed Central

Everett, Meredith V; Seeb, James E

2014-01-01

Understanding how organisms interact with their environments is increasingly important for conservation efforts in many species, especially in light of highly anticipated climate changes. One method for understanding this relationship is to use genetic maps and QTL mapping to detect genomic regions linked to phenotypic traits of importance for adaptation. We used high-throughput genotyping by sequencing (GBS) to both detect and map thousands of SNPs in haploid Chinook salmon (Oncorhynchus tshawytscha). We next applied this map to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon. Using these techniques, we mapped 3534 SNPs in 34 linkage groups which is consistent with the haploid chromosome number for Chinook salmon. We successfully detected three QTL for temperature tolerance and one QTL for body size at the experiment-wide level, as well as additional QTL significant at the chromosome-wide level. The use of haploids coupled with GBS provides a robust pathway to rapidly develop genomic resources in nonmodel organisms; these QTL represent preliminary progress toward linking traits of conservation interest to regions in the Chinook salmon genome. PMID:24822082

Physical and genetic map of Streptococcus thermophilus A054.

PubMed Central

Roussel, Y; Pebay, M; Guedon, G; Simonet, J M; Decaris, B

1994-01-01

The three restriction endonucleases SfiI, BssHII, and SmaI were found to generate fragments with suitable size distributions for mapping the genome of Streptococcus thermophilus A054. A total of 5, 8, and 24 fragments were produced with SfiI, BssHII, and SmaI, respectively. An average genome size of 1,824 kb was determined by summing the total fragment sizes obtained by digestions with these three enzymes. Partial and multiple digestions of genomic DNA in conjunction with Southern hybridization were used to map SfiI, BssHII, and SmaI fragments. All restriction fragments were arranged in a unique circular chromosome. Southern hybridization analysis with specific probes allowed 23 genetic markers to be located on the restriction map. Among them, six rrn loci were precisely located. The area of the chromosome containing the ribosomal operons was further detailed by mapping some of the ApaI and SgrAI sites. Comparison of macrorestriction patterns from three clones derived from strain A054 revealed two variable regions in the chromosome. One was associated with the tandem rrnD and rrnE loci, and the other was mapped in the region of the lactose operon. Images PMID:8002562

Social-Ecological Patterns of Soil Heavy Metals Based on a Self-Organizing Map (SOM): A Case Study in Beijing, China

PubMed Central

Wang, Binwu; Li, Hong; Sun, Danfeng

2014-01-01

The regional management of trace elements in soils requires understanding the interaction between the natural system and human socio-economic activities. In this study, a social-ecological patterns of heavy metals (SEPHM) approach was proposed to identify the heavy metal concentration patterns and processes in different ecoregions of Beijing (China) based on a self-organizing map (SOM). Potential ecological risk index (RI) values of Cr, Ni, Zn, Hg, Cu, As, Cd and Pb were calculated for 1,018 surface soil samples. These data were averaged in accordance with 253 communities and/or towns, and compared with demographic, agriculture structure, geomorphology, climate, land use/cover, and soil-forming parent material to discover the SEPHM. Multivariate statistical techniques were further applied to interpret the control factors of each SEPHM. SOM application clustered the 253 towns into nine groups on the map size of 12 × 7 plane (quantization error 1.809; topographic error, 0.0079). The distribution characteristics and Spearman rank correlation coefficients of RIs were strongly associated with the population density, vegetation index, industrial and mining land percent and road density. The RIs were relatively high in which towns in a highly urbanized area with large human population density exist, while low RIs occurred in mountainous and high vegetation cover areas. The resulting dataset identifies the SEPHM of Beijing and links the apparent results of RIs to driving factors, thus serving as an excellent data source to inform policy makers for legislative and land management actions. PMID:24690947

Impact craters on Venus: An overview from Magellan observations

NASA Technical Reports Server (NTRS)

Schaber, G. G.; Strom, R. G.; Moore, H. J.; Soderblom, L. A.; Kirk, R. L.; Chadwick, D. J.; Dawson, D. D.; Gaddis, L. R.; Boyce, J. M.; Russell, J.

1992-01-01

Magellan has revealed an ensemble of impact craters on Venus that is unique in many important ways. We have compiled a database describing 842 craters on 89 percent of the planet's surface mapped through orbit 2578 (the craters range in diameter from 1.5 to 280 km). We have studied the distribution, size-frequency, morphology, and geology of these craters both in aggregate and, for some craters, in more detail. We have found the following: (1) the spatial distribution of craters is highly uniform; (2) the size-density distribution of craters with diameters greater than or equal to 35 km is consistent with a 'production' population having a surprisingly young age of about 0.5 Ga (based on the estimated population of Venus-crossing asteroids); (3) the spectrum of crater modification differs greatly from that on other planets--62 percent of all craters are pristine, only 4 percent volcanically embayed, and the remainder affected by tectonism, but none are severely and progressively depleted based on size-density distribution extrapolated from larger craters; (4) large craters have a progression of morphologies generally similar to those on other planets, but small craters are typically irregular or multiple rather than bowl shaped; (5) diffuse radar-bright or -dark features surround some craters, and about 370 similar diffuse 'splotches' with no central crater are observed whose size-density distribution is similar to that of small craters; and (6) other features unique to Venus include radar-bright or -dark parabolic arcs opening westward and extensive outflows originating in crater ejecta.

Genetic Variation in TLR Genes in Ugandan and South African Populations and Comparison with HapMap Data

PubMed Central

Randhawa, April Kaur; Horne, David J.; Adams, Mark D.; Shey, Muki; Barnholtz-Sloan, Jill; Mayanja-Kizza, Harriet; Kaplan, Gilla; Hanekom, Willem A.; Boom, W. Henry; Hawn, Thomas R.; Stein, Catherine M.

2012-01-01

Genetic epidemiological studies of complex diseases often rely on data from the International HapMap Consortium for identification of single nucleotide polymorphisms (SNPs), particularly those that tag haplotypes. However, little is known about the relevance of the African populations used to collect HapMap data for study populations conducted elsewhere in Africa. Toll-like receptor (TLR) genes play a key role in susceptibility to various infectious diseases, including tuberculosis. We conducted full-exon sequencing in samples obtained from Uganda (n = 48) and South Africa (n = 48), in four genes in the TLR pathway: TLR2, TLR4, TLR6, and TIRAP. We identified one novel TIRAP SNP (with minor allele frequency [MAF] 3.2%) and a novel TLR6 SNP (MAF 8%) in the Ugandan population, and a TLR6 SNP that is unique to the South African population (MAF 14%). These SNPs were also not present in the 1000 Genomes data. Genotype and haplotype frequencies and linkage disequilibrium patterns in Uganda and South Africa were similar to African populations in the HapMap datasets. Multidimensional scaling analysis of polymorphisms in all four genes suggested broad overlap of all of the examined African populations. Based on these data, we propose that there is enough similarity among African populations represented in the HapMap database to justify initial SNP selection for genetic epidemiological studies in Uganda and South Africa. We also discovered three novel polymorphisms that appear to be population-specific and would only be detected by sequencing efforts. PMID:23112821

New Constraints on the Rock Size Distribution on the Moon from Diviner Infrared Measurements

NASA Astrophysics Data System (ADS)

Elder, C. M.; Hayne, P. O.; Piqueux, S.; Bandfield, J. L.; Ghent, R. R.; Williams, J. P.; Paige, D. A.

2015-12-01

Most of the Moon's surface is covered by fine-grained regolith produced by impacts, but rocks of various sizes are also present. Rock abundances can be used to distinguish different surface units and quantify the ages of craters [1,2]. Furthermore, the size distribution of a population of rocks reflects the process by which they were formed and fragmented [3]. Knowing the distribution of rock sizes on the Moon can improve our understanding of regolith generation, evolution, and distribution, can be used to select landing sites, and can provide insight into the processes that have shaped the lunar surface. The high thermal inertia of rocks compared to fine-grained regolith leads to multiple temperatures within the field of view of nighttime multispectral data returned from the Lunar Reconnaissance Orbiter (LRO) Diviner thermal radiometer. This data has been used to map the rock abundance across the lunar surface [1]. However, the derived rock abundance is not constant over the course of the lunar night; small rocks cool faster than large rocks and eventually become indistinguishable from regolith using Diviner data. Thus the detectable rock abundance will decrease over the course of the lunar night. Here we use this change in measured rock abundance with time to constrain the size distribution of rock fragments, and map its variation across the lunar surface. We will show results from this study and discuss the implications for the geologic processes shaping the lunar surface. [1] Bandfield J. L. et al. (2011) JGR, 116, E00H02. [2] Ghent R. R. et al. (2014) Geology, 42, no. 12, 1059-1062. [3] Hartmann W. K. (1969) Icarus, 10, 201-213. Part of this work was performed at the Jet Propulsion Laboratory, California Institute of Technology under contract with the National Aeronautics and Space Administration.

The scaling of human interactions with city size.

PubMed

Schläpfer, Markus; Bettencourt, Luís M A; Grauwin, Sébastian; Raschke, Mathias; Claxton, Rob; Smoreda, Zbigniew; West, Geoffrey B; Ratti, Carlo

2014-09-06

The size of cities is known to play a fundamental role in social and economic life. Yet, its relation to the structure of the underlying network of human interactions has not been investigated empirically in detail. In this paper, we map society-wide communication networks to the urban areas of two European countries. We show that both the total number of contacts and the total communication activity grow superlinearly with city population size, according to well-defined scaling relations and resulting from a multiplicative increase that affects most citizens. Perhaps surprisingly, however, the probability that an individual's contacts are also connected with each other remains largely unaffected. These empirical results predict a systematic and scale-invariant acceleration of interaction-based spreading phenomena as cities get bigger, which is numerically confirmed by applying epidemiological models to the studied networks. Our findings should provide a microscopic basis towards understanding the superlinear increase of different socioeconomic quantities with city size, that applies to almost all urban systems and includes, for instance, the creation of new inventions or the prevalence of certain contagious diseases. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Deformation-mechanism map for nanocrystalline metals by molecular-dynamics simulation.

PubMed

Yamakov, V; Wolf, D; Phillpot, S R; Mukherjee, A K; Gleiter, H

2004-01-01

Molecular-dynamics simulations have recently been used to elucidate the transition with decreasing grain size from a dislocation-based to a grain-boundary-based deformation mechanism in nanocrystalline f.c.c. metals. This transition in the deformation mechanism results in a maximum yield strength at a grain size (the 'strongest size') that depends strongly on the stacking-fault energy, the elastic properties of the metal, and the magnitude of the applied stress. Here, by exploring the role of the stacking-fault energy in this crossover, we elucidate how the size of the extended dislocations nucleated from the grain boundaries affects the mechanical behaviour. Building on the fundamental physics of deformation as exposed by these simulations, we propose a two-dimensional stress-grain size deformation-mechanism map for the mechanical behaviour of nanocrystalline f.c.c. metals at low temperature. The map captures this transition in both the deformation mechanism and the related mechanical behaviour with decreasing grain size, as well as its dependence on the stacking-fault energy, the elastic properties of the material, and the applied stress level.

Beamline 10.3.2 at ALS: a hard X-ray microprobe for environmental and materials sciences.

PubMed

Marcus, Matthew A; MacDowell, Alastair A; Celestre, Richard; Manceau, Alain; Miller, Tom; Padmore, Howard A; Sublett, Robert E

2004-05-01

Beamline 10.3.2 at the ALS is a bend-magnet line designed mostly for work on environmental problems involving heavy-metal speciation and location. It offers a unique combination of X-ray fluorescence mapping, X-ray microspectroscopy and micro-X-ray diffraction. The optics allow the user to trade spot size for flux in a size range of 5-17 microm in an energy range of 3-17 keV. The focusing uses a Kirkpatrick-Baez mirror pair to image a variable-size virtual source onto the sample. Thus, the user can reduce the effective size of the source, thereby reducing the spot size on the sample, at the cost of flux. This decoupling from the actual source also allows for some independence from source motion. The X-ray fluorescence mapping is performed with a continuously scanning stage which avoids the time overhead incurred by step-and-repeat mapping schemes. The special features of this beamline are described, and some scientific results shown.

Development and genetic characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) population of wild × cultivated barley

USDA-ARS?s Scientific Manuscript database

The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population ...

Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations.

PubMed

Teo, Yik-Ying; Sim, Xueling; Ong, Rick T H; Tan, Adrian K S; Chen, Jieming; Tantoso, Erwin; Small, Kerrin S; Ku, Chee-Seng; Lee, Edmund J D; Seielstad, Mark; Chia, Kee-Seng

2009-11-01

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.

Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations

PubMed Central

Teo, Yik-Ying; Sim, Xueling; Ong, Rick T.H.; Tan, Adrian K.S.; Chen, Jieming; Tantoso, Erwin; Small, Kerrin S.; Ku, Chee-Seng; Lee, Edmund J.D.; Seielstad, Mark; Chia, Kee-Seng

2009-01-01

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser. PMID:19700652

Role of patch size, disease, and movement in rapid extinction of bighorn sheep

USGS Publications Warehouse

Singer, F.J.; Zeigenfuss, L.C.; Spicer, L.

2001-01-01

The controversy (Berger 1990, 1999; Wehausen 1999) over rapid extinction in bighorn sheep (Ovis canadensis) has focused on population size alone as a correlate to persistence time. We report on the persistence and population performance of 24 translocated populations of bighorn sheep. Persistence in these sheep was strongly correlated with larger patch sizes, greater distance to domestic sheep, higher population growth rates, and migratory movements, as well as to larger population sizes. Persistence was also positively correlated with larger average home-range size (p = 0.058, n = 10 translocated populations) and home-range size of rams (p = 0.087, n = 8 translocated populations). Greater home-range size and dispersal rates of bighorn sheep were positively correlated to larger patches. We conclude that patch size and thus habitat carrying capacity, not population size per se, is the primary correlate to both population performance and persistence. Because habitat carrying capacity defines the upper limit to population size, clearly the amount of suitable habitat in a patch is ultimately linked to population size. Larger populations (250+ animals) were more likely to recover rapidly to their pre-epizootic survey number following an epizootic (p = 0.019), although the proportion of the population dying in the epizootic also influenced the probability of recovery (p = 0.001). Expensive management efforts to restore or increase bighorn sheep populations should focus on large habitat patches located ≥23 km from domestic sheep, and less effort should be expended on populations in isolated, small patches of habitat.

Temporal and spatial stability of red-tailed hawk territories in the Luquillo Experimental Forest, Puerto Rico

USGS Publications Warehouse

Boal, C.W.; Snyder, H.A.; Bibles, Brent D.; Estabrook, T.S.

2003-01-01

We mapped Red-tailed Hawk (Buteo jamaicensis) territories in the Luquillo Experimental Forest (LEF) of Puerto Rico in 1998. We combined our 1998 data with that collected during previous studies of Red-tailed Hawks in the LEF to examine population numbers and spatial stability of territorial boundaries over a 26-yr period. We also investigated potential relationships between Red-tailed Hawk territory sizes and topographic and climatic factors. Mean size of 16 defended territories during 1998 was 124.3 ?? 12.0 ha, which was not significantly different from our calculations of mean territory sizes derived from data collected in 1974 and 1984. Aspect and slope influenced territory size with the smallest territories having high slope and easterly aspects. Territory size was small compared to that reported for other parts of the species' range. In addition, there was remarkably little temporal change in the spatial distribution, area, and boundaries of Red-tailed Hawk territories among the study periods. Further, there was substantial boundary overlap (21-27%) between defended territories among the different study periods. The temporal stability of the spatial distribution of Red-tailed Hawk territories in the study area leads us to believe the area might be at or near saturation.

Effects of weather on the abundance and distribution on populations of 103 breeding bird species across the United States

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.

A standard photomap of ovarian nurse cell chromosomes and inversion polymorphism in Anopheles beklemishevi.

PubMed

Artemov, Gleb N; Gordeev, Mikhail I; Kokhanenko, Alina A; Moskaev, Anton V; Velichevskaya, Alena I; Stegniy, Vladimir N; Sharakhov, Igor V; Sharakhova, Maria V

2018-03-27

Anopheles beklemishevi is a member of the Maculipennis group of malaria mosquitoes that has the most northern distribution among other members of the group. Although a cytogenetic map for the larval salivary gland chromosomes of this species has been developed, a high-quality standard cytogenetic photomap that enables genomics and population genetics studies of this mosquito at the adult stage is still lacking. In this study, a cytogenetic map for the polytene chromosomes of An. beklemishevi from ovarian nurse cells was developed using high-resolution digital imaging from field collected mosquitoes. PCR-amplified DNA probes for fluorescence in situ hybridization (FISH) were designed based on the genome of An. atroparvus. The DNA probe obtained by microdissection procedures from the breakpoint region was labelled in a DOP-PCR reaction. Population analysis was performed on 371 specimens collected in 18 locations. We report the development of a high-quality standard photomap for the polytene chromosomes from ovarian nurse cells of An. beklemishevi. To confirm the suitability of the map for physical mapping, several PCR-amplified probes were mapped to the chromosomes of An. beklemishevi using FISH. In addition, we identified and mapped DNA probes to flanking regions of the breakpoints of two inversions on chromosome X of this species. Inversion polymorphism was determined in 13 geographically distant populations of An. beklemishevi. Four polymorphic inversions were detected. The positions of common chromosomal inversions were indicated on the map. The study constructed a standard photomap for ovarian nurse cell chromosomes of An. beklemishevi and tested its suitability for physical genome mapping and population studies. Cytogenetic analysis determined inversion polymorphism in natural populations of An. beklemishevi related to this species' adaptation.

Metallothionein Gene Duplications and Metal Tolerance in Natural Populations of Drosophila melanogaster

PubMed Central

Maroni, G.; Wise, J.; Young, J. E.; Otto, E.

1987-01-01

A search for duplications of the Drosophila melanogaster metallothionein gene (Mtn) yielded numerous examples of this type of chromosomal rearrangement. These duplications are distributed widely—we found them in samples from four continents, and they are functional—larvae carrying Mtn duplications produce more Mtn RNA and tolerate increased cadmium and copper concentrations. Six different duplication types were characterized by restriction-enzyme analyses using probes from the Mtn region. The restriction maps show that in four cases the sequences, ranging in size between 2.2 and 6.0 kb, are arranged as direct, tandem repeats; in two other cases, this basic pattern is modified by the insertion of a putative transposable element into one of the repeated units. Duplications of the D. melanogaster metallothionein gene such as those that we found in natural populations may represent early stages in the evolution of a gene family. PMID:2828157

Mapping of plume deposits and surface composition on Enceladus

NASA Astrophysics Data System (ADS)

Nordheim, T. A.; Scipioni, F.; Cruikshank, D. P.; Clark, R. N.,; Hand, K. P.

2017-01-01

A major result of the Cassini mission was the discovery that the small mid-sized moon Enceladus is presently geological active[Dougherty et al., 2006; Porco et al., 2006; Spencer et al., 2006; Hansen et al., 2008]. This activity results in plumes of water vapor and ice emanating from a series of fractures ("Tiger Stripes") at the moon's South Pole. Some fraction of plume material escapes the moon's gravity and populates the E-ring as well as ultimately providing a source of fresh plasma in the Saturnian magnetosphere [Pontius and Hill, 2006; Kempf et al., 2010]. However, a significant portion of plume material is redeposited on Enceladus and thus provides a source of surface contaminants. By studying the near-infrared spectral signatures of these contaminants we may put new constraints on the composition of the plumes and, ultimately, their source, which is currently believed to be Enceladus's global sub-surface ocean [Iess et al., 2014]. Here we present preliminary results from our analysis of observations from the Visual and Infrared Mapping Spectrometer (VIMS) [Brown et al., 2005] onboard Cassini and mapping of plume deposits across the surface of Enceladus. We have investigated the global variation of the water ice Fresnel peak at 3.1 μm, which may be used as an indicator of ice crystallinity [Hansen & McCord, 2004; Jaumann et al., 2008; Newman et al., 2008]. We have also investigated the slope of the 1.11-2.25 μm spectral region, which serves as an indicator of water ice grain size for small grains (< 100 μm) as well as the presence of contaminants [e.g. Filacchione et al., 2010]. Finally, we have identified and mapped an absorption feature centered at 3.25 μm that may be related to organic contaminants, represented by the band depth of the fundamental C-H stretch [e.g. Cruikshank et al., 2014; Scipioni et al., 2014].

Uncertainty in Population Estimates for Endangered Animals and Improving the Recovery Process.

PubMed

Haines, Aaron M; Zak, Matthew; Hammond, Katie; Scott, J Michael; Goble, Dale D; Rachlow, Janet L

2013-08-13

United States recovery plans contain biological information for a species listed under the Endangered Species Act and specify recovery criteria to provide basis for species recovery. The objective of our study was to evaluate whether recovery plans provide uncertainty (e.g., variance) with estimates of population size. We reviewed all finalized recovery plans for listed terrestrial vertebrate species to record the following data: (1) if a current population size was given, (2) if a measure of uncertainty or variance was associated with current estimates of population size and (3) if population size was stipulated for recovery. We found that 59% of completed recovery plans specified a current population size, 14.5% specified a variance for the current population size estimate and 43% specified population size as a recovery criterion. More recent recovery plans reported more estimates of current population size, uncertainty and population size as a recovery criterion. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty compared to reptiles and amphibians. We suggest the use of calculating minimum detectable differences to improve confidence when delisting endangered animals and we identified incentives for individuals to get involved in recovery planning to improve access to quantitative data.

Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus.

PubMed

Wang, Xiaodong; Wang, Hao; Long, Yan; Li, Dianrong; Yin, Yongtai; Tian, Jianhua; Chen, Li; Liu, Liezhao; Zhao, Weiguo; Zhao, Yajun; Yu, Longjiang; Li, Maoteng

2013-01-01

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.

Identification of QTLs Associated with Oil Content in a High-Oil Brassica napus Cultivar and Construction of a High-Density Consensus Map for QTLs Comparison in B. napus

PubMed Central

Long, Yan; Li, Dianrong; Yin, Yongtai; Tian, Jianhua; Chen, Li; Liu, Liezhao; Zhao, Weiguo; Zhao, Yajun; Yu, Longjiang; Li, Maoteng

2013-01-01

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between ‘KenC-8’ and ‘N53-2’, two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64–17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus. PMID:24312482

The demographic consequences of growing older and bigger in oyster populations.

PubMed

Moore, Jacob L; Lipcius, Romuald N; Puckett, Brandon; Schreiber, Sebastian J

2016-10-01

Structured population models, particularly size- or age-structured, have a long history of informing conservation and natural resource management. While size is often easier to measure than age and is the focus of many management strategies, age-structure can have important effects on population dynamics that are not captured in size-only models. However, relatively few studies have included the simultaneous effects of both age- and size-structure. To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age- and size-structured IPM, using a population of Crassostrea gigas oysters in the northeastern Pacific Ocean. We analyzed sensitivity of model results across values of local retention that give populations decreasing in size to populations increasing in size. We found that age- and size-structured models yielded the best fit to the demographic data and provided more reliable results about long-term demography. Elasticity analysis showed that population growth rate was most sensitive to changes in the survival of both large (>175 mm shell length) and small (<75 mm shell length) oysters, indicating that a maximum size limit, in addition to a minimum size limit, could be an effective strategy for maintaining a sustainable population. In contrast, the purely size-structured model did not detect the importance of large individuals. Finally, patterns in stable age and stable size distributions differed between populations decreasing in size due to limited local retention and populations increasing in size due to high local retention. These patterns can be used to determine population status and restoration success. The methodology described here provides general insight into the necessity of including both age- and size-structure into modeling frameworks when using population models to inform restoration and management decisions. © 2016 by the Ecological Society of America.

Mapping cell populations in flow cytometry data for cross‐sample comparison using the Friedman–Rafsky test statistic as a distance measure

PubMed Central

Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu

2015-01-01

Abstract Flow cytometry (FCM) is a fluorescence‐based single‐cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap‐FR, a novel method for cell population mapping across FCM samples. FlowMap‐FR is based on the Friedman–Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap‐FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap‐FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap‐FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap‐FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap‐FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback–Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL‐distance in distinguishing equivalent from nonequivalent cell populations. FlowMap‐FR was also employed as a distance metric to match cell populations delineated by manual gating across 30 FCM samples from a benchmark FlowCAP data set. An F‐measure of 0.88 was obtained, indicating high precision and recall of the FR‐based population matching results. FlowMap‐FR has been implemented as a standalone R/Bioconductor package so that it can be easily incorporated into current FCM data analytical workflows. © 2015 International Society for Advancement of Cytometry PMID:26274018

Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones.

PubMed

Clément, D; Lanaud, C; Sabau, X; Fouet, O; Le Cunff, L; Ruiz, E; Risterucci, A M; Glaszmann, J C; Piffanelli, P

2004-05-01

We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

Novel 3D ultrasound image-based biomarkers based on a feature selection from a 2D standardized vessel wall thickness map: a tool for sensitive assessment of therapies for carotid atherosclerosis

NASA Astrophysics Data System (ADS)

Chiu, Bernard; Li, Bing; Chow, Tommy W. S.

2013-09-01

With the advent of new therapies and management strategies for carotid atherosclerosis, there is a parallel need for measurement tools or biomarkers to evaluate the efficacy of these new strategies. 3D ultrasound has been shown to provide reproducible measurements of plaque area/volume and vessel wall volume. However, since carotid atherosclerosis is a focal disease that predominantly occurs at bifurcations, biomarkers based on local plaque change may be more sensitive than global volumetric measurements in demonstrating efficacy of new therapies. The ultimate goal of this paper is to develop a biomarker that is based on the local distribution of vessel-wall-plus-plaque thickness change (VWT-Change) that has occurred during the course of a clinical study. To allow comparison between different treatment groups, the VWT-Change distribution of each subject must first be mapped to a standardized domain. In this study, we developed a technique to map the 3D VWT-Change distribution to a 2D standardized template. We then applied a feature selection technique to identify regions on the 2D standardized map on which subjects in different treatment groups exhibit greater difference in VWT-Change. The proposed algorithm was applied to analyse the VWT-Change of 20 subjects in a placebo-controlled study of the effect of atorvastatin (Lipitor). The average VWT-Change for each subject was computed (i) over all points in the 2D map and (ii) over feature points only. For the average computed over all points, 97 subjects per group would be required to detect an effect size of 25% that of atorvastatin in a six-month study. The sample size is reduced to 25 subjects if the average were computed over feature points only. The introduction of this sensitive quantification technique for carotid atherosclerosis progression/regression would allow many proof-of-principle studies to be performed before a more costly and longer study involving a larger population is held to confirm the treatment efficacy.

Big Bang Bifurcation Analysis and Allee Effect in Generic Growth Functions

NASA Astrophysics Data System (ADS)

Leonel Rocha, J.; Taha, Abdel-Kaddous; Fournier-Prunaret, D.

2016-06-01

The main purpose of this work is to study the dynamics and bifurcation properties of generic growth functions, which are defined by the population size functions of the generic growth equation. This family of unimodal maps naturally incorporates a principal focus of ecological and biological research: the Allee effect. The analysis of this kind of extinction phenomenon allows to identify a class of Allee’s functions and characterize the corresponding Allee’s effect region and Allee’s bifurcation curve. The bifurcation analysis is founded on the performance of fold and flip bifurcations. The dynamical behavior is rich with abundant complex bifurcation structures, the big bang bifurcations of the so-called “box-within-a-box” fractal type being the most outstanding. Moreover, these bifurcation cascades converge to different big bang bifurcation curves with distinct kinds of boxes, where for the corresponding parameter values several attractors are associated. To the best of our knowledge, these results represent an original contribution to clarify the big bang bifurcation analysis of continuous 1D maps.

TOGA COARE Satellite data summaries available on the World Wide Web

NASA Technical Reports Server (NTRS)

Chen, S. S.; Houze, R. A., Jr.; Mapes, B. E.; Brodzick, S. R.; Yutler, S. E.

1995-01-01

Satellite data summary images and analysis plots from the Tropical Ocean Global Atmosphere Coupled Ocean-Atmosphere Response Experiment (TOGA COARE), which were initially prepared in the field at the Honiara Operations Center, are now available on the Internet via World Wide Web browsers such as Mosaic. These satellite data summaries consist of products derived from the Japanese Geosynchronous Meteorological Satellite IR data: a time-size series of the distribution of contiguous cold cloudiness areas, weekly percent high cloudiness (PHC) maps, and a five-month time-longitudinal diagram illustrating the zonal motion of large areas of cold cloudiness. The weekly PHC maps are overlaid with weekly mean 850-hPa wind calculated from the European Centre for Medium-Range Weather Forecasts (ECMWF) global analysis field and can be viewed as an animation loop. These satellite summaries provide an overview of spatial and temporal variabilities of the cloud population and a large-scale context for studies concerning specific processes of various components of TOGA COARE.

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era.

PubMed

Gao, Feng; Ming, Chen; Hu, Wangjie; Li, Haipeng

2016-06-01

Genetic recombination is a very important evolutionary mechanism that mixes parental haplotypes and produces new raw material for organismal evolution. As a result, information on recombination rates is critical for biological research. In this paper, we introduce a new extremely fast open-source software package (FastEPRR) that uses machine learning to estimate recombination rate [Formula: see text] (=[Formula: see text]) from intraspecific DNA polymorphism data. When [Formula: see text] and the number of sampled diploid individuals is large enough ([Formula: see text]), the variance of [Formula: see text] remains slightly smaller than that of [Formula: see text] The new estimate [Formula: see text] (calculated by averaging [Formula: see text] and [Formula: see text]) has the smallest variance of all cases. When estimating [Formula: see text], the finite-site model was employed to analyze cases with a high rate of recurrent mutations, and an additional method is proposed to consider the effect of variable recombination rates within windows. Simulations encompassing a wide range of parameters demonstrate that different evolutionary factors, such as demography and selection, may not increase the false positive rate of recombination hotspots. Overall, accuracy of FastEPRR is similar to the well-known method, LDhat, but requires far less computation time. Genetic maps for each human population (YRI, CEU, and CHB) extracted from the 1000 Genomes OMNI data set were obtained in less than 3 d using just a single CPU core. The Pearson Pairwise correlation coefficient between the [Formula: see text] and [Formula: see text] maps is very high, ranging between 0.929 and 0.987 at a 5-Mb scale. Considering that sample sizes for these kinds of data are increasing dramatically with advances in next-generation sequencing technologies, FastEPRR (freely available at http://www.picb.ac.cn/evolgen/) is expected to become a widely used tool for establishing genetic maps and studying recombination hotspots in the population genomic era. Copyright © 2016 Gao et al.

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome.

PubMed

Zhang, Li; Luo, Jiang-Tao; Hao, Ming; Zhang, Lian-Quan; Yuan, Zhong-Wei; Yan, Ze-Hong; Liu, Ya-Xi; Zhang, Bo; Liu, Bao-Long; Liu, Chun-Ji; Zhang, Huai-Gang; Zheng, You-Liang; Liu, Deng-Cai

2012-08-13

A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.

Numerical equilibrium analysis for structured consumer resource models.

PubMed

de Roos, A M; Diekmann, O; Getto, P; Kirkilionis, M A

2010-02-01

In this paper, we present methods for a numerical equilibrium and stability analysis for models of a size structured population competing for an unstructured resource. We concentrate on cases where two model parameters are free, and thus existence boundaries for equilibria and stability boundaries can be defined in the (two-parameter) plane. We numerically trace these implicitly defined curves using alternatingly tangent prediction and Newton correction. Evaluation of the maps defining the curves involves integration over individual size and individual survival probability (and their derivatives) as functions of individual age. Such ingredients are often defined as solutions of ODE, i.e., in general only implicitly. In our case, the right-hand sides of these ODE feature discontinuities that are caused by an abrupt change of behavior at the size where juveniles are assumed to turn adult. So, we combine the numerical solution of these ODE with curve tracing methods. We have implemented the algorithms for "Daphnia consuming algae" models in C-code. The results obtained by way of this implementation are shown in the form of graphs.

The aquatic turtle assemblage inhabiting a highly altered landscape in southeast Missouri

USGS Publications Warehouse

Glorioso, Brad M.; Vaughn, Allison J.; Waddle, J. Hardin

2010-01-01

Turtles are linked to energetic food webs as both consumers of plants and animals and prey for many species. Turtle biomass in freshwater systems can be an order of magnitude greater than that of endotherms. Therefore, declines in freshwater turtle populations can change energy transfer in freshwater systems. Here we report on a mark–recapture study at a lake and adjacent borrow pit in a relict tract of bottomland hardwood forest in the Mississippi River floodplain in southeast Missouri, which was designed to gather baseline data, including sex ratio, size structure, and population size, density, and biomass, for the freshwater turtle population. Using a variety of capture methods, we captured seven species of freshwater turtles (snapping turtle Chelydra serpentina; red-eared slider Trachemys scripta; southern painted turtle Chrysemys dorsalis; river cooter Pseudemys concinna; false map turtle Graptemys pseudogeographica; eastern musk turtle Sternotherus odoratus; spiny softshell Apalone spinifera) comprising four families (Chelydridae, Emydidae, Kinosternidae, Trinoychidae). With the exception of red-eared sliders, nearly all individuals captured were adults. Most turtles were captured by baited hoop-nets, and this was the only capture method that caught all seven species. The unbaited fyke net was very successful in the borrow pit, but only captured four of the seven species. Basking traps and deep-water crawfish nets had minimal success. Red-eared sliders had the greatest population estimate (2,675), density (205/ha), and biomass (178 kg/ha). Two species exhibited a sex-ratio bias: snapping turtles C. serpentina in favor of males, and spiny softshells A. spinifera in favor of females.

Sustainable Sizing.

PubMed

Robinette, Kathleen M; Veitch, Daisy

2016-08-01

To provide a review of sustainable sizing practices that reduce waste, increase sales, and simultaneously produce safer, better fitting, accommodating products. Sustainable sizing involves a set of methods good for both the environment (sustainable environment) and business (sustainable business). Sustainable sizing methods reduce (1) materials used, (2) the number of sizes or adjustments, and (3) the amount of product unsold or marked down for sale. This reduces waste and cost. The methods can also increase sales by fitting more people in the target market and produce happier, loyal customers with better fitting products. This is a mini-review of methods that result in more sustainable sizing practices. It also reviews and contrasts current statistical and modeling practices that lead to poor fit and sizing. Fit-mapping and the use of cases are two excellent methods suited for creating sustainable sizing, when real people (vs. virtual people) are used. These methods are described and reviewed. Evidence presented supports the view that virtual fitting with simulated people and products is not yet effective. Fit-mapping and cases with real people and actual products result in good design and products that are fit for person, fit for purpose, with good accommodation and comfortable, optimized sizing. While virtual models have been shown to be ineffective for predicting or representing fit, there is an opportunity to improve them by adding fit-mapping data to the models. This will require saving fit data, product data, anthropometry, and demographics in a standardized manner. For this success to extend to the wider design community, the development of a standardized method of data collection for fit-mapping with a globally shared fit-map database is needed. It will enable the world community to build knowledge of fit and accommodation and generate effective virtual fitting for the future. A standardized method of data collection that tests products' fit methodically and quantitatively will increase our predictive power to determine fit and accommodation, thereby facilitating improved, effective design. These methods apply to all products people wear, use, or occupy. © 2016, Human Factors and Ergonomics Society.

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data

PubMed Central

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest. PMID:26958859

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data.

PubMed

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.

An Appraisal of Female Sex Work in Nigeria - Implications for Designing and Scaling Up HIV Prevention Programmes

PubMed Central

Ikpeazu, Akudo; Momah-Haruna, Amaka; Madu Mari, Baba; Thompson, Laura H.; Ogungbemi, Kayode; Daniel, Uduak; Aboki, Hafsatu; Isac, Shajy; Gorgens, Marelize; Mziray, Elizabeth; Njie, Ndella; Akala, Francisca Ayodeji; Emmanuel, Faran; Odek, Willis Omondi; Blanchard, James F.

2014-01-01

Background The HIV epidemic in Nigeria is complex with diverse factors driving the epidemic. Accordingly, Nigeria's National Agency for the Control of AIDS is coordinating a large-scale initiative to conduct HIV epidemic appraisals across all states. These appraisals will help to better characterize the drivers of the epidemic and ensure that the HIV prevention programmes match the local epidemic context, with resources allocated to interventions that have the greatest impact locally. Currently, the mapping and size estimation of Female Sex Workers (FSWs) - a major component of the appraisal has been completed in seven states. These states are using the data generated to plan, prioritize and scale-up sub-national HIV prevention programmes. Methodology It involved a two-level process of identifying and validating locations where FSWs solicit and/or meet clients (“hotspots”). In the first level, secondary key informants were interviewed to collect information about the geographic location and description of the hotspots. For the second level, FSWs were interviewed at each hotspot and information on population size estimates, typologies and operational dynamics of the FSWs were collected. Results Across the seven states, a total of 17,266 secondary key informants and 5,732 FSWs were interviewed. 10,233 hotspots were identified with an estimated 126,489 FSWs ranging from 5,920 in Anambra to 46,691 in Lagos. The most common hotspots were bars/nightclubs (30%), hotels/lodges (29.6%), streets (16.6%), and brothels (14.6%). Furthermore, the population density of FSWs (per thousand adult men) across the states ranged from 2 in Anambra to 17 in the Federal Capital Territory. Conclusion FSW populations in Nigeria are large and diverse, with substantial differences between and within states. Improved understanding of the location, population size, density, organizational typologies and clients of sex work has informed and is central to Nigeria's planning process for scaling up focused HIV prevention programmes. PMID:25118691

An appraisal of female sex work in Nigeria--implications for designing and scaling up HIV prevention programmes.

PubMed

Ikpeazu, Akudo; Momah-Haruna, Amaka; Madu Mari, Baba; Thompson, Laura H; Ogungbemi, Kayode; Daniel, Uduak; Aboki, Hafsatu; Isac, Shajy; Gorgens, Marelize; Mziray, Elizabeth; Njie, Ndella; Akala, Francisca Ayodeji; Emmanuel, Faran; Odek, Willis Omondi; Blanchard, James F

2014-01-01

The HIV epidemic in Nigeria is complex with diverse factors driving the epidemic. Accordingly, Nigeria's National Agency for the Control of AIDS is coordinating a large-scale initiative to conduct HIV epidemic appraisals across all states. These appraisals will help to better characterize the drivers of the epidemic and ensure that the HIV prevention programmes match the local epidemic context, with resources allocated to interventions that have the greatest impact locally. Currently, the mapping and size estimation of Female Sex Workers (FSWs)--a major component of the appraisal has been completed in seven states. These states are using the data generated to plan, prioritize and scale-up sub-national HIV prevention programmes. It involved a two-level process of identifying and validating locations where FSWs solicit and/or meet clients ("hotspots"). In the first level, secondary key informants were interviewed to collect information about the geographic location and description of the hotspots. For the second level, FSWs were interviewed at each hotspot and information on population size estimates, typologies and operational dynamics of the FSWs were collected. Across the seven states, a total of 17,266 secondary key informants and 5,732 FSWs were interviewed. 10,233 hotspots were identified with an estimated 126,489 FSWs ranging from 5,920 in Anambra to 46,691 in Lagos. The most common hotspots were bars/nightclubs (30%), hotels/lodges (29.6%), streets (16.6%), and brothels (14.6%). Furthermore, the population density of FSWs (per thousand adult men) across the states ranged from 2 in Anambra to 17 in the Federal Capital Territory. FSW populations in Nigeria are large and diverse, with substantial differences between and within states. Improved understanding of the location, population size, density, organizational typologies and clients of sex work has informed and is central to Nigeria's planning process for scaling up focused HIV prevention programmes.

An Atlas of ShakeMaps and population exposure catalog for earthquake loss modeling

USGS Publications Warehouse

Allen, T.I.; Wald, D.J.; Earle, P.S.; Marano, K.D.; Hotovec, A.J.; Lin, K.; Hearne, M.G.

2009-01-01

We present an Atlas of ShakeMaps and a catalog of human population exposures to moderate-to-strong ground shaking (EXPO-CAT) for recent historical earthquakes (1973-2007). The common purpose of the Atlas and exposure catalog is to calibrate earthquake loss models to be used in the US Geological Survey's Prompt Assessment of Global Earthquakes for Response (PAGER). The full ShakeMap Atlas currently comprises over 5,600 earthquakes from January 1973 through December 2007, with almost 500 of these maps constrained-to varying degrees-by instrumental ground motions, macroseismic intensity data, community internet intensity observations, and published earthquake rupture models. The catalog of human exposures is derived using current PAGER methodologies. Exposure to discrete levels of shaking intensity is obtained by correlating Atlas ShakeMaps with a global population database. Combining this population exposure dataset with historical earthquake loss data, such as PAGER-CAT, provides a useful resource for calibrating loss methodologies against a systematically-derived set of ShakeMap hazard outputs. We illustrate two example uses for EXPO-CAT; (1) simple objective ranking of country vulnerability to earthquakes, and; (2) the influence of time-of-day on earthquake mortality. In general, we observe that countries in similar geographic regions with similar construction practices tend to cluster spatially in terms of relative vulnerability. We also find little quantitative evidence to suggest that time-of-day is a significant factor in earthquake mortality. Moreover, earthquake mortality appears to be more systematically linked to the population exposed to severe ground shaking (Modified Mercalli Intensity VIII+). Finally, equipped with the full Atlas of ShakeMaps, we merge each of these maps and find the maximum estimated peak ground acceleration at any grid point in the world for the past 35 years. We subsequently compare this "composite ShakeMap" with existing global hazard models, calculating the spatial area of the existing hazard maps exceeded by the combined ShakeMap ground motions. In general, these analyses suggest that existing global, and regional, hazard maps tend to overestimate hazard. Both the Atlas of ShakeMaps and EXPO-CAT have many potential uses for examining earthquake risk and epidemiology. All of the datasets discussed herein are available for download on the PAGER Web page ( http://earthquake.usgs.gov/ eqcenter/pager/prodandref/ ). ?? 2009 Springer Science+Business Media B.V.

Mapping Urban Risk: Flood Hazards, Race, & Environmental Justice In New York”

PubMed Central

Maantay, Juliana; Maroko, Andrew

2009-01-01

This paper demonstrates the importance of disaggregating population data aggregated by census tracts or other units, for more realistic population distribution/location. A newly-developed mapping method, the Cadastral-based Expert Dasymetric System (CEDS), calculates population in hyper-heterogeneous urban areas better than traditional mapping techniques. A case study estimating population potentially impacted by flood hazard in New York City compares the impacted population determined by CEDS with that derived by centroid-containment method and filtered areal weighting interpolation. Compared to CEDS, 37 percent and 72 percent fewer people are estimated to be at risk from floods city-wide, using conventional areal weighting of census data, and centroid-containment selection, respectively. Undercounting of impacted population could have serious implications for emergency management and disaster planning. Ethnic/racial populations are also spatially disaggregated to determine any environmental justice impacts with flood risk. Minorities are disproportionately undercounted using traditional methods. Underestimating more vulnerable sub-populations impairs preparedness and relief efforts. PMID:20047020

Introgression Makes Waves in Inferred Histories of Effective Population Size.

PubMed

Hawks, John

2017-01-01

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent "wave" of larger effective population sizes, found in both African and non-African populations, that appears to reflect events prior to the last 100,000 years. I carried out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have visible effects on the inference of effective population size.

Experimental colitis is exacerbated by concomitant infection with Mycobacterium avium ssp. paratuberculosis.

PubMed

Suwandi, Abdulhadi; Bargen, Imke; Roy, Bishnudeo; Pils, Marina C; Krey, Martina; Zur Lage, Susanne; Basler, Tina; Rohde, Manfred; Falk, Christine S; Hornef, Mathias W; Goethe, Ralph; Weiss, Siegfried

2014-11-01

Crohn's disease (CD) is a chronic inflammatory disorder of the human gastrointestinal tract. Although genetic, immunological, environmental, and bacterial factors have been implicated, the pathogenesis is incompletely understood. The histopathological appearance of CD strikingly resembles Johne's disease, a ruminant inflammatory bowel disease, caused by Mycobacterium avium ssp. paratuberculosis (MAP), but a causative role of MAP in CD has not been established. In this work, we hypothesized that MAP might exacerbate an already existing intestinal disease. We combined dextran sulfate sodium (DSS)-induced colitis with MAP infection in mice and monitored the immune response and bacterial count in different organs. An increased size of liver and spleen was observed in DSS-treated and MAP-infected animals (DSS + MAP) as compared with DSS-treated uninfected (DSS + PBS) mice. Similarly, DSS treatment increased the number and size of MAP-induced liver granulomas and enhanced the MAP counts in enteric tissue. MAP infection in turn delayed the mucosal healing of DSS-induced tissue damage. Finally, high numbers of MAP were found in mesenteric fat tissue causing large granuloma and necrotic regions. Taken together, we present an in vivo model to study the role of MAP infection in CD. Our results confirm the hypothesis that MAP is able to exacerbate existing intestinal inflammation.

Local extinction and recolonization, species effective population size, and modern human origins.

PubMed

Eller, Elise; Hawks, John; Relethford, John H

2004-10-01

A primary objection from a population genetics perspective to a multiregional model of modern human origins is that the model posits a large census size, whereas genetic data suggest a small effective population size. The relationship between census size and effective size is complex, but arguments based on an island model of migration show that if the effective population size reflects the number of breeding individuals and the effects of population subdivision, then an effective population size of 10,000 is inconsistent with the census size of 500,000 to 1,000,000 that has been suggested by archeological evidence. However, these models have ignored the effects of population extinction and recolonization, which increase the expected variance among demes and reduce the inbreeding effective population size. Using models developed for population extinction and recolonization, we show that a large census size consistent with the multiregional model can be reconciled with an effective population size of 10,000, but genetic variation among demes must be high, reflecting low interdeme migration rates and a colonization process that involves a small number of colonists or kin-structured colonization. Ethnographic and archeological evidence is insufficient to determine whether such demographic conditions existed among Pleistocene human populations, and further work needs to be done. More realistic models that incorporate isolation by distance and heterogeneity in extinction rates and effective deme sizes also need to be developed. However, if true, a process of population extinction and recolonization has interesting implications for human demographic history.

A first AFLP-Based Genetic Linkage Map for Brine Shrimp Artemia franciscana and Its Application in Mapping the Sex Locus

PubMed Central

De Vos, Stephanie; Bossier, Peter; Van Stappen, Gilbert; Vercauteren, Ilse; Sorgeloos, Patrick; Vuylsteke, Marnik

2013-01-01

We report on the construction of sex-specific linkage maps, the identification of sex-linked markers and the genome size estimation for the brine shrimp Artemia franciscana. Overall, from the analysis of 433 AFLP markers segregating in a 112 full-sib family we identified 21 male and 22 female linkage groups (2n = 42), covering 1,041 and 1,313 cM respectively. Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage map. Eight sex-linked AFLP marker alleles were inherited from the female parent, supporting the hypothesis of a WZ–ZZ sex-determining system. The haploid Artemia genome size was estimated to 0.93 Gb by flow cytometry. The produced Artemia linkage maps provide the basis for further fine mapping and exploring of the sex-determining region and are a possible marker resource for mapping genomic loci underlying phenotypic differences among Artemia species. PMID:23469207

Genetic Diversity in Introduced Populations with an Allee Effect

PubMed Central

Wittmann, Meike J.; Gabriel, Wilfried; Metzler, Dirk

2014-01-01

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations. PMID:25009147

Mapping, fine mapping, and molecular dissection of quantitative trait Loci in domestic animals.

PubMed

Georges, Michel

2007-01-01

Artificial selection has created myriad breeds of domestic animals, each characterized by unique phenotypes pertaining to behavior, morphology, physiology, and disease. Most domestic animal populations share features with isolated founder populations, making them well suited for positional cloning. Genome sequences are now available for most domestic species, and with them a panoply of tools including high-density single-nucleotide polymorphism panels. As a result, domestic animal populations are becoming invaluable resources for studying the molecular architecture of complex traits and of adaptation. Here we review recent progress and issues in the positional identification of genes underlying complex traits in domestic animals. As many phenotypes studied in animals are quantitative, we focus on mapping, fine mapping, and cloning of quantitative trait loci.

Population structure of the hydrocoral Millepora platyphylla in habitats experiencing different flow regimes in Moorea, French Polynesia

PubMed Central

Mercière, Alexandre; Vermeij, Mark J. A.; Planes, Serge

2017-01-01

While the fire coral Millepora platyphylla is an important component of Indo-Pacific reefs, where it thrives in a wide range of environments, the ecological and biological processes driving its distribution and population structure are not well understood. Here, we quantified this species’ population structure in five habitats with contrasting hydrodynamic regimes in Moorea, French Polynesia; two in the fore reef: mid and upper slopes, and three in the lagoon: back, fringing and patch reefs. A total of 3651 colonies of fire corals were mapped and measured over 45,000 m2 of surveyed reef. Due to the species’ sensitivity to fragmentation in response to strong water movement, hydrodynamic conditions (e.g. waves, pass and lagoonal circulation) corresponded to marked differences in colony size distributions, morphology and recruitment dynamics among habitats. The size structure varied among reef habitats with higher proportions of larger colonies in calm nearshore reefs (fringing and patch reefs), while populations were dominated by smaller colonies in the exposed fore reefs. The highest densities of fire corals were recorded in fore reef habitats (0.12–0.20 n.m-2) where the proportion of recruits and juveniles was higher at mid slope populations (49.3%) than on the upper slope near where waves break (29.0%). In the latter habitat, most colonies grew as vertical sheets on encrusting bases making them more vulnerable to colony fragmentation, whereas fire corals were encrusting or massive in all other habitats. The lowest densities of M. platyphylla occurred in lagoonal habitats (0.02–0.04 n.m-2) characterized by a combination of low water movement and other physical and biological stressors. This study reports the first evidence of population structure of fire corals in two common reef environments and illustrates the importance of water flow in driving population dynamic processes of these reef-building species. PMID:28273119

Population structure of the hydrocoral Millepora platyphylla in habitats experiencing different flow regimes in Moorea, French Polynesia.

PubMed

Dubé, Caroline E; Mercière, Alexandre; Vermeij, Mark J A; Planes, Serge

2017-01-01

While the fire coral Millepora platyphylla is an important component of Indo-Pacific reefs, where it thrives in a wide range of environments, the ecological and biological processes driving its distribution and population structure are not well understood. Here, we quantified this species' population structure in five habitats with contrasting hydrodynamic regimes in Moorea, French Polynesia; two in the fore reef: mid and upper slopes, and three in the lagoon: back, fringing and patch reefs. A total of 3651 colonies of fire corals were mapped and measured over 45,000 m2 of surveyed reef. Due to the species' sensitivity to fragmentation in response to strong water movement, hydrodynamic conditions (e.g. waves, pass and lagoonal circulation) corresponded to marked differences in colony size distributions, morphology and recruitment dynamics among habitats. The size structure varied among reef habitats with higher proportions of larger colonies in calm nearshore reefs (fringing and patch reefs), while populations were dominated by smaller colonies in the exposed fore reefs. The highest densities of fire corals were recorded in fore reef habitats (0.12-0.20 n.m-2) where the proportion of recruits and juveniles was higher at mid slope populations (49.3%) than on the upper slope near where waves break (29.0%). In the latter habitat, most colonies grew as vertical sheets on encrusting bases making them more vulnerable to colony fragmentation, whereas fire corals were encrusting or massive in all other habitats. The lowest densities of M. platyphylla occurred in lagoonal habitats (0.02-0.04 n.m-2) characterized by a combination of low water movement and other physical and biological stressors. This study reports the first evidence of population structure of fire corals in two common reef environments and illustrates the importance of water flow in driving population dynamic processes of these reef-building species.

Noise pollution mapping approach and accuracy on landscape scales.

PubMed

Iglesias Merchan, Carlos; Diaz-Balteiro, Luis

2013-04-01

Noise mapping allows the characterization of environmental variables, such as noise pollution or soundscape, depending on the task. Strategic noise mapping (as per Directive 2002/49/EC, 2002) is a tool intended for the assessment of noise pollution at the European level every five years. These maps are based on common methods and procedures intended for human exposure assessment in the European Union that could be also be adapted for assessing environmental noise pollution in natural parks. However, given the size of such areas, there could be an alternative approach to soundscape characterization rather than using human noise exposure procedures. It is possible to optimize the size of the mapping grid used for such work by taking into account the attributes of the area to be studied and the desired outcome. This would then optimize the mapping time and the cost. This type of optimization is important in noise assessment as well as in the study of other environmental variables. This study compares 15 models, using different grid sizes, to assess the accuracy of the noise mapping of the road traffic noise at a landscape scale, with respect to noise and landscape indicators. In a study area located in the Manzanares High River Basin Regional Park in Spain, different accuracy levels (Kappa index values from 0.725 to 0.987) were obtained depending on the terrain and noise source properties. The time taken for the calculations and the noise mapping accuracy results reveal the potential for setting the map resolution in line with decision-makers' criteria and budget considerations. Copyright © 2013 Elsevier B.V. All rights reserved.

Mapping Vulnerability to Disasters in Latin America and the Caribbean, 1900-2007

USGS Publications Warehouse

Maynard-Ford, Miriam C.; Phillips, Emily C.; Chirico, Peter G.

2008-01-01

The vulnerability of a population and its infrastructure to disastrous events is a factor of both the probability of a hazardous event occurring and the community's ability to cope with the resulting impacts. Therefore, the ability to accurately identify vulnerable populations and places in order to prepare for future hazards is of critical importance for disaster mitigation programs. This project created maps of higher spatial resolution of vulnerability to disaster in Latin America and the Caribbean from 1900 to 2007 by mapping disaster data by first-level administrative boundaries with the objective of identifying geographic trends in regional occurrences of disasters and vulnerable populations. The method of mapping by administrative level is an improvement on displaying and analyzing disasters at the country level and shows the relative intensity of vulnerability within and between countries in the region. Disaster mapping at the country level produces only a basic view of which countries experience various types of natural disasters. Through disaggregation, the data show which geographic areas of these countries, including populated areas, are historically most susceptible to different hazard types.

Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population

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

Escamilla, M.A.; Reus, V.I.; Smith, L.B.

1996-05-31

Linkage disequilibrium (LD) analysis provides a powerful means for screening the genome to map the location of disease genes, such as those for bipolar disorder (BP). As described in this paper, the population of the Central Valley of Costa Rica, which is descended from a small number of founders, should be suitable for LD mapping; this assertion is supported by reconstruction of extended haplotypes shared by distantly related individuals in this population suffering low-frequency hearing loss (LFHL1), which has previously been mapped by linkage analysis. A sampling strategy is described for applying LD methods to map genes for BP, andmore » clinical and demographic characteristics of an initially collected sample are discussed. This sample will provide a complement to a previously collected set of Costa Rican BP families which is under investigation using standard linkage analysis. 42 refs., 4 figs., 2 tabs.« less

A New Material Mapping Procedure for Quantitative Computed Tomography-Based, Continuum Finite Element Analyses of the Vertebra

PubMed Central

Unnikrishnan, Ginu U.; Morgan, Elise F.

2011-01-01

Inaccuracies in the estimation of material properties and errors in the assignment of these properties into finite element models limit the reliability, accuracy, and precision of quantitative computed tomography (QCT)-based finite element analyses of the vertebra. In this work, a new mesh-independent, material mapping procedure was developed to improve the quality of predictions of vertebral mechanical behavior from QCT-based finite element models. In this procedure, an intermediate step, called the material block model, was introduced to determine the distribution of material properties based on bone mineral density, and these properties were then mapped onto the finite element mesh. A sensitivity study was first conducted on a calibration phantom to understand the influence of the size of the material blocks on the computed bone mineral density. It was observed that varying the material block size produced only marginal changes in the predictions of mineral density. Finite element (FE) analyses were then conducted on a square column-shaped region of the vertebra and also on the entire vertebra in order to study the effect of material block size on the FE-derived outcomes. The predicted values of stiffness for the column and the vertebra decreased with decreasing block size. When these results were compared to those of a mesh convergence analysis, it was found that the influence of element size on vertebral stiffness was less than that of the material block size. This mapping procedure allows the material properties in a finite element study to be determined based on the block size required for an accurate representation of the material field, while the size of the finite elements can be selected independently and based on the required numerical accuracy of the finite element solution. The mesh-independent, material mapping procedure developed in this study could be particularly helpful in improving the accuracy of finite element analyses of vertebroplasty and spine metastases, as these analyses typically require mesh refinement at the interfaces between distinct materials. Moreover, the mapping procedure is not specific to the vertebra and could thus be applied to many other anatomic sites. PMID:21823740

An integrated chromosome map of microsatellite markers and inversion breakpoints for an Asian malaria mosquito, Anopheles stephensi.

PubMed

Kamali, Maryam; Sharakhova, Maria V; Baricheva, Elina; Karagodin, Dmitrii; Tu, Zhijian; Sharakhov, Igor V

2011-01-01

Anopheles stephensi is one of the major vectors of malaria in the Middle East and Indo-Pakistan subcontinent. Understanding the population genetic structure of malaria mosquitoes is important for developing adequate and successful vector control strategies. Commonly used markers for inferring anopheline taxonomic and population status include microsatellites and chromosomal inversions. Knowledge about chromosomal locations of microsatellite markers with respect to polymorphic inversions could be useful for better understanding a genetic structure of natural populations. However, fragments with microsatellites used in population genetic studies are usually too short for successful labeling and hybridization with chromosomes. We designed new primers for amplification of microsatellite loci identified in the A. stephensi genome sequenced with next-generation technologies. Twelve microsatellites were mapped to polytene chromosomes from ovarian nurse cells of A. stephensi using fluorescent in situ hybridization. All microsatellites hybridized to unique locations on autosomes, and 7 of them localized to the largest arm 2R. Ten microsatellites were mapped inside the previously described polymorphic chromosomal inversions, including 4 loci located inside the widespread inversion 2Rb. We analyzed microsatellite-based population genetic data available for A. stephensi in light of our mapping results. This study demonstrates that the chromosomal position of microsatellites may affect estimates of population genetic parameters and highlights the importance of developing physical maps for nonmodel organisms.

Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.

PubMed

Raghavan, Chitra; Mauleon, Ramil; Lacorte, Vanica; Jubay, Monalisa; Zaw, Hein; Bonifacio, Justine; Singh, Rakesh Kumar; Huang, B Emma; Leung, Hei

2017-06-07

Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations. Copyright © 2017 Raghavan et al.

Genetic structure in contemporary south Tyrolean isolated populations revealed by analysis of Y-chromosome, mtDNA, and Alu polymorphisms.

PubMed

Pichler, Irene; Mueller, Jakob C; Stefanov, Stefan A; De Grandi, Alessandro; Volpato, Claudia Beu; Pinggera, Gerd K; Mayr, Agnes; Ogriseg, Martin; Ploner, Franz; Meitinger, Thomas; Pramstaller, Peter P

2006-08-01

Most of the inhabitants of South Tyrol in the eastern Italian Alps can be considered isolated populations because of their physical separation by mountain barriers and their sociocultural heritage. We analyzed the genetic structure of South Tyrolean populations using three types of genetic markers: Y-chromosome, mitochondrial DNA (mtDNA), and autosomal Alu markers. Using random samples taken from the populations of Val Venosta, Val Pusteria, Val Isarco, Val Badia, and Val Gardena, we calculated genetic diversity within and among the populations. Microsatellite diversity and unique event polymorphism diversity (on the Y chromosome) were substantially lower in the Ladin-speaking population of Val Badia compared to the neighboring German-speaking populations. In contrast, the genetic diversity of mtDNA haplotypes was lowest for the upper Val Venosta and Val Pusteria. These data suggest a low effective population size, or little admixture, for the gene pool of the Ladin-speaking population from Val Badia. Interestingly, this is more pronounced for Ladin males than for Ladin females. For the pattern of genetic Alu variation, both Ladin samples (Val Gardena and Val Badia) are among the samples with the lowest diversity. An admixture analysis of one German-speaking valley (Val Venosta) indicates a relatively high genetic contribution of Ladin origin. The reduced genetic diversity and a high genetic differentiation in the Rhaetoroman- and German-speaking South Tyrolean populations may constitute an important basis for future medical genetic research and gene mapping studies in South Tyrol.

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

PubMed Central

2012-01-01

Background Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents. PMID:23126659

A high resolution spatial population database of Somalia for disease risk mapping.

PubMed

Linard, Catherine; Alegana, Victor A; Noor, Abdisalan M; Snow, Robert W; Tatem, Andrew J

2010-09-14

Millions of Somali have been deprived of basic health services due to the unstable political situation of their country. Attempts are being made to reconstruct the health sector, in particular to estimate the extent of infectious disease burden. However, any approach that requires the use of modelled disease rates requires reasonable information on population distribution. In a low-income country such as Somalia, population data are lacking, are of poor quality, or become outdated rapidly. Modelling methods are therefore needed for the production of contemporary and spatially detailed population data. Here land cover information derived from satellite imagery and existing settlement point datasets were used for the spatial reallocation of populations within census units. We used simple and semi-automated methods that can be implemented with free image processing software to produce an easily updatable gridded population dataset at 100 × 100 meters spatial resolution. The 2010 population dataset was matched to administrative population totals projected by the UN. Comparison tests between the new dataset and existing population datasets revealed important differences in population size distributions, and in population at risk of malaria estimates. These differences are particularly important in more densely populated areas and strongly depend on the settlement data used in the modelling approach. The results show that it is possible to produce detailed, contemporary and easily updatable settlement and population distribution datasets of Somalia using existing data. The 2010 population dataset produced is freely available as a product of the AfriPop Project and can be downloaded from: http://www.afripop.org.

A high resolution spatial population database of Somalia for disease risk mapping

PubMed Central

2010-01-01

Background Millions of Somali have been deprived of basic health services due to the unstable political situation of their country. Attempts are being made to reconstruct the health sector, in particular to estimate the extent of infectious disease burden. However, any approach that requires the use of modelled disease rates requires reasonable information on population distribution. In a low-income country such as Somalia, population data are lacking, are of poor quality, or become outdated rapidly. Modelling methods are therefore needed for the production of contemporary and spatially detailed population data. Results Here land cover information derived from satellite imagery and existing settlement point datasets were used for the spatial reallocation of populations within census units. We used simple and semi-automated methods that can be implemented with free image processing software to produce an easily updatable gridded population dataset at 100 × 100 meters spatial resolution. The 2010 population dataset was matched to administrative population totals projected by the UN. Comparison tests between the new dataset and existing population datasets revealed important differences in population size distributions, and in population at risk of malaria estimates. These differences are particularly important in more densely populated areas and strongly depend on the settlement data used in the modelling approach. Conclusions The results show that it is possible to produce detailed, contemporary and easily updatable settlement and population distribution datasets of Somalia using existing data. The 2010 population dataset produced is freely available as a product of the AfriPop Project and can be downloaded from: http://www.afripop.org. PMID:20840751

High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens.

PubMed

Hu, Xin-Sheng; Yeh, Francis C; Hu, Yang; Deng, Li-Ting; Ennos, Richard A; Chen, Xiaoyang

2017-02-22

Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (G st  = 0.05 ± 0.049). The smallest divergence is among African populations (G st  = 0.0081 ± 0.0025), with increased divergence among non-African populations (G st  = 0.0217 ± 0.0109) and then among African and non-African populations (G st  = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.

Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions

PubMed Central

2013-01-01

Background Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extreme example of copy number variation, but their structure and function is largely understudied. Here, we describe a detailed study of six autosomal and two X chromosomal MSRs among 270 HapMap individuals from Central Europe, Asia and Africa. Copy number variation, stability and genetic heterogeneity of the autosomal macrosatellite repeats RS447 (chromosome 4p), MSR5p (5p), FLJ40296 (13q), RNU2 (17q) and D4Z4 (4q and 10q) and X chromosomal DXZ4 and CT47 were investigated. Results Repeat array size distribution analysis shows that all of these MSRs are highly polymorphic with the most genetic variation among Africans and the least among Asians. A mitotic mutation rate of 0.4-2.2% was observed, exceeding meiotic mutation rates and possibly explaining the large size variability found for these MSRs. By means of a novel Bayesian approach, statistical support for a distinct multimodal rather than a uniform allele size distribution was detected in seven out of eight MSRs, with evidence for equidistant intervals between the modes. Conclusions The multimodal distributions with evidence for equidistant intervals, in combination with the observation of MSR-specific constraints on minimum array size, suggest that MSRs are limited in their configurations and that deviations thereof may cause disease, as is the case for facioscapulohumeral muscular dystrophy. However, at present we cannot exclude that there are mechanistic constraints for MSRs that are not directly disease-related. This study represents the first comprehensive study of MSRs in different human populations by applying novel statistical methods and identifies commonalities and differences in their organization and function in the human genome. PMID:23496858

Two-Year-Old Children Interpret Abstract, Purely Geometric Maps

ERIC Educational Resources Information Center

Winkler-Rhoades, Nathan; Carey, Susan C.; Spelke, Elizabeth S.

2013-01-01

In two experiments, 2.5-year-old children spontaneously used geometric information from 2D maps to locate objects in a 3D surface layout, without instruction or feedback. Children related maps to their corresponding layouts even though the maps differed from the layouts in size, mobility, orientation, dimensionality, and perspective, and even when…

47 CFR 22.947 - Five year build-out period.

Code of Federal Regulations, 2010 CFR

2010-10-01

... full size map, a reduced map, and an exhibit showing technical data relevant to determination of the system's CGSA. Separate maps must be submitted for each market into which the CGSA extends, showing the extension area in the adjacent market. Maps showing extension areas must be labeled (i.e. marked with the...

Using Mental Map Principles to Interpret American Indian Cartography

ERIC Educational Resources Information Center

Mitchell, Martin D.

2014-01-01

The understanding of maps drawn or significantly influenced by American Indians fosters critical thinking, cultural diversity, and awareness of a much-neglected topic in cartography. Line styles, scale depiction, and the sizing of individual entities are discussed in the context of applying principles from mental maps to American Indian maps and…

Struvite pyrolysate recycling combined with dry pyrolysis for ammonium removal from wastewater.

PubMed

Yu, Rongtai; Geng, Jinju; Ren, Hongqiang; Wang, Yanru; Xu, Ke

2013-03-01

The dry pyrolysis of magnesium ammonium phosphate (MAP) with NaOH powder for ammonium release was investigated, as well as the utility of MAP pyrolysate recycling. The identities of the MAP pyrolysate and its derivatives were experimentally validated. The results showed that the pyrolysate was amorphous magnesium hydrogen phosphate (MgHPO4) and magnesium pyrophosphate (Mg2P2O7). The best molar ratio of sodium hydroxide (NaOH) powder to ammonium was 1:1, at 110°C for 3h. The optimum pH for pyrolysate recycling was 9.5. The ammonia removal ratio could be maintained above 80% with MAP pyrolysate recycling. Seed crystal inoculation increased the rate of MAP crystallization by 20.86%, as well as the MAP grain size (2.08nm with seeding versus 1.72nm without). MAP particle size with NaOH treatment decreased: d(0.5)=19.34μm versus d(0.5)=30.35μm for direct pyrolysis. The results demonstrated that crystal growth was controlled by adding NaOH during MAP pyrolysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Estimating the size of hidden populations using respondent-driven sampling data: Case examples from Morocco

PubMed Central

Johnston, Lisa G; McLaughlin, Katherine R; Rhilani, Houssine El; Latifi, Amina; Toufik, Abdalla; Bennani, Aziza; Alami, Kamal; Elomari, Boutaina; Handcock, Mark S

2015-01-01

Background Respondent-driven sampling is used worldwide to estimate the population prevalence of characteristics such as HIV/AIDS and associated risk factors in hard-to-reach populations. Estimating the total size of these populations is of great interest to national and international organizations, however reliable measures of population size often do not exist. Methods Successive Sampling-Population Size Estimation (SS-PSE) along with network size imputation allows population size estimates to be made without relying on separate studies or additional data (as in network scale-up, multiplier and capture-recapture methods), which may be biased. Results Ten population size estimates were calculated for people who inject drugs, female sex workers, men who have sex with other men, and migrants from sub-Sahara Africa in six different cities in Morocco. SS-PSE estimates fell within or very close to the likely values provided by experts and the estimates from previous studies using other methods. Conclusions SS-PSE is an effective method for estimating the size of hard-to-reach populations that leverages important information within respondent-driven sampling studies. The addition of a network size imputation method helps to smooth network sizes allowing for more accurate results. However, caution should be used particularly when there is reason to believe that clustered subgroups may exist within the population of interest or when the sample size is small in relation to the population. PMID:26258908

Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

PubMed

Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

2014-10-01

Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

Detailed photometric analysis of young star groups in the galaxy NGC 300

NASA Astrophysics Data System (ADS)

Rodríguez, M. J.; Baume, G.; Feinstein, C.

2016-10-01

Aims: The purpose of this work is to understand the global characteristics of the stellar populations in NGC 300. In particular, we focused our attention on searching young star groups and study their hierarchical organization. The proximity and orientation of this Sculptor Group galaxy make it an ideal candidate for this study. Methods: The research was conducted using archival point spread function (PSF) fitting photometry measured from images in multiple bands obtained with the Advanced Camera for Surveys of the Hubble Space Telescope (ACS/HST). Using the path linkage criterion (PLC), we cataloged young star groups and analyzed them from the observation of individual stars in the galaxy NGC 300. We also built stellar density maps from the bluest stars and applied the SExtractor code to identify overdensities. This method provided an additional tool for the detection of young stellar structures. By plotting isocontours over the density maps and comparing the two methods, we could infer and delineate the hierarchical structure of the blue population in the galaxy. For each region of a detected young star group, we estimated the size and derived the radial surface density profiles for stellar populations of different color (blue and red). A statistical decontamination of field stars was performed for each region. In this way it was possible to build the color-magnitude diagrams (CMD) and compare them with theoretical evolutionary models. We also constrained the present-day mass function (PDMF) per group by estimating a value for its slope. Results: The blue population distribution in NGC 300 clearly follows the spiral arms of the galaxy, showing a hierarchical behavior in which the larger and loosely distributed structures split into more compact and denser ones over several density levels. We created a catalog of 1147 young star groups in six fields of the galaxy NGC 300, in which we present their fundamental characteristics. The mean and the mode radius values obtained from the size distribution are both 25 pc, in agreement with the value for the Local Group and nearby galaxies. Additionally, we found an average PDMF slope that is compatible with the Salpeter value. Full Table 2 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/594/A34

EGFR mutation incidence in non-small-cell lung cancer of adenocarcinoma histology: a systematic review and global map by ethnicity (mutMapII)

PubMed Central

Midha, Anita; Dearden, Simon; McCormack, Rose

2015-01-01

Mutations in the epidermal growth factor receptor (EGFR) gene are commonly observed in non-small-cell lung cancer (NSCLC), particularly in tumors of adenocarcinoma (ADC) histology (NSCLC/ADC). Robust data exist regarding the prevalence of EGFR mutations in Western and Asian patients with NSCLC/ADC, yet there is a lack of data for patients of other ethnicities. This review collated available data with the aim of creating a complete, global picture of EGFR mutation frequency in patients with NSCLC/ADC by ethnicity. Worldwide literature reporting EGFR mutation frequency in patients with NSCLC/ADC was reviewed, to create a map of the world populated with EGFR mutation frequency by country (a ‘global EGFR mutMap’). A total of 151 worldwide studies (n=33162 patients with NSCLC/ADC, of which 9749 patients had EGFR mutation-positive NSCLC/ADC) were included. There was substantial variation in EGFR mutation frequency between studies, even when grouped by geographic region or individual country. As expected, the Asia-Pacific NSCLC/ADC subgroup had the highest EGFR mutation frequency (47% [5958/12819; 87 studies; range 20%-76%]) and the lowest EGFR mutation frequency occurred in the Oceania NSCLC/ADC subgroup (12% [69/570; 4 studies; range 7%-36%]); however, comparisons between regions were limited due to the varying sizes of the patient populations studied. In all regional (geographic) subgroups where data were available, EGFR mutation frequency in NSCLC/ADC was higher in women compared with men, and in never-compared with ever-smokers. This review provides the foundation for a global map of EGFR mutation frequency in patients with NSCLC/ADC. The substantial lack of data from several large geographic regions of the world, notably Africa, the Middle East, Central Asia, and Central and South America, highlights a potential lack of routine mutation testing and the need for further investigations in these regions. PMID:26609494

Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design

PubMed Central

Zhang, Zheng; Dai, Zhijun; Chen, Yuan; Yuan, Xiong; Yuan, Zheming; Tang, Wenbang; Li, Lanzhi; Hu, Zhongli

2017-01-01

The use of heterosis has considerably increased the productivity of many crops; however, the biological mechanism underpinning the technique remains elusive. The North Carolina design III (NCIII) and the triple test cross (TTC) are powerful and popular genetic mating design that can be used to decipher the genetic basis of heterosis. However, when using the NCIII design with the present quantitative trait locus (QTL) mapping method, if epistasis exists, the estimated additive or dominant effects are confounded with epistatic effects. Here, we propose a two-step approach to dissect all genetic effects of QTL and digenic interactions on a whole genome without sacrificing statistical power based on an augmented TTC (aTTC) design. Because the aTTC design has more transformation combinations than do the NCIII and TTC designs, it greatly enriches the QTL mapping for studying heterosis. When the basic population comprises recombinant inbred lines (RIL), we can use the same materials in the NCIII design for aTTC-design QTL mapping with transformation combination Z1, Z2, and Z4 to obtain genetic effect of QTL and digenic interactions. Compared with RIL-based TTC design, RIL-based aTTC design saves time, money, and labor for basic population crossed with F1. Several Monte Carlo simulation studies were carried out to confirm the proposed approach; the present genetic parameters could be identified with high statistical power, precision, and calculation speed, even at small sample size or low heritability. Additionally, two elite rice hybrid datasets for nine agronomic traits were estimated for real data analysis. We dissected the genetic effects and calculated the dominance degree of each QTL and digenic interaction. Real mapping results suggested that the dominance degree in Z2 that mainly characterize heterosis showed overdominance and dominance for QTL and digenic interactions. Dominance and overdominance were the major genetic foundations of heterosis in rice. PMID:29240818

Grain size mapping in shallow rivers using spectral information: a lab spectroradiometry perspective

NASA Astrophysics Data System (ADS)

Niroumand-Jadidi, Milad; Vitti, Alfonso

2017-10-01

Every individual attribute of a riverine environment defines the overall spectral signature to be observed by an optical sensor. The spectral characteristic of riverbed is influenced not only by the type but also the roughness of substrates. Motivated by this assumption, potential of optical imagery for mapping grain size of shallow rivers (< 1 m deep) is examined in this research. The previous studies concerned with grain size mapping are all built upon the texture analysis of exposed bed material using very high resolution (i.e. cm resolution) imagery. However, the application of texturebased techniques is limited to very low altitude sensors (e.g. UAVs) to ensure the sufficient spatial resolution. Moreover, these techniques are applicable only in the presence of exposed substrates along the river channel. To address these drawbacks, this study examines the effectiveness of spectral information to make distinction among grain sizes for submerged substrates. Spectroscopic experiments are performed in controlled condition of a hydraulic lab. The spectra are collected over a water flume in a range of water depths and bottoms with several grain sizes. A spectral convolution is performed to match the spectra to WorldView-2 spectral bands. The material type of substrates is considered the same for all the experiments with only variable roughness/size of grains. The spectra observed over dry beds revealed that the brightness/reflectance increases with the grain size across all the spectral bands. Based on this finding, the above-water spectra over a river channel are simulated considering different grain sizes in the bottom. A water column correction method is then used to retrieve the bottom reflectances. Then the inferred bottom reflectances are clustered to segregate among grain sizes. The results indicate high potential of the spectral approach for clustering grain sizes (overall accuracy of 92%) which opens up some horizons for mapping this valuable attribute of rivers using remotely sensed data.

Community Size Effects on Epidemic Spreading in Multiplex Social Networks.

PubMed

Liu, Ting; Li, Ping; Chen, Yan; Zhang, Jie

2016-01-01

The dynamical process of epidemic spreading has drawn much attention of the complex network community. In the network paradigm, diseases spread from one person to another through the social ties amongst the population. There are a variety of factors that govern the processes of disease spreading on the networks. A common but not negligible factor is people's reaction to the outbreak of epidemics. Such reaction can be related information dissemination or self-protection. In this work, we explore the interactions between disease spreading and population response in terms of information diffusion and individuals' alertness. We model the system by mapping multiplex networks into two-layer networks and incorporating individuals' risk awareness, on the assumption that their response to the disease spreading depends on the size of the community they belong to. By comparing the final incidence of diseases in multiplex networks, we find that there is considerable mitigation of diseases spreading for full phase of spreading speed when individuals' protection responses are introduced. Interestingly, the degree of community overlap between the two layers is found to be critical factor that affects the final incidence. We also analyze the consequences of the epidemic incidence in communities with different sizes and the impacts of community overlap between two layers. Specifically, as the diseases information makes individuals alert and take measures to prevent the diseases, the effective protection is more striking in small community. These phenomena can be explained by the multiplexity of the networked system and the competition between two spreading processes.

Community Size Effects on Epidemic Spreading in Multiplex Social Networks

PubMed Central

Liu, Ting; Li, Ping; Chen, Yan; Zhang, Jie

2016-01-01

The dynamical process of epidemic spreading has drawn much attention of the complex network community. In the network paradigm, diseases spread from one person to another through the social ties amongst the population. There are a variety of factors that govern the processes of disease spreading on the networks. A common but not negligible factor is people’s reaction to the outbreak of epidemics. Such reaction can be related information dissemination or self-protection. In this work, we explore the interactions between disease spreading and population response in terms of information diffusion and individuals’ alertness. We model the system by mapping multiplex networks into two-layer networks and incorporating individuals’ risk awareness, on the assumption that their response to the disease spreading depends on the size of the community they belong to. By comparing the final incidence of diseases in multiplex networks, we find that there is considerable mitigation of diseases spreading for full phase of spreading speed when individuals’ protection responses are introduced. Interestingly, the degree of community overlap between the two layers is found to be critical factor that affects the final incidence. We also analyze the consequences of the epidemic incidence in communities with different sizes and the impacts of community overlap between two layers. Specifically, as the diseases information makes individuals alert and take measures to prevent the diseases, the effective protection is more striking in small community. These phenomena can be explained by the multiplexity of the networked system and the competition between two spreading processes. PMID:27007112

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Science.gov Websites

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A comparative analysis of chaotic particle swarm optimizations for detecting single nucleotide polymorphism barcodes.

PubMed

Chuang, Li-Yeh; Moi, Sin-Hua; Lin, Yu-Da; Yang, Cheng-Hong

2016-10-01

Evolutionary algorithms could overcome the computational limitations for the statistical evaluation of large datasets for high-order single nucleotide polymorphism (SNP) barcodes. Previous studies have proposed several chaotic particle swarm optimization (CPSO) methods to detect SNP barcodes for disease analysis (e.g., for breast cancer and chronic diseases). This work evaluated additional chaotic maps combined with the particle swarm optimization (PSO) method to detect SNP barcodes using a high-dimensional dataset. Nine chaotic maps were used to improve PSO method results and compared the searching ability amongst all CPSO methods. The XOR and ZZ disease models were used to compare all chaotic maps combined with PSO method. Efficacy evaluations of CPSO methods were based on statistical values from the chi-square test (χ 2 ). The results showed that chaotic maps could improve the searching ability of PSO method when population are trapped in the local optimum. The minor allele frequency (MAF) indicated that, amongst all CPSO methods, the numbers of SNPs, sample size, and the highest χ 2 value in all datasets were found in the Sinai chaotic map combined with PSO method. We used the simple linear regression results of the gbest values in all generations to compare the all methods. Sinai chaotic map combined with PSO method provided the highest β values (β≥0.32 in XOR disease model and β≥0.04 in ZZ disease model) and the significant p-value (p-value<0.001 in both the XOR and ZZ disease models). The Sinai chaotic map was found to effectively enhance the fitness values (χ 2 ) of PSO method, indicating that the Sinai chaotic map combined with PSO method is more effective at detecting potential SNP barcodes in both the XOR and ZZ disease models. Copyright © 2016 Elsevier B.V. All rights reserved.

The rationale and cost-effectiveness of a confirmatory mapping tool for lymphatic filariasis: Examples from Ethiopia and Tanzania

PubMed Central

Pelletreau, Sonia; Barbre, Kira A.; Deming, Michael S.; Rebollo, Maria P.

2017-01-01

Endemicity mapping is required to determining whether a district requires mass drug administration (MDA). Current guidelines for mapping LF require that two sites be selected per district and within each site a convenience sample of 100 adults be tested for antigenemia or microfilaremia. One or more confirmed positive tests in either site is interpreted as an indicator of potential transmission, prompting MDA at the district-level. While this mapping strategy has worked well in high-prevalence settings, imperfect diagnostics and the transmission potential of a single positive adult have raised concerns about the strategy’s use in low-prevalence settings. In response to these limitations, a statistically rigorous confirmatory mapping strategy was designed as a complement to the current strategy when LF endemicity is uncertain. Under the new strategy, schools are selected by either systematic or cluster sampling, depending on population size, and within each selected school, children 9–14 years are sampled systematically. All selected children are tested and the number of positive results is compared against a critical value to determine, with known probabilities of error, whether the average prevalence of LF infection is likely below a threshold of 2%. This confirmatory mapping strategy was applied to 45 districts in Ethiopia and 10 in Tanzania, where initial mapping results were considered uncertain. In 42 Ethiopian districts, and all 10 of the Tanzanian districts, the number of antigenemic children was below the critical cutoff, suggesting that these districts do not require MDA. Only three Ethiopian districts exceeded the critical cutoff of positive results. Whereas the current World Health Organization guidelines would have recommended MDA in all 55 districts, the present results suggest that only three of these districts requires MDA. By avoiding unnecessary MDA in 52 districts, the confirmatory mapping strategy is estimated to have saved a total of $9,293,219. PMID:28976981

The rationale and cost-effectiveness of a confirmatory mapping tool for lymphatic filariasis: Examples from Ethiopia and Tanzania.

PubMed

Gass, Katherine M; Sime, Heven; Mwingira, Upendo J; Nshala, Andreas; Chikawe, Maria; Pelletreau, Sonia; Barbre, Kira A; Deming, Michael S; Rebollo, Maria P

2017-10-01

Endemicity mapping is required to determining whether a district requires mass drug administration (MDA). Current guidelines for mapping LF require that two sites be selected per district and within each site a convenience sample of 100 adults be tested for antigenemia or microfilaremia. One or more confirmed positive tests in either site is interpreted as an indicator of potential transmission, prompting MDA at the district-level. While this mapping strategy has worked well in high-prevalence settings, imperfect diagnostics and the transmission potential of a single positive adult have raised concerns about the strategy's use in low-prevalence settings. In response to these limitations, a statistically rigorous confirmatory mapping strategy was designed as a complement to the current strategy when LF endemicity is uncertain. Under the new strategy, schools are selected by either systematic or cluster sampling, depending on population size, and within each selected school, children 9-14 years are sampled systematically. All selected children are tested and the number of positive results is compared against a critical value to determine, with known probabilities of error, whether the average prevalence of LF infection is likely below a threshold of 2%. This confirmatory mapping strategy was applied to 45 districts in Ethiopia and 10 in Tanzania, where initial mapping results were considered uncertain. In 42 Ethiopian districts, and all 10 of the Tanzanian districts, the number of antigenemic children was below the critical cutoff, suggesting that these districts do not require MDA. Only three Ethiopian districts exceeded the critical cutoff of positive results. Whereas the current World Health Organization guidelines would have recommended MDA in all 55 districts, the present results suggest that only three of these districts requires MDA. By avoiding unnecessary MDA in 52 districts, the confirmatory mapping strategy is estimated to have saved a total of $9,293,219.

Population differences in the rate of proliferation of international HapMap cell lines.

PubMed

Stark, Amy L; Zhang, Wei; Zhou, Tong; O'Donnell, Peter H; Beiswanger, Christine M; Huang, R Stephanie; Cox, Nancy J; Dolan, M Eileen

2010-12-10

The International HapMap Project is a resource for researchers containing genotype, sequencing, and expression information for EBV-transformed lymphoblastoid cell lines derived from populations across the world. The expansion of the HapMap beyond the four initial populations of Phase 2, referred to as Phase 3, has increased the sample number and ethnic diversity available for investigation. However, differences in the rate of cellular proliferation between the populations can serve as confounders in phenotype-genotype studies using these cell lines. Within the Phase 2 populations, the JPT and CHB cell lines grow faster (p < 0.0001) than the CEU or YRI cell lines. Phase 3 YRI cell lines grow significantly slower than Phase 2 YRI lines (p < 0.0001), with no widespread genetic differences based on common SNPs. In addition, we found significant growth differences between the cell lines in the Phase 2 ASN populations and the Han Chinese from the Denver metropolitan area panel in Phase 3 (p < 0.0001). Therefore, studies that separate HapMap panels into discovery and replication sets must take this into consideration. Copyright © 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

High Diversity of Genes for Nonhost Resistance of Barley to Heterologous Rust Fungi

PubMed Central

Jafary, Hossein; Albertazzi, Giorgia; Marcel, Thierry C.; Niks, Rients E.

2008-01-01

Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley–Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes. PMID:18430953

Beta Regio - Phoebe Regio on Venus: Geologic mapping with the Magellan data

NASA Technical Reports Server (NTRS)

Nikishin, A. M.; Borozdin, V. K.; Bobina, N. N.; Burba, G. A.

1993-01-01

The geologic maps of C1-15N283 and C1-00N283 sheets were produced (preliminary versions) with Magellan SAR images. This work was undertaken as a part of Russia's contribution into C1 geologic mapping efforts. The scale of the original maps is 1:8,000,000, and the maps are reproduced here at a reduced size.

Utilizing the ultrasensitive Schistosoma up-converting phosphor lateral flow circulating anodic antigen (UCP-LF CAA) assay for sample pooling-strategies.

PubMed

Corstjens, Paul L A M; Hoekstra, Pytsje T; de Dood, Claudia J; van Dam, Govert J

2017-11-01

Methodological applications of the high sensitivity genus-specific Schistosoma CAA strip test, allowing detection of single worm active infections (ultimate sensitivity), are discussed for efficient utilization in sample pooling strategies. Besides relevant cost reduction, pooling of samples rather than individual testing can provide valuable data for large scale mapping, surveillance, and monitoring. The laboratory-based CAA strip test utilizes luminescent quantitative up-converting phosphor (UCP) reporter particles and a rapid user-friendly lateral flow (LF) assay format. The test includes a sample preparation step that permits virtually unlimited sample concentration with urine, reaching ultimate sensitivity (single worm detection) at 100% specificity. This facilitates testing large urine pools from many individuals with minimal loss of sensitivity and specificity. The test determines the average CAA level of the individuals in the pool thus indicating overall worm burden and prevalence. When requiring test results at the individual level, smaller pools need to be analysed with the pool-size based on expected prevalence or when unknown, on the average CAA level of a larger group; CAA negative pools do not require individual test results and thus reduce the number of tests. Straightforward pooling strategies indicate that at sub-population level the CAA strip test is an efficient assay for general mapping, identification of hotspots, determination of stratified infection levels, and accurate monitoring of mass drug administrations (MDA). At the individual level, the number of tests can be reduced i.e. in low endemic settings as the pool size can be increased as opposed to prevalence decrease. At the sub-population level, average CAA concentrations determined in urine pools can be an appropriate measure indicating worm burden. Pooling strategies allowing this type of large scale testing are feasible with the various CAA strip test formats and do not affect sensitivity and specificity. It allows cost efficient stratified testing and monitoring of worm burden at the sub-population level, ideally for large-scale surveillance generating hard data for performance of MDA programs and strategic planning when moving towards transmission-stop and elimination.

Channel mapping river miles 29–62 of the Colorado River in Grand Canyon National Park, Arizona, May 2009

USGS Publications Warehouse

Kaplinski, Matt; Hazel, Joseph E.; Grams, Paul E.; Kohl, Keith; Buscombe, Daniel D.; Tusso, Robert B.

2017-03-23

Bathymetric, topographic, and grain-size data were collected in May 2009 along a 33-mi reach of the Colorado River in Grand Canyon National Park, Arizona. The study reach is located from river miles 29 to 62 at the confluence of the Colorado and Little Colorado Rivers. Channel bathymetry was mapped using multibeam and singlebeam echosounders, subaerial topography was mapped using ground-based total-stations, and bed-sediment grain-size data were collected using an underwater digital microscope system. These data were combined to produce digital elevation models, spatially variable estimates of digital elevation model uncertainty, georeferenced grain-size data, and bed-sediment distribution maps. This project is a component of a larger effort to monitor the status and trends of sand storage along the Colorado River in Grand Canyon National Park. This report documents the survey methods and post-processing procedures, digital elevation model production and uncertainty assessment, and procedures for bed-sediment classification, and presents the datasets resulting from this study.

Mapping South San Francisco Bay's seabed diversity for use in wetland restoration planning

USGS Publications Warehouse

Fregoso, Theresa A.; Jaffe, B.; Rathwell, G.; Collins, W.; Rhynas, K.; Tomlin, V.; Sullivan, S.

2006-01-01

Data for an acoustic seabed classification were collected as a part of a California Coastal Conservancy funded bathymetric survey of South Bay in early 2005.  A QTC VIEW seabed classification system recorded echoes from a sungle bean 50 kHz echosounder.  Approximately 450,000 seabed classification records were generated from an are of of about 30 sq. miles.  Ten district acoustic classes were identified through an unsupervised classification system using principle component and cluster analyses.  One hundred and sixty-one grab samples and forty-five benthic community composition data samples collected in the study area shortly before and after the seabed classification survey, further refined the ten classes into groups based on grain size.  A preliminary map of surficial grain size of South Bay was developed from the combination of the seabed classification and the grab and benthic samples.  The initial seabed classification map, the grain size map, and locations of sediment samples will be displayed along with the methods of acousitc seabed classification.

Determining size and dispersion of minimum viable populations for land management planning and species conservation

NASA Astrophysics Data System (ADS)

Lehmkuhl, John F.

1984-03-01

The concept of minimum populations of wildlife and plants has only recently been discussed in the literature. Population genetics has emerged as a basic underlying criterion for determining minimum population size. This paper presents a genetic framework and procedure for determining minimum viable population size and dispersion strategies in the context of multiple-use land management planning. A procedure is presented for determining minimum population size based on maintenance of genetic heterozygosity and reduction of inbreeding. A minimum effective population size ( N e ) of 50 breeding animals is taken from the literature as the minimum shortterm size to keep inbreeding below 1% per generation. Steps in the procedure adjust N e to account for variance in progeny number, unequal sex ratios, overlapping generations, population fluctuations, and period of habitat/population constraint. The result is an approximate census number that falls within a range of effective population size of 50 500 individuals. This population range defines the time range of short- to long-term population fitness and evolutionary potential. The length of the term is a relative function of the species generation time. Two population dispersion strategies are proposed: core population and dispersed population.

Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents.

PubMed

Ulloa, Mauricio; Hulse-Kemp, Amanda M; De Santiago, Luis M; Stelly, David M; Burke, John J

2017-01-01

High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton ( Gossypium hirsutum L., "2n = 52"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F 2 , a recombinant inbred line (RIL), and reciprocal RIL population, from "Phytogen 72" and "Stoneville 474" cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD) 1 arisen from the merging of 2 genomes ("A" Old World and "D" New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the A t and D t subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the D t subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral A t -subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum . However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid A t and D t subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI G hirsutum assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in G hirsutum with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.

Urbanization and depopulation in the Alps.

PubMed

Batzing, W; Perlik, M; Dekleva, M

1996-11-01

Demographic developments in the European Alpine region are analyzed over the period 1870-1990. The region is defined as including parts of Germany, France, Italy, Liechtenstein, Austria, Switzerland, and Slovenia. "Studies of growth, stagnation, decline, commune size, and altitude in almost 6,000 communes are presented on three colored maps.... It is apparent that two highly divergent processes are at work and, accordingly, statistical mean values reveal little of importance. Approximately one-half of Alpine Europe is undergoing general economic and demographic growth and has experienced significant increase in population since the end of the agricultural era. This development has taken place primarily in low-lying valleys and basins and in areas bordering the Alps that have good access to transport routes. Tourism is not as widespread as generally assumed and is usually characterized by a punctate pattern. Only in the western part of the Eastern Alps does tourism account for widespread population growth at higher altitudes; elsewhere the Alps have not been affected by modern development and the economy and population are declining, with some areas in danger of becoming completely abandoned. The results challenge the earlier concept of the Alps as a rural region, once populated by peasants, where tourism now plays a major role." (EXCERPT)

Snake River Plain Geothermal Play Fairway Analysis - Phase 1 Raster Files

DOE Data Explorer

John Shervais

2015-10-09

Snake River Plain Play Fairway Analysis - Phase 1 CRS Raster Files. This dataset contains raster files created in ArcGIS. These raster images depict Common Risk Segment (CRS) maps for HEAT, PERMEABILITY, AND SEAL, as well as selected maps of Evidence Layers. These evidence layers consist of either Bayesian krige functions or kernel density functions, and include: (1) HEAT: Heat flow (Bayesian krige map), Heat flow standard error on the krige function (data confidence), volcanic vent distribution as function of age and size, groundwater temperature (equivalue interval and natural breaks bins), and groundwater T standard error. (2) PERMEABILTY: Fault and lineament maps, both as mapped and as kernel density functions, processed for both dilational tendency (TD) and slip tendency (ST), along with data confidence maps for each data type. Data types include mapped surface faults from USGS and Idaho Geological Survey data bases, as well as unpublished mapping; lineations derived from maximum gradients in magnetic, deep gravity, and intermediate depth gravity anomalies. (3) SEAL: Seal maps based on presence and thickness of lacustrine sediments and base of SRP aquifer. Raster size is 2 km. All files generated in ArcGIS.

Choropleth map legend design for visualizing community health disparities.

PubMed

Cromley, Robert G; Cromley, Ellen K

2009-09-24

Disparities in health outcomes across communities are a central concern in public health and epidemiology. Health disparities research often links differences in health outcomes to other social factors like income. Choropleth maps of health outcome rates show the geographical distribution of health outcomes. This paper illustrates the use of cumulative frequency map legends for visualizing how the health events are distributed in relation to social characteristics of community populations. The approach uses two graphs in the cumulative frequency legend to highlight the difference between the raw count of the health events and the raw count of the social characteristic like low income in the geographical areas of the map. The approach is applied to mapping publicly available data on low birth weight by town in Connecticut and Lyme disease incidence by town in Connecticut in relation to income. The steps involved in creating these legends are described in detail so that health analysts can adopt this approach. The different health problems, low birth weight and Lyme disease, have different cumulative frequency signatures. Graphing poverty population on the cumulative frequency legends revealed that the poverty population is distributed differently with respect to the two different health problems mapped here. Cumulative frequency legends can be useful supplements for choropleth maps. These legends can be constructed using readily available software. They contain all of the information found in standard choropleth map legends, and they can be used with any choropleth map classification scheme. Cumulative frequency legends effectively communicate the proportion of areas, the proportion of health events, and/or the proportion of the denominator population in which the health events occurred that falls within each class interval. They illuminate the context of disease through graphing associations with other variables.

LA-ICP-MS trace element mapping: insights into the crystallisation history of a metamorphic garnet population

NASA Astrophysics Data System (ADS)

George, Freya; Gaidies, Fred

2017-04-01

In comparison to our understanding of major element zoning, relatively little is known about the incorporation of trace elements into metamorphic garnet. Given their extremely slow diffusivities and sensitivity to changing mineral assemblages, the analysis of the distribution of trace elements in garnet has the potential to yield a wealth of information pertaining to interfacial attachment mechanisms during garnet crystallisation, the mobility of trace elements in both garnet and the matrix, and trace element geochronology. Due to advances in the spatial resolution and analytical precision of modern microbeam techniques, small-scale trace element variations can increasingly be documented and used to inform models of metamorphic crystallisation. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) in particular, can be used to rapidly quantify a wide range of elemental masses as a series of laser rasters, producing large volumes of spatially constrained trace element data. In this study, we present LA-ICP-MS maps of trace element concentrations from numerous centrally-sectioned garnets representative of the crystal size-distribution of a single sample's population. The study sample originates from the garnet-grade Barrovian zone of the Lesser Himalayan Sequence in Sikkim, northeast India, and has been shown to have crystallised garnet within a single assemblage between 515 ˚C and 565˚C, with no evidence for accessory phase reaction over the duration of garnet growth. Previous models have indicated that the duration of garnet crystallisation was extremely rapid (<1 Myr), with negligible diffusional homogenisation of major divalent cations. Consequently, the trace element record likely documents the primary zonation generated during garnet growth. In spite of straightforward (i.e. concentrically-zoned) major element garnet zonation, trace elements maps are characterised by significant complexity and variability. Y and the heavy rare earth elements are strongly enriched in crystal cores, where there is overprinting of the observed internal fabric, and exhibit numerous concentric annuli towards crystal rims. Conversely, the medium rare earth elements (e.g. Gd, Eu and Sm) exhibit bowl-shaped zoning from core to rim, with no annuli, and core and rim compositions of the medium rare earth elements are the same throughout the population within crystals of differing size. Cr exhibits pronounced spiral zoning, and the average Cr content increases towards garnet rims. In all cases, spirals are centered on the geometric core of the crystals. These LA-ICP-MS maps highlight the complexity of garnet growth over a single prograde event, and indicate that there is still much to be learnt from the analysis of garnet using ever-improving analytical methods. We explore the potential causes of the variations in the distribution of trace elements in garnet, and assess how these zoning patterns may be used to refine our understanding of the intricacies of garnet crystallisation and the spatial and temporal degree of trace element equilibration during metamorphism.

High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut.

PubMed

Agarwal, Gaurav; Clevenger, Josh; Pandey, Manish K; Wang, Hui; Shasidhar, Yaduru; Chu, Ye; Fountain, Jake C; Choudhary, Divya; Culbreath, Albert K; Liu, Xin; Huang, Guodong; Wang, Xingjun; Deshmukh, Rupesh; Holbrook, C Corley; Bertioli, David J; Ozias-Akins, Peggy; Jackson, Scott A; Varshney, Rajeev K; Guo, Baozhu

2018-04-10

Whole-genome resequencing (WGRS) of mapping populations has facilitated development of high-density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the 'T' population (Tifrunner × GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Reduced fecundity in small populations of the rare plant Gentianopsis ciliate (Gentianaceae)

USGS Publications Warehouse

Kery, M.; Matthies, D.

2004-01-01

Habitat destruction is the main cause for the biodiversity crisis. Surviving populations are often fragmented, i.e., small and isolated from each other. Reproduction of plants in small populations is often reduced, and this has been attributed to inbreeding depression, reduced attractiveness for pollinators, and reduced habitat quality in small populations. Here we present data on the effects of fragmentation on the rare, self-compatible perennial herb Gentianopsis ciliata (Gentianaceae), a species with very small and presumably well-dispersed seeds. We studied the relationship between population size, plant size, and the number of flowers produced in 63 populations from 1996-1998. In one of the years, leaf and flower size and the number of seeds produced per fruit was studied in a subset of 25 populations. Plant size, flower size, and the number of seeds per fruit and per plant increased with population size, whereas leaf length and the number of flowers per plant did not. The effects of population size on reproduction and on flower size remained significant if the effects were adjusted for differences in plant size, indicating that they could not be explained by differences in habitat quality. The strongly reduced reproduction in small populations may be due to pollination limitation, while the reduced flower size could indicate genetic effects.

Reduced fecundity in small populations of the rare plant Gentianopsis ciliate (Gentianaceae)

USGS Publications Warehouse

Robbins, C.S.

1983-01-01

Habitat destruction is the main cause for the biodiversity crisis. Surviving populations are often fragmented, i.e., small and isolated from each other. Reproduction of plants in small populations is often reduced, and this has been attributed to inbreeding depression, reduced attractiveness for pollinators, and reduced habitat quality in small populations. Here we present data on the effects of fragmentation on the rare, self-compatible perennial herb Gentianopsis ciliata (Gentianaceae), a species with very small and presumably well-dispersed seeds. We studied the relationship between population size, plant size, and the number of flowers produced in 63 populations from 1996-1998. In one of the years, leaf and flower size and the number of seeds produced per fruit was studied in a subset of 25 populations. Plant size, flower size, and the number of seeds per fruit and per plant increased with population size, whereas leaf length and the number of flowers per plant did not. The effects of population size on reproduction and on flower size remained significant if the effects were adjusted for differences in plant size, indicating that they could not be explained by differences in habitat quality. The strongly reduced reproduction in small populations may be due to pollination limitation, while the reduced flower size could indicate genetic effects.

Quasar Accretion Disk Sizes With Continuum Reverberation Mapping From the Dark Energy Survey

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

Mudd, D.; et al.

We present accretion disk size measurements for 15 luminous quasars atmore » $$0.7 \\leq z \\leq 1.9$$ derived from $griz$ light curves from the Dark Energy Survey. We measure the disk sizes with continuum reverberation mapping using two methods, both of which are derived from the expectation that accretion disks have a radial temperature gradient and the continuum emission at a given radius is well-described by a single blackbody. In the first method we measure the relative lags between the multiband light curves, which provides the relative time lag between shorter and longer wavelength variations. The second method fits the model parameters for the canonical Shakura-Sunyaev thin disk directly rather than solving for the individual time lags between the light curves. Our measurements demonstrate good agreement with the sizes predicted by this model for accretion rates between 0.3-1 times the Eddington rate. These results are also in reasonable agreement with disk size measurements from gravitational microlensing studies of strongly lensed quasars, as well as other photometric reverberation mapping results.« less

The contribution of stimulus frequency and recency to set-size effects.

PubMed

van 't Wout, Félice

2018-06-01

Hick's law describes the increase in choice reaction time (RT) with the number of stimulus-response (S-R) mappings. However, in choice RT experiments, set-size is typically confounded with stimulus recency and frequency: With a smaller set-size, each stimulus occurs on average more frequently and more recently than with a larger set-size. To determine to what extent stimulus recency and frequency contribute to the set-size effect, stimulus set-size was manipulated independently of stimulus recency and frequency, by keeping recency and frequency constant for a subset of the stimuli. Although this substantially reduced the set-size effect (by approximately two-thirds for these stimuli), it did not eliminate it. Thus, the time required to retrieve an S-R mapping from memory is (at least in part) determined by the number of alternatives. In contrast, a recent task switching study (Van 't Wout et al. in Journal of Experimental Psychology: Learning, Memory & Cognition., 41, 363-376, 2015) using the same manipulation found that the time required to retrieve a task-set from memory is not influenced by the number of alternatives per se. Hence, this experiment further supports a distinction between two levels of representation in task-set control: The level of task-sets, and the level of S-R mappings.

The spatial distribution of threats to plant species with extremely small populations

NASA Astrophysics Data System (ADS)

Wang, Chunjing; Zhang, Jing; Wan, Jizhong; Qu, Hong; Mu, Xianyun; Zhang, Zhixiang

2017-03-01

Many biological conservationists take actions to conserve plant species with extremely small populations (PSESP) in China; however, there have been few studies on the spatial distribution of threats to PSESP. Hence, we selected distribution data of PSESP and made a map of the spatial distribution of threats to PSESP in China. First, we used the weight assignment method to evaluate the threat risk to PSESP at both country and county scales. Second, we used a geographic information system to map the spatial distribution of threats to PSESP, and explored the threat factors based on linear regression analysis. Finally, we suggested some effective conservation options. We found that the PSESP with high values of protection, such as the plants with high scientific research values and ornamental plants, were threatened by over-exploitation and utilization, habitat fragmentation, and a small sized wild population in broad-leaved forests and bush fallows. We also identified some risk hotspots for PSESP in China. Regions with low elevation should be given priority for ex- and in-situ conservation. Moreover, climate change should be considered for conservation of PSESP. To avoid intensive over-exploitation or utilization and habitat fragmentation, in-situ conservation should be practiced in regions with high temperatures and low temperature seasonality, particularly in the high risk hotspots for PSESP that we proposed. Ex-situ conservation should be applied in these same regions, and over-exploitation and utilization of natural resources should be prevented. It is our goal to apply the concept of PSESP to the global scale in the future.

Does source population size affect performance in new environments?

PubMed Central

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

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

PubMed Central

Parker, Heidi G.; Kukekova, Anna V.; Akey, Dayna T.; Goldstein, Orly; Kirkness, Ewen F.; Baysac, Kathleen C.; Mosher, Dana S.; Aguirre, Gustavo D.; Acland, Gregory M.; Ostrander, Elaine A.

2007-01-01

The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. We then use the multibreed approach to fine-map Collie eye anomaly (cea), a complex disorder of ocular development that was initially mapped to a 3.9-cM region on canine chromosome 37. Combined genotypes from affected individuals from four breeds of a single breed group significantly narrowed the candidate gene region to a 103-kb interval spanning only four genes. Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage. PMID:17916641

Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.

PubMed Central

Gong, L.; Stift, G.; Kofler, R.; Pachner, M.

2008-01-01

Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Ölkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety “Lady Godiva” (O5) and the Italian crookneck variety “Bianco Friulano” (CN), which are the parents of our previous F2 mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0750-2) contains supplementary material, which is available to authorized users. PMID:18379753

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

USGS Publications Warehouse

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

2005-01-01

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

Genetic dissection of sorghum grain quality traits using diverse and segregating populations.

PubMed

Boyles, Richard E; Pfeiffer, Brian K; Cooper, Elizabeth A; Rauh, Bradley L; Zielinski, Kelsey J; Myers, Matthew T; Brenton, Zachary; Rooney, William L; Kresovich, Stephen

2017-04-01

Coordinated association and linkage mapping identified 25 grain quality QTLs in multiple environments, and fine mapping of the Wx locus supports the use of high-density genetic markers in linkage mapping. There is a wide range of end-use products made from cereal grains, and these products often demand different grain characteristics. Fortunately, cereal crop species including sorghum [Sorghum bicolor (L.) Moench] contain high phenotypic variation for traits influencing grain quality. Identifying genetic variants underlying this phenotypic variation allows plant breeders to develop genotypes with grain attributes optimized for their intended usage. Multiple sorghum mapping populations were rigorously phenotyped across two environments (SC Coastal Plain and Central TX) in 2 years for five major grain quality traits: amylose, starch, crude protein, crude fat, and gross energy. Coordinated association and linkage mapping revealed several robust QTLs that make prime targets to improve grain quality for food, feed, and fuel products. Although the amylose QTL interval spanned many megabases, the marker with greatest significance was located just 12 kb from waxy (Wx), the primary gene regulating amylose production in cereal grains. This suggests higher resolution mapping in recombinant inbred line (RIL) populations can be obtained when genotyped at a high marker density. The major QTL for crude fat content, identified in both a RIL population and grain sorghum diversity panel, encompassed the DGAT1 locus, a critical gene involved in maize lipid biosynthesis. Another QTL on chromosome 1 was consistently mapped in both RIL populations for multiple grain quality traits including starch, crude protein, and gross energy. Collectively, these genetic regions offer excellent opportunities to manipulate grain composition and set up future studies for gene validation.

HapMap tagSNP transferability in multiple populations: general guidelines

PubMed Central

Xing, Jinchuan; Witherspoon, David J.; Watkins, W. Scott; Zhang, Yuhua; Tolpinrud, Whitney; Jorde, Lynn B.

2008-01-01

This PDF receipt will only be used as the basis for generating PubMed Central (PMC) documents. PMC documents will be made available for review after conversion (approx. 2–3 weeks time). Any corrections that need to be made will be done at that time. No materials will be released to PMC without the approval of an author. Only the PMC documents will appear on PubMed Central -- this PDF Receipt will not appear on PubMed Central. Linkage disequilibrium (LD) has received much recent attention because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r2 >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations. PMID:18482828

High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

PubMed Central

2013-01-01

Background The availability of a large expressed sequence tags (EST) resource and recent advances in high-throughput genotyping technology have made it possible to develop highly multiplexed SNP arrays for multi-objective genetic applications, including the construction of meiotic maps. Such approaches are particularly useful in species with a large genome size, precluding the use of whole-genome shotgun assembly with current technologies. Results In this study, a 12 k-SNP genotyping array was developed for maritime pine from an extensive EST resource assembled into a unigene set. The offspring of three-generation outbred and inbred mapping pedigrees were then genotyped. The inbred pedigree consisted of a classical F2 population resulting from the selfing of a single inter-provenance (Landes x Corsica) hybrid tree, whereas the outbred pedigree (G2) resulted from a controlled cross of two intra-provenance (Landes x Landes) hybrid trees. This resulted in the generation of three linkage maps based on SNP markers: one from the parental genotype of the F2 population (1,131 markers in 1,708 centimorgan (cM)), and one for each parent of the G2 population (1,015 and 1,110 markers in 1,447 and 1,425 cM for the female and male parents, respectively). A comparison of segregation patterns in the progeny obtained from the two types of mating (inbreeding and outbreeding) led to the identification of a chromosomal region carrying an embryo viability locus with a semi-lethal allele. Following selfing and segregation, zygote mortality resulted in a deficit of Corsican homozygous genotypes in the F2 population. This dataset was also used to study the extent and distribution of meiotic recombination along the length of the chromosomes and the effect of sex and/or genetic background on recombination. The genetic background of trees in which meiotic recombination occurred was found to have a significant effect on the frequency of recombination. Furthermore, only a small proportion of the recombination hot- and cold-spots were common to all three genotypes, suggesting that the spatial pattern of recombination was genetically variable. Conclusion This study led to the development of classical genomic tools for this ecologically and economically important species. It also identified a chromosomal region bearing a semi-lethal recessive allele and demonstrated the genetic variability of recombination rate over the genome. PMID:23597128

MAP - a mapping and analysis program for harvest planning

Treesearch

Robert N. Eli; Chris B. LeDoux; Penn A. Peters

1984-01-01

The Northeastern Forest Experiment Station and the Department of Civil Engineering at West Virginia University are cooperating in the development of a Mapping and Analysis Program, to be named MAP. The goal of this computer software package is to significantly improve the planning and harvest efficiency of small to moderately sized harvest units located in mountainous...

Predictive Mapping of Forest Attributes on the Fishlake National Forest

Treesearch

Tracey S. Frescino; Gretchen G. Moisen

2005-01-01

Forest land managers increasingly need maps of forest characteristics to aid in planning and management. A set of 30-m resolution maps was prepared for the Fishlake National Forest by modeling FIA plot variables as nonparametric functions of ancillary digital data. The set includes maps of volume, biomass, growth, stand age, size, crown cover, and various aspen...

Demographic history and rare allele sharing among human populations.

PubMed

Gravel, Simon; Henn, Brenna M; Gutenkunst, Ryan N; Indap, Amit R; Marth, Gabor T; Clark, Andrew G; Yu, Fuli; Gibbs, Richard A; Bustamante, Carlos D

2011-07-19

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence.

Demographic history and rare allele sharing among human populations

PubMed Central

Gravel, Simon; Henn, Brenna M.; Gutenkunst, Ryan N.; Indap, Amit R.; Marth, Gabor T.; Clark, Andrew G.; Yu, Fuli; Gibbs, Richard A.; Bustamante, Carlos D.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Sudbrak, Ralf; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Sherry, Stephen T.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Auton, Adam; Iqbal, Zamin; Lunter, Gerton; Marchini, Jonathan L.; Moutsianas, Loukas; Myers, Simon; Tumian, Afidalina; Desany, Brian; Knight, James; Winer, Roger; Craig, David W.; Beckstrom-Sternberg, Steve M.; Christoforides, Alexis; Kurdoglu, Ahmet A.; Pearson, John V.; Sinari, Shripad A.; Tembe, Waibhav D.; Haussler, David; Hinrichs, Angie S.; Katzman, Sol J.; Kern, Andrew; Kuhn, Robert M.; Przeworski, Molly; Hernandez, Ryan D.; Howie, Bryan; Kelley, Joanna L.; Melton, S. Cord; Abecasis, Gonçalo R.; Li, Yun; Anderson, Paul; Blackwell, Tom; Chen, Wei; Cookson, William O.; Ding, Jun; Kang, Hyun Min; Lathrop, Mark; Liang, Liming; Moffatt, Miriam F.; Scheet, Paul; Sidore, Carlo; Snyder, Matthew; Zhan, Xiaowei; Zöllner, Sebastian; Awadalla, Philip; Casals, Ferran; Idaghdour, Youssef; Keebler, John; Stone, Eric A.; Zilversmit, Martine; Jorde, Lynn; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Sahinalp, S. Cenk; Sudmant, Peter H.; Mardis, Elaine R.; Chen, Ken; Chinwalla, Asif; Ding, Li; Koboldt, Daniel C.; McLellan, Mike D.; Dooling, David; Weinstock, George; Wallis, John W.; Wendl, Michael C.; Zhang, Qunyuan; Durbin, Richard M.; Albers, Cornelis A.; Ayub, Qasim; Balasubramaniam, Senduran; Barrett, Jeffrey C.; Carter, David M.; Chen, Yuan; Conrad, Donald F.; Danecek, Petr; Dermitzakis, Emmanouil T.; Hu, Min; Huang, Ni; Hurles, Matt E.; Jin, Hanjun; Jostins, Luke; Keane, Thomas M.; Le, Si Quang; Lindsay, Sarah; Long, Quan; MacArthur, Daniel G.; Montgomery, Stephen B.; Parts, Leopold; Stalker, James; Tyler-Smith, Chris; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Balasubramanian, Suganthi; Bjornson, Robert; Du, Jiang; Grubert, Fabian; Habegger, Lukas; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Li, Yingrui; Luo, Ruibang; Marth, Gabor T.; Garrison, Erik P.; Kural, Deniz; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; McCarroll, Steven A.; Banks, Eric; DePristo, Mark A.; Handsaker, Robert E.; Hartl, Chris; Korn, Joshua M.; Li, Heng; Nemesh, James C.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Degenhardt, Jeremiah; Kaganovich, Mark; Clarke, Laura; Smith, Richard E.; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Humphray, Sean; Cheetham, R. Keira; Eberle, Michael; Kahn, Scott; Murray, Lisa; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Peckham, Heather E.; Sun, Yongming A.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Xiao, Chunlin; Iqbal, Zamin; Desany, Brian; Blackwell, Tom; Snyder, Matthew; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Chen, Ken; Chinwalla, Asif; Ding, Li; McLellan, Mike D.; Wallis, John W.; Hurles, Matt E.; Conrad, Donald F.; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Du, Jiang; Grubert, Fabian; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Gibbs, Richard A.; Bainbridge, Matthew; Challis, Danny; Coafra, Cristian; Dinh, Huyen; Kovar, Christie; Lee, Sandy; Muzny, Donna; Nazareth, Lynne; Reid, Jeff; Sabo, Aniko; Yu, Fuli; Yu, Jin; Marth, Gabor T.; Garrison, Erik P.; Indap, Amit; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Ward, Alistair N.; Wu, Jiantao; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Garimella, Kiran V.; Hartl, Chris; Shefler, Erica; Sougnez, Carrie L.; Wilkinson, Jane; Clark, Andrew G.; Gravel, Simon; Grubert, Fabian; Clarke, Laura; Flicek, Paul; Smith, Richard E.; Zheng-Bradley, Xiangqun; Sherry, Stephen T.; Khouri, Hoda M.; Paschall, Justin E.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Katzman, Sol J.; Abecasis, Gonçalo R.; Blackwell, Tom; Mardis, Elaine R.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Koboldt, Daniel C.; Durbin, Richard M.; Balasubramaniam, Senduran; Coffey, Allison; Keane, Thomas M.; MacArthur, Daniel G.; Palotie, Aarno; Scott, Carol; Stalker, James; Tyler-Smith, Chris; Gerstein, Mark B.; Balasubramanian, Suganthi; Chakravarti, Aravinda; Knoppers, Bartha M.; Abecasis, Gonçalo R.; Bustamante, Carlos D.; Gharani, Neda; Gibbs, Richard A.; Jorde, Lynn; Kaye, Jane S.; Kent, Alastair; Li, Taosha; McGuire, Amy L.; McVean, Gil A.; Ossorio, Pilar N.; Rotimi, Charles N.; Su, Yeyang; Toji, Lorraine H.; TylerSmith, Chris; Brooks, Lisa D.; Felsenfeld, Adam L.; McEwen, Jean E.; Abdallah, Assya; Juenger, Christopher R.; Clemm, Nicholas C.; Collins, Francis S.; Duncanson, Audrey; Green, Eric D.; Guyer, Mark S.; Peterson, Jane L.; Schafer, Alan J.; Abecasis, Gonçalo R.; Altshuler, David L.; Auton, Adam; Brooks, Lisa D.; Durbin, Richard M.; Gibbs, Richard A.; Hurles, Matt E.; McVean, Gil A.

2011-01-01

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

Modelling the UNAIDS 90-90-90 treatment cascade for gay, bisexual and other men who have sex with men in South Africa: using the findings of a data triangulation process to map a way forward.

PubMed

Scheibe, Andrew; Grasso, Michael; Raymond, Henry Fisher; Manyuchi, Albert; Osmand, Thomas; Lane, Tim; Struthers, Helen

2018-03-01

A data triangulation exercise was carried out between 2013 and 2015 to assess the HIV epidemic and response among gay, bisexual and other men who have sex with men (GBMSM) in South Africa. We used the findings to assess progress in achieving the UNAIDS 90-90-90 goals for GBMSM in the country. Three scenarios were developed using different GBMSM population factors (2.0, 3.5 and 5.0% of males aged ≥15) to estimate the population size, HIV prevalence of 13.2-49.5%, and 68% of GBMSM knowing their status. Due to data gaps, general population data were used as estimates of GBMSM on antiretroviral therapy (ART) and virologically suppressed (25.7 and 84.0%, respectively). The biggest gap is access to ART. To address the data gap we recommend developing data collection tools, indicators, and further quantification of HIV cascades. Targeted testing, linkage to services and scaled-up prevention interventions (including pre-exposure prophylaxis) are also required.

Mapping the Spread of Methamphetamine Abuse in California From 1995 to 2008

PubMed Central

Ponicki, William R.; Remer, Lillian G.; Waller, Lance A.; Zhu, Li; Gorman, Dennis M.

2013-01-01

Objectives. From 1983 to 2008, the incidence of methamphetamine abuse and dependence (MA) presenting at hospitals in California increased 13-fold. We assessed whether this growth could be characterized as a drug epidemic. Methods. We geocoded MA discharges to residential zip codes from 1995 through 2008. We related discharges to population and environmental characteristics using Bayesian Poisson conditional autoregressive models, correcting for small area effects and spatial misalignment and enabling an assessment of contagion between areas. Results. MA incidence increased exponentially in 3 phases interrupted by implementation of laws limiting access to methamphetamine precursors. MA growth from 1999 through 2008 was 17% per year. MA was greatest in areas with larger White or Hispanic low-income populations, small household sizes, and good connections to highway systems. Spatial misalignment was a source of bias in estimated effects. Spatial autocorrelation was substantial, accounting for approximately 80% of error variance in the model. Conclusions. From 1995 through 2008, MA exhibited signs of growth and spatial spread characteristic of drug epidemics, spreading most rapidly through low-income White and Hispanic populations living outside dense urban areas. PMID:23078474

Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

PubMed

Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

2012-08-01

White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

Population demographics and genetic diversity in remnant and translocated populations of sea otters

USGS Publications Warehouse

Bodkin, James L.; Ballachey, Brenda E.; Cronin, M.A.; Scribner, K.T.

1999-01-01

The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter (Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Metochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (r = -0.741, p = 0.038) and minimum population size (r = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, altough growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.

Subnormalized states and trace-nonincreasing maps

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

Cappellini, Valerio; Sommers, Hans-Juergen; Zyczkowski, Karol

2007-05-15

We investigate the set of completely positive, trace-nonincreasing linear maps acting on the set M{sub N} of mixed quantum states of size N. Extremal point of this set of maps are characterized and its volume with respect to the Hilbert-Schmidt (HS) (Euclidean) measure is computed explicitly for an arbitrary N. The spectra of partially reduced rescaled dynamical matrices associated with trace-nonincreasing completely positive maps belong to the N cube inscribed in the set of subnormalized states of size N. As a by-product we derive the measure in M{sub N} induced by partial trace of mixed quantum states distributed uniformly withmore » respect to the HS measure in M{sub N{sup 2}}.« less

Development of a Mapped Diabetes Community Program Guide for a Safety Net Population

PubMed Central

Zallman, Leah; Ibekwe, Lynn; Thompson, Jennifer W.; Ross-Degnan, Dennis; Oken, Emily

2014-01-01

Purpose Enhancing linkages between patients and community programs is increasingly recognized as a method for improving physical activity, nutrition and weight management. Although interactive mapped community program guides may be beneficial, there remains a dearth of articles that describe the processes and practicalities of creating such guides. This article describes the development of an interactive, web-based mapped community program guide at a safety net institution and the lessons learned from that process. Conclusions This project demonstrated the feasibility of creating two maps – a program guide and a population health map. It also revealed some key challenges and lessons for future work in this area, particularly within safety-net institutions. Our work underscores the need for developing partnerships outside of the health care system and the importance of employing community-based participatory methods. In addition to facilitating improvements in individual wellness, mapping community programs also has the potential to improve population health management by healthcare delivery systems such as hospitals, health centers, or public health systems, including city and state departments of health. PMID:24752180

Evidence for r- and K-selection in a wild bird population: a reciprocal link between ecology and evolution.

PubMed

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).

Preliminary geologic map of the Perris 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Digital preparation by Bovard, Kelly R.; Alvarez, Rachel M.

2003-01-01

Open-File Report 03-270 contains a digital geologic map database of the Perris 7.5’ quadrangle, Riverside County, California that includes: 1. ARC/INFO (Environmental Systems Research Institute, http://www.esri.com) version 7.2.1 coverages of the various elements of the geologic map. 2. A Postscript file to plot the geologic map on a topographic base, and containing a Correlation of Map Units diagram (CMU), a Description of Map Units (DMU), and an index map. 3. Portable Document Format (.pdf) files of: a. A Readme file b. The same graphic as described in 2 above. Test plots have not produced precise 1:24,000- scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formationname, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc.

Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies.

PubMed

Yamaguchi-Kabata, Yumi; Nakazono, Kazuyuki; Takahashi, Atsushi; Saito, Susumu; Hosono, Naoya; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki

2008-10-01

Because population stratification can cause spurious associations in case-control studies, understanding the population structure is important. Here, we examined Japanese population structure by "Eigenanalysis," using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster includes most of the individuals from Okinawa. The SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were found in the HLA region in chromosome 6. The nonsynonymous SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were the Val/Ala polymorphism (rs3827760) in the EDAR gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the ABCC11 gene, associated with ear-wax type. Genetic differentiation was observed, even among different regions in Honshu Island, the largest island of Japan. Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large.

Novel Population Specific Autosomal Copy Number Variation and Its Functional Analysis amongst Negritos from Peninsular Malaysia

PubMed Central

Mokhtar, Siti Shuhada; Marshall, Christian R.; Phipps, Maude E.; Thiruvahindrapuram, Bhooma; Lionel, Anath C.; Scherer, Stephen W.; Peng, Hoh Boon

2014-01-01

Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia. PMID:24956385

Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.

PubMed

Mokhtar, Siti Shuhada; Marshall, Christian R; Phipps, Maude E; Thiruvahindrapuram, Bhooma; Lionel, Anath C; Scherer, Stephen W; Peng, Hoh Boon

2014-01-01

Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.

Quaternary Geologic Map of the Regina 4 Degrees x 6 Degrees Quadrangle, United States and Canada

USGS Publications Warehouse

Fullerton, David S.; Christiansen, Earl A.; Schreiner, Bryan T.; Colton, Roger B.; Clayton, Lee; Bush, Charles A.; Fullerton, David S.

2007-01-01

For scientific purposes, the map differentiates Quaternary surficial deposits and materials on the basis of clast lithology or composition, matrix texture or particle size, structure, genesis, stratigraphic relations, engineering geologic properties, and relative age, as shown on the correlation diagram and indicated in the 'Description of Map Units'. Deposits of some constructional landforms, such as end moraines, are distinguished as map units. Deposits of erosional landforms, such as outwash terraces, are not distinguished, although glaciofluvial, ice-contact, fluvial, and lacustrine deposits that are mapped may be terraced. Differentiation of sequences of fluvial and glaciofluvial deposits at this scale is not possible. For practical purposes, the map is a surficial materials map. Materials are distinguished on the basis of lithology or composition, texture or particle size, and other physical, chemical, and engineering characteristics. It is not a map of soils that are recognized and classified in pedology or agronomy. Rather, it is a generalized map of soils as recognized in engineering geology, or of substrata or parent materials in which pedologic or agronomic soils are formed. As a materials map, it serves as a base from which a variety of maps for use in planning engineering, land-use planning, or land-management projects can be derived and from which a variety of maps relating to earth surface processes and Quaternary geologic history can be derived.

Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines.

PubMed

Wang, Ju; McClean, Phillip E; Lee, Rian; Goos, R Jay; Helms, Ted

2008-04-01

Association mapping is an alternative to mapping in a biparental population. A key to successful association mapping is to avoid spurious associations by controlling for population structure. Confirming the marker/trait association in an independent population is necessary for the implementation of the marker in other genetic studies. Two independent soybean populations consisting of advanced breeding lines representing the diversity within maturity groups 00, 0, and I were screened in multi-site, replicated field trials to discover molecular markers associated with iron deficiency chlorosis (IDC), a major yield-limiting factor in soybean. Lines with extreme phenotypes were initially screened to identify simple sequence repeat (SSR) markers putatively associated with the IDC. Marker data collected from all lines were used to control for population structure and kinship relationships. Single factor analysis of variance (SFA) and mixed linear model (MLM) analyses were used to discover marker/trait associations. The MLM analyses, which include population structure, kinship or both factors, reduced the number of markers significantly associated with IDC by 50% compared with SFA. With the MLM approach, three markers were found to be associated with IDC in the first population. Two of these markers, Satt114 and Satt239, were also found to be associated with IDC in the second confirmation population. For both populations, those lines with the tolerance allele at both these two marker loci had significantly lower IDC scores than lines with one or no tolerant alleles.

Direction of Translation and Size of Bacteriophage φX174 Cistrons

PubMed Central

Benbow, Robert M.; Mayol, Robert F.; Picchi, Joanna C.; Sinsheimer, Robert L.

1972-01-01

Translation of the bacteriophage φX174 genome follows cistron order D-E-F-G-H-A-B-C. To establish this, the position of a nonsense mutation on the genetic map was compared with the physical size (molecular weight) of the appropriate protein fragment generated in nonpermissive cells. Distances on the φX174 genetic map and distances on a physical map constructed from the molecular weights of φX174 proteins and protein fragments are proportional over most of the genome with the exception of the high recombination region within cistron A. Images PMID:16789133

GIS Database and Google Map of the Population at Risk of Cholangiocarcinoma in Mueang Yang District, Nakhon Ratchasima Province of Thailand.

PubMed

Kaewpitoon, Soraya J; Rujirakul, Ratana; Joosiri, Apinya; Jantakate, Sirinun; Sangkudloa, Amnat; Kaewthani, Sarochinee; Chimplee, Kanokporn; Khemplila, Kritsakorn; Kaewpitoon, Natthawut

2016-01-01

Cholangiocarcinoma (CCA) is a serious problem in Thailand, particularly in the northeastern and northern regions. Database of population at risk are need required for monitoring, surveillance, home health care, and home visit. Therefore, this study aimed to develop a geographic information system (GIS) database and Google map of the population at risk of CCA in Mueang Yang district, Nakhon Ratchasima province, northeastern Thailand during June to October 2015. Populations at risk were screened using the Korat CCA verbal screening test (KCVST). Software included Microsoft Excel, ArcGIS, and Google Maps. The secondary data included the point of villages, sub-district boundaries, district boundaries, point of hospital in Mueang Yang district, used for created the spatial databese. The populations at risk for CCA and opisthorchiasis were used to create an arttribute database. Data were tranfered to WGS84 UTM ZONE 48. After the conversion, all of the data were imported into Google Earth using online web pages www.earthpoint.us. Some 222 from a 4,800 population at risk for CCA constituted a high risk group. Geo-visual display available at following www.google.com/maps/d/u/0/ edit?mid=zPxtcHv_iDLo.kvPpxl5mAs90 and hl=th. Geo-visual display 5 layers including: layer 1, village location and number of the population at risk for CCA; layer 2, sub-district health promotion hospital in Mueang Yang district and number of opisthorchiasis; layer 3, sub-district district and the number of population at risk for CCA; layer 4, district hospital and the number of population at risk for CCA and number of opisthorchiasis; and layer 5, district and the number of population at risk for CCA and number of opisthorchiasis. This GIS database and Google map production process is suitable for further monitoring, surveillance, and home health care for CCA sufferers.

Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.)

PubMed Central

Wei, Chunhua; Chen, Xiner; Wang, Zhongyuan; Liu, Qiyan; Li, Hao; Zhang, Yong; Ma, Jianxiang; Yang, Jianqiang

2017-01-01

The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies. PMID:28704497

Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.).

PubMed

Wei, Chunhua; Chen, Xiner; Wang, Zhongyuan; Liu, Qiyan; Li, Hao; Zhang, Yong; Ma, Jianxiang; Yang, Jianqiang; Zhang, Xian

2017-01-01

The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies.

Aedes aegypti Global Suitability Maps Using a Water Container Energy Balance Model for Dengue Risk Applications

NASA Astrophysics Data System (ADS)

Steinhoff, D.

2015-12-01

Dengue infections are estimated to total nearly 400 million per year worldwide, with both the geographic range and the magnitude of infections having increased in the past 50 years. The primary dengue vector mosquito Aedes aegypti is closely associated with humans. It lives exclusively in urban and semi-urban areas, preferentially bites humans, and spends its developmental stages in artificial water containers. Climate regulates the development of Ae. aegypti immature mosquitoes in artificial containers. Potential containers for Ae. aegypti immature development include, but are not limited to, small sundry items (e.g., bottles, cans, plastic containers), buckets, tires, barrels, tanks, and cisterns. Successful development of immature mosquitoes from eggs to larvae, pupae, and eventually adults is largely dependent on the availability of water and the thermal properties of the water in the containers. Recent work has shown that physics-based approaches toward modeling container water properties are promising for resolving the complexities of container water dynamics and the effects on immature mosquito development. An energy balance container model developed by the author, termed the Water Height And Temperature in Container Habitats Energy Model (WHATCH'EM), solves for water temperature and height for user-specified containers with readily available weather data. Here we use WHATCH'EM with NASA Earth Science products used as input to construct global suitability maps based on established water temperature ranges for immature Ae. aegypti mosquitoes. A proxy for dengue risk is provided from habitat suitability, but also population estimates, as Ae. aegypti is closely associated with human activity. NASA gridded Global Population of the World data is used to mask out rural areas with low dengue risk. Suitability maps are illustrated for a variety of containers (size, material, color) and shading scenarios.

Titan2D simulations of dome-collapse pyroclastic flows for crisis assessments on Montserrat

NASA Astrophysics Data System (ADS)

Widiwijayanti, C.; Voight, B.; Hidayat, D.; Patra, A.; Pitman, E.

2010-12-01

The Soufriere Hills Volcano (SHV), Montserrat, has experienced numerous episodes of lava dome collapses since 1995. Collapse volumes range from small rockfalls to major dome collapses (as much as ~200 M m3). Problems arise in hazards mitigation, particularly in zoning for populated areas. Determining the likely extent of flowage deposits in various scenarios is important for hazards zonation, provision of advice by scientists, and decision making by public officials. Towards resolution of this issue we have tested the TITAN2D code, calibrated parameters for an SHV database, and using updated topography have provided flowage maps for various scenarios and volume classes from SHV, for use in hazards assessments. TITAN2D is a map plane (depth averaged) simulator of granular flow and yields mass distributions over a DEM. Two Coulomb frictional parameters (basal and internal frictions) and initial source conditions (volume, source location, and source geometry) of single or multiple pulses in a dome-collapse type event control behavior of the flow. Flow kinematics are captured, so that the dynamics of flow can be examined spatially from frame to frame, or as a movie. Our hazard maps include not only the final deposit, but also areas inundated by moving debris prior to deposition. Simulations from TITAN2D were important for analysis of crises in the period 2007-2010. They showed that any very large mass released on the north slope would be strongly partitioned by local topography, and thus it was doubtful that flows of very large size (>20 M m3) could be generated in the Belham River drainage. This partitioning effect limited runout toward populated areas. These effects were interpreted to greatly reduce the down-valley risk of ash-cloud surges.

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

PubMed Central

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

2018-01-01

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

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

PubMed

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

2018-05-01

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

A parametric ribcage geometry model accounting for variations among the adult population.

PubMed

Wang, Yulong; Cao, Libo; Bai, Zhonghao; Reed, Matthew P; Rupp, Jonathan D; Hoff, Carrie N; Hu, Jingwen

2016-09-06

The objective of this study is to develop a parametric ribcage model that can account for morphological variations among the adult population. Ribcage geometries, including 12 pair of ribs, sternum, and thoracic spine, were collected from CT scans of 101 adult subjects through image segmentation, landmark identification (1016 for each subject), symmetry adjustment, and template mesh mapping (26,180 elements for each subject). Generalized procrustes analysis (GPA), principal component analysis (PCA), and regression analysis were used to develop a parametric ribcage model, which can predict nodal locations of the template mesh according to age, sex, height, and body mass index (BMI). Two regression models, a quadratic model for estimating the ribcage size and a linear model for estimating the ribcage shape, were developed. The results showed that the ribcage size was dominated by the height (p=0.000) and age-sex-interaction (p=0.007) and the ribcage shape was significantly affected by the age (p=0.0005), sex (p=0.0002), height (p=0.0064) and BMI (p=0.0000). Along with proper assignment of cortical bone thickness, material properties and failure properties, this parametric ribcage model can directly serve as the mesh of finite element ribcage models for quantifying effects of human characteristics on thoracic injury risks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Variation of short tandem repeats within and between species belonging to the Canidae family.

PubMed

Fredholm, M; Winterø, A K

1995-01-01

Frequency distribution and allele size in 20 canine microsatellite loci were analyzed in 33 flat-coated retrievers, 32 dachshunds, 10 red foxes, and 10 Arctic foxes. Overall, the major difference between the two dog breeds was the relative allele frequencies rather than the size ranges of alleles at the individual locus. The average heterozygosity within the two dog breeds was not significantly different. Since the average heterozygosity at several polymorphic loci is a relative measure of heterogeneity within the population, analysis of heterozygosity within microsatellite loci is suggested as a measure for the diversity of populations. Eighty percent (16 of 20) of the canine microsatellite primer pairs amplified corresponding loci in the two fox species. This reflects a very high sequence conservation within the Canidae family relative to findings in, for instance, the Muridae family. This indicates that it will be possible to utilize the well-characterized fox karyotype instead of the dog karyotype as a step towards physical mapping of the dog genome. Analysis of exclusion power and probabilities of genetic identity between unrelated animals by use of the seven most informative loci demonstrated that it will be possible to assemble a panel of microsatellite loci that is effective for parentage analysis in all breeds.

The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question.

PubMed

Jacquemin, Julie; Bhatia, Dharminder; Singh, Kuldeep; Wing, Rod A

2013-05-01

The wild relatives of rice contain a virtually untapped reservoir of traits that can be used help drive the 21st century green revolution aimed at solving world food security issues by 2050. To better understand and exploit the 23 species of the Oryza genus the rice research community is developing foundational resources composed of: 1) reference genomes and transcriptomes for all 23 species; 2) advanced mapping populations for functional and breeding studies; and 3) in situ conservation sites for ecological, evolutionary and population genomics. To this end, 16 genome sequencing projects are currently underway, and all completed assemblies have been annotated; and several advanced mapping populations have been developed, and more will be generated, mapped, and phenotyped, to uncover useful alleles. As wild Oryza populations are threatened by human activity and climate change, we also discuss the urgent need for sustainable in situ conservation of the genus. Copyright © 2013 Elsevier Ltd. All rights reserved.

LPmerge: an R package for merging genetic maps by linear programming.

PubMed

Endelman, Jeffrey B; Plomion, Christophe

2014-06-01

Consensus genetic maps constructed from multiple populations are an important resource for both basic and applied research, including genome-wide association analysis, genome sequence assembly and studies of evolution. The LPmerge software uses linear programming to efficiently minimize the mean absolute error between the consensus map and the linkage maps from each population. This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved. When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts. LPmerge is on CRAN at http://cran.r-project.org/web/packages/LPmerge. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mapping geomorphic process domains to predict hillslope sediment size distribution using remotely-sensed data and field sampling, Inyo Creek, California

NASA Astrophysics Data System (ADS)

Leclere, S.; Sklar, L. S.; Genetti, J. R.

2014-12-01

The size distribution of sediments produced on hillslopes and supplied to channels depends on the geomorphic processes that weather, detach and transport rock fragments down slopes. Little in the way of theory or data is available to predict patterns in hillslope size distributions at the catchment scale from topographic and geologic maps. Here we use aerial imagery and a variety of remote sensing techniques to map and categorize geomorphic landscape units (GLUs) by inferred sediment production process regime, across the steep mountain catchment of Inyo Creek, eastern Sierra Nevada, California. We also use field measurements of particle size and local geomorphic attributes to test and refine GLU determinations. Across the 2 km of relief in this catchment, landcover varies from bare bedrock cliffs at higher elevations to vegetated, regolith-covered convex slopes at lower elevations. Hillslope gradient could provide a simple index of sediment production process, from rock spallation and landsliding at highest slopes, to tree-throw and other disturbance-driven soil production processes at lowest slopes. However, many other attributes are needed for a more robust predictive model, including elevation, curvature, aspect, drainage area, and color. We combine tools from ArcGIS, ERDAS Imagine and Envi with groundtruthing field work to find an optimal combination of attributes for defining sediment production GLUs. Key challenges include distinguishing: weathered from freshly eroded bedrock, boulders from intact bedrock, and landslide deposits from talus slopes. We take advantage of emerging technologies that provide new ways of conducting fieldwork and comparing field data to mapping solutions. In particular, cellphone GPS is approaching the accuracy of dedicated GPS systems and the ability to geo-reference photos simplifies field notes and increases accuracy of later map creation. However, the predictive power of the GLU mapping approach is limited by inherent uncertainty in remotely sensed data and aerial imagery. This work is a contribution toward the long-term goal of reliable and automated mapping of hillslope sediment size distributions for use in sediment budgets and hazard delineation, and for understanding the feedbacks between climate, erosion and topography that drive sediment production.

Mapping of yellow mosaic virus (YMV) resistance in soybean (Glycine max L. Merr.) through association mapping approach.

PubMed

Kumar, Bhupender; Talukdar, Akshay; Verma, Khushbu; Bala, Indu; Harish, G D; Gowda, Sarmrat; Lal, S K; Sapra, R L; Singh, K P

2015-02-01

Yellow Mosaic Virus (YMV) is a serious disease of soybean. Resistance to YMV was mapped in 180 soybean genotypes through association mapping approach using 121 simple sequence repeats (SSR) and four resistance gene analogue (RGA)-based markers. The association mapping population (AMP) (96 genotypes) and confirmation population (CP) (84 genotypes) was tested for resistance to YMV at hot-spot consecutively for 3 years (2007-2009). The genotypes exhibited significant variability for YMV resistance (P < 0.01). Molecular genotyping and population structure analysis with 'admixture' co-ancestry model detected seven optimal sub-populations in the AMP. Linkage disequilibrium (LD) between the markers extended up to 35 and 10 cM with r2 > 0.15, and >0.25, respectively. The 4 RGA-based markers showed no association with YMV resistance. Two SSR markers, Satt301 and GMHSP179 on chromosome 17 were found to be in significant LD with YMV resistance. Contingency Chi-square test confirmed the association (P < 0.01) and the utility of the markers was validated in the CP. It would pave the way for marker assisted selection for YMV resistance in soybean. This is the first report of its kind in soybean.

A High-Resolution InDel (Insertion–Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea

PubMed Central

Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.

2016-01-01

Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major genomic regions harboring each of pod number and seed yield robust QTLs (15–28% phenotypic variation explained) were identified on chromosomes 2, 4, and 6. The integration of genetic and physical maps at these QTLs mapped on chromosomes scaled-down the long major QTL intervals into high-resolution short pod number and seed yield robust QTL physical intervals (0.89–2.94 Mb) which were essentially got validated in multiple genetic backgrounds of two chickpea mapping populations. The genome-wide InDel markers including natural allelic variants and genomic loci/genes delineated at major six especially in one colocalized novel congruent robust pod number and seed yield robust QTLs mapped on a high-density consensus genetic map were found most promising in chickpea. These functionally relevant molecular tags can drive marker-assisted genetic enhancement to develop high-yielding cultivars with increased seed/pod number and yield in chickpea. PMID:27695461

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

PubMed Central

2012-01-01

Background Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. Conclusions Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut. PMID:23140574

A Genomewide Admixture Mapping Panel for Hispanic/Latino Populations

PubMed Central

Mao, Xianyun ; Bigham, Abigail W. ; Mei, Rui ; Gutierrez, Gerardo ; Weiss, Ken M. ; Brutsaert, Tom D. ; Leon-Velarde, Fabiola ; Moore, Lorna G. ; Vargas, Enrique ; McKeigue, Paul M. ; Shriver, Mark D. ; Parra, Esteban J. 

2007-01-01

Admixture mapping (AM) is a promising method for the identification of genetic risk factors for complex traits and diseases showing prevalence differences among populations. Efficient application of this method requires the use of a genomewide panel of ancestry-informative markers (AIMs) to infer the population of origin of chromosomal regions in admixed individuals. Genomewide AM panels with markers showing high frequency differences between West African and European populations are already available for disease-gene discovery in African Americans. However, no such a map is yet available for Hispanic/Latino populations, which are the result of two-way admixture between Native American and European populations or of three-way admixture of Native American, European, and West African populations. Here, we report a genomewide AM panel with 2,120 AIMs showing high frequency differences between Native American and European populations. The average intermarker genetic distance is ∼1.7 cM. The panel was identified by genotyping, with the Affymetrix GeneChip Human Mapping 500K array, a population sample with European ancestry, a Mesoamerican sample comprising Maya and Nahua from Mexico, and a South American sample comprising Aymara/Quechua from Bolivia and Quechua from Peru. The main criteria for marker selection were both high information content for Native American/European ancestry (measured as the standardized variance of the allele frequencies, also known as “f value”) and small frequency differences between the Mesoamerican and South American samples. This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas. PMID:17503334

Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.).

PubMed

Zhu, Yufeng; Yin, Yanfei; Yang, Keqiang; Li, Jihong; Sang, Yalin; Huang, Long; Fan, Shu

2015-08-18

Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. High-density genetic maps for walnut containing 16 LGs were constructed using the SLAF-seq method with an F1 population. One QTL for walnut anthracnose resistance was identified based on the map. The results will aid molecular marker-assisted breeding and walnut resistance genes identification.

Exploiting induced variation to dissect quantitative traits in barley.

PubMed

Druka, Arnis; Franckowiak, Jerome; Lundqvist, Udda; Bonar, Nicola; Alexander, Jill; Guzy-Wrobelska, Justyna; Ramsay, Luke; Druka, Ilze; Grant, Iain; Macaulay, Malcolm; Vendramin, Vera; Shahinnia, Fahimeh; Radovic, Slobodanka; Houston, Kelly; Harrap, David; Cardle, Linda; Marshall, David; Morgante, Michele; Stein, Nils; Waugh, Robbie

2010-04-01

The identification of genes underlying complex quantitative traits such as grain yield by means of conventional genetic analysis (positional cloning) requires the development of several large mapping populations. However, it is possible that phenotypically related, but more extreme, allelic variants generated by mutational studies could provide a means for more efficient cloning of QTLs (quantitative trait loci). In barley (Hordeum vulgare), with the development of high-throughput genome analysis tools, efficient genome-wide identification of genetic loci harbouring mutant alleles has recently become possible. Genotypic data from NILs (near-isogenic lines) that carry induced or natural variants of genes that control aspects of plant development can be compared with the location of QTLs to potentially identify candidate genes for development--related traits such as grain yield. As yield itself can be divided into a number of allometric component traits such as tillers per plant, kernels per spike and kernel size, mutant alleles that both affect these traits and are located within the confidence intervals for major yield QTLs may represent extreme variants of the underlying genes. In addition, the development of detailed comparative genomic models based on the alignment of a high-density barley gene map with the rice and sorghum physical maps, has enabled an informed prioritization of 'known function' genes as candidates for both QTLs and induced mutant genes.

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.

PubMed

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.

On the absence of a correlation between population size and 'toolkit size' in ethnographic hunter-gatherers.

PubMed

Aoki, Kenichi

2018-04-05

In apparent contradiction to the theoretically predicted effect of population size on the quality/quantity of material culture, statistical analyses on ethnographic hunter-gatherers have shown an absence of correlation between population size and toolkit size. This has sparked a heated, if sometimes tangential, debate as to the usefulness of the theoretical models and as to what modes of cultural transmission humans are capable of and hunter-gatherers rely on. I review the directly relevant theoretical literature and argue that much of the confusion is caused by a mismatch between the theoretical variable and the empirical observable. I then confirm that a model incorporating the appropriate variable does predict a positive association between population size and toolkit size for random oblique, vertical, best-of- K , conformist, anticonformist, success bias and one-to-many cultural transmission, with the caveat that for all populations sampled, the population size has remained constant and toolkit size has reached the equilibrium for this population size. Finally, I suggest three theoretical scenarios, two of them involving variable population size, that would attenuate or eliminate this association and hence help to explain the empirical absence of correlation.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Linkage mapping in a watermelon population segregating for fusarium wilt resistance

Treesearch

Leigh K. Hawkins; Fenny Dane; Thomas L. Kubisiak; Billy B. Rhodes; Robert L. Jarret

2001-01-01

Isozyme, randomly amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR) markers were used to generate a linkage map in an F2 and F3 watermelon (Citrullus lanatus (Thumb.) Matsum. & Nakai) population derived from a cross between the fusarium wilt (Fusarium oxysporum f....

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

PubMed

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.

Domestic well locations and populations served in the contiguous U.S.: 1990

USGS Publications Warehouse

Johnson, Tyler; Belitz, Kenneth

2017-01-01

We estimate the location and population served by domestic wells in the contiguous United States in two ways: (1) the “Block Group Method” or BGM, uses data from the 1990 census, and (2) the “Road-Enhanced Method” or REM, refines the locations by using a buffer expansion and shrinkage technique along roadways to define areas where domestic wells exist. The fundamental assumption is that houses (and therefore domestic wells) are located near a named road. The results are presented as two nationally-consistent domestic-well population datasets.While both methods can be considered valid, the REM map is more precise in locating domestic wells; the REM map has a smaller amount of spatial bias (Type 1 and Type 2 errors nearly equal vs biased in Type 1), total error (10.9% vs 23.7%), and distance error (2.0 km vs 2.7 km), when comparing the REM and BGM maps to a calibration map in California. However, the BGM map is more inclusive of all potential locations for domestic wells. Independent domestic well datasets from the USGS, and the States of MN, NV, and TX show that the BGM captures about 5 to 10% more wells than the REM.One key difference between the BGM and the REM is the mapping of low density areas. The REM reduces areas mapped as low density by 57%, concentrating populations into denser regions. Therefore, if one is trying to capture all of the potential areas of domestic-well usage, then the BGM map may be more applicable. If location is more imperative, then the REM map is better at identifying areas of the landscape with the highest probability of finding a domestic well. Depending on the purpose of a study, a combination of both maps can be used.

A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts

PubMed Central

Shirasawa, Kenta; Hand, Melanie L.; Henderson, Steven T.; Okada, Takashi; Johnson, Susan D.; Taylor, Jennifer M.; Spriggs, Andrew; Siddons, Hayley; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Koltunow, Anna M. G.

2015-01-01

Background and Aims Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. Methods RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. Key Results A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. Conclusions A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations. PMID:25538115

Making It Count: Improving Estimates of the Size of Transgender and Gender Nonconforming Populations.

PubMed

Deutsch, Madeline B

2016-06-01

An accurate estimate of the number of transgender and gender nonconforming people is essential to inform policy and funding priorities and decisions. Historical reports of population sizes of 1 in 4000 to 1 in 50,000 have been based on clinical populations and likely underestimate the size of the transgender population. More recent population-based studies have found a 10- to 100-fold increase in population size. Studies that estimate population size should be population based, employ the two-step method to allow for collection of both gender identity and sex assigned at birth, and include measures to capture the range of transgender people with nonbinary gender identities.