WorldWideScience

Sample records for understanding population structure

  1. Understanding cooperative behavior in structurally disordered populations

    Science.gov (United States)

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

    2016-06-01

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

  2. Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers.

    Science.gov (United States)

    Arnau, Gemma; Bhattacharjee, Ranjana; Mn, Sheela; Chair, Hana; Malapa, Roger; Lebot, Vincent; K, Abraham; Perrier, Xavier; Petro, Dalila; Penet, Laurent; Pavis, Claudie

    2017-01-01

    Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods.

  3. Lagrangian Flow Network: a new tool to evaluate connectivity and understand the structural complexity of marine populations

    Science.gov (United States)

    Rossi, V.; Dubois, M.; Ser-Giacomi, E.; Monroy, P.; Lopez, C.; Hernandez-Garcia, E.

    2016-02-01

    Assessing the spatial structure and dynamics of marine populations is still a major challenge for ecologists. The necessity to manage marine resources from a large-scale perspective and considering the whole ecosystem is now recognized but the absence of appropriate tools to address these objectives limits the implementation of globally pertinent conservation planning. Inspired from Network Theory, we present a new methodological framework called Lagrangian Flow Network which allows a systematic characterization of multi-scale dispersal and connectivity of early life history stages of marine organisms. The network is constructed by subdividing the basin into an ensemble of equal-area subregions which are interconnected through the transport of propagules by ocean currents. The present version allows the identification of hydrodynamical provinces and the computation of various connectivity proxies measuring retention and exchange of larvae. Due to our spatial discretization and subsequent network representation, as well as our Lagrangian approach, further methodological improvements are handily accessible. These future developments include a parametrization of habitat patchiness, the implementation of realistic larval traits and the consideration of abiotic variables (e.g. temperature, salinity, planktonic resources...) and their effects on larval production and survival. While the model is potentially tunable to any species whose biological traits and ecological preferences are precisely known, it can also be used in a more generic configuration by efficient computing and analysis of a large number of experiments with relevant ecological parameters. It permits a better characterization of population connectivity at multiple scales and it informs its ecological and managerial interpretations.

  4. Understanding influences of culture and history on mtDNA variation and population structure in three populations from Assam, Northeast India.

    Science.gov (United States)

    Rej, Peter H; Deka, Ranjan; Norton, Heather L

    2017-05-06

    Positioned at the nexus of India, China, and Southeast Asia, Northeast India is presumed to have served as a channel for land-based human migration since the Upper Pleistocene. Assam is the largest state in the Northeast. We characterized the genetic background of three populations and examined the ways in which their population histories and cultural practices have influenced levels of intrasample and intersample variation. We examined sequence data from the mtDNA hypervariable control region and selected diagnostic mutations from the coding region in 128 individuals from three ethnic groups currently living in Assam: two Scheduled tribes (Sonowal Kachari and Rabha), and the non-Scheduled Tai Ahom. The populations of Assam sampled here express mtDNA lineages indicative of South Asian, Southeast Asian, and East Asian ancestry. We discovered two completely novel haplogroups in Assam that accounted for 6.2% of the lineages in our sample. We also identified a new subhaplogroup of M9a that is prevalent in the Sonowal Kachari of Assam (19.1%), but not present in neighboring Arunachal Pradesh, indicating substantial regional population structuring. Employing a large comparative dataset into a series of multidimensional scaling (MDS) analyses, we saw the Rabha cluster with populations sampled from Yunnan Province, indicating that the historical matrilineality of the Rabha has maintained lineages from Southern China. Assam has undergone multiple colonization events in the time since the initial peopling event, with populations from Southern China and Southeast Asia having the greatest influence on maternal lineages in the region. © 2017 Wiley Periodicals, Inc.

  5. Understanding how lake populations of arctic char are structured and function with special consideration of the potential effects of climate change: a multi-faceted approach.

    Science.gov (United States)

    Budy, Phaedra; Luecke, Chris

    2014-09-01

    Size dimorphism in fish populations, both its causes and consequences, has been an area of considerable focus; however, uncertainty remains whether size dimorphism is dynamic or stabilizing and about the role of exogenous factors. Here, we explored patterns among empirical vital rates, population structure, abundance and trend, and predicted the effects of climate change on populations of arctic char (Salvelinus alpinus) in two lakes. Both populations cycle dramatically between dominance by small (≤300 mm) and large (>300 mm) char. Apparent survival (Φ) and specific growth rates (SGR) were relatively high (40-96%; SGR range 0.03-1.5%) and comparable to those of conspecifics at lower latitudes. Climate change scenarios mimicked observed patterns of warming and resulted in temperatures closer to optimal for char growth (15.15 °C) and a longer growing season. An increase in consumption rates (28-34%) under climate change scenarios led to much greater growth rates (23-34%). Higher growth rates predicted under climate change resulted in an even greater predicted amplitude of cycles in population structure as well as an increase in reproductive output (Ro) and decrease in generation time (Go). Collectively, these results indicate arctic char populations (not just individuals) are extremely sensitive to small changes in the number of ice-free days. We hypothesize years with a longer growing season, predicted to occur more often under climate change, produce elevated growth rates of small char and act in a manner similar to a "resource pulse," allowing a sub-set of small char to "break through," thus setting the cycle in population structure.

  6. Structural image and video understanding

    NARCIS (Netherlands)

    Lou, Z.

    2016-01-01

    In this thesis, we have discussed how to exploit the structures in several computer vision topics. The five chapters addressed five computer vision topics using the image structures. In chapter 2, we proposed a structural model to jointly predict the age, expression and gender of a face. By modeling

  7. Understanding Content-and-Structure

    NARCIS (Netherlands)

    Kamps, J.; Marx, M.J.; de Rijke, M.; Sigurbjörnsson, B.; Trotman, A.; Lalmas, M.; Fuhr, N.

    2005-01-01

    Document-centric XML is a mixture of text and structure. +With the increased availability of document-centric XML content comes a need for query facilities in which both structural constraints and constraints on the content of the documents can be expressed. This has generated considerable interest

  8. Understanding the Structure of Bones

    Science.gov (United States)

    ... structure of bone is very similar to reinforced concrete that is used to make a building or ... a defective blueprint is produced that tells the cell to produce deformed collagen, resulting in bad collagen ...

  9. Understanding the structure of chocolate

    International Nuclear Information System (INIS)

    Schenk, H.; Peschar, R.

    2004-01-01

    Crystallization of cocoa-butter in the β phase from the melt under static conditions is only possible using the memory effect of cocoa-butter. Under all other conditions polymorphs with lower melting temperatures develop, whereas the β phase is the preferred one in chocolate. SAXS experiments proved 1,3-distearoyl-2-oleoylglycerol seeds with triple chain-length packing initiate the β-crystallization. Models for the different phases may be based on the crystal structure determinations of triacylglycerols. A new, patented, way of chocolate making is in development in which the traditional tempering process is replaced by another pre-crystallization process. The process is based on the use of seed crystals in the liquid phase and driven by a feedback system

  10. Intraspecific competition delays recovery of population structure.

    Science.gov (United States)

    Liess, Matthias; Foit, Kaarina

    2010-04-01

    Ecotoxicological field studies have shown that total abundance and biomass often recover shortly after pulsed toxicant stress. In contrast, population structure showed comparatively long-term alterations before reaching pre-treatment conditions. We investigated two mechanisms that may explain the prolonged recovery of population structure: latent toxicant effects on life-history traits on the individual level and competition on the population level. To test these hypotheses we exposed populations of Daphnia magna to a pulse of the pyrethroid Fenvalerate. For several generations the populations were kept at two different degrees of competition: strong competition at carrying capacity and reduced competition maintained by simulated predation. After disturbance due to Fenvalerate exposure, biomass recovered after 14-17 days. In contrast, size structure characterised by a lack of large and dominance of small organisms recovered after 43 days in populations with strong competition. Size structure recovered twice faster in populations with reduced competition. We explain this as follows: due to toxicant induced mortality, food availability and consequently birth rate increased and populations were dominated by small individuals. In populations without predation, these cohorts grew and eventually exerted high intraspecific competition that (i) stopped further growth of juveniles and (ii) increased mortality of adults. These demographic processes were mainly responsible for the prolonged recovery of size structure. In contrast, for populations with predation, the regular harvest of individuals reduced competition. Juveniles developed continuously, allowing a fast recovery of size structure in these dynamic populations. In risk assessment the duration for populations to recover from (toxicant) stress, is crucial for the determination of ecological acceptable effects. We conclude that competition needs to be considered in order to understand and predict recovery of size

  11. Understanding the population dimension in development planning.

    Science.gov (United States)

    Rivera, P C

    1983-01-01

    In the Philippines initial efforts to adopt population policies focused on reducing rapid population growth through fertility control. The history of the national population welfare congress, which started in 1978, reflects this emphasis on family planning as a major deterrent to rapid population growth. It was only in recent years that the 2-way relationship between population and development came to be better appreciated. The 6th National Populaton Welfare Congress was a response to this need to broaden the scope of population concerns and integrate the population dimension into development planning. This viewpoint regards population not as a demand variable but as a factor that can be influenced by economic and social development. Dr. Mercedes B. Concepcion, dean of the University of the Philippines Population Institute (UPPI), discussed population trends, prospects, and problems in a paper presented before the 6th congress. In 1980, she said, the Philippine population was 48.1 million persons, up by 11.4 million persons or 31%, over the3l.7 million enumerated in 1970. While the rate of populated growth remains high, data indicate a decreasing post-World War II trend, from 3.06% in 1948-60 to 2.68% in 1975-80. The proportion of the population below 15 has dropped by 2 percentage points, while the number of persons in the working ages 15-64 has increased. In 1 of the 3 group sessions during the congress, the participants tried to define the Philippines' population distribution goals, the requirement of an urban-rural balance, and priority intervention areas. In that session 2 main papers were presented -- one on human settlements and urbanization and the other on macroeconomic policies and their spatial implications. In another sessionplanners and researchers examined the socioeconomic and demographic impact of development programs, specifically the impact of rural electrification on fertility change in Misamis Oriental, a province in Southern Philippines. In the

  12. Population structure of the Classic period Maya.

    Science.gov (United States)

    Scherer, Andrew K

    2007-03-01

    This study examines the population structure of Classic period (A.D. 250-900) Maya populations through analysis of odontometric variation of 827 skeletons from 12 archaeological sites in Mexico, Guatemala, Belize, and Honduras. The hypothesis that isolation by distance characterized Classic period Maya population structure is tested using Relethford and Blangero's (Hum Biol 62 (1990) 5-25) approach to R matrix analysis for quantitative traits. These results provide important biological data for understanding ancient Maya population history, particularly the effects of the competing Tikal and Calakmul hegemonies on patterns of lowland Maya site interaction. An overall F(ST) of 0.018 is found for the Maya area, indicating little among-group variation for the Classic Maya sites tested. Principal coordinates plots derived from the R matrix analysis show little regional patterning in the data, though the geographic outliers of Kaminaljuyu and a pooled Pacific Coast sample did not cluster with the lowland Maya sites. Mantel tests comparing the biological distance matrix to a geographic distance matrix found no association between genetic and geographic distance. In the Relethford-Blangero analysis, most sites possess negative or near-zero residuals, indicating minimal extraregional gene flow. The exceptions were Barton Ramie, Kaminaljuyu, and Seibal. A scaled R matrix analysis clarifies that genetic drift is a consideration for understanding Classic Maya population structure. All results indicate that isolation by distance does not describe Classic period Maya population structure. (c) 2006 Wiley-Liss, Inc.

  13. Using Network Sampling and Recruitment Data to Understand Social Structures Related to Community Health in a Population of People Who Inject Drugs in Rural Puerto Rico.

    Science.gov (United States)

    Coronado-García, Mayra; Thrash, Courtney R; Welch-Lazoritz, Melissa; Gauthier, Robin; Reyes, Juan Carlos; Khan, Bilal; Dombrowski, Kirk

    2017-06-01

    This research examined the social network and recruitment patterns of a sample of people who inject drugs (PWIDs) in rural Puerto Rico, in an attempt to uncover systematic clustering and between-group social boundaries that potentially influence disease spread. Respondent driven sampling was utilized to obtain a sample of PWID in rural Puerto Rico. Through eight initial "seeds", 317 injection drug users were recruited. Using recruitment patterns of this sample, estimates of homophily and affiliation were calculated using RDSAT. Analyses showed clustering within the social network of PWID in rural Puerto Rico. In particular, females showed a very high tendency to recruit male PWID, which suggests low social cohesion among female PWID. Results for (believed) HCV status at the time of interview indicate that HCV+ individuals were less likely to interact with HCV- individuals or those who were unaware of their status, and may be acting as "gatekeepers" to prevent disease spread. Individuals who participated in a substance use program were more likely to affiliate with one another. The use of speedballs was related to clustering within the network, in which individuals who injected this mixture were more likely to affiliate with other speedball users. Social clustering based on several characteristics and behaviors were found within the IDU population in rural Puerto Rico. RDS was effective in not only garnering a sample of PWID in rural Puerto Rico, but also in uncovering social clustering that can potentially influence disease spread among this population.

  14. Structure of African elephant populations

    DEFF Research Database (Denmark)

    Siegismund, H R; Arctander, P

    1996-01-01

    The structure of elephant populations from east and south Africa has been analyzed by Georgiadis et al. (1994) on the basis of restriction site variation of mitochondrial DNA. They used F statistics based on identity by descent in tests for subdivision and reached the conclusion that there was a ......The structure of elephant populations from east and south Africa has been analyzed by Georgiadis et al. (1994) on the basis of restriction site variation of mitochondrial DNA. They used F statistics based on identity by descent in tests for subdivision and reached the conclusion...

  15. Evolutionary dynamics in structured populations

    Science.gov (United States)

    Nowak, Martin A.; Tarnita, Corina E.; Antal, Tibor

    2010-01-01

    Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces. PMID:20008382

  16. Understanding structural conservation through materials science:

    DEFF Research Database (Denmark)

    Fuster-López, Laura; Krarup Andersen, Cecil

    2014-01-01

    provide both explanation and prediction of failure in materials. It has therefore shown to be an effective method for developing useful solutions to conservation problems. Since materials science and mechanics can help conservators predict the long term consequences of their treatments and provide them......Mechanical properties and the structure of materials are key elements in understanding how structural interventions in conservation treatments affect cultural heritage objects. In this context, engineering mechanics can help determine the strength and stability found in art objects as it can...... with tools to avoid future problems, it should be present in all conservation-restoration training programs to help promote students’ understanding of the degradation mechanisms in cultural materials (and their correlation with chemical and biological degradation) as well as the implications behind...

  17. [Genetic structure of natural populations

    International Nuclear Information System (INIS)

    1988-01-01

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

  18. Investigating Student Understanding of the Universe: Structure

    Science.gov (United States)

    Hayes, Virginia; Coble, K.; Nickerson, M.; Cochran, G.; Camarillo, C. T.; Bailey, J. M.; McLin, K. M.; Cominsky, L. R.

    2011-05-01

    Chicago State University (CSU) offers an introductory astronomy course that services students from a variety of majors including pre-service teachers. At CSU, we have been investigating methods and tools that will improve student conceptual understanding in astronomy for this diverse group of students. We have analyzed pre-course surveys, pre-course essays, exams, and interviews in an effort to better understand the ideas and difficulties in understanding that students have in regards to the structure of the universe. Analysis of written essays has revealed that our students do have some knowledge of the objects in the universe, but interviews inform us that their understanding of the structure of the universe is superficial. This project is a part of a larger study; also see our posters on student ideas about dark matter, the age and expansion of the universe, and perceptions of astronomical sizes and distances. This work was supported by NASA ROSES E/PO Grant #NNXlOAC89G, as well as by the Illinois Space Grant Consortium and National Science Foundation CCLI Grant #0632563 at Chicago State University and the Fermi E/PO program at Sonoma State University.

  19. Visualising the demographic factors which shape population age structure

    Directory of Open Access Journals (Sweden)

    Tom Wilson

    2016-09-01

    Full Text Available Background: The population pyramid is one of the most popular tools for visualising population age structure. However, it is difficult to discern from the diagram the relative effects of different demographic components on the size of age-specific populations, making it hard to understand exactly how a population's age structure is formed. Objective: The aim of this paper is to introduce a type of population pyramid which shows how births, deaths, and migration have shaped a population's age structure. Methods: Births, deaths, and population data were obtained from the Human Mortality Database and the Australian Bureau of Statistics. A variation on the conventional population pyramid, termed here a components-of-change pyramid, was created. Based on cohort population accounts, it illustrates how births, deaths, and net migration have created the population of each age group. A simple measure which summarises the impact of net migration on age structure is also suggested. Results: Example components-of-change pyramids for several countries and subnational regions are presented, which illustrate how births, deaths, and net migration have fashioned current population age structures. The influence of migration is shown to vary greatly between populations. Conclusions: The new type of pyramid aids interpretation of a population's age structure and helps to understand its demographic history over the last century.

  20. Conclusions, synthesis, and future directions: understanding sources of population change

    Science.gov (United States)

    Esler, Daniel N.; Flint, Paul L.; Derksen, Dirk V.; Savard, Jean-Pierre L.; Eadie, John M.

    2015-01-01

    The material in this volume reflects the burgeoning interest in sea ducks, both as study species with compelling and unique ecological attributes and as taxa of conservation concern. In this review, we provide perspective on the current state of sea duck knowledge by highlighting key findings in the preceding chapters that are of particular value for understanding or influencing population change. We also introduce a conceptual model that characterizes links among topics covered by individual chapters and places them in the context of demographic responses. Finally, we offer recommendations for areas of future research that we suggest will have importance for understanding and managing sea duck population dynamics.

  1. High school students' understanding and problem solving in population genetics

    Science.gov (United States)

    Soderberg, Patti D.

    This study is an investigation of student understanding of population genetics and how students developed, used and revised conceptual models to solve problems. The students in this study participated in three rounds of problem solving. The first round involved the use of a population genetics model to predict the number of carriers in a population. The second round required them to revise their model of simple dominance population genetics to make inferences about populations containing three phenotype variations. The third round of problem solving required the students to revise their model of population genetics to explain anomalous data where the proportions of males and females with a trait varied significantly. As the students solved problems, they were involved in basic scientific processes as they observed population phenomena, constructed explanatory models to explain the data they observed, and attempted to persuade their peers as to the adequacy of their models. In this study, the students produced new knowledge about the genetics of a trait in a population through the revision and use of explanatory population genetics models using reasoning that was similar to what scientists do. The students learned, used and revised a model of Hardy-Weinberg equilibrium to generate and test hypotheses about the genetics of phenotypes given only population data. Students were also interviewed prior to and following instruction. This study suggests that a commonly held intuitive belief about the predominance of a dominant variation in populations is resistant to change, despite instruction and interferes with a student's ability to understand Hardy-Weinberg equilibrium and microevolution.

  2. Understanding Sleep Disorders in a College Student Population.

    Science.gov (United States)

    Jensen, Dallas R.

    2003-01-01

    College students' sleep habits are changing dramatically, and related sleep problems are increasing. Reviews the current literature on sleep problems, focusing on the college student population. The unique challenges of college settings are discussed as they apply to understanding sleep problems, and suggestions are made for professionals who work…

  3. Ordering structured populations in multiplayer cooperation games

    Science.gov (United States)

    Peña, Jorge; Wu, Bin; Traulsen, Arne

    2016-01-01

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

  4. Dominance and population structure of freshwater crabs ...

    African Journals Online (AJOL)

    ... the availability of refugia for specific/different size classes. Intraspecific aggression, predation and refuge availability are probable strong selection pressures in determining population structures of wild populations of P. perlatus. Keywords: Dominance. linear hierarchy, population structure, refuge availability, rivers, South ...

  5. Complexity and simplification in understanding recruitment in benthic populations

    KAUST Repository

    Pineda, Jesús

    2008-11-13

    Research of complex systems and problems, entities with many dependencies, is often reductionist. The reductionist approach splits systems or problems into different components, and then addresses these components one by one. This approach has been used in the study of recruitment and population dynamics of marine benthic (bottom-dwelling) species. Another approach examines benthic population dynamics by looking at a small set of processes. This approach is statistical or model-oriented. Simplified approaches identify "macroecological" patterns or attempt to identify and model the essential, "first-order" elements of the system. The complexity of the recruitment and population dynamics problems stems from the number of processes that can potentially influence benthic populations, including (1) larval pool dynamics, (2) larval transport, (3) settlement, and (4) post-settlement biotic and abiotic processes, and larval production. Moreover, these processes are non-linear, some interact, and they may operate on disparate scales. This contribution discusses reductionist and simplified approaches to study benthic recruitment and population dynamics of bottom-dwelling marine invertebrates. We first address complexity in two processes known to influence recruitment, larval transport, and post-settlement survival to reproduction, and discuss the difficulty in understanding recruitment by looking at relevant processes individually and in isolation. We then address the simplified approach, which reduces the number of processes and makes the problem manageable. We discuss how simplifications and "broad-brush first-order approaches" may muddle our understanding of recruitment. Lack of empirical determination of the fundamental processes often results in mistaken inferences, and processes and parameters used in some models can bias our view of processes influencing recruitment. We conclude with a discussion on how to reconcile complex and simplified approaches. Although it

  6. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  7. Understanding population growth in the peri-urban region.

    Science.gov (United States)

    Ford, T

    1999-01-01

    This article advocates a new approach to understanding periurban population growth. A conceptual model is developed that identifies four distinct growth processes: suburbanization, counterurbanization, population retention, and centripetal migration. Each of these growth processes acts differently on particular population subgroups. The differences are reflected in variations in the spatial manifestation of periurban growth within Australia. Suburbanization process is differentiated from counterurbanization by employing three indicators of suburbanization. The first indicator includes the broad situation of the periurban destination and is defined as in-migration from the metropolitan area to adjacent, accessible periurban locations. The second indicator lies in the assessment of the commuting and social linkages with the metropolitan maintained by migrants. The third indicator is the nature of the migrants' residential destination site. Counterurbanization is largely seen to be a shift in population down the urban hierarchy to smaller centers and localities beyond the existing metropolitan boundaries. Furthermore, the article discusses the four indicators that distinguish counterurbanization from suburbanization. Another important process contributing to periurban growth is population retention. Two key indicators that lie in the measurement of increased period of residence and reduced rates of out-migration overtime characterize this process.

  8. Population structure of Atlantic Mackerel (Scomber scombrus)

    DEFF Research Database (Denmark)

    Jansen, Teunis; Gislason, Henrik

    2013-01-01

    model where the population structure of mackerel is described as a dynamic cline, rather than as connected contingents. Temporal changes in hydrography and mackerel behavior may affect the steepness of the cline at various locations. The new interpretation of the population structure of Atlantic...

  9. Population Structure of West Greenland Narwhals

    DEFF Research Database (Denmark)

    Riget, F.; Dietz, R.; Møller, P.

    The hypothesis that different populations of narwhals in the West Greenland area exist has been tested by different biomarkers (metal and organochlorine concentrations, stable isotopes and DNA). Samples of muscle, liver, kidney, blubber and skin tissues of narwhals from West Greenland have been...... isotopes could not support the population structure with two West Greenland populations suggested by the genetic study....

  10. Understanding Microbial Communities: Function, Structure and Dynamics

    Science.gov (United States)

    2015-02-11

    microbial communities: Function, structure and dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to...dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to December 2014. The programme involved over 150...Communities: Function, Structure and Dynamics’, at the Isaac Newton Institute, Cambridge University, UK, from 19th August 2014 – 19th December 2014

  11. Understanding water's anomalies with locally favoured structures.

    Science.gov (United States)

    Russo, John; Tanaka, Hajime

    2014-04-02

    Water is a complex liquid that displays a surprising array of unusual properties, the most famous being the density maximum at about 4 °C. The origin of these anomalies is still a matter of debate, and so far a quantitative description of water's phase behaviour starting from the molecular arrangements is still missing. Here we report a study of the microscopic structural features of water as obtained from computer simulations. We identify locally favoured structures having a high degree of translational order in the second shell, and a two-state model is used to describe the behaviour of liquid water over a wide region of the phase diagram. Furthermore, we show that locally favoured structures not only have translational order in the second shell but also contain five-membered rings of hydrogen-bonded molecules. This suggests their mixed character: the former helps crystallization, whereas the latter causes frustration against crystallization.

  12. Population structure and adaptation in fishes

    DEFF Research Database (Denmark)

    Limborg, Morten

    . Comprehensive genetic analyses on the small pelagic fish European sprat (Sprattus sprattus) revealed significant population structure throughout its distribution with an overall pattern of reduced connectivity across environmental transition zones. Population structure reflected both historical separations over......Marine fishes represent a valuable resource for the global economy and food consumption. Accordingly, many species experience high levels of exploitation necessitating effective management plans. However, long term sustainability may be jeopardized from insufficient knowledge about intra......-specific population structure and adaptive divergence. The large population sizes and high migration rates common to most marine fishes impede the differentiating effect of genetic drift, having led to expectations of no population structure and that the occurrence of local adaptation should be rare in these species...

  13. Symbolic trephinations and population structure

    Directory of Open Access Journals (Sweden)

    László Szathmáry

    2006-12-01

    Full Text Available The sample examined consists of 19 skulls with symbolic trephinations and 86 skulls without trepanations dated from the X century. Skulls were all excavated in the Great Hungarian Plain in the Carpathian Basin, which was occupied by the Hungarian conquerors at the end of the IX century. The variations of 12 cranial dimensions of the trephined skulls were investigated and compared to the skulls without trepanations after performing a discriminant analysis. The classification results evince that the variability of non-trephined skulls shows a more homogeneous and a more characteristic picture of their own group than the trephined samples, which corresponds to the notion, formed by archaeological evidence and written historical sources, of a both ethnically and socially differing population of the Hungarian conquerors. According to historical research, a part of the population was of Finno-Ugric origin, while the military leading layer of society can be brought into connection with Turkic ethnic groups. All the same, individuals dug up with rich grave furniture and supposed to belong to this upper stratum of society are primarily characterized by the custom of symbolic trephination, and, as our results demonstrate, craniologically they seem to be more heterogeneous.

  14. Understanding water's anomalies with locally favored structures

    OpenAIRE

    Russo, John; Tanaka, Hajime

    2013-01-01

    Water is a complex structured liquid of hydrogen-bonded molecules that displays a surprising array of unusual properties, also known as water anomalies, the most famous being the density maximum at about $4^\\circ$C. The origin of these anomalies is still a matter of debate, and so far a quantitative description of water's phase behavior starting from the molecular arrangements is still missing. Here we provide a simple physical description from microscopic data obtained through computer simul...

  15. Structured Open Urban Data: Understanding the Landscape.

    Science.gov (United States)

    Barbosa, Luciano; Pham, Kien; Silva, Claudio; Vieira, Marcos R; Freire, Juliana

    2014-09-01

    A growing number of cities are now making urban data freely available to the public. Besides promoting transparency, these data can have a transformative effect in social science research as well as in how citizens participate in governance. These initiatives, however, are fairly recent and the landscape of open urban data is not well known. In this study, we try to shed some light on this through a detailed study of over 9,000 open data sets from 20 cities in North America. We start by presenting general statistics about the content, size, nature, and popularity of the different data sets, and then examine in more detail structured data sets that contain tabular data. Since a key benefit of having a large number of data sets available is the ability to fuse information, we investigate opportunities for data integration. We also study data quality issues and time-related aspects, namely, recency and change frequency. Our findings are encouraging in that most of the data are structured and published in standard formats that are easy to parse; there is ample opportunity to integrate different data sets; and the volume of data is increasing steadily. But they also uncovered a number of challenges that need to be addressed to enable these data to be fully leveraged. We discuss both our findings and issues involved in using open urban data.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

  18. Structural shell analysis understanding and application

    CERN Document Server

    Blaauwendraad, Johan

    2014-01-01

    The mathematical description of the properties of a shell is much more elaborate than those of beam and plate structures. Therefore many engineers and architects are unacquainted with aspects of shell behaviour and design, and are not familiar with sufficiently reliable shell theories for the different shell types as derived in the middle of the 20th century. Rather than contributing to theory development, this university textbook focuses on architectural and civil engineering schools. Of course, practising professionals will profit from it as well. The book deals with thin elastic shells, in particular with cylindrical, conical and spherical types, and with elliptic and hyperbolic paraboloids. The focus is on roofs, chimneys, pressure vessels and storage tanks. Special attention is paid to edge bending disturbance zones, which is indispensable knowledge in FE meshing. A substantial part of the book results from research efforts in the mid 20th century at Delft University of Technology. As such, it is a valua...

  19. Genetic structure of Potentilla acaulis (Rosaceae) populations ...

    African Journals Online (AJOL)

    Genetic structure of Potentilla acaulis (Rosaceae) populations based on randomly amplified polymorphic DNA (RAPD) in habitat fragmented grassland of northern ... attention from a conservation point of view and it should be considered as a conservation strategy to increasing gene exchange among isolated populations.

  20. Assessing population structure: FST and related measures

    NARCIS (Netherlands)

    Meirmans, P.G.; Hedrick, P.W.

    2011-01-01

    Although FST is widely used as a measure of population structure, it has been criticized recently because of its dependency on within-population diversity. This dependency can lead to difficulties in interpretation and in the comparison of estimates among species or among loci and has led to the

  1. Mechanisms of Population Structuring in Giant Australian Cuttlefish Sepia apama

    OpenAIRE

    Payne, Nicholas L.; Snelling, Edward P.; Semmens, Jayson M.; Gillanders, Bronwyn M.

    2013-01-01

    While a suite of approaches have been developed to describe the scale, rate and spatial structure of exchange among populations, a lack of mechanistic understanding will invariably compromise predictions of population-level responses to ecosystem modification. In this study, we measured the energetics and sustained swimming capacity of giant Australian cuttlefish Sepia apama and combined these data with information on the life-history strategy, behaviour and circulation patterns experienced b...

  2. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae.

    Directory of Open Access Journals (Sweden)

    Laura Cristina Multini

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

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

    Science.gov (United States)

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

    2016-01-01

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

  4. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Among the mixed models analysed, mixed linear model (MLM) identified 21 quantitative trait loci for lint percentage and seed quality traits, such as seed protein and oil. Establishing genetic diversity, population structure and marker trait associations for the seed quality traits could be valuable in understanding the genetic ...

  5. Understanding the Implications of Neural Population Activity on Behavior

    Science.gov (United States)

    Briguglio, John

    Learning how neural activity in the brain leads to the behavior we exhibit is one of the fundamental questions in Neuroscience. In this dissertation, several lines of work are presented to that use principles of neural coding to understand behavior. In one line of work, we formulate the efficient coding hypothesis in a non-traditional manner in order to test human perceptual sensitivity to complex visual textures. We find a striking agreement between how variable a particular texture signal is and how sensitive humans are to its presence. This reveals that the efficient coding hypothesis is still a guiding principle for neural organization beyond the sensory periphery, and that the nature of cortical constraints differs from the peripheral counterpart. In another line of work, we relate frequency discrimination acuity to neural responses from auditory cortex in mice. It has been previously observed that optogenetic manipulation of auditory cortex, in addition to changing neural responses, evokes changes in behavioral frequency discrimination. We are able to account for changes in frequency discrimination acuity on an individual basis by examining the Fisher information from the neural population with and without optogenetic manipulation. In the third line of work, we address the question of what a neural population should encode given that its inputs are responses from another group of neurons. Drawing inspiration from techniques in machine learning, we train Deep Belief Networks on fake retinal data and show the emergence of Garbor-like filters, reminiscent of responses in primary visual cortex. In the last line of work, we model the state of a cortical excitatory-inhibitory network during complex adaptive stimuli. Using a rate model with Wilson-Cowan dynamics, we demonstrate that simple non-linearities in the signal transferred from inhibitory to excitatory neurons can account for real neural recordings taken from auditory cortex. This work establishes and tests

  6. Structured population models in biology and epidemiology

    CERN Document Server

    Ruan, Shigui

    2008-01-01

    This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

  7. Coexistence of competing stage-structured populations.

    KAUST Repository

    Fujiwara, Masami

    2011-10-05

    This paper analyzes the stability of a coexistence equilibrium point of a model for competition between two stage-structured populations. In this model, for each population, competition for resources may affect any one of the following population parameters: reproduction, juvenile survival, maturation rate, or adult survival. The results show that the competitive strength of a population is affected by (1) the ratio of the population parameter influenced by competition under no resource limitation (maximum compensatory capacity) over the same parameter under a resource limitation due to competition (equilibrium rate) and (2) the ratio of interspecific competition over intraspecific competition; this ratio was previously shown to depend on resource-use overlap. The former ratio, which we define as fitness, can be equalized by adjusting organisms\\' life history strategies, thereby promoting coexistence. We conclude that in addition to niche differentiation among populations, the life history strategies of organisms play an important role in coexistence.

  8. Population structure of ice-breeding seals.

    Science.gov (United States)

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

    2008-07-01

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

  9. Structural stability of nonlinear population dynamics

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

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

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

    Science.gov (United States)

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

    1999-01-01

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

  11. Genetic structure of Potentilla acaulis (Rosaceae) populations ...

    African Journals Online (AJOL)

    Jane

    2011-07-18

    Jul 18, 2011 ... Ecol. 10: 1811-1819. Bohonak AJ (1999). Dispersal, gene flow, and population structure. Q. Rev. Biol., 74: 21-45. Chen S, Xia T, Chen S, Zhou Y (2005). RAPD Profiling in Detecting. Genetic Variation in Endemic Coelonema (Brassicaceae) of Qinghai-. Tibet Plateau of China. Biochem. Genet., 43: 189-201.

  12. Population structure of Staphylococcus aureus in China

    NARCIS (Netherlands)

    Yan, Xiaomei

    2015-01-01

    The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance

  13. Understanding the population genetics of Plasmodium vivax is essential for malaria control and elimination

    Directory of Open Access Journals (Sweden)

    Arnott Alicia

    2012-01-01

    Full Text Available Abstract Traditionally, infection with Plasmodium vivax was thought to be benign and self-limiting, however, recent evidence has demonstrated that infection with P. vivax can also result in severe illness and death. Research into P. vivax has been relatively neglected and much remains unknown regarding the biology, pathogenesis and epidemiology of this parasite. One of the fundamental factors governing transmission and immunity is parasite diversity. An understanding of parasite population genetic structure is necessary to understand the epidemiology, diversity, distribution and dynamics of natural P. vivax populations. In addition, studying the population structure of genes under immune selection also enables investigation of the dynamic interplay between transmission and immunity, which is crucial for vaccine development. A lack of knowledge regarding the transmission and spread of P. vivax has been particularly highlighted in areas where malaria control and elimination programmes have made progress in reducing the burden of Plasmodium falciparum, yet P. vivax remains as a substantial obstacle. With malaria elimination back on the global agenda, mapping of global and local P. vivax population structure is essential prior to establishing goals for elimination and the roll-out of interventions. A detailed knowledge of the spatial distribution, transmission and clinical burden of P. vivax is required to act as a benchmark against which control targets can be set and measured. This paper presents an overview of what is known and what is yet to be fully understood regarding P. vivax population genetics, as well as the importance and application of P. vivax population genetics studies.

  14. Sustaining salmonid populations: A caring understanding of naturalness of taxa

    Science.gov (United States)

    Nielsen, Jennifer L.; Regier, Henry A.; Knudsen, E. Eric

    2004-01-01

    Species of the family of Salmonidae occur naturally in Northern Hemisphere waters that remain clear and cool to cold in summer. For purposes of reproduction, salmonids generally behaviorally respond to the currents of streams and lakes in recently glaciated areas. For feeding and maturation, many larger species migrate into existing systems of large lakes, seas, and oceans. The subfamilies include Salmoninae, Coregoninae, and Thymallinae. In many locales and regions of the hemisphere, numerous species of these subfamilies evolved and self-organized into species flocks or taxocenes of bewildering complexity. For example, any individual species may play different or unique ecological roles in different taxocenes. The northern Pacific and Atlantic Ocean ecosystems, with their seas and tributaries, each contained a metacomplex of such taxocenes that, in their natural state some centuries ago, resembled each other but differed in many ways. Humans have valued all species of this family for subsistence, ceremonial, naturalist, gustatory, angling, and commercial reasons for centuries. Modern progressive humans (MPHs), whose industrial and commercial enterprises have gradually spread over this hemisphere in recent time, now affect aquatic ecosystems at all scales from local to global. These human effects mingle in complex ways that together induce uniquely natural salmonid taxocenes to disintegrate with the loss of species, including those groups least tolerant to human manipulations, but extending more recently to those taxa more adapted to anthropogenic change. As we leave the modern era, dominated by MPHs, will we find ways to live sustainably with salmonid taxocenes that still exhibit self-organizational integrity, or will only individual, isolated populations of salmonid species, derived from those most tolerant of MPHs, survive? To achieve future sustainability of salmonids, we suggest implementation of a search for intuitive knowledge based on faith in the wisdom of

  15. Tools to Understand Structural Property Relationships for Wood Cell Walls

    Science.gov (United States)

    Joseph E. Jakes; Daniel J. Yelle; Charles R. Frihart

    2011-01-01

    Understanding structure-property relationships for wood cell walls has been hindered by the complex polymeric structures comprising these cell walls and the difficulty in assessing meaningful mechanical property measurements of individual cell walls. To help overcome these hindrances, we have developed two experimental methods: 1) two-dimensional solution state nuclear...

  16. Understanding how discrete populations of hypothalamic neurons orchestrate complicated behavioral states

    Directory of Open Access Journals (Sweden)

    Allison eGraebner

    2015-08-01

    Full Text Available A major question in systems neuroscience is how a single population of neurons can interact with the rest of the brain to orchestrate complex behavioral states. The hypothalamus contains many such discrete neuronal populations that individually regulate arousal, feeding, and drinking. For example, hypothalamic neurons that express hypocretin (Hcrt neuropeptides can sense homeostatic and metabolic factors affecting wakefulness and orchestrate organismal arousal. Neurons that express agouti-related protein (AgRP can sense the metabolic needs of the body and orchestrate a state of hunger. The organum vasculosum of the lamina terminalis (OVLT can detect the hypertonicity of blood and orchestrate a state of thirst. Each hypothalamic population is sufficient to generate complicated behavioral states through the combined efforts of distinct efferent projections. The principal challenge to understanding these brain systems is therefore to determine the individual roles of each downstream projection for each behavioral state. In recent years, the development and application of temporally precise, genetically encoded tools have greatly improved our understanding of the structure and function of these neural systems. This review will survey recent advances in our understanding of how these individual hypothalamic populations can orchestrate complicated behavioral states due to the combined efforts of individual downstream projections.

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

    Science.gov (United States)

    Buffoni, Giuseppe; Pasquali, Sara

    2007-04-01

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

  18. Phytophthora infestans population structure: a worldwide scale

    Directory of Open Access Journals (Sweden)

    Martha Cárdenas Toquica

    2012-05-01

    Full Text Available Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase and Pep (Peptidase, the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and the mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America expanding on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.

  19. Phytophthora infestans population structure: A worldwide scale

    International Nuclear Information System (INIS)

    Cardenas, Martha; Danies, Giovanna; Tabima, Javier; Bernal, Adriana; Restrepo, Silvia

    2012-01-01

    Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of the pathogen's population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase) and Pep (Pep tidase), the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America, expanding it on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.

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

    Science.gov (United States)

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

    2014-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Paul Verdu

    2014-08-01

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

  2. Toward a Better Understanding of Population Genetics: Pop!World--A Virtual, Inquiry-Based Tool for Teaching Population Genetics

    Science.gov (United States)

    Poulin, Jessica; Ramamurthy, Bina; Dittmar, Katharina

    2013-01-01

    Population genetics is fundamental to understanding evolutionary theory, and is taught in most introductory biology/evolution courses. Many students are unaware that understanding this topic requires pertinent knowledge

  3. Ethnicity and Population Structure in Personal Naming Networks

    Science.gov (United States)

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

    2011-01-01

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

  4. Comparative population structure of cavity-nesting sea ducks

    Science.gov (United States)

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

    2014-01-01

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

  5. Trading Stages: Life Expectancies in Structured Populations

    Science.gov (United States)

    Tuljapurkar, Shripad; Coulson, Tim; Horvitz, Carol

    2012-01-01

    Interest in stage-and age structured models has recently increased because they can describe quantitative traits such as size that are left out of age-only demography. Available methods for the analysis of effects of vital rates on lifespan in stage-structured models have not been widely applied because they are hard to use and interpret, and tools for age and stage structured populations are missing. We present easily interpretable expressions for the sensitivities and elasticities of life expectancy to vital rates in age-stage models, and illustrate their application with two biological examples. Much of our approach relies on trading of time and mortality risk in one stage for time and risk in others. Our approach contributes to the new framework of the study of age- and stage-structured biodemography. PMID:22664576

  6. The scale of population structure in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Alexander Platt

    2010-02-01

    Full Text Available The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

  7. Mechanisms of population structuring in giant australian Cuttlefish Sepia apama.

    Directory of Open Access Journals (Sweden)

    Nicholas L Payne

    Full Text Available While a suite of approaches have been developed to describe the scale, rate and spatial structure of exchange among populations, a lack of mechanistic understanding will invariably compromise predictions of population-level responses to ecosystem modification. In this study, we measured the energetics and sustained swimming capacity of giant Australian cuttlefish Sepia apama and combined these data with information on the life-history strategy, behaviour and circulation patterns experienced by the species to predict scales of connectivity throughout parts of their range. The swimming capacity of adult and juvenile S. apama was poor compared to most other cephalopods, with most individuals incapable of maintaining swimming above 15 cm s(-1. Our estimate of optimal swimming speed (6-7 cm s(-1 and dispersal potential were consistent with the observed fine-scale population structure of the species. By comparing observed and predicted population connectivity, we identified several mechanisms that are likely to have driven fine-scale population structure in this species, which will assist in the interpretation of future population declines.

  8. Mechanisms of population structuring in giant australian Cuttlefish Sepia apama.

    Science.gov (United States)

    Payne, Nicholas L; Snelling, Edward P; Semmens, Jayson M; Gillanders, Bronwyn M

    2013-01-01

    While a suite of approaches have been developed to describe the scale, rate and spatial structure of exchange among populations, a lack of mechanistic understanding will invariably compromise predictions of population-level responses to ecosystem modification. In this study, we measured the energetics and sustained swimming capacity of giant Australian cuttlefish Sepia apama and combined these data with information on the life-history strategy, behaviour and circulation patterns experienced by the species to predict scales of connectivity throughout parts of their range. The swimming capacity of adult and juvenile S. apama was poor compared to most other cephalopods, with most individuals incapable of maintaining swimming above 15 cm s(-1). Our estimate of optimal swimming speed (6-7 cm s(-1)) and dispersal potential were consistent with the observed fine-scale population structure of the species. By comparing observed and predicted population connectivity, we identified several mechanisms that are likely to have driven fine-scale population structure in this species, which will assist in the interpretation of future population declines.

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

    Science.gov (United States)

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

    2007-02-01

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

  10. Metabolic competition as a driver of bacterial population structure.

    Science.gov (United States)

    Watkins, Eleanor R; Maiden, Martin Cj; Gupta, Sunetra

    2016-10-01

    Understanding the processes whereby diversity arises and is maintained in pathogen populations is pivotal for designing disease control interventions. A particular problem is the maintenance of strain structure in bacterial pathogen populations despite frequent genetic exchange. Although several theoretical frameworks have been put forward to explain this widespread phenomenon, few have focused on the role of genes encoding metabolic functions, despite an increasing recognition of their importance in pathogenesis and transmission. In this article, we review the literature for evidence of metabolic niches within the host and discuss theoretical frameworks which examine ecological interactions between metabolic genes. We contend that metabolic competition is an important phenomenon which contributes to the maintenance of population structure and diversity of many bacterial pathogens.

  11. Population structure of Staphylococcus aureus in China

    OpenAIRE

    Yan, Xiaomei

    2015-01-01

    The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance against rifampicin doubled to 68%. Staphylococcal food poisoning (SFP) is frequent in China. Two predominant S. aureus lineages, ST6 and ST943, were identified causing outbreaks of SFP in Southern China...

  12. Population and Resource Control Measures: A Conceptual Framework for Understanding and Implementation

    Science.gov (United States)

    2009-12-01

    COVERED Master’s Thesis 4. TITLE AND SUBTITLE Population and Resource Control Measures: A Conceptual Framework for Understanding and Implementation...successful use of population and resource control measures. If utilized correctly, PRCMs are powerful operational tools that can be used to break...NUMBER OF PAGES 71 14. SUBJECT TERMS Population and resource control measures, Population control , Counterinsurgency, COIN, Population

  13. Effects of demographic structure on key properties of stochastic density-independent population dynamics.

    Science.gov (United States)

    Vindenes, Yngvild; Sæther, Bernt-Erik; Engen, Steinar

    2012-12-01

    The development of stochastic demography has largely been based on age structured populations, although other types of demographic structure, especially permanent and dynamic heterogeneity, are likely common in natural populations. The combination of stochasticity and demographic structure is a challenge for analyses of population dynamics and extinction risk, because the population structure will fluctuate around the stable structure and the population size shows transient fluctuations. However, by using a diffusion approximation for the total reproductive value, density-independent dynamics of structured populations can be described with only three population parameters: the expected population growth rate, the environmental variance and the demographic variance. These parameters depend on population structure via the state-specific vital rates and transition rates. Once they are found, the diffusion approximation represents a substantial reduction in model complexity. Here, we review and compare the key population parameters across a wide range of demographic structure, from the case of no structure to the most general case of dynamic heterogeneity, and for both discrete and continuous types. We focus on the demographic variance, but also show how environmental stochasticity can be included. This study brings together results from recent models, each considering a specific type of population structure, and places them in a general framework for structured populations. Comparison across different types of demographic structure reveals that the reproductive value is an essential concept for understanding how population structure affects stochastic dynamics and extinction risk. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. Selection of Cooperation in Spatially Structured Populations

    Science.gov (United States)

    Yang, Hyunmo; Ghim, Cheol-Min

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

  15. Structural Approaches to Sequence Evolution Molecules, Networks, Populations

    CERN Document Server

    Bastolla, Ugo; Roman, H. Eduardo; Vendruscolo, Michele

    2007-01-01

    Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

  16. Understanding metallic bonding: Structure, process and interaction by Rasch analysis

    Science.gov (United States)

    Cheng, Maurice M. W.; Oon, Pey-Tee

    2016-08-01

    This paper reports the results of a survey of 3006 Year 10-12 students on their understandings of metallic bonding. The instrument was developed based on Chi's ontological categories of scientific concepts and students' understanding of metallic bonding as reported in the literature. The instrument has two parts. Part one probed into students' understanding of metallic bonding as (a) a submicro structure of metals, (b) a process in which individual metal atoms lose their outermost shell electrons to form a 'sea of electrons' and octet metal cations or (c) an all-directional electrostatic force between delocalized electrons and metal cations, that is, an interaction. Part two assessed students' explanation of malleability of metals, for example (a) as a submicro structural rearrangement of metal atoms/cations or (b) based on all-directional electrostatic force. The instrument was validated by the Rasch Model. Psychometric assessment showed that the instrument possessed reasonably good properties of measurement. Results revealed that it was reliable and valid for measuring students' understanding of metallic bonding. Analysis revealed that the structure, process and interaction understandings were unidimensional and in an increasing order of difficulty. Implications for the teaching of metallic bonding, particular through the use of diagrams, critiques and model-based learning, are discussed.

  17. Russian Population Ethnic Structure: Trends and Transformations

    Directory of Open Access Journals (Sweden)

    Safronov S.

    2015-08-01

    Full Text Available Based on the census data from 1989, 2002 and 2010, the article analyzes the evolution of the ethnic structure of the population of the post-Soviet Russia from the territorial perspective. The stability of the ethnic structure of the “Russian mega nucleus” and indigenization of the national regions are considered in view of the differences in migration trends during the two inter-census periods and the socioeconomic situation in the regions. The urbanization rate of major ethnic groups is an indirect indicator of the prospects of traditional “primordial” ethnic identities in different ethnic groups. Special attention is paid to new trends — an increase in the number of people refraining from answering the question about their ethnic identity or giving an unclear answer. Alongside serious census errors, this phenomenon can be a result of growing complexity of the ethnic identity structures and the processes of modernization, which occur at different rates in Russian and national regions. Based on the 2010 census data, the article analyses the differences in polyethnicity between the rural and urban population, which are accounted for by the historical background, particularities of regional development, settlement features, and migration processes of the past two decades.

  18. Understanding the structure and electronic properties of N-doped ...

    Indian Academy of Sciences (India)

    2014-11-12

    Nov 12, 2014 ... Understanding the structure and electronic properties of N-doped graphene nanoribbons upon hydrogen saturation. MICHAEL MANANGHAYA. Department of Chemical Engineering, De La Salle University, 2401 Taft Ave, Manila 1004 Philippines e-mail: mikemananghaya@gmail.com. MS received 31 May ...

  19. Understanding and Representing Changing Work Structures and Practices through Art

    Science.gov (United States)

    Wieland, Stacey M. B.

    2018-01-01

    Courses: Organizational Communication, Advanced Organizational Communication, Organizing Work, Management/Organizational History. Objectives: This activity will help students to understand major shifts in the organization of work and creatively represent changing work structures and practices. An optional follow-up assignment is included. A…

  20. Origin and population structure of the Icelanders.

    Science.gov (United States)

    Williams, J T

    1993-04-01

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

  1. Liberal Liability. Understanding Students’ Conceptions of Gender Structures

    Directory of Open Access Journals (Sweden)

    Linda Murstedt

    2014-04-01

    Full Text Available Research has shown that teaching gender theories tends to be an educational challenge and elicits student resistance. However, little is known about students’ learning processes in social science. This study aims to explore these learning processes by drawing on feminist pedagogy and conceptual change theory. The results show that when students are asked to perform analysis from a structural gender perspective, they recurrently introduce other explanatory frameworks based on non-structural understandings. The students’ learning processes involve reformulating questions and making interpretations based on liberal understandings of power, freedom of choice and equality. We argue that this process is due to the hegemonic position of the liberal paradigm as well as to the dominant ideas about science. Clarifying the underlying presumptions of a liberal perspective and a structural perspective may help students to recognise applied premises and enable them to distinguish relevant explanations.

  2. Evolutionary genomics and population structure of Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Koushik Das

    2014-11-01

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

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

    Science.gov (United States)

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

    2017-06-01

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

  4. How population structure shapes neighborhood segregation.

    Science.gov (United States)

    Bruch, Elizabeth E

    2014-03-01

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

  5. Exploiting Fast-Variables to Understand Population Dynamics and Evolution

    Science.gov (United States)

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

    2017-11-01

    We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

  6. Population and evolutionary dynamics in spatially structured seasonally varying environments.

    Science.gov (United States)

    Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

    2018-03-25

    Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

  7. Understanding Peripheral Bat Populations Using Maximum-Entropy Suitability Modeling.

    Science.gov (United States)

    Barnhart, Paul R; Gillam, Erin H

    2016-01-01

    Individuals along the periphery of a species distribution regularly encounter more challenging environmental and climatic conditions than conspecifics near the center of the distribution. Due to these potential constraints, individuals in peripheral margins are expected to change their habitat and behavioral characteristics. Managers typically rely on species distribution maps when developing adequate management practices. However, these range maps are often too simplistic and do not provide adequate information as to what fine-scale biotic and abiotic factors are driving a species occurrence. In the last decade, habitat suitability modelling has become widely used as a substitute for simplistic distribution mapping which allows regional managers the ability to fine-tune management resources. The objectives of this study were to use maximum-entropy modeling to produce habitat suitability models for seven species that have a peripheral margin intersecting the state of North Dakota, according to current IUCN distributions, and determine the vegetative and climatic characteristics driving these models. Mistnetting resulted in the documentation of five species outside the IUCN distribution in North Dakota, indicating that current range maps for North Dakota, and potentially the northern Great Plains, are in need of update. Maximum-entropy modeling showed that temperature and not precipitation were the variables most important for model production. This fine-scale result highlights the importance of habitat suitability modelling as this information cannot be extracted from distribution maps. Our results provide baseline information needed for future research about how and why individuals residing in the peripheral margins of a species' distribution may show marked differences in habitat use as a result of urban expansion, habitat loss, and climate change compared to more centralized populations.

  8. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Issue 4. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation ... Keywords. agarwood; conservation; home gardens; genetic diversity; population genetic structure; amplified fragment length polymorphism.

  9. Understanding the defect structure of solution grown zinc oxide

    International Nuclear Information System (INIS)

    Liew, Laura-Lynn; Sankar, Gopinathan; Handoko, Albertus D.; Goh, Gregory K.L.; Kohara, Shinji

    2012-01-01

    Zinc oxide (ZnO) is a wide bandgap semiconducting oxide with many potential applications in various optoelectronic devices such as light emitting diodes (LEDs) and field effect transistors (FETs). Much effort has been made to understand the ZnO structure and its defects. However, one major issue in determining whether it is Zn or O deficiency that provides ZnO its unique properties remains. X-ray absorption spectroscopy (XAS) is an ideal, atom specific characterization technique that is able to probe defect structure in many materials, including ZnO. In this paper, comparative studies of bulk and aqueous solution grown (≤90 °C) ZnO powders using XAS and x-ray pair distribution function (XPDF) techniques are described. The XAS Zn–Zn correlation and XPDF results undoubtedly point out that the solution grown ZnO contains Zn deficiency, rather than the O deficiency that were commonly reported. This understanding of ZnO short range order and structure will be invaluable for further development of solid state lighting and other optoelectronic device applications. - Graphical abstract: Highlights: ► ZnO powders have been synthesized through an aqueous solution method. ► Defect structure studied using XAS and XPDF. ► Zn–Zn correlations are less in the ZnO powders synthesized in solution than bulk. ► Zn vacancies are present in the powders synthesized. ► EXAFS and XPDF, when used complementary, are useful characterization techniques.

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

    Science.gov (United States)

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

    2015-08-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  12. New protein structures provide an updated understanding of phenylketonuria.

    Science.gov (United States)

    Jaffe, Eileen K

    2017-08-01

    Phenylketonuria (PKU) and less severe hyperphenylalaninemia (HPA) constitute the most common inborn error of amino acid metabolism, and is most often caused by defects in phenylalanine hydroxylase (PAH) function resulting in accumulation of Phe to neurotoxic levels. Despite the success of dietary intervention in preventing permanent neurological damage, individuals living with PKU clamor for additional non-dietary therapies. The bulk of disease-associated mutations are PAH missense variants, which occur throughout the entire 452 amino acid human PAH protein. While some disease-associated mutations affect protein structure (e.g. truncations) and others encode catalytically dead variants, most have been viewed as defective in protein folding/stability. Here we refine this view to address how PKU-associated missense variants can perturb the equilibrium among alternate native PAH structures (resting-state PAH and activated PAH), thus shifting the tipping point of this equilibrium to a neurotoxic Phe concentration. This refined view of PKU introduces opportunities for the design or discovery of therapeutic pharmacological chaperones that can help restore the tipping point to healthy Phe levels and how such a therapeutic might work with or without the inhibitory pharmacological chaperone BH 4 . Dysregulation of an equilibrium of architecturally distinct native PAH structures departs from the concept of "misfolding", provides an updated understanding of PKU, and presents an enhanced foundation for understanding genotype/phenotype relationships. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Advancing environmentally explicit structured population models of plants

    DEFF Research Database (Denmark)

    Ehrlén, Johan; Morris, William; von Euler, Tove

    2016-01-01

    The relationship between the performance of individuals and the surrounding environment is fundamental in ecology and evolutionary biology. Assessing how abiotic and biotic environmental factors influence demographic processes is necessary to understand and predict population dynamics, as well...... as species distributions and abundances. We searched the literature for studies that have linked abiotic and biotic environmental factors to vital rates and, using structured demographic models, population growth rates of plants. We found 136 studies that had examined the environmental drivers of plant...... demography. The number of studies has been increasing rapidly in recent years. Based on the reviewed studies, we identify and discuss several major gaps in our knowledge of environmentally driven demography of plants. We argue that some drivers may have been underexplored and that the full potential...

  14. Toxoplasma and Africa: One Parasite, Two Opposite Population Structures.

    Science.gov (United States)

    Galal, Lokman; Ajzenberg, Daniel; Hamidović, Azra; Durieux, Marie-Fleur; Dardé, Marie-Laure; Mercier, Aurélien

    2018-02-01

    Exploring the genetic diversity of Toxoplasma gondii is essential for an understanding of its worldwide distribution and the determinants of its evolution. Africa remains one of the least studied areas of the world regarding T. gondii genetic diversity. This review has compiled published data on T. gondii strains from Africa to generate a comprehensive map of their continent-wide geographical distribution. The emerging picture about T. gondii strain distribution in Africa suggests a geographical separation of the parasite populations across the continent. We discuss the potential role of a number of factors in shaping this structure. We finally suggest the next steps towards a better understanding of Toxoplasma epidemiology in Africa in light of the strains circulating on this continent. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Understanding the Structural Basis of Adhesion GPCR Functions.

    Science.gov (United States)

    Araç, Demet; Sträter, Norbert; Seiradake, Elena

    2016-01-01

    Unlike conventional G-protein-coupled receptors (GPCRs), adhesion GPCRs (aGPCRs) have large extracellular regions that are autoproteolytically cleaved from their membrane-embedded seven-pass transmembrane helices. Autoproteolysis occurs within the conserved GPCR-Autoproteolysis INducing (GAIN) domain that is juxtaposed to the transmembrane domain and cleaves the last beta strand of the GAIN domain. The other domains of the extracellular region are variable and specific to each aGPCR and are likely involved in adhering to various ligands. Emerging evidence suggest that extracellular regions may modulate receptor function and that ligand binding to the extracellular regions may induce receptor activation via multiple mechanisms. Here, we summarize current knowledge about the structural understanding for the extracellular regions of aGPCRs and discuss their possible functional roles that emerge from the available structural information.

  16. Using decision trees to understand structure in missing data.

    Science.gov (United States)

    Tierney, Nicholas J; Harden, Fiona A; Harden, Maurice J; Mengersen, Kerrie L

    2015-06-29

    Demonstrate the application of decision trees--classification and regression trees (CARTs), and their cousins, boosted regression trees (BRTs)--to understand structure in missing data. Data taken from employees at 3 different industrial sites in Australia. 7915 observations were included. The approach was evaluated using an occupational health data set comprising results of questionnaires, medical tests and environmental monitoring. Statistical methods included standard statistical tests and the 'rpart' and 'gbm' packages for CART and BRT analyses, respectively, from the statistical software 'R'. A simulation study was conducted to explore the capability of decision tree models in describing data with missingness artificially introduced. CART and BRT models were effective in highlighting a missingness structure in the data, related to the type of data (medical or environmental), the site in which it was collected, the number of visits, and the presence of extreme values. The simulation study revealed that CART models were able to identify variables and values responsible for inducing missingness. There was greater variation in variable importance for unstructured as compared to structured missingness. Both CART and BRT models were effective in describing structural missingness in data. CART models may be preferred over BRT models for exploratory analysis of missing data, and selecting variables important for predicting missingness. BRT models can show how values of other variables influence missingness, which may prove useful for researchers. Researchers are encouraged to use CART and BRT models to explore and understand missing data. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  17. Understanding surface structure and chemistry of single crystal lanthanum aluminate

    KAUST Repository

    Pramana, Stevin S.

    2017-03-02

    The surface crystallography and chemistry of a LaAlO3 single crystal, a material mainly used as a substrate to deposit technologically important thin films (e.g. for superconducting and magnetic devices), was analysed using surface X-ray diffraction and low energy ion scattering spectroscopy. The surface was determined to be terminated by Al-O species, and was significantly different from the idealised bulk structure. Termination reversal was not observed at higher temperature (600 °C) and chamber pressure of 10−10 Torr, but rather an increased Al-O occupancy occurred, which was accompanied by a larger outwards relaxation of Al from the bulk positions. Changing the oxygen pressure to 10−6 Torr enriched the Al site occupancy fraction at the outermost surface from 0.245(10) to 0.325(9). In contrast the LaO, which is located at the next sub-surface atomic layer, showed no chemical enrichment and the structural relaxation was lower than for the top AlO2 layer. Knowledge of the surface structure will aid the understanding of how and which type of interface will be formed when LaAlO3 is used as a substrate as a function of temperature and pressure, and so lead to improved design of device structures.

  18. Temporal structure of neuronal population oscillations with empirical model decomposition

    International Nuclear Information System (INIS)

    Li Xiaoli

    2006-01-01

    Frequency analysis of neuronal oscillation is very important for understanding the neural information processing and mechanism of disorder in the brain. This Letter addresses a new method to analyze the neuronal population oscillations with empirical mode decomposition (EMD). Following EMD of neuronal oscillation, a series of intrinsic mode functions (IMFs) are obtained, then Hilbert transform of IMFs can be used to extract the instantaneous time frequency structure of neuronal oscillation. The method is applied to analyze the neuronal oscillation in the hippocampus of epileptic rats in vivo, the results show the neuronal oscillations have different descriptions during the pre-ictal, seizure onset and ictal periods of the epileptic EEG at the different frequency band. This new method is very helpful to provide a view for the temporal structure of neural oscillation

  19. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

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

    Directory of Open Access Journals (Sweden)

    Luciano Miranda

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

  1. Population genetic structure and phylogeography of the mud-flat ...

    African Journals Online (AJOL)

    Yomi

    2012-01-27

    FST) revealed significant genetic structure in the 10 populations of H. tientsinensis and H. latimera. For all populations, the AMOVA showed three different groups in the marginal seas of East Asia. Within-lineage variation was ...

  2. Understanding Underrepresented Populations in the Business School Pipeline. GMAC® Research Report RR-16-02

    Science.gov (United States)

    Daniel, Rhonda; Caruthers, Devina

    2016-01-01

    This white paper, "Understanding Underrepresented Populations in the Business School Pipeline," examines the shifting US racial and ethnic demographics and projected growth among US minority populations and the challenges--and incentives--these developments pose for US business schools to increase the opportunities for minority students…

  3. Integrating population and genetic monitoring to understand changes in the abundance of a threatened seabird

    Science.gov (United States)

    Catalina Vásquez-Carrillo; R. William Henry; Laird Henkel; M. Zachariah. Peery

    2013-01-01

    Population monitoring programs for threatened species are rarely designed to disentangle the effects of movements from changes in birth and death rates on estimated trends in abundance. Here, we illustrate how population and genetic monitoring can be integrated to understand the cause of large changes in the abundance of a threatened species of seabird, the Marbled...

  4. Genetic population structure of harbour seals in the United Kingdom and neighbouring waters

    NARCIS (Netherlands)

    Olsen, Morten Tange; Islas, Valentina; Graves, Jeff A.; Onoufriou, Aubrie; Vincent, Cecile; Brasseur, Sophie; Frie, Anne Kirstine; Hall, Ailsa J.

    2017-01-01

    In the United Kingdom (UK), several harbour seal (Phoca vitulina) populations have been declining over the past decade. In order to understand the effect of these changes in abundance, this study seeks to determine the population structure of harbour seals in the UK, and in Scotland in particular,

  5. Genetic variation and population structure in Oryza ...

    Indian Academy of Sciences (India)

    We assessed the nature and distribution of genetic variation among 11 populations of O. malampuzhaensis using random amplified polymorphic DNA markers. The analysis revealed low genetic variation in O. malampuzhaensis. Cluster analysis of pairwise genetic distances of populations revealed three distinct clusters ...

  6. Underground population defense structures in China

    Energy Technology Data Exchange (ETDEWEB)

    Wukasch, E.

    The design and construction ofunderground shelters to protect the Chinese population in the event of nuclear war are described. Built in the style of World War II air raid shelters and designed as neighborhood defense facilities, these are not judged to be adequate for nuclear defense needs, particularly the needs of urban populations. However, 80% of China's population is rural and 1/3 of this has lived underground for centuries in cliff dwellings and atrium houses. It is, therefore, concluded that China's rural population has a better chance the the population of any other country for long-term survival from the later consequences, as well as the immediate shock, of an urban nuclear attack. (LCL)

  7. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  8. Understanding physical activity participation in spinal cord injured populations: Three narrative types for consideration

    Directory of Open Access Journals (Sweden)

    Anthony Papathomas

    2015-08-01

    Full Text Available The aim of this study was to identity the types of physical activity narratives drawn upon by active spinal injured people. More than 50 h of semi-structured life-story interview data, collected as part of larger interdisciplinary program of disability lifestyle research, was analysed for 30 physically active male and female spinal cord injury (SCI participants. A structural narrative analysis of data identified three narrative types which people with SCI draw on: (1 exercise is restitution, (2 exercise is medicine, and (3 exercise is progressive redemption. These insights contribute new knowledge by adding a unique narrative perspective to existing cognitive understanding of physical activity behaviour in the spinal cord injured population. The implications of this narrative typology for developing effective positive behavioural change interventions are critically discussed. It is concluded that the identified narratives types may be constitutive, as well as reflective, of physical activity experiences and therefore may be a useful tool on which to base physical activity promotion initiatives.

  9. Understanding physical activity participation in spinal cord injured populations: Three narrative types for consideration.

    Science.gov (United States)

    Papathomas, Anthony; Williams, Toni L; Smith, Brett

    2015-01-01

    The aim of this study was to identity the types of physical activity narratives drawn upon by active spinal injured people. More than 50 h of semi-structured life-story interview data, collected as part of larger interdisciplinary program of disability lifestyle research, was analysed for 30 physically active male and female spinal cord injury (SCI) participants. A structural narrative analysis of data identified three narrative types which people with SCI draw on: (1) exercise is restitution, (2) exercise is medicine, and (3) exercise is progressive redemption. These insights contribute new knowledge by adding a unique narrative perspective to existing cognitive understanding of physical activity behaviour in the spinal cord injured population. The implications of this narrative typology for developing effective positive behavioural change interventions are critically discussed. It is concluded that the identified narratives types may be constitutive, as well as reflective, of physical activity experiences and therefore may be a useful tool on which to base physical activity promotion initiatives.

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

    Science.gov (United States)

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

  11. Estimating population age structure using otolith morphometrics

    DEFF Research Database (Denmark)

    Doering-Arjes, P.; Cardinale, M.; Mosegaard, Henrik

    2008-01-01

    Traditional age reading is a rather subjective method that lacks true reproducibility, producing ageing error that propagates up to stock assessment. One alternative is represented by the use of otolith morphometrics as a predictor of age. An important issue with such a method is that it requires...... known-age fish individuals. Here we used known-age Atlantic cod (Gadus morhua) from the Faroe Bank and Faroe Plateau stocks. Cod populations usually show quite large variation in growth rates and otolith shape. We showed that including otolith morphometrics into ageing processes has the potential...... populations. The intercalibration method was successful but generalization from one stock to another remains problematic. The development of an otolith growth model is needed for generalization if an operational method for different populations is required in the future....

  12. Genetic approaches to understanding the population-level impact of wind energy development on migratory bats

    Energy Technology Data Exchange (ETDEWEB)

    Vonhof, Maarten J. [Western Michigan Univ., Kalamazoo MI (United States); Russell, Amy L. [Grand Valley State Univ. Allendale, MI (United States)

    2013-09-30

    Documented fatalities of bats at wind turbines have raised serious concerns about the future impacts of increased wind power development on populations of migratory bat species. Yet there is little data on bat population sizes and trends to provide context for understanding the consequences of mortality due to wind power development. Using a large dataset of both nuclear and mitochondrial DNA variation for eastern red bats, we demonstrated that: 1) this species forms a single, panmictic population across their range with no evidence for the historical use of divergent migratory pathways by any portion of the population; 2) the effective size of this population is in the hundreds of thousands to millions; and 3) for large populations, genetic diversity measures and at least one coalescent method are insensitive to even very high rates of population decline over long time scales and until population size has become very small. Our data provide important context for understanding the population-level impacts of wind power development on affected bat species.

  13. Understanding the mechanisms behind coking pressure: Relationship to pore structure

    Energy Technology Data Exchange (ETDEWEB)

    John J. Duffy; M. Castro Diaz; Colin E. Snape; Karen M. Steel; Merrick R. Mahoney [University of Nottingham, Nottingham (United Kingdom). Nottingham Fuel and Energy Centre, School of Chemical, Environmental and Mining Engineering

    2007-09-15

    Three low volatile coals A, B and C with oven wall pressures of 100 kPa, 60 kPa and 20 kPa respectively were investigated using high-temperature rheometry, {sup 1}H NMR, thermogravimetric analysis and SEM, with the primary aim to better understand the mechanisms behind the coking pressure phenomenon. Rheometer plate displacement measurements ({Delta}L) have shown differences in the expansion and contraction behaviour of the three coals, which seem to correlate with changes in rheological properties; while SEM images have shown that the expansion process coincides with development of pore structure. It is considered that the point of maximum plate height ({Delta}L{sub max}) prior to contraction may be indicative of a cell opening or pore network forming process, based on analogies with other foam systems. Such a process may be considered important for coking pressure since it provides a potential mechanism for volatile escape, relieving internal gas pressure and inducing charge contraction. For coal C, which has the highest fluidity {delta}L{sub max} occurs quite early in the softening process and consequently a large degree of contraction is observed; while for the lower fluidity coal B, the process is delayed since pore development and consequently wall thinning progress at a slower rate. When {Delta}L{sub max} is attained, a lower degree of contraction is observed because the event occurs closer to resolidification where the increasing viscosity/elasticity can stabilise the expanded pore structure. For coal A which is relatively high fluidity, but also high coking pressure, a greater degree of swelling is observed prior to cell rupture, which may be due to greater fluid elasticity during the expansion process. This excessive expansion is considered to be a potential reason for its high coking pressure. 58 refs., 15 figs., 1 tab.

  14. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... Meconopsis quintuplinervia is regarded as a valuable medicinal plant in Tibetan medicinal system. This species is distributed in Qinghai, Xizang, Sichuan, Shanxi ,Gansu and Hubei provinces of the People's. Republic of China. Genetic variation of 16 M. quintuplinervia populations sampled from Qinghai ...

  15. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    This species is distributed in Qinghai, Xizang, Sichuan, Shanxi ,Gansu and Hubei provinces of the People's Republic of China. Genetic variation of ... Nei's coefficient of differentiation (GST) was found to be high (0.2320), also confirming the relatively high level of genetic differentiation within populations. By UPGMA cluster ...

  16. Extensive population genetic structure in the giraffe

    Science.gov (United States)

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

    2007-01-01

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

  17. Extensive population genetic structure in the giraffe

    Directory of Open Access Journals (Sweden)

    Grether Gregory F

    2007-12-01

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

  18. Genetic variation and population structure in Oryza ...

    Indian Academy of Sciences (India)

    Genetically isolated smaller populations and a narrow genetic base in O. malampuzhaensis point to its vulnerability to genetic drift and genetic depauperation. Thus O. malampuzhaensis appears to be under the threat of extinction and needs to be conserved by use of suitable methods. The present study also identified ...

  19. Population Structure and Reproduction of Pseudione elongata ...

    African Journals Online (AJOL)

    production (bacteria and microalgae) may thus provide the shrimp with more abundant and diverse food, increasing several population fitness parameters. However .... was based on the number of stage II embryos and epicaridium larvae in each brood (adapted from the definitions proposed by Penha-Lopes et al., 2009).

  20. On some quasilinear structured population models

    NARCIS (Netherlands)

    Getto, P.

    2005-01-01

    The object of my research was the mathematical analysis of a class of population models in which the effect of differences of individuals (in e.g. age, size or position in space) on their physiological development, mortality and reproduction is assumed to play an important role. Such models, which

  1. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

  2. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  3. A Structure for Population Education: Goals, Generalizations, and Behavioral Objectives.

    Science.gov (United States)

    Lane, Mary Turner; Wileman, Ralph E.

    This book is written to assist anyone who wants to learn about, teach, or plan curricula for population education. A structure is provided that educators can use for first graders or for high school students. Chapter 1 identifies the population phenomenon and the need to study it. Chapter 2 gives the elements of the structure: goals,…

  4. Modeling evolutionary games in populations with demographic structure

    DEFF Research Database (Denmark)

    Li, Xiang-Yi; Giaimo, Stefano; Baudisch, Annette

    2015-01-01

    interactions, but usually omits life history and the demographic structure of the population. Here we show how an integration of both aspects can substantially alter the underlying evolutionary dynamics. We study the replicator dynamics of strategy interactions in life stage structured populations. Individuals...

  5. Population Genetic Structure and Gene Flow Among Nigerian Goats ...

    African Journals Online (AJOL)

    Population Genetic structure in 200 indigenous goats sampled across four states from the South-Western and South Southern region of Nigeria was assessed using 7 microsatellite DNA markers. Observed Analysis of molecular genetic variation (AMOVA) was higher within populations (3.47) than among populations (1.84) ...

  6. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  7. Using Instruments to Understand Argument Structure: Evidence for Gradient Representation

    Science.gov (United States)

    Rissman, Lilia; Rawlins, Kyle; Landau, Barbara

    2015-01-01

    The arguments of a verb are commonly assumed to correspond to the event participants specified by the verb. That is, drink has two arguments because drink specifies two participants: someone who drinks and something that gets drunk. This correspondence does not appear to hold, however, in the case of instrumental participants, e.g. John drank the soda with a straw. Verbs such as slice and write have been argued to specify an instrumental participant, even though instruments do not pattern like arguments given other criteria. In this paper, we investigated how instrumental verbs are represented, testing the hypothesis that verbs such as slice encode three participants in the same way that dative verbs such as lend encode three participants. In two experiments English-speakers reported their judgments about the number of participants specified by a verb, e.g. that drink specifies two participants. These judgments indicate that slice does not encode three distinct arguments. Nonetheless, some verbs were systematically more likely to elicit the judgment that the instrument is specified by the verb, a pattern that held across individual subjects. To account for these findings, we propose that instruments are not independent verbal arguments but are represented in a gradient away: an instrument may be a more or less salient part of the force exerted by an agent. These results inform our understanding of the relationship between argument structure and event representation, raising questions concerning the role of arguments in language processing and learning. PMID:26057832

  8. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course.

    Science.gov (United States)

    Jaswal, Sheila S; O'Hara, Patricia B; Williamson, Patrick L; Springer, Amy L

    2013-01-01

    Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. © 2013 by The International Union of Biochemistry and Molecular Biology.

  9. Identifying the number of population clusters with structure: problems and solutions.

    Science.gov (United States)

    Gilbert, Kimberly J

    2016-05-01

    The program structure has been used extensively to understand and visualize population genetic structure. It is one of the most commonly used clustering algorithms, cited over 11,500 times in Web of Science since its introduction in 2000. The method estimates ancestry proportions to assign individuals to clusters, and post hoc analyses of results may indicate the most likely number of clusters, or populations, on the landscape. However, as has been shown in this issue of Molecular Ecology Resources by Puechmaille (), when sampling is uneven across populations or across hierarchical levels of population structure, these post hoc analyses can be inaccurate and identify an incorrect number of population clusters. To solve this problem, Puechmaille () presents strategies for subsampling and new analysis methods that are robust to uneven sampling to improve inferences of the number of population clusters. © 2016 John Wiley & Sons Ltd.

  10. Population structure of Han nationality in Central-Southern China.

    Science.gov (United States)

    Liu, Qiu-Ling; Chen, Ye-Fei; He, Xin; Shi, Yan-Wei; Wu, Wei-Wei; Zhao, Hu; Lu, De-Jian

    2017-07-01

    Knowledge of population structure is very important for forensic genetics. However, the population substructure in Central-Southern China Han nationality has still not been fully described. In this study, we investigated the genetic diversity of 15 forensic autosomal STR loci from 6879 individuals in 12 Han populations subdivided by administrative provinces in Central-Southern China. The statistical analysis of genetic variation showed that genetic differentiation among these populations was very small with a F st value of 0.0009. The Discriminant Analysis of Principal Components (DAPC) showed that there were no obvious population clusters in Central-Southern China Han population. In practice, the population structure effect in Central-Southern China Han population can be negligible in forensic identification and paternity testing. Copyright © 2017. Published by Elsevier B.V.

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

    Science.gov (United States)

    Wollenberg, M S; Ruby, E G

    2009-01-01

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

  12. Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

    Directory of Open Access Journals (Sweden)

    Jiali Zhao

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

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

    DEFF Research Database (Denmark)

    Macedo Viana, Flavia Daniela; Jensen, Christopher Erik; Macey, Michael

    2016-01-01

    . Although several studies have addressed the Verminephrobacter diversity between worm species, the intra-species diversity of the symbiont population has never been investigated. To address symbiont population structure, we used a multi-locus sequence typing (MLST) approach on Verminephrobacter isolated...... from two contrasting ecological types of earthworm hosts: the high population density, fast reproducing compost worms, Eisenia andrei and E. fetida, and the low-density, slow reproducing Aporrectodea tuberculata, commonly found in garden soils; for both types, three distinct populations were...... across host individuals from the same population. Thus, host ecology shapes the population structure of the Verminephrobacter symbionts. The homogeneous symbiont populations in the compost worms indicate that Verminephrobacter can be transferred bi-parentally or via leaky horizontal transmission in high...

  14. Integrating Model-Based Learning and Animations for Enhancing Students' Understanding of Proteins Structure and Function

    Science.gov (United States)

    Barak, Miri; Hussein-Farraj, Rania

    2013-04-01

    This paper describes a study conducted in the context of chemistry education reforms in Israel. The study examined a new biochemistry learning unit that was developed to promote in-depth understanding of 3D structures and functions of proteins and nucleic acids. Our goal was to examine whether, and to what extent teaching and learning via model-based learning and animations of biomolecules affect students' chemical understanding. Applying the mixed methods research paradigm, pre- and post-questionnaires as well as class-observations were employed in the collection, analysis, and interpretation of data. The research population included 175 grade twelve students, divided into three research groups: (a) hands-on exploration of animations, (b) teacher's demonstrations of animations, (c) traditional learning using textbooks. Findings indicated that the integration of model-based learning and 3D animations enhanced students' understanding of proteins' structure and function and their ability to transfer across different levels of chemistry understanding. Findings also indicated that teachers' demonstrations of animations may enhance students' `knowledge'—a low order thinking skill; however, in order to enhance higher levels of thinking, students should be able to explore 3D animations on their own. Applying constructivist and interpretative analysis of the data, three themes were raised, corresponding to cognitive, affective, and social aspects of learning while exploring web-based models and animations.

  15. Understanding Metallic Bonding: Structure, Process and Interaction by Rasch Analysis

    Science.gov (United States)

    Cheng, Maurice M. W.; Oon, Pey-Tee

    2016-01-01

    This paper reports the results of a survey of 3006 Year 10-12 students on their understandings of metallic bonding. The instrument was developed based on Chi's ontological categories of scientific concepts and students' understanding of metallic bonding as reported in the literature. The instrument has two parts. Part one probed into students'…

  16. Understanding Structural Features of Microbial Lipases–-An Overview

    Directory of Open Access Journals (Sweden)

    John Geraldine Sandana Mala

    2008-01-01

    Full Text Available The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ returns only 93 hits (as of September 2007 and, the NCBI database ( http://www.ncbi.nlm.nih.gov reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.

  17. Population activity structure of excitatory and inhibitory neurons.

    Science.gov (United States)

    Bittner, Sean R; Williamson, Ryan C; Snyder, Adam C; Litwin-Kumar, Ashok; Doiron, Brent; Chase, Steven M; Smith, Matthew A; Yu, Byron M

    2017-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  19. Population structure age of Paraná state between 1970 and 2010

    Directory of Open Access Journals (Sweden)

    Eduardo de Pintor

    2014-06-01

    Full Text Available The theory of demographic transition began with an effort of Frank Notestein (1945 to understand the demographic changes that were occurring in Western Europe since the late nineteenth century. The demographic transition is the transition between two scenarios of population growth, which changes the age structure of the population. The aim of the article is to discuss the evolution of population structure age of Paraná state between 1970 and 2010. The changes in the age structure of the Paraná indicate a reduction in the share of young population and increasing aging population, an increase in the relative weight of the elderly population. Public policies on education, health, social security and labor market should consider the current change in the age structure. Thus, the aim of this study was to analyze the change in the age structure of the population of the state of Paraná. For this we used data Censuses of the Brazilian Institute of Geography and Statistics (IBGE on the age distribution of urban and rural Paraná and its Mesoregions. It was concluded that the change in structure occurs group widespread in all Mesoregions state. However, it occurs unevenly between urban and rural population.

  20. HOW POPULATION STRUCTURE SHAPES NEIGHBORHOOD SEGREGATION*

    Science.gov (United States)

    Bruch, Elizabeth E.

    2014-01-01

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

  1. Dynamics of a structured neuron population

    International Nuclear Information System (INIS)

    Pakdaman, Khashayar; Salort, Delphine; Perthame, Benoît

    2010-01-01

    We study the dynamics of assemblies of interacting neurons. For large fully connected networks, the dynamics of the system can be described by a partial differential equation reminiscent of age-structure models used in mathematical ecology, where the 'age' of a neuron represents the time elapsed since its last discharge. The nonlinearity arises from the connectivity J of the network. We prove some mathematical properties of the model that are directly related to qualitative properties. On the one hand, we prove that it is well-posed and that it admits stationary states which, depending upon the connectivity, can be unique or not. On the other hand, we study the long time behaviour of solutions; both for small and large J, we prove the relaxation to the steady state describing asynchronous firing of the neurons. In the middle range, numerical experiments show that periodic solutions appear expressing re-synchronization of the network and asynchronous firing

  2. Understanding Local Structure versus Long-Range Structure: The Case of UO2.

    Science.gov (United States)

    Desgranges, Lionel; Ma, Yue; Garcia, Philippe; Baldinozzi, Gianguido; Siméone, David; Fischer, Henry E

    2018-02-09

    A recent trend in the development of new optimized materials makes use of crystalline domains having nanometer sizes for which characterization methods at the atomic scale are mandatory. Amongst them is pair-distribution function analysis (PDF-analysis), a diffraction technique that has already shown that a short-range or "local" atomic structure of a given domain, having a lower symmetry than the average long-range structure, often exists in many compounds having valuable properties for industrial applications, such as pyrochlores, spinels, and doped ceria among others. However, the manner by which these domains are arranged to produce the average long-range structure is still an open question. Herein, the first structural model that accounts for both the local structure (inside a given domain) and the long-range structure (averaged over all domains) that is observed in the PDF of uranium dioxide is presented. The structural model describes domain walls in such a way as to preserve the uranium coordination polyhedron and to obey the needed symmetry rules. The proper description of domain walls is an important step in the understanding and the modelling of nanostructured materials. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Dynamics of a physiologically structured population in a time-varying environment

    DEFF Research Database (Denmark)

    Heilmann, Irene Louise Torpe; Starke, Jens; Andersen, Ken Haste

    2016-01-01

    Physiologically structured population models have become a valuable tool to model the dynamics of populations. In a stationary environment such models can exhibit equilibrium solutions as well as periodic solutions. However, for many organisms the environment is not stationary, but varies more...... or less regularly. In order to understand the interaction between an external environmental forcing and the internal dynamics in a population, we examine the response of a physiologically structured population model to a periodic variation in the food resource. We explore the addition of forcing in two...... cases: (A) where the population dynamics is in equilibrium in a stationary environment, and (B) where the population dynamics exhibits a periodic solution in a stationary environment. When forcing is applied in case A, the solutions are mainly periodic. In case B the forcing signal interacts...

  4. Estimating density dependence from time series of population age structure.

    Science.gov (United States)

    Lande, Russell; Engen, Steinar; Saether, Bernt-Erik; Coulson, Tim

    2006-07-01

    Population fluctuations are caused by demographic and environmental stochasticity, time lags due to life history, and density dependence. We model a general life history allowing density dependence within and among age or stage classes in a population undergoing small or moderate fluctuations around a stable equilibrium. We develop a method for estimating the overall strength of density dependence measured by the rate of return toward equilibrium, and we also consider a simplified population description and forecasting using the density-dependent reproductive value. This generality comes at the cost of requiring a time series of the population age or stage structure instead of a univariate time series of adult or total population size. The method is illustrated by analyzing the dynamics of a fully censused population of red deer (Cervus elaphus) based on annual fluctuations of age structure through 21 years.

  5. Population genetic structure in wild and aquaculture populations of Hemibarbus maculates inferred from microsatellites markers

    Directory of Open Access Journals (Sweden)

    Linlin Li

    2017-03-01

    Full Text Available The objective of this study was to investigate 4 aquaculture populations Shanghai (SH, Hangzhou (HZ, Kaihua (KH and Xianju (XJ and one wild population Yingshan (YS of spotted barbell (Hemibarbus maculates to assess their genetic diversity level and investigate the genetic structure of the populations. The dendrogram and STRUCTURE revealed that the populations XJ, KH, and HZ jointly formed one cluster, to which the populations SH and YS were sequentially adhered. The genetic diversity of the cultured populations maintained better, possible due to favourable hatchery conditions that decreased the effect of environmental selection present in wild populations. The results of the present study will contribute to the management of spotted barbell genetic resources, but also demonstrates how the genetic diversity of freshwater species is vulnerable to human activity.

  6. Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats

    Science.gov (United States)

    Bryce A. Richardson; Marcus V. Warwell; Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald

    2010-01-01

    To assess threats or predict responses to disturbances, or both, it is essential to recognize and characterize the population structures of forest species in relation to changing environments. Appropriate management of these genetic resources in the future will require (1) understanding the existing genetic diversity/variation and population structure of forest trees...

  7. Genetic variation and population structure of interleukin genes ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 86; Issue 3. Genetic variation and population structure of interleukin genes among seven ethnic populations from Karnataka, India. Srilakshmi M. Raj Diddahally R. Govindaraju Ranajit Chakraborty. Research Article Volume 86 Issue 3 December 2007 pp 189-194 ...

  8. Genetic diversity and population structure of blue-crested lizard ...

    Indian Academy of Sciences (India)

    Weerachai Saijuntha

    2017-06-19

    Jun 19, 2017 ... VNm(HM425545)) published by Hartmann et al. (2013) were included. Pairwise genetic differentiation between populations with φST (using genetic distances with the. Kimura algorithm) and population structure patterns based on analysis of molecular variance (AMOVA) were conducted using Arlequin ver.

  9. Genetic diversity and population structure of leaf-nosed bat ...

    African Journals Online (AJOL)

    Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

  10. Population genetic structure of coral reef species Plectorhinchus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-03

    Jun 3, 2008 ... 510300 P.R. China. Accepted 24 April, 2008. The population genetic structure and the dispersal ability of Plectorhinchus flavomaculatus from South. China Sea were examined with a 464 bp segment of mtDNA control region. A total of 116 .... θ1 (θ before and after the population growth) and τ (time since.

  11. Genetic diversity and population structure of Caragana microphylla ...

    African Journals Online (AJOL)

    Caragana microphylla Lam. is a long-lived shrub species in the semi-arid, arid and desert regions. To determine the genetic diversity and population structure of C. microphylla Lam., 17 wild populations from the central and eastern part of Inner Mongolia were analyzed by inter-simple sequence repeat. 18 primers produced ...

  12. Population structure in an anadromous fish Tenualosa ilisha using ...

    African Journals Online (AJOL)

    WATER INDIA

    2013-05-29

    May 29, 2013 ... there is little or no movement between rivers and little intermingling of three populations. Thus, aim of the study was to analyze population structure of commercially important tropical anadromous fish T. ilisha from Ganga and Hooghly using mitochondrial DNA cytochrome b gene sequence polymorphism.

  13. Population structure and expansion of kuruma shrimp ( Penaeus ...

    African Journals Online (AJOL)

    Sequence analyses on the specific intron from the elongation factor-1α gene were conducted to examine the population genetic structure and expansion of kuruma shrimp (Penaeus japonicus) off Taiwan. Five populations including 119 individuals were separately sampled from the north of East China Sea (ECS), west of ...

  14. Understanding the structure of data when planning for analysis ...

    African Journals Online (AJOL)

    Human beings and other living creatures tend to exist within organisational structures, such as families, schools, and business organisations. In an educational system, for example, students exist within a hierarchical social structure that can include classroom, grade level, school, school district and country. Data obtained ...

  15. Population structure and genome-wide patterns of variation in Ireland and Britain.

    Science.gov (United States)

    O'Dushlaine, Colm T; Morris, Derek; Moskvina, Valentina; Kirov, George; Gill, Michael; Corvin, Aiden; Wilson, James F; Cavalleri, Gianpiero L

    2010-11-01

    Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654 individuals from Ireland, Britain (with regional sampling in Scotland), Bulgaria, Portugal, Sweden and the Utah HapMap collection. Our results indicate a subtle but clear genetic structure across Britain and Ireland, although levels of structure were reduced in comparison with average cross-European structure. We observed slightly elevated levels of LD and homozygosity in the Irish population compared with neighbouring European populations. We also report on a cline of HD across Europe with greatest levels in southern populations and lowest levels in Ireland and Scotland. These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants.

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

    Directory of Open Access Journals (Sweden)

    Morgana Vighi

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Prasanna HC

    2010-09-01

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

  19. A Theoretical Approach to Understanding Population Dynamics with Seasonal Developmental Durations

    Science.gov (United States)

    Lou, Yijun; Zhao, Xiao-Qiang

    2017-04-01

    There is a growing body of biological investigations to understand impacts of seasonally changing environmental conditions on population dynamics in various research fields such as single population growth and disease transmission. On the other side, understanding the population dynamics subject to seasonally changing weather conditions plays a fundamental role in predicting the trends of population patterns and disease transmission risks under the scenarios of climate change. With the host-macroparasite interaction as a motivating example, we propose a synthesized approach for investigating the population dynamics subject to seasonal environmental variations from theoretical point of view, where the model development, basic reproduction ratio formulation and computation, and rigorous mathematical analysis are involved. The resultant model with periodic delay presents a novel term related to the rate of change of the developmental duration, bringing new challenges to dynamics analysis. By investigating a periodic semiflow on a suitably chosen phase space, the global dynamics of a threshold type is established: all solutions either go to zero when basic reproduction ratio is less than one, or stabilize at a positive periodic state when the reproduction ratio is greater than one. The synthesized approach developed here is applicable to broader contexts of investigating biological systems with seasonal developmental durations.

  20. Spatial Genetic Structure and Mitochondrial DNA Phylogeography of Argentinean Populations of the Grasshopper Dichroplus elongatus

    OpenAIRE

    Rosetti, Natalia; Remis, Maria Isabel

    2012-01-01

    Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of ...

  1. Genetic Variation and Population Structure in Native Americans

    Science.gov (United States)

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

    2007-01-01

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

  2. Genetic variation and population structure in native Americans.

    Directory of Open Access Journals (Sweden)

    Sijia Wang

    2007-11-01

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

  3. Canadian Provincial Population Growth: Fertility, Migration, and Age Structure Effects

    Directory of Open Access Journals (Sweden)

    Edmonston, Barry

    2009-01-01

    Full Text Available AbstractThe effect of changes in rates of mortality, fertility, and migration depend not only on the age specific patterns and levels of these rates, but on the age structure of the population. In orderto remove the influences of the age structure and concentrate on the impact of the demographic rates themselves, a common practice is to analyze the influences of the rates for a standard age structure. This paper adapts the general approach of using a standard age structure to a stationary population equivalent (SPE model, and analyzes current population change, using the SPE model, for provinces of Canada. Below-replacement fertility levels are only partially offset by net immigration. The SPE model evidences the decrease in the eventual provincial populations brought about by the below replacement fertility. Out-migration for some provincesto other areas of Canada accentuates their eventual population decreases.RésuméLes effets des changements des taux de mortalité, fécondité, et de migration dépendent non seulement des modèles par âge et des niveaux de ces taux, mais aussi de la structure par âge de la population. Pour éliminer les influences de la structure par âge et se concentrer sur les effets des taux démographiques mêmes, une pratique courante est d’analyser les influences des taux par une structure par âge de norme. Cet article adapte l’approche générale de la structure parâge à un modèle de population stationnaire équivalente (PSE. Cet article analyse les changements de population, en utilisant le modèle de PSE, dans les provinces canadiennes. Le taux de fécondité inférieur au seuil de reproduction de la population n’est que légèrement compensé par l’immigration nette. Le modèle de PSE démontre le déclin des populations provinciales éventuelles causé par le taux de fécondité inférieur au seuil de reproduction de la population. Le taux d’émigration entre certaines provinces et reste du

  4. The role of social and ecological processes in structuring animal populations

    NARCIS (Netherlands)

    Farine, D.R.; Firth, J.A.; Aplin, L.M.; Crates, R.A.; Culina, Antica; Garroway, Colin J.; Hinde, C.A.

    2015-01-01

    Both social and ecological factors influence population process and structure, with resultant consequences for phenotypic selection on individuals. Understanding the scale and relative contribution of these two factors is thus a central aim in evolutionary ecology. In this study, we develop a

  5. Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis

    NARCIS (Netherlands)

    Pang, W.; Li, X.; Choi, S.R.; Dhandapani, V.; Im, S.; Park, M.Y.; Jang, C.S.; Yang, M.S.; Ham, I.K.; Lee, E.M.; Kim, W.; Lee, S.S.; Bonnema, A.B.; Park, S.; Piao, Z.; Lim, Y.P.

    2015-01-01

    Brassica rapa is an economically important crop with a wide range of morphologies. Developing a set of fixed lines and understanding their diversity has been challenging, but facilitates resource conservation. We investigated the genetic diversity and population structure of 238 fixed lines of leafy

  6. Hierarchical population structure in greater sage-grouse provides insight into management boundary delineation

    Science.gov (United States)

    Todd B. Cross; David E. Naugle; John C. Carlson; Michael K. Schwartz

    2016-01-01

    Understanding population structure is important for guiding ongoing conservation and restoration efforts. The greater sage-grouse (Centrocercus urophasianus) is a species of concern distributed across 1.2 million km2 of western North America. We genotyped 1499 greater sagegrouse from 297 leks across Montana, North Dakota and South Dakota using a 15 locus...

  7. The population structure of wild sorghum species in agro-ecological ...

    African Journals Online (AJOL)

    There is need to understand the genetic structure of wild sorghums that grow alongside cultivated traditional sorghum varieties in order to assess the potential effect of crop genes in wild populations. In this study, 175 wild sorghum samples were collected from 13 agroecological zones (AEZs) from three counties in Western ...

  8. Amplification on Undirected Population Structures: Comets Beat Stars.

    Science.gov (United States)

    Pavlogiannis, Andreas; Tkadlec, Josef; Chatterjee, Krishnendu; Nowak, Martin A

    2017-03-06

    The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Bénédicte Coupat-Goutaland

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

  11. Biobanking for research: a survey of patient population attitudes and understanding

    OpenAIRE

    Rahm, Alanna Kulchak; Wrenn, Michelle; Carroll, Nikki M.; Feigelson, Heather Spencer

    2013-01-01

    Population-based biobanks are a critical resource for genetic research. It is important to know what potential participants understand about the risks and benefits of providing samples in order to ensure adequate informed consent. Kaiser Permanente Colorado (KPCO) is currently planning a biobank where adult members would be asked to contribute an additional tube of blood during a routine blood draw. Adult KPCO members in clinic waiting rooms were asked to read an informational brochure and in...

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

    Science.gov (United States)

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

    2014-01-01

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

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

    NARCIS (Netherlands)

    de Roos, A.M.; Persson, L.

    2003-01-01

    In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and

  14. Understanding the proton's spin structure

    Energy Technology Data Exchange (ETDEWEB)

    Myhrer, Fred [Univ. of South Carolina, Columbia, SC (United States); Thomas, Anthony W. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); College of William and Mary, Williamsburg, VA (United States)

    2010-02-01

    We discuss the tremendous progress that has been towards an understanding of how the spin of the proton is distributed on its quark and gluon constituents. This is a problem that began in earnest twenty years ago with the discovery of the proton "spin crisis" by the European Muon Collaboration. The discoveries prompted by that original work have given us unprecedented insight into the amount of spin carried by polarized gluons and the orbital angular momentum of the quarks.

  15. Fundamental understanding and rational design of high energy structural microbatteries

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuxing; Li, Qiuyan; Cartmell, Samuel; Li, Huidong; Mendoza, Sarah; Zhang, Ji-Guang; Deng, Zhiqun Daniel; Xiao, Jie

    2018-01-01

    Microbatteries play a critical role in determining the lifetime of downsized sensors, wearable devices and medical applications, etc. More often, structural batteries are required from the perspective of aesthetics and space utilization, which is however rarely explored. Herein, we discuss the fundamental issues associated with the rational design of practically usable high energy microbatteries. The tubular shape of the cell further allows the flexible integration of microelectronics. A functioning acoustic micro-transmitter continuously powered by this tubular battery has been successfully demonstrated. Multiple design features adopted to accommodate large mechanical stress during the rolling process are discussed providing new insights in designing the structural microbatteries for emerging technologies.

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

    Directory of Open Access Journals (Sweden)

    Sitthi-amorn Chitr

    2009-07-01

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

  17. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    Science.gov (United States)

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

    2016-02-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  18. Genetic structure of introduced populations: 120-year-old DNA footprint of historic introduction in an insular small mammal population

    Science.gov (United States)

    Simpson, Siobhan; Blampied, Nick; Peniche, Gabriela; Dozières, Anne; Blackett, Tiffany; Coleman, Stephen; Cornish, Nina; Groombridge, Jim J

    2013-01-01

    Wildlife populations have been introduced to new areas by people for centuries, but this human-mediated movement can disrupt natural patterns of genetic structure by altering patterns of gene flow. Insular populations are particularly prone to these influences due to limited opportunities for natural dispersal onto islands. Consequently, understanding how genetic patterns develop in island populations is important, particularly given that islands are frequently havens for protected wildlife. We examined the evolutionary origins and extent of genetic structure within the introduced island population of red squirrels (Sciurus vulgaris) on the Channel Island of Jersey using mitochondrial DNA (mtDNA) control region sequence and nuclear microsatellite genotypes. Our findings reveal two different genetic origins and a genetic architecture reflective of the introductions 120 years ago. Genetic structure is marked within the maternally inherited mtDNA, indicating slow dispersal of female squirrels. However, nuclear markers detected only weak genetic structure, indicating substantially greater male dispersal. Data from both mitochondrial and nuclear markers support historic records that squirrels from England were introduced to the west of the island and those from mainland Europe to the east. Although some level of dispersal and introgression across the island between the two introductions is evident, there has not yet been sufficient gene flow to erase this historic genetic “footprint.” We also investigated if inbreeding has contributed to high observed levels of disease, but found no association. Genetic footprints of introductions can persist for considerable periods of time and beyond traditional timeframes of wildlife management. PMID:23532702

  19. Using a structured morbidity and mortality meeting to understand the ...

    African Journals Online (AJOL)

    2013-11-04

    Nov 4, 2013 ... We report our experience with these meetings. Methods. A structured template was developed for each morbidity and mortality meeting. We used a grid to analyse mortality and classify the death as: (i) death expected/death unexpected; and (ii) death unpreventable/death preventable. Individual cases were ...

  20. Understanding Protein-Protein Interactions Using Local Structural Features

    DEFF Research Database (Denmark)

    Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier

    2013-01-01

    of this classification suggests that the balance between favoring and disfavoring structural features determines if a pair of proteins interacts or not. Our results are in agreement with previous works and support the funnel-like intermolecular energy landscape theory that explains PPIs. We have used these features...

  1. Understanding Practices in Mathematics Education: Structure and Text

    Science.gov (United States)

    Morgan, Candia

    2014-01-01

    The practices of mathematics education can be investigated at a wide variety of levels: from the actions of individual students or teachers through classroom interactions, school structures, curriculum specifications and materials, teacher development programmes and local, national or international systems of instruction and assessment. These…

  2. Understanding the structure and electronic properties of N-doped ...

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Structures and electronic properties of zigzag graphene nanoribbon (ZGNR) with pyridine (3NVZGNR) functionalized by Scandium (Sc) at the edge were studied through quantum chemical calculations in the formalism of density-functional theory (DFT). Pyridine-like nitrogen defects is very crucial for ...

  3. Schools as Racial Spaces: Understanding and Resisting Structural Racism

    Science.gov (United States)

    Blaisdell, Benjamin

    2016-01-01

    Analyzing schools as racial spaces can help researchers examine the role of teachers in the perpetuation of structural racism in schools. Based on ethnographic and autoethnographic work, this article offers examples of schools as racial spaces, spaces where whiteness controlled access. It also highlights four teachers who pursued racial equity in…

  4. Understanding and quantifying urban forest structure, functions, and value

    Science.gov (United States)

    David J. Nowak; Daniel E. Crane; Jeffrey T. Walton; Daniel B. Twardus; John F. Dwyer

    2002-01-01

    Trees in urban areas can have a significant impact on human health and the environment. Unfortunately, there is relatively little data about the structure, health, functions, and long-term changes in this important resource. In the United States, a number of efforts are underway to assess urban forest attributes at the local to national scales. In addition, tools are...

  5. Using a structured morbidity and mortality meeting to understand the ...

    African Journals Online (AJOL)

    Background. Several authors have suggested that the traditional surgical morbidity and mortality meeting be developed as a tool to identify surgical errors and turn them into learning opportunities for staff. We report our experience with these meetings. Methods. A structured template was developed for each morbidity and ...

  6. Effect of Population Structure Change on Carbon Emission in China

    Directory of Open Access Journals (Sweden)

    Wen Guo

    2016-03-01

    Full Text Available This paper expanded the Logarithmic Mean Divisia Index (LMDI model through the introduction of urbanization, residents’ consumption, and other factors, and decomposed carbon emission changes in China into carbon emission factor effect, energy intensity effect, consumption inhibitory factor effect, urbanization effect, residents’ consumption effect, and population scale effect, and then explored contribution rates and action mechanisms of the above six factors on change in carbon emissions in China. Then, the effect of population structure change on carbon emission was analyzed by taking 2003–2012 as a sample period, and combining this with the panel data of 30 provinces in China. Results showed that in 2003–2012, total carbon emission increased by 4.2117 billion tons in China. The consumption inhibitory factor effect, urbanization effect, residents’ consumption effect, and population scale effect promoted the increase in carbon emissions, and their contribution ratios were 27.44%, 12.700%, 74.96%, and 5.90%, respectively. However, the influence of carbon emission factor effect (−2.54% and energy intensity effect (−18.46% on carbon emissions were negative. Population urbanization has become the main population factor which affects carbon emission in China. The “Eastern aggregation” phenomenon caused the population scale effect in the eastern area to be significantly higher than in the central and western regions, but the contribution rate of its energy intensity effect (−11.10 million tons was significantly smaller than in the central (−21.61 million tons and western regions (−13.29 million tons, and the carbon emission factor effect in the central area (−3.33 million tons was significantly higher than that in the eastern (−2.00 million tons and western regions (−1.08 million tons. During the sample period, the change in population age structure, population education structure, and population occupation structure

  7. The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins.

    Science.gov (United States)

    Younger, Jane L; Clucas, Gemma V; Kao, Damian; Rogers, Alex D; Gharbi, Karim; Hart, Tom; Miller, Karen J

    2017-08-01

    Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions, particularly whether the Ross Sea, a major stronghold for the species, is isolated or not. We assessed emperor penguin population structure using 4,596 genome-wide single nucleotide polymorphisms (SNPs), characterized in 110 individuals (10-16 per colony) from eight colonies around Antarctica. In contrast to a previous conclusion that emperor penguins are panmictic around the entire continent, we find that emperor penguins comprise at least four metapopulations, and that the Ross Sea is clearly a distinct metapopulation. Using larger sample sizes and a thorough assessment of the limitations of different analytical methods, we have shown that population structure within emperor penguins does exist and argue that its recognition is vital for the effective conservation of the species. We discuss the many difficulties that molecular ecologists and managers face in the detection and interpretation of subtle population structure using large SNP data sets, and argue that subtle structure should be taken into account when determining management strategies for threatened species, until accurate estimates of demographic connectivity among populations can be made. © 2017 John Wiley & Sons Ltd.

  8. Hydrogen/deuterium substitution methods: understanding water structure in solution

    International Nuclear Information System (INIS)

    Soper, A.K.

    1993-01-01

    The hydrogen/deuterium substitution method has been used for different applications, such as the short range order between water molecules in a number of different environments (aqueous solutions of organic molecules), or to study the partial structure factors of water at high pressure and temperature. The absolute accuracy that can be obtained remains uncertain, but important qualitative information can be obtained on the local organization of water in aqueous solution. Some recent results with pure water, methanol and dimethyl sulphoxide (DMSO) solutions are presented. It is shown that the short range water structure is not greatly affected by most solutes except at high concentrations and when the solute species has its own distinctive interaction with water (such as a dissolved small ion). 3 figs., 14 refs

  9. Understanding `galaxy groups' as a unique structure in the universe

    Science.gov (United States)

    Paul, S.; John, R. S.; Gupta, P.; Kumar, H.

    2017-10-01

    'Galaxy groups' have hardly been realized as a separate class of objects with specific characteristics in the structural hierarchy. The presumption that the self-similarity of dark matter structures is a valid prescription for the baryonic universe at all scales has rendered smaller structures undetectable by current observational facilities, leading to lesser dedicated studies on them. Some recent reports that indicate a deviation from LX-T scaling in groups compared to clusters have motivated us to study their physical properties in depth. In this article, we report the extensive study on physical properties of groups in comparison to the clusters through cosmological hydrodynamic plus N-body simulations using enzo 2.2 code. As additional physics, radiative cooling, heating due to supernova and star motions, star formation and stellar feedback have been implemented. We have produced a mock sample of 362 objects with mass ranging from 5 × 1012 M⊙ to 2.5 × 1015 M⊙. Strikingly, we have found that objects with mass below ˜8 × 1013 M⊙ do not follow any of the cluster self-similar laws in hydrostatics, not even in thermal and non-thermal energies. Two distinct scaling laws are observed to be followed with breaks at ˜8 × 1013 M⊙ for mass, ˜1 keV for temperature and ˜1 Mpc for radius. This places groups as a distinct entity in the hierarchical structures, well demarcated from clusters. This study reveals that groups are mostly far away from virialization, suggesting the need for formulating new models for deciphering their physical parameters. They are also shown to have high turbulence and more non-thermal energy stored, indicating better visibility in the non-thermal regime.

  10. Understanding 'Galaxy Groups' as a Unique Structure in the Universe

    Science.gov (United States)

    John, Reju Sam; Paul, Surajit; Gupta, Prateek; Kumar, Harish

    2017-07-01

    'Galaxy groups' have hardly been realized as a separate class of objects with specific characteristics in the structural hierarchy of the universe. The presumption that the self-similarity of dark matter structures is a valid prescription for the baryonic universe also at all scales has rendered smaller structures undetectable by current observational facilities, leading to lesser dedicated studies on them. Some recent reports on deviation of {L_x}-T scaling in groups from that of clusters have motivated us to study their physical properties in depth. In this article, we report the extensive study on physical properties of groups in comparison with clusters through cosmological hydrodynamic plus N-body simulations using ENZO 2.2 code. We have included cooling and heating physics and star formation feedback in the simulation. And produced a mock sample of 362 objects with mass ranging from 5×10^{12} M_{⊙} to 2.5×10^{15} M_{⊙}. Strikingly, we have found that objects with a mass below ˜ 8×10^{13} M_{⊙} do not follow any of the cluster self-similar laws in hydrostatics, not even in thermal and non-thermal regimes. Two distinct scaling laws are observed to be followed with breaks at ˜ 6-8× 10^{13} M_{⊙} for mass, ˜1 keV for temperature and ˜1 Mpc for radius. This places groups as a distinct entity in the hierarchical structures, well demarcated from clusters. This study reveals that groups are mostly far away from virialization, suggesting the need for formulating new models for deciphering their physical parameters. They are also shown to have high turbulence and more non-thermal energy stored, indicating better visibility in the non-thermal regime.

  11. Genetic population structure of the vulnerable bog fritillary butterfly.

    Science.gov (United States)

    Vandewoestijne, S; Baguette, M

    2004-01-01

    Populations of the bog fritillary butterfly Proclossiana eunomia (Lepidoptera, Nymphalidae) occur in patchy habitat in central and western Europe. P. eunomia is a vulnerable species in the Belgian Ardennes and the number of occupied sites has significantly decreased in this region since the 1960s. RAPD (random amplified polymorphic DNA) markers were used to study the consequences of habitat loss and fragmentation on the genetic population structure of this species. Gene diversity was lower in populations with smaller population sizes. Genetic subdivision was high (Fst=0.0887) considering the small spatial scale of this study (150 km2). The most geographically isolated population was also the most genetically differentiated one. The genetic population structure and genetic differentiation detected in this study were explained by (1) differences in altitude of the sampled locations and, (2) lower dispersal propensity and dispersal rate in fragmented landscapes versus continuous landscapes. Results from the RAPD analyses were compared with a previous allozyme based study on the same populations. The results of this study suggest that increased fragmentation has lead to a greater genetic differentiation between remaining P. eunomia populations.

  12. [Analysis on age structure and dynamics of Kindonia uniflora populations].

    Science.gov (United States)

    Zhang, Wenhui; Li, Jingxia; Li, Hong; Liu, Xiangjun

    2004-04-01

    Kindonia uniflora is a perennial clone herbaceous plant, and also, a native endangered plant in China. This paper studied its age structure, life table and survivorship curve in different habitats in Taibai mountain area. The results indicated that the age structure and dynamics of K. uniflora populations in the Betula utilis forest at altitude 2500-2700 m, in the Abies fargesii forest at altitude 2700-2900 m, and in the Larix chinensis forest at altitude 2900-3100 m had the similar pattern and developing tendency. The number of younger ramets at 1-2 years old or older than 5 years was less, and the number of ramets at 3-5 years old was the highest in the age structures. The negative values of dx (dead number), qx (mortality rate) and Kx (Killing rate) in the life table showed the increasing rate of the population sizes during the age stage. The survivorship curve of K. uniflora populations in different habitats belonged to Deevey C after 3-5 years old. The mortality rate of populations during 5-10 years stage was higher, and was stable after 10 years old. As for the characters of asexual propagation and clone growth, the rhizomes of the populations were in humus of soil, and developed and expanded as guerilla line style. During growth season, only one leaf grew above ground at every inter-node, and the population growth and development were rarely influenced by external factors. The forest communities, such as Betula utilis, Abies fargesii and Larix chinensis forest, in which K. uniflora populations lived, were at middle or higher mountain, where there were rarely disturbance from human being. Therefore, the habitats for K. uniflora populations to live were relatively stable. As the altitude increased, the disturbances from human being became less, the density of K. uniflora populations increased, the life cycle expanded, the peak of population death delayed, and the population living strategy changed to adapt to the habitats. K. uniflora populations preferred to

  13. Landscape, population structure and genetic diversity of Stomoxys calcitrans

    Directory of Open Access Journals (Sweden)

    Dsouli Aymes N.

    2009-03-01

    Full Text Available To investigate whether different landscapes could affect genetic diversity and structure of the cosmopolitan diptera Stomoxys calcitrans, populations from Gabon and southern France were studied using dominant amplified fragment length polymorphism (AFLP markers. Gabon is characterized by a forested closed landscape, and southern France by an open Mediterranean landscape. The genetic diversity between Gabon and France populations did not differ significantly (P > 0.05. Contrary to our expectation, this study shows a moderate level of genetic differentiation between these two distant countries (Fst = 0.0979 and a low genetic structure among Gabonese and French populations (Fst = 0.0291 and 0.0275 respectively. This result could indicate the capacities of S. calcitrans populations to sustain a high level of gene flow, despite geographic distance and isolation.

  14. Identification of genetic and epigenetic marks involved in population structure.

    Science.gov (United States)

    Liu, Jingyu; Hutchison, Kent; Perrone-Bizzozero, Nora; Morgan, Marilee; Sui, Jing; Calhoun, Vince

    2010-10-07

    Population structure is well known as a prevalent and important factor in genetic studies, but its relevance in epigenetics is unclear. Very little is known about the affected epigenetic markers and their connections with genetics. In this study we assessed the impact of population diversity on genome wide single nucleotide polymorphisms (SNPs) and DNA methylation levels in 196 participants from five ethnic groups, using principle and independent component analyses. Three population stratification factors (PSFs) were identified in the genomic SNP dataset, accounting for a relatively large portion of total variance (6%). In contrast, only one PSF was identified in genomic methylation dataset accounting for 0.2% of total variance. This methylation PSF, however, was significantly correlated with the largest SNP PSF (r = 0.72, ppopulation stratification, and suggest that the interrelationship between genetic and epigenetic population structure is mediated via complex multiple gene interactions in shared biological processes, through possibly, SNP-dependent modulation and ID2 repressor function.

  15. Ultrathin (Understanding the processing, structure, and physical and electrical limits

    Science.gov (United States)

    Green, M. L.; Gusev, E. P.; Degraeve, R.; Garfunkel, E. L.

    2001-09-01

    The outstanding properties of SiO2, which include high resistivity, excellent dielectric strength, a large band gap, a high melting point, and a native, low defect density interface with Si, are in large part responsible for enabling the microelectronics revolution. The Si/SiO2 interface, which forms the heart of the modern metal-oxide-semiconductor field effect transistor, the building block of the integrated circuit, is arguably the worlds most economically and technologically important materials interface. This article summarizes recent progress and current scientific understanding of ultrathin (understanding of the limits of these gate dielectrics, i.e., how their continuously shrinking thickness, dictated by integrated circuit device scaling, results in physical and electrical property changes that impose limits on their usefulness. We observe, in conclusion, that although Si microelectronic devices will be manufactured with SiO2 and Si-O-N for the foreseeable future, continued scaling of integrated circuit devices, essentially the continued adherence to Moore's law, will necessitate the introduction of an alternate gate dielectric once the SiO2 gate dielectric thickness approaches ˜1.2 nm. It is hoped that this article will prove useful to members of the silicon microelectronics community, newcomers to the gate dielectrics field, practitioners in allied fields, and graduate students. Parts of this article have been adapted from earlier articles by the authors [L. Feldman, E. P. Gusev, and E. Garfunkel, in Fundamental Aspects of Ultrathin Dielectrics on Si-based Devices, edited by E. Garfunkel, E. P. Gusev, and A. Y. Vul' (Kluwer, Dordrecht, 1998), p. 1 [Ref. 1]; E. P. Gusev, H. C. Lu, E. Garfunkel, T. Gustafsson, and M. Green, IBM J. Res. Dev. 43, 265 (1999) [Ref. 2]; R. Degraeve, B. Kaczer, and G. Groeseneken, Microelectron. Reliab. 39, 1445 (1999) [Ref. 3].

  16. From structure of the complex to understanding of the biology

    Energy Technology Data Exchange (ETDEWEB)

    Rossmann, Michael G., E-mail: mr@purdue.edu [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)

    2007-01-01

    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

  17. Population genetic structure in natural and reintroduced beaver (Castor fiber populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Kautenburger, R.

    2008-12-01

    Full Text Available Castor fiber Linnaeus, 1758 is the only indigenous species of the genus Castor in Europe and Asia. Due to extensive hunting until the beginning of the 20th century, the distribution of the formerly widespread Eurasian beaver was dramatically reduced. Only a few populations remained and these were in isolated locations, such as the region of the German Elbe River. The loss of genetic diversity in small or captive populations throughgenetic drift and inbreeding is a severe conservation problem. However, the reintroduction of beaver populations from several regions in Europe has shown high viability and populations today are growing fast. In the present study we analysed the population genetic structure of a natural and two reintroduced beaver populations in Germany and Austria. Furthermore, we studied the genetic differentiation between two beaver species, C. fiber and the American beaver (C. canadensis, using RAPD (Random Amplified Polymorphic DNA as a genetic marker. The reintroduced beaver populations of different origins and the autochthonous population of the Elbe River showed a similar low genetic heterogeneity. There was an overall high genetic similarity in the species C. fiber, and no evidence was found for a clear subspecific structure in the populations studied.

  18. Understanding the structure of nuclei at finite temperatures

    International Nuclear Information System (INIS)

    Baktash, C.

    1988-01-01

    The purpose of this commentary is to briefly review several works on nuclear structure and to enumerate a few of the difficulties encountered in the interpretation of the experimental results. To be brief, comments are confined to the studies in the particle-bound regime, i.e., a temperature range of T ≤ 1 MeV. Among the interesting topics to be addressed in this temperature range are the question of thermal fluctuations, and the variations of the pairing correlations, shape parameters, nuclear collectivity, and rotational damping width with spin and excitation energy

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

    Science.gov (United States)

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

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

  20. Population, Environment, and Climate in the Albertine Rift: Understanding Local Impacts of Regional Change

    Science.gov (United States)

    Hartter, J.; Ryan, S. J.; Diem, J.; Palace, M. W.

    2012-12-01

    Climate change is of critical concern for conservation and to develop appropriate policies and responses, it is important not only to anticipate the nature of changes, but also how they are perceived, interpreted and adapted to by local people. The Albertine Rift in East Africa is one of the most threatened biodiversity hotspots due to dense settlement, extreme poverty, and land conversion. We synthesize ongoing NSF-CNH research, where Ugandan park landscapes are examined to understand the impacts of climate change on livelihoods. Kibale National Park, the main study site, exemplifies the challenges facing many parks because of its isolation within a densely populated agricultural landscape. Three separate household surveys (n=251, 130, 100) reveal that the most perceived benefits provided by Kibale were ecosystem services and farmers cite rainfall as one of the park's most important benefits, but are also concerned with variable precipitation. Analysis of 30+ years of daily rainfall station data shows total rainfall has not changed significantly, but timing and transitions of seasons and intra-seasonal distribution are highly variable, which may contribute to changes in farming schedules and threaten food security. Further, the contrast between land use/cover change over 25 years around the park and the stability of forest within the park underscores the need to understand this landscape for future sustainability planning and the inevitable population growth outside its boundaries. Understanding climate change impacts and feedbacks to and from socio-ecological systems are important to address the dual challenge of biodiversity conservation and poverty alleviation.

  1. Modeling structured population dynamics using data from unmarked individuals

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2008-06-01

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

  3. Population structure of larch forests in the Urals

    Energy Technology Data Exchange (ETDEWEB)

    Putenikhin, V.P.; Farukshina, G.G. [Russian Academy of Sciences, Ufa (Russian Federation). Botanical Garden Inst.

    1995-12-31

    The variability and population structure of larch (Larix sukaczewii Dyl.) naturally growing in the Urals was studied on the basis of biometric analysis of generative organs. The obtained results point to the existence of 11 phenotypically different local populations of Larix sukaczewii in the Urals. Four populations are identified in the South Urals: Marginal, central, high-mountainous, south-uralian and Bashkircis-uralian. Middle-uralian, Perm cis-uralian, central north-uralian and high-mountainous north-uralian populations are determined in the Middle and the North Urals. Three populations of Larix sukaczewii are identified in the Sub-Polar and the Polar Urals: Subpolar-uralian, Pechora-Thiman cisuralian and polar-uralian. 8 refs, 2 tabs

  4. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the m......The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... importance to disease management issues highlighted....

  5. Understanding the Mixing Phenomena - from Structural Stability to Chaos

    Directory of Open Access Journals (Sweden)

    Adela Ionescu

    2011-01-01

    Full Text Available Nowadays, computational fluid dynamics (CFD becomes
    more and more mature. In the same time, it becomes more and more difficult to contribute fundamental research to it. Although the software tools in this area are increasing in importance, the way how CFD develops remain unpredictable, and it is part of what makes it an exciting and attractive discipline. The mixing phenomena - and the mixing theory - are using more and more CFD tools. This modern theory issued in the flow kinematics after hundred of years of stability study, has mathematical methods and techniques which are developing a continuous signi¯cant relation between turbulence and chaos. The turbulence is an important feature of dynamic systems with few freedom degrees, the so-called far from equilibrium systems. These are widespread between the models of excitable media. The present paper exhibits some recent results of the turbulent mixing study, based on computational tools of MAPLE11 soft. The data would be statistically analyzed, in order to construct a significant guideline in understanding the transition from stability to
    chaos in these excitable media.

  6. Chronic irradiation as an ecological factor affecting genetic population structure

    International Nuclear Information System (INIS)

    Kal'chenko, V.A.; Kalabushkin, B.A.; Rubanovich, A.V.

    1991-01-01

    Genetic structure of two Centaurea scabiosa L. populations was studied by frequency distribution of leucine aminopeptidase (LAP) locus genotypes. The experimental population has been growing under conditions of chronic irradiation, with the dose per generation amounting to 1.2 to 25.5 Gy. In it, mutational variants are observed with a frequency of 5.4.10(-3)-4.5.10(-2) per generation (as compared to control population frequency at 5.4.10(-4)). Indexes for heterozygosity, mean number of genotypes, and effective number of alleles were higher in the experimental population. Segregation analysis revealed no differences in viability in the control population, and all genotypic combinations were found to be nearly neutral. In the experimental population, however, significant differences in relative viability of the genotypes were disclosed. The relative viability of heterozygotes for mutant allele C' was nearly maximum, while heterozygotes for other mutant alleles showed minimum viability. We reach the conclusion that the differences in genetic structure of the populations under investigation can be explained by the chronic irradiation factor that brought out differences in adaptability of both normal and mutant genotypes. The suggestion is that intra-locus interactions of the C' allele with normal alleles determine plant resistance to a wide range of unfavorable environmental conditions

  7. Urban decline within the region: Understanding the intra-regional differentiation in urban population development in the declining regions Saarland and Southern-Limburg

    NARCIS (Netherlands)

    Hoekveld, J.J.

    2014-01-01

    Urban decline, urban shrinkage and population decline are a few terms which describe the transformation processes currently going on in many cities and regions throughout the world. We are beginning to understand the driving forces of these urban transformation processes - such as structural

  8. Genomic epidemiology and population structure of Neisseria gonorrhoeae from remote highly endemic Western Australian populations.

    Science.gov (United States)

    Al Suwayyid, Barakat A; Coombs, Geoffrey W; Speers, David J; Pearson, Julie; Wise, Michael J; Kahler, Charlene M

    2018-02-27

    Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Western Australia (WA). Unlike isolates from the major Australian population centres, the remote community isolates have low rates of antimicrobial resistance (AMR). Population structure and whole-genome comparison of 59 isolates from the Western Australian N. gonorrhoeae collection were used to investigate relatedness of isolates cultured in the metropolitan and remote areas. Core genome phylogeny, multilocus sequencing typing (MLST), N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) in addition to hierarchical clustering of sequences were used to characterize the isolates. Population structure analysis of the 59 isolates together with 72 isolates from an international collection, revealed six population groups suggesting that N. gonorrhoeae is a weakly clonal species. Two distinct population groups, Aus1 and Aus2, represented 63% of WA isolates and were mostly composed of the remote community isolates that carried no chromosomal AMR genotypes. In contrast, the Western Australian metropolitan isolates were frequently multi-drug resistant and belonged to population groups found in the international database, suggesting international transmission of the isolates. Our study suggests that the population structure of N. gonorrhoeae is distinct between the communities in remote and metropolitan WA. Given the high rate of AMR in metropolitan regions, ongoing surveillance is essential to ensure the enduring efficacy of the empiric gonorrhoea treatment in remote WA.

  9. Detailed genetic structure of European bitterling populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Veronika Bartáková

    2015-11-01

    Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

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

    Directory of Open Access Journals (Sweden)

    Zewdu Edea

    2017-12-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  12. [Some understandings about the population development of the minorities in China].

    Science.gov (United States)

    Zhou, Q; Xiong, Y

    1982-05-29

    China is a Socialist country which is composed of numerous ethnic groups. In addition to the Han people, there are 55 minorities in various parts of China. Since liberation (1949), the lives of the minorities have improved greatly. There has also been reasonable advancement in their local economic situation, cultural and educational establishments, and health care, and the population growth among ethnic minorities has also increased rapidly. At the present time, the rate of population growth among the minorities is extremely high, and the age structure of the minority population is young. The custom of early marriage and having children at a young age is still popular. The levels of economic development, cultural and educational establishments and medical and health care are still too low to satisfy current needs of the local people. Within a short period of time, population growth among the minorities may reach among climax, and the problem of overpopulation may become more serious. This new trend is not encouraging for the economic and cultural development of the minority people. In order to protect the economic situation of the minority population, various rules and regulations should be established according to local situations, and work in family planning and birth control is also urgently needed for the minorities.

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

    Science.gov (United States)

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

    2011-04-05

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

  14. The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland

    Science.gov (United States)

    Price, Alkes L.; Helgason, Agnar; Palsson, Snaebjorn; Stefansson, Hreinn; St. Clair, David; Andreassen, Ole A.; Reich, David; Kong, Augustine; Stefansson, Kari

    2009-01-01

    The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation. PMID:19503599

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

    Science.gov (United States)

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

    2011-01-01

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

  16. Diversity and population structure of red rice germplasm in Bangladesh.

    Science.gov (United States)

    Islam, M Z; Khalequzzaman, M; Prince, M F R K; Siddique, M A; Rashid, E S M H; Ahmed, M S U; Pittendrigh, B R; Ali, M P

    2018-01-01

    While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs.

  17. Population genetic structure of Meccus longipennis (Hemiptera, Reduviidae, Triatominae), vector of Chagas disease in West Mexico.

    Science.gov (United States)

    Brenière, Simone Frédérique; Waleckx, Etienne; Magallón-Gastélum, Ezequiel; Bosseno, Marie-France; Hardy, Xavier; Ndo, Cyrille; Lozano-Kasten, Felipe; Barnabé, Christian; Kengne, Pierre

    2012-03-01

    The originally wild species of the Meccus complex are important vectors of Chagas disease in Mexico. In West Mexico, Meccus longipennis plays an important epidemiological role. To understand the genetic structure of the domestic and wild populations of this species, a preliminary study with five polymorphic microsatellite loci was conducted. The population genetics analysis showed high structuring between peridomestic biotopes, with breeding subunits detected in a single peridomestic structure. In the wild environment, two genetic patterns were observed according to the biotope, possible breeding subunits in large rocky formations and a larger panmictic unit in agropastoral areas, suggesting considerable dispersal of bugs in this biotope. Moreover, the discovery of two foci of wild populations at the edge of Guadalajara city raises the question of new urban areas where the phenomenon of bug incursions into households could constitute a risk of transmission of Chagas disease. Copyright © 2011 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2014-10-01

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

  19. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A.

  20. Fecundity and Population Structure of Cockles, Anadara antiquata L ...

    African Journals Online (AJOL)

    The fecundity and population structure of the cockle, Anadara antiquataL., from sandy/muddy intertidal habitats in the intertidal of Ocean Road beach was examined from January to December 2001. A. antiquata is hand harvested, for domestic consumption, mainly by women and children, with the empty shells sold to ...

  1. Genetic variation and population structure of willowy flounder ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-11-05

    Nov 5, 2008 ... The first hypervariable region (HVR-1) of the mitochondrial DNA control region was utilized for determination of genetic variation and population structure in willowy flounder (Tanakius kitaharai) collected from Aomori, Ibaraki and Niigata. A total of 35 haplotypes were detected among 66 individuals.

  2. Dynamique de structuration spatio-temporelle des populations de ...

    African Journals Online (AJOL)

    Dynamique de structuration spatio-temporelle des populations de familles de macroinvertébrés dans un continuum lac de barrage-effluent-fleuve issu de périmètre irrigué. Bassin de la Volta (Burkina Faso)

  3. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

  4. Population structure and association mapping studies for important ...

    Indian Academy of Sciences (India)

    2014-12-18

    Dec 18, 2014 ... The Q matrix was constructed following the model-based approach as described by Pritchard et al. (2000) and Falush et al. (2003) which is implemented in the software Structure (Pritchard et al. 2000; http://pritch.bsd.uchicago.edu). For analysis of the data, set parameters of the population admixture model.

  5. Genetic diversity and population structure of 10 Chinese indigenous ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 89; Issue 1. Genetic diversity and population structure of 10 Chinese indigenous egg-type duck breeds assessed by microsatellite polymorphism. Li Hui-Fang Song Wei-Tao Shu Jing-Ting Chen Kuan-Wei Zhu Wen-Qi Han Wei Xu Wen-Juan. Research Article Volume 89 Issue 1 ...

  6. Molecular epidemiology and population structure of bovine Streptococcus uberis

    DEFF Research Database (Denmark)

    Rato, M G; Bexiga, R; Nunes, S F

    2008-01-01

    The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

  7. Genetic variation and population structure of interleukin genes ...

    Indian Academy of Sciences (India)

    these factors may have important clinical consequences and thus, impact on community genetics (Bittles 2001, 2002). A number of complex genetic disorders such as, coronary heart disease, cancer, psychiatric disorders and asthma, have been. Keywords. population structure; interleukin genes; ethnic variation; Karnataka.

  8. Population Genetic Structure and Connectivity of the Abundant Sea ...

    African Journals Online (AJOL)

    The aim of this study was to examine the fine-scale genetic structure and connectivity in the sea urchin, Diadema setosum, population around Unguja, Zanzibar, using AFLP. We found evidence of different genetic clusters, high migration between the sites and high genetic diversity within the sites. These findings indicate ...

  9. Population genetic structure of coral reef species Plectorhinchus ...

    African Journals Online (AJOL)

    The population genetic structure and the dispersal ability of Plectorhinchus flavomaculatus from South China Sea were examined with a 464 bp segment of mtDNA control region. A total of 116 individuals were collected from 12 coral reefs in Xisha, Zhongsha and Nansha archipelagos and 22 haplotypes were obtained.

  10. Population genetic structure and demographic history of small ...

    African Journals Online (AJOL)

    Small yellow croaker, Larimichthys polyactis (Bleeker, 1877), a commercially important benthopelagic fish, is widely distributed in the Bohai, Yellow and East China Seas. To evaluate the population genetic structure and demographic history of L. polyactis, we sequenced the complete mitochondrial deoxyribonucleic acid ...

  11. Aspects of population structure of Parechinus angulosus Leske ...

    African Journals Online (AJOL)

    Aspects of population structure of Parechinus angulosus Leske, around the Cape Peninsula. A.H. Fricke ... cularly in view of the severe impact on kelp beds in Cali- fornia and on the east coast of Canada by ..... (Fig. 5). Food resources for the early stages of Parechinus are most plentiful in an upwelling area such as ...

  12. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    fire7-

    2016-12-28

    Dec 28, 2016 ... Population structure for 120 common bean accessions from different growing regions of Ethiopia and. 3 Kenyan cultivars compared to Andean and Mesoamerican control genotypes at K = 2 to K = 5. Predetermined group names indicated below figure are: Amhara = Genotypes from Amhara Regional State; ...

  13. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    user

    2011-02-28

    Feb 28, 2011 ... Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. Ting Ji, Ling Yin and Guohong Chen*. College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China. Accepted 18 January, 2011. Using 21 microsatellite markers ...

  14. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination...

  15. Transmission intensity and malaria vector population structure in ...

    African Journals Online (AJOL)

    Abstract. A 1-year longitudinal study was conducted in Magugu in Babati district, northern Tanzania to determine malaria vector population structure and malaria transmission indices. Mosquitoes were sampled using the Centre for Disease Control (CDC) light traps. A total of 110,357 adult female mosquitoes were collected.

  16. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  17. Genetic population structure of the Japanese mitten crab Eriocheir ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... divergence between these two groups (Okinawa and main islands of Japan) is equivalent to the genetic distance between congeneric species. Our results failed to demonstrate significant geographical structure in main islands of Japan, indicating that populations of Japanese mitten crab are capable of.

  18. Population structure and genetic trends for indigenous African beef ...

    African Journals Online (AJOL)

    The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger, Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher than 88.5% in the first ...

  19. Population structure and recruitment of penaeid shrimps in ...

    African Journals Online (AJOL)

    This study characterizes the population structure and identifies nursery areas and recruitment seasons of penaeid shrimps in the Pungué river estuary of Mozambique. Shrimp samples were obtained from 12 trawl stations at monthly intervals during 2004. Six species were found, two of which (Fenneropenaeus indicus and ...

  20. Fine population structure analysis method for genomes of many.

    Science.gov (United States)

    Pan, Xuedong; Wang, Yi; Wong, Emily H M; Telenti, Amalio; Venter, J Craig; Jin, Li

    2017-10-03

    Fine population structure can be examined through the clustering of individuals into subpopulations. The clustering of individuals in large sequence datasets into subpopulations makes the calculation of subpopulation specific allele frequency possible, which may shed light on selection of candidate variants for rare diseases. However, as the magnitude of the data increases, computational burden becomes a challenge in fine population structure analysis. To address this issue, we propose fine population structure analysis (FIPSA), which is an individual-based non-parametric method for dissecting fine population structure. FIPSA maximizes the likelihood ratio of the contingency table of the allele counts multiplied by the group. We demonstrated that its speed and accuracy were superior to existing non-parametric methods when the simulated sample size was up to 5,000 individuals. When applied to real data, the method showed high resolution on the Human Genome Diversity Project (HGDP) East Asian dataset. FIPSA was independently validated on 11,257 human genomes. The group assignment given by FIPSA was 99.1% similar to those assigned based on supervised learning. Thus, FIPSA provides high resolution and is compatible with a real dataset of more than ten thousand individuals.

  1. Intertidal population structure of the edible mollusc Turbo sarmaticus ...

    African Journals Online (AJOL)

    The intertidal population structure of the large edible gastropod Turbo sarmaticus was examined at four sites along the Eastern Cape Province of South Africa. One site was free from exploitation, two were subjected to low levels of exploitation and one was heavily exploited. Within the intertidal zone at all sites there was a ...

  2. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering impor- tant repositories of biological diversity, the genetic ...

  3. Comparison of the population structure and life-history parameters ...

    African Journals Online (AJOL)

    Blacktail seabream Diplodus capensis were sampled from proximate (10 km apart) exploited and unexploited areas in southern Angola to compare their population structures and life-history parameters. Females dominated the larger size and older age classes in the unexploited area. In the exploited area the length and ...

  4. Short communication Population structure and genetic trends for ...

    African Journals Online (AJOL)

    user

    2016-05-23

    May 23, 2016 ... Abstract. The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger,. Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher ...

  5. Global population structure and demographic history of the grey seal

    DEFF Research Database (Denmark)

    Klimova, A.; Phillips, C. D.; Fietz, Katharina

    2014-01-01

    Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habit...

  6. Genetic variation and population structure of willowy flounder ...

    African Journals Online (AJOL)

    The first hypervariable region (HVR-1) of the mitochondrial DNA control region was utilized for determination of genetic variation and population structure in willowy flounder (Tanakius kitaharai) collected from Aomori, Ibaraki and Niigata. A total of 35 haplotypes were detected among 66 individuals with a total of 30 variable ...

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

    Science.gov (United States)

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

    2012-01-01

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

  8. An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

    Science.gov (United States)

    Uyulgan, Melis Arzu; Akkuzu, Nalan

    2016-01-01

    The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

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

    Science.gov (United States)

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

    2014-06-01

    Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH-Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford.edu/structure.html. Copyright © 2014 by the Genetics Society of America.

  10. Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics.

    Science.gov (United States)

    Kim, Jae In; Na, Sungsoo; Eom, Kilho

    2011-01-15

    Normal mode analysis (NMA) with coarse-grained model, such as elastic network model (ENM), has allowed the quantitative understanding of protein dynamics. As the protein size is increased, there emerges the expensive computational process to find the dynamically important low-frequency normal modes due to diagonalization of massive Hessian matrix. In this study, we have provided the domain decomposition-based structural condensation method that enables the efficient computations on low-frequency motions. Specifically, our coarse-graining method is established by coupling between model condensation (MC; Eom et al., J Comput Chem 2007, 28, 1400) and component mode synthesis (Kim et al., J Chem Theor Comput 2009, 5, 1931). A protein structure is first decomposed into substructural units, and then each substructural unit is coarse-grained by MC. Once the NMA is implemented to coarse-grained substructural units, normal modes and natural frequencies for each coarse-grained substructural unit are assembled by using geometric constraints to provide the normal modes and natural frequencies for whole protein structure. It is shown that our coarse-graining method enhances the computational efficiency for analysis of large protein complexes. It is clearly suggested that our coarse-graining method provides the B-factors of 100 large proteins, quantitatively comparable with those obtained from original NMA, with computational efficiency. Moreover, the collective behaviors and/or the correlated motions for model proteins are well delineated by our suggested coarse-grained models, quantitatively comparable with those computed from original NMA. It is implied that our coarse-grained method enables the computationally efficient studies on conformational dynamics of large protein complex.

  11. Evolutionary dynamics for persistent cooperation in structured populations

    Science.gov (United States)

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

    2015-06-01

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

  12. Population genetic structure in a social landscape: barley in a traditional Ethiopian agricultural system.

    Science.gov (United States)

    Samberg, Leah H; Fishman, Lila; Allendorf, Fred W

    2013-12-01

    Conservation strategies are increasingly driven by our understanding of the processes and patterns of gene flow across complex landscapes. The expansion of population genetic approaches into traditional agricultural systems requires understanding how social factors contribute to that landscape, and thus to gene flow. This study incorporates extensive farmer interviews and population genetic analysis of barley landraces (Hordeum vulgare) to build a holistic picture of farmer-mediated geneflow in an ancient, traditional agricultural system in the highlands of Ethiopia. We analyze barley samples at 14 microsatellite loci across sites at varying elevations and locations across a contiguous mountain range, and across farmer-identified barley types and management strategies. Genetic structure is analyzed using population-based and individual-based methods, including measures of population differentiation and genetic distance, multivariate Principal Coordinate Analysis, and Bayesian assignment tests. Phenotypic analysis links genetic patterns to traits identified by farmers. We find that differential farmer management strategies lead to markedly different patterns of population structure across elevation classes and barley types. The extent to which farmer seed management appears as a stronger determinant of spatial structure than the physical landscape highlights the need for incorporation of social, landscape, and genetic data for the design of conservation strategies in human-influenced landscapes.

  13. Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China.

    Science.gov (United States)

    Yi, Shaokui; Li, Yanhe; Shi, Linlin; Zhang, Long; Li, Qingbin; Chen, Jing

    2018-04-03

    The red swamp crayfish (Procambarus clarkii) is one of the most economically important farmed aquatic species in China. However, it is also a famous invasive species in the world. This invasive species was dispersed most via human activities including intentional or unintentional carry in China. Thus, P. clarkii naturally distributed in China provides us a desirable mode to investigate the genetic structure of an invasive species dispersed mainly by human-mediated factors. To reveal the impact of human-mediated dispersal on genetic structure of P. clarkii in China, a total of 22,043 genome-wide SNPs were obtained from approximately 7.4 billion raw reads using 2b-RAD technique in this study. An evident pattern of population genetic structure and the asymmetrical migrational rates between different regions were observed with 22 populations based on these SNPs. This study provide a better understanding of the population genetic structure and demographic history of P. clarkii populations in China, inferring that anthropogenic factors (aquaculture or by accident) and ecological factors (e.g., complicated topography and climatic environment), as well as its special biological traits could account for the current population structure pattern and dispersal history of P. clarkii.

  14. Evolutionary game dynamics in populations with heterogenous structures.

    Directory of Open Access Journals (Sweden)

    Wes Maciejewski

    2014-04-01

    Full Text Available Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations. An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative behaviours. In this article we show that such a conclusion largely depends on the individual-level interactions that take place. In particular, averaging payoffs garnered through game interactions rather than accumulating the payoffs can altogether remove the cooperative advantage of heterogeneous graphs while such a difference does not affect the outcome on homogeneous structures. In addition, the rate at which game interactions occur can alter the evolutionary outcome. Less interactions allow heterogeneous graphs to support more cooperation than homogeneous graphs, while higher rates of interactions make homogeneous and heterogeneous graphs virtually indistinguishable in their ability to support cooperation. Most importantly, we show that common measures of evolutionary advantage used in homogeneous populations, such as a comparison of the fixation probability of a rare mutant to that of the resident type, are no longer valid in heterogeneous populations. Heterogeneity causes a bias in where mutations occur in the population which affects the mutant's fixation probability. We derive the appropriate measures for heterogeneous populations that account for this bias.

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2015-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Khulekhani Sedwell Khanyile

    2015-02-01

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

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

    Science.gov (United States)

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

    2013-03-05

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

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

    Science.gov (United States)

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

    2013-07-01

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

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

    Science.gov (United States)

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

    2006-01-01

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

  1. Population structure of barley landrace populations and gene-flow with modern varieties.

    Directory of Open Access Journals (Sweden)

    Elisa Bellucci

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

  2. Understanding anti-tuberculosis drug efficacy: rethinking bacterial populations and how we model them

    Directory of Open Access Journals (Sweden)

    Dimitrios Evangelopoulos

    2015-03-01

    Full Text Available Tuberculosis still remains a global health emergency, claiming 1.5 million lives in 2013. The bacterium responsible for this disease, Mycobacterium tuberculosis (M.tb, has successfully survived within hostile host environments, adapting to immune defence mechanisms, for centuries. This has resulted in a disease that is challenging to treat, requiring lengthy chemotherapy with multi-drug regimens. One explanation for this difficulty in eliminating M.tb bacilli in vivo is the disparate action of antimicrobials on heterogeneous populations of M.tb, where mycobacterial physiological state may influence drug efficacy. In order to develop improved drug combinations that effectively target diverse mycobacterial phenotypes, it is important to understand how such subpopulations of M.tb are formed during human infection. We review here the in vitro and in vivo systems used to model M.tb subpopulations that may persist during drug therapy, and offer aspirations for future research in this field.

  3. Population structure in the Mediterranean basin: a Y chromosome perspective.

    Science.gov (United States)

    Capelli, C; Redhead, N; Romano, V; Calì, F; Lefranc, G; Delague, V; Megarbane, A; Felice, A E; Pascali, V L; Neophytou, P I; Poulli, Z; Novelletto, A; Malaspina, P; Terrenato, L; Berebbi, A; Fellous, M; Thomas, M G; Goldstein, D B

    2006-03-01

    The Mediterranean region has been characterised by a number of pre-historical and historical demographic events whose legacy on the current genetic landscape is still a matter of debate. In order to investigate the degree of population structure across the Mediterranean, we have investigated Y chromosome variation in a large dataset of Mediterranean populations, 11 of which are first described here. Our analyses identify four main clusters in the Mediterranean that can be labelled as North Africa, Arab, Central-East and West Mediterranean. In particular, Near Eastern samples tend to separate according to the presence of Arab Y chromosome lineages, suggesting that the Arab expansion played a major role in shaping the current genetic structuring within the Fertile Crescent.

  4. Dynamics of N-person snowdrift games in structured populations.

    Science.gov (United States)

    Santos, Marta D; Pinheiro, Flávio L; Santos, Francisco C; Pacheco, Jorge M

    2012-12-21

    In many real-life situations, the completion of a task by a group toward achieving a common goal requires the cooperation of at least some of its members, who share the required workload. Such cases are conveniently modeled by the N-person snowdrift game, an example of a Public Goods Game. Here we study how an underlying network of contacts affects the evolutionary dynamics of collective action modeled in terms of such a Public Goods Game. We analyze the impact of different types of networks in the global, population-wide dynamics of cooperators and defectors. We show that homogeneous social structures enhance the chances of coordinating toward stable levels of cooperation, while heterogeneous network structures create multiple internal equilibria, departing significantly from the reference scenario of a well-mixed, structureless population. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Population estimates of extended family structure and size.

    Science.gov (United States)

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

    2008-01-01

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

  6. Structured populations of the oriental fruit moth in an agricultural ecosystem.

    Science.gov (United States)

    Torriani, Marco V G; Mazzi, Dominique; Hein, Silke; Dorn, Silvia

    2010-07-01

    Intercontinental trade has led to multiple introductions of invasive pest species at a global scale. Molecular analyses of the structure of populations support the understanding of ecological strategies and evolutionary patterns that promote successful biological invasions. The oriental fruit moth, Grapholita (= Cydia) molesta, is a cosmopolitan and economically destructive pest of stone and pome fruits, expanding its distribution range concomitantly with global climate warming. We used ten newly developed polymorphic microsatellite markers to examine the genetic structure of G. molesta populations in an agricultural ecosystem in the Emilia-Romagna region of northern Italy. Larvae collected in eight sampling sites were assigned to a mosaic of five populations with significant intra-regional structure. Inferred measures of gene flow within populations implicated both active dispersal, and passive dispersal associated with accidental anthropogenic displacements. Small effective population sizes, coupled with high inbreeding levels, highlighted the effect of orchard management practices on the observed patterns of genetic variation within the sampling sites. Isolation by distance did not appear to play a major role at the spatial scale considered. Our results provide new insights into the population genetics and dynamics of an invasive pest species at a regional scale.

  7. Estimation of genetic structure of a Mycosphaerella musicola population using inter-simple sequence repeat markers.

    Science.gov (United States)

    Peixouto, Y S; Dórea Bragança, C A; Andrade, W B; Ferreira, C F; Haddad, F; Oliveira, S A S; Darosci Brito, F S; Miller, R N G; Amorim, E P

    2015-07-17

    Among the diseases affecting banana (Musa sp), yellow Sigatoka, caused by the fungal pathogen Mycosphaerella musicola Leach, is considered one of the most important in Brazil, causing losses throughout the year. Understanding the genetic structure of pathogen populations will provide insight into the life history of pathogens, including the evolutionary processes occurring in agrosystems. Tools for estimating the possible emergence of pathogen variants with altered pathogenicity, virulence, or aggressiveness, as well as resistance to systemic fungicides, can also be developed from such data. The objective of this study was to analyze the genetic diversity and population genetics of M. musicola in the main banana-producing regions in Brazil. A total of 83 isolates collected from different banana cultivars in the Brazilian states of Bahia, Rio Grande do Norte, and Minas Gerais were evaluated using inter-simple sequence repeat markers. High variability was detected between the isolates, and 85.5% of the haplotypes were singletons in the populations. The highest source of genetic diversity (97.22%) was attributed to variations within populations. Bayesian cluster analysis revealed the presence of 2 probable ancestral groups, however, showed no relationship to population structure in terms of collection site, state of origin, or cultivar. Similarly, we detected noevidence of genetic recombination between individuals within different states, indicating that asexual cycles play a major role in M. musicola reproduction and that long-distance dispersal of the pathogen is the main factor contributing to the lack of population structure in the fungus.

  8. Population genetic structure and demographic history of the black fly vector, Simulium nodosum in Thailand.

    Science.gov (United States)

    Chaiyasan, P; Pramual, P

    2016-09-01

    An understanding of the genetic structure and diversity of vector species is crucial for effective control and management. In this study, mitochondrial DNA sequences were used to examine the genetic structure, diversity and demographic history of a black fly vector, Simulium nodosum Puri (Diptera: Simuliidae), in Thailand. A total of 145 sequences were obtained from 10 sampling locations collected across geographical ranges in the country. Low genetic diversity was found in populations of S. nodosum that could be explained by the recent population history of this species. Demographic history analysis revealed a signature of demographic expansion dating back to only 2600-5200 years ago. Recent population expansion in S. nodosum possibly followed an increase in agriculture that enabled its hosts', humans and domestic animals, densities to increase. Alternatively, the Thai populations could be a derivative of an older expansion event in the more northern populations. Mitochondrial DNA genealogy revealed no genetically divergent lineages, which agrees with the previous cytogenetic study. Genetic structure analyses found that only 27% of the pairwise comparisons were significantly different. The most likely explanation for the pattern of genetic structuring is the effect of genetic drift because of recent colonization. © 2016 The Royal Entomological Society.

  9. Development of paradigms for the dynamics of structured populations

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  11. Graphical and demographic synopsis of the captive cohort method for estimating population age structure in the wild.

    Science.gov (United States)

    Carey, James R; Müller, Hans-Georg; Wang, Jane-Ling; Papadopoulos, Nikos T; Diamantidis, Alexandros; Koulousis, Nikos A

    2012-10-01

    The purpose of this paper is to complement the literature concerned with the captive cohort method for estimating age structure including (1) graphic techniques to visualize and thus better understand the underlying life table identity in which the age structure of a stationary population equals the time-to-death distribution of the individuals within it; (2) re-derive the basic model for estimating age structure in non-stationary population in demographic rather than statistical notation; and (3) describe a simplified method for estimating changes in the mean age of a wild population. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Insular Celtic population structure and genomic footprints of migration.

    Science.gov (United States)

    Byrne, Ross P; Martiniano, Rui; Cassidy, Lara M; Carrigan, Matthew; Hellenthal, Garrett; Hardiman, Orla; Bradley, Daniel G; McLaughlin, Russell L

    2018-01-01

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

  13. Insular Celtic population structure and genomic footprints of migration.

    Directory of Open Access Journals (Sweden)

    Ross P Byrne

    2018-01-01

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

  14. Understanding support for complementary and alternative medicine in general populations: use and perceived efficacy.

    Science.gov (United States)

    Stoneman, Paul; Sturgis, Patrick; Allum, Nick

    2013-09-01

    Proponents of complementary and alternative medicine argue that these treatments can be used with great effect in addition to, and sometimes instead of, conventional medicine, a position which has drawn sustained opposition from those who advocate an evidence-based approach to the evaluation of treatment efficacy. Using recent survey data from the United Kingdom, this article seeks to establish a clearer understanding of the nature of the public's relationship with complementary and alternative medicine within the general population by focusing on beliefs about the perceived effectiveness of homeopathy, in addition to its reported use. Using recent data from the United Kingdom, we initially demonstrate that reported use and perceived effectiveness are far from coterminous and argue that for a proper understanding of the motivations underpinning public support of complementary and alternative medicine, consideration of both reported use and perceived effectiveness is necessary. We go on to demonstrate that although the profile of homeopathy users differs from those who support this form of medicine, neither outcome is dependent upon peoples' levels of knowledge about science. Instead, the results suggest a far greater explanatory role for need and concerns about conventional medicine.

  15. Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

  16. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  17. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Directory of Open Access Journals (Sweden)

    Mauricio Lima

    Full Text Available Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors. Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

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

    Science.gov (United States)

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

    2017-06-01

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

  19. The doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridization

    KAUST Repository

    Eriksson, Anders

    2014-03-13

    Distinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure. 2014 The Author.

  20. Inter-chromosomal variation in the pattern of human population genetic structure

    Directory of Open Access Journals (Sweden)

    Baye Tesfaye M

    2011-05-01

    Full Text Available Abstract Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC, cluster, discriminant, fixation index (FST and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homogeneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (OCA2, hect domain and RLD 2 (HERC2, ectodysplasin A receptor (EDAR and solute carrier family 45, member 2 (SLC45A2. These genes are associated with melanin production, which is involved in the development of skin and hair colour, skin cancer and eye pigmentation. We also identified the genes encoding interferon-γ (IFNG and death-associated protein kinase 1 (DAPK1, which are associated with cell death, inflammatory and immunological diseases. An in-depth understanding of these genomic regions may help to explain variations in adaptation to different environments. Our approach offers a comprehensive strategy for analysing chromosome-based population structure and differentiation, and demonstrates the

  1. Population size-structure-dependent fitness and ecosystem consequences in Trinidadian guppies.

    Science.gov (United States)

    Bassar, Ronald D; Heatherly, Thomas; Marshall, Michael C; Thomas, Steven A; Flecker, Alexander S; Reznick, David N

    2015-07-01

    Decades of theory and recent empirical results have shown that evolutionary, population, community and ecosystem properties are the result of feedbacks between ecological and evolutionary processes. The vast majority of theory and empirical research on these eco-evolutionary feedbacks has focused on interactions among population size and mean traits of populations. However, numbers and mean traits represent only a fraction of the possible feedback dimensions. Populations of many organisms consist of different size classes that differ in their impact on the environment and each other. Moreover, rarely do we know the map of ecological pathways through which changes in numbers or size structure cause evolutionary change. The goal of this study was to test the role of size structure in eco-evolutionary feedbacks of Trinidadian guppies and to begin to build an eco-evolutionary map along this unexplored dimension. We used a factorial experiment in mesocosms wherein we crossed high- and low-predation guppy phenotypes with population size structure. We tested the ability of changes in size structure to generate selection on the demographic rates of guppies using an integral projection model (IPM). To understand how fitness differences among high- and low-predation phenotypes may be generated, we measured the response of the biomass of lower trophic levels and nutrient cycling to the different phenotype and size structure treatments. We found a significant interaction between guppy phenotype and the size structure treatments for absolute fitness. Size structure had a very large effect on invertebrate biomass in the mesocosms, but there was little or no effect of the phenotype. The effect of size structure on algal biomass depended on guppy phenotype, with no difference in algal biomass in populations with more, smaller guppies, but a large decrease in algal biomass in mesocosms with phenotypes adapted to low-predation risk. These results indicate an important role for size

  2. What do children know and understand about universal gravitation? Structural and developmental aspects

    NARCIS (Netherlands)

    Frappart, S.; Raijmakers, M.; Frède, V.

    2014-01-01

    Children's understanding of universal gravitation starts at an early age but changes until adulthood, which makes it an interesting topic for studying the development and structure of knowledge. Children's understanding of gravitation was tested for a variety of contexts and across a wide age range

  3. Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations

    Science.gov (United States)

    Freese, Peter D.; Korolev, Kirill S.; Jiménez, José I.; Chen, Irene A.

    2014-02-01

    Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.

  4. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc; Binh, Nguyen Trong

    2013-01-01

    Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese...... indigenous cattle populations, using microsatellite markers. A total of 410 individuals from six indigenous cattle populations and an exotic breed was characterized using 27 microsatellite markers A total of 362 alleles was detected and the number of alleles per locus ranged from 8 (INRA005 and ILSTS005......) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean FIS=0.05) and genetic differentiation (mean FST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected...

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    Shen, A

    1984-01-01

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

  7. Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): Natural replicate tests of post-Pleistocene evolution

    Science.gov (United States)

    Morris-Pocock, J. A.; Taylor, S.A.; Birt, T.P.; Damus, M.; Piatt, John F.; Warheit, K.I.; Friesen, Vicki L.

    2008-01-01

    Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east-west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east-west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa. ?? 2008 The Authors.

  8. Gut microbiome populations are associated with structure-specific changes in white matter architecture.

    Science.gov (United States)

    Ong, Irene M; Gonzalez, Jose G; McIlwain, Sean J; Sawin, Emily A; Schoen, Andrew J; Adluru, Nagesh; Alexander, Andrew L; Yu, John-Paul J

    2018-01-10

    Altered gut microbiome populations are associated with a broad range of neurodevelopmental disorders including autism spectrum disorder and mood disorders. In animal models, modulation of gut microbiome populations via dietary manipulation influences brain function and behavior and has been shown to ameliorate behavioral symptoms. With striking differences in microbiome-driven behavior, we explored whether these behavioral changes are also accompanied by corresponding changes in neural tissue microstructure. Utilizing diffusion tensor imaging, we identified global changes in white matter structural integrity occurring in a diet-dependent manner. Analysis of 16S ribosomal RNA sequencing of gut bacteria also showed changes in bacterial populations as a function of diet. Changes in brain structure were found to be associated with diet-dependent changes in gut microbiome populations using a machine learning classifier for quantitative assessment of the strength of microbiome-brain region associations. These associations allow us to further test our understanding of the gut-brain-microbiota axis by revealing possible links between altered and dysbiotic gut microbiome populations and changes in brain structure, highlighting the potential impact of diet and metagenomic effects in neuroimaging.

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

    Directory of Open Access Journals (Sweden)

    Eric G. Johnson

    2016-12-01

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

  10. Sea otter population structure and ecology in Alaska

    Science.gov (United States)

    Bodkin, James L.; Monson, Daniel H.

    2002-01-01

    environmental conditions. During the past decade, using molecular genetics, researchers have been trying to understand how sea otter populations might differ throughout the North Pacific and what effects population reductions and recovery have had on population genetics. Also, as a result of the varying degree of recovery among isolated populations, we have the opportunity to contrast life history attributes (such as condition, reproduction, and survival) among populations throughout their range. These contrasts may be useful in developing methods to assess the status of populations where traditional methods of surveying abundance are difficult and expensive.

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

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

  13. Multi-layered population structure in Island Southeast Asians

    Science.gov (United States)

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

    2016-01-01

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

  14. A new eigenfunction spatial analysis describing population genetic structure.

    Science.gov (United States)

    Diniz-Filho, José Alexandre Felizola; Diniz, João Vitor Barnez P L; Rangel, Thiago Fernando; Soares, Thannya Nascimento; Telles, Mariana Pires de Campos; Collevatti, Rosane Garcia; Bini, Luis Mauricio

    2013-12-01

    Several methods of spatial analyses have been proposed to infer the relative importance of evolutionary processes on genetic population structure. Here we show how a new eigenfunction spatial analysis can be used to model spatial patterns in genetic data. Considering a sample of n local populations, the method starts by modeling the response variable (allele frequencies or phenotypic variation) against the eigenvectors sequentially extracted from a geographic distance matrix (n × n). The relationship between the coefficient of determination (R(2)) of the models and the cumulative eigenvalues, which we named the spatial signal-representation (SSR) curve, can be more efficient than Moran's I correlograms in describing different patterns. The SSR curve was also applied to simulated data (under distinct scenarios of population differentiation) and to analyze spatial patterns in alleles from microsatellite data for 25 local populations of Dipteryx alata, a tree species endemic to the Brazilian Cerrado. The SSR curves are consistent with previous phylogeographical patterns of the species, revealing combined effects of isolation-by-distance and range expansion. Our analyses demonstrate that the SSR curve is a useful exploratory tool for describing spatial patterns of genetic variability and for selecting spatial eigenvectors for models aiming to explain spatial responses to environmental variables and landscape features.

  15. Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

    Science.gov (United States)

    Xie, Guo-Wen; Wang, De-Lian; Yuan, Yong-Ming; Ge, Xue-Jun

    2005-04-01

    Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

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

    Science.gov (United States)

    Cushing, J M; Henson, Shandelle M

    2018-02-03

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

  17. Spatial genetic structure and mitochondrial DNA phylogeography of Argentinean populations of the grasshopper Dichroplus elongatus.

    Science.gov (United States)

    Rosetti, Natalia; Remis, Maria Isabel

    2012-01-01

    Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD) and partial sequences of the cytochrome oxydase 1 (COI) mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the genetic loss

  18. Spatial genetic structure and mitochondrial DNA phylogeography of Argentinean populations of the grasshopper Dichroplus elongatus.

    Directory of Open Access Journals (Sweden)

    Natalia Rosetti

    Full Text Available Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD and partial sequences of the cytochrome oxydase 1 (COI mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the

  19. Combining computational chemistry and crystallography for a better understanding of the structure of cellulose

    Science.gov (United States)

    The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially the molecular shape is inferred from the crystal structures of m...

  20. Understanding Structure-Property Relations of Compressed Glasses through Relaxation Studies

    DEFF Research Database (Denmark)

    Smedskjær, Morten Mattrup; Svenson, Mouritz Nolsøe; Youngman, Randall E.

    When a glassy material or its liquid state is subjected to sufficiently high pressure, significant changes can take place in the short- and medium-range structure, vibrational density of states, and physical properties. It is crucial to determine and understand the structure-property relations un...

  1. Technological and structural change : Understanding economic growth in countries and regions

    NARCIS (Netherlands)

    Diodato, D.

    2017-01-01

    The research aims at improving our understanding of the link between economic structure and growth, by tackling a number of open questions. First, it asks whether economic structure – meaning the distribution of production factors among different industries – can significantly explain differences in

  2. Understanding herding based on a co-evolutionary model for strategy and game structure

    International Nuclear Information System (INIS)

    Wang, Tao; Huang, Keke; Cheng, Yuan; Zheng, Xiaoping

    2015-01-01

    Highlights: •We model herding effect in emergency from perspective of evolutionary game theory. •Rational subpopulation survives only when the game parameter is significantly large. •Herding effect may arise if the relative rewarding for rational agents is small. •Increasing the relative rewarding for rational agents will prevent herding effect. •The evolution result is unstable if the game parameter approaches critical points. -- Abstract: So far, there has been no conclusion on the mechanism for herding, which is often discussed in the academia. Assuming escaping behavior of individuals in emergency is rational rather than out of panic according to recent findings in social psychology, we investigate the behavioral evolution of large crowds from the perspective of evolutionary game theory. Specifically, evolution of the whole population divided into two subpopulations, namely the co-evolution of strategy and game structure, is numerically simulated based on the game theoretical models built and the evolutionary rule designed, and a series of phenomena including extinction of one subpopulation and herding effect are predicted in the proposed framework. Furthermore, if the rewarding for rational agents becomes significantly larger than that for emotional ones, herding effect will disappear. It is exciting that some phase transition points with interesting properties for the system can be found. In addition, our model framework is able to explain the fact that it is difficult for mavericks to prevail in society. The current results of this work will be helpful in understanding and restraining herding effect in real life

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Matthew W Blair

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

  5. Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars.

    Science.gov (United States)

    Glassmire, Andrea E; Jeffrey, Christopher S; Forister, Matthew L; Parchman, Thomas L; Nice, Chris C; Jahner, Joshua P; Wilson, Joseph S; Walla, Thomas R; Richards, Lora A; Smilanich, Angela M; Leonard, Michael D; Morrison, Colin R; Simbaña, Wilmer; Salagaje, Luis A; Dodson, Craig D; Miller, Jim S; Tepe, Eric J; Villamarin-Cortez, Santiago; Dyer, Lee A

    2016-10-01

    Chemically mediated plant-herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry and host-specialized caterpillars in the genus Eois (Geometridae: Larentiinae) and associated parasitoid wasps and flies. In addition, we used a genotyping-by-sequencing approach to examine the genetic structure of one abundant caterpillar species, Eois encina, in relation to host phytochemical variation. We found substantive concentration differences among three major secondary metabolites, and these differences in chemistry predicted caterpillar and parasitoid community structure among host plant populations. Furthermore, E. encina populations located at high elevations were genetically different from other populations. They fed on plants containing high concentrations of prenylated benzoic acid. Thus, phytochemistry potentially shapes caterpillar and wasp community composition and geographic variation in species interactions, both of which can contribute to diversification of plants and insects. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  6. Migration, distribution and population (stock) structure of shallow-water hake (Merluccius capensis) in the Benguela Current Large Marine Ecosystem inferred using a geostatistical population model

    DEFF Research Database (Denmark)

    Jansen, Teunis; Kristensen, Kasper; Kainge, Paulus Inekela

    2016-01-01

    Shallow-water hake (Merluccius capensis) is of considerable ecological and economic importance in the Benguela Current Large Marine Ecosystem in South Africa and Namibia. Optimal management of the resource is currently constrained by the limited understanding of migration patterns and population....../nursery areas, through the juvenile phase and the adults' migration to the spawning areas outside/upstream of the nursery areas. This revealed some previously unknown migration patterns and indicated natal homing and the existence of three primary population components in the region, namely the Walvis (central...... and population (stock) structure of M. capensis in the Benguela Current Large Marine Ecosystem....

  7. Do differences in the administrative structure of populations confound comparisons of geographic health inequalities?

    LENUS (Irish Health Repository)

    Jackson, Andrew L

    2010-08-18

    Abstract Background Geographical health inequalities are naturally described by the variation in health outcomes between areas (e.g. mortality rates). However, comparisons made between countries are hampered by our lack of understanding of the effect of the size of administrative units, and in particular the modifiable areal unit problem. Our objective was to assess how differences in geographic and administrative units used for disseminating data affect the description of health inequalities. Methods Retrospective study of standard populations and deaths aggregated by administrative regions within 20 European countries, 1990-1991. Estimated populations and deaths in males aged 0-64 were in 5 year age bands. Poisson multilevel modelling was conducted of deaths as standardised mortality ratios. The variation between regions within countries was tested for relationships with the mean region population size and the unequal distribution of populations within each country measured using Gini coefficients. Results There is evidence that countries whose regions vary more in population size show greater variation and hence greater apparent inequalities in mortality counts. The Gini coefficient, measuring inequalities in population size, ranged from 0.1 to 0.5 between countries; an increase of 0.1 was accompanied by a 12-14% increase in the standard deviation of the mortality rates between regions within a country. Conclusions Apparently differing health inequalities between two countries may be due to differences in geographical structure per se, rather than having any underlying epidemiological cause. Inequalities may be inherently greater in countries whose regions are more unequally populated.

  8. Population structure of Serpula lacrymans in Europe with an outlook to the French population.

    Science.gov (United States)

    Maurice, Sundy; Skrede, Inger; LeFloch, Gaetan; Barbier, Georges; Kauserud, Håvard

    2014-01-01

    In this study the genetic variation and population structure in a French population of the dry rot fungus S. lacrymans was investigated using 14 microsatellites markers and compared to the rest of Europe. In that comparison the French population possessed the same allelic diversity as rest of Europe. A weak geographic structuring of the genetic variation was observed across Europe, where the French isolates to some extent separated from the rest of Europe, indicating that weak barriers to gene flow exists. Eighty percent of the isolates had unique multilocus microsatellite genotypes, which corresponds to high recombination and dispersal by sexual spores. Deviations from Hardy-Weinberg expectations were observed in multiple loci. In most loci there was an excess of heterozygotes, which could be due to either non-random mating, presence of more than two nuclei in the secondary mycelia or another unrecognized process. A total of six vegetative compatibility (VC) groups were present in Europe, out of which four were sampled in France. One VC group was over-represented in France while two others were underrepresented, as compared to the rest of Europe. © 2014 by The Mycological Society of America.

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

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  10. Hierarchical spatial genetic structure in a distinct population segment of greater sage-grouse

    Science.gov (United States)

    Oyler-McCance, Sara J.; Casazza, Michael L.; Fike, Jennifer A.; Coates, Peter S.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus) within the Bi-State Management Zone (area along the border between Nevada and California) are geographically isolated on the southwestern edge of the species’ range. Previous research demonstrated that this population is genetically unique, with a high proportion of unique mitochondrial DNA (mtDNA) haplotypes and with significant differences in microsatellite allele frequencies compared to populations across the species’ range. As a result, this population was considered a distinct population segment (DPS) and was recently proposed for listing as threatened under the U.S. Endangered Species Act. A more comprehensive understanding of the boundaries of this genetically unique population (where the Bi-State population begins) and an examination of genetic structure within the Bi-State is needed to help guide effective management decisions. We collected DNA from eight sampling locales within the Bi-State (N = 181) and compared those samples to previously collected DNA from the two most proximal populations outside of the Bi-State DPS, generating mtDNA sequence data and amplifying 15 nuclear microsatellites. Both mtDNA and microsatellite analyses support the idea that the Bi-State DPS represents a genetically unique population, which has likely been separated for thousands of years. Seven mtDNA haplotypes were found exclusively in the Bi-State population and represented 73 % of individuals, while three haplotypes were shared with neighboring populations. In the microsatellite analyses both STRUCTURE and FCA separate the Bi-State from the neighboring populations. We also found genetic structure within the Bi-State as both types of data revealed differences between the northern and southern part of the Bi-State and there was evidence of isolation-by-distance. STRUCTURE revealed three subpopulations within the Bi-State consisting of the northern Pine Nut Mountains (PNa), mid Bi-State, and White Mountains (WM) following a

  11. [Plant potyvirus evolution: the survey of the genetic structure of populations].

    Science.gov (United States)

    Ohshima, Kazusato

    2012-01-01

    The Potyvirus is the largest genus of the largest family of plant RNA viruses, the Potyviridae. The potyviruses infect not only dicotyledonous but also monocotyledonous plants. The potyvirus phylogeny shows that the genus probably originated from a virus of monocotyledonous plants and that it first diverged approximately 7250 years ago in Southwest Eurasia or North Africa. Turnip mosaic virus (TuMV) belongs to the genus Potyvirus and infects a wide range of plant species, most from the family Brassicaceae. TuMV is most studied a potyvirus species for molecular evolution and the genetic structure of populations. The use of computer programs for better understanding of the evolution and the genetic structures of populations of potyviruses and TuMV are illustrated.

  12. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the m......The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

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

    Science.gov (United States)

    Laird, Robert A; Schamp, Brandon S

    2015-01-21

    Intransitive competition occurs when competing strategies cannot be listed in a hierarchy, but rather form loops-as in the game rock-paper-scissors. Due to its cyclic competitive replacement, competitive intransitivity promotes strategy coexistence, both in rock-paper-scissors and in higher-richness communities. Previous work has shown that this intransitivity-mediated coexistence is strongly influenced by spatially explicit interactions, compared to when populations are well mixed. Here, we extend and broaden this line of research and examine the impact on coexistence of intransitive competition taking place on a continuum of small-world networks linking spatial lattices and regular random graphs. We use simulations to show that the positive effect of competitive intransitivity on strategy coexistence holds when competition occurs on networks toward the spatial end of the continuum. However, in networks that are sufficiently disordered, increasingly violent fluctuations in strategy frequencies can lead to extinctions and the prevalence of monocultures. We further show that the degree of disorder that leads to the transition between these two regimes is positively dependent on population size; indeed for very large populations, intransitivity-mediated strategy coexistence may even be possible in regular graphs with completely random connections. Our results emphasize the importance of interaction structure in determining strategy dynamics and diversity. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Microsatellite based genetic structure of regional transboundary Istrian sheep breed populations in Croatia and Slovenia

    Directory of Open Access Journals (Sweden)

    Beatriz Gutierrez-Gil

    2015-02-01

    Full Text Available Istrian dairy sheep is a local breed essential for the identity and development of the Northern- Adriatic karstic region through high-quality products, primarily the hard sheep artisanal cheese. Border changes fragmented the initial Istrian dairy sheep population in three genetically isolated sub-populations in Italy (1000 animals, Slovenia (1150 animals and Croatia (2500 animals. Due to the drastic reduction of their population sizes and fragmentation, the populations in Croatia and Slovenia are included in governmentally supported conservation programs. The initial subpopulation in Italy was restored after near extinction with stock from Slovenia, and is used today in meat production. The aim of this study was to provide an initial understanding of the current genetic structure and distribution of the genetic variability that exists in Istrian sheep by analysing individuals sampled in two regional groups of Istrian sheep from Croatia and Slovenia. Cres island sheep and Lika pramenka sheep were used as out-groups for comparison. Genetic differentiation was analysed using factorial correspondence analysis and structure clustering over 26 microsatellite loci for a total of 104 sheep belonging to three breeds from Croatia and Slovenia. Factorial correspondence analysis and clustering-based structure analysis both showed three distinct populations: Lika pramenka sheep, Cres island sheep and Istrian sheep. We did not find a marked genetic divergence of the regional groups of Istrian sheep. Istrian sheep regional group from Slovenia showed lower genetic variability compared to the one from Croatia. Variability and structure information obtained in this study considered alongside with socio-cultural-contexts and economic goals for the Istrian sheep reared in Croatia and Slovenia indicate that the cross-border exchange of genetic material of animals carrying private alleles among populations would maintain these alleles at low frequencies and minimize

  15. High genetic diversity and structured populations of the oriental fruit moth in its range of origin.

    Science.gov (United States)

    Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

    2013-01-01

    The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.

  16. High genetic diversity and structured populations of the oriental fruit moth in its range of origin.

    Directory of Open Access Journals (Sweden)

    Yan Zheng

    Full Text Available The oriental fruit moth Grapholita ( = Cydia molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.

  17. Advanced understanding on electronic structure of molecular semiconductors and their interfaces

    Science.gov (United States)

    Akaike, Kouki

    2018-03-01

    Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

  18. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

    Science.gov (United States)

    Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F

    2012-01-01

    Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

  19. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

    Directory of Open Access Journals (Sweden)

    Martina Temunović

    Full Text Available Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM. We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

  20. Population structure of Reyna Creole cattle in Nicaragua.

    Science.gov (United States)

    Corrales, Roldan; Näsholm, Anna; Malmfors, Birgitta; Philipsson, Jan

    2010-10-01

    Reyna Creole cattle originated from Bos taurus cattle brought to Latin America during the Spanish colonization in the fifteenth century and are the only remaining local breed in Nicaragua. However, the current genetic status of this breed is unknown. Therefore, the population structure of three recorded Reyna Creole herds in Nicaragua was studied to estimate their level of inbreeding, effective population size, and generation intervals. Data from 2,609 animals born between 1958 and 2007 were analyzed. A pedigree completeness index higher than 0.8 was required to obtain reliable estimates of the level of inbreeding, and this criterion was met for 367 animals (14%) in two herds. The average level of inbreeding was 13.0%, with values ranging from 0% to 43.8% for individual animals. One of the herds had an average inbreeding level of 21.6%, primarily due to long periods in which the same bulls were used for mating, leading to excessive frequencies of matings between closely related animals. The effective population size differed between years and ranged from 28 to 46 animals, showing that the Reyna Creole cattle breed is endangered, close to critical status. The average generation interval was 6.9 years with values as high as 19.1 years for some sires that were used for artificial insemination over a long period of time. Due to the high level of inbreeding and small population size, urgent actions are required for the development of a breeding program to protect the breed and support its sustainable utilization.

  1. Stability patterns for a size-structured population model and its stage-structured counterpart

    DEFF Research Database (Denmark)

    Zhang, Lai; Pedersen, Michael; Lin, Zhigui

    2015-01-01

    delayed system consisting of a renewal equation for the consumer population birth rate and a delayed differential equation for the resource. Results show that the size- and stage-structured models differ considerably with respect to equilibrium stability, although the two models have completely identical...

  2. Evolutionary game dynamics in a growing structured population

    International Nuclear Information System (INIS)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir; Traulsen, Arne

    2009-01-01

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  3. Physical models have gender-specific effects on student understanding of protein structure-function relationships.

    Science.gov (United States)

    Forbes-Lorman, Robin M; Harris, Michelle A; Chang, Wesley S; Dent, Erik W; Nordheim, Erik V; Franzen, Margaret A

    2016-07-08

    Understanding how basic structural units influence function is identified as a foundational/core concept for undergraduate biological and biochemical literacy. It is essential for students to understand this concept at all size scales, but it is often more difficult for students to understand structure-function relationships at the molecular level, which they cannot as effectively visualize. Students need to develop accurate, 3-dimensional mental models of biomolecules to understand how biomolecular structure affects cellular functions at the molecular level, yet most traditional curricular tools such as textbooks include only 2-dimensional representations. We used a controlled, backward design approach to investigate how hand-held physical molecular model use affected students' ability to logically predict structure-function relationships. Brief (one class period) physical model use increased quiz score for females, whereas there was no significant increase in score for males using physical models. Females also self-reported higher learning gains in their understanding of context-specific protein function. Gender differences in spatial visualization may explain the gender-specific benefits of physical model use observed. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 44(4):326-335, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

  4. The construction of an amino acid network for understanding protein structure and function.

    Science.gov (United States)

    Yan, Wenying; Zhou, Jianhong; Sun, Maomin; Chen, Jiajia; Hu, Guang; Shen, Bairong

    2014-06-01

    Amino acid networks (AANs) are undirected networks consisting of amino acid residues and their interactions in three-dimensional protein structures. The analysis of AANs provides novel insight into protein science, and several common amino acid network properties have revealed diverse classes of proteins. In this review, we first summarize methods for the construction and characterization of AANs. We then compare software tools for the construction and analysis of AANs. Finally, we review the application of AANs for understanding protein structure and function, including the identification of functional residues, the prediction of protein folding, analyzing protein stability and protein-protein interactions, and for understanding communication within and between proteins.

  5. Understanding the Connection Between Traumatic Brain Injury and Alzheimer’s Disease: A Population Based Medical Record Review Analysis

    Science.gov (United States)

    2016-10-01

    AWARD NUMBER: W81XWH-15-1-0573 TITLE: Understanding the Connection Between Traumatic Brain Injury and Alzheimer’s Disease: A Population -Based...Sep 2015 - 14 Sep 2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Understanding the Connection Between Traumatic Brain Injury and Alzheimer’s Disease...A Population -Based Medical Record Review Analysis 5b. GRANT NUMBER W81XWH-15-1-0573 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Allen W. Brown 5d

  6. A structural equation modeling analysis of students' understanding in basic mathematics

    Science.gov (United States)

    Oktavia, Rini; Arif, Salmawaty; Ferdhiana, Ridha; Yuni, Syarifah Meurah; Ihsan, Mahyus

    2017-11-01

    This research, in general, aims to identify incoming students' understanding and misconceptions of several basic concepts in mathematics. The participants of this study are the 2015 incoming students of Faculty of Mathematics and Natural Science of Syiah Kuala University, Indonesia. Using an instrument that were developed based on some anecdotal and empirical evidences on students' misconceptions, a survey involving 325 participants was administered and several quantitative and qualitative analysis of the survey data were conducted. In this article, we discuss the confirmatory factor analysis using Structural Equation Modeling (SEM) on factors that determine the new students' overall understanding of basic mathematics. The results showed that students' understanding on algebra, arithmetic, and geometry were significant predictors for their overall understanding of basic mathematics. This result supported that arithmetic and algebra are not the only predictors of students' understanding of basic mathematics.

  7. Genetic diversity and population structure of native maize populations in Latin America and the Caribbean.

    Science.gov (United States)

    Bedoya, Claudia A; Dreisigacker, Susanne; Hearne, Sarah; Franco, Jorge; Mir, Celine; Prasanna, Boddupalli M; Taba, Suketoshi; Charcosset, Alain; Warburton, Marilyn L

    2017-01-01

    This study describes the genetic diversity and population structure of 194 native maize populations from 23 countries of Latin America and the Caribbean. The germplasm, representing 131 distinct landraces, was genetically characterized as population bulks using 28 SSR markers. Three main groups of maize germplasm were identified. The first, the Mexico and Southern Andes group, highlights the Pre-Columbian and modern exchange of germplasm between North and South America. The second group, Mesoamerica lowland, supports the hypothesis that two separate human migration events could have contributed to Caribbean maize germplasm. The third, the Andean group, displayed early introduction of maize into the Andes, with little mixing since then, other than a regional interchange zone active in the past. Events and activities in the pre- and post-Columbian Americas including the development and expansion of pre-Columbian cultures and the arrival of Europeans to the Americas are discussed in relation to the history of maize migration from its point of domestication in Mesoamerica to South America and the Caribbean through sea and land routes.

  8. Genetic structure of fragmented November moth (Lepidoptera: Geometridae) populations in farmland

    DEFF Research Database (Denmark)

    Wynne, Ian Robert; Loxdale, Hugh D.; Brookes, Cliff P.

    2003-01-01

    allozymes, conservation genetics, Epirrita dilutata, Epirrita christyi, molecular markers, habitat fragmentation, population genetic structure......allozymes, conservation genetics, Epirrita dilutata, Epirrita christyi, molecular markers, habitat fragmentation, population genetic structure...

  9. Dispersal and population structure of a New World predator, the army ant Eciton burchellii

    DEFF Research Database (Denmark)

    Berghoff, S M; Kronauer, D J C; Edwards, K J

    2008-01-01

    barriers, which might have severe impacts on population structure and lead to population decline. Using nuclear microsatellite markers and mitochondrial sequences, we investigated genetic differentiation in a fragmented population in the Panama Canal area. While nuclear markers showed little...

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

    DEFF Research Database (Denmark)

    Hartvig, Martin; Andersen, Ken Haste

    2013-01-01

    on the maximum adult sizes and population size distributions. We explore the assembly and potential for coexistence of small communities where all species experience ontogenetic trophic niche shifts. The life-history of each species is described by a physiologically structured model and species identity...... is characterized by the trait: size at maturation. We show that a single species can exist in two different states: a ‘resource driven state’ and a ‘cannibalistic state’ with a large scope for emergent Allee effects and bistable states. Two species can coexist in two different configurations: in a ‘competitive...... coexistence’ state when the ratio between sizes at maturation of the two species is less than a predator–prey mass ratio and the resource level is low to intermediate, or in a ‘trophic ladder’ state if the ratio of sizes at maturation is larger than the predator–prey mass ratio at all resource levels. While...

  11. ASSESSMENT OF CHAROLAIS BULLS POPULATION STRUCTURE BASED ON SNPs ANALYSES

    Directory of Open Access Journals (Sweden)

    Nina Moravčíková

    2014-02-01

    Full Text Available The aim of this study was identification of SNPs in leptin (LEP, leptin receptor (LEPR, growth hormone (GH and specific pituitary transcription factor (Pit-1 genes in order to analyze genetic structure of Charolais bulls’ population. The total numbers of genomic DNA samples were taken from 52 breeding bulls and analyzed by PCR-RFLP method. After digestion with restriction enzymes were detected in bulls’ population alleles with frequency: LEP/Sau3AI A 0.83 and B 0.17 (±0.037; LEPR/BseGI C 0.95 and T 0.05 (±0.021, GH/AluI L 0.62 and V 0.38 (±0.048 and Pit1/HinfI A 0.40 and B 0.60 (±0.048. Based on the observed vs. expected genotypes frequencies population across loci were in Hardy-Weinberg equilibrium (P>0.05, only in case of Pit-1 locus was detected disequilibrium. Predominant were in analyzed breeding bulls LEP/Sau3AIAA (0.69, LEPR/T945MCC (0.90, GH/AluILL (0.43 and Pit-1/HinfIAB (0.65 genotypes. The observed heterozygosity of SNPs was also transferred to the low (LEP/Sau3AI/0.248 and LEPR/T945M/0.088 or median polymorphic information content (GH/AluI/0.366 and Pit-1/HinfI/0.370. Within genetic variability estimating negative (LEPR/T945M and Pit-1/HinfI and positive values (LEP/Sau3AI and GH/AluI of fixation indexes FIS indicating slight heterozygote excess or deficiency based on analyzed genetic marker were observed.

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

    Science.gov (United States)

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

    2013-01-01

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

  13. Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers.

    Science.gov (United States)

    Kumar, Vinay; Shukla, Sanjeev K; Mathew, Jose; Sharma, Deepak

    2015-01-01

    The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ▵K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.

  14. Genetic population structure of muskellunge in the Great Lakes

    Science.gov (United States)

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

    2013-01-01

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

  15. Implementation of Structured Inquiry Based Model Learning toward Students' Understanding of Geometry

    Science.gov (United States)

    Salim, Kalbin; Tiawa, Dayang Hjh

    2015-01-01

    The purpose of this study is implementation of a structured inquiry learning model in instruction of geometry. The model used is a model with a quasi-experimental study amounted to two classes of samples selected from the population of the ten classes with cluster random sampling technique. Data collection tool consists of a test item…

  16. Colony social structure in native and invasive populations of the social wasp Vespula pensylvanica

    Science.gov (United States)

    Hanna, Cause; Cook, Erin D.; Thompson, Ariel R.; Dare, Lyndzey E.; Palaski, Amanda L.; Foote, David; Goodisman, Michael A. D.

    2014-01-01

    Social insects rank among the most invasive of terrestrial species. The success of invasive social insects stems, in part, from the flexibility derived from their social behaviors. We used genetic markers to investigate if the social system of the invasive wasp, Vespula pensylvanica, differed in its introduced and native habitats in order to better understand variation in social phenotype in invasive social species. We found that (1) nestmate workers showed lower levels of relatedness in introduced populations than native populations, (2) introduced colonies contained workers produced by multiple queens whereas native colonies contained workers produced by only a single queen, (3) queen mate number did not differ significantly between introduced and native colonies, and (4) workers from introduced colonies were frequently produced by queens that originated from foreign nests. Thus, overall, native and introduced colonies differed substantially in social phenotype because introduced colonies more frequently contained workers produced by multiple, foreign queens. In addition, the similarity in levels of genetic variation in introduced and native habitats, as well as observed variation in colony social phenotype in native populations, suggest that colony structure in invasive populations may be partially associated with social plasticity. Overall, the differences in social structure observed in invasive V. pensylvanica parallel those in other, distantly related invasive social insects, suggesting that insect societies often develop similar social phenotypes upon introduction into new habitats.

  17. Do Students Understand Our Course Structure? Implications for Important Classroom Attitudes and Behavior

    Science.gov (United States)

    Elicker, Joelle D.; Foust, Michelle Singer; Perry, Jennifer L.

    2015-01-01

    The complexity of a course's structure may influence how well students understand what is expected of them. Using the foundation of the industrial/organizational (I/O) psychology literature, the authors modified a measure of "Perceived System Knowledge" (Williams & Levy, 1992) for employee performance appraisal to be appropriate for…

  18. Using Concrete & Representational Experiences to Understand the Structure of DNA: A Four-Step Instructional Framework

    Science.gov (United States)

    Harrell, Pamela Esprivalo; Richards, Debbie; Collins, James; Taylor, Sarah

    2005-01-01

    A description of learning experience that uses a four-step instrumentational framework involving concrete and representational experiences to promote conceptual understanding of abstract biological concepts by a series of closely-related activities is presented. The students are introduced to the structure and implications of DNA using four…

  19. Urban ecological stewardship: understanding the structure, function and network of community-based urban land management

    Science.gov (United States)

    Erika s. Svendsen; Lindsay K. Campbell

    2008-01-01

    Urban environmental stewardship activities are on the rise in cities throughout the Northeast. Groups participating in stewardship activities range in age, size, and geography and represent an increasingly complex and dynamic arrangement of civil society, government and business sectors. To better understand the structure, function and network of these community-based...

  20. Integrating Model-Based Learning and Animations for Enhancing Students' Understanding of Proteins Structure and Function

    Science.gov (United States)

    Barak, Miri; Hussein-Farraj, Rania

    2013-01-01

    This paper describes a study conducted in the context of chemistry education reforms in Israel. The study examined a new biochemistry learning unit that was developed to promote in-depth understanding of 3D structures and functions of proteins and nucleic acids. Our goal was to examine whether, and to what extent teaching and learning via…

  1. Teacher's Understanding, Perceptions, and Experiences of Students in Foster Care: A Forgotten Population

    Science.gov (United States)

    Watson-Davis, Darneika

    2010-01-01

    The purpose of this study is to examine elementary teacher's understanding, perceptions, and experiences of working with students in foster care. The researcher examined whether teachers are informed about students in foster care, determined teacher's understanding of the foster care system, and how their students are affected. The results…

  2. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).

    Science.gov (United States)

    Li, Pirui; Zhang, Fei; Chen, Sumei; Jiang, Jiafu; Wang, Haibin; Su, Jiangshuo; Fang, Weimin; Guan, Zhiyong; Chen, Fadi

    2016-06-01

    Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.

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

    Science.gov (United States)

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

    2016-01-01

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

  4. Surviving winter: Food, but not habitat structure, prevents crashes in cyclic vole populations.

    Science.gov (United States)

    Johnsen, Kaja; Boonstra, Rudy; Boutin, Stan; Devineau, Olivier; Krebs, Charles J; Andreassen, Harry P

    2017-01-01

    Vole population cycles are a major force driving boreal ecosystem dynamics in northwestern Eurasia. However, our understanding of the impact of winter on these cycles is increasingly uncertain, especially because climate change is affecting snow predictability, quality, and abundance. We examined the role of winter weather and snow conditions, the lack of suitable habitat structure during freeze-thaw periods, and the lack of sufficient food as potential causes for winter population crashes. We live-trapped bank voles Myodes glareolus on 26 plots (0.36 ha each) at two different elevations (representing different winter conditions) in southeast Norway in the winters 2013/2014 and 2014/2015. We carried out two manipulations: supplementing six plots with food to eliminate food limitation and six plots with straw to improve habitat structure and limit the effect of icing in the subnivean space. In the first winter, all bank voles survived well on all plots, whereas in the second winter voles on almost all plots went extinct except for those receiving supplemental food. Survival was highest on the feeding treatment in both winters, whereas improving habitat structure had no effect. We conclude that food limitation was a key factor in causing winter population crashes.

  5. Bipartite graphs as models of population structures in evolutionary multiplayer games.

    Science.gov (United States)

    Peña, Jorge; Rochat, Yannick

    2012-01-01

    By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

  6. Population Structure and Genomic Breed Composition in an Angus–Brahman Crossbred Cattle Population

    Directory of Open Access Journals (Sweden)

    Mesfin Gobena

    2018-03-01

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

  7. Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures

    Directory of Open Access Journals (Sweden)

    Rui Li

    2016-05-01

    Full Text Available Although thousands of long non-coding RNAs (lncRNAs have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure–function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq, selective 2′-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq, parallel analysis of RNA structure (PARS, and fragmentation sequencing (FragSeq. The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level.

  8. Effects of Structural Transparency in System Dynamics Simulators on Performance and Understanding

    Directory of Open Access Journals (Sweden)

    Birgit Kopainsky

    2015-10-01

    Full Text Available Prior exploration is an instructional strategy that has improved performance and understanding in system-dynamics-based simulators, but only to a limited degree. This study investigates whether model transparency, that is, showing users the internal structure of models, can extend the prior exploration strategy and improve learning even more. In an experimental study, participants in a web-based simulation learned about and managed a small developing nation. All participants were provided the prior exploration strategy but only half received prior exploration embedded in a structure-behavior diagram intended to make the underlying model’s structure more transparent. Participants provided with the more transparent strategy demonstrated better understanding of the underlying model. Their performance, however, was the equivalent to those in the less transparent condition. Combined with previous studies, our results suggest that while prior exploration is a beneficial strategy for both performance and understanding, making the model structure transparent with structure-behavior diagrams is more limited in its effect.

  9. Using Model Building in Structural Engineering to Enhance Understanding of Construction Principles and Methods

    Directory of Open Access Journals (Sweden)

    Niall Holmes

    2013-05-01

    Full Text Available This paper presents a new model building exercise in a second year module in the Department of Civil & Structural Engineering in the Dublin Institute of Technology (DIT. The activity aimed to improve students’ understanding of structural engineering, construction principles and methods. It allowed students to practically apply lecture material and construct a scaled model giving them an opportunity to study and visualise a real structure and generate their own ideas on how it should be assembled within a constructivist active learning environment. As a result, lectures were found to be more interactive and students more engaged in the discussions and provided a pathway to bridge the gap between theory (presented in lectures and the reality of their professions, which can aid them in their graduate careers. It is hoped that this type of active learning can be used in other engineering programmes to improve student understanding and as an opportunity to better apply lecture material to the real world.

  10. Predation and physical environment structure the density and population size structure of zebra mussels

    OpenAIRE

    Naddafi, Rahmat; Pettersson, Kurt; Eklöv, Peter

    2010-01-01

    The zebra mussel (Dreissena polymorpha) provides one example of successful invaders in novel environments. However, little attention has been devoted to exploring the factors regulating zebra mussel density and population size structure at the local scale. We tested effects of physicochemical factors and fish predation on the density of zebra mussels at several sites and between years in a natural lake. Water depth and roach (Rutilus rutilus) density were the most important variables affectin...

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

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    Rocío Pineda-Martos

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  13. Genetic structure and diversity of animal populations exposed to metal pollution.

    Science.gov (United States)

    Mussali-Galante, Patricia; Tovar-Sánchez, Efraín; Valverde, Mahara; Rojas, Emilio

    2014-01-01

    ecotoxicological studies. Collectively, these points are designed to provide more accurate data and a deeper understanding of the relationship between alterations in genetic diversity of impacted populations and metal exposures. In particular, we believe that the exact nature of all tested chemical pollutants be clearly described, biomarkers be included, sentinel organisms be used, testing be performed at multiple experimental sites, reference populations be sampled in close geographical proximity to where pollution occurs, and genetic structure parameters and high-throughput technology be more actively employed. Furthermore, we propose a new class of biomarkers,termed "biomarkers of permanent effect," which may include measures of genetic variability in impacted populations.

  14. Genetic structuring among silverside fish (Atherinella brasiliensis) populations from different Brazilian regions

    Science.gov (United States)

    da Silva Cortinhas, Maria Cristina; Kersanach, Ralf; Proietti, Maíra; Dumont, Luiz Felipe Cestari; D'Incao, Fernando; Lacerda, Ana Luzia F.; Prata, Pedro Sanmartin; Matoso, Daniele Aparecida; Noleto, Rafael Bueno; Ramsdorf, Wanessa; Boni, Talge Aiex; Prioli, Alberto José; Cestari, Marta Margarete

    2016-09-01

    Estuaries are dynamic environments, key for the survival of innumerous ecologically or economically important fish species. Among these species are Neotropical silversides (Atherinella brasiliensis), which are resident and abundant in Brazilian estuaries and used as a complementary source of income and food for local communities. To better understand silverside populations in Brazil, we evaluated the genetic diversity, structure and demography of fish sampled at six estuaries from the northeastern to the southern coast, using Random Amplified Polymorphic DNA and mitochondrial DNA (D-loop) markers. High haplotype diversities (h ranging from 0.75 to 0.99) were found in all populations except Carapebus, located in Southeast Brazil (h = 0.54). A total of 69 mtDNA haplotypes were found, with Itaparica (Northeast Brazil) and Carapebus presenting only exclusive haplotypes, while some were shared among populations in the South. Strong regional structure was observed, with very high differentiation between Itaparica and Carapebus, as well as among these two populations and the ones from the Southern region (Paranaguá, Conceição, Camacho and Patos). Among southern areas, low/moderate structure was detected. Most populations showed unimodal mismatch distributions indicating recent demographic expansion, while Carapebus presented a multimodal distribution characteristic of a stable or bottlenecked population. Times since possible population expansion were highest in Itaparica (32,500 ya) and Carapebus (29,540 ya), while in the Southern region longest time was observed at Conceição (25,540 ya) and shortest at Patos (9720 ya). In a general manner, haplotype diversities were directly related to times since population expansions; again, Carapebus was the exception, displaying long time since expansion but low diversity, possibly due to a recent bottleneck caused by the isolation and human impacts this lagoon is subject to. Isolation by Distance was significant for Itaparica

  15. Population Genetic Structure of the Endangered Kaiser's Mountain Newt, Neurergus kaiseri (Amphibia: Salamandridae.

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    Hossein Farasat

    Full Text Available Species often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in an endemic and critically endangered stream breeding mountain newt, Neurergus kaiseri, within its entire range in southwestern Iran. We identified two geographic regions based on phylogenetic relationships using Bayesian inference and maximum likelihood of 779 bp mtDNA (D-loop in 111 individuals from ten of twelve known breeding populations. This analysis revealed a clear divergence between northern populations, located in more humid habitats at higher elevation, and southern populations, from drier habitats at lower elevations regions. From seven haplotypes found in these populations none was shared between the two regions. Analysis of molecular variance (AMOVA of N. kaiseri indicates that 94.03% of sequence variation is distributed among newt populations and 5.97% within them. Moreover, a high degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.94, P = 0.002. The positive and significant correlation between geographic and genetic distances (r = 0.61, P = 0.002 following controlling for environmental distance suggests an important influence of geographic divergence of the sites in shaping the genetic variation and may provide tools for a possible conservation based prioritization policy for the endangered species.

  16. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae on the Canary Islands

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    Ye Sun

    2017-06-01

    Full Text Available Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat. The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote and western islands (EI Hierro, La Palma, La Gomera, Tenerife, this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  17. Using satellite telemetry to define spatial population structure in polar bears in the Norwegian and western Russian Arctic

    Science.gov (United States)

    Mauritzen, Mette; Derocher, Andrew E.; Wiig, Øystein; Belikov, Stanislav; Boltunov, Andrei N.; Garner, Gerald W.

    2002-01-01

    1. Animal populations, defined by geographical areas within a species’ distribution where population dynamics are largely regulated by births and deaths rather than by migration from surrounding areas, may be the correct unit for wildlife management. However, in heterogeneous landscapes varying habitat quality may yield subpopulations with distinct patterns in resource use and demography significant to the dynamics of populations.2. To define the spatial population structure of polar bears Ursus maritimus in the Norwegian and western Russian Arctic, and to assess the existence of a shared population between the two countries, we analysed satellite telemetry data obtained from 105 female polar bears over 12 years.3. Using both cluster analyses and home-range estimation methods, we identified five population units inhabiting areas with different sea-ice characteristics and prey availability.4. The continuous distribution of polar bear positions indicated that the different subpopulations formed one continuous polar bear population in the Norwegian and western Russian Arctic. Hence, Norway and Russia have a shared management responsibility.5. The spatial population structure identified will provide a guide for evaluating geographical patterns in polar bear ecology, the dynamics of polar bear–seal relationships and the effects of habitat alteration due to climate change. The work illustrates the importance of defining population borders and subpopulation structure in understanding the dynamics and management of larger animals.

  18. Population Structure and the Colonization Route of One of the Oldest North American Invasive Insects: Stories from the Worn Road of the Hessian Fly, Mayetiola destructor (Say)

    OpenAIRE

    Morton, Philip K.; Schemerhorn, Brandon J.

    2013-01-01

    An integral part to understanding the biology of an invasive species is determining its origin, particularly in pest species. As one of the oldest known invasive species, the goals of this study were to evaluate the evidence of a westward expansion of Hessian fly into North America, from a potential singular introduction event, and the population genetic structure of current populations. Levels of genetic diversity and population structure in the Hessian fly were compared across North America...

  19. Combining clinical and population-level data to understand the health of neighborhoods.

    Science.gov (United States)

    Chambers, Earle C; Wong, Barbara C; Riley, Rachael W; Hollingsworth, Nicole; Blank, Arthur E; Myers, Christa; Bedell, Jane; Selwyn, Peter A

    2015-03-01

    From February through December 2012, we examined responses to health behavior questions integrated into the electronic medical record of primary care centers in the Bronx, New York in the context of New York City Community Health Survey data. We saw a higher proportion of unhealthy behaviors among patients than among the neighborhood population. Analyzing clinical data in the neighborhood context can better target at-risk populations.

  20. Understanding long-term fruit fly (Diptera: Tephritidae) population dynamics: implications for areawide management.

    Science.gov (United States)

    Aluja, Martín; Ordano, Mariano; Guillén, Larissa; Rull, Juan

    2012-06-01

    Fruit flies (Diptera: Tephritidae) are devastating agricultural pests worldwide but studies on their long-term population dynamics are sparse. Our aim was to determine the mechanisms driving long-term population dynamics as a prerequisite for ecologically based areawide pest management. The population density of three pestiferous Anastrepha species [Anastrepha ludens (Loew), Anastrepha obliqua (Macquart), and Anastrepha serpentina (Wiedemann)] was determined in grapefruit (Citrus x paradisi Macfad.), mango (Mangifera indica L.), and sapodilla [Manilkara zapota (L.) P. Royen] orchards in central Veracruz, México, on a weekly basis over an 11-yr period. Fly populations exhibited relatively stable dynamics over time. Population dynamics were mainly driven by a direct density-dependent effect and a seasonal feedback process. We discovered direct and delayed influences that were correlated with both local (rainfall and air temperature) and global climatic variation (El Niño Southern Oscillation [ENSO] and North Atlantic Oscillation [NAO]), and detected differences among species and location of orchards with respect to the magnitude and nature (linear or nonlinear) of the observed effects, suggesting that highly mobile pest outbreaks become uncertain in response to significant climatic events at both global and local levels. That both NAO and ENSO affected Anastrepha population dynamics, coupled with the high mobility of Anastrepha adults and the discovery that when measured as rate of population change, local population fluctuations exhibited stable dynamics over time, suggests potential management scenarios for the species studied lie beyond the local scale and should be approached from an areawide perspective. Localized efforts, from individual growers will probably prove ineffective, and nonsustainable.

  1. Plasmodium vivax Population Structure and Transmission Dynamics in Sabah Malaysia

    Science.gov (United States)

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

    2013-01-01

    Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (F ST  = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI  = 1.38) and KK (mean MOI  = 1.19). However, population diversity remained moderate (H E  = 0.583 in KM and H E  = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (I A S >0.5 [Ppopulation appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for malaria elimination. PMID:24358203

  2. Worldwide population genetic structure of the oriental fruit moth (Grapholita molesta), a globally invasive pest.

    Science.gov (United States)

    Kirk, Heather; Dorn, Silvia; Mazzi, Dominique

    2013-03-25

    Invasive pest species have large impacts on agricultural crop yields, and understanding their population dynamics is important for ensuring food security. The oriental fruit moth Grapholita molesta is a cosmopolitan pest of stone and pome fruit species including peach and apple, and historical records indicate that it has invaded North and South America, Europe, Australia and Africa from its putative native range in Asia over the past century. We used 13 microsatellite loci, including nine newly developed markers, to characterize global population structure of G. molesta. Approximately 15 individuals from each of 26 globally distributed populations were genotyped. A weak but significant global pattern of isolation-by-distance was found, and G. molesta populations were geographically structured on a continental scale. Evidence does not support that G. molesta was introduced to North America from Japan as previously proposed. However, G. molesta was probably introduced from North America to The Azores, South Africa, and Brazil, and from East Asia to Australia. Shared ancestry was inferred between populations from Western Europe and from Brazil, although it remains unresolved whether an introduction occurred from Europe to Brazil, or vice versa. Both genetic diversity and levels of inbreeding were surprisingly high across the range of G. molesta and were not higher or lower overall in introduced areas compared to native areas. There is little evidence for multiple introductions to each continent (except in the case of South America), or for admixture between populations from different origins. Cross-continental introductions of G. molesta appear to be infrequent, which is surprising given its rapid worldwide expansion over the past century. We suggest that area-wide spread via transport of fruits and other plant materials is a major mechanism of ongoing invasion, and management efforts should therefore target local and regional farming communities and distribution

  3. Evaluation of genetic population structure of smallmouth bass in the Susquehanna River basin, Pennsylvania

    Science.gov (United States)

    Schall, Megan K.; Bartron, Meredith L.; Wertz, Timothy; Niles, Jonathan M.; Shaw, Cassidy H.; Wagner, Tyler

    2017-01-01

    The Smallmouth Bass Micropterus dolomieu was introduced into the Susquehanna River basin, Pennsylvania, nearly 150 years ago. Since introduction, it has become an economically and ecologically important species that supports popular recreational fisheries. It is also one of the most abundant top predators in the system. Currently, there is no information on the level of genetic diversity or genetic structuring that may have occurred since introduction. An understanding of genetic diversity is important for the delineation of management units and investigation of gene flow at various management scales. The goals of this research were to investigate population genetic structure of Smallmouth Bass at sites within the Susquehanna River basin and to assess genetic differentiation relative to Smallmouth Bass at an out-of-basin site (Allegheny River, Pennsylvania) located within the species’ native range. During spring 2015, fin clips (n = 1,034) were collected from adults at 11 river sites and 13 tributary sites in the Susquehanna River basin and at one site on the Allegheny River. Fin clips were genotyped at 12 polymorphic microsatellite loci. Based on our results, adults sampled throughout the Susquehanna River basin did not represent separate genetic populations. There were only subtle differences in genetic diversity among sites (mean pairwise genetic differentiation index FST = 0.012), and there was an overall lack of population differentiation (K = 3 admixed populations). The greatest genetic differentiation was observed between fish collected from the out-of-basin site and those from the Susquehanna River basin sites. Knowledge that separate genetic populations of Smallmouth Bass do not exist in the Susquehanna River basin is valuable information for fisheries management in addition to providing baseline genetic data on an introduced sport fish population.

  4. Octopus vulgaris (Cuvier, 1797 in the Mediterranean Sea: Genetic Diversity and Population Structure.

    Directory of Open Access Journals (Sweden)

    Daniele De Luca

    Full Text Available The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.

  5. Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure.

    Science.gov (United States)

    De Luca, Daniele; Catanese, Gaetano; Procaccini, Gabriele; Fiorito, Graziano

    2016-01-01

    The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.

  6. MOLECULAR STRUCTURE OF AMYOTROPHIC LATERAL SCLEROSIS IN RUSSIAN POPULATION

    Directory of Open Access Journals (Sweden)

    N. Yu. Abramycheva

    2016-01-01

    Full Text Available Materials and methods. 285 Russian patients with amyotrophic lateral sclerosis (ALS including 260 patients with a sporadic form and 25 with a familial form were examined for mutations in SOD1, C9orf72, TARDBP,  ANG and other genes and the presence of associations among polymorphic sites in ATXN2 (polyCAG and VEGF (-2578С/А genes.Molecular genetic analysis was performed using direct sequencing, fragment analysis and real-time polymerase chain reaction. On the last stage, rare ALS candidate genes were evaluated using a next generation sequencing (NGS panel.Results. Total rate of the identified mutations in the examined ALS cohort was 9.5 %. The most frequently observed defects were mutations in the SOD1 (24.0 % in familial ALS and 4.6 % in sporadic ALS and C9orf72 (pathological hexanucleotide repeat expansion was identified in 1.8 % cases of ALS, all sporadic genes. The TARDBP gene didn’t contain any mutations, though in the ALS group deletion c.715-126delG located in intron 5 of the TARDBP gene was significantly over-represented – 38.0 % vs. 26.6 % (χ2 = 13.17; р = 0.002. Mutations in the ANG gene were identified in 1.05 % of ALS patients (all cases were sporadic. In 1 (0.35 % sporadic case a G1082A mutation in the DCTN1 gene was identified. The examined group significantly more frequently carried a risk allele of the ATXN2 gene with an “intermediate” (28–33  number of CAG repeats – 5.0 % vs. 1.7 % in the control group (χ2 = 3.89; р = 0.0486. In Russian ALS patients, an association between the disease and the presence of a risk А-allele and homozygote genotype А/А of -2578С/А polymorphism in the VEGF gene was identified (χ2 = 7.14; р = 0.008 and χ2 = 13.46; р = 0.001 for the rates in the ALS population and in the control population, respectively, which is confirmed by the odds ratio.Conclusion. In the current article, molecular structure of ALS in the Russian population was examined, rates of individual genetic forms

  7. Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism.

    Science.gov (United States)

    Welin, Martin; Nordlund, Pär

    2010-05-21

    Interactions are the foundation of life at the molecular level. In the plethora of activities in the cell, the evolution of enzyme specificity requires the balancing of appropriate substrate affinity with a negative selection, in order to minimize interactions with other potential substrates in the cell. To understand the structural basis for enzyme specificity, the comparison of structural and biochemical data between enzymes within pathways using similar substrates and effectors is valuable. Nucleotide metabolism is one of the largest metabolic pathways in the human cell and is of outstanding therapeutic importance since it activates and catabolises nucleoside based anti-proliferative drugs and serves as a direct target for anti-proliferative drugs. In recent years the structural coverage of the enzymes involved in human nucleotide metabolism has been dramatically improved and is approaching completion. An important factor has been the contribution from the Structural Genomics Consortium (SGC) at Karolinska Institutet, which recently has solved 33 novel structures of enzymes and enzyme domains in human nucleotide metabolism pathways and homologs thereof. In this review we will discuss some of the principles for substrate specificity of enzymes in human nucleotide metabolism illustrated by a selected set of enzyme families where a detailed understanding of the structural determinants for specificity is now emerging. 2010. Published by Elsevier Inc.

  8. Understanding specificity in metabolic pathways-Structural biology of human nucleotide metabolism

    International Nuclear Information System (INIS)

    Welin, Martin; Nordlund, Paer

    2010-01-01

    Interactions are the foundation of life at the molecular level. In the plethora of activities in the cell, the evolution of enzyme specificity requires the balancing of appropriate substrate affinity with a negative selection, in order to minimize interactions with other potential substrates in the cell. To understand the structural basis for enzyme specificity, the comparison of structural and biochemical data between enzymes within pathways using similar substrates and effectors is valuable. Nucleotide metabolism is one of the largest metabolic pathways in the human cell and is of outstanding therapeutic importance since it activates and catabolises nucleoside based anti-proliferative drugs and serves as a direct target for anti-proliferative drugs. In recent years the structural coverage of the enzymes involved in human nucleotide metabolism has been dramatically improved and is approaching completion. An important factor has been the contribution from the Structural Genomics Consortium (SGC) at Karolinska Institutet, which recently has solved 33 novel structures of enzymes and enzyme domains in human nucleotide metabolism pathways and homologs thereof. In this review we will discuss some of the principles for substrate specificity of enzymes in human nucleotide metabolism illustrated by a selected set of enzyme families where a detailed understanding of the structural determinants for specificity is now emerging.

  9. Evolution of the population structure of Venturia inaequalis, the apple scab fungus, associated with the domestication of its host.

    Science.gov (United States)

    Gladieux, Pierre; Zhang, Xiu-Guo; Róldan-Ruiz, Isabel; Caffier, Valérie; Leroy, Thibault; Devaux, Martine; Van Glabeke, Sabine; Coart, Els; Le Cam, Bruno

    2010-02-01

    Evaluating the impact of plant domestication on the population structure of the associated pathogens provides an opportunity to increase our understanding of how and why diseases emerge. Here, we investigated the evolution of the population structure of the apple scab fungus Venturia inaequalis in response to the domestication of its host. Inferences were drawn from multilocus microsatellite data obtained from samples collected on (i) the Central Asian Malus sieversii, the main progenitor of apple, (ii) the European crabapple, Malus sylvestris, a secondary progenitor of apple, and (iii) the cultivated apple, Malus x domestica, in orchards from Europe and Central Asia. Using clustering methods, we identified three distinct populations: (i) a large European population on domesticated and wild apples, (ii) a large Central Asian population on domesticated and wild apples in urban and agricultural areas, and (iii) a more geographically restricted population in M. sieversii forests growing in the eastern mountains of Kazakhstan. Unique allele richness and divergence time estimates supported a host-tracking co-evolutionary scenario in which this latter population represents a relict of the ancestral populations from which current populations found in human-managed habitats were derived. Our analyses indicated that the domestication of apple induced a significant change in the genetic differentiation of populations of V. inaequalis in its centre of origin, but had little impact on its population dynamics and mating system. We discuss how the structure of the apple-based agrosystem may have restricted changes in the population structure of the fungus in response to the domestication of its host.

  10. Genetic structure of autochthonous populations of Meso-America: Mexico.

    Science.gov (United States)

    Lisker, R; Ramírez, E; Babinsky, V

    1996-06-01

    We analyze the possible effect of gene flow on the genetic structure of present-day Mexicans. For this purpose we reviewed previous admixture estimates for various Indian and Mestizo groups. Several facts seem clear: (1) There are no pure Indian groups in Mexico, because all Indian groups show variable degrees of admixture, mostly with whites (range, 0.088 in the Huichol to 0.373 in the Huasteco); (2) the main ancestral contribution to the noncoastal lower middle class Mestizo populations is Indian (above 50%) so that from a genetic standpoint Indians and lower middle class Mestizos are not much different; and (3) black ancestry is quite high on the coasts, ranging from 0.127 to 0.405 on the east coast, and is present in other Mestizos, ranging in large urban centers from 0.027 in Oaxaca to 0.107 in Puebla and in smaller cities from 0.08 in Tlaxcala to 0.181 in Cuanalán.

  11. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

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    Suzana Cláudia Silveira Martins

    2016-01-01

    Full Text Available There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation.

  12. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

    2011-01-01

      It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...... experienced a bottleneck resulting from a recent population decline. The significant heterozygote excess observed in the Svalbard sample might be attributed to the low effective population size, which could initiate future population inbreeding effects. This phenomenon has not been reported earlier from other...

  13. Populations of models: A new approach for understanding the mechanisms of atrial fibrillation

    Energy Technology Data Exchange (ETDEWEB)

    Liberos, A.; Bueno-Orovio, A.; Rodrigo, M.; Ravens, U.; Hernandez, I.; Fernandez-Aviles, F.; Guillem, M.S.; Rodriguez, B.; Climent, A.M.

    2016-07-01

    Inter-subject variability explains the diverging effects to pharmacological treatments of AF reported in the literature. A population of 173 mathematical models of remodeled human atrial tissue with realistic inter–subject variability was developed based on action potential recordings of 149 patients diagnosed with AF. The ranges of 6 biomarkers measured from the patchclamp studies were appropriately covered. The resulting population shows that multiple combinations of variations in the ionic conductances result in AF models that cover the range of biomarkers measured experimentally. Introducing restrictions associated with pacing rate limits the number of models, restricts calcium transient amplitudes, and shows significant differences in the distribution of variation of parameters associated with INa, IKr and INaK ionic currents. Populations of models will improve the development of new antiarrhythmic treatments preventing undesired effects associated with differences between individuals. (Author)

  14. Population and demographic structure of Ixodes scapularis Say in the eastern United States.

    Directory of Open Access Journals (Sweden)

    Joyce M Sakamoto

    Full Text Available INTRODUCTION: The most significant vector of tick-borne pathogens in the United States is Ixodes scapularis Say (the blacklegged tick. Previous studies have identified significant genetic, behavioral and morphological differences between northern vs. southern populations of this tick. Because tick-borne pathogens are dependent on their vectors for transmission, a baseline understanding of the vector population structure is crucial to determining the risks and epidemiology of pathogen transmission. METHODS: We investigated population genetic variation of I. scapularis populations in the eastern United States using a multilocus approach. We sequenced and analyzed the mitochondrial COI and 16S genes and three nuclear genes (serpin2, ixoderin B and lysozyme from wild specimens. RESULTS: We identified a deep divergence (3-7% in I. scapularis COI gene sequences from some southern specimens, suggesting we had sampled a different Ixodes species. Analysis of mitochondrial 16S rRNA sequences did not support this hypothesis and indicated that all specimens were I. scapularis. Phylogenetic analysis and analysis of molecular variance (AMOVA supported significant differences between northern vs. southern populations. Demographic analysis suggested that northern populations had experienced a bottleneck/expansion event sometime in the past, possibly associated with Pleistocene glaciation events. CONCLUSIONS: Similar to other studies, our data support the division of northern vs. southern I. scapularis genetic lineages, likely due to differences in the demographic histories between these geographic regions. The deep divergence identified in some COI gene sequences highlights a potential hazard of relying solely on COI for species identification ("barcoding" and population genetics in this important vector arthropod.

  15. The effect of isolation, fragmentation, and population bottlenecks on song structure of a Hawaiian honeycreeper

    Science.gov (United States)

    Pang-Ching, Joshua M.; Paxton, Kristina L.; Paxton, Eben H.; Pack, Adam A.; Hart, Patrick J.

    2018-01-01

    Little is known about how important social behaviors such as song vary within and among populations for any of the endemic Hawaiian honeycreepers. Habitat loss and non‐native diseases (e.g., avian malaria) have resulted in isolation and fragmentation of Hawaiian honeycreepers within primarily high elevation forests. In this study, we examined how isolation of Hawai'i ‘amakihi (Chlorodrepanis virens) populations within a fragmented landscape influences acoustic variability in song. In the last decade, small, isolated populations of disease tolerant ‘amakihi have been found within low elevation forests, allowing us to record ‘amakihi songs across a large elevational gradient (10–1800 m) that parallels disease susceptibility on Hawai'i island. To understand underlying differences among populations, we examined the role of geographic distance, elevation, and habitat structure on acoustic characteristics of ‘amakihi songs. We found that the acoustic characteristics of ‘amakihi songs and song‐type repertoires varied most strongly across an elevational gradient. Differences in ‘amakihi song types were primarily driven by less complex songs (e.g., fewer frequency changes, shorter songs) of individuals recorded at low elevation sites compared to mid and high elevation populations. The reduced complexity of ‘amakihi songs at low elevation sites is most likely shaped by the effects of habitat fragmentation and a disease‐driven population bottleneck associated with avian malaria, and maintained through isolation, localized song learning and sharing, and cultural drift. These results highlight how a non‐native disease through its influence on population demographics may have also indirectly played a role in shaping the acoustic characteristics of a species.

  16. Understanding and meeting the needs of the older population: a global challenge.

    Science.gov (United States)

    Bergman, Howard; Karunananthan, Sathya; Robledo, Luis M G; Brodsky, Jenny; Chan, Piu; Cheung, Maria; Bovet, Pascal

    2013-01-01

    In the past century, there has been a significant rise in life expectancy in almost all regions of the world, contributing to an increasingly older population. The aging of the population, in conjunction with urbanization and industrialization, has resulted in an important epidemiological transition marked by a widespread increase in the prevalence of chronic diseases and their sequelae. Current trends suggest that the transition will have a greater impact on developing countries compared to developed countries. An adequate response to the transition requires a strong emphasis on primary prevention and adequate resource allocation.

  17. UNDERSTANDING AND MANAGING BIODIVERSITY IN RELATION TO NATIVE CRAYFISH POPULATIONS IN EUROPE

    Directory of Open Access Journals (Sweden)

    GHERARDI F.

    2003-04-01

    Full Text Available The loss or diminution of European crayfish populations because of both habitat deterioration and competition with alien crayfish – also responsible for the dissemination of the crayfish plague – would reduce the biodiversity at the species level. The topic “What is meant by biodiversity?” in the context of native freshwater crayfish in Europe was discussed during the Kilkenny CRAYNET meeting in order to make the point about the varied meanings of biodiversity from genes and individuals to population levels.

  18. Understanding the GPCR biased signaling through G protein and arrestin complex structures.

    Science.gov (United States)

    Zhou, X Edward; Melcher, Karsten; Xu, H Eric

    2017-08-01

    G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and are important drug targets for many human diseases. The determination of the 3-D structure of GPCRs and their signaling complexes has promoted our understanding of GPCR biology and provided templates for structure-based drug discovery. In this review, we focus on the recent structure work on GPCR signaling complexes, the β2-adrenoreceptor-Gs and the rhodopsin-arrestin complexes in particular, and highlight the structural features of GPCR complexes involved in G protein- and arrestin-mediated signal transduction. The crystal structures reveal distinct structural mechanisms by which GPCRs recruit a G protein and an arrestin. A comparison of the two complex structures provides insight into the molecular mechanism of functionally selective GPCR signaling, and a structural basis for the discovery of G protein- and arrestin-biased treatments of human diseases related to GPCR signal transduction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Genetic diversity and population structure in the Leishmania guyanensis vector Lutzomyia anduzei (Diptera, Psychodidae) from the Brazilian Amazon.

    Science.gov (United States)

    Scarpassa, Vera Margarete; Figueiredo, Adrya da Silva; Alencar, Ronildo Baiatone

    2015-04-01

    Lutzomyia (Nyssomyia) anduzei has been recognized as a secondary vector of Leishmania guyanensis in the Brazilian Amazon region. Since L. anduzei is anthropophilic, co-exists in areas of high leishmaniasis transmission and has been found infected with L. guyanensis, the understanding of the vector population structure and of the process responsible for it is paramount to the vector management and control efforts. In this study we analyzed 74 and 67 sequences of the COI and Cytb loci, respectively, from mitochondrial DNA, aiming to estimate the intra-population genetic variability and population structure in six L. anduzei samples from the Brazilian Amazon region. For COI, we found 58 haplotypes, low to high (FST=0.0310-0.4128) and significant (P=0.0033) genetic structure, and reduced gene flow among populations. The haplotype network yielded many reticulations that likely resulted from hypervariability in the locus. For Cytb, we observed 27 haplotypes, low to moderate (FST=0.0077-0.1954) and nonsignificant (P>0.05) genetic structure for the majority of comparisons and extensive gene flow among populations, in line with the haplotypes network data. AMOVA analysis indicated that most of the variation occurred within populations (83.41%, 90.94%); nevertheless, there were significant differences (ΦST=0.0906-0.1659; P=0.00098; P=0.00000) among them for both loci. The Mantel test showed that the genetic structure is not associated to an isolation-by-distance (IBD) model in either of both loci. These data suggest that L. anduzei is genetically very diverse. The genetic structure lacking IBD may be due to adaptation to local habitats and the low dispersal capacity of the sandflies, and both could lead to population fragmentation and geographic isolation. These findings have important implications for epidemiology, surveillance and vector control and may be a first step in understanding the evolutionary history of this species. Copyright © 2015 Elsevier B.V. All rights

  20. Towards a general, population-level understanding of eco-evolutionary change

    NARCIS (Netherlands)

    Smallegange, I.M.; Coulson, T.

    2013-01-01

    Most population-level studies of eco-evolutionary dynamics assume that evolutionary change occurs in response to ecological change and vice versa. However, a growing number of papers report simultaneous ecological and evolutionary change, suggesting that the eco-evolutionary consequences of

  1. Determining the drivers of population structure in a highly urbanized landscape to inform conservation planning.

    Science.gov (United States)

    Thomassen, Henri A; Harrigan, Ryan J; Semple Delaney, Kathleen; Riley, Seth P D; Serieys, Laurel E K; Pease, Katherine; Wayne, Robert K; Smith, Thomas B

    2018-02-01

    Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home-range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11-81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions. © 2017 Society for Conservation Biology.

  2. Employment status and health: understanding the health of the economically inactive population in Scotland

    Directory of Open Access Journals (Sweden)

    Brown Judith

    2012-07-01

    Full Text Available Abstract Background Although the association between health and unemployment has been well examined, less attention has been paid to the health of the economically inactive (EI population. Scotland has one of the worst health records compared to any Western European country and the EI population account for 23% of the working age population. The aim of this study is to investigate and compare the health outcomes and behaviours of the employed, unemployed and the EI populations (further subdivided into the permanently sick, looking after home and family [LAHF] and others in Scotland. Methods Using data from the 2003 Scottish Health Survey, the differences in health and health behaviours among the employed, unemployed and the subgroups of the EI population were examined. Results Both low educational attainment and residence in a deprived community were more likely in the permanently sick group. The LAHF and the unemployed showed worse self-reported health and limiting longstanding illness compared to the employed but no significant differences were observed between these groups. The permanently sick group had significantly poorer health outcomes than all the other economic groups. Similar to the unemployed and LAHF they are more likely to smoke than the employed but less likely (along with LAHF and ‘others’ to exhibit heavy alcohol consumption. Interestingly, the LAHF showed better mental health than the rest of the EI group, but a similar mental health status to the unemployed. On the physical health element of lung function, the LAHF were no worse than the employed. Conclusion While on-going health promotion and vocational rehabilitation efforts need to be directed towards all, our data suggests that the EI group is at higher risk and policies and strategies directed at this group may need particular attention.

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

    Science.gov (United States)

    2010-01-01

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

  4. Structural validation of the Self-Compassion Scale with a German general population sample

    NARCIS (Netherlands)

    Coroiu, A.; Kwakkenbos, C.M.C.; Moran, C.; Thombs, B.D.; Albani, C.; Bourkas, S.; Zenger, M.; Brahler, E.; Körner, A.

    2018-01-01

    Background: Published validation studies have reported different factor structures for the Self-Compassion Scale (SCS). The objective of this study was to assess the factor structure of the SCS in a large general population sample representative of the German population. Methods: A German population

  5. The Pathology of structure of explanations in understanding of literary texts

    Directory of Open Access Journals (Sweden)

    Mahyar Alavi Moghaddam

    2011-02-01

    Full Text Available Abstract Traditional and non-scientific classification shade to educational and research Persian literature and literary education and research haven't grown up. The aim of explanation of text is to rub off difficulties and to lead reader to deep understanding. In semantics studies of understanding and interpretation of text, to familiar with the place of meaning in literary tradition and new approaches of criticism, the acceptance of multi meaning in interpretation texts are necessary. The role of interpreter is very important, because he can relate between the world of text and the world of reader and so between semantic horizon of writer and poet and mental horizon.   We can step in analysing interpretation of Hafez' poem and pathology of this area, because of expanding of research about Hafez and his explanations. There are four difficulties in these explanations: structural, semantic, lexical and figural. In this article, we will pay attention to just structural difficulties. These structural difficulties are unversatility system, incomprehensiveness, nonalaystic of explanations, mistake methods in educating and to ignore relation between Hafez's Verses in semantic texture of Ghazal. Certainly, it is necessary to pay scientific, analytic criticism in Hafez's explanations as one of the areas in understanding of his poems.

  6. Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers.

    Directory of Open Access Journals (Sweden)

    Shanmugapriya Arumugasundaram

    Full Text Available Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r(2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r(2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.

  7. Population Structure of Vibrio fischeri within the Light Organs of Euprymna scolopes Squid from Two Oahu (Hawaii) Populations▿ †

    Science.gov (United States)

    Wollenberg, M. S.; Ruby, E. G.

    2009-01-01

    We resolved the intraspecific diversity of Vibrio fischeri, the bioluminescent symbiont of the Hawaiian sepiolid squid Euprymna scolopes, at two previously unexplored morphological and geographical scales. These scales ranged from submillimeter regions within the host light organ to the several kilometers encompassing two host populations around Oahu. To facilitate this effort, we employed both novel and standard genetic and phenotypic assays of light-organ symbiont populations. A V. fischeri-specific fingerprinting method and five phenotypic assays were used to gauge the genetic richness of V. fischeri populations; these methods confirmed that the symbiont population present in each adult host's light organ is polyclonal. Upon statistical analysis of these genetic and phenotypic population data, we concluded that the characteristics of symbiotic populations were more similar within individual host populations than between the two distinct Oahu populations of E. scolopes, providing evidence that local geographic symbiont population structure exists. Finally, to better understand the genesis of symbiont diversity within host light organs, the process of symbiosis initiation in newly hatched juvenile squid was examined both experimentally and by mathematical modeling. We concluded that, after the juvenile hatches, only one or two cells of V. fischeri enter each of six internal epithelium-lined crypts present in the developing light organ. We hypothesize that the expansion of different, crypt-segregated, clonal populations creates the polyclonal adult light-organ population structure observed in this study. The stability of the luminous-bacterium-sepiolid squid mutualism in the presence of a polyclonal symbiont population structure is discussed in the context of contemporary evolutionary theory. PMID:18997024

  8. High spoligotype diversity within a Mycobacterium bovis population: Clues to understanding the demography of the pathogen in Europe

    OpenAIRE

    Rodriguez, Sabrina; Romero, Beatriz; Bezos, Javier; de Juan, Lucia; Alvarez, Julio; Castellanos, Elena; Moya, Nuria; Lozano, Francisco; Gonzalez, Sergio; Luis Saez-Llorente, Jose; Mateos, Ana; Dominguez, Lucas; Aranaz, Alicia

    2010-01-01

    Abstract Mycobacterium bovis is the main causative agent of bovine tuberculosis. This zoonotic disease produces important economic losses and must be considered a threat to endangered animal species and public health. This study was performed (1) to assess the degree of diversity of the Spanish M. bovis isolates and its effect on the epidemiology of the infection, and (2) to understand the connection of M. bovis populations within a European context. In this report we resume the DV...

  9. A CRISPR-based MLST Scheme for Understanding the Population Biology and Epidemiology of Salmonella Enterica

    Science.gov (United States)

    2015-05-26

    N. Shariat, R. E. Timme, J. B. Pettengill, R. Barrangou, E. G. Dudley. Characterization and evolution of Salmonella CRISPR - Cas systems...Barrangou, Edward G. Dudley. Characterization of CRISPR - Cas in Salmonella, 3rd European CRISPR meeting. 14-MAY-14, . : , Margaret K. Kirchner, Nikki... CRISPRs Beyond subtyping approaches, we were motivated to understand the biology of CRISPR - Cas systems in Salmonella. We performed in-depth sequence

  10. Dynamic Analytical Capability to Better Understand and Anticipate Extremist Shifts Within Populations under Authoritarian Regimes.

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, Michael Lewis [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-11-01

    The purpose of this work is to create a generalizable data- and theory-supported capability to better understand and anticipate (with quantifiable uncertainty): 1) how the dynamics of allegiance formations between various groups and society are impacted by active conflict and by third-party interventions and 2) how/why extremist allegiances co-evolve over time due to changing geopolitical, sociocultural, and military conditions.

  11. Microgeographic Population Structuring of Culex quinquefasciatus (Diptera: Culicidae) From São Paulo, Brazil.

    Science.gov (United States)

    Wilke, André Barretto Bruno; de Carvalho, Gabriela Cristina; Marrelli, Mauro Toledo

    2017-11-07

    The continuing worldwide increase in urbanization can potentially have a major impact on the epidemiology of vector-borne diseases, as anthropogenic changes to the environment are known to favor a few species of mosquitoes that can thrive in urban environments. Culex quinquefasciatus Say (Diptera: Culicidae) is found extensively in urban habitats, where it lives in degraded, polluted areas and is often the only species of mosquito capable to surviving under such conditions. Traditional mosquito control strategies no longer have the desired effect due to the several factors such as insecticide resistance, abundance of breeding sites, lack of proper sewage and sanitation, and absence of natural predator, leading Cx. quinquefasciatus populations to increase its numbers in cities. In this study, five Cx. quinquefasciatus populations were analyzed using 12 microsatellite markers to investigate whether the dynamics of these populations are being modulated by urbanization and how they are structured in the city of São Paulo, Brazil. Our results indicate that only one of the study populations (the population from Anhanguera Park) exhibited evidence of expansion. The populations from Ibirapuera Park and Piqueri Park, the most urbanized regions of the areas studied, did not show signs of expansion. A better understanding of the mechanisms involved in the dispersal of Cx. quinquefasciatus and its colonization of new areas, as well as the species' demographic patterns and how these are associated with urbanization, particularly in areas undergoing a rural-to-urban transformation, such as Anhanguera Park, is of great importance for mosquito control. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Ontogenetic niche shifts and flexible behavior in size-structured populations

    NARCIS (Netherlands)

    de Roos, A.M.; Leonardsson, K.; Persson, L.; Mittelbach, G.G.

    2002-01-01

    Flexible behavior has been shown to have substantial affects on population dynamics in unstructured models. We investigate the influence of flexible bahavior on the dynamics of a size-structured population using a physiologically structured modeling approach. Individuals of the size-structured

  13. Toward a Demographic Understanding of Incarceration Disparities: Race, Ethnicity, and Age Structure.

    Science.gov (United States)

    Vogel, Matt; Porter, Lauren C

    2016-01-01

    Non-Hispanic blacks and Hispanics in the United States are more likely to be incarcerated than non-Hispanic whites. The risk of incarceration also varies with age, and there are striking differences in age distributions across racial/ethnic groups. Guided by these trends, the present study examines the extent to which differences in age structure account for incarceration disparities across racial and ethnic groups. We apply two techniques commonly employed in the field of demography, age-standardization and decomposition, to data provided by the Bureau of Justice Statistics and the 2010 decennial census to assess the contribution of age structure to racial and ethnic disparities in incarceration. The non-Hispanic black and Hispanic incarceration rates in 2010 would have been 13-20 % lower if these groups had age structures identical to that of the non-Hispanic white population. Moreover, age structure accounts for 20 % of the Hispanic/white disparity and 8 % of the black/white disparity. The comparison of crude incarceration rates across racial/ethnic groups may not be ideal because these groups boast strikingly different age structures. Since the risk of imprisonment is tied to age, criminologists should consider adjusting for age structure when comparing rates of incarceration across groups.

  14. Multifunctional light escaping architecture inspired by compound eye surface structures: From understanding to experimental demonstration.

    Science.gov (United States)

    Song, Young Min; Park, Gyeong Cheol; Jang, Sung Jun; Ha, Jong Hoon; Yu, Jae Su; Lee, Yong Tak

    2011-03-14

    We present bioinspired artificial compound eye surface structures that consist of antireflective subwavelength structures (SWSs) on hexagonally patterned microstructures (MSs), for the purpose of efficient light escaping inside light-emitting materials/devices. Theoretical understanding and geometrical optimization of SWSs on MSs are described together with rigorous coupled-wave analysis. As a proof of this concept, AlGaInP red light-emitting diodes (LEDs) with SWS/MSs were fabricated, and a light output power enhancement of 72.47% was achieved as compared to that of conventional LEDs. The artificial compound eye structures are not limited to LEDs, and the fabrication process is compatible with most semiconductor device manufacturing processes; hence, this concept opens up new possibilities for improving the optical performance of various optoelectronic device applications.

  15. A Pilot Study Using Mixed GPS/Narrative Interview Methods to Understand Geospatial Behavior in Homeless Populations.

    Science.gov (United States)

    North, Carol S; Wohlford, Sarah E; Dean, Denis J; Black, Melissa; Balfour, Margaret E; Petrovich, James C; Downs, Dana L; Pollio, David E

    2017-08-01

    Tracking the movements of homeless populations presents methodological difficulties, but understanding their movements in space and time is needed to inform optimal placement of services. This pilot study developed, tested, and refined methods to apply global positioning systems (GPS) technology paired with individual narratives to chronicle the movements of homeless populations. Detail of methods development and difficulties encountered and addressed, and geospatial findings are provided. A pilot sample of 29 adults was recruited from a low-demand homeless shelter in the downtown area of Fort Worth, Texas. Pre- and post-deployment interviews provided participant characteristics and planned and retrospectively-reported travels. Only one of the first eight deployments returned with sufficient usable data. Ultimately 19 participants returned the GPS device with >20 h of usable data. Protocol adjustments addressing methodological difficulties achieved 81 % of subsequent participants returning with sufficient usable data. This study established methods and demonstrated feasibility for tracking homeless population travels.

  16. UNDERSTANDING THE STRUCTURE OF THE HOT INTERSTELLAR MEDIUM IN NORMAL EARLY-TYPE GALAXIES.

    Science.gov (United States)

    Traynor, Liam; Kim, Dong-Woo; Chandra Galaxy Atlas

    2018-01-01

    The hot interstellar medium (ISM) of early-type galaxies (ETG's) provides crucial insight into the understanding of their formation and evolution. Mechanisms such as type Ia supernovae heating, AGN feedback, deepening potential depth through dark matter assembly and ramp-pressure stripping are known to affect the structure of the ISM. By using temperature maps and radial temperature profiles of the hot ISM from ~70 ETG's with archival Chandra data, it is possible to classify the galaxy's ISM into common structural types. This is extended by using 3D fitting of the radial temperature profile in order to provide models that further constrain the structural types. Five structural types are present, negative (temperature decreases with radii), positive (temperature increases with radii), hybrid-dip (temperature decreases at small radii and increases at large radii), hybrid-bump (inverse of hybrid-dip) and quasi-isothermal (temperature is constant at all radii). This work will be continued by 1) determining which mechanisms are present in which galaxies and 2) analysing the model parameters between galaxies within each structural type to determine whether each type can be described by a single set of model parameters, indicating that the same physical processes are responsible for creating that structural type.

  17. Understanding human thiol dioxygenase enzymes: structure to function, and biology to pathology.

    Science.gov (United States)

    Sarkar, Bibekananda; Kulharia, Mahesh; Mantha, Anil K

    2017-04-01

    Amino acid metabolism is a significant metabolic activity in humans, especially of sulphur-containing amino acids, methionine and cysteine (Cys). Cys is cytotoxic and neurotoxic in nature; hence, mammalian cells maintain a constant intracellular level of Cys. Metabolism of Cys is mainly regulated by two thiol dioxygenases: cysteine dioxygenase (CDO) and 2-aminoethanethiol dioxygenase (ADO). CDO and ADO are the only human thiol dioxygenases reported with a role in Cys metabolism and localized to mitochondria. This metabolic pathway is important in various human disorders, as it is responsible for the synthesis of antioxidant glutathione and is also for the synthesis of hypotaurine and taurine. CDO is the most extensively studied protein, whose high-resolution crystallographic structures have been solved. As compared to CDO, ADO is less studied, even though it has a key role in cysteamine metabolism. To further understand ADO's structure and function, the three-dimensional structures have been predicted from I-TASSER and SWISS-MODEL servers and validated with PROCHECK software. Structural superimposition approach using iPBA web server further confirmed near-identical structures (including active sites) for the predicted protein models of ADO as compared to CDO. In addition, protein-protein interaction and their association in patho-physiology are crucial in understanding protein functions. Both ADO and CDO interacting partner profiles have been presented using STRING database. In this study, we have predicted a 3D model structure for ADO and summarized the biological roles and the pathological consequences which are associated with the altered expression and functioning of ADO and CDO in case of cancer, neurodegenerative disorders and other human diseases. © 2017 The Authors. International Journal of Experimental Pathology © 2017 International Journal of Experimental Pathology.

  18. Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (Rangifer tarandus) in China.

    Science.gov (United States)

    Ju, Yan; Liu, Huamiao; Rong, Min; Zhang, Ranran; Dong, Yimeng; Zhou, Yongna; Xing, Xiumei

    2018-04-16

    Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal K and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.

  19. Genetic diversity and population structure of Anastrepha striata (Diptera: Tephritidae) in three natural regions of southwestern Colombia using mitochondrial sequences.

    Science.gov (United States)

    Gallo-Franco, Jenny Johana; Velasco-Cuervo, Sandra Marcela; Aguirre-Ramirez, Elkin; González Obando, Ranulfo; Carrejo, Nancy Soraya; Toro-Perea, Nelson

    2017-02-01

    Anastrepha striata is widely distributed across the Americas and is a pest of economically important crops, especially crops of the Myrtaceae family. Insect population structures can be influenced by the presence of physical barriers or characteristics associated with habitat differences. This study evaluated the effect of the Western Andes on the population structure of A. striata. Individuals were collected from Psidium guajava fruits from three natural regions of southwestern Colombia (Pacific Coast, mountainous region and the inter-Andean valley of the Cauca River). Based on a 1318 bp concatenated of the genes Cytochrome Oxidase subunit I (COI) and NADH dehydrogenase subunit 6 (ND6), 14 haplotypes with few changes among them (between 1 and 3) were found. There was only one dominant haplotype in all three regions. No genetic structure associated with the three eco-geographical regions of the study was found. Moreover, the Western Andes are not an effective barrier for the genetic isolation of the populations from the Pacific Coast compared with the inter-Andean valley populations. This genetic homogeneity could be partially due to anthropogenic intervention, which acts as a dispersal agent of infested fruits. Another hypothesis to explain the lack of structure would be the relatively recent arrival of A. striata to the region, as indicated by an analysis of the demographic history, which reveals a process of population expansion. This study represents the first attempt to understand the population genetics of A. striata in Colombia and could contribute to the integral management of this pest.

  20. Population genetic structure of the sidespot barb, Barbus neefi, from ...

    African Journals Online (AJOL)

    Allozyme analysis was used to determine patterns of genetic variation within and between populations of Barbus neefi. The products of 29 loci were analysed, with 17 loci being monomorphic in all populations. The genetic variability estimates compared well with values reported in the literature. The percentage of ...

  1. Understanding the GOLD 2011 Strategy as applied to a real-world COPD population

    DEFF Research Database (Denmark)

    Vestbo, J.; Vogelmeier, C.; Small, M.

    2014-01-01

    Study objectives: The aim of this analysis was to understand the implications of the GOLD 2011 multidimensional system for the assessment and management of COPD, using data from a real-world observational study. Methods: Data were drawn from the Adelphi Respiratory Disease Specific Programme...... burden, increased airflow limitation and exacerbation, and further illustrated the importance of including exacerbation history in the assessment of COPD to identify patients at high risk. As based on data from current clinical practice, this study also highlighted the frequent and potentially...

  2. Effect of selection on green pea hybrid population structure

    Directory of Open Access Journals (Sweden)

    В. М. Стригун

    2013-05-01

    Full Text Available The article features the results of variability study for one of the productivity characteristics in green pea, namely «number of seeds in the seedpod» for hybrid  populations and for the selections made thereof. Statistical methods of analysis have established the levels of variability for the characteristics in F2 original population , the impact of the selection completed within F2 onto the variability of F3 hybrid population. This shows the efficiency of repeated selection from F3 population and its impact onto the level of expersiioon of the characteristic being studied in the resulting F6 population. As a conclusion, a good time is set for practical breeding with the characteristic of «number of seeds in a seedpod» for  the selection, as well as for the methods for achieving its stable expression, that is to facilitate the decrease of durations and means for the tests conduct.

  3. Genetic Diversity and Structure of Domestic Cavy (Cavia Porcellus) Populations From Smallholder Farms in Southern Cameroon

    OpenAIRE

    Ayagirwe, Basengere; Meutchieye, Felix; Djikeng, Appolinaire; Skilton, Robert; Osama, Sarah; Manjeli, Yacouba

    2017-01-01

    Although domestic cavies are widely used in sub-Saharan Africa as a source of meat and income, there are only a few studies of their population structure and genetic relatedness. This seminal study was designed with the main objective to assess the genetic diversity and determine the population structure of cavy populations from Cameroon to guide the development of a cavy improvement program. Sixteen microsatellite markers were used to genotype 109 individuals from five cavy populations (Wour...

  4. Geographic structure of Plasmodium vivax: microsatellite analysis of parasite populations from Sri Lanka, Myanmar, and Ethiopia

    DEFF Research Database (Denmark)

    Gunawardena, Sharmini; Karunaweera, Nadira D; Ferreira, Marcelo U

    2010-01-01

    Genetic diversity and population structure of Plasmodium vivax parasites can predict the origin and spread of novel variants within a population enabling population specific malaria control measures. We analyzed the genetic diversity and population structure of 425 P. vivax isolates from Sri Lanka.......8610 in Sri Lanka. Significant linkage disequilibrium was maintained. Population structure showed two clusters (Asian and African) according to geography and ancestry. Strong clustering of outbreak isolates from Sri Lanka and Ethiopia was observed. Predictive power of ancestry using two-thirds of the isolates...

  5. Establishing the solubility and local structure(s) of Amorphous Calcium Carbonate (ACC): Toward an understanding of invertebrate biomineralization

    Science.gov (United States)

    Mergelsberg, S. T.; Ulrich, R. N.; Michel, F. M.; Dove, P. M.

    2017-12-01

    Recent advances in high-resolution imaging show the widespreadd occurrence of multistep pathways to mineralization in biological and geological settings (De Yoreo et al., 2015, Science). For example, carbonate biomineralization often involves precipitation of amorphous calcium carbonate (ACC) as a reactive intermediate that subsequently transforms to crystalline products with diverse structures. Although current carbonate mineral proxies are based upon the composition of final crystalline products, the final signatures may be recording the properties of the initial amorphous phase. Thus, it is critical to establish the physical properties of ACC and understand the factors that influence its evolution to final products at conditions that approximate biological environments. This disconnect limits our ability to build a process-based understanding of when/how minor and trace elements are recorded in mineral composition proxies. In this experimental study, we quantified the chemical and physical properties of ACC and its evolution to final products. We first determined ACC solubility under controlled chemical conditions using a new type of flow-through reactor developed by our research group (Blue and Dove, 2015, GCA; Blue et al., 2017, GCA). The experimental design varied Mg concentration and total alkalinity while maintaining a mild pH that approximates biological environments. ACC solubility was measured at specific time points during the precipitation (from super- and undersaturated conditions) and during its subsequent evolution. Parallel experiments characterized the structure of the corresponding amorphous products using in situ pair distribution function (PDF) and small-angle x-ray scattering (SAXS) analyses. The measurements demonstrate at least two types of ACC can be produced by tuning Mg concentration and alkalinity. Each "phase" exhibits distinct short-range ordering that demonstrates structure-specific solubility. We also find temporal changes in the

  6. Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis

    Directory of Open Access Journals (Sweden)

    Kittlein Marcelo J

    2010-01-01

    Full Text Available Abstract Background The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation. In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales. Results Our results show that dispersal in C. australis is not restricted at regional spatial scales (~ 4 km. Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females. Conclusions Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (~ 4 km and small (less than 1 km spatial scales despite apparently

  7. Understanding barotrauma in fish passing hydro structures: a global strategy for sustainable development of water resources

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Richard S.; Colotelo, Alison HA; Pflugrath, Brett D.; Boys, Craig A.; Baumgartner, Lee J.; Deng, Zhiqun; Silva, Luiz G.; Brauner, Colin J.; Mallen-Cooper, Martin; Phonekhampeng, Oudom; Thorncraft, Garry; Singhanouvong, Douangkham

    2014-03-24

    Freshwater fishes are one of the most imperiled groups of vertebrates and species declines have been linked to a number of anthropogenic influences. This is alarming as the diversity and stability of populations are at risk. In addition, freshwater fish serve as important protein sources, particularly in developing countries. One of the focal activities thought to influence freshwater fish population declines is water resource development, which is anticipated to increase over the next several decades. For fish encountering hydro structures, such as passing through hydroturbines, there may be a rapid decrease in pressure which can lead to injuries commonly referred to as barotraumas. The authors summarize the research to date that has examined the effects of rapid pressure changes on fish and outline the most important factors to consider (i.e., swim bladder morphology, depth of acclimation, migration pattern and life stage) when examining the susceptibility of barotraumas for fish of interest.

  8. Understanding the regulation of coding and noncoding transcription in cell populations.

    Science.gov (United States)

    Beilharz, Traude Helene

    2016-05-01

    Whole transcriptome analyses have unveiled the uncomfortable truth that we know less about how transcription is regulated then we thought. In addition to its role in classic promoter-driven transcription of coding RNA, it is now clear that RNA Pol II also drives abundant expression of noncoding RNA. For the majority of this the functional significance remains unclear. Moreover, its regulation and impact are hard to predict because it often proceeds in unexpected ways from cryptic promoters, including by driving convergent antisense transcription from within 3' UTRs. This review suggests that its time to rethink how we envisage gene expression by inclusion of the regulatory architecture of the full genetic locus, and expanding our thinking to encompass the fact that we generally study cells within heterogeneous populations.

  9. Towards a better understanding of biomarker response in field survey: a case study in eight populations of zebra mussels.

    Science.gov (United States)

    Pain-Devin, S; Cossu-Leguille, C; Geffard, A; Giambérini, L; Jouenne, T; Minguez, L; Naudin, B; Parant, M; Rodius, F; Rousselle, P; Tarnowska, K; Daguin-Thiébaut, C; Viard, F; Devin, S

    2014-10-01

    In order to provide reliable information about responsiveness of biomarkers during environmental monitoring, there is a need to improve the understanding of inter-population differences. The present study focused on eight populations of zebra mussels and aimed to describe how variable are biomarkers in different sampling locations. Biomarkers were investigated and summarised through the Integrated Biomarker Response (IBR index). Inter-site differences in IBR index were analysed through comparisons with morphological data, proteomic profiles and genetic background of the studied populations. We found that the IBR index was a good tool to inform about the status of sites. It revealed higher stress in more polluted sites than in cleaner ones. It was neither correlated to proteomic profiles nor to genetic background, suggesting a stronger influence of environment than genes. Meanwhile, morphological traits were related to both environment and genetic background influence. Together these results attest the benefit of using biological tools to better illustrate the status of a population and highlight the need of consider inter-population difference in their baselines. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    Science.gov (United States)

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

  11. Genetic diversity and genetic structure of the Siberian roe deer (Capreolus pygargus) populations from Asia.

    Science.gov (United States)

    Lee, Yun Sun; Markov, Nickolay; Voloshina, Inna; Argunov, Alexander; Bayarlkhagva, Damdingiin; Oh, Jang Geun; Park, Yong-Su; Min, Mi-Sook; Lee, Hang; Kim, Kyung Seok

    2015-08-18

    The roe deer, Capreolus sp., is one of the most widespread meso-mammals of Palearctic distribution, and includes two species, the European roe deer, C. capreolus inhabiting mainly Europe, and the Siberian roe deer, C. pygargus, distributed throughout continental Asia. Although there are a number of genetic studies concerning European roe deer, the Siberian roe deer has been studied less, and none of these studies use microsatellite markers. Natural processes have led to genetic structuring in wild populations. To understand how these factors have affected genetic structure and connectivity of Siberian roe deer, we investigated variability at 12 microsatellite loci for Siberian roe deer from ten localities in Asia. Moderate levels of genetic diversity (H(E) = 0.522 to 0.628) were found in all populations except in Jeju Island, South Korea, where the diversity was lowest (H(E) = 0.386). Western populations showed relatively low genetic diversity and higher degrees of genetic differentiation compared with eastern populations (mean Ar = 3.54 (east), 2.81 (west), mean F(ST) = 0.122). Bayesian-based clustering analysis revealed the existence of three genetically distinct groups (clusters) for Siberian roe deer, which comprise of the Southeastern group (Mainland Korea, Russian Far East, Trans-Baikal region and Northern part of Mongolia), Northwestern group (Western Siberia and Ural in Russia) and Jeju Island population. Genetic analyses including AMOVA (F(RT) = 0.200), Barrier and PCA also supported genetic differentiation among regions separated primarily by major mountain ridges, suggesting that mountains played a role in the genetic differentiation of Siberian roe deer. On the other hand, genetic evidence also suggests an ongoing migration that may facilitate genetic admixture at the border areas between two groups. Our results reveal an apparent pattern of genetic differentiation among populations inhabiting Asia, showing moderate levels of genetic diversity with an

  12. From patterns to causal understanding: Structural equation modeling (SEM) in soil ecology

    Science.gov (United States)

    Eisenhauer, Nico; Powell, Jeff R; Grace, James B.; Bowker, Matthew A.

    2015-01-01

    In this perspectives paper we highlight a heretofore underused statistical method in soil ecological research, structural equation modeling (SEM). SEM is commonly used in the general ecological literature to develop causal understanding from observational data, but has been more slowly adopted by soil ecologists. We provide some basic information on the many advantages and possibilities associated with using SEM and provide some examples of how SEM can be used by soil ecologists to shift focus from describing patterns to developing causal understanding and inspiring new types of experimental tests. SEM is a promising tool to aid the growth of soil ecology as a discipline, particularly by supporting research that is increasingly hypothesis-driven and interdisciplinary, thus shining light into the black box of interactions belowground.

  13. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    . Aerva tomentosa,. Coccinia grandis,. Cenchrus ciliaris and Panicum turgidum. Figure 1. Map showing the locations of six analyzed populations of C. decidua in. Saudi Arabia: Khor Assos, Raudhat Khuraim, Hawayer Assos, ...

  14. Genetic structure of populations of Mugil cephalus using RAPD ...

    African Journals Online (AJOL)

    , Andhra Pradesh and Tamil Nadu in India was studied using randomly amplified polymorphic DNA (RAPD) markers. Five selective primers provided distinct and consistent RAPD profiles in all the four populations. The bands in the range 400 ...

  15. DEMOGRAPHY AND SPATIAL POPULATION STRUCTURE IN CALIFORNIA TIGER SALAMANDER

    Science.gov (United States)

    Although the causes of many amphibian declines remain mysterious, there is general agreement that human habitat alteration represents the greatest threat to amphibian populations. In January 2000 the US Fish and Wildlife Service proposed listing Santa Barbara County California Ti...

  16. Similar levels of diversity and population Structure in superflock and ...

    African Journals Online (AJOL)

    superflock cichlid fishes from Lake Victoria, Africa. ... Tropical Freshwater Biology ... We use DNA microsatellite loci to estimate neutral genetic diversity and the level of gene flow among populations of two cichlid species from southern Lake Victoria, ...

  17. Influence of mouth status on population structure of southern African ...

    African Journals Online (AJOL)

    Two species, Gilchristella aestuaria and Glossogobius callidus, displayed normally distributed populations throughout, with recruitment/abundance peaks between spring and autumn, and were unaffected by open mouth and extended marine connection conditions. Atherina breviceps, however, displayed multiple modal ...

  18. Ecology and Population Structure of Vibrionaceae in the Coastal Ocean

    Science.gov (United States)

    2010-02-01

    populations. The members of the Vibrio genus were used as a model system because they are an important part of the bacterioplankton community and extensive...Polz, M.F. (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton . Science, 320, 1081-1085. Huq, A...Sarma-Rupavtarm, R., Distel, D.L., & Polz, M.F. (2005) Genotypic diversity within a natural coastal bacterioplankton population. Science, 307, 1311

  19. [Age estimation and age structure of Cycas fairylakea population in Shenzhen City].

    Science.gov (United States)

    Wang, Dian-Pei; Ji, Shu-Yi; Chen, Fei-Peng; Peng, Shao-Lin

    2007-03-01

    Based on the structural characteristics of Cycas trunk, including vegetative leaf base scars, sporophyll concave rings, and average occurrence probabilities of vegetative leaf and sporophyll, a method for the age estimation of Cycas fairylakea population was developed, and the age of each individual was calculated. Three approaches, i.e., age structure diagram, age distribution curve and curve estimation were used to study the age structure of C. fairylakea population at genet and clone population levels. The age structure diagram showed that the clone population of C. fairylakea was stable, but the genet population was in declining. However, both of the clone and genet populations were in declining when using the other two approaches. It was considered that the C. fairylakea population was in declining, and needed an urgent protection.

  20. Escherichia coli Population Structure and Antibiotic Resistance at a Buffalo/Cattle Interface in Southern Africa.

    Science.gov (United States)

    Mercat, Mathilde; Clermont, Olivier; Massot, Méril; Ruppe, Etienne; de Garine-Wichatitsky, Michel; Miguel, Eve; Valls Fox, Hugo; Cornelis, Daniel; Andremont, Antoine; Denamur, Erick; Caron, Alexandre

    2015-12-28

    At a human/livestock/wildlife interface, Escherichia coli populations were used to assess the risk of bacterial and antibiotic resistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibiotic resistance of E. coli commensal populations and the resistant Enterobacteriaceae carriage of sympatric African buffalo (Syncerus caffer caffer) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results (i) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, dominated by B1 (44.5%) and E (29.0%) phylogroups, with some variability in A phylogroup presence (from 1.9 to 12%); (ii) identified a significant gradient of antibiotic resistance from isolated buffalo to buffalo in contact with cattle and cattle populations expressed as the Murray score among Enterobacteriaceae (0.146, 0.258, and 0.340, respectively) and as the presence of tetracycline-, trimethoprim-, and amoxicillin-resistant subdominant E. coli strains (0, 5.7, and 38%, respectively); (iii) evidenced the dissemination of tetracycline, trimethoprim, and amoxicillin resistance genes (tet, dfrA, and blaTEM-1) in 26 isolated subdominant E. coli strains between nearby buffalo and cattle populations, that led us (iv) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and toward wildlife. The study of antibiotic resistance dissemination in multihost systems and at anthropized/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using E. coli as a tool for the identification of pathogen transmission pathway in multihost systems. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  1. Genetic diversity and population structure of Lantana camara in India indicates multiple introductions and gene flow.

    Science.gov (United States)

    Ray, A; Quader, S

    2014-05-01

    Lantana camara is a highly invasive plant, which has spread over 60 countries and island groups of Asia, Africa and Australia. In India, it was introduced in the early nineteenth century, since when it has expanded and gradually established itself in almost every available ecosystem. We investigated the genetic diversity and population structure of this plant in India in order to understand its introduction, subsequent range expansion and gene flow. A total of 179 individuals were sequenced at three chloroplast loci and 218 individuals were genotyped for six nuclear microsatellites. Both chloroplasts (nine haplotypes) and microsatellites (83 alleles) showed high genetic diversity. Besides, each type of marker confirmed the presence of private polymorphism. We uncovered low to medium population structure in both markers, and found a faint signal of isolation by distance with microsatellites. Bayesian clustering analyses revealed multiple divergent genetic clusters. Taken together, these findings (i.e. high genetic diversity with private alleles and multiple genetic clusters) suggest that Lantana was introduced multiple times and gradually underwent spatial expansion with recurrent gene flow. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  2. Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure.

    Science.gov (United States)

    Albaina, A; Iriondo, M; Velado, I; Laconcha, U; Zarraonaindia, I; Arrizabalaga, H; Pardo, M A; Lutcavage, M; Grant, W S; Estonba, A

    2013-12-01

    The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST  = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.

  3. Population structure, behavior, and current threats to the sarus crane (Grus antigone antigone in Nepal

    Directory of Open Access Journals (Sweden)

    Kamal Raj Gosai

    2016-09-01

    Full Text Available The sarus crane (Grus antigone antigone is listed as “vulnerable” in the International Union for Conservation of Nature (IUCN Red List of Threatened Species. Sarus cranes are distributed in the lowlands, but most live outside protected areas, especially in agricultural areas and wetlands of Nepal. The continuous expansion of agricultural land and the reduction of wetland habitats pose the greatest threats to the conservation of the species. We studied the sarus crane in the Rupandehi District of Nepal to understand their population structure, behavior, and current threats. We used the line (i.e., road transect method from August 2013 to February 2014. The study area contained 147 sarus cranes. Agricultural land and wetland areas contained the highest number of sarus cranes. Our analysis showed that the population of sarus crane in the area has declined since 2007. Most sarus cranes lived in pairs. A single flock contained 13 cranes at maximum. Sarus crane behavior was not significantly different before and after the breeding seasons. Human–sarus crane conflict began when cranes started utilizing agricultural areas. The main threats to the hatching success and survival of sarus cranes in the Rupendehi District are egg theft and the hunting of cranes for meat. The findings of this study establish baseline information on the overall conservation status, habitat availability, and ecological behavior of sarus cranes in the district. We propose regular surveys to monitor sarus crane population levels in the face of multiple anthropogenic threats to their survival.

  4. Structure and dynamics of silver fir (Abies alba Mill. population in forest communities of the Świętokrzyski National Park. I. The population structure

    Directory of Open Access Journals (Sweden)

    Maria Mazur

    2014-01-01

    Full Text Available The paper presents the spatial, age and size structures of individuals in silver fir population. The studies were conducted in fir forest and Carpathian beechwood. It was found that fir trees were distributed randomly, whereas seedlings, new growth and up-growth had clumped distribution. The growth and development of individuals in aggregations and outside them were analysed. The stress was put on the impact of spatial structure on the process of population regeneration. Age pyramid was flat with its base very wide. About 40% of trees in the population were dead.

  5. Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus

    OpenAIRE

    Mariette, Stéphanie; Tavaud, Muriel; Arunyawat, Uraiwan; Capdeville, Gaëlle; Millan, Muriel; Salin, Franck

    2010-01-01

    Abstract Background Domestication and breeding involve the selection of particular phenotypes, limiting the genomic diversity of the population and creating a bottleneck. These effects can be precisely estimated when the location of domestication is established. Few analyses have focused on understanding the genetic consequences of domestication and breeding in fruit trees. In this study, we aimed to analyse genetic structure and changes in the diversity in sweet cherry Prunus avium L. Result...

  6. A perfect storm: the combined effects on population fluctuations of autocorrelated environmental noise, age structure, and density dependence.

    Science.gov (United States)

    Wilmers, Christopher C; Post, Eric; Hastings, Alan

    2007-05-01

    While it is widely appreciated that climate can affect the population dynamics of various species, a mechanistic understanding of how climate interacts with life-history traits to influence population fluctuations requires development. Here we build a general density-dependent age-structured model that accounts for differential responses in life-history traits to increasing population density. We show that as the temporal frequency of favorable environmental conditions increases, population fluctuations also increase provided that unfavorable environmental conditions still occur. As good years accumulate and the number of individuals in a population increases, successive life-history traits become vulnerable to density dependence once a return to unfavorable conditions prevails. The stronger this ratcheting of density dependence in life-history traits by autocorrelated climatic conditions, the larger the population fluctuations become. Highly fecund species, and those in which density dependence occurs in juvenile and adult vital rates at similar densities, are most sensitive to increases in the frequency of favorable conditions. Understanding the influence of global warming on temporal correlation in regional environmental conditions will be important in identifying those species liable to exhibit increased population fluctuations that could lead to their extinction.

  7. Understanding the structural drivers governing glass-water interactions in borosilicate based model bioactive glasses.

    Science.gov (United States)

    Stone-Weiss, Nicholas; Pierce, Eric M; Youngman, Randall E; Gulbiten, Ozgur; Smith, Nicholas J; Du, Jincheng; Goel, Ashutosh

    2018-01-01

    The past decade has witnessed a significant upsurge in the development of borate and borosilicate based resorbable bioactive glasses owing to their faster degradation rate in comparison to their silicate counterparts. However, due to our lack of understanding about the fundamental science governing the aqueous corrosion of these glasses, most of the borate/borosilicate based bioactive glasses reported in the literature have been designed by "trial-and-error" approach. With an ever-increasing demand for their application in treating a broad spectrum of non-skeletal health problems, it is becoming increasingly difficult to design advanced glass formulations using the same conventional approach. Therefore, a paradigm shift from the "trial-and-error" approach to "materials-by-design" approach is required to develop new-generations of bioactive glasses with controlled release of functional ions tailored for specific patients and disease states, whereby material functions and properties can be predicted from first principles. Realizing this goal, however, requires a thorough understanding of the complex sequence of reactions that control the dissolution kinetics of bioactive glasses and the structural drivers that govern them. While there is a considerable amount of literature published on chemical dissolution behavior and apatite-forming ability of potentially bioactive glasses, the majority of this literature has been produced on silicate glass chemistries using different experimental and measurement protocols. It follows that inter-comparison of different datasets reveals inconsistencies between experimental groups. There are also some major experimental challenges or choices that need to be carefully navigated to unearth the mechanisms governing the chemical degradation behavior and kinetics of boron-containing bioactive glasses, and to accurately determine the composition-structure-property relationships. In order to address these challenges, a simplified

  8. Understanding the Global Structure and Evolution of Coronal Mass Ejections in the Solar Wind

    Science.gov (United States)

    Riley, Pete

    2004-01-01

    This report summarizes the technical progress made during the first six months of the second year of the NASA Living with a Star program contract Understanding the global structure and evolution of coronal mass ejections in the solar wind, between NASA and Science Applications International Corporation, and covers the period November 18, 2003 - May 17,2004. Under this contract SAIC has conducted numerical and data analysis related to fundamental issues concerning the origin, intrinsic properties, global structure, and evolution of coronal mass ejections in the solar wind. During this working period we have focused on a quantitative assessment of 5 flux rope fitting techniques. In the following sections we summarize the main aspects of this work and our proposed investigation plan for the next reporting period. Thus far, our investigation has resulted in 6 refereed scientific publications and we have presented the results at a number of scientific meetings and workshops.

  9. A Study to Understand the Potential Vulnerabilities to the Foundations of Historic Structures in Coastal Areas

    Science.gov (United States)

    Hall, C. L.; Curran, B.; Jefferson, M.; Routhier, M.; Mulukutla, G. K.

    2011-12-01

    Sea level rise, one of the most important manifestations of climate change is expected to result in increased coastal erosion and storm surge flooding. This work reports on a project undertaken to assess the vulnerability of foundations of historic structures in coastal areas to the potential consequences from climate change resulting from increased storm surge flooding. Foundations of historic buildings are especially vulnerable to the seepage and ground water intrusion. Many historic structures themselves are used to house valuable historic collections making it all the important to preserve and protect these structures. Data collected from a field subsurface geophysical survey, geospatial field survey, and a simulation to understand the hydrological conditions of the site useful to build an understanding of threats to foundations of historic structures located on the coast. The study site chosen for this project is the Strawbery Banke Living History Museum, in Portsmouth, NH. Located very close to the banks of the Piscataqua River at its meeting point with the Atlantic Ocean, it consists of many buildings of historical importance dating as far back as 1690. Upstream of the river is the tidal estuary system, the Great Bay which itself is formed by a confluence of seven major rivers, making it a highly dynamic, tide-dominated body of fresh and saltwater. Strawbery Banke is representative of historic structures, located on the Northeastern coast of the US, that will likely be impacted by climate change. The primary threat to the sub-structures for the site is Puddle Dock; a tidal inlet , that lies at the heart of the facility, that once provided direct river access to Strawbery Banke (and since filled around 1900). Results from the long term deployment of in -situ water level loggers in test wells, temperature and relative humidity sensors, and a ground penetration radar survey of the Puddle Dock, along with the detailed fine-scale elevation survey of the site

  10. Understanding the structure of Exmoor's peatland ecosystems using laser-scanning technologies

    Science.gov (United States)

    Luscombe, D. J.; Anderson, K.; Wetherelt, A.; Grand-Clement, E.; Le-Feuvre, N.; Smith, D.; Brazier, R. E.

    2012-04-01

    Upland blanket peatlands in the UK are of high conservation value and in an intact state, provide important landscape services, such as carbon sequestration and flood attenuation. The drainage of many such wetlands for agricultural reclamation has resulted in changes to upland blanket mire topography, ecology, hydrological processes and carbon fluxes. There is a need for spatially explicit monitoring approaches at peatland sites in the UK as although there has been a national effort to restore drained peat uplands, baseline and post restoration monitoring of changes to ecosystem structure and function is largely absent. Climate change policy and the emerging carbon markets also necessitate the need for enhanced system understanding to inform carbon targets and understand the impacts of restoration. Exmoor is the focus of this research because many areas of upland peat have, in the past, been extensively drained through government "moorland reclamation" programs. A large restoration project funded by South West Water is currently underway in association with Exmoor National Park, The Environment Agency and Natural England. Exmoor also provides an analogue for other westerly peatlands in the British Isles in terms of its climate, ecology and drainage characteristics. Our approach employed airborne LiDAR data gathered by the Environment Agency Geomatics Group coupled with Terrestrial Laser Scanning (TLS) surveys. LiDAR data were processed to produce digital surface models (DSM) of the peatland surface at a 0.5m resolution. These data were further interrogated to separate vegetation structures and geomorphic features such as man-made drainage channels which have damaged the peatland. Over small extents the LiDAR derived DSM surface was then compared to a TLS derived DSM to examine the ability of these models to describe fine scale vegetation and geomorphic structure, which could then be extrapolated to larger spatial extents. Exploration of the data has shown that

  11. Population structure of the Southeast Asian river catfish Mystus nemurus.

    Science.gov (United States)

    Usmani, S; Tan, S G; Siraj, S S; Yusoff, K

    2003-12-01

    A total of 143 microsatellites were isolated from Mystus nemurus using a 5' anchored polymerase chain reaction technique or the random amplified hybridization microsatellite method, the first set of microsatellite markers developed for the Southeast Asian river catfish. Twenty polymorphic microsatellite loci were used as markers for population characterization of M. nemurus from six different geographical locations in Malaysia (Perak, Kedah, Johor, UPM, Sarawak and Terengganu). The number of alleles per locus ranged from 2 to 11 with 6.3 as the average number of alleles per locus. Characterization of the populations showed relatively high levels of genetic variation compared with previous studies using allozyme markers. The highest genetic similarity was found between Perak and Kedah, while the highest genetic distance was found between Terengganu and Kedah. The majority of clustering was in accordance with geographical locations and the histories of the populations. Microsatellite analysis indicated that the Sarawak population might be genetically closer to the Peninsular Malaysian populations than has been previously shown by other molecular marker studies.

  12. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Directory of Open Access Journals (Sweden)

    Sajjad Ahmad

    2015-06-01

    Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  13. Mini-review: Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance

    Directory of Open Access Journals (Sweden)

    Mi Li

    2016-11-01

    Full Text Available Lignin, a complex aromatic polymer in terrestrial plants, contributes significantly to biomass recalcitrance to microbial and/or enzymatic deconstruction. To reduce biomass recalcitrance, substantial endeavors have been exerted on pretreatment and lignin engineering in the past few decades. Lignin removal and/or alteration of lignin structure have been shown to result in reduced biomass recalcitrance with improved cell wall digestibility. While high lignin content is usually a barrier to a cost-efficient application of bioresource to biofuels, the direct correlation of lignin structure and its concomitant properties with biomass remains unclear due to the complexity of cell wall and lignin structure. Advancement in application of biorefinery to production of biofuels, chemicals, and biomaterials necessitates a fundamental understanding of the relationship of lignin structure and biomass recalcitrance. In this mini-review, we focus on recent investigations on the influence of lignin chemical properties on bioprocessability— pretreatment and enzymatic hydrolysis of biomass. Specifically, lignin-enzyme interaction and the effects of lignin compositional units, hydroxycinnamates, and lignin functional groups on biomass recalcitrance have been highlighted, which will be useful not only in addressing biomass recalcitrance but also in deploying renewable lignocelluloses efficiently.

  14. Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

    Science.gov (United States)

    Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto

    2010-01-01

    Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643

  15. Household structure vs. composition: Understanding gendered effects on educational progress in rural South Africa

    Directory of Open Access Journals (Sweden)

    Sangeetha Madhavan

    2017-12-01

    Full Text Available Background: Demographers have long been interested in the relationship between living arrangements and gendered outcomes for children in sub-Saharan Africa. Most research conflates household structure with composition and has revealed little about the pathways that link these components to gendered outcomes. Objective: We offer a conceptual approach that differentiates structure from composition with a focus on gendered processes that operate in the household in rural South Africa. Methods: We use data from the 2002 round of the Agincourt Health and Socio-Demographic Surveillance System. Our analytical sample includes 22,997 children aged 6‒18 who were neither parents themselves nor lived with a partner or partner's family. We employ ordinary least squares regression models to examine the effects of structure and composition on educational progress of girls and boys. Results: Non-nuclear structures are associated with similar negative effects for both boys and girls compared to children growing up in nuclear households. However, the presence of other kin in the absence of one or both parents results in gendered effects favouring boys. Conclusions: The absence of any gendered effects when using a household structure typology suggests that secular changes to attitudes about gender equity trump any specific gendered processes stemming from particular configurations. On the other hand, gendered effects that appear when one or both parents are absent show that traditional gender norms and/or resource constraints continue to favour boys. Contribution: We have shown the value of unpacking household structure to better understand how gender norms and gendered resource allocations are linked to an important outcome for children in sub-Saharan Africa.

  16. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    Representatives of both Andean and Mesoamerican gene pools were identified by STRUCTURE software analysis, as well as a high proportion of hybrid accessions as evidenced by a STRUCTURE K = 2 preset. At the optimum K = 5 preset value, mixed membership of Andean and Mesoamerican genotypes in some of the ...

  17. Variation in population structure and life-history parameters of ...

    African Journals Online (AJOL)

    The age structure of female steentjies was truncated in the exploited area but the male age structure was unaffected, possibly because of the poor relationship between size and age of males caused by accelerated growth-at-sex-change. There were no differences in the size- and age-at-sex-change between the reserve ...

  18. New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

    Science.gov (United States)

    Doyle, Jacqueline M.; Bell, Douglas A.; Bloom, Peter H.; Emmons, Gavin; Fesnock, Amy; Katzner, Todd; LePre, Larry; Leonard, Kolbe; SanMiguel, Phillip; Westerman, Rick; DeWoody, J. Andrew

    2018-01-01

    BackgroundManagement requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.ResultsWe sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.ConclusionsOur study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating

  19. Strong Migration Limit for Games in Structured Populations: Applications to Dominance Hierarchy and Set Structure

    Directory of Open Access Journals (Sweden)

    Dhaker Kroumi

    2015-09-01

    Full Text Available In this paper, we deduce a condition for a strategy S1 to be more abundant on average at equilibrium under weak selection than another strategy S2 in a population structured into a finite number of colonies of fixed proportions as the population size tends to infinity. It is assumed that one individual reproduces at a time with some probability depending on the payoff received in pairwise interactions within colonies and between colonies and that the offspring replaces one individual chosen at random in the colony into which the offspring migrates. It is shown that an expected weighted average equilibrium frequency of S1 under weak symmetric strategy mutation between S1 and S2 is increased by weak selection if an expected weighted payoff of S1 near neutrality exceeds the corresponding expected weighted payoff of S2. The weights are given in terms of reproductive values of individuals in the different colonies in the neutral model. This condition for S1 to be favoured by weak selection is obtained from a strong migration limit of the genealogical process under neutrality for a sample of individuals, which is proven using a two-time scale argument. The condition is applied to games between individuals in colonies with linear or cyclic dominance and between individuals belonging to groups represented by subsets of a given set.

  20. Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population.

    Science.gov (United States)

    Tay, Chin Yen; Mitchell, Hazel; Dong, Quanjiang; Goh, Khean-Lee; Dawes, Ian W; Lan, Ruiting

    2009-06-19

    Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture. Seventy eight H. pylori isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST) of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified H. pylori ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the H. pylori populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates. The majority of the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. The Malay population, known to have a low infection rate of H. pylori, was likely to be initially H. pylori free and gained the pathogen only recently from cross infection from other populations.

  1. Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population

    Directory of Open Access Journals (Sweden)

    Dawes Ian W

    2009-06-01

    Full Text Available Abstract Background Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture. Results Seventy eight H. pylori isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified H. pylori ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the H. pylori populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates. Conclusion The majority of the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. The Malay population, known to have a low infection rate of H. pylori, was likely to be initially H. pylori free and gained the pathogen only recently from cross infection from other populations.

  2. Population structure and genetic diversity in insular populations of Nasutitermes takasagoensis (Isoptera: Termitidae) analyzed by AFLP markers.

    Science.gov (United States)

    García, Julio; Maekawa, Kiyoto; Miura, Toru; Matsumoto, Tadao

    2002-10-01

    Dispersal ability and degree of inbreeding in a population can indirectly be assessed using genetic markers. In general, it was suggested that winged termites are not able to fly distances greater than several hundred meters. Here, amplified fragment length polymorphism (AFLP) was used to analyze genetic diversity, population substructure, and gene flow among insular populations of the termite Nasutitermes takasagoensis (Isoptera: Termitidae) in the Yaeyama Islands, Okinawa, Japan. Samples were collected from 77 nests on seven islands of the Yaeyama Group. Using three primer combinations a total of 155 bands were generated with 78 (50%) polymorphic bands. Genetic distance and G(st) values among insular populations were calculated. Relatively high genetic diversity and low values of G (st), suggest there is moderate subpopulation structure. Based on these results, we discussed two possibilities; first, winged termites are able to fly over distances of several kilometers, and second, these results were obtained because insular populations share a recent common origin.

  3. Genetic variability and structure of an isolated population of ...

    Indian Academy of Sciences (India)

    ... 0.621); we also found a small population size (Ne = 8.8), the presence of historical (M = 0.486) and recent bottlenecks under IAM and TPM models, with a low, but significantcoefficient of inbreeding (FIS = −0.451). This information will help us to raise conservation strategies of this microendemic mole salamander species.

  4. Research Article Molecular variation and population structure in ...

    Indian Academy of Sciences (India)

    微软用户

    firstly for effective and sustainable development. At the same time, ex situ measures, such as those individuals with rare alleles, to maintain the relationships between individuals and populations are also proposed. Key words Limonium bicolor, genetic diversity, SSR, AFLP, plant conservation. Introduction. The Limonium is ...

  5. Analysis of genetic diversity and population structure among exotic ...

    African Journals Online (AJOL)

    The present study was performed to study genetic relationships and population differentiation of 90 introduced sugarcane accessions in Ethiopia by means of 22 SSR molecular markers. The 22 SSR markers amplified a total of 260 alleles, of which 230 were polymorphic with a mean of 10.45 alleles per SSR locus.

  6. Genetic variation and population structure of interleukin genes ...

    Indian Academy of Sciences (India)

    results of phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data on these ethnic groups. .... relatively homogeneous culture, but to different caste clus- ters, priest (Brahmins: .... members of the South Asian diaspora in western societies. Thus, as pointed out by ...

  7. Population structure and growth of polydorid polychaetes that infest ...

    African Journals Online (AJOL)

    Polydorid polychaetes can infest cultured abalone thereby reducing productivity. In order to effectively control these pests, their reproductive biology must be understood. The population dynamics and reproduction of polydorids infesting abalone Haliotis midae from two farms in South Africa is described using a ...

  8. Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

    African Journals Online (AJOL)

    Administrator

    2Farm Forestry Programme, Kenya Forestry Research Institute, P. O. Box 20412, Nairobi, Kenya. Accepted 5 ... were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between ...

  9. Genetic diversity and population structure of the marbled rockfish ...

    Indian Academy of Sciences (India)

    water pollution. The only genetic work on the rockfishes was undertaken by Dong et al. (2008) in Zhejiang, People's. Republic of China. This study used eight enzyme markers and reported a low level of polymorphism of only 27.78%. The objective of the present study was to assess the genetic diversity within populations ...

  10. Euphausiid population structure and grazing in the Antarctic Polar ...

    African Journals Online (AJOL)

    The daily ration estimates of autotrophic carbon for the euphausiids suggest that phytoplankton represent a minor component in their diets, with only the sub-adult E. vallentini consuming sufficient phytoplankton to meet their daily carbon requirements. Keywords: euphausiid; ingestion; Polar Frontal Zone; population ...

  11. The population structure of Ukraine in relation to the ...

    African Journals Online (AJOL)

    Background: The taste sensitivity to phenylthiocarbamide (PTC) is one of the classical genetic markers in human studies. PTC is of great interest from the medical point of view since a number of associations of the taster status with human diseases have been found. The aim of our study was to evaluate the population ...

  12. Some aspects of the morphology, population structure and larval ...

    African Journals Online (AJOL)

    The parasite has a high prevalence of infection (68,9%) in the X. laevis population studied and shows a preference for attachment in the anterior duodenum. Approximately 76% of the worms recovered were juveniles. Coracidia had an LT50 of 6 h and transmission is thought to take place in darkness at the sediment/water ...

  13. Genetic structure of natural populations: Final technical report

    International Nuclear Information System (INIS)

    Ayala, F.J.

    1987-01-01

    We determined the LD 50 for individuals with any one of four genetic constitutions. The LD 50 was in kR units (S and F refer to the two common alleles found in natural populations and N is a mull allele) S/S 5.31, F/F 4.61, S/F 4.19, N/N 3.16. These results are as expected under the hypothesis the SOD is involved in radio-resistance and the degree of protection is a function of SOD specific activity. S codes for an allozyme that has the highest in vitro specific activity while N reduces the amount of enzyme to 3.5% of the normal level. Natural selection experiments in population cages were carried out for 13 generations. In control populations, the frequency of the S allele decreases from the initial frequency of 0.50 to an equilibrium value 0.1 to 0.2 in about 10 generations. In populations with the larvae receiving 4 KR in each generation, s reaches an equilibrium frequency of 0.6; when the irradiation was no longer applied, the frequency of S started declining, eventually reaching 0.1 to 0.2. These results corroborate the hypothesis that SOD protects against irradiation and that the degree of protection is correlated by the in vitro specific activity of the allozymes. 29 refs., 4 tabs

  14. Relating Kirtland's warbler population to changing landscape composition and structure

    Science.gov (United States)

    John R. Probst; Jerry Weinrich

    1993-01-01

    The population of male Kirtland's warbler (Dendroica kirtlandil) in the breeding season has averaged 206 from 1971 to 1987. The Kirtland's warbler occupies dense jack pine (Pinus banksiana) barrens from 5 to 23 years old and from 1.4 to 5.0 m high, formerly of wildfire origin. In 1984, 73% of the males censused were found in habitat naturally regenerated from...

  15. The genetic structure of Leishmania infantum populations in Brazil and its possible association with the transmission cycle of visceral leishmaniasis.

    Directory of Open Access Journals (Sweden)

    Gabriel Eduardo Melim Ferreira

    Full Text Available Leishmania infantum is the etiologic agent of visceral leishmaniasis (VL in the Americas, Mediterranean basin and West and Central Asia. Although the geographic structure of L. infantum populations from the Old World have been described, few studies have addressed the population structure of this parasite in the Neotropical region. We employed 14 microsatellites to analyze the population structure of the L. infantum strains isolated from humans and dogs from most of the Brazilian states endemic for VL and from Paraguay. The results indicate a low genetic diversity, high inbreeding estimates and a depletion of heterozygotes, which together indicate a predominantly clonal breeding system, but signs of sexual events are also present. Three populations were identified from the clustering analysis, and they were well supported by F statistics inferences and partially corroborated by distance-based. POP1 (111 strains was observed in all but one endemic area. POP2 (31 strains is also well-dispersed, but it was the predominant population in Mato Grosso (MT. POP3 (31 strains was less dispersed, and it was observed primarily in Mato Grosso do Sul (MS. Strains originated from an outbreak of canine VL in Southern Brazil were grouped in POP1 with those from Paraguay, which corroborates the hypothesis of dispersal from Northeastern Argentina and Paraguay. The distribution of VL in MS seems to follow the west-east construction of the Bolivia-Brazil pipeline from Corumbá municipality. This may have resulted in a strong association of POP3 and Lutzomyia cruzi, which is the main VL vector in Corumbá, and a dispersion of this population in this region that was shaped by human interference. This vector also occurs in MT and may influence the structure of POP2. This paper presents significant advances in the understanding of the population structure of L. infantum in Brazil and its association with eco-epidemiological aspects of VL.

  16. The Genetic Structure of Leishmania infantum Populations in Brazil and Its Possible Association with the Transmission Cycle of Visceral Leishmaniasis

    Science.gov (United States)

    Ferreira, Gabriel Eduardo Melim; dos Santos, Barbara Neves; Dorval, Maria Elizabeth Cavalheiros; Ramos, Tereza Pompilio Bastos; Porrozzi, Renato; Peixoto, Alexandre Afranio; Cupolillo, Elisa

    2012-01-01

    Leishmania infantum is the etiologic agent of visceral leishmaniasis (VL) in the Americas, Mediterranean basin and West and Central Asia. Although the geographic structure of L. infantum populations from the Old World have been described, few studies have addressed the population structure of this parasite in the Neotropical region. We employed 14 microsatellites to analyze the population structure of the L. infantum strains isolated from humans and dogs from most of the Brazilian states endemic for VL and from Paraguay. The results indicate a low genetic diversity, high inbreeding estimates and a depletion of heterozygotes, which together indicate a predominantly clonal breeding system, but signs of sexual events are also present. Three populations were identified from the clustering analysis, and they were well supported by F statistics inferences and partially corroborated by distance-based. POP1 (111 strains) was observed in all but one endemic area. POP2 (31 strains) is also well-dispersed, but it was the predominant population in Mato Grosso (MT). POP3 (31 strains) was less dispersed, and it was observed primarily in Mato Grosso do Sul (MS). Strains originated from an outbreak of canine VL in Southern Brazil were grouped in POP1 with those from Paraguay, which corroborates the hypothesis of dispersal from Northeastern Argentina and Paraguay. The distribution of VL in MS seems to follow the west-east construction of the Bolivia-Brazil pipeline from Corumbá municipality. This may have resulted in a strong association of POP3 and Lutzomyia cruzi, which is the main VL vector in Corumbá, and a dispersion of this population in this region that was shaped by human interference. This vector also occurs in MT and may influence the structure of POP2. This paper presents significant advances in the understanding of the population structure of L. infantum in Brazil and its association with eco-epidemiological aspects of VL. PMID:22606248

  17. ObStruct: A Method to Objectively Analyse Factors Driving Population Structure Using Bayesian Ancestry Profiles

    Science.gov (United States)

    Gayevskiy, Velimir; Klaere, Steffen; Knight, Sarah; Goddard, Matthew R.

    2014-01-01

    Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin) correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses. PMID:24416362

  18. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    Directory of Open Access Journals (Sweden)

    Velimir Gayevskiy

    Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  19. Generation time, net reproductive rate, and growth in stage-age-structured populations

    DEFF Research Database (Denmark)

    Steiner, Uli; Tuljapurkar, Shripad; Coulson, Tim

    2014-01-01

    to age-structured populations. Here we generalize this result to populations structured by stage and age by providing a new, unique measure of reproductive timing (Tc) that, along with net reproductive rate (R0), has a direct mathematical relationship to and approximates growth rate (r). We use simple...... examples to show how reproductive timing Tc and level R0 are shaped by stage dynamics (individual trait changes), selection on the trait, and parent-offspring phenotypic correlation. We also show how population structure can affect dispersion in reproduction among ages and stages. These macroscopic...... features of the life history determine population growth rate r and reveal a complex interplay of trait dynamics, timing, and level of reproduction. Our results contribute to a new framework of population and evolutionary dynamics in stage-and-age-structured populations....

  20. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    DEFF Research Database (Denmark)

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.

    2009-01-01

    Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from...... and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...... landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North–South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin...

  1. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    2015-03-12

    Mar 12, 2015 ... Ashok Badigannavar and Gerald O. Myers these traits in conventional cotton breeding programmes. Genetic mapping provides a useful tool to understand the architecture of quantitative traits at the molecular level. DNA markers linked to QTL controlling seed protein content have been identified in soybean ...

  2. Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population

    Science.gov (United States)

    Antolin, Michael F.; Van Horne, Beatrice; Berger, Michael D.

    2001-01-01

    Piute ground squirrels (Spermophilus mollis) are distributed continuously in habitat dominated by native shrubs and perennial grasses in the Snake River Birds of Prey National Conservation Area in Idaho, U.S.A. This habitat is being fragmented and replaced by exotic annual plants, changing it to a wildfire-dominated system that provides poor habitat for ground squirrels. To assess potential effects of this fragmentation on ground squirrel populations, we combined an estimate of effective population size (Ne) based upon a demographic study with a population genetic analysis. The study area included three subpopulations separated from each other by 8–13 km. The ratio of effective population size to census number (Ne/N) was 0.57. Combining Ne/N with dispersal distances from a radio-tracking study, we calculated that neighborhood size was 62.2 ha, which included between 204 and 480 individuals. Our population genetic analysis (based on randomly amplified polymorphic DNA (RAPD) and microsatellite markers) showed relatively low levels of genetic differentiation (Qpopulations 0.07–0.10) between subpopulations and no inbreeding within subpopulations (f = 0.0003). These estimates of population subdivision translate into an effective migration rate (Nem) of 2.3–3.3 per year, which represents a high level of gene flow. Invasion by exotics will reduce the overall productivity of the habitat, and will lead to isolation among subpopulations if favorable habitat patches become isolated.

  3. Historical Population Structure of Central Valley Steelhead and Its Alteration by Dams

    Directory of Open Access Journals (Sweden)

    Steven T. Lindley

    2006-02-01

    Full Text Available Effective conservation and recovery planning for Central Valley steelhead requires an understanding of historical population structure. We describe the historical structure of the Central Valley steelhead evolutionarily significant unit using a multi-phase modeling approach. In the first phase, we identify stream reaches possibly suitable for steelhead spawning and rearing using a habitat model based on environmental envelopes (stream discharge, gradient, and temperature that takes a digital elevation model and climate data as inputs. We identified 151 patches of potentially suitable habitat with more than 10 km of stream habitat, with a total of 25,500 km of suitable habitat. We then measured the distances among habitat patches, and clustered together patches within 35 km of each other into 81 distinct habitat patches. Groups of fish using these 81 patches are hypothesized to be (or to have been independent populations for recovery planning purposes. Consideration of climate and elevation differences among the 81 habitat areas suggests that there are at least four major subdivisions within the Central Valley steelhead ESU that correspond to geographic regions defined by the Sacramento River basin, Suisun Bay area tributaries, San Joaquin tributaries draining the Sierra Nevada, and lower-elevation streams draining to the Buena Vista and Tulare basins, upstream of the San Joaquin River. Of these, it appears that the Sacramento River basin was the main source of steelhead production. Presently, impassable dams block access to 80% of historically available habitat, and block access to all historical spawning habitat for about 38% of the historical populations of steelhead.

  4. Understanding the structure of nanocatalysts with high resolution scanning/transmission electron microscopy

    International Nuclear Information System (INIS)

    Francis, L D; Rivas, J; José-Yacamán, M

    2014-01-01

    Nanomaterials including nanoparticles, nanowires and nanotubes play an important role in heterogeneous catalysis. Thanks to the rapid improvement of the electron microscopic techniques and with the advent of aberration corrected electron microscopy as well as theoretical methodologies, the potential effects induced by nanocatalysts are better understood than before by unravelling their atomic structure. A brief introduction to advanced electron microscopic techniques namely aberration corrected scanning transmission electron microscopy (Cs-STEM) is presented and subsequently two examples of nanocatalysts are considered in the present review. The first example will focus on the study of bimetallic/core-shell nanoalloys. In heterogeneous catalysis, catalysts containing two or more metals might show significantly different catalytic properties compared to the parent metals and thus are widely utilized in several catalytic reactions. Atom-by-atom insights of the nanoalloy based catalysts ex: Au-Pd will be described in the present review using a combination of advanced electron microscopic and spectroscopic techniques. A related example on the understanding of bimetallic clusters by HAADF-STEM will also be presented in addition to nanoparticles. In the second case understanding the structure of transition metal chalcogenide based nanocatalysts by HRTEM and aberration corrected STEM, for the case of MoS 2 will be discussed. MoS 2 -based catalysts serve as model catalysts and are employed in the hydrodesulphurisations (HDS) reactions in the removal of sulphur from gasoline and related petrochemical products. They have been studied in various forms including nanowires, nanotubes and nanoplates. Their structure, atomic insights and as a consequence elucidation of their corresponding catalytic activity are thus important

  5. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    Ivoire. However, no study on the genetic diversity of the species has been performed to date. This study aims at analyzing the diversity and genetic structure of 35 maize accessions using 10 microsatellite markers. These accessions are from ...

  6. Understanding how self-management interventions work for disadvantaged populations living with chronic conditions: protocol for a realist synthesis.

    Science.gov (United States)

    Mills, Susan L; Pumarino, Javiera; Clark, Nancy; Carroll, Simon; Dennis, Sarah; Koehn, Sharon; Yu, Tricia; Davis, Connie; Fong, Maylene

    2014-07-01

    Self-management programmes are complex interventions aimed at improving the way individuals self-manage chronic conditions, but there are questions about the overall impact of these programmes on disadvantaged populations, in terms of their capacity to engage with and receive the benefits from these initiatives. Given the increased resources being directed towards self-management initiatives, clinicians and policy makers need knowledge on how self-management interventions work for these populations. Most systematic reviews of self-management interventions do not consider the complex interactions between implementation contexts, intervention strategies, and mechanisms that influence how self-management interventions work in real life for disadvantaged groups. To address the need for better understanding of these mechanisms and to create context-relevant knowledge, we are conducting a realist synthesis of evidence on self-management interventions for disadvantaged populations living with chronic conditions. The primary research question is: What are the key mechanisms operating in chronic condition self-management interventions among disadvantaged populations? In this protocol, we outline the steps we will take to identify the programme theory for self-management interventions and candidate middle-range theories; to search for evidence in academic and grey literature; to appraise and extract the collected evidence; to synthesise and interpret the findings to generate key context-mechanism-outcome configurations and to disseminate results to relevant stakeholder and to peer-review publications. Understandings of how chronic conditions self-management interventions work among disadvantaged populations is essential knowledge for clinicians and other decision makers who need to know which programmes they should implement for which groups. Results will also benefit medical researchers who want to direct effort towards current gaps in knowledge in order to advance the self

  7. Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae) in China: two gene pools inferred by microsatellites.

    Science.gov (United States)

    Ma, Yajun; Yang, Manni; Fan, Yong; Wu, Jing; Ma, Ying; Xu, Jiannong

    2011-01-01

    Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet. This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy-Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F(ST) = 0.156). Pairwise differentiation between populations were lower within clusters (F(ST) = 0.008-0.028 in cluster I and F(ST) = 0.004-0.048 in cluster II) than between clusters (F(ST) = 0.120-0.201). A reduced gene flow (Nm = 1-1.7) was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite) across sampled populations. Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population perturbations could be the factors affecting the population differentiation. The

  8. Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae in China: two gene pools inferred by microsatellites.

    Directory of Open Access Journals (Sweden)

    Yajun Ma

    Full Text Available BACKGROUND: Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet. METHODOLOGY/PRINCIPAL FINDINGS: This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy-Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F(ST = 0.156. Pairwise differentiation between populations were lower within clusters (F(ST = 0.008-0.028 in cluster I and F(ST = 0.004-0.048 in cluster II than between clusters (F(ST = 0.120-0.201. A reduced gene flow (Nm = 1-1.7 was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite across sampled populations. CONCLUSIONS/SIGNIFICANCE: Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population

  9. Landscape structure mediates the effects of a stressor on field vole populations

    DEFF Research Database (Denmark)

    Dalkvist, Trine; Topping, Chris J.; Sibly, Richard M.

    2013-01-01

    Spatio-temporal landscape heterogeneity has rarely been considered in population-level impact assessments. Here we test whether landscape heterogeneity is important by examining the case of a pesticide applied seasonally to orchards which may affect non-target vole populations, using a validated...... results show that accurate prediction of population impact cannot be achieved without taking account of landscape structure. The specifics of landscape structure and habitat connectivity are likely always important in mediating the effects of stressors....

  10. Sus scrofa: Population Structure, Reproduction and Condition in Tropical North Eastern Australia

    Directory of Open Access Journals (Sweden)

    NELSON, John E.

    2009-01-01

    Full Text Available Three feral pig populations inhabiting contrasting environments along the north easterncoast of Australia have been investigated with respect to population structure, individual condition andreproduction. The population on Prince of Wales Island contains a large proportion of juvenile andsub-adult pigs but lacks pigs in the higher age classes. Individuals also breed at an earlier age thananimals of the mainland populations. Pig populations on Cape York Peninsula show a largerproportion of older animals and feral pigs living in rainforest habitats show a low proportion ofanimals in very young and very old age classes. Pigs from the lowland rainforest population are inbetter condition than those of the other populations for most of the year, reflecting the availability offood all year round in this environment. Differences in the population structure of the threepopulations are discussed with respect to fecundity and several mortality factors such as predation anddiseases/parasites.

  11. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  12. Transferrin variation and genetic structure of reindeer populations in Scandinavia

    Directory of Open Access Journals (Sweden)

    Knut H. Røed

    1987-06-01

    Full Text Available Polyacrylamide gel electrophoresis was used to analyse transferrin variation in herds of semi-domestic reindeer from Scandinavia. The results are compared with previously reported values for other populations of both semi-domestic and wild reindeer using the same techniques as in the present study. In all populations the number of alleles was high, ranging from seven to eleven, and the heterozygosity was correspondingly high, with a mean of 0.749. This high genetic variation in all populations suggests that inbreeding is not widespread among Scandinavian reindeer. The pattern of allele frequency distribution indicates a high degree of genetic heterogeneity in the transferrin locus, both between the different semi-domestic herds and between the different wild populations. The mean value of genetic distance was 0.069 between semi-domestic herds and 0.091 between wild populations. Between semi-domestic and wild populations the genetic distance was particularly high, with a mean of 0.188. This high value was mainly due to a different pattern in the distribution of the two most common transferrin alleles: Tfu was most common among semi-domestic herds, while TfEI was most common among wild populations. These differences in transferrin allele distribution are discussed in relation to possible different origins of semi-domestic and wild reindeer in Scandinavia, or alternatively, to different selection forces acting on transferrin genotypes in semi-domestic and wild populations.Transferrin-variasjon og genetisk struktur hos rein i Skandinavia.Abstact in Norwegian / Sammendrag: Transferrin-variasjon i tamreinflokker ble analysert ved hjelp av polyacrylamid gel elektroforese. Resultatene er sammenlignet med verdier som tidligere er beskrevet for både tamrein og villrein hvor det ble benyttet samme metode som i denne undersøkelsen. I alle populasjonene ble det registrert et høyt antall alleler (7-11 og heterozygositeten var tilsvarende høy med en

  13. Genetic structure of honeybee populations from southern Brazil and Uruguay

    Directory of Open Access Journals (Sweden)

    Diniz Nilza Maria

    2003-01-01

    Full Text Available Apis mellifera scutellata was introduced to Brazil in 1956 and Africanized honeybee populations have now spread from Argentina to the southwestern United States. Temperate climatic restrictions seem to be a natural limit to Africanized honeybee expansion around parallels 35° to 40° SL. We used allozyme loci (Mdh-1 and Hk-1 and mtDNA haplotypes to characterize honeybee populations in southern Brazil and Uruguay and define a possible transition area between Africanized and European bees. Samples of 194 bee colonies were collected from ten localities between 30°-35° SL and 52°-59° WL. The mtDNA restriction patterns of these colonies were obtained through digestion of the mitochondrial genome by Eco RI, or by digestion by Bgl II and Xba I of the cytochrome B locus and the COI-COII intergenic region, respectively. The distribution limit of African bee colonies, i.e., those populations with only the African mtDNA haplotype and with a high proportion of African genes as shown by allozyme analysis, is located in northern Uruguay, with a hybridization zone located farther south in Uruguay. A gradual cline from north to south was observed, confirmed by mtDNA, racial admixture, and genetic distance analyses. No evidence of either gametic disequilibrium between nuclear markers or cytonuclear disequilibrium among the nuclear and mtDNA genotypes was detected, suggesting that the hybridization process has been completed.

  14. Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

    Directory of Open Access Journals (Sweden)

    Guillermo Velo-Antón

    Full Text Available The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa. We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4 and microsatellite markers (32 loci and a subset of 12 loci. Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24 with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.

  15. Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

    Science.gov (United States)

    Velo-Antón, Guillermo; Godinho, Raquel; Campos, João Carlos; Brito, José Carlos

    2014-01-01

    The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.

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

    OpenAIRE

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

    2010-01-01

    Fine-scale population structure characterizes most continents and is especially pronounced in non-cosmopolitan populations. Roughly half of the world's population remains non-cosmopolitan and even populations within cities often assort along ethnic and linguistic categories. Barriers to random mating can be ecologically extreme, such as the Sahara Desert, or cultural, such as the Indian caste system. In either case, subpopulations accumulate genetic differences if the barrier is maintained ov...

  17. Altitudinal population structure and microevolution of the malaria vector Anopheles cruzii (Diptera: Culicidae).

    Science.gov (United States)

    Lorenz, Camila; Marques, Tatiani Cristina; Sallum, Maria Anice Mureb; Suesdek, Lincoln

    2014-12-16

    In Brazil, the autochthonous transmission of extra-Amazonian malaria occurs mainly in areas of the southeastern coastal Atlantic Forest, where Anopheles cruzii is the primary vector. In these locations, the population density of the mosquito varies with altitude (5-263 m above sea level), prompting us to hypothesise that gene flow is also unevenly distributed. Describing the micro-geographical and temporal biological variability of this species may be a key to understanding the dispersion of malaria in the region. We explored the homogeneity of the An. cruzii population across its altitudinal range of distribution using wing shape and mtDNA gene analysis. We also assessed the stability of wing geometry over time. Larvae were sampled from lowland (5-20 m) and hilltop (81-263 m) areas in a primary Atlantic Forest region, in the municipality of Cananéia (State of São Paulo, Brazil). The right wings of males and females were analysed by standard geometric morphometrics. Eighteen landmarks were digitised for each individual and a discriminant analysis was used to compare samples from the hilltop and lowland. A 400-bp DNA fragment of the mitochondrial cytochrome oxidase gene subunit I (CO-I) was PCR-amplified and sequenced. Wing shapes were distinct between lowland and hilltop population samples. Results of cross-validated tests based on Mahalanobis distances showed that the individuals from both micro-environments were correctly reclassified in a range of 54-96%. The wings of hilltop individuals were larger. The CO-I gene was highly polymorphic (haplotypic diversity = 0.98) and altitudinally structured (Фst = 0.085 and Jaccard = 0.033). We found 60 different haplotypes but only two were shared by the lowland and hilltop populations. Wing shape changed over the brief study period (2009-2013). Wing geometry and CO-I gene analysis indicated that An. cruzii is vertically structured. Wing shape varied rapidly, but altitude structure was maintained. Future

  18. Impact of population age structure on Wolbachia transgene driver efficacy: ecologically complex factors and release of genetically modified mosquitoes.

    Science.gov (United States)

    Rasgon, Jason L; Scott, Thomas W

    2004-07-01

    Wolbachia symbionts hold theoretical promise as a way to drive transgenes into insect vector populations for disease prevention. For simplicity, current models of Wolbachia dynamics and spread ignore ecologically complex factors such as the age structure of vector populations and overlapping vector generations. We developed a model including these factors to assess their impact on the process of Wolbachia spread into populations of three mosquito species (Anopheles gambiae, Aedes aegypti and Culex pipiens). Depending on the mosquito species, Wolbachia parameters, released mosquito life stage and initial age structure of the target population, the number of Wolbachia-infected mosquitoes that we predict would need to be released ranged from less than the threshold calculated by the simple model to a 10-30-fold increase. Transgenic releases into age-structured populations, which is an expectation for wild mosquitoes, will be difficult and depending on the circumstances may not be economically or logistically feasible due to the large number of infected mosquitoes that must be released. Our results support the perspective that understanding ecological factors is critical for designing transgenic vector-borne disease control strategies.

  19. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    Science.gov (United States)

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  20. Political Market Orientation: A Framework for Understanding Relationship Structures in Political Parties

    DEFF Research Database (Denmark)

    Ormrod, Robert P.; Savigny, Heather

    2012-01-01

    This article is motivated by the growing need to integrate the current political science and marketing literature in order to provide a deeper understanding of the behaviour of political actors and their relationships with relevant stakeholder groups. In our article, we demonstrate how Ormrod......’s conceptual model of political market orientation complements political science models of party organization by drawing attention to the competing interests of stakeholders in shaping party strategy and organizational structure. We treat parties as a multitude of actors rather than as monolithic entities...... and thus address the dearth of literature on the micro foundations of parties. Whilst the underlying conceptualization of a political market orientation draws on the management-based ‘relationship marketing’ approach, we acknowledge that the commercial and political contexts are not isomorphic, and thus we...

  1. The right friends in the right places: Understanding network structure as a predictor of voluntary turnover.

    Science.gov (United States)

    Ballinger, Gary A; Cross, Rob; Holtom, Brooks C

    2016-04-01

    Research examining the relationship between social networks and employee retention has focused almost exclusively on the number of direct links and generally found that having more ties decreases the likelihood of turnover. The present research moves beyond simple measures of network centrality to investigate the relationship between 2 additional, and theoretically distinct, facets of social capital and voluntary turnover. In 2 organizations, we found consistent evidence of a negative relationship between reputation, as measured by relationships with highly sought-out others (incoming eigenvector centrality) and voluntary turnover. Further, we found that the negative relationship between brokerage (structural holes) and turnover is significant, but only for higher-level employees. The theoretical and practical implications of expanding the suite of social capital measures to understand voluntary turnover are discussed. (c) 2016 APA, all rights reserved).

  2. The everyday lives of video game developers: Experimentally understanding underlying systems/structures

    Directory of Open Access Journals (Sweden)

    Casey O'Donnell

    2009-03-01

    Full Text Available This essay examines how tensions between work and play for video game developers shape the worlds they create. The worlds of game developers, whose daily activity is linked to larger systems of experimentation and technoscientific practice, provide insights that transcend video game development work. The essay draws on ethnographic material from over 3 years of fieldwork with video game developers in the United States and India. It develops the notion of creative collaborative practice based on work in the fields of science and technology studies, game studies, and media studies. The importance of, the desire for, or the drive to understand underlying systems and structures has become fundamental to creative collaborative practice. I argue that the daily activity of game development embodies skills fundamental to creative collaborative practice and that these capabilities represent fundamental aspects of critical thought. Simultaneously, numerous interests have begun to intervene in ways that endanger these foundations of creative collaborative practice.

  3. Genetic Identification and Population Structure of Juvenile Mullet ...

    African Journals Online (AJOL)

    Abstract—There is a growing demand for wild caught juvenile fish to supply the market for aquaculture. We investigated the local genetic structure of juvenile mullets collected at five sites around Bagamoyo (Tanzanian mainland) and. Zanzibar, East Africa. Fish were caught at low tide using a seine net in the same manner ...

  4. Genetic structure and variability within and among populations of the ...

    African Journals Online (AJOL)

    This study investigates the genetic diversity and the structure of the most dominant native fat-tailed Tunisian sheep breed (Barbarine, BAR) using microsatellite markers. Blood samples from 183 BAR animals, belonging to 4 subpopulations according to phenotypic traits, were collected across all regions in Tunisia.

  5. Population genetic structure and phylogeography of the mud-flat ...

    African Journals Online (AJOL)

    Genetic structure and evolutionary demography of the mud-flat crabs (Helice tientsinensis and H. latimera) were investigated using sequence data of mitochondrial cytochrome c oxidase I (COI) gene. Samples of 213 individuals were collected from nine localities over most of the species' range along the coast of China seas ...

  6. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    pc

    2016-11-02

    Nov 2, 2016 ... (Chen et al., 2012) and quinoa (Bazile et al., 2014). This study aims at assessing the variability and genetic structure of local varieties of Ivorian maize using microsatellite markers. The results of the assessment can contribute to the ex situ conservation and the development of selection strategies in order to ...

  7. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    ... organization of genetic diversity. The Andean and Mesoamerican genotypes were present in similar frequencies (51 vs. 49%, respectively). All SSR markers tested were polymorphic with mean polymorphism information content (PIC) of 0.8. The model-based cluster analysis of SSR diversity in the STRUCTURE software ...

  8. Genetic population structuring and demographic history of red ...

    African Journals Online (AJOL)

    Climatic oscillations during the Pleistocene ice ages in the Northwestern Pacific produced great changes in species' geographical distribution and abundance, which could be expected to have genetic consequences in marine fishes. In order to estimate the demographic history and genetic structure of Epinephelus akaara ...

  9. Population fluctuations and community structure of small mammals ...

    African Journals Online (AJOL)

    Small mammals were live trapped monthly over a three year period in a subtropical grassland in Swaziland. Seven species of small mammals were recorded from the study grid. There were significant seasonal and inter annual differences in rodent numbers, breeding intensity and community structure. Mastomys natalensis ...

  10. Harvesting Renewable Resources of Population with Size Structure and Diffusion

    Directory of Open Access Journals (Sweden)

    Qiang-Jun Xie

    2014-01-01

    Full Text Available The aim of this work is to explore the optimal exploitation way for a biological resources model incorporating individual’s size difference and spatial effects. The existence of a unique nonnegative solution to the state system is shown by means of Banach’s fixed point theorem, and the continuous dependence of the population density with the harvesting effort is given. The optimal harvesting strategy is established via normal cone and adjoint system technique. Some conditions are found to assure that there is only one optimal policy.

  11. Geographical structure and differential natural selection among North European populations

    DEFF Research Database (Denmark)

    McEvoy, Brian P; Montgomery, Grant W; McRae, Allan F

    2009-01-01

    from F(ST)-based analysis of genic and nongenic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps...... reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to the HLA-G gene on chromosome 6. Evidence of the sweep extends over a 8-Mb/3.5-cM region. Overall, the results illustrate the power of dense genotype and sample...

  12. Population Structure and Incidence of Virus Infection in Free-Living Populations of Cucurbita Pepo

    Science.gov (United States)

    To assess the imact of virus resistance transgene introgression into wild, free-living populations, it is important to characterize the potential benefit(s) that those transgenes might confer on such poulations. Transgenic virus-resistant Cucurbita pepo L. (squash) cultivars have been commercialize...

  13. Understanding the reaction of nuclear graphite with molecular oxygen: Kinetics, transport, and structural evolution

    Science.gov (United States)

    Kane, Joshua J.; Contescu, Cristian I.; Smith, Rebecca E.; Strydom, Gerhard; Windes, William E.

    2017-09-01

    For the next generation of nuclear reactors, HTGRs specifically, an unlikely air ingress warrants inclusion in the license applications of many international regulators. Much research on oxidation rates of various graphite grades under a number of conditions has been undertaken to address such an event. However, consequences to the reactor result from the microstructural changes to the graphite rather than directly from oxidation. The microstructure is inherent to a graphite's properties and ultimately degradation to the graphite's performance must be determined to establish the safety of reactor design. To understand the oxidation induced microstructural change and its corresponding impact on performance, a thorough understanding of the reaction system is needed. This article provides a thorough review of the graphite-molecular oxygen reaction in terms of kinetics, mass and energy transport, and structural evolution: all three play a significant role in the observed rate of graphite oxidation. These provide the foundations of a microstructurally informed model for the graphite-molecular oxygen reaction system, a model kinetically independent of graphite grade, and capable of describing both the observed and local oxidation rates under a wide range of conditions applicable to air-ingress.

  14. Population dynamics of Eldana saccharina Walker (Lepidoptera: Pyralidae): application of a biophysical model to understand phenological variation in an agricultural pest.

    Science.gov (United States)

    Kleynhans, E; Barton, M G; Conlong, D E; Terblanche, J S

    2017-08-08

    Understanding pest population dynamics and seasonal phenology is a critical component of modern integrated pest-management programs. Accurate forecasting allows timely, cost-effective interventions, including maximum efficacy of, for example, biological control and/or sterile insect technique. Due to the variation in life stage-related sensitivity toward climate, insect pest population abundance models are often not easily interpreted or lack direct relevance to management strategies in the field. Here we apply a process-based (biophysical) model that incorporates climate data with life stage-dependent physiology and life history to attempt to predict Eldana saccharina life stage and generation turnover in sugarcane fields. Fitness traits are modelled at two agricultural locations in South Africa that differ in average temperature (hereafter a cold and a warm site). We test whether the life stage population structures in the field entering winter and local climate during winter directly affect development rates, and therefore interact to determine the population dynamics and phenological responses of E. saccharina in subsequent spring and summer seasons. The model predicts that: (1) E. saccharina can cycle through more generations at the warm site where fewer hours of cold and heat stress are endured, and (2) at the cold site, overwintering as pupae (rather than larvae) confer higher relative fitness and fecundity in the subsequent summer adult moths. The model predictions were compared with a large dataset of field observations from scouting records. Model predictions for larval presence (or absence) generally overlapped well with positive (or negative) scout records. These results are important for integrated pest management strategies by providing a useful foundation for future population dynamics models, and are applicable to a variety of agricultural landscapes, but especially the sugarcane industry of South Africa.

  15. Hundred years of genetic structure in a sediment revived diatom population

    DEFF Research Database (Denmark)

    Haernstroem, Karolina; Ellegaard, Marianne; Andersen, Thorbjørn Joest

    2011-01-01

    This paper presents research on the genetic structure and diversity of populations of a common marine protist and their changes over time. The bloom-forming diatom Skeletonema marinoi was used as a model organism. Strains were revived from anoxic discrete layers of a 210Pb-dated sediment core...... and of the effect of environmental fluctuations. The results showed a stable population structure among and within the examined sediment layers, and a similar genetic structure has been maintained over thousands of generations. However, established populations from inside the fjord were highly differentiated from...... open-sea populations. Despite constant water exchange and influx of potential colonizers into the fjord, the populations do not mix. One fjord population, accumulated in 1980, was significantly differentiated from the other groups of strains isolated from the fjord. This differentiation could have...

  16. Understanding uncertainties in non-linear population trajectories: a Bayesian semi-parametric hierarchical approach to large-scale surveys of coral cover.

    Directory of Open Access Journals (Sweden)

    Julie Vercelloni

    Full Text Available Recently, attempts to improve decision making in species management have focussed on uncertainties associated with modelling temporal fluctuations in populations. Reducing model uncertainty is challenging; while larger samples improve estimation of species trajectories and reduce statistical errors, they typically amplify variability in observed trajectories. In particular, traditional modelling approaches aimed at estimating population trajectories usually do not account well for nonlinearities and uncertainties associated with multi-scale observations characteristic of large spatio-temporal surveys. We present a Bayesian semi-parametric hierarchical model for simultaneously quantifying uncertainties associated with model structure and parameters, and scale-specific variability over time. We estimate uncertainty across a four-tiered spatial hierarchy of coral cover from the Great Barrier Reef. Coral variability is well described; however, our results show that, in the absence of additional model specifications, conclusions regarding coral trajectories become highly uncertain when considering multiple reefs, suggesting that management should focus more at the scale of individual reefs. The approach presented facilitates the description and estimation of population trajectories and associated uncertainties when variability cannot be attributed to specific causes and origins. We argue that our model can unlock value contained in large-scale datasets, provide guidance for understanding sources of uncertainty, and support better informed decision making.

  17. Genetic structure and phenotypic variation in wild populations of the medicinal tetraploid species Bromelia antiacantha (Bromeliaceae).

    Science.gov (United States)

    Zanella, Camila Martini; Bruxel, Manuela; Paggi, Gecele Matos; Goetze, Márcia; Buttow, Miriam Valli; Cidade, Fernanda Witt; Bered, Fernanda

    2011-09-01

    The patterns of genetic structure in plant populations are mainly related to the species life history and breeding system, and knowledge of these patterns is necessary for the management, use, and conservation of biological diversity. Polyploidy is considered an important mode of evolution in plants, but few studies have evaluated genetic structure of polyploid populations. We studied the patterns of genetic structure and morphological variation of Bromelia antiacantha (Bromeliaceae) populations, a polyploid terrestrial species. • Microsatellite markers and morphological analyses were used to explore patterns of genetic and morphological diversity in wild populations of B. antiacantha. • The results of our simple-sequence repeat analyses supported that B. antiacantha is a polyploid species. The inbreeding coefficients were high and significant in all populations (F(IS) = 0.431), indicating homozygote excess. Bromelia antiacantha showed high levels of genetic differentiation among populations (F(ST) = 0.224) and therefore was highly structured. High morphological variation was observed in fruit phenotypic traits in the populations studied. • The levels of genetic diversity and the pattern of the population's structure may be related to the low recruitment of seeds, clonal reproduction, and the population's colonization history. The genetic and morphological variability displayed in this study are important issues in planning the conservation and exploitation of this resource in a sustainable way.

  18. Corruption and population health outcomes: an analysis of data from 133 countries using structural equation modeling.

    Science.gov (United States)

    Factor, Roni; Kang, Minah

    2015-09-01

    The current study aims to develop a theoretical framework for understanding the antecedents of corruption and the effects of corruption on various health indicators. Using structural equation models, we analyzed a multinational dataset of 133 countries that included three main groups of variables--antecedents of corruption, corruption measures, and health indicators. Controlling for various factors, our results suggest that corruption rises as GDP per capita falls and as the regime becomes more autocratic. Higher corruption is associated with lower levels of health expenditure as a percentage of GDP per capita, and with poorer health outcomes. Countries with higher GDP per capita and better education for women have better health outcomes regardless of health expenditures and regime type. Our results suggest that there is no direct relationship between health expenditures and health outcomes after controlling for the other factors in the model. Our study enhances our understanding of the conceptual and theoretical links between corruption and health outcomes in a population, including factors that may mediate how corruption can affect health outcomes.

  19. Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain.

    Science.gov (United States)

    Pérez-Figueroa, A; Fernández, C; Amaro, R; Hermida, M; San Miguel, E

    2015-08-01

    Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N(e)) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N(e) estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N(e) estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30-56 and 47-56 for the Rato and Guisande Rivers, respectively. Estimated census size (N(c)) for the Rato River was 880 individuals. This yielded a N(e)/N(c) estimate of 3-6 % for temporal estimation of N(e), which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.

  20. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.