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Sample records for comparing genetic structure

  1. AB Initio Protein Tertiary Structure Prediction: Comparative-Genetic Algorithm with Graph Theoretical Methods

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S. K.

    2001-04-20

    During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.

  2. Comparative genetic mapping between clementine, pummelo and sweet orange and the interspecicic structure of the Clementine genome

    Science.gov (United States)

    Comparative genetic mapping between clementine, pummelo and sweet orange and the interspecicic structure of the Clementine genome The availability of a saturated genetic map of Clementine was identified by the International Citrus Genome Consortium as an essential prerequisite to assist the assembly...

  3. A Comparative Study of Genetic and Firefly Algorithms for Sensor Placement in Structural Health Monitoring

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    Guang-Dong Zhou

    2015-01-01

    Full Text Available Optimal sensor placement (OSP is an important task during the implementation of sophisticated structural health monitoring (SHM systems for large-scale structures. In this paper, a comparative study between the genetic algorithm (GA and the firefly algorithm (FA in solving the OSP problem is conducted. To overcome the drawback related to the inapplicability of the FA in optimization problems with discrete variables, some improvements are proposed, including the one-dimensional binary coding system, the Hamming distance between any two fireflies, and the semioriented movement scheme; also, a simple discrete firefly algorithm (SDFA is developed. The capabilities of the SDFA and the GA in finding the optimal sensor locations are evaluated using two disparate objective functions in a numerical example with a long-span benchmark cable-stayed bridge. The results show that the developed SDFA can find the optimal sensor configuration with high reliability. The comparative study indicates that the SDFA outperforms the GA in terms of algorithm complexity, computational efficiency, and result quality. The optimization mechanism of the FA has the potential to be extended to a wide range of optimization problems.

  4. The use of carcasses for the analysis of cetacean population genetic structure: a comparative study in two dolphin species.

    Science.gov (United States)

    Bilgmann, Kerstin; Möller, Luciana M; Harcourt, Robert G; Kemper, Catherine M; Beheregaray, Luciano B

    2011-01-01

    Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully

  5. Comparative analysis of riverscape genetic structure in rare, threatened and common freshwater mussels

    Science.gov (United States)

    Galbraith, Heather S.; Zanatta, David T; Wilson, Chris C.

    2015-01-01

    Freshwater mussels (Bivalvia: Unionoida) are highly imperiled with many species on the verge of local extirpation or global extinction. This study investigates patterns of genetic structure and diversity in six species of freshwater mussels in the central Great Lakes region of Ontario, Canada. These species vary in their conservation status (endangered to not considered at risk), life history strategy, and dispersal capabilities. Evidence of historical genetic connectivity within rivers was ubiquitous across species and may reflect dispersal abilities of host fish. There was little to no signature of recent disturbance events or bottlenecks, even in endangered species, likely as a function of mussel longevity and historical population sizes (i.e., insufficient time for genetic drift to be detectable). Genetic structure was largely at the watershed scale suggesting that population augmentation via translocation within rivers may be a useful conservation tool if needed, while minimizing genetic risks to recipient sites. Recent interest in population augmentation via translocation and propagation may rely on these results to inform management of unionids in the Great Lakes region.

  6. Comparative genetic structure of two mangrove species in Caribbean and Pacific estuaries of Panama

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    Cerón-Souza Ivania

    2012-10-01

    Full Text Available Abstract Background Mangroves are ecologically important and highly threatened forest communities. Observational and genetic evidence has confirmed the long distance dispersal capacity of water-dispersed mangrove seeds, but less is known about the relative importance of pollen vs. seed gene flow in connecting populations. We analyzed 980 Avicennia germinans for 11 microsatellite loci and 940 Rhizophora mangle for six microsatellite loci and subsampled two non-coding cpDNA regions in order to understand population structure, and gene flow within and among four major estuaries on the Caribbean and Pacific coasts of Panama. Results Both species showed similar rates of outcrossing (t= 0.7 in A. germinans and 0.8 in R. mangle and strong patterns of spatial genetic structure within estuaries, although A. germinans had greater genetic structure in nuclear and cpDNA markers (7 demes > 4 demes and Sp= 0.02 > 0.002, and much greater cpDNA diversity (Hd= 0.8 > 0.2 than R. mangle. The Central American Isthmus serves as an exceptionally strong barrier to gene flow, with high levels nuclear (FST= 0.3-0.5 and plastid (FST= 0.5-0.8 genetic differentiation observed within each species between coasts and no shared cpDNA haplotypes between species on each coast. Finally, evidence of low ratios of pollen to seed dispersal (r = −0.6 in A. germinans and 7.7 in R. mangle, coupled with the strong observed structure in nuclear and plastid DNA among most estuaries, suggests low levels of gene flow in these mangrove species. Conclusions We conclude that gene dispersal in mangroves is usually limited within estuaries and that coastal geomorphology and rare long distance dispersal events could also influence levels of structure.

  7. Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae, comparing one exploratory and two Bayesian-model-based methods

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    Carolina L. Pometti

    2014-01-01

    Full Text Available Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations. GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12. STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

  8. Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods.

    Science.gov (United States)

    Pometti, Carolina L; Bessega, Cecilia F; Saidman, Beatriz O; Vilardi, Juan C

    2014-03-01

    Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

  9. Comparative Analysis of Population Genetic Structure in Bemisia tabaci (Gennadius) Biotypes B and Q Based on ISSR Marker

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; WAN Fang-hao; XU Bao-yun; WU Qing-jun; ZHANG You-jun

    2008-01-01

    Bemisia tabaci (Gennadius) biotypes B and Q are two invasive biotypes in the species complex. The comparison of the population genetic structure of the two biotypes is of significance to show their invasive mechanism and to their control. The intersimple sequence repeats (ISSR) marker was used to analyze the 16 B-biotype populations and 4 Q-biotype populations worldwide with a Trialeurodes vaporariorum population in Shanxi Province, China, and a B. tabaci non-B/Q-biotype population in Zhejiang Province, China, was used as control populations. The analysis of genetic diversity showed that the diversity indexes of biotype Q including Nei's gene diversity index, Shannon informative index, and the percentage of polymorphic loci were higher than those of biotype B. The high genetic diversity of biotype Q might provide the genetic basis for the excellent ecological adaptation. Cluster analysis suggested that the ISSR could not be used in the phylogenetic analysis though it could easily distinguish the biotypes of B. tabaci. The difference of the population genetic structure between the biotype B and the biotype Q exists based on the ISSR marker. Meanwhile, the results suggested that the molecular marker has its limitation in the phylogenetic analysis among the biotypes of B. tabaci.

  10. Comparative phylogeography and genetic structure of Vanuatu birds: control region variation in a rail, a dove, and a passerine.

    Science.gov (United States)

    Kirchman, Jeremy J; Franklin, James D

    2007-04-01

    We examined variation in mitochondrial control region (Domain I) sequences in three distantly related species of birds found on multiple islands in Vanuatu: the Buff-banded Rail Gallirallus philippensis (n=21, 433bp), the Emerald Dove Chalcophaps indica (n=21, 513bp), and the Streaked Fantail Rhipidura spilodera (n=17, 326bp). Nucleotide and haplotype diversity were similar in all three species and showed little to no geographic structure within Vanuatu. Estimates of demographic parameters, tests for excess rare alleles, and the structure of both haplotype networks and pairwise mismatch distributions support a hypothesis of recent colonization and subsequent expansion in C. indica and R. spilodera but not in G. philippensis. Phylogenetic analyses suggest that G. philippensis samples from Vanuatu are polyphyletic, and further indicate that this species has had a more complex history of colonization than do the other two species. Estimated divergence times of alleles sampled in Vanuatu suggest there may be slight differences among species in the timing of colonization of Vanuatu despite differences in flight ability and presumed dispersal ability. In all three species, current populations probably derive from colonists that arrived several million years after the islands formed. Our comparisons illustrate the potential of direct genetic analyses of to highlight historical differences among co-distributed species with similar levels of phenotypic variation.

  11. Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map.

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    Li, Ximei; Jin, Xin; Wang, Hantao; Zhang, Xianlong; Lin, Zhongxu

    2016-06-01

    A high-density linkage map was constructed using 1,885 newly obtained loci and 3,747 previously published loci, which included 5,152 loci with 4696.03 cM in total length and 0.91 cM in mean distance. Homology analysis in the cotton genome further confirmed the 13 expected homologous chromosome pairs and revealed an obvious inversion on Chr10 or Chr20 and repeated inversions on Chr07 or Chr16. In addition, two reciprocal translocations between Chr02 and Chr03 and between Chr04 and Chr05 were confirmed. Comparative genomics between the tetraploid cotton and the diploid cottons showed that no major structural changes exist between DT and D chromosomes but rather between AT and A chromosomes. Blast analysis between the tetraploid cotton genome and the mixed genome of two diploid cottons showed that most AD chromosomes, regardless of whether it is from the AT or DT genome, preferentially matched with the corresponding homologous chromosome in the diploid A genome, and then the corresponding homologous chromosome in the diploid D genome, indicating that the diploid D genome underwent converted evolution by the diploid A genome to form the DT genome during polyploidization. In addition, the results reflected that a series of chromosomal translocations occurred among Chr01/Chr15, Chr02/Chr14, Chr03/Chr17, Chr04/Chr22, and Chr05/Chr19.

  12. Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability.

    Science.gov (United States)

    Jump, A S; Rico, L; Coll, M; Peñuelas, J

    2012-06-01

    Identification and quantification of spatial genetic structure (SGS) within populations remains a central element of understanding population structure at the local scale. Understanding such structure can inform on aspects of the species' biology, such as establishment patterns and gene dispersal distance, in addition to sampling design for genetic resource management and conservation. However, recent work has identified that variation in factors such as sampling methodology, population characteristics and marker system can all lead to significant variation in SGS estimates. Consequently, the extent to which estimates of SGS can be relied on to inform on the biology of a species or differentiate between experimental treatments is open to doubt. Following on from a recent report of unusually extensive SGS when assessed using amplified fragment length polymorphisms in the tree Fagus sylvatica, we explored whether this marker system led to similarly high estimates of SGS extent in other apparently similar populations of this species. In the three populations assessed, SGS extent was even stronger than this previously reported maximum, extending up to 360 m, an increase in up to 800% in comparison with the generally accepted maximum of 30-40 m based on the literature. Within this species, wide variation in SGS estimates exists, whether quantified as SGS intensity, extent or the Sp parameter. Consequently, we argue that greater standardization should be applied in sample design and SGS estimation and highlight five steps that can be taken to maximize the comparability between SGS estimates.

  13. Comparative genetics in the grasses

    OpenAIRE

    Gale, Michael D.; Devos, Katrien M.

    1998-01-01

    Genetic mapping of wheat, maize, and rice and other grass species with common DNA probes has revealed remarkable conservation of gene content and gene order over the 60 million years of radiation of Poaceae. The linear organization of genes in some nine different genomes differing in basic chromosome number from 5 to 12 and nuclear DNA amount from 400 to 6,000 Mb, can be described in terms of only 25 “rice linkage blocks.” The extent to which this intergenomic coli...

  14. Wideband Direction of Arrival (DOA Estimation: A Comparative Study of Wideband MUSIC Method, Joint Diagonalization Structure (JDS Method and Beam-Space Genetic Algorithm (BGA

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    Sandeep Santosh

    2016-09-01

    Full Text Available In this paper, a comparative study of Wideband MUSIC method, Joint Diagonalization Structure (JDS method and Beam-Space Genetic Algorithm (BGA is presented with respect to resolution probability and Root mean square error (RMSE evaluated in both low and high Signal-to-Noise ratio (SNR regions. The simulation results show that BGA has higher resolution probability than the JDS method and Wideband MUSIC method in low SNR region while in the high SNR region, Wideband MUSIC has higher resolution probability followed by BGA and JDS method. RMSE is smallest for BGA as compared to JDS and Wideband MUSIC in low SNR region. In the high SNR region, Wideband MUSIC has smallest RMSE followed by BGA and JDS method.

  15. Coalgebraic structure of genetic inheritance.

    Science.gov (United States)

    Tian, Jianjun; Li, Bai-Lian

    2004-09-01

    Although in the broadly defined genetic algebra, multiplication suggests a forward direction of from parents to progeny, when looking from the reverse direction, it also suggests to us a new algebraic structure-coalge- braic structure, which we call genetic coalgebras. It is not the dual coalgebraic structure and can be used in the construction of phylogenetic trees. Math- ematically, to construct phylogenetic trees means we need to solve equations x([n]) = a, or x([n]) = b. It is generally impossible to solve these equations inalgebras. However, we can solve them in coalgebras in the sense of tracing back for their ancestors. A thorough exploration of coalgebraic structure in genetics is apparently necessary. Here, we develop a theoretical framework of the coalgebraic structure of genetics. From biological viewpoint, we defined various fundamental concepts and examined their elementary properties that contain genetic significance. Mathematically, by genetic coalgebra, we mean any coalgebra that occurs in genetics. They are generally noncoassociative and without counit; and in the case of non-sex-linked inheritance, they are cocommutative. Each coalgebra with genetic realization has a baric property. We have also discussed the methods to construct new genetic coalgebras, including cocommutative duplication, the tensor product, linear combinations and the skew linear map, which allow us to describe complex genetic traits. We also put forward certain theorems that state the relationship between gametic coalgebra and gametic algebra. By Brower's theorem in topology, we prove the existence of equilibrium state for the in-evolution operator.

  16. Ocean currents help explain population genetic structure

    Science.gov (United States)

    White, Crow; Selkoe, Kimberly A.; Watson, James; Siegel, David A.; Zacherl, Danielle C.; Toonen, Robert J.

    2010-01-01

    Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management. PMID:20133354

  17. Comparative genetic structure in pines: evolutionary and conservation consequences Estructura genética comparada en pinos: consecuencias evolutivas y para la conservación

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    PATRICIA DELGADO

    2002-03-01

    Full Text Available Pines have been the focus of several studies that estimate population genetic parameters using both allozymes and chloroplast single sequence repeats (SSRs. Also, the genus has also been recently studied using molecular systematics so that we now have a more clear understanding of their evolutionary history. With this background we studied comparatively the genetic structure in pines. Expected heterozygosity is particularly constant with a 99 % confidence interval between 0.19 and 0.23 in species that have been studied until now using allozymes. There is a significant proportion of species (9/41 that show high population differentiation estimates (Fst = or larger than 0.15 and five of these have large and wingless seeds probably associated with low densities, bird dispersal mechanisms and resistance to water stress. These species include the North American pinyon pines. Outcrossing rates are also constant among species from both subgenus Pinus and subgenus Strobus, which probably reflects a selective limit to the amount of deleterious alleles that can be maintained in pine species and this also affects inbreeding levels. We also explored the data published using microsatellites in pines and conclude that these markers uncover a higher proportion of variation and genetic differentiation as expected and that the evolutionary models that are used to derive the population genetic structure estimators should take into account other sources of mutation (point mutations, larger insertions and or deletions and duplications to better understand the comparative applications of these molecular markersLos pinos han sido el objeto de varios estudios para estimar los parámetros genéticos de la población utilizando tanto aloenzimas como fragmentos repetidos de secuencia sencilla (RSSs de cloroplasto. Este género también ha sido estudiado recientemente utilizando sistemática molecular de tal manera que ahora tenemos un entendimiento más claro de su

  18. Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence.

    Science.gov (United States)

    Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

    2017-08-16

    Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae). Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation. Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances. Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations. © 2017 Botanical Society of America.

  19. Global MLST of Salmonella Typhi Revisited in Post-Genomic Era: Genetic conservation, Population Structure and Comparative genomics of rare sequence types

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    Kien-Pong eYap

    2016-03-01

    Full Text Available Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus Sequence Typing (MLST is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2 co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC and tviD that may explain the variations that differentiate between seemingly successful (widespread and unsuccessful (poor dissemination S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

  20. Genetic network models: a comparative study

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    van Someren, Eugene P.; Wessels, Lodewyk F. A.; Reinders, Marcel J. T.

    2001-06-01

    Currently, the need arises for tools capable of unraveling the functionality of genes based on the analysis of microarray measurements. Modeling genetic interactions by means of genetic network models provides a methodology to infer functional relationships between genes. Although a wide variety of different models have been introduced so far, it remains, in general, unclear what the strengths and weaknesses of each of these approaches are and where these models overlap and differ. This paper compares different genetic modeling approaches that attempt to extract the gene regulation matrix from expression data. A taxonomy of continuous genetic network models is proposed and the following important characteristics are suggested and employed to compare the models: inferential power; predictive power; robustness; consistency; stability and computational cost. Where possible, synthetic time series data are employed to investigate some of these properties. The comparison shows that although genetic network modeling might provide valuable information regarding genetic interactions, current models show disappointing results on simple artificial problems. For now, the simplest models are favored because they generalize better, but more complex models will probably prevail once their bias is more thoroughly understood and their variance is better controlled.

  1. Somatically acquired structural genetic differences

    DEFF Research Database (Denmark)

    Magaard Koldby, Kristina; Nygaard, Marianne; Christensen, Kaare;

    2016-01-01

    Structural genetic variants like copy number variants (CNVs) comprise a large part of human genetic variation and may be inherited as well as somatically acquired. Recent studies have reported the presence of somatically acquired structural variants in the human genome and it has been suggested t...... with age.European Journal of Human Genetics advance online publication, 20 April 2016; doi:10.1038/ejhg.2016.34.......Structural genetic variants like copy number variants (CNVs) comprise a large part of human genetic variation and may be inherited as well as somatically acquired. Recent studies have reported the presence of somatically acquired structural variants in the human genome and it has been suggested...... that they may accumulate in elderly individuals. To further explore the presence and the age-related acquisition of somatic structural variants in the human genome, we investigated CNVs acquired over a period of 10 years in 86 elderly Danish twins as well as CNV discordances between co-twins of 18 monozygotic...

  2. Population genetic structure and ecotoxicology.

    OpenAIRE

    Guttman, S I

    1994-01-01

    Electrophoretic analyses of population genetic structure, both in the laboratory and in the field, have documented significant shifts in allozyme genotype frequencies in a variety of aquatic taxa as a result of environmental impacts. Studies are documented which indicate that contaminants may select for individuals with tolerant allozyme genotypes, causing the potential loss of individuals with sensitive genotypes. This may diminish the genetic variability and fitness of affected populations ...

  3. Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites.

    Science.gov (United States)

    Schueler, Silvio; Tusch, Alexandra; Scholz, Florian

    2006-10-01

    Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the

  4. Genetic structure of chimpanzee populations.

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    Celine Becquet

    2007-04-01

    Full Text Available Little is known about the history and population structure of our closest living relatives, the chimpanzees, in part because of an extremely poor fossil record. To address this, we report the largest genetic study of the chimpanzees to date, examining 310 microsatellites in 84 common chimpanzees and bonobos. We infer three common chimpanzee populations, which correspond to the previously defined labels of "western," "central," and "eastern," and find little evidence of gene flow between them. There is tentative evidence for structure within western chimpanzees, but we do not detect distinct additional populations. The data also provide historical insights, demonstrating that the western chimpanzee population diverged first, and that the eastern and central populations are more closely related in time.

  5. A comparative phylogenetic study of genetics and folk music.

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    Pamjav, Horolma; Juhász, Zoltán; Zalán, Andrea; Németh, Endre; Damdin, Bayarlkhagva

    2012-04-01

    Computer-aided comparison of folk music from different nations is one of the newest research areas. We were intrigued to have identified some important similarities between phylogenetic studies and modern folk music. First of all, both of them use similar concepts and representation tools such as multidimensional scaling for modelling relationship between populations. This gave us the idea to investigate whether these connections are merely accidental or if they mirror population migrations from the past. We raised the question; does the complex structure of musical connections display a clear picture and can this system be interpreted by the genetic analysis? This study is the first to systematically investigate the incidental genetic background of the folk music context between different populations. Paternal (42 populations) and maternal lineages (56 populations) were compared based on Fst genetic distances of the Y chromosomal and mtDNA haplogroup frequencies. To test this hypothesis, the corresponding musical cultures were also compared using an automatic overlap analysis of parallel melody styles for 31 Eurasian nations. We found that close musical relations of populations indicate close genetic distances (folk music; maternal lineages have a more important role in folk music traditions than paternal lineages. Furthermore, the combination of these disciplines establishing a new interdisciplinary research field of "music-genetics" can be an efficient tool to get a more comprehensive picture on the complex behaviour of populations in prehistoric time.

  6. Genetic structure of nine horse populations

    Directory of Open Access Journals (Sweden)

    Monika Burócziová

    2008-01-01

    Full Text Available In the present study was estimate the genetic diversity and relationships among nine horses breeds in Czech and Slovak Republic.In conclusion, the main objective of study was to show the level of genetic distance among the horse breeds with different history of breeding of each country. Furthermore, it should be clarified whether these populations and subpopulations are distinct enough from each other to justify defining separate breeds. This research concerns the variability of microsatellite markers in genotypes of horse. We compared the genetic diversity and distance among nine horse breeds Czech and Slovak Warmblood both of Czech origin, Slovak Warmblood of Slovak origin, Hucul, Hafling, Furioso, Noriker, Silesian Noriker and Bohemian-Moravian Belgian Horse.In total, 932 animals were genotyped for 17 microsatellites markers (AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, HTG6, HMS2, HTG7, ASB17, ASB23, CA425, HMS1, LEX3 recommended by the International Society of Animal Genetics.In the different population size, the allele frequencies, observed and expected heterozygosity, test for deviations from Hardy-Weinberg equilibrium and Polymorphism information content have been calculated for each breed. We analyzed genetic distance and diversity among them on the base of the dataset of highly polymorphic set of microsatellites representing all autozomes using set of PowerMar­ker v3.25 analysis tools and Structure 2.2. programme for results comparison.

  7. Genetic Structure of the Spanish Population

    Directory of Open Access Journals (Sweden)

    Gutiérrez Marta

    2010-05-01

    Full Text Available Abstract Background Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias. Results In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV analyses, and have compared these estimates of the Spanish population with existing data from similar efforts. Conclusions In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community.

  8. A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca), Pumas (Puma concolor), and Ocelots (Leopardus pardalis) in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone.

    Science.gov (United States)

    Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J

    2016-01-01

    With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis). We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09), followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16), and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08). We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.

  9. A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca, Pumas (Puma concolor, and Ocelots (Leopardus pardalis in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone.

    Directory of Open Access Journals (Sweden)

    Claudia Wultsch

    Full Text Available With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca, pumas (Puma concolor, and ocelots (Leopardus pardalis. We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09, followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16, and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08. We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.

  10. Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers

    Directory of Open Access Journals (Sweden)

    Magdalena Szenejko

    2016-09-01

    Full Text Available Background Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. Methods The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA. Results The low value of Dice’s coefficient (0.369 along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. Discussion The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.

  11. Predicting Protein Structure Using Parallel Genetic Algorithms.

    Science.gov (United States)

    1994-12-01

    34 IEEE Transactions on Systems, Man and Cybernetics, 10(9) (September 1980). 16. De Jong, Kenneth A. "On Using Genetic Algoriths to Search Program...By " Predicting rotein Structure D istribticfiar.. ................ Using Parallel Genetic Algorithms ,Avaiu " ’ •"... Dist THESIS I IGeorge H...iiLite-d Approved for public release; distribution unlimited AFIT/ GCS /ENG/94D-03 Predicting Protein Structure Using Parallel Genetic Algorithms

  12. Structural similarity of genetically interacting proteins

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    Nussinov Ruth

    2008-07-01

    Full Text Available Abstract Background The study of gene mutants and their interactions is fundamental to understanding gene function and backup mechanisms within the cell. The recent availability of large scale genetic interaction networks in yeast and worm allows the investigation of the biological mechanisms underlying these interactions at a global scale. To date, less than 2% of the known genetic interactions in yeast or worm can be accounted for by sequence similarity. Results Here, we perform a genome-scale structural comparison among protein pairs in the two species. We show that significant fractions of genetic interactions involve structurally similar proteins, spanning 7–10% and 14% of all known interactions in yeast and worm, respectively. We identify several structural features that are predictive of genetic interactions and show their superiority over sequence-based features. Conclusion Structural similarity is an important property that can explain and predict genetic interactions. According to the available data, the most abundant mechanism for genetic interactions among structurally similar proteins is a common interacting partner shared by two genetically interacting proteins.

  13. Structural health monitoring using genetic fuzzy systems

    CERN Document Server

    Pawar, Prashant M

    2014-01-01

    The high profile of structural health monitoring (SHM) will add urgency to this detailed treatment of intelligent SHM development and implementation via the evolutionary system, which uses a genetic algorithm to automate the development of the fuzzy system.

  14. Comparing Consumer Attitudes towards Genetically Modified Food in Europe

    OpenAIRE

    2002-01-01

    As biotechnology evolves new methods of genetic engineering are now being applied to the production and processing of foods. This paper is trying to explore the attitudes of the European consumers towards genetic modification of food. Using survey data of the EU member countries the proposed research paper is planned to have a threefold output: 1) providing a comparative ranking of the EU member countries in relation to the prevalence of rejection of genetically modified food, 2) uncovering i...

  15. (Genetic structure of natural populations)

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Introduction to Protein Structure through Genetic Diseases

    Science.gov (United States)

    Schneider, Tanya L.; Linton, Brian R.

    2008-01-01

    An illuminating way to learn about protein function is to explore high-resolution protein structures. Analysis of the proteins involved in genetic diseases has been used to introduce students to protein structure and the role that individual mutations can play in the onset of disease. Known mutations can be correlated to changes in protein…

  17. Introduction to Protein Structure through Genetic Diseases

    Science.gov (United States)

    Schneider, Tanya L.; Linton, Brian R.

    2008-01-01

    An illuminating way to learn about protein function is to explore high-resolution protein structures. Analysis of the proteins involved in genetic diseases has been used to introduce students to protein structure and the role that individual mutations can play in the onset of disease. Known mutations can be correlated to changes in protein…

  18. Predicting complex mineral structures using genetic algorithms.

    Science.gov (United States)

    Mohn, Chris E; Kob, Walter

    2015-10-28

    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  19. 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...

  20. A genetic algorithm for structure-activity relationships: software implementation

    CERN Document Server

    Jantschi, Lorentz

    2009-01-01

    The design and the implementation of a genetic algorithm are described. The applicability domain is on structure-activity relationships expressed as multiple linear regressions and predictor variables are from families of structure-based molecular descriptors. An experiment to compare different selection and survival strategies was designed and realized. The genetic algorithm was run using the designed experiment on a set of 206 polychlorinated biphenyls searching on structure-activity relationships having known the measured octanol-water partition coefficients and a family of molecular descriptors. The experiment shows that different selection and survival strategies create different partitions on the entire population of all possible genotypes.

  1. GENETIC CONSEQUENCES OF SEED DISPERSAL IN THREE SYMPATRIC FOREST HERBS. I. HIERARCHICAL POPULATION-GENETIC STRUCTURE.

    Science.gov (United States)

    Williams, Charles F; Guries, Raymond P

    1994-06-01

    To examine the effects of seed dispersal on spatial genetic structure, we compare three sympatric species of forest herbs in the family Apiaceae whose fruits differ widely in morphological adaptations for animal-attached dispersal. Cryptotaenia canadensis has smooth fruits that are gravity dispersed, whereas Osmorhiza claytonii and Sanicula odorata fruits have appendages that facilitate their attachment to animals. The relative seed-dispersal ability among species, measured as their ability to remain attached to mammal fur, is ranked Sanicula > Osmorhiza > Cryptotaenia. We use a nested hierarchical sampling design to analyze genetic structure at spatial scales ranging from a few meters to hundreds of kilometers. Genetic differentiation among population subdivisions, estimated by average genetic distance and hierarchical F-statistics, has an inverse relationship with dispersal ability such that Cryptotaenia > Osmorhiza > Sanicula. In each species, genetic differentiation increases with distance among population subdivisions. Stochastic variation in gene flow, arising from seed dispersal by attachment to animals, may partly explain the weak relationship between pairwise spatial and genetic distance among populations and heterogeneity in estimates of single locus F-statistics. A hierarchical island model of gene flow is invoked to describe the effects of seed dispersal on population genetic structure. Seed dispersal is the predominant factor affecting variation in gene flow among these ecologically similar, taxonomically related species. © 1994 The Society for the Study of Evolution.

  2. The genetic structure of the Swedish population.

    Directory of Open Access Journals (Sweden)

    Keith Humphreys

    Full Text Available Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise F(st indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to

  3. Comparative genetics of the rdar morphotype in Salmonella.

    Science.gov (United States)

    White, A P; Surette, M G

    2006-12-01

    The Salmonella rdar morphotype is a distinct, rough and dry colony morphology formed by the extracellular interaction of thin aggregative fimbriae (Tafi or curli), cellulose, and other polysaccharides. Cells in rdar colonies are more resistant to desiccation and exogenous stresses, which is hypothesized to aid in the passage of pathogenic Salmonella spp. between hosts. Here we analyzed the genetic and phenotypic conservation of the rdar morphotype throughout the entire Salmonella genus. The rdar morphotype was conserved in 90% of 80 isolates representing all 7 Salmonella groups; however, the frequency was only 31% in a reference set of 16 strains (Salmonella reference collection C [SARC]). Comparative gene expression analysis was used to separate cis- and trans-acting effects on promoter activity for the 16 SARC strains, focusing on the 780-bp intergenic region containing divergent promoters for the master regulator of the rdar morphotype (agfD) and the Tafi structural genes (agfB). Surprisingly, promoter functionality was conserved in most isolates, and loss of the phenotype was due primarily to defects in trans-acting regulatory factors. We hypothesize that trans differences have been caused by domestication, whereas cis differences, detected for Salmonella enterica subsp. arizonae isolates, may reflect an evolutionary change in lifestyle. Our results demonstrate that the rdar morphotype is conserved throughout the salmonellae, but they also emphasize that regulation is an important source of variability among isolates.

  4. Community structure and population genetics of Eastern Mediterranean polychaetes

    Directory of Open Access Journals (Sweden)

    Giorgos eChatzigeorgiou

    2014-10-01

    Full Text Available Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1776 during two successive years at two locations in northern Crete (Aegean Sea and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community.

  5. Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed

    Science.gov (United States)

    Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

    2012-01-01

    Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations. PMID:23139883

  6. Regeneration Methods Affect Genetic Variation and Structure in Shortleaf Pine (Pinus Echinata Mill.)

    Science.gov (United States)

    Rajiv G. Raja; Charles G. Tauer; Robert F. Wittwer; Yinghua Huang

    1998-01-01

    The effects of regene ration methods on genetic diversity and structure in shortleaf pine (Pinus echinata Mill.) were examined by quantifying the changes in genetic composition of shortleaf pine stands following harvest by monitoring changes in allele number and frequency at heterozygous loci over time. The results were also compared to the genetic...

  7. Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens

    DEFF Research Database (Denmark)

    Timms, Richard T.; Menzies, Sam A.; Tchasovnikarova, Iva A.

    2016-01-01

    The application of forward genetic screens to cultured human cells represents a powerful method to study gene function. The repurposing of the bacterial CRISPR/Cas9 system provides an effective method to disrupt gene function in mammalian cells, and has been applied to genome-wide screens. Here, we...... compare the efficacy of genome-wide CRISPR/Cas9-mediated forward genetic screens versus gene-trap mutagenesis screens in haploid human cells, which represent the existing ‘gold standard’ method. This head-to-head comparison aimed to identify genes required for the endoplasmic reticulum....../3-associated disulphide reductase. Genome-wide CRISPR/Cas9-mediated screens together with haploid genetic screens provide a powerful addition to the forward genetic toolbox....

  8. Genetic Synthesis of New Reversible/Quantum Ternary Comparator

    Directory of Open Access Journals (Sweden)

    DEIBUK, V.

    2015-08-01

    Full Text Available Methods of quantum/reversible logic synthesis are based on the use of the binary nature of quantum computing. However, multiple-valued logic is a promising choice for future quantum computer technology due to a number of advantages over binary circuits. In this paper we have developed a synthesis of ternary reversible circuits based on Muthukrishnan-Stroud gates using a genetic algorithm. The method of coding chromosome is presented, and well-grounded choice of algorithm parameters allowed obtaining better circuit schemes of one- and n-qutrit ternary comparators compared with other methods. These parameters are quantum cost of received reversible devices, delay time and number of constant input (ancilla lines. Proposed implementation of the genetic algorithm has led to reducing of the device delay time and the number of ancilla qutrits to 1 and 2n-1 for one- and n-qutrits full comparators, respectively. For designing of n-qutrit comparator we have introduced a complementary device which compares output functions of 1-qutrit comparators.

  9. Genetic structure of spatial and verbal working memory.

    Science.gov (United States)

    Ando, J; Ono, Y; Wright, M J

    2001-11-01

    Working memory (WM) encompasses both short-term memory (storage) and executive functions that play an essential role in all forms of cognition. In this study, the genetic structure of storage and executive functions engaged in both a spatial and verbal WM span task is investigated using a twin sample. The sample consists of 143 monozygotic (MZ) and 93 dizygotic (DZ) Japanese twin pairs, ages 16 to 29 years. In 155 (87 MZ, 62 DZ) of these pairs, cognitive ability scores from the Kyodai Japanese IQ test are also obtained. The phenotypic relationship between WM and cognitive ability is confirmed (r = 0.26-0.44). Individual differences in WM storage and executive functions are found to be significantly influenced by genes, with heritability estimates all moderately high (43%-49%), and estimates for cognitive ability comparable to previous studies (65%). A large part of the genetic variance in storage and executive functions in both spatial and verbal modalities is due to a common genetic factor that accounts for 11% to 43% of the variance. In the reduced sample, this common genetic factor accounts for 64% and 26% of the variance in spatial and verbal cognitive ability, respectively. Additional genetic variance in WM (7%-30%) is due to modality specific factors (spatial and verbal) and a storage specific factor that may be particularly important for the verbal modality. None of the variance in cognitive ability is accounted for by the modality and storage genetic factors, suggesting these may be specific to WM.

  10. Hitchhiker's guide to genetic diversity in socially structured populations

    Institute of Scientific and Technical Information of China (English)

    L.S.PREMO

    2012-01-01

    When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking.A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration.Under conditions in which genetic and cultural variants are transmitted symmetrically,neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking.Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity,and it may be applicable to humans as well.This paper provides a critical review of recent models of both types of hitchhiking in socially structured populations.The models' assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species,and vice versa [Current Zoology 58 (1):287-297,2012].

  11. 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.

  12. The Genetic Structure of Marijuana and Hemp.

    Science.gov (United States)

    Sawler, Jason; Stout, Jake M; Gardner, Kyle M; Hudson, Darryl; Vidmar, John; Butler, Laura; Page, Jonathan E; Myles, Sean

    2015-01-01

    Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana), which contain high amounts of the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC), are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica) are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains.

  13. The Genetic Structure of Marijuana and Hemp.

    Directory of Open Access Journals (Sweden)

    Jason Sawler

    Full Text Available Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana, which contain high amounts of the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC, are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains.

  14. The Genetic Structure of Marijuana and Hemp

    Science.gov (United States)

    Sawler, Jason; Stout, Jake M.; Gardner, Kyle M.; Hudson, Darryl; Vidmar, John; Butler, Laura; Page, Jonathan E.; Myles, Sean

    2015-01-01

    Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana), which contain high amounts of the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC), are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica) are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains. PMID:26308334

  15. Beyond the thale: comparative genomics and genetics of Arabidopsis relatives.

    Science.gov (United States)

    Koenig, Daniel; Weigel, Detlef

    2015-05-01

    For decades a small number of model species have rightly occupied a privileged position in laboratory experiments, but it is becoming increasingly clear that our knowledge of biology is greatly improved when informed by a broader diversity of species and evolutionary context. Arabidopsis thaliana has been the primary model organism for plants, benefiting from a high-quality reference genome sequence and resources for reverse genetics. However, recent studies have made a group of species also in the Brassicaceae family and closely related to A. thaliana a focal point for comparative molecular, genomic, phenotypic and evolutionary studies. In this Review, we emphasize how such studies complement continued study of the model plant itself, provide an evolutionary perspective and summarize our current understanding of genetic and phenotypic diversity in plants.

  16. [Molecular genetic analysis of wild soybean (Glycine soja Sieb. & Zucc.) population structure in anthropogenic and natural landscapes of Primorskii krai].

    Science.gov (United States)

    Nedoluzhko, A V; Tikhonov, A V; Dorokhov, D B

    2008-08-01

    The data are presented on genetic population structure of wild soybean growing in natural and anthropogenically disturbed landscapes of Primorskii krai of the Russian Federation. Comparative analysis showed that wild soybean populations exposed to anthropogenic influence exhibited lower genetic diversity than natural populations. Recommendations on conservation of the wild plant gene pools using comparative data on population genetic structures are made.

  17. Spatial genetic structure of a symbiotic beetle-fungal system: toward multi-taxa integrated landscape genetics.

    Directory of Open Access Journals (Sweden)

    Patrick M A James

    Full Text Available Spatial patterns of genetic variation in interacting species can identify shared features that are important to gene flow and can elucidate co-evolutionary relationships. We assessed concordance in spatial genetic variation between the mountain pine beetle (Dendroctonus ponderosae and one of its fungal symbionts, Grosmanniaclavigera, in western Canada using neutral genetic markers. We examined how spatial heterogeneity affects genetic variation within beetles and fungi and developed a novel integrated landscape genetics approach to assess reciprocal genetic influences between species using constrained ordination. We also compared landscape genetic models built using Euclidean distances based on allele frequencies to traditional pair-wise Fst. Both beetles and fungi exhibited moderate levels of genetic structure over the total study area, low levels of structure in the south, and more pronounced fungal structure in the north. Beetle genetic variation was associated with geographic location while that of the fungus was not. Pinevolume and climate explained beetle genetic variation in the northern region of recent outbreak expansion. Reciprocal genetic relationships were only detectedin the south where there has been alonger history of beetle infestations. The Euclidean distance and Fst-based analyses resulted in similar models in the north and over the entire study area, but differences between methods in the south suggest that genetic distances measures should be selected based on ecological and evolutionary contexts. The integrated landscape genetics framework we present is powerful, general, and can be applied to other systems to quantify the biotic and abiotic determinants of spatial genetic variation within and among taxa.

  18. The Genetic Structure of Milkfish (Chanos chanos) Stocks from ...

    African Journals Online (AJOL)

    Yudha T Adiputra

    2012-02-14

    Feb 14, 2012 ... waters. AFLP analyses may reveal historical patterns of milkfish genetic population structure in ... categorize their population of origin to design a long term management ..... Systematic, distribution, genetics and life history of.

  19. Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept.

    Science.gov (United States)

    Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

    2016-04-01

    Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating

  20. Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses.

    Science.gov (United States)

    Lauber, Chris; Gorbalenya, Alexander E

    2012-04-01

    Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

  1. Comparative Genetics of Floral Morphology in Diploid and Allotetraploid Gossypium

    Institute of Scientific and Technical Information of China (English)

    CHEE Peng W

    2008-01-01

    @@ The cultivated Gossypium A genome diploid species G.arboreum and G.herbaceum and the allotetraploid species G.hirsutum and G.barbadense share common morphology for various floral traits,which offers an ideal system in which to investigate genetic mechanisms that differentiate diploid and tetraploid genomes.For example,knowing how a single phenotype behaves in the diploids,and comparing the same trait with different dosage effects in the tetraploids,may provide a means to study inter- and intra-genomic interactions in the polyploid genome.

  2. Comparative Transmission Genetics of Introgressed Chromatin in Gossypium Species

    Institute of Scientific and Technical Information of China (English)

    WAGHMARE Vijay N; RONG Jun-kang; ROGERS Carl J; BOWERS John E; PATERSON Andrew H

    2008-01-01

    @@ Wild relatives and un-adapted germplasm of crop species harbors several adaptive traits.Introgression of genes for economic and adaptive traits brings in novel genetic variation into the gene pools of many crops including cotton.We compared patterns of introgression into polyploid Gossypium hirsuture from its sister G.tomentosum,and from G.barbadense representing a different clade tracing to the same polyploidization.Advanced-generation populations,resulting from recurrent backcrossing to G.hirsutum,show a paucity of G.tomentosum alleles and severe deficiencies of homozygotes.

  3. Comparative design of structures concepts and methodologies

    CERN Document Server

    Lin, Shaopei

    2016-01-01

    This book presents comparative design as an approach to the conceptual design of structures. Primarily focusing on reasonable structural performance, sustainable development and architectural aesthetics, it features detailed studies of structural performance through the composition and de-composition of these elements for a variety of structures, such as high-rise buildings, long-span crossings and spatial structures. The latter part of the book addresses the theoretical basis and practical implementation of knowledge engineering in structural design, and a case-based fuzzy reasoning method is introduced to illustrate the concept and method of intelligent design. The book is intended for civil engineers, structural designers and architects, as well as senior undergraduate and graduate students in civil engineering and architecture. Shaopei Lin and Zhen Huang are both Professors at the Department of Civil Engineering, Shanghai Jiao Tong University, China.

  4. Structural deterioration of tendon collagen in genetic muscular dystrophy.

    Science.gov (United States)

    Stinson, R H

    1975-08-19

    The structure of gastrocnemius tendons from chickens with genetically induced muscular dystrophy has been studied by low-angle X-ray diffraction. Compared with normal samples there is poor alignment of collagen within the tendons. This difference is quite pronounced at eight weeks when the affected birds are still in comparatively good physical condition. Similar changes have been reported for birds with nutritionally induced muscular dystrophy (Bartlett, M. W., Egelstaff, P. A., Holden, T. M., Stinson, R. H. and Sweeny, P. R. (1973) Biochim. Biophys. Acta 328, 213-220).

  5. Genetic structure of West Greenland populations of lumpfish Cyclopterus lumpus

    DEFF Research Database (Denmark)

    Mayoral, Elsa Garcia; Olsen, M.; Hedeholm, R.

    2016-01-01

    In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow for identifica......In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow...... for identification of origin of C. lumpus in Greenlandic waters, genetic assignment analysis was performed for 86 C. lumpus sampled on a feeding migration. Significant structuring with isolation by distance was observed in the West Greenland samples and two major subpopulations, north and south, were suggested...

  6. Comparative Protein Structure Modeling Using MODELLER.

    Science.gov (United States)

    Webb, Benjamin; Sali, Andrej

    2016-06-20

    Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.

  7. Comparative Landscape Genetics of Three Closely Related Sympatric Hesperid Butterflies with Diverging Ecological Traits

    Science.gov (United States)

    Engler, Jan O.; Balkenhol, Niko; Filz, Katharina J.; Habel, Jan C.; Rödder, Dennis

    2014-01-01

    To understand how landscape characteristics affect gene flow in species with diverging ecological traits, it is important to analyze taxonomically related sympatric species in the same landscape using identical methods. Here, we present such a comparative landscape genetic study involving three closely related Hesperid butterflies of the genus Thymelicus that represent a gradient of diverging ecological traits. We analyzed landscape effects on their gene flow by deriving inter-population connectivity estimates based on different species distribution models (SDMs), which were calculated from multiple landscape parameters. We then used SDM output maps to calculate circuit-theoretic connectivity estimates and statistically compared these estimates to actual genetic differentiation in each species. We based our inferences on two different analytical methods and two metrics of genetic differentiation. Results indicate that land use patterns influence population connectivity in the least mobile specialist T. acteon. In contrast, populations of the highly mobile generalist T. lineola were panmictic, lacking any landscape related effect on genetic differentiation. In the species with ecological traits in between those of the congeners, T. sylvestris, climate has a strong impact on inter-population connectivity. However, the relative importance of different landscape factors for connectivity varies when using different metrics of genetic differentiation in this species. Our results show that closely related species representing a gradient of ecological traits also show genetic structures and landscape genetic relationships that gradually change from a geographical macro- to micro-scale. Thus, the type and magnitude of landscape effects on gene flow can differ strongly even among closely related species inhabiting the same landscape, and depend on their relative degree of specialization. In addition, the use of different genetic differentiation metrics makes it possible to

  8. 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,

  9. Agreeing Probability Measures for Comparative Probability Structures

    NARCIS (Netherlands)

    P.P. Wakker (Peter)

    1981-01-01

    textabstractIt is proved that fine and tight comparative probability structures (where the set of events is assumed to be an algebra, not necessarily a σ-algebra) have agreeing probability measures. Although this was often claimed in the literature, all proofs the author encountered are not valid

  10. Comparing a Coevolutionary Genetic Algorithm for Multiobjective Optimization

    Science.gov (United States)

    Lohn, Jason D.; Kraus, William F.; Haith, Gary L.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    We present results from a study comparing a recently developed coevolutionary genetic algorithm (CGA) against a set of evolutionary algorithms using a suite of multiobjective optimization benchmarks. The CGA embodies competitive coevolution and employs a simple, straightforward target population representation and fitness calculation based on developmental theory of learning. Because of these properties, setting up the additional population is trivial making implementation no more difficult than using a standard GA. Empirical results using a suite of two-objective test functions indicate that this CGA performs well at finding solutions on convex, nonconvex, discrete, and deceptive Pareto-optimal fronts, while giving respectable results on a nonuniform optimization. On a multimodal Pareto front, the CGA finds a solution that dominates solutions produced by eight other algorithms, yet the CGA has poor coverage across the Pareto front.

  11. Genetic population structures of the blue starfish Linckia laevigata and its gastropod ectoparasite Thyca crystallina

    National Research Council Canada - National Science Library

    Kochzius, M; Seidel, C; Hauschild, J; Kirchhoff, S; Mester, P; Meyer-Wachsmuth, I; Nuryanto, A; Timm, J

    2009-01-01

    ... lead to congruent patterns. We studied the comparative genetic population structure based on partial sequences of the mitochondrial cytochrome oxidase I gene of the blue starfish Linckia laevigata and its gastropod ectoparasite...

  12. Comparing anisotropic displacement parameters in protein structures.

    Science.gov (United States)

    Merritt, E A

    1999-12-01

    The increasingly widespread use of synchrotron-radiation sources and cryo-preparation of samples in macromolecular crystallography has led to a dramatic increase in the number of macromolecular structures determined at atomic or near-atomic resolution. This permits expansion of the structural model to include anisotropic displacement parameters U(ij) for individual atoms. In order to explore the physical significance of these parameters in protein structures, it is useful to be able to compare quantitatively the electron-density distribution described by the refined U(ij) values associated with corresponding crystallographically independent atoms. This paper presents the derivation of an easily calculated correlation coefficient in real space between two atoms modeled with anisotropic displacement parameters. This measure is used to investigate the degree of similarity between chemically equivalent but crystallographically independent atoms in the set of protein structural models currently available from the Protein Data Bank.

  13. Flexibility of the genetic code with respect to DNA structure

    DEFF Research Database (Denmark)

    Baisnée, P. F.; Baldi, Pierre; Brunak, Søren

    2001-01-01

    Motivation. The primary function of DNA is to carry genetic information through the genetic code. DNA, however, contains a variety of other signals related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, nucleosome positioning and DNA...... structure. Here we study the relationship between the genetic code and DNA structure and address two questions. First, to which degree does the degeneracy of the genetic code and the acceptable amino acid substitution patterns allow for the superimposition of DNA structural signals to protein coding...... sequences? Second, is the origin or evolution of the genetic code likely to have been constrained by DNA structure? Results. We develop an index for code flexibility with respect to DNA structure. Using five different di- or tri-nucleotide models of sequence-dependent DNA structure, we show...

  14. Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro.

    Science.gov (United States)

    Zancolli, Giulia; Rödel, Mark-Oliver; Steffan-Dewenter, Ingolf; Storfer, Andrew

    2014-10-01

    Estimating population connectivity and species' abilities to disperse across the landscape is crucial for understanding the long-term persistence of species in changing environments. Surprisingly, few landscape genetic studies focused on tropical regions despite the alarming extinction rates within these ecosystems. Here, we compared the influence of landscape features on the distribution of genetic variation of an Afromontane frog, Amietia wittei, with that of its more broadly distributed lowland congener, Amietia angolensis, on Mt. Kilimanjaro, Tanzania. We predicted high gene flow in the montane species with movements enhanced through terrestrial habitats of the continuous rainforest. In contrast, dispersal might be restricted to aquatic corridors and reduced by anthropogenic disturbance in the lowland species. We found high gene flow in A. wittei relative to other montane amphibians. Nonetheless, gene flow was lower than in the lowland species which showed little population structure. Least-cost path analysis suggested that dispersal is facilitated by stream networks in both species, but different landscape features were identified to influence connectivity among populations. Contrary to a previous study, gene flow in the lowland species was negatively correlated with the presence of human settlements. Also, genetic subdivision in A. wittei did not coincide with specific physical barriers as in other landscape genetic studies, suggesting that factors other than topography may contribute to population divergence. Overall, these results highlight the importance of a comparative landscape genetic approach for assessing the influence of the landscape matrix on population connectivity, particularly because nonintuitive results can alter the course of conservation and management.

  15. Comparative studies on some genetic characteristics among four large yellow croaker (Pseudosciaena crocea) populations

    Institute of Scientific and Technical Information of China (English)

    WANG Dexiang; WANG Jun; DING Shaoxiong; SU Yongquan

    2007-01-01

    The genetic structure was compared among four large yellow croaker (Pseudosciaena crocea) populations, an important aquaculture species in China. RAPD and ISSR results show that the genetic distances between domestic stocks and their wild counterparts are significantly larger than those between the three wild stocks. The sequence of mtDNA cyt b shows that the three wild populations share the same sequence, with differences in the four bases from the cultured stock: two transitions [ 57 ( C-T), 291 (G-A) ] and two transversions [ 66 (C-G) ,223 (A-C) ]. Cluster analysis reveals that the domestic stock has diverged from its parental wild stock [ Min-Yuedong (Fujian Province-eastern Guangdong Province, China) stock]. Results demonstrate that 20 a of domestication of the Pseudosciaena crocea stock has resulted in significant genetic changes.

  16. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    pc

    2016-11-02

    Nov 2, 2016 ... diversity and genetic structure of 35 maize accessions using 10 microsatellite markers. These accessions ... In addition, they provide new sources of resistance to ..... http://taylor0.biology.ucla.edu/structureHarvester/.The .... environment and in other areas. ..... Molecular population genetics and evolution. In:.

  17. The Knowledge Structure of Mendelian Genetics.

    Science.gov (United States)

    Collins, Angelo; Stewart, James H.

    1989-01-01

    Examines the content knowledge of genetics as it is organized for solving effect-to-cause problems. Reviews proposed reasons explaining why students find genetics difficult to learn. Explains dominant and codominant inheritance patterns, multiple alleles, and X-linkage. (RT)

  18. Plant genetics shapes inquiline community structure across spatial scales.

    Science.gov (United States)

    Crutsinger, Gregory M; Cadotte, Marc W; Sanders, Nathan J

    2009-04-01

    Recent research in community genetics has examined the effects of intraspecific genetic variation on species diversity in local communities. However, communities can be structured by a combination of both local and regional processes and to date, few community genetics studies have examined whether the effects of instraspecific genetic variation are consistent across levels of diversity. In this study, we ask whether host-plant genetic variation structures communities of arthropod inquilines within distinct habitat patches--rosette leaf galls on tall goldenrod (Solidago altissima). We found that genetic variation determined inquiline diversity at both local and regional spatial scales, but that trophic-level responses varied independently of one another. This result suggests that herbivores and predators likely respond to heritable plant traits at different spatial scales. Together, our results show that incorporating spatial scale is essential for predicting the effects of genetically variable traits on different trophic levels and levels of diversity within the communities that depend on host plants.

  19. Structure and genetics of circular bacteriocins.

    Science.gov (United States)

    van Belkum, Marco J; Martin-Visscher, Leah A; Vederas, John C

    2011-08-01

    Circular bacteriocins are antimicrobial peptides produced by a variety of Gram-positive bacteria. They are part of a growing family of ribosomally synthesized peptides with a head-to-tail cyclization of their backbone that are found in mammals, plants, fungi and bacteria and are exceptionally stable. These bacteriocins permeabilize the membrane of sensitive bacteria, causing loss of ions and dissipation of the membrane potential. Most circular bacteriocins probably adopt a common 3D structure consisting of four or five α-helices encompassing a hydrophobic core. This review compares the various structures, as well as the gene clusters that encode circular bacteriocins, and discusses the biogenesis of this unique class of bacteriocins.

  20. Genetic and environmental structure of Cloninger's temperament and character dimensions.

    Science.gov (United States)

    Ando, Juko; Suzuki, Atsunobu; Yamagata, Shinji; Kijima, Nobuhiko; Maekawa, Hiroko; Ono, Yutaka; Jang, Kerry L

    2004-08-01

    The multivariate genetic and environmental structure of Cloninger's Temperament and Character Inventory (TCI) was investigated in a sample of 617 pairs of adolescent and young adult twins from Japan. Additive genetic factors accounted for 22% to 49% of the variability on all TCI temperament scales. Although the theory predicts lower heritability for the character scales, all character subscales had a substantial genetic contribution, and nonshared environmental influences accounted for the remainder. Multivariate genetic analyses showed that several subscales used to define one dimension shared a common genetic basis with subscales defining others. Using the degree of shared genetic influence as the basis to rearrange the TCI subscales into new dimensions, it was possible to create genetically independent scales. The implications for personality measurement, theory, and molecular genetic research are discussed.

  1. Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus×domestica) genetic resources.

    Science.gov (United States)

    Patzak, Josef; Paprštein, František; Henychová, Alena; Sedlák, Jiří

    2012-09-01

    The aim of this study was to compare traditional hierarchical clustering techniques and principal coordinate analysis (PCoA) with the model-based Bayesian cluster analyses in relation to subpopulation differentiation based on breeding history and geographical origin of apple (Malus×domestica Borkh.) cultivars and landraces. We presented the use of a set of 10 microsatellite (SSR) loci for genetic diversity structure analyses of 273 apple accessions from national genetic resources. These SSR loci yielded a total of 113 polymorphic SSR alleles, with 5-18 alleles per locus. SSR molecular data were successfully used in binary and allelic input format for all genetic diversity analyses, but allelic molecular data did not reveal reliable results with the NTSYS-pc and BAPS softwares. A traditional cluster analysis still provided an easy and effective way for determining genetic diversity structure in the apple germplasm collection. A model-based Bayesian analysis also provided the clustering results in accordance to traditional cluster analysis, but the analyses were distorted by the presence of a dominant group of apple genetic resources owing to the narrow origin of the apple genome. PCoA confirmed that there were no noticeable differences in genetic diversity structure of apple genetic resources during the breeding history. The results of our analyses are useful in the context of enhancing apple collection management, sampling of core collections, and improving breeding processes.

  2. Genetic resources of teak (Tectona grandis Linn. f.)—strong genetic structure among natural populations

    DEFF Research Database (Denmark)

    Hansen, Ole Kim; Changtragoon, Suchitra; Ponoy, Bundit;

    2015-01-01

    Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India...... had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern...... of the findings for conservation and use of genetic resources of the species are discussed....

  3. Genetic diversity and genetic structure of different types of natural populations in Osmanthus fragrans Lour. and the relationships with sex ratio, population structure, and geographic isolation.

    Science.gov (United States)

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhao, Hongbo; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of N e , H e , and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity.

  4. Genetic Diversity and Genetic Structure of Different Types of Natural Populations in Osmanthus fragrans Lour. and the Relationships with Sex Ratio, Population Structure, and Geographic Isolation

    Directory of Open Access Journals (Sweden)

    Shaoqing Hu

    2014-01-01

    Full Text Available Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites, once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of Ne, He, and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... including the populations distributed in same location together in every group. ... Key words: Meconopsis quintuplinervia Regel, genetic diversity, random amplified ..... in its original center, and Banma population located in ...

  6. Implications of population structure and ancestry on asthma genetic studies.

    Science.gov (United States)

    Ortega, Victor E; Meyers, Deborah A

    2014-10-01

    The frequency and severity of asthma differ between different racial and ethnic groups. An understanding of the genetic basis for these differences could constitute future genetic biomarker panels for predicting asthma risk and progression in individuals from different ethnic groups. The recent mixing of different ancestries during the European colonization of the Americas and the African slave trade has resulted in the complex population structures identified in different ethnic groups. These population structures represent varying degrees of genetic diversity which impacts the allele frequency of individual variants and, thus, how the gene variation is utilized in genetic association studies. In this review, we will discuss the basis for the complex population structures of modern human genomes and the impact of genetic diversity on genetic studies in different ethnic groups. We will also highlight the potential for admixture and rare variant-based genetic studies to identify novel genetic loci for asthma susceptibility and severity. The ability to account for the consequences of genetic diversity in different racial and ethnic groups will be critical in developing genetic profiles for personalized or precision medicine approaches tailored to asthmatic patients from different ethnic groups.

  7. A New Genetic Algorithm Methodology for Design Optimization of Truss Structures: Bipopulation-Based Genetic Algorithm with Enhanced Interval Search

    Directory of Open Access Journals (Sweden)

    Tugrul Talaslioglu

    2009-01-01

    Full Text Available A new genetic algorithm (GA methodology, Bipopulation-Based Genetic Algorithm with Enhanced Interval Search (BGAwEIS, is introduced and used to optimize the design of truss structures with various complexities. The results of BGAwEIS are compared with those obtained by the sequential genetic algorithm (SGA utilizing a single population, a multipopulation-based genetic algorithm (MPGA proposed for this study and other existing approaches presented in literature. This study has two goals: outlining BGAwEIS's fundamentals and evaluating the performances of BGAwEIS and MPGA. Consequently, it is demonstrated that MPGA shows a better performance than SGA taking advantage of multiple populations, but BGAwEIS explores promising solution regions more efficiently than MPGA by exploiting the feasible solutions. The performance of BGAwEIS is confirmed by better quality degree of its optimal designations compared to algorithms proposed here and described in literature.

  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. Local genetic structure in a white-bearded manakin population.

    Science.gov (United States)

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present.

  10. Population genetic structure of Aedes albopictus in Penang, Malaysia.

    Science.gov (United States)

    Zawani, M K N; Abu, H A; Sazaly, A B; Zary, S Y; Darlina, M N

    2014-10-07

    The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.

  11. Correlation between genetic and geographic structure in Europe

    DEFF Research Database (Denmark)

    Lao, Oscar; Lu, Timothy T; Nothnagel, Michael;

    2008-01-01

    Understanding the genetic structure of the European population is important, not only from a historical perspective, but also for the appropriate design and interpretation of genetic epidemiological studies. Previous population genetic analyses with autosomal markers in Europe either had a wide g...... Europe. By including the widely used CEPH from Utah (CEU) samples into our analysis, we could show that these individuals represent northern and western Europeans reasonably well, thereby confirming their assumed regional ancestry....

  12. Bioclimatic regions influence genetic structure of four Jordanian Stipa species.

    Science.gov (United States)

    Hamasha, H R; Schmidt-Lebuhn, A N; Durka, W; Schleuning, M; Hensen, I

    2013-09-01

    Strong environmental gradients can affect the genetic structure of plant populations, but little is known as to whether closely related species respond similarly or idiosyncratically to ecogeographic variation. We analysed the extent to which gradients in temperature and rainfall shape the genetic structure of four Stipa species in four bioclimatic regions in Jordan. Genetic diversity, differentiation and structure of Stipa species were investigated using amplified fragment length polymorphism (AFLP) molecular markers. For each of the four study species, we sampled 120 individuals from ten populations situated in distinct bioclimatic regions and assessed the degree of genetic diversity and genetic differentiation within and among populations. The widespread ruderals Stipa capensis and S. parviflora had higher genetic diversity than the geographically restricted semi-desert species S. arabica and S. lagascae. In three of the four species, genetic diversity strongly decreased with precipitation, while genetic diversity increased with temperature in S. capensis. Most genetic diversity resided among populations in the semi-desert species (Φ(ST) = 0.572/0.595 in S. arabica/lagascae) but within populations in the ruderal species (Φ(ST) = 0.355/0.387 S. capensis/parviflora). Principal coordinate analysis (PCoA) and STRUCTURE analysis showed that Stipa populations of all species clustered ecogeographically. A genome scan revealed that divergent selection at particular AFLP loci contributed to genetic differentiation. Irrespective of their different life histories, Stipa species responded similarly to the bioclimatic gradient in Jordan. We conclude that, in addition to predominant random processes, steep climatic gradients might shape the genetic structure of plant populations.

  13. Original Paper Patterns of genetic structure and phenotypic diversity ...

    African Journals Online (AJOL)

    Patterns of genetic structure and phenotypic diversity in sorghum landraces in relation to farmers' management in Burkina Faso ... the role of farmer practices in phenotypic and genetic evolution of sorghum. ... varieties to marginal environments such as ...... Supporting the Convention on Biological ... A new method to.

  14. Analysis of genetic structure of white croaker using amplified ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... The population with the highest Nei's genetic diversity and. Shannon diversity index ... fish assemblages off the coasts of China and Japan, supporting an ..... genetic distances. graphic structure of populations may be influenced by ... the sea-level-induced environmental signal was amplified in the marginal ...

  15. Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar

    NARCIS (Netherlands)

    Goedbloed, D.J.; Hooft, van W.F.; Megens, H.J.W.C.; Langenbeck, K.; Lutz, W.; Crooijmans, R.P.M.A.; Wieren, van S.E.; Ydenberg, R.C.; Prins, H.H.T.

    2013-01-01

    Background: Population genetic studies focus on natural dispersal and isolation by landscape barriers as the main drivers of genetic population structure. However, anthropogenic factors such as reintroductions, translocations and wild x domestic hybridization may also have strong effects on genetic

  16. Comparative genetic study of intratumoral heterogenous MYCN amplified neuroblastoma versus aggressive genetic profile neuroblastic tumors.

    Science.gov (United States)

    Berbegall, A P; Villamón, E; Piqueras, M; Tadeo, I; Djos, A; Ambros, P F; Martinsson, T; Ambros, I M; Cañete, A; Castel, V; Navarro, S; Noguera, R

    2016-03-17

    Intratumoral heterogeneous MYCN amplification (hetMNA) is an unusual event in neuroblastoma with unascertained biological and clinical implications. Diagnosis is based on the detection of MYCN amplification surrounded by non-amplified tumor cells by fluorescence in situ hybridization (FISH). To better define the genetic features of hetMNA tumors, we studied the Spanish cohort of neuroblastic tumors by FISH and single nucleotide polymorphism arrays. We compared hetMNA tumors with homogeneous MNA (homMNA) and nonMNA tumors with 11q deletion (nonMNA w11q-). Of 1091 primary tumors, 28 were hetMNA by FISH. Intratumoral heterogeneity of 1p, 2p, 11q and 17q was closely associated with hetMNA tumors when analyzing different pieces for each case. For chromosome 2, 16 cases showed 2p intact, 4 focal gain at 2p24.3 and 8 MNA. The lengths of the smallest regions of overlap (SROs) for 2p gains and 1p deletions were between the SRO lengths observed in homMNA and nonMNA w11q- tumors. Co-occurrence of 11q- and +17q was frequently found with the largest SROs for both aberrations. The evidence for and frequency of different genetic subpopulations representing a hallmark of the hetMNA subgroup of NB indicates, on one hand, the presence of a considerable genetic instability with different SRO of either gains and losses compared with those of the other NB groups and highlights and, on the other hand, the need for multiple sampling from distant and macroscopically and microscopically distinct tumor areas. Narrowing down the different SRO for both deletions and gains in NB groups would be crucial to pinpointing the candidate gene(s) and the critical gene dosage with prognostic and therapeutic significance. This complexity of segmental chromosomal aberration patterns reinforces the necessity for a larger cohort study using FISH and pangenomic techniques to develop a suitable therapeutic strategy for these patients.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... However, few studies have focused on the population genetic structures of ... There are two main demographic strategies for benthic estuarine macro- .... differentiation existed in the two populations of Okinawa. Pairwise FST ...

  18. A heterogeneity test for fine-scale genetic structure.

    Science.gov (United States)

    Smouse, Peter E; Peakall, Rod; Gonzales, Eva

    2008-07-01

    For organisms with limited vagility and/or occupying patchy habitats, we often encounter nonrandom patterns of genetic affinity over relatively small spatial scales, labelled fine-scale genetic structure. Both the extent and decay rate of that pattern can be expected to depend on numerous interesting demographic, ecological, historical, and mating system factors, and it would be useful to be able to compare different situations. There is, however, no heterogeneity test currently available for fine-scale genetic structure that would provide us with any guidance on whether the differences we encounter are statistically credible. Here, we develop a general nonparametric heterogeneity test, elaborating on standard autocorrelation methods for pairs of individuals. We first develop a 'pooled within-population' correlogram, where the distance classes (lags) can be defined as functions of distance. Using that pooled correlogram as our null-hypothesis reference frame, we then develop a heterogeneity test of the autocorrelations among different populations, lag-by-lag. From these single-lag tests, we construct an analogous test of heterogeneity for multilag correlograms. We illustrate with a pair of biological examples, one involving the Australian bush rat, the other involving toadshade trillium. The Australian bush rat has limited vagility, and sometimes occupies patchy habitat. We show that the autocorrelation pattern diverges somewhat between continuous and patchy habitat types. For toadshade trillium, clonal replication in Piedmont populations substantially increases autocorrelation for short lags, but clonal replication is less pronounced in mountain populations. Removal of clonal replicates reduces the autocorrelation for short lags and reverses the sign of the difference between mountain and Piedmont correlograms.

  19. Architectural DNA: A genetic exploration of complex structures

    NARCIS (Netherlands)

    Van Embden Andres, M.V.; Turrin, M.; Von Buelow, P.

    2011-01-01

    The approach demonstrated in this paper uses Evolutionary Computation (EC) to enhance and modify structural form based on biological micro structures.The forms are modified to conform to new boundary conditions associated with architectural structures.The process is based on a Genetic Algorithm (GA)

  20. Architectural DNA: A genetic exploration of complex structures

    NARCIS (Netherlands)

    Van Embden Andres, M.V.; Turrin, M.; Von Buelow, P.

    2011-01-01

    The approach demonstrated in this paper uses Evolutionary Computation (EC) to enhance and modify structural form based on biological micro structures.The forms are modified to conform to new boundary conditions associated with architectural structures.The process is based on a Genetic Algorithm (GA)

  1. Common genetic variants influence human subcortical brain structures

    OpenAIRE

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro,; Desrivieres, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences(1). Subcortical brain regions form circuits with cortical areas to coordinate movement(2), learning, memory(3) and motivation(4), and altered circuits can lead to abnormal behaviour and disease(5). To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume de...

  2. Family Competition Pheromone Genetic Algorithm for Comparative Genome Assembly

    Institute of Scientific and Technical Information of China (English)

    Chien-Hao Su; Chien-Shun Chiou; Jung-Che Kuo; Pei-Jen Wang; Cheng-Yan Kao; Hsueh-Ting Chu

    2014-01-01

    Genome assembly is a prerequisite step for analyzing next generation sequencing data and also far from being solved. Many assembly tools have been proposed and used extensively. Majority of them aim to assemble sequencing reads into contigs; however, we focus on the assembly of contigs into scaffolds in this paper. This is called scaffolding, which estimates the relative order of the contigs as well as the size of the gaps between these contigs. Pheromone trail-based genetic algorithm (PGA) was previously proposed and had decent performance according to their paper. From our previous study, we found that family competition mechanism in genetic algorithm is able to further improve the results. Therefore, we propose family competition pheromone genetic algorithm (FCPGA) and demonstrate the improvement over PGA.

  3. A genetic algorithm approach in interface and surface structure optimization

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jian [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    The thesis is divided into two parts. In the first part a global optimization method is developed for the interface and surface structures optimization. Two prototype systems are chosen to be studied. One is Si[001] symmetric tilted grain boundaries and the other is Ag/Au induced Si(111) surface. It is found that Genetic Algorithm is very efficient in finding lowest energy structures in both cases. Not only existing structures in the experiments can be reproduced, but also many new structures can be predicted using Genetic Algorithm. Thus it is shown that Genetic Algorithm is a extremely powerful tool for the material structures predictions. The second part of the thesis is devoted to the explanation of an experimental observation of thermal radiation from three-dimensional tungsten photonic crystal structures. The experimental results seems astounding and confusing, yet the theoretical models in the paper revealed the physics insight behind the phenomena and can well reproduced the experimental results.

  4. Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India

    Directory of Open Access Journals (Sweden)

    Sarwar Azam

    2016-01-01

    Full Text Available Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis.

  5. Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India

    Science.gov (United States)

    Azam, Sarwar; Rao, Sashi Bhushan; Jakka, Padmaja; NarasimhaRao, Veera; Bhargavi, Bindu; Gupta, Vivek Kumar

    2016-01-01

    Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis. PMID:27525259

  6. Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India.

    Science.gov (United States)

    Azam, Sarwar; Rao, Sashi Bhushan; Jakka, Padmaja; NarasimhaRao, Veera; Bhargavi, Bindu; Gupta, Vivek Kumar; Radhakrishnan, Girish

    2016-01-01

    Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis.

  7. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  8. Genetic structure of arbuscular mycorrhizal populations in fallow and cultivated soils

    DEFF Research Database (Denmark)

    Rosendahl, Søren; Matzen, Hans

    2008-01-01

    protein-coding genes GmFOX2 and GmTOR2 were used as co-dominant genetic markers together with the large subunit (LSU) rDNA. The gene diversity and genetic structure of Glomus mosseae, Glomus geosporum and Glomus caledonium were compared within and between the fields. •  Spores of G. caledonium and G...... be attributed to variation between plots rather than subplots, suggesting that the lack of soil cultivation resulted in more heterogeneous population genetic structures. Analyses of haplotype networks of the fungi suggested a subdivision of G. mosseae haplotypes between the two fields, whereas no such division...

  9. Comparative sequence-structure analysis of Aves insulin.

    Science.gov (United States)

    Islam, Md Mirazul; Aktaruzzaman, M; Mohamed, Zahurin

    2015-01-01

    Normal blood glucose level depends on the availability of insulin and its ability to bind insulin receptor (IR) that regulates the downstream signaling pathway. Insulin sequence and blood glucose level usually vary among animals due to species specificity. The study of genetic variation of insulin, blood glucose level and diabetics symptoms development in Aves is interesting because of its optimal high blood glucose level than mammals. Therefore, it is of interest to study its evolutionary relationship with other mammals using sequence data. Hence, we compiled 32 Aves insulin from GenBank to compare its sequence-structure features with phylogeny for evolutionary inference. The analysis shows long conserved motifs (about 14 residues) for functional inference. These sequences show high leucine content (20%) with high instability index (>40). Amino acid position 11, 14, 16 and 20 are variable that may have contribution to binding to IR. We identified functionally critical variable residues in the dataset for possible genetic implication. Structural models of these sequences were developed for surface analysis towards functional representation. These data find application in the understanding of insulin function across species.

  10. Patient accounts of diagnostic testing for familial hypercholesterolaemia: comparing responses to genetic and non-genetic testing methods

    Directory of Open Access Journals (Sweden)

    Hollands Gareth J

    2012-09-01

    Full Text Available Abstract Background Continuing developments in genetic testing technology together with research revealing gene-disease associations have brought closer the potential for genetic screening of populations. A major concern, as with any screening programme, is the response of the patient to the findings of screening, whether the outcome is positive or negative. Such concern is heightened for genetic testing, which it is feared may elicit stronger reactions than non-genetic testing. Methods This paper draws on thematic analysis of 113 semi-structured interviews with 39 patients being tested for familial hypercholesterolaemia (FH, an inherited predisposition to early-onset heart disease. It examines the impact of disease risk assessments based on both genetic and non-genetic information, or solely non-genetic information. Results The impact of diagnostic testing did not seem to vary according to whether or not genetic information was used. More generally, being given a positive or negative diagnosis of FH had minimal discernible impact on people's lives as they maintained the continuity of their beliefs and behaviour. Conclusions The results suggest that concerns about the use of genetic testing in this context are unfounded, a conclusion that echoes findings from studies in this and other health contexts.

  11. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...... eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79......% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations....

  12. Emergent patterns of population genetic structure for a coral reef community.

    Science.gov (United States)

    Selkoe, Kimberly A; Gaggiotti, Oscar E; Bowen, Brian W; Toonen, Robert J

    2014-06-01

    What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R2=0.22), but accounting for higher FST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global FST (adjusted R2=0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species-specific abundance and migration patterns and/or seascape and historical factors.

  13. Distinct Genetic Influences on Cortical and Subcortical Brain Structures

    Science.gov (United States)

    Wen, Wei; Thalamuthu, Anbupalam; Mather, Karen A.; Zhu, Wanlin; Jiang, Jiyang; de Micheaux, Pierre Lafaye; Wright, Margaret J.; Ames, David; Sachdev, Perminder S.

    2016-09-01

    This study examined the heritability of brain grey matter structures in a subsample of older adult twins (93 MZ and 68 DZ twin pairs; mean age 70 years) from the Older Australian Twins Study. The heritability estimates of subcortical regions ranged from 0.41 (amygdala) to 0.73 (hippocampus), and of cortical regions, from 0.55 (parietal lobe) to 0.78 (frontal lobe). Corresponding structures in the two hemispheres were influenced by the same genetic factors and high genetic correlations were observed between the two hemispheric regions. There were three genetically correlated clusters, comprising (i) the cortical lobes (frontal, temporal, parietal and occipital lobes); (ii) the basal ganglia (caudate, putamen and pallidum) with weak genetic correlations with cortical lobes, and (iii) the amygdala, hippocampus, thalamus and nucleus accumbens grouped together, which genetically correlated with both basal ganglia and cortical lobes, albeit relatively weakly. Our study demonstrates a complex but patterned and clustered genetic architecture of the human brain, with divergent genetic determinants of cortical and subcortical structures, in particular the basal ganglia.

  14. The Structure of Trade in Genetic Resources: Implications for the International ABS Regime Negotiation

    Directory of Open Access Journals (Sweden)

    Mikyung Yun

    2010-06-01

    Full Text Available The intensive exploitation of genetic resources at the international level has led to a negotiation of an international regime on Access and Benefit-Sharing (ABS of genetic resources. Due to lack of systematic data, little is known about the structure of trade in genetic resources to inform the negotiators. This study attempts to shed a greater insight into genetic resources trade in the pharmaceutical sector in Korea, mainly relying on interviews of industry practitioners and scientists in related fields. The study finds that Korea is mainly a genetic resource importer, but that pharmaceutical firms rarely carry out bioprospecting directly, relying on semi-processed biochemicals imports trough agents. Therefore, the impact of the to-be negotiated international ABS negotiation will be larger if derivatives are included in its scope. However, the general impact on the economy as a whole would be small, given the small share of genetic resources trade compared to total trade volumes.

  15. Comparative Genetics of the rdar Morphotype in Salmonella▿

    OpenAIRE

    2006-01-01

    The Salmonella rdar morphotype is a distinct, rough and dry colony morphology formed by the extracellular interaction of thin aggregative fimbriae (Tafi or curli), cellulose, and other polysaccharides. Cells in rdar colonies are more resistant to desiccation and exogenous stresses, which is hypothesized to aid in the passage of pathogenic Salmonella spp. between hosts. Here we analyzed the genetic and phenotypic conservation of the rdar morphotype throughout the entire Salmonella genus. The r...

  16. Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

    Science.gov (United States)

    Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

    2012-01-01

    Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

  17. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Directory of Open Access Journals (Sweden)

    Sascha van der Meer

    Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  18. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Science.gov (United States)

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

    Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  19. COMPARATIVE ANALYSIS OF STEEL AND ALUMINUM STRUCTURES

    Directory of Open Access Journals (Sweden)

    Josip Peko

    2016-12-01

    Full Text Available This study examined steel and aluminum variants of modern exhibition structures in which the main design requirements include low weight (increased span/depth ratio, transportation, and construction and durability (resistance to corrosion. This included a design situation in which the structural application of aluminum alloys provided an extremely convenient and practical solution. Viability of an aluminum structure depends on several factors and requires a detailed analysis. The overall conclusion of the study indicated that aluminum can be used as a structural material and as a viable alternative to steel for Croatian snow and wind load values and evidently in cases in which positive properties of aluminum are required for structural design. Furthermore, a structural fire analysis was conducted for an aluminum variant structure by using a zone model for realistic fire analysis. The results suggested that passive fire protection for the main structural members was not required in the event of areal fire with duration of 60 min.

  20. Geographic variation and genetic structure in Spotted Owls

    Science.gov (United States)

    Haig, Susan M.; Wagner, R.S.; Forsman, E.D.; Mullins, Thomas D.

    2001-01-01

    We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.

  1. 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.

  2. Genetic structure and diversity of Shorea obtusa (Dipterocarpaceae) in Thailand

    Institute of Scientific and Technical Information of China (English)

    Chadaporn SENAKUN; Suchitra CHANGTRAGOON; Pairot PRAMUAL; Preecha PRATHEPHA

    2011-01-01

    Shorea obtusa is a keystone species of the dry deciduous dipterocarp forest in Thailand. In this study,the genetic structure and diversity of this species were evaluated by means of five microsatellite markers. A total of 146 trees were collected from five populations encompassing major forest regions of Thailand. High levels of genetic diversity were found among the five populations with the average He of 0.664. Genetic differentiations between populations, although significant, were low with approximately 3% of genetic variation partitioned among populations. This may indicate that the populations sampled were recently part of a continuous population. A tree constructed using the unweighted pair group method with arithmetic average, based on Nei's genetic distance, divided the populations into three groups. This separation was consistent with the altitudinal zonation of the populations,thus indicating that altitude might play a significant role in the genetic structure of S. obtusa. Areas of high genetic diversity were identified which could be considered priorities for conservation.

  3. Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation

    Directory of Open Access Journals (Sweden)

    Gianola Daniel

    2007-09-01

    Full Text Available Abstract Multivariate linear models are increasingly important in quantitative genetics. In high dimensional specifications, factor analysis (FA may provide an avenue for structuring (covariance matrices, thus reducing the number of parameters needed for describing (codispersion. We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (covariance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model.

  4. Structural chromosomal anomalies detected by prenatal genetic diagnosis: our experience.

    Science.gov (United States)

    Farcaş, Simona; Crişan, C D; Andreescu, Nicoleta; Stoian, Monica; Motoc, A G M

    2013-01-01

    The prenatal diagnosis is currently widely spread and facilitates the acquiring of important genetic information about the fetus by a rate extremely accelerate and considered without precedent. In this paper, we like to present our experience concerning the genetic diagnosis and counseling offered for pregnancies in which a structural chromosomal aberration was found. The study group is formed by 528 prenatal samples of amniotic fluid and chorionic villi, received by our laboratory from 2006 through October 2012 for cytogenetic diagnosis. The appropriate genetic investigation was selected based on the indications for prenatal diagnosis. The cases with structural chromosomal anomalies and polymorphic variants were analyzed as regard to the maternal age, gestational age, referral indications and type of chromosomal anomaly found. A total number of 21 structural chromosomal anomalies and polymorphic variants were identified in the study group. Out of 21 structural chromosomal anomalies and polymorphic variants, six deletions and microdeletions, four situations with abnormal long "p" arm of acrocentric chromosomes, two duplications, two reciprocal translocations, two inversions, two additions, one Robertsonian translocation associating trisomy 13, one 9q heteromorphism and one complex chromosome rearrangement were noticed. To the best of our knowledge, this is the first Romanian study in which the diagnostic strategies and the management of the prenatal cases with structural rearrangements are presented. The data provided about the diagnosis strategy and the management of the prenatal cases with structural chromosomal anomalies represents a useful tool in genetic counseling of pregnancies diagnosed with rare structural chromosomal anomalies.

  5. Genetic diversity and population structure of cucumber (Cucumis sativus L..

    Directory of Open Access Journals (Sweden)

    Jing Lv

    Full Text Available Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

  6. Genetic structuring across marine biogeographic boundaries in rocky shore invertebrates.

    Science.gov (United States)

    Villamor, Adriana; Costantini, Federica; Abbiati, Marco

    2014-01-01

    Biogeography investigates spatial patterns of species distribution. Discontinuities in species distribution are identified as boundaries between biogeographic areas. Do these boundaries affect genetic connectivity? To address this question, a multifactorial hierarchical sampling design, across three of the major marine biogeographic boundaries in the central Mediterranean Sea (Ligurian-Tyrrhenian, Tyrrhenian-Ionian and Ionian-Adriatic) was carried out. Mitochondrial COI sequence polymorphism of seven species of Mediterranean benthic invertebrates was analysed. Two species showed significant genetic structure across the Tyrrhenian-Ionian boundary, as well as two other species across the Ionian Sea, a previously unknown phylogeographic barrier. The hypothesized barrier in the Ligurian-Tyrrhenian cannot be detected in the genetic structure of the investigated species. Connectivity patterns across species at distances up to 800 km apart confirmed that estimates of pelagic larval dispersal were poor predictors of the genetic structure. The detected genetic discontinuities seem more related to the effect of past historical events, though maintained by present day oceanographic processes. Multivariate statistical tools were used to test the consistency of the patterns across species, providing a conceptual framework for across-species barrier locations and strengths. Additional sequences retrieved from public databases supported our findings. Heterogeneity of phylogeographic patterns shown by the 7 investigated species is relevant to the understanding of the genetic diversity, and carry implications for conservation biology.

  7. Genetic structuring across marine biogeographic boundaries in rocky shore invertebrates.

    Directory of Open Access Journals (Sweden)

    Adriana Villamor

    Full Text Available Biogeography investigates spatial patterns of species distribution. Discontinuities in species distribution are identified as boundaries between biogeographic areas. Do these boundaries affect genetic connectivity? To address this question, a multifactorial hierarchical sampling design, across three of the major marine biogeographic boundaries in the central Mediterranean Sea (Ligurian-Tyrrhenian, Tyrrhenian-Ionian and Ionian-Adriatic was carried out. Mitochondrial COI sequence polymorphism of seven species of Mediterranean benthic invertebrates was analysed. Two species showed significant genetic structure across the Tyrrhenian-Ionian boundary, as well as two other species across the Ionian Sea, a previously unknown phylogeographic barrier. The hypothesized barrier in the Ligurian-Tyrrhenian cannot be detected in the genetic structure of the investigated species. Connectivity patterns across species at distances up to 800 km apart confirmed that estimates of pelagic larval dispersal were poor predictors of the genetic structure. The detected genetic discontinuities seem more related to the effect of past historical events, though maintained by present day oceanographic processes. Multivariate statistical tools were used to test the consistency of the patterns across species, providing a conceptual framework for across-species barrier locations and strengths. Additional sequences retrieved from public databases supported our findings. Heterogeneity of phylogeographic patterns shown by the 7 investigated species is relevant to the understanding of the genetic diversity, and carry implications for conservation biology.

  8. Genetic structure and differentiation of the Italian catria horse.

    Science.gov (United States)

    Bigi, Daniele; Perrotta, Giovanna

    2012-01-01

    Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P origin with Maremmano and Italian Heavy Draught. Genetic relationships among Catria and the other breeds are consistent with the breed's documented history. The data and information found here can be utilized in the organization of conservation programmes planned to reduce inbreeding and to minimize loss of genetic variability.

  9. Comparing Factor Structures of Adolescent Psychopathology

    Science.gov (United States)

    Verona, Edelyn; Javdani, Shabnam; Sprague, Jenessa

    2011-01-01

    Research on the structure of adolescent psychopathology can provide information on broad factors that underlie different forms of maladjustment in youths. Multiple studies from the literature on adult populations suggest that 2 factors, Internalizing and Externalizing, meaningfully comprise the factor structure of adult psychopathology (e.g.,…

  10. Comparing Factor Structures of Adolescent Psychopathology

    Science.gov (United States)

    Verona, Edelyn; Javdani, Shabnam; Sprague, Jenessa

    2011-01-01

    Research on the structure of adolescent psychopathology can provide information on broad factors that underlie different forms of maladjustment in youths. Multiple studies from the literature on adult populations suggest that 2 factors, Internalizing and Externalizing, meaningfully comprise the factor structure of adult psychopathology (e.g.,…

  11. 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

  12. Genetic structure in four West African population groups.

    Science.gov (United States)

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

    2005-06-24

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

  13. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  14. 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

  15. Structural and genetic diversity in antibody repertoires from diverse species.

    Science.gov (United States)

    de los Rios, Miguel; Criscitiello, Michael F; Smider, Vaughn V

    2015-08-01

    The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes.

  16. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.

  17. Comparing mannose binding lectin genetic diversity in intracellular ...

    African Journals Online (AJOL)

    SERVER

    2007-09-05

    Sep 5, 2007 ... mannose binding lectin level for susceptibility to intracellular pathogens. Key words: .... The distribution of alleles and genotypes between groups were compared using ... Frequency of promoter variants and position +4 (Table.

  18. Genetic Structure Analysis of Human Remains from Khitan Noble Necropolis

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Ancient DNA was extracted from 13 skeletal remains from the burial groups of Khitan nobles, which were excavated in northeast China. The hypervariable segment I sequences ( HVS Ⅰ ) of the mitochondrial DNA control region, in the 13 individuals, were used as genetic markers to determine the genetic relationships between the individuals and the genetic affinity to other interrelated populations by using the known database of mtDNA. Based on the phylogenetic analysis of these ancient DNA sequences, the genetic structures of two Khitan noble kindreds were obtained, including the Yel Yuzhi's kindred and the Xiao He's kindred. Furthermore, the relationships between the Khitan nobles and some modern interrelated populations were analyzed. On the basis of the result of the analysis, the gene flows of the ancient Khitans and their demographic expansion in history was deduced.

  19. How does farmer connectivity influence livestock genetic structure?

    DEFF Research Database (Denmark)

    Berthouly, C; Do, Duy Ngoc; Thévenon, S

    2009-01-01

    Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between...... farmers and their husbandry practices will define the farmer's network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were......, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies....

  20. Large-scale natural disturbance alters genetic population structure of the sailfin molly, Poecilia latipinna.

    Science.gov (United States)

    Apodaca, Joseph J; Trexler, Joel C; Jue, Nathaniel K; Schrader, Matthew; Travis, Joseph

    2013-02-01

    Many inferences about contemporary rates of gene flow are based on the assumption that the observed genetic structure among populations is stable. Recent studies have uncovered several cases in which this assumption is tenuous. Most of those studies have focused on the effects that regular environmental fluctuations can have on genetic structure and gene flow patterns. Occasional catastrophic disturbances could also alter either the distribution of habitat or the spatial distribution of organisms in a way that affects population structure. However, evidence of such effects is sparse in the literature because it is difficult to obtain. Hurricanes, in particular, have the potential to exert dramatic effects on population structure of organisms found on islands or coral reefs or in near shore and coastal habitats. Here we draw on a historic genetic data set and new data to suggest that the genetic structure of sailfin molly (Poecilia latipinna) populations in north Florida was altered dramatically by an unusually large and uncommon type of storm surge associated with Hurricane Dennis in 2005. We compare the spatial pattern of genetic variation in these populations after Hurricane Dennis to the patterns described in an earlier study in this same area. We use comparable genetic data from another region of Florida, collected in the same two periods, to estimate the amount of change expected from typical temporal variation in population structure. The comparative natural history of sailfin mollies in these two regions indicates that the change in population structure produced by the storm surge is not the result of many local extinctions with recolonization from a few refugia but emerged from a pattern of mixing and redistribution.

  1. Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens

    DEFF Research Database (Denmark)

    Timms, Richard T.; Menzies, Sam A.; Tchasovnikarova, Iva A.;

    2016-01-01

    The application of forward genetic screens to cultured human cells represents a powerful method to study gene function. The repurposing of the bacterial CRISPR/Cas9 system provides an effective method to disrupt gene function in mammalian cells, and has been applied to genome-wide screens. Here, ...

  2. Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

    Science.gov (United States)

    Yan, Yu-Bin; Duke, Norm C.; Sun, Mei

    2016-01-01

    Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

  3. Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

    Directory of Open Access Journals (Sweden)

    Yu-Bin Yan

    2016-09-01

    Full Text Available Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, R. mucronata, and R. stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

  4. Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.

    Science.gov (United States)

    Hodoğlugil, Uğur; Mahley, Robert W

    2012-03-01

    Turkey has experienced major population movements. Population structure and genetic relatedness of samples from three regions of Turkey, using over 500,000 SNP genotypes, were compared together with Human Genome Diversity Panel (HGDP) data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analysed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K=3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42-49), 40% European (95% CI, 36-44) and 15% Central Asian (95% CI, 13-16), whereas at K=4 the genetic ancestry of the Turks was 38% European (95% CI, 35-42), 35% Middle Eastern (95% CI, 33-38), 18% South Asian (95% CI, 16-19) and 9% Central Asian (95% CI, 7-11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul and Kayseri) were superimposed, without clear subpopulation structure, suggesting sample homogeneity. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns. © 2012 The Authors Annals of Human Genetics © 2012 Blackwell Publishing Ltd/University College London.

  5. Common genetic variants influence human subcortical brain structures.

    Science.gov (United States)

    Hibar, Derrek P; Stein, Jason L; Renteria, Miguel E; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S; Armstrong, Nicola J; Bernard, Manon; Bohlken, Marc M; Boks, Marco P; Bralten, Janita; Brown, Andrew A; Chakravarty, M Mallar; Chen, Qiang; Ching, Christopher R K; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H; Olde Loohuis, Loes M; Luciano, Michelle; Macare, Christine; Mather, Karen A; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L; Roiz-Santiañez, Roberto; Rose, Emma J; Salami, Alireza; Sämann, Philipp G; Schmaal, Lianne; Schork, Andrew J; Shin, Jean; Strike, Lachlan T; Teumer, Alexander; van Donkelaar, Marjolein M J; van Eijk, Kristel R; Walters, Raymond K; Westlye, Lars T; Whelan, Christopher D; Winkler, Anderson M; Zwiers, Marcel P; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M H; Hartberg, Cecilie B; Haukvik, Unn K; Heister, Angelien J G A M; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C M; Lopez, Lorna M; Makkinje, Remco R R; Matarin, Mar; Naber, Marlies A M; McKay, D Reese; Needham, Margaret; Nugent, Allison C; Pütz, Benno; Royle, Natalie A; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S L; van Hulzen, Kimm J E; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A; Bastin, Mark E; Brodaty, Henry; Bulayeva, Kazima B; Carless, Melanie A; Cichon, Sven; Corvin, Aiden; Curran, Joanne E; Czisch, Michael; de Zubicaray, Greig I; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D; Erk, Susanne; Fedko, Iryna O; Ferrucci, Luigi; Foroud, Tatiana M; Fox, Peter T; Fukunaga, Masaki; Gibbs, J Raphael; Göring, Harald H H; Green, Robert C; Guelfi, Sebastian; Hansell, Narelle K; Hartman, Catharina A; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G; Heslenfeld, Dirk J; Hoekstra, Pieter J; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W; Kochunov, Peter; Kwok, John B; Lawrie, Stephen M; Liu, Xinmin; Longo, Dan L; McMahon, Katie L; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W; Mostert, Jeanette C; Mühleisen, Thomas W; Nalls, Michael A; Nichols, Thomas E; Nilsson, Lars G; Nöthen, Markus M; Ohi, Kazutaka; Olvera, Rene L; Perez-Iglesias, Rocio; Pike, G Bruce; Potkin, Steven G; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D; Rujescu, Dan; Schnell, Knut; Schofield, Peter R; Smith, Colin; Steen, Vidar M; Sussmann, Jessika E; Thalamuthu, Anbupalam; Toga, Arthur W; Traynor, Bryan J; Troncoso, Juan; Turner, Jessica A; Valdés Hernández, Maria C; van 't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J A; van Tol, Marie-Jose; Veltman, Dick J; Wassink, Thomas H; Westman, Eric; Zielke, Ronald H; Zonderman, Alan B; Ashbrook, David G; Hager, Reinmar; Lu, Lu; McMahon, Francis J; Morris, Derek W; Williams, Robert W; Brunner, Han G; Buckner, Randy L; Buitelaar, Jan K; Cahn, Wiepke; Calhoun, Vince D; Cavalleri, Gianpiero L; Crespo-Facorro, Benedicto; Dale, Anders M; Davies, Gareth E; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C; Espeseth, Thomas; Gollub, Randy L; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W J H; Roffman, Joshua L; Sisodiya, Sanjay M; Smoller, Jordan W; van Bokhoven, Hans; van Haren, Neeltje E M; Völzke, Henry; Walter, Henrik; Weiner, Michael W; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A; Blangero, John; Boomsma, Dorret I; Brouwer, Rachel M; Cannon, Dara M; Cookson, Mark R; de Geus, Eco J C; Deary, Ian J; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E; Francks, Clyde; Glahn, David C; Grabe, Hans J; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E; Jönsson, Erik G; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M; Ophoff, Roel A; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S; Saykin, Andrew J; Simmons, Andy

    2015-04-01

    The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

  6. Genetic population structuring and demographic history of red ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-10-20

    Oct 20, 2008 ... In order to estimate the demographic history and genetic structure of. Epinephelus ... using DNA sequence data from the 5' end of the control region. ... on the aquaculture and biology of E. akaara, and Deng ... evolutionary history of the species. .... at low frequency are more likely to be new, θл is a useful.

  7. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivieres, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Loohuis, Loes M. Olde; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santianez, Roberto; Rose, Emma J.; Salami, Alireza; Saemann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Puetz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Goering, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzah, Eva; Melle, Ingrid; Mahnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Muehleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Noethen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdes Hernandez, Maria C.; van't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffman, Wolfgang; Hosten, Norbert; Kahn, Rene S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Mueller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Voelzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernandez, Guillen; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Pol, Hilleke E. Hulshoff; Joensson, Erik G.; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S.; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M.; Ophoff, Roel A.; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S.; Saykin, Andrew J.; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M.; Weale, Michael E.; Weinberger, Daniel R.; Adams, Hieab H. H.; Launer, Lenore J.; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L.; Becker, James T.; Yanek, Lisa; van der Lee, Sven J.; Ebling, Maritza; Fischl, Bruce; Longstreth, W. T.; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N.; van Duijn, Cornelia M.; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C.; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M. Arfan; Martin, Nicholas G.; Wright, Margaret J.; Schumann, Gunter; Franke, Barbara; Thompson, Paul M.; Medland, Sarah E.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences(1). Subcortical brain regions form circuits with cortical areas to coordinate movement(2), learning, memory(3) and motivation(4), and altered circuits can lead to abnormal behaviour and disease(5). To investigat

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

    Science.gov (United States)

    Multini, Laura Cristina; 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. PMID:27598889

  9. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    D.P. Hibar (Derrek); J.L. Stein; M.E. Rentería (Miguel); A. Arias-Vásquez (Alejandro); S. Desrivières (Sylvane); N. Jahanshad (Neda); R. Toro (Roberto); K. Wittfeld (Katharina); L. Abramovic (Lucija); M. Andersson (Micael); B. Aribisala (Benjamin); N.J. Armstrong (Nicola J.); M. Bernard (Manon); M.M. Bohlken (Marc M.); M.P.M. Boks (Marco); L.B.C. Bralten (Linda); A.A. Brown (Andrew); M.M. Chakravarty (M. Mallar); Q. Chen (Qiang); C.R.K. Ching (Christopher); G. Cuellar-Partida (Gabriel); A. den Braber (Anouk); S. Giddaluru (Sudheer); A.L. Goldman (Aaron L.); O. Grimm (Oliver); T. Guadalupe (Tulio); J. Hass (Johanna); G. Woldehawariat (Girma); A.J. Holmes (Avram); M. Hoogman (Martine); D. Janowitz (Deborah); T. Jia (Tianye); S. Kim (Shinseog); M. Klein (Marieke); B. Kraemer (Bernd); P.H. Lee (Phil H.); L.M. Olde Loohuis (Loes M.); M. Luciano (Michelle); C. MacAre (Christine); R. Mather; M. Mattheisen (Manuel); Y. Milaneschi (Yuri); K. Nho (Kwangsik); M. Papmeyer (Martina); A. Ramasamy (Adaikalavan); S.L. Risacher (Shannon); R. Roiz-Santiañez (Roberto); E.J. Rose (Emma); A. Salami (Alireza); P.G. Sämann (Philipp); L. Schmaal (Lianne); N.J. Schork (Nicholas); J. Shin (Jean); V.M. Strike (Vanessa); A. Teumer (Alexander); M.M.J. Van Donkelaar (Marjolein M. J.); K.R. van Eijk (Kristel); R.K. Walters (Raymond); L.T. Westlye (Lars); C.D. Whelan (Christopher); A.M. Winkler (Anderson); M.P. Zwiers (Marcel); S. Alhusaini (Saud); L. Athanasiu (Lavinia); S.M. Ehrlich (Stefan); M. Hakobjan (Marina); C.B. Hartberg (Cecilie B.); U.K. Haukvik (Unn); A.J.G.A.M. Heister (Angelien J. G. A. M.); D. Hoehn (David); D. Kasperaviciute (Dalia); D.C. Liewald (David C.); L.M. Lopez (Lorna); R.R.R. Makkinje (Remco R. R.); M. Matarin (Mar); M.A.M. Naber (Marlies A. M.); D. Reese McKay; M. Needham (Margaret); A.C. Nugent (Allison); B. Pütz (Benno); N.A. Royle (Natalie); L. Shen (Li); R. Sprooten (Roy); D. Trabzuni (Danyah); S.S.L. Van Der Marel (Saskia S. L.); K.J.E. Van Hulzen (Kimm J. E.); E. Walton (Esther); A. Björnsson (Asgeir); L. Almasy (Laura); D. Ames (David); S. Arepalli (Sampath); A.A. Assareh; M.E. Bastin (Mark); H. Brodaty (Henry); K. Bulayeva (Kazima); M.A. Carless (Melanie); S. Cichon (Sven); A. Corvin (Aiden); J.E. Curran (Joanne); M. Czisch (Michael); G.I. de Zubicaray (Greig); A. Dillman (Allissa); A. Duggirala (Aparna); M.D. Dyer (Matthew); S. Erk; I. Fedko (Iryna); L. Ferrucci (Luigi); T. Foroud (Tatiana); P.T. Fox (Peter); M. Fukunaga (Masaki); J. Raphael Gibbs; H.H.H. Göring (Harald H.); R.C. Green (Robert C.); S. Guelfi (Sebastian); N.K. Hansell (Narelle); C.A. Hartman (Catharina); K. Hegenscheid (Katrin); J. Heinz (Judith); D.G. Hernandez (Dena); D.J. Heslenfeld (Dirk); P.J. Hoekstra (Pieter); F. Holsboer; G. Homuth (Georg); J.J. Hottenga (Jouke Jan); M. Ikeda (Masashi); C.R. Jack Jr. (Clifford); S. Jenkinson (Sarah); R. Johnson (Robert); R. Kanai (Ryota); M. Keil (Maria); J.W. Kent (Jack W.); P. Kochunov (Peter); J.B. Kwok (John B.); S. Lawrie (Stephen); X. Liu (Xinmin); D.L. Longo (Dan L.); K.L. Mcmahon (Katie); E. Meisenzahl (Eva); I. Melle (Ingrid); S. Mohnke (Sebastian); G.W. Montgomery (Grant); J.C. Mostert (Jeanette C.); T.W. Mühleisen (Thomas); M.A. Nalls (Michael); T.E. Nichols (Thomas); L.G. Nilsson; M.M. Nöthen (Markus); K. Ohi (Kazutaka); R.L. Olvera (Rene); R. Perez-Iglesias (Rocio); G. Bruce Pike; S.G. Potkin (Steven); I. Reinvang (Ivar); S. Reppermund; M. Rietschel (M.); N. Seiferth (Nina); G.D. Rosen (Glenn D.); D. Rujescu (Dan); K. Schnell (Kerry); C.J. Schofield (Christopher); C. Smith (Colin); V.M. Steen (Vidar); J. Sussmann (Jessika); A. Thalamuthu (Anbupalam); A.W. Toga (Arthur W.); B. Traynor (Bryan); J.C. Troncoso (Juan); J. Turner (Jessica); M.C. Valdés Hernández (Maria); D. van 't Ent (Dennis); M.P. van der Brug (Marcel); N.J. van der Wee (Nic); M.J.D. van Tol (Marie-José); D.J. Veltman (Dick); A.M.J. Wassink (Annemarie); E. Westman (Eric); R.H. Zielke (Ronald H.); A.B. Zonderman (Alan B.); D.G. Ashbrook (David G.); R. Hager (Reinmar); L. Lu (Lu); F.J. Mcmahon (Francis J); D.W. Morris (Derek W); R.W. Williams (Robert W.); H.G. Brunner; M. Buckner; J.K. Buitelaar (Jan K.); W. Cahn (Wiepke); V.D. Calhoun Vince D. (V.); G. Cavalleri (Gianpiero); B. Crespo-Facorro (Benedicto); A.M. Dale (Anders); G.E. Davies (Gareth); N. Delanty; C. Depondt (Chantal); S. Djurovic (Srdjan); D.A. Drevets (Douglas); T. Espeseth (Thomas); R.L. Gollub (Randy); B.C. Ho (Beng ); W. Hoffmann (Wolfgang)

    2015-01-01

    textabstractThe highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate

  10. Host genetics and population structure effects on parasitic disease.

    Science.gov (United States)

    Williams-Blangero, Sarah; Criscione, Charles D; VandeBerg, John L; Correa-Oliveira, Rodrigo; Williams, Kimberly D; Subedi, Janardan; Kent, Jack W; Williams, Jeff; Kumar, Satish; Blangero, John

    2012-03-19

    Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for Trypanosoma cruzi infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of Ascaris worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for T. cruzi infection were found.

  11. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    Hibar, D.P.; Stein, J.L.; Renteria, M.E.; Arias Vasquez, A.; Desrivieres, S.; Jahanshad, N.; Toro, R.; Wittfeld, K.; Abramovic, L.; Andersson, M.; Aribisala, B.S.; Armstrong, N.J.; Bernard, M.; Bohlken, M.M.; Boks, M.P.; Bralten, J.; Brown, A.A.; Chakravarty, M.M.; Chen, Q.; Ching, C.R.; Cuellar-Partida, G.; Braber, A.; Giddaluru, S.; Goldman, A.L.; Grimm, O.; Guadalupe, T.; Hass, J.; Woldehawariat, G.; Holmes, A.J.; Hoogman, M.; Janowitz, D.; Jia, T.; Kim, S.; Klein, M.; Kraemer, B.; Lee, P.H.; Olde Loohuis, L.M.; Luciano, M.; Macare, C.; Mather, K.A.; Mattheisen, M.; Milaneschi, Y.; Nho, K.; Papmeyer, M.; Ramasamy, A.; Risacher, S.L.; Roiz-Santianez, R.; Rose, E.J.; Salami, A.; Samann, P.G.; Schmaal, L.; Schork, A.J.; Shin, J.; Strike, L.T.; Teumer, A.; Donkelaar, M.M.J. van; Eijk, K.R. van; Walters, R.K.; Westlye, L.T.; Whelan, C.D.; Winkler, A.M.; Zwiers, M.P.; Alhusaini, S.; Athanasiu, L.; Ehrlich, S.; Hakobjan, M.M.; Hartberg, C.B.; Haukvik, U.K.; Heister, A.J.; Hoehn, D.; Kasperaviciute, D.; Liewald, D.C.; Lopez, L.M.; Makkinje, R.R.; Matarin, M.; Naber, M.; McKay, D.R.; Needham, M.; Nugent, A.C.; Putz, B.; Royle, N.A.; Shen, L.; Sprooten, E.; Trabzuni, D.; Marel, S.S. van der; Hulzen, K.J.E. van; Walton, E.; Wolf, C.; Almasy, L.; Ames, D.; Arepalli, S.; Assareh, A.A.; Bastin, M.E.; Brodaty, H.; Bulayeva, K.B.; Carless, M.A.; Cichon, S.; Corvin, A.; Curran, J.E.; Czisch, M.; Fisher, S.E.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common

  12. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivieres, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Loohuis, Loes M. Olde; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santianez, Roberto; Rose, Emma J.; Salami, Alireza; Saemann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Puetz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Goering, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzah, Eva; Melle, Ingrid; Mahnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Muehleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Noethen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdes Hernandez, Maria C.; van't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffman, Wolfgang; Hosten, Norbert; Kahn, Rene S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Mueller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Voelzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernandez, Guillen; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Pol, Hilleke E. Hulshoff; Joensson, Erik G.; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S.; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M.; Ophoff, Roel A.; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S.; Saykin, Andrew J.; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M.; Weale, Michael E.; Weinberger, Daniel R.; Adams, Hieab H. H.; Launer, Lenore J.; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L.; Becker, James T.; Yanek, Lisa; van der Lee, Sven J.; Ebling, Maritza; Fischl, Bruce; Longstreth, W. T.; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N.; van Duijn, Cornelia M.; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C.; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M. Arfan; Martin, Nicholas G.; Wright, Margaret J.; Schumann, Gunter; Franke, Barbara; Thompson, Paul M.; Medland, Sarah E.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences(1). Subcortical brain regions form circuits with cortical areas to coordinate movement(2), learning, memory(3) and motivation(4), and altered circuits can lead to abnormal behaviour and disease(5). To

  13. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    User

    2013-11-06

    Nov 6, 2013 ... origin of breeding populations, molecular marker informa-. *Corresponding .... on the phenotypic characteristics of each local breed (Desai, 1962). ..... Development of a genetic map of the chicken with markers of ... variation and population structure of Italian native sheep breeds ... evolutionary studies. Mol.

  14. Common genetic variants influence human subcortical brain structures

    Science.gov (United States)

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Olde Loohuis, Loes M.; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santiañez, Roberto; Rose, Emma J.; Salami, Alireza; Sämann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Pütz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Göring, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Mühleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Nöthen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdés Hernández, Maria C.; van ’t Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Völzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E.; Jönsson, Erik G.; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S.; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M.; Ophoff, Roel A.; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S.; Saykin, Andrew J.; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M.; Weale, Michael E.; Weinberger, Daniel R.; Adams, Hieab H. H.; Launer, Lenore J.; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L.; Becker, James T.; Yanek, Lisa; van der Lee, Sven J.; Ebling, Maritza; Fischl, Bruce; Longstreth, W. T.; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N.; van Duijn, Cornelia M.; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C.; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M. Arfan; Martin, Nicholas G.; Wright, Margaret J.; Schumann, Gunter; Franke, Barbara; Thompson, Paul M.; Medland, Sarah E.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences1. Subcortical brain regions form circuits with cortical areas to coordinate movement2, learning, memory3 and motivation4, and altered circuits can lead to abnormal behaviour and disease2. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume5 and intracranial volume6. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10−33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability inhuman brain development, and may help to determine mechanisms of neuropsychiatric dysfunction. PMID:25607358

  15. Population genetic structure of a colonising, triploid weed, Hieracium lepidulum.

    Science.gov (United States)

    Chapman, H; Robson, B; Pearson, M L

    2004-03-01

    Understanding the breeding system and population genetic structure of invasive weed species is important for biocontrol, and contributes to our understanding of the evolutionary processes associated with invasions. Hieracium lepidulum is an invasive weed in New Zealand, colonising a diverse range of habitats including native Nothofagus forest, pine plantations, scrubland and tussock grassland. It is competing with native subalpine and alpine grassland and herbfield vegetation. H. lepidulum is a triploid, diplosporous apomict, so theoretically all seed is clonal, and there is limited potential for the creation of variation through recombination. We used intersimple sequence repeats (ISSRs) to determine the population genetic structure of New Zealand populations of H. lepidulum. ISSR analysis of five populations from two regions in the South Island demonstrated high intrapopulation genotypic diversity, and high interpopulation genetic structuring; PhiST = 0.54 over all five populations. No private alleles were found in any of the five populations, and allelic differentiation was correlated to geographic distance. Cladistic compatibility analysis indicated that both recombination and mutation were important in the creation of genotypic diversity. Our data will contribute to any biocontrol program developed for H. lepidulum. It will also be a baseline data set for future comparisons of genetic structure during the course of H. lepidulum invasions.

  16. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    D.P. Hibar (Derrek); J.L. Stein; M.E. Rentería (Miguel); A. Arias-Vásquez (Alejandro); S. Desrivières (Sylvane); N. Jahanshad (Neda); R. Toro (Roberto); K. Wittfeld (Katharina); L. Abramovic; M. Andersson (Micael); B. Aribisala (Benjamin); N.J. Armstrong (Nicola J.); M. Bernard (Manon); M.M. Bohlken (Marc M.); M.P.M. Boks (Marco); L.B.C. Bralten (Linda); A.A. Brown (Andrew); M.M. Chakravarty (M. Mallar); Q. Chen (Qiang); C.R.K. Ching (Christopher); G. Cuellar-Partida (Gabriel); A. den Braber (Anouk); S. Giddaluru (Sudheer); A.L. Goldman (Aaron L.); O. Grimm (Oliver); T. Guadalupe (Tulio); J. Hass (Johanna); G. Woldehawariat (Girma); A.J. Holmes (Avram); M. Hoogman (Martine); D. Janowitz (Deborah); T. Jia (Tianye); S. Kim (Shinseog); M. Klein (Marieke); B. Kraemer (Bernd); P.H. Lee (Phil H.); L.M. Olde Loohuis (Loes M.); M. Luciano (Michelle); C. MacAre (Christine); R. Mather; M. Mattheisen (Manuel); Y. Milaneschi (Yuri); K. Nho (Kwangsik); M. Papmeyer (Martina); A. Ramasamy (Adaikalavan); S.L. Risacher (Shannon); R. Roiz-Santiañez (Roberto); E.J. Rose (Emma); A. Salami (Alireza); P.G. Sämann (Philipp); L. Schmaal (Lianne); N.J. Schork (Nicholas); J. Shin (Jean); V.M. Strike (Vanessa); A. Teumer (Alexander); M.M.J. Van Donkelaar (Marjolein M. J.); K.R. van Eijk (Kristel); R.K. Walters (Raymond); L.T. Westlye (Lars); C.D. Whelan (Christopher); A.M. Winkler (Anderson); M.P. Zwiers (Marcel); S. Alhusaini (Saud); L. Athanasiu (Lavinia); S.M. Ehrlich (Stefan); M. Hakobjan (Marina); C.B. Hartberg (Cecilie B.); U.K. Haukvik (Unn); A.J.G.A.M. Heister (Angelien J. G. A. M.); D. Hoehn (David); D. Kasperaviciute (Dalia); D.C. Liewald (David C.); L.M. Lopez (Lorna); R.R.R. Makkinje (Remco R. R.); M. Matarin (Mar); M.A.M. Naber (Marlies A. M.); D. Reese McKay; M. Needham (Margaret); A.C. Nugent (Allison); B. Pütz (Benno); N.A. Royle (Natalie); L. Shen (Li); R. Sprooten (Roy); D. Trabzuni (Danyah); S.S.L. Van Der Marel (Saskia S. L.); K.J.E. Van Hulzen (Kimm J. E.); E. Walton (Esther); A. Björnsson (Asgeir); L. Almasy (Laura); D. Ames (David); S. Arepalli (Sampath); A.A. Assareh; M.E. Bastin (Mark); H. Brodaty (Henry); K. Bulayeva (Kazima); M.A. Carless (Melanie); S. Cichon (Sven); A. Corvin (Aiden); J.E. Curran (Joanne); M. Czisch (Michael); G.I. de Zubicaray (Greig); A. Dillman (Allissa); A. Duggirala (Aparna); M.D. Dyer (Matthew); S. Erk; I. Fedko (Iryna); L. Ferrucci (Luigi); T. Foroud (Tatiana); P.T. Fox (Peter); M. Fukunaga (Masaki); J. Raphael Gibbs; H.H.H. Göring (Harald H.); R.C. Green (Robert C.); S. Guelfi (Sebastian); N.K. Hansell (Narelle); C.A. Hartman (Catharina); K. Hegenscheid (Katrin); J. Heinz (Judith); D.G. Hernandez (Dena); D.J. Heslenfeld (Dirk); P.J. Hoekstra (Pieter); F. Holsboer; G. Homuth (Georg); J.J. Hottenga (Jouke Jan); M. Ikeda (Masashi); C.R. Jack Jr. (Clifford); S. Jenkinson (Sarah); R. Johnson (Robert); R. Kanai (Ryota); M. Keil (Maria); J.W. Kent (Jack W.); P. Kochunov (Peter); J.B. Kwok (John B.); S. Lawrie (Stephen); X. Liu (Xinmin); D.L. Longo (Dan L.); K.L. Mcmahon (Katie); E. Meisenzahl (Eva); I. Melle (Ingrid); S. Mohnke (Sebastian); G.W. Montgomery (Grant); J.C. Mostert (Jeanette C.); T.W. Mühleisen (Thomas); M.A. Nalls (Michael); T.E. Nichols (Thomas); L.G. Nilsson; M.M. Nöthen (Markus); K. Ohi (Kazutaka); R.L. Olvera (Rene); R. Perez-Iglesias (Rocio); G. Bruce Pike; S.G. Potkin (Steven); I. Reinvang (Ivar); S. Reppermund; M. Rietschel (M.); N. Seiferth (Nina); G.D. Rosen (Glenn D.); D. Rujescu (Dan); K. Schnell (Kerry); C.J. Schofield (Christopher); C. Smith (Colin); V.M. Steen (Vidar); J. Sussmann (Jessika); A. Thalamuthu (Anbupalam); A.W. Toga (Arthur W.); B. Traynor (Bryan); J.C. Troncoso (Juan); J. Turner (Jessica); M.C. Valdés Hernández (Maria); D. van 't Ent (Dennis); M.P. van der Brug (Marcel); N.J. van der Wee (Nic); M.J.D. van Tol (Marie-José); D.J. Veltman (Dick); A.M.J. Wassink (Annemarie); E. Westman (Eric); R.H. Zielke (Ronald H.); A.B. Zonderman (Alan B.); D.G. Ashbrook (David G.); R. Hager (Reinmar); L. Lu (Lu); F.J. Mcmahon (Francis J); D.W. Morris (Derek W); R.W. Williams (Robert W.); H.G. Brunner; M. Buckner; J.K. Buitelaar (Jan K.); W. Cahn (Wiepke); V.D. Calhoun Vince D. (V.); G. Cavalleri (Gianpiero); B. Crespo-Facorro (Benedicto); A.M. Dale (Anders); G.E. Davies (Gareth); N. Delanty; C. Depondt (Chantal); S. Djurovic (Srdjan); D.A. Drevets (Douglas); T. Espeseth (Thomas); R.L. Gollub (Randy); B.C. Ho (Beng ); W. Hoffmann (Wolfgang); N. Hosten (Norbert); R. Kahn; S. Le Hellard (Stephanie); A. Meyer-Lindenberg; B. Müller-Myhsok (B.); M. Nauck (Matthias); L. Nyberg (Lars); M. Pandolfo (Massimo); B.W.J.H. Penninx (Brenda); J.L. Roffman (Joshua); S.M. Sisodiya (Sanjay); J.W. Smoller; H. van Bokhoven (Hans); N.E.M. van Haren (Neeltje E.); H. Völzke (Henry); H.J. Walter (Henrik); M.W. Weiner (Michael); W. Wen (Wei); T.J.H. White (Tonya); I. Agartz (Ingrid); O.A. Andreassen (Ole A.); J. Blangero (John); D.I. Boomsma (Dorret); R.M. Brouwer (Rachel); D.M. Cannon (Dara); M.R. Cookson (Mark); E.J.C. de Geus (Eco); I.J. Deary (Ian J.); D.J. Donohoe (Dennis); G. Fernandez (Guillén); S.E. Fisher (Simon); C. Francks (Clyde); D.C. Glahn (David); H.J. Grabe (Hans Jörgen); O. Gruber (Oliver); J. Hardy (John); R. Hashimoto (Ryota); H.E. Hulshoff Pol (Hilleke); E.G. Jönsson (Erik); I. Kloszewska (Iwona); S. Lovestone (Simon); V.S. Mattay (Venkata S.); P. Mecocci (Patrizia); C. McDonald (Colm); A.M. McIntosh (Andrew); R.A. Ophoff (Roel); T. Paus (Tomas); Z. Pausova (Zdenka); M. Ryten (Mina); P.S. Sachdev (Perminder); A.J. Saykin (Andrew); A. Simmons (Andrew); A. Singleton (Andrew); H. Soininen (H.); J.M. Wardlaw (J.); M.E. Weale (Michael); D.R. Weinberger (Daniel); H.H.H. Adams (Hieab); L.J. Launer (Lenore); S. Seiler (Stephan); R. Schmidt (Reinhold); G. Chauhan (Ganesh); C.L. Satizabal (Claudia L.); J.T. Becker (James); L.R. Yanek (Lisa); S. van der Lee (Sven); M. Ebling (Maritza); B. Fischl (Bruce); W.T. Longstreth Jr; D. Greve (Douglas); R. Schmidt (Reinhold); P. Nyquist (Paul); L.N. Vinke (Louis N.); C.M. van Duijn (Cock); L. Xue (Luting); B. Mazoyer (Bernard); J.C. Bis (Joshua); V. Gudnason (Vilmundur); S. Seshadri (Sudha); M.A. Ikram (Arfan); N.G. Martin (Nicholas); M.J. Wright (Margaret); G. Schumann (Gunter); B. Franke (Barbara); P.M. Thompson (Paul); S.E. Medland (Sarah Elizabeth)

    2015-01-01

    textabstractThe highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate h

  17. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    NARCIS (Netherlands)

    Lv, J.; Qi, J.; Shi, Q.; Shen, D.; Zhang, S.; Shao, G.; Li, H.; Sun, Z.; Weng, Y.; Shang, Y.; Gu, X.; Li, X.; Zhu, X.; Zhang, J.; Treuren, van R.; Dooijeweert, van W.; Zhang, Z.; Huang, S.

    2012-01-01

    Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also incl

  18. The role of river drainages in shaping the genetic structure of capybara populations.

    Science.gov (United States)

    Byrne, María Soledad; Quintana, Rubén Darío; Bolkovic, María Luisa; Cassini, Marcelo H; Túnez, Juan Ignacio

    2015-12-01

    The capybara, Hydrochoerus hydrochaeris, is an herbivorous rodent widely distributed throughout most of South American wetlands that lives closely associated with aquatic environments. In this work, we studied the genetic structure of the capybara throughout part of its geographic range in Argentina using a DNA fragment of the mitochondrial control region. Haplotypes obtained were compared with those available for populations from Paraguay and Venezuela. We found 22 haplotypes in 303 individuals. Hierarchical AMOVAs were performed to evaluate the role of river drainages in shaping the genetic structure of capybara populations at the regional and basin scales. In addition, two landscape genetic models, isolation by distance and isolation by resistance, were used to test whether genetic distance was associated with Euclidean distance (i.e. isolation by distance) or river corridor distance (i.e. isolation by resistance) at the basin scale. At the regional scale, the results of the AMOVA grouping populations by mayor river basins showed significant differences between them. At the basin scale, we also found significant differences between sub-basins in Paraguay, together with a significant correlation between genetic and river corridor distance. For Argentina and Venezuela, results were not significant. These results suggest that in Paraguay, the current genetic structure of capybaras is associated with the lack of dispersion corridors through permanent rivers. In contrast, limited structuring in Argentina and Venezuela is likely the result of periodic flooding facilitating dispersion.

  19. Comparative population genetic analysis of brackish- and freshwater populations of Eurasian perch (Perca fluviatilis L.: implication for fish forensics.

    Directory of Open Access Journals (Sweden)

    Lilian Pukk

    2015-11-01

    Full Text Available Understanding the genetic population structure of commercially important fish species is crucial for developing biologically sound management and conservation strategies. Genetic information can be also useful for fighting against illegal fishing and fish trade. Here, we studied commercially important brackish and freshwater populations of Eurasian perch (Perca fluviatilis L. in Estonia, to describe the genetic divergence among populations and evaluate the power of 16 microsatellite markers to assign individual fish and group of fish to their population of origin. To do so, a total of 785 individuals caught from 13 different sites in the Baltic Sea and four locations in Lake Peipus were analyzed. We found significant differences in genetic diversity between brackish and freshwater populations with Baltic Sea samples showing slightly lower allelic richness and heterozygosity compared to Lake Peipus. We also observed moderate genetic differentiation among populations (overall FST=0.034. Individual self-assignment tests assigned large proportion of individuals correctly back to freshwater or coastal origin (Lake Peipus: 87.1%; Baltic Sea: 89.4%. Also, when evaluating the origin of group of individuals, it was possible to identify the origin of the brackish and freshwater fish groups with very high confidence (log 10 LR > 2 when sample size was larger than 15. Our results demonstrate the power of highly variable genetic markers separating two commercially most important Eurasian perch stocks in Estonia and the usefulness of assignment tests to successfully identify the genetic origin of fish.

  20. Structural change in OECD comparative advantage

    NARCIS (Netherlands)

    Brakman, Steven; Inklaar, Robert; Van Marrewijk, Charles

    2013-01-01

    In the post-war period, the goods composition of trade in Organisation for Economic Cooperation and Development (OECD) countries has changed considerably. We analyze the evolution of comparative advantage using a detailed trade data set and a new analytical tool: the Harmonic Mass index (HM index),

  1. An investigation of the statistical power of neutrality tests based on comparative and population genetic data

    DEFF Research Database (Denmark)

    Zhai, Weiwei; Nielsen, Rasmus; Slatkin, Montgomery

    2009-01-01

    In this report, we investigate the statistical power of several tests of selective neutrality based on patterns of genetic diversity within and between species. The goal is to compare tests based solely on population genetic data with tests using comparative data or a combination of comparative...... selection. The Hudson-Kreitman-Aguadé test is the most powerful test for detecting positive selection among the population genetic tests investigated, whereas McDonald-Kreitman test typically has more power to detect negative selection. We discuss our findings in the light of the discordant results obtained...

  2. Fine-scaled human genetic structure revealed by SNP microarrays.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Witherspoon, David J; Zhang, Yuhua; Guthery, Stephen L; Thara, Rangaswamy; Mowry, Bryan J; Bulayeva, Kazima; Weiss, Robert B; Jorde, Lynn B

    2009-05-01

    We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

  3. Genetic structure and phylogeography of European catfish (Silurus glanis) populations.

    Science.gov (United States)

    Triantafyllidis, A; Krieg, F; Cottin, C; Abatzopoulos, T J; Triantaphyllidis, C; Guyomard, R

    2002-06-01

    The genetic structure of Silurus glanis (Europe's largest freshwater fish species) across most of its natural distribution was investigated using 10 microsatellite loci. The revealed levels of genetic diversity were much higher than previous allozyme and restriction fragment length polymorphism mitochondrial DNA analyses had shown; relative levels of variability among populations were however, in good agreement with the previous studies. Populations from large basins (Volga and Danube rivers) were the most polymorphic, while samples from the smaller Greek rivers, which are more prone to genetic bottleneck, exhibited the lowest levels of genetic diversity. Microsatellite multilocus genotyping permitted the assignment of individual fish to their population of origin with a score as high as 98.3%. Despite the great genetic differentiation of S. glanis populations, no consistent pattern of geographical structuring was revealed, in contrast to previous studies of European freshwater fish species. A model of isolation by distance seems more probable and a hypothesis of recent dispersion from only one glacial refugium is proposed. The discovery of the highest levels of microsatellite and mitochondrial diversity in the Volga sample and the presence of river connections, during the Pleistocene, between this area and all major areas of the present catfish distribution, place this refugium around the Ponto-Caspian region. Combining these data with those from previous studies, a number of markers are now available to monitor wild and hatchery populations even at the individual level.

  4. Assessment of the effects of genetically modified potatoes on structure and functioning of soil fungal communities

    NARCIS (Netherlands)

    Hannula, Emilia

    2012-01-01

    This thesis investigates the effects of genetic modification of the starch quality in potato on the structure and function of the soil fungal community via changes in root-exudates and litter composition, and compares the observed differences between the GM- and its parental variety in the context o

  5. Testing the influence of habituation on genetic structure of brown bear (Ursus arctos

    Directory of Open Access Journals (Sweden)

    Ancuţa Cotovelea

    2015-04-01

    Full Text Available Adult bear individuals live solitary and haveprolonged parent–offspring relationships, therefore the share of learned skills compared to the inherited ones is much larger than in other carnivores. This promotes acquisition of deviated behavior and simultaneously establishment of a kinship structure. However, deviated bear behavior and human food conditioning are the symptoms of habituation. The aim of this paper is to test the genetic structuring of habituated and non-habituated individuals located in the central region of Romania (Braşov and Prahova districts, a hotspot in terms of human-bear conflicts. Seven microsatellites were used to genotype 145 samples (ear clips and tissue, out of which 82 were classified as habituated and 63 as wild individuals, respectively. Our results suggest the presence of kinship structures in habituated bear group and a reduction of genetic diversity (He = 0.75, while the group located in the wild registered a higher genetic diversity (He = 0.78 and more private alleles. The genetic differentiation suggested by the Neighbor joining cluster analysis has been strengthened by the two percent (AMOVA differences between the two groups and highlights the negative impact of brown bear kinship structure, caused by the human expansion on wilderness. The genetic analyses indicated that the two groups share genetic variants due to the dispersal and breeding patterns of male adult bears. The emergence of genetic differences between the two groups can be avoided by preventing bears to become human-food conditioned; over time, kinship structure can pose a threat to genetic diversity.

  6. Physiological vagility: correlations with dispersal and population genetic structure of amphibians.

    Science.gov (United States)

    Hillman, Stanley S; Drewes, Robert C; Hedrick, Michael S; Hancock, Thomas V

    2014-01-01

    Physiological vagility represents the capacity to move sustainably and is central to fully explaining the processes involved in creating fine-scale genetic structure of amphibian populations, because movement (vagility) and the duration of movement determine the dispersal distance individuals can move to interbreed. The tendency for amphibians to maintain genetic differentiation over relatively short distances (isolation by distance) has been attributed to their limited dispersal capacity (low vagility) compared with other vertebrates. Earlier studies analyzing genetic isolation and population differentiation with distance treat all amphibians as equally vagile and attempt to explain genetic differentiation only in terms of physical environmental characteristics. We introduce a new quantitative metric for vagility that incorporates aerobic capacity, body size, body temperature, and the cost of transport and is independent of the physical characteristics of the environment. We test our metric for vagility with data for dispersal distance and body mass in amphibians and correlate vagility with data for genetic differentiation (F'(ST)). Both dispersal distance and vagility increase with body size. Differentiation (F'(ST)) of neutral microsatellite markers with distance was inversely and significantly (R2=0.61) related to ln vagility. Genetic differentiation with distance was not significantly related to body mass alone. Generalized observations are validated with several specific amphibian studies. These results suggest that interspecific differences in physiological capacity for movement (vagility) can contribute to genetic differentiation and metapopulation structure in amphibians.

  7. Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park.

    Science.gov (United States)

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

    2014-04-01

    Roads can fragment and isolate wildlife populations, which will eventually decrease genetic diversity within populations. Wildlife crossing structures may counteract these impacts, but most crossings are relatively new, and there is little evidence that they facilitate gene flow. We conducted a three-year research project in Banff National Park, Alberta, to evaluate the effectiveness of wildlife crossings to provide genetic connectivity. Our main objective was to determine how the Trans-Canada Highway and crossing structures along it affect gene flow in grizzly (Ursus arctos) and black bears (Ursus americanus). We compared genetic data generated from wildlife crossings with data collected from greater bear populations. We detected a genetic discontinuity at the highway in grizzly bears but not in black bears. We assigned grizzly bears that used crossings to populations north and south of the highway, providing evidence of bidirectional gene flow and genetic admixture. Parentage tests showed that 47% of black bears and 27% of grizzly bears that used crossings successfully bred, including multiple males and females of both species. Differentiating between dispersal and gene flow is difficult, but we documented gene flow by showing migration, reproduction and genetic admixture. We conclude that wildlife crossings allow sufficient gene flow to prevent genetic isolation.

  8. Genetic Structure and Indica/Japonica Component Changes in Major Inbred Rice Varieties in China

    Institute of Scientific and Technical Information of China (English)

    YU Ping; YUAN Xiao-ping; XU Qun; WANG Cai-hong; YU Han-yong; WANG Yi-ping; TANG Sheng-xiang

    2013-01-01

    We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties,and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from the 1950s to the 1990s in China.The genetic structure analysis showed that these rice varieties were distinctly divided into two populations,indica and japonica.The sub-structure of indica varieties was more complex than that of japonica ones.Among the various lines,late-season indica and early season japonica varieties had simpler genetic backgrounds.The seasonal ecotypes were not quite consistent with the subtypes of genetic structure.Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica/japonica components.The differences in indica/japonica components among the five decades were not significant,except for late-season indica varieties in the 1990s,which had a significantly higher japonica component.These results will help to understand the genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China.

  9. 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.

  10. Healing Temperature of Hybrid Structures Based on Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    赵中伟; 陈志华; 刘红波

    2016-01-01

    The healing temperature of suspen-dome with stacked arches(SDSA)and arch-supported single-layer lattice shell structures was investigated based on the genetic algorithm. The temperature field of arch under solar radiation was derived by FLUENT to investigate the influence of solar radiation on the determination of the healing temperature. Moreover, a multi-scale model was established to apply the complex temperature field under solar radiation. The change in the mechanical response of these two kinds of structures with the healing temperature was discussed. It can be concluded that solar radiation has great influence on the healing temperature, and the genetic algorithm can be effectively used in the optimization of the healing temperature for hybrid structures.

  11. Comparative Study of Diagrid Structures with Conventional Frame Structures

    Directory of Open Access Journals (Sweden)

    Manthan I. Shah

    2016-05-01

    Full Text Available In modern age, the decrease of available free land and increase of land prices along with the wide spread of urban area has made architects and engineers to develop the cities vertically. For vertical growth, the only option is to construct the buildings as high as possible. It is a task of a structural designer to make the desired building stand and stable throughout its life. There are various structural systems for tall buildings, among them diagrid system is selected for this work. Diagrid is an exterior structural system which resists the lateral forces by axial actions of diagonals provided in periphery. Statistical analysis of tall buildings in India is carried out and presented for buildings having height more than 150 m or 40 storeys. Parametric study and detailed comparison of diagrid structural system with respect to conventional frame is carried out for symmetrical buildings. In this study seven steel buildings of identical base area and loadings with different heights are designed for optimum sections for both structural systems diagrid and conventional frame in ETABS. Various parameters like fundamental time period, maximum top storey lateral displacement, maximum base shear, steel weight, percentage differences in change of steel weight, maximum storey displacement and maximum storey drift are considered in this study. A Diagrid structure performs well than conventional frame structures and increase in steel weight with increase in height of building is considerably less in diagrid structures

  12. Meningeal Hemangiopericytomas and Meningomas: a Comparative Immunohistochemical and Genetic Study.

    Science.gov (United States)

    Trabelsi, Saoussen; Mama, Nadia; Chourabi, Maroua; Mastouri, Maroua Haddaji; Ladib, Mohamed; Popov, Sergey; Burford, Anna; Mokni, Moncef; Tlili, Kalthoum; Krifa, Hedi; Jones, Chris; Yacoubi, Mohamed Tahar; Saad, Ali; Brahim, Dorra H'mida-Ben

    2015-01-01

    The meningeal hemangiopericytoma (MHPC) is a vascular tumor arising from pericytes. Most intracranial MHPCs resemble meningiomas (MNGs) in their clinical presentation and histological features and may therefore be misdiagnosed, despite important differences in prognosis. We report 8 cases of MHPC and 5 cases of MNG collected from 2007 to 2011 from the Neuro-Surgery and Histopathology departments. All 13 samples were re reviewed by two independent pathologists and investigated by immunohistochemistry (IHC) using mesenchymal, epithelial and neuro-glial markers. Additionally, we screened all tumors for a large panel of chromosomal alterations using multiplex ligation probe amplification (MLPA). Presence of the NAB2-STAT6 fusion gene was inferred by immunohistochemical staining for STAT6. Compared with MNG, MHPCs showed strong VIM (100% of cases), CD99 (62%), bcl-2 (87%), and p16 (75%) staining but only focal positivity with EMA (33%) and NSE (37%). The p21 antibody was positive in 62% of MHPC and less than 1% in all MNGs. MLPA data did not distinguish HPC from MNG, with PTEN loss and ERBB2 gain found in both. By contrast, STAT6 nuclear staining was observed in 3 MHPC cases and was absent from MNG. MNG and MHPC comprise a spectrum of tumors that cannot be easily differentiated based on histopathology. The presence of STAT6 nuclear positivity may however be a useful diagnostic marker.

  13. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

    Science.gov (United States)

    Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

    2014-01-01

    Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

  14. Comparison of algorithms to infer genetic population structure from unlinked molecular markers.

    Science.gov (United States)

    Peña-Malavera, Andrea; Bruno, Cecilia; Fernandez, Elmer; Balzarini, Monica

    2014-08-01

    Identifying population genetic structure (PGS) is crucial for breeding and conservation. Several clustering algorithms are available to identify the underlying PGS to be used with genetic data of maize genotypes. In this work, six methods to identify PGS from unlinked molecular marker data were compared using simulated and experimental data consisting of multilocus-biallelic genotypes. Datasets were delineated under different biological scenarios characterized by three levels of genetic divergence among populations (low, medium, and high FST) and two numbers of sub-populations (K=3 and K=5). The relative performance of hierarchical and non-hierarchical clustering, as well as model-based clustering (STRUCTURE) and clustering from neural networks (SOM-RP-Q). We use the clustering error rate of genotypes into discrete sub-populations as comparison criterion. In scenarios with great level of divergence among genotype groups all methods performed well. With moderate level of genetic divergence (FST=0.2), the algorithms SOM-RP-Q and STRUCTURE performed better than hierarchical and non-hierarchical clustering. In all simulated scenarios with low genetic divergence and in the experimental SNP maize panel (largely unlinked), SOM-RP-Q achieved the lowest clustering error rate. The SOM algorithm used here is more effective than other evaluated methods for sparse unlinked genetic data.

  15. Genetic mapping and comparative expression analysis of transcription factors in cotton.

    Science.gov (United States)

    Chen, Xuemei; Jin, Xin; Li, Ximei; Lin, Zhongxu

    2015-01-01

    Transcription factors (TFs) play an important role in the regulation of plant growth and development. The study of the structure and function of TFs represents a research frontier in plant molecular biology. The findings of these studies will provide significant information regarding genetic improvement traits in crops. Currently, a large number of TFs have been cloned, and their function has been verified. However, relatively few studies that genetically map TFs in cotton are available. To genetically map TFs in cotton in this study, specific primers were designed for TF genes that were published in the Plant Transcription Factor Database. A total of 977 TF primers were obtained, and 31 TF polymorphic loci were mapped on 15 cotton chromosomes. These polymorphic loci were clearly preferentially distributed on chromosomes 5, 11, 19 and 20; and TFs from the same family mapped to homologous cotton chromosomes. In-silico mapping verified that many mapped TFs were mapped on their corresponding chromosomes or their homologous chromosomes' corresponding chromosomes in the diploid genomes. QTL mapping for fiber quality revealed that TF-Ghi005602-2 mapped on Chr19 was associated with fiber length. Eighty-five TF genes were selected for RT-PCR analysis, and 4 TFs were selected for qRT-PCR analysis, revealing unique expression patterns across different stages of fiber development between the mapping parents. Our data offer an overview of the chromosomal distribution of TFs in cotton, and the comparative expression analysis between Gossypium hirsutum and G. barbadense provides a rough understanding of the regulation of TFs during cotton fiber development.

  16. Genetic structure among 50 species of the northeastern Pacific rocky intertidal community.

    Directory of Open Access Journals (Sweden)

    Ryan P Kelly

    Full Text Available Comparing many species' population genetic patterns across the same seascape can identify species with different levels of structure, and suggest hypotheses about the processes that cause such variation for species in the same ecosystem. This comparative approach helps focus on geographic barriers and selective or demographic processes that define genetic connectivity on an ecosystem scale, the understanding of which is particularly important for large-scale management efforts. Moreover, a multispecies dataset has great statistical advantages over single-species studies, lending explanatory power in an effort to uncover the mechanisms driving population structure. Here, we analyze a 50-species dataset of Pacific nearshore invertebrates with the aim of discovering the most influential structuring factors along the Pacific coast of North America. We collected cytochrome c oxidase I (COI mtDNA data from populations of 34 species of marine invertebrates sampled coarsely at four coastal locations in California, Oregon, and Alaska, and added published data from 16 additional species. All nine species with non-pelagic development have strong genetic structure. For the 41 species with pelagic development, 13 show significant genetic differentiation, nine of which show striking FST levels of 0.1-0.6. Finer scale geographic investigations show unexpected regional patterns of genetic change near Cape Mendocino in northern California for five of the six species tested. The region between Oregon and Alaska is a second focus of intraspecific genetic change, showing differentiation in half the species tested. Across regions, strong genetic subdivision occurs more often than expected in mid-to-high intertidal species, a result that may reflect reduced gene flow due to natural selection along coastal environmental gradients. Finally, the results highlight the importance of making primary research accessible to policymakers, as unexpected barriers to marine

  17. Public attitudes towards genetic testing revisited: comparing opinions between 2002 and 2010

    Science.gov (United States)

    Henneman, Lidewij; Vermeulen, Eric; van El, Carla G; Claassen, Liesbeth; Timmermans, Danielle R M; Cornel, Martina C

    2013-01-01

    Ten years after the Human Genome Project, medicine is still waiting for many of the promised benefits, and experts have tempered their high expectations. Public opinion on genetic testing has generally been favourable but is this still the case? The aim of this study is to compare public experiences, beliefs and expectations concerning genetic testing over the years (2002 vs 2010). A cross-sectional questionnaire survey was conducted using the Dutch Health Care Consumer Panel in 2002 and 2010. Responses to questions in identical wording were compared. In 2002 and 2010, 817 (63%) and 978 (70%) members responded, respectively. Awareness and reported use of genetic tests remained stable over time. In 2010, more respondents expected genetic testing to become more widely applied, believed that knowledge about the genetic background of disease helps people live longer, and that testing should be promoted more intensively. In 2010, they were also more interested in their own genetic make-up. On the one hand, the concern that a dichotomy would emerge between people with ‘good genes' and ‘bad genes' was higher. On the other hand, respondents thought that insurance companies would be less likely to demand a genetic test in order to calculate health insurance premiums. In conclusion, the results suggest that in 8 years, expectations of benefits and potential use of genetic testing have been raised among the public, resulting in more positive opinions. Worries on inequity remain, although worries about premium differentiation by insurance companies have decreased. PMID:23249955

  18. Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

    NARCIS (Netherlands)

    Cascante-Marín, A.; Oostermeijer, G.; Wolf, J.; Fuchs, E.J.

    2014-01-01

    Information on genetic variation and its distribution in tropical plant populations relies mainly on studies of ground-rooted species, while genetic information of epiphytic plants is still limited. Particularly, the effect of forest successional condition on genetic diversity and structure of

  19. Structure analysis of the La Guajira-Colombia population: a genetic, demographic and genealogical overview.

    Science.gov (United States)

    Rojas, M Y; Alonso, L A; Sarmiento, V A; Eljach, L Y; Usaquén, W

    2013-03-01

    This study examined whether cultural factors, as compared to geographical distance, have produced a population sub-structure among different groups from the La Guajira population (Amerindian Wayúu and other resident groups) that co-exist within the same region. The aims of this study were to analyse this population to discover whether cultural barriers result in the sub-structure, to evaluate whether there is a genetic drift effect and to describe migration dynamics using a genetic, genealogical and demographic approach. This study examined a sample of 290 individuals who were grouped based on a genealogical criterion to distinguish between native individuals and migrants. Using demographic information, the age and gender structure of the population and genetic drift estimators were analysed. Using 15 autosomal microsatellites, heterozygosity, Hardy-Weinberg equilibrium (HWE), inbreeding, sub-structure, recent migration rate and genetic relationships were also evaluated using a Principal Component analysis (PCA) using reference populations. La Guajira is a young population that is growing and exposed to a moderate effect of genetic drift (Neme 11.903). The Wayúu are highly diverse (Ho 0.727) and different from other groups, with the exception of Wayúu-Guajiro. This trend was also observed in other Amerindian populations. This study found a high level of admixture and gene flow within the Wayúu population despite cultural differences. Thus, although the Wayúu population differs from other population groups, it is not an isolated population.

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

    Science.gov (United States)

    Hruschka, Daniel J; Hadley, Craig; Brewis, Alexandra A; Stojanowski, Christopher M

    2015-01-01

    Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28). However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74). Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

  1. Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish, Belodontichthys truncatus Kottelat & Ng, 1999 (Siluriformes: Siluridae, from Mekong Basin

    Directory of Open Access Journals (Sweden)

    Surapon Yodsiri

    2017-01-01

    Full Text Available The Mekong River and its tributaries possess the second highest diversity in fish species in the world. However, the fish biodiversity in this river is threatened by several human activities, such as hydropower plant construction. Understanding the genetic diversity and genetic structure of the species is important for natural resource management. Belodontichthys truncatus Kottelat & Ng is endemic to the Mekong River basin and is an important food source for people in this area. In this study, the genetic diversity, genetic structure, and demographic history of the twisted-jaw fish, B. truncatus, were investigated using mitochondrial cytochrome b gene sequences. A total of 124 fish specimens were collected from 10 locations in the Mekong and its tributaries. Relatively high genetic diversity was found in populations of B. truncatus compared to other catfish species in the Mekong River. The genetic structure analysis revealed that a population from the Chi River in Thailand was genetically significantly different from other populations, which is possibly due to the effect of genetic drift. Demographic history analysis indicated that B. truncatus has undergone recent demographic expansion dating back to the end of the Pleistocene glaciation.

  2. Surface Appendages of Archaea: Structure, Function, Genetics and Assembly

    Directory of Open Access Journals (Sweden)

    Sarah Siu

    2013-01-01

    Full Text Available Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including archaella, certain pili and sugar binding structures termed bindosomes. In addition, there are widespread posttranslational modifications of archaellins and pilins with N-linked glycans, with some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer, biofilm formation, and possible intercellular communication. Sometimes functions are co-dependent on other surface structures. These structures and the regulation of their assembly are important features that allow various Archaea, including thermoacidophilic, hyperthermophilic, halophilic, and anaerobic ones, to survive and thrive in the extreme environments that are commonly inhabited by members of this domain.

  3. Using an alignment of fragment strings for comparing protein structures

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Kolodny, Rachel

    2007-01-01

    MOTIVATION: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. This type of representation can be a p...

  4. Novel genetic algorithm search procedure for LEED surface structure determination.

    Science.gov (United States)

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E

    2014-06-04

    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  5. Analysis of genetic structure and relationship among nine indigenous Chinese chicken populations by the Structure program

    Indian Academy of Sciences (India)

    H. F. Li; W. Han; Y. F. Zhu; J. T. Shu; X. Y. Zhang; K. W. Chen

    2009-08-01

    The multi-locus model-based clustering method Structure program was used to infer the genetic structure of nine indigenous Chinese chicken (Gallus gallus) populations based on 16 microsatellite markers. Twenty runs were carried out at each chosen value of predefined cluster numbers $(K)$ under admixture model. The Structure program properly inferred the presence of genetic structure with 0.999 probabilities. The genetic structure not only indicated that the nine kinds of chicken populations were defined actually by their locations, phenotypes or culture, but also reflected the underlying genetic variations. At $K = 2$, nine chicken populations were divided into two main clusters, one light-body type, including Chahua chicken (CHA), Tibet chicken (TIB), Xianju chicken (XIA), Gushi chicken (GUS) and Baier chicken (BAI); and the other heavy-body type, including Beijing You chicken (YOU), Xiaoshan chicken (XIA), Luyuan chicken (LUY) and Dagu chicken (DAG). GUS and DAG were divided into independent clusters respectively when equaled 4, 5, or 6. XIA and BIA chicken, XIA and LUY chicken, TIB and CHA chicken still clustered together when equaled 6, 7, and 8, respectively. These clustering results were consistent with the breeding directions of the nine chicken populations. The Structure program also identified migrants or admixed individuals. The admixed individuals were distributed in all the nine chicken populations, while migrants were only distributed in TIB, XIA and LUY populations. These results indicated that the clustering analysis using the Structure program might provide an accurate representation of the genetic relationship among the breeds.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Valentina Coia

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

  9. Comparative Genome of GK and Wistar Rats Reveals Genetic Basis of Type 2 Diabetes.

    Directory of Open Access Journals (Sweden)

    Tiancheng Liu

    Full Text Available The Goto-Kakizaki (GK rat, which has been developed by repeated inbreeding of glucose-intolerant Wistar rats, is the most widely studied rat model for Type 2 diabetes (T2D. However, the detailed genetic background of T2D phenotype in GK rats is still largely unknown. We report a survey of T2D susceptible variations based on high-quality whole genome sequencing of GK and Wistar rats, which have generated a list of GK-specific variations (228 structural variations, 2660 CNV amplification and 2834 CNV deletion, 1796 protein affecting SNVs or indels by comparative genome analysis and identified 192 potential T2D-associated genes. The genes with variants are further refined with prior knowledge and public resource including variant polymorphism of rat strains, protein-protein interactions and differential gene expression. Finally we have identified 15 genetic mutant genes which include seven known T2D related genes (Tnfrsf1b, Scg5, Fgb, Sell, Dpp4, Icam1, and Pkd2l1 and eight high-confidence new candidate genes (Ldlr, Ccl2, Erbb3, Akr1b1, Pik3c2a, Cd5, Eef2k, and Cpd. Our result reveals that the T2D phenotype may be caused by the accumulation of multiple variations in GK rat, and that the mutated genes may affect biological functions including adipocytokine signaling, glycerolipid metabolism, PPAR signaling, T cell receptor signaling and insulin signaling pathways. We present the genomic difference between two closely related rat strains (GK and Wistar and narrow down the scope of susceptible loci. It also requires further experimental study to understand and validate the relationship between our candidate variants and T2D phenotype. Our findings highlight the importance of sequenced-based comparative genomics for investigating disease susceptibility loci in inbreeding animal models.

  10. Genetic population structure of Anopheles gambiae in Equatorial Guinea

    Directory of Open Access Journals (Sweden)

    Caccone Adalgisa

    2007-10-01

    Full Text Available Abstract Background Patterns of genetic structure among mosquito vector populations in islands have received particular attention as these are considered potentially suitable sites for experimental trials on transgenic-based malaria control strategies. In this study, levels of genetic differentiation have been estimated between populations of Anopheles gambiae s.s. from the islands of Bioko and Annobón, and from continental Equatorial Guinea (EG and Gabon. Methods Genotyping of 11 microsatellite loci located in chromosome 3 was performed in three island samples (two in Bioko and one in Annobón and three mainland samples (two in EG and one in Gabon. Four samples belonged to the M molecular form and two to the S-form. Microsatellite data was used to estimate genetic diversity parameters, perform demographic equilibrium tests and analyse population differentiation. Results High levels of genetic differentiation were found between the more geographically remote island of Annobón and the continent, contrasting with the shallow differentiation between Bioko island, closest to mainland, and continental localities. In Bioko, differentiation between M and S forms was higher than that observed between island and mainland samples of the same molecular form. Conclusion The observed patterns of population structure seem to be governed by the presence of both physical (the ocean and biological (the M-S form discontinuity barriers to gene flow. The significant degree of genetic isolation between M and S forms detected by microsatellite loci located outside the "genomic islands" of speciation identified in A. gambiae s.s. further supports the hypothesis of on-going incipient speciation within this species. The implications of these findings regarding vector control strategies are discussed.

  11. On Natural Genetic Engineering: Structural Dynamism in Random Boolean Networks

    CERN Document Server

    Bull, Larry

    2012-01-01

    This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include changes in node connectivity based upon the current cell state, e.g., via transposable elements. The underlying behaviour of the resulting dynamical networks is investigated before their evolvability is explored using a version of the NK model of fitness landscapes. Structural dynamism is found to be selected for in non-stationary environments and subsequently shown capable of providing a mechanism for evolutionary innovation when such reorganizations are inherited.

  12. Detecting structural breaks in time series via genetic algorithms

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Fischer, Paul; Hilbert, Astrid

    2016-01-01

    Detecting structural breaks is an essential task for the statistical analysis of time series, for example, for fitting parametric models to it. In short, structural breaks are points in time at which the behaviour of the time series substantially changes. Typically, no solid background knowledge...... and mutation operations for this problem, we conduct extensive experiments to determine good choices for the parameters and operators of the genetic algorithm. One surprising observation is that use of uniform and one-point crossover together gave significantly better results than using either crossover...

  13. Pollution and genetic structure of North American populations of the common dandelion (Taraxacum officinale).

    Science.gov (United States)

    Keane, Brian; Collier, Matthew H; Rogstad, Steven H

    2005-06-01

    Assessing the genetic structure of natural populations differentially impacted by anthropogenic contaminants can be a useful tool for evaluating the population genetic consequences of exposure to pollution. In this study, measures of genetic diversity at variable-number-tandem-repeat loci in six dandelion populations (3 urban and 3 rural) showed patterns that may have been influenced by exposure to environmental contaminants. Mean genetic similarity among individuals within a population was significantly and positively correlated with increasing levels of airborne particulate matter (< or = 10 microm, PM10) and soil concentrations of four metals (Cd, Fe, Ni and Pb). In addition, mean genetic similarity was always significantly higher at the urban sites compared to rural sites. There was a significant negative correlation between the number of genotypes at a site and increasing amounts of PM10, concentrations of five soil metals (Cd, Cu, Fe, Ni and Pb), leaf tissue levels of Fe and a significant positive correlation between the extent of clonality at a site and levels of PM10 and soil concentrations of five metals (Cd, Cu, Fe, Ni and Pb). Although, this study does not directly establish a causal link between the specific contaminants detected at the study sites and differences in genetic diversity, our data are consistent with the hypothesis that pollution-induced selection has contributed in some fashion to the lower genetic diversity found at the urban sites.

  14. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

    Science.gov (United States)

    Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

    2016-11-14

    Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (HE = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (HE = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher genetic

  15. 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

  16. Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

    NARCIS (Netherlands)

    Wild, Philipp S.; Felix, Janine F.; Schillert, Arne; Teumer, Alexander; Chen, Ming-Huei; Leening, Maarten J. G.; Voelker, Uwe; Grossmann, Vera; Brody, Jennifer A.; Irvin, Marguerite R.; Shah, Sanjiv J.; Pramana, Setia; Lieb, Wolfgang; Schmidt, Reinhold; Stanton, Alice V.; Malzahn, Doerthe; Smith, Albert Vernon; Sundstrom, Johan; Minelli, Cosetta; Ruggiero, Daniela; Lyytikainen, Leo-Pekka; Tiller, Daniel; Smith, J. Gustav; Monnereau, Claire; Di Tullio, Marco R.; Musani, Solomon K.; Morrison, Alanna C.; Pers, Tune H.; Morley, Michael; Kleber, Marcus E.; Aragam, Jayashri; Benjamin, Emelia J.; Bis, Joshua C.; Bisping, Egbert; Broeckel, Ulrich; Cheng, Susan; Deckers, Jaap W.; Del Greco, Fabiola; Edelmann, Frank; Fornage, Myriam; Franke, Lude; Friedrich, Nele; Harris, Tamara B.; Hofer, Edith; Hofman, Albert; Huang, Jie; Hughes, Alun D.; Kahonen, Mika; Kruppa, Jochen; Lackner, Karl J.; Lannfelt, Lars; Laskowski, Rafael; Launer, Lenore J.; Leosdottir, Margret; Lin, Honghuang; Lindgren, Cecilia M.; Loley, Christina; MacRae, Calum A.; Mascalzoni, Deborah; Mayet, Jamil; Medenwald, Daniel; Morris, Andrew P.; Mueller, Christian; Mueller-Nurasyid, Martina; Nappo, Stefania; Nilsson, Peter M.; Nuding, Sebastian; Nutile, Teresa; Peters, Annette; Pfeufer, Arne; Pietzner, Diana; Pramstaller, Peter P.; Raitakari, Olli T.; Rice, Kenneth M.; Rivadeneira, Fernando; Rotter, Jerome I.; Ruohonen, Saku T.; Sacco, Ralph L.; Samdarshi, Tandaw E.; Schmidt, Helena; Sharp, Andrew S. P.; Shields, Denis C.; Sorice, Rossella; Sotoodehnia, Nona; Stricker, Bruno H.; Surendran, Praveen; Thom, Simon; Toeglhofer, Anna M.; Uitterlinden, Andre G.; Wachter, Rolf; Voelzke, Henry; Ziegler, Andreas; Muenzel, Thomas; Maerz, Winfried; Cappola, Thomas P.; Hirschhorn, Joel N.; Mitchell, Gary F.; Smith, Nicholas L.; Fox, Ervin R.; Dueker, Nicole D.; Jaddoe, Vincent W. V.; Melander, Olle; Russ, Martin; Lehtimaki, Terho; Ciullo, Marina; Hicks, Andrew A.; Lind, Lars; Gudnason, Vilmundur; Pieske, Burkert; Barron, Anthony J.; Zweiker, Robert; Schunkert, Heribert; Ingelsson, Erik; Liu, Kiang; Arnett, Donna K.; Psaty, Bruce M.; Blankenberg, Stefan; Larson, Martin G.; Felix, Stephan B.; Franco, Oscar H.; Zeller, Tanja; Vasan, Ramachandran S.; Doerr, Marcus

    2017-01-01

    BACKGROUND. Understanding the genetic architecture of cardiac structure and function may help to prevent and treat heart disease. This investigation sought to identify common genetic variations associated with inter-individual variability in cardiac structure and function. METHODS. A GWAS

  17. Population genetic structure of Venezuelan chiropterophilous columnar cacti (Cactaceae).

    Science.gov (United States)

    Nassar, Jafet M; Hamrick, J L; Fleming, Theodore H

    2003-11-01

    We conducted allozyme surveys of three Venezuelan self-incompatible chiropterophilous columnar cacti: two diploid species, Stenocereus griseus and Cereus repandus, and one tetraploid, Pilosocereus lanuginosus. The three cacti are pollinated by bats, and both bats and birds disperse seeds. Population sampling comprised two spatial scales: all Venezuelan arid zones (macrogeographic) and two arid regions in northwestern Venezuela (regional). Ten to 15 populations and 17-23 loci were analyzed per species. Estimates of genetic diversity were compared with those of other allozyme surveys in the Cactaceae to examine how bat-mediated gene dispersal affects the population genetic attributes of the three cacti. Genetic diversity was high for both diploid (P(s) = 94.1-100, P(p) = 56.7-72.3, H(s) = 0.182-0.242, H(p) = 0.161-0.205) and tetraploid (P(s) = 93.1, P(p) = 76.1, H(s) = 0.274, H(p) = 0.253) species. Within-population heterozygote deficit was detected in the three cacti at macrogeographic (F(IS) = 0.145-0.182) and regional (F(IS) = 0.057-0.174) levels. Low genetic differentiation was detected at both macrogeographic (G(ST) = 0.043-0.126) and regional (G(ST) = 0.009-0.061) levels for the three species, suggesting substantial gene flow among populations. Gene exchange among populations seems to be regulated by distance among populations. Our results support the hypothesis that bat-mediated gene dispersal confers high levels of genetic exchange among populations of the three columnar cacti, a process that enhances levels of genetic diversity within their populations.

  18. 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.

  19. 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.

  20. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

    Full Text Available To determine the genetic diversity of durum wheat, 41 accessions from Morocco, Ethiopia, Turkey, Lebanon, Kazakhstan, China, and Mongolia were analyzed through Inter-Simple Sequence Repeats (ISSR molecular markers. Out of the used twenty primers, 15 primers that included a considerable polymorphism were selected for the analyses. Among the genotypes under study, 163 fragments (73.7% were polymorph. Several indexes were used to determine the most appropriate primers. While UBC812, UBC864, UBC840, and UBC808 primers were among those markers which produced the highest number of bands and polymorphic bands, they also dedicated the highest rate of polymorphic index content (PIC. These primers also possessed the highest amounts of effective multiplex ratio (EMR and marker index (MI. Therefore, these primers can be recommended for genetic evaluation of the durum wheat. The results of cluster analysis and principle component analysis indicated that the observed genetic diversity in wheat materials under study is geographically structured. The results also indicated that the genetic diversity index based on ISSR markers was higher for Turkey, Lebanon, Morocco, and Ethiopia accessions than for other countries. The high level of polymorphism in this collections durum wheat would agree with the suggestion that Fertile Crescent and parts of Africa are first possible diversity center of this crop.

  1. Fine-scale genetic structure in Pinus clausa (Pinaceae) populations: effects of disturbance history.

    Science.gov (United States)

    Parker, K C; Hamrick, J L; Parker, A J; Nason, J D

    2001-07-01

    Spatial autocorrelation analyses of 12 allozyme loci were used to compare genetic structure within populations of two varieties of Pinus clausa. P. clausa var. immuginata populations tend to be uneven-aged, with continuous recruitment in small gaps created by wind damage, whereas P. clausa var. clausa populations are more even-aged, with recruitment postdating periodic canopy fires. Three var. immuginata populations and three matched pairs of var. clausa populations, including both a mature and a nearby recently burned population, were examined. Aggregation of multilocus genotypes at small distances was evident in all young var. clausa populations. Little inbreeding was apparent among juveniles or adults in these populations; their genetic structure is likely to have resulted from limited seed dispersal. Genotypes were not significantly spatially structured in nearby matched mature populations. Genetic structure was less evident in var. immuginata populations. Aggregated genotypes were only apparent in the population where patches included juveniles of similar ages; dense juvenile clumps in the other two var. immuginata populations comprised a variety of ages. Interannual variability in allele frequencies of surviving seedlings may account for the absence of genetic structure in these populations.

  2. Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa.

    Science.gov (United States)

    Kyndt, Tina; Assogbadjo, Achille E; Hardy, Olivier J; Glele Kakaï, Romain; Sinsin, Brice; Van Damme, Patrick; Gheysen, Godelieve

    2009-05-01

    This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.

  3. Geography has more influence than language on maternal genetic structure of various northeastern Thai ethnicities.

    Science.gov (United States)

    Kutanan, Wibhu; Ghirotto, Silvia; Bertorelle, Giorgio; Srithawong, Suparat; Srithongdaeng, Kanokpohn; Pontham, Nattapon; Kangwanpong, Daoroong

    2014-09-01

    Several literatures have shown the influence of geographic and linguistic factors in shaping genetic variation patterns, but their relative impact, if any, in the very heterogeneous northeastern region of Thailand has not yet been studied. This area, called Isan, is geographically structured in two wide basins, the Sakon Nakorn Basin and the Korat Basin, serving today as home to diverse ethnicities encompassing two different linguistic families, that is, the Austro-Asiatic; Suay (Kui), Mon, Chaobon (Nyahkur), So and Khmer, and the Tai-Kadai; Saek, Nyaw, Phu Tai, Kaleung and Lao Isan. In this study, we evaluated the relative role of geographic distance and barriers as well as linguistic differences as possible causes affecting the maternal genetic distances among northeastern Thai ethnicities. A 596-bp segment of the hypervariable region I mitochondrial DNA was utilized to elucidate the genetic structure and biological affinity from 433 individuals. Different statistical analyses agreed in suggesting that most ethnic groups in the Sakon Nakorn Basin are closely related. Mantel test revealed that genetic distances were highly associated to geographic (r = 0.445, P0.01) distances. Three evolutionary models were compared by Approximate Bayesian Computation. The posterior probability of the scenario, which assumed an initial population divergence possibly related to reduced gene flow among basins, was equal or higher than 0.87. All analyses exhibited concordant results supporting that geography was the most relevant factor in determining the maternal genetic structure of northeastern Thai populations.

  4. A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

    Directory of Open Access Journals (Sweden)

    Ollitrault Patrick

    2012-11-01

    Full Text Available Abstract Background Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP, Simple Sequence Repeats (SSR and Insertion-Deletion (Indel markers. An initial medium density reference map (961 markers for 1084.1 cM of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high

  5. A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping.

    Science.gov (United States)

    Ollitrault, Patrick; Terol, Javier; Chen, Chunxian; Federici, Claire T; Lotfy, Samia; Hippolyte, Isabelle; Ollitrault, Frédérique; Bérard, Aurélie; Chauveau, Aurélie; Cuenca, Jose; Costantino, Gilles; Kacar, Yildiz; Mu, Lisa; Garcia-Lor, Andres; Froelicher, Yann; Aleza, Pablo; Boland, Anne; Billot, Claire; Navarro, Luis; Luro, François; Roose, Mikeal L; Gmitter, Frederick G; Talon, Manuel; Brunel, Dominique

    2012-11-05

    Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should

  6. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Cardoso Márcio Z

    2011-01-01

    Full Text Available Abstract Background Brazil's Atlantic Forest is a biodiversity hotspot endangered by severe habitat degradation and fragmentation. Habitat fragmentation is expected to reduce dispersal among habitat patches resulting in increased genetic differentiation among populations. Here we examined genetic diversity and differentiation among populations of two Heliconius butterfly species in the northern portion of Brazil's Atlantic Forest to estimate the potential impact of habitat fragmentation on population connectivity in butterflies with home-range behavior. Results We generated microsatellite, AFLP and mtDNA sequence data for 136 Heliconius erato specimens from eight collecting locations and 146 H. melpomene specimens from seven locations. Population genetic analyses of the data revealed high levels of genetic diversity in H. erato relative to H. melpomene, widespread genetic differentiation among populations of both species, and no evidence for isolation-by-distance. Conclusions These results are consistent with the hypothesis that the extensive habitat fragmentation along Brazil's Atlantic Forest has reduced dispersal of Heliconius butterflies among neighboring habitat patches. The results also lend support to the observation that fine-scale population genetic structure may be common in Heliconius. If such population structure also exists independent of human activity, and has been common over the evolutionary history of Heliconius butterflies, it may have contributed to the evolution of wing pattern diversity in the genus.

  7. A Discussion on Possible Indicators Related to Genetic Structure Changes in Plant Germplasm Conservation

    Institute of Scientific and Technical Information of China (English)

    GAI Jun-yi

    2004-01-01

    The purpose of the present paper is to study and develop indicators and procedures for the evaluation of genetic structure changes in germplasm conservation due to social and natural environment reasons.Some basic concepts in germplasm study were introduced at first. Then, six kinds of indicators for genetic diversity as a measure of genetic potential of a germplasm collection were presented, i.e.,numbers of different entities at certain level, evenness of the entity distribution, genetic similarityand genetic distance, genetic variance and genetic coefficient of variation, multivariate genetic variation indices, and coefficient of parentage. It was pointed out that genetic dispersion did not provide a complete concept of genetic diversity if without any information from genetic richness. Based on the above, the indicators for genetic erosion as the genetic structure changes of germplasm conservation due to social reasons, the indicators of genetic vulnerability as the genetic structure changes of germplasm conservation due to environmental stresses, the measurement of genetic drift and genetic shift as the genetic structure changes of germplasm collection during reproduction or seed increase were reviewed and developed. Furthermore, the estimation procedures of the indicators by using molecular markers were suggested. Finally, the case studies on suitable conservation sample size of self-pollinated and open-pollinated populations were given for reference.

  8. Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus and leopard cat (Prionailurus bengalensis in India.

    Directory of Open Access Journals (Sweden)

    Shomita Mukherjee

    Full Text Available BACKGROUND: Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus and leopard cat (Prionailurus bengalensis. Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. METHODOLOGY/PRINCIPAL FINDINGS: We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b. Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F(ST of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. CONCLUSIONS/SIGNIFICANCE: Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.

  9. Differential effects of landscape-level environmental features on genetic structure in three codistributed tree species in Central America.

    Science.gov (United States)

    Poelchau, Monica F; Hamrick, J L

    2012-10-01

    Landscape genetic studies use spatially explicit population genetic information to determine the physical and environmental causes of population genetic structure on regional scales. Comparative studies that identify common barriers to gene flow across multiple species within a community are important to both understand the evolutionary trajectories of populations and prioritize habitat conservation. Here, we use a comparative landscape genetic approach to ask whether gradients in temperature or precipitation seasonality structure genetic variation across three codistributed tree species in Central America, or whether a simpler (geographic distance) or more complex, species-specific environmental niche model is necessary to individually explain population genetic structure. Using descriptive statistics and causal modelling, we find that different factors best explain genetic distance in each of the three species: environmental niche distance in Bursera simaruba, geographic distance in Ficus insipida and historical barriers to gene flow or cryptic reproductive barriers for Brosimum alicastrum. This study confirms suggestions from previous studies of Central American tree species that imply that population genetic structure of trees in this region is determined by complex interactions of both historical and current barriers to gene flow.

  10. Population structure and genetic diversity of moose in Alaska.

    Science.gov (United States)

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P moose in Alaska with population expansion from interior Alaska westward toward the coast.

  11. Genetic structure characterization of Chileans reflects historical immigration patterns.

    Science.gov (United States)

    Eyheramendy, Susana; Martinez, Felipe I; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M

    2015-03-17

    Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

  12. The genetic population structure of northern Sweden and its implications for mapping genetic diseases.

    Science.gov (United States)

    Einarsdottir, Elisabet; Egerbladh, Inez; Beckman, Lars; Holmberg, Dan; Escher, Stefan A

    2007-11-01

    The northern Swedish population has a history of admixture of three ethnic groups and a dramatic population growth from a relatively small founder population. This has resulted in founder effects that together with unique resources for genealogical analyses provide excellent conditions for genetic mapping of monogenic diseases. Several recent examples of successful mapping of genetic factors underlying susceptibility to complex diseases have suggested that the population of northern Sweden may also be an important tool for efficient mapping of more complex phenotypes. A potential factor contributing to these effects may be population sub-isolates within the large river valleys, constituting a central geographic characteristic of this region. We here provide evidence that marriage patterns as well as the distribution of gene frequencies in a set of marker loci are compatible with this notion. The possible implications of this population structure on linkage- and association based strategies for identifying genes contributing risk to complex diseases are discussed.

  13. Evolution and physics in comparative protein structure modeling.

    Science.gov (United States)

    Fiser, András; Feig, Michael; Brooks, Charles L; Sali, Andrej

    2002-06-01

    From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.

  14. Spatial structure of morphological and neutral genetic variation in Brook Trout

    Science.gov (United States)

    Kazyak, David C.; Hilderbrand, Robert H.; Keller, Stephen R.; Colaw, Mark C.; Holloway, Amanda E.; Morgan, Raymond P.; King, Timothy L.

    2015-01-01

    Brook Trout Salvelinus fontinalis exhibit exceptional levels of life history variation, remarkable genetic variability, and fine-scale population structure. In many cases, neighboring populations may be highly differentiated from one another to an extent that is comparable with species-level distinctions in other taxa. Although genetic samples have been collected from hundreds of populations and tens of thousands of individuals, little is known about whether differentiation at neutral markers reflects phenotypic differences among Brook Trout populations. We compared differentiation in morphology and neutral molecular markers among populations from four geographically proximate locations (all within 24 km) to examine how genetic diversity covaries with morphology. We found significant differences among and/or within streams for all three morphological axes examined and identified the source stream of many individuals based on morphology (52.3% classification efficiency). Although molecular and morphological differentiation among streams ranged considerably (mean pairwise FST: 0.023–0.264; pairwise PST: 0.000–0.339), the two measures were not significantly correlated. While in some cases morphological characters appear to have diverged to a greater extent than expected by neutral genetic drift, many traits were conserved to a greater extent than were neutral genetic markers. Thus, while Brook Trout exhibit fine-scale spatial patterns in both morphology and neutral genetic diversity, these types of biological variabilities are being structured by different ecological and evolutionary processes. The relative influences of genetic drift versus selection and phenotypic plasticity in shaping morphology appear to vary among populations occupying nearby streams.

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

    Directory of Open Access Journals (Sweden)

    Jingyu Liu

    Full Text Available 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, p<1E-23. We then investigated the top contributing markers in these two linked PSFs. The SNP PSF predominantly consists of 8 SNPs from three genes, SLC45A2, HERC2 and CTNNA2, known to encode skin/hair/eye color. The methylation PSF includes 48 methylated sites in 44 genes coding for basic molecular functions, including transcription regulation, DNA binding, cytokine, and transferase activity. Among them, 8 sites are either hypo- or hyper-methylated correlating to minor alleles of SNPs in the SNP PSF. We found that the genes in SNP and methylation PSFs share common biological processes including sexual/multicellular organism reproduction, cell-cell signaling and cytoskeleton organization. We further investigated the transcription regulatory network operating at these genes and identified that most of genes closely interact with ID2, which encodes for a helix-loop-helix inhibitor of DNA binding. Overall, our results show a significant correlation between genetic and epigenetic population stratification, and suggest that the interrelationship between genetic and epigenetic population structure is mediated via complex multiple

  16. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica.

    Directory of Open Access Journals (Sweden)

    Nicholas John Deacon

    Full Text Available Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses.High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation.Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by

  17. Frequency selective surface structure optimized by genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    Lu Jun; Wang Jian-Bo; Sun Guan-Cheng

    2009-01-01

    Frequency selective surface(FSS)is a two-dimensional periodic structure which has prominent characteristics of bandpass or bandblock when interacting with electromagnetic waves.In this paper,the thickness,the dielectric constant,the element graph and the arrangement periodicity of an FSS medium are investigated by Genetic Algorithm(GA)when an electromagnetic wave is incident on the FSS at a wide angle,and an optimized FSS structure and transmission characteristics are obtained.The results show that the optimized structure has better stability in relation to incident angle of electromagnetic wave and preserves the stability of centre frequency even at an incident angle as large as 80°,thereby laying the foundation for the application of FSS to curved surfaces at wide angles.

  18. Genetic algorithms for optimal design and control of adaptive structures

    CERN Document Server

    Ribeiro, R; Dias-Rodrigues, J; Vaz, M

    2000-01-01

    Future High Energy Physics experiments require the use of light and stable structures to support their most precise radiation detection elements. These large structures must be light, highly stable, stiff and radiation tolerant in an environment where external vibrations, high radiation levels, material aging, temperature and humidity gradients are not negligible. Unforeseen factors and the unknown result of the coupling of environmental conditions, together with external vibrations, may affect the position stability of the detectors and their support structures compromising their physics performance. Careful optimization of static and dynamic behavior must be an essential part of the engineering design. Genetic Algorithms ( GA) belong to the group of probabilistic algorithms, combining elements of direct and stochastic search. They are more robust than existing directed search methods with the advantage of maintaining a population of potential solutions. There is a class of optimization problems for which Ge...

  19. The genetic structure of an invasive pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae.

    Directory of Open Access Journals (Sweden)

    Aline S Guidolin

    Full Text Available The Asian citrus psyllid Diaphorina citri is currently the major threat to the citrus industry as it is the vector of Candidatus Liberibacter, the causal agent of huanglongbing disease (HLB. D. citri is native to Asia and now colonizes the Americas. Although it has been known in some countries for a long time, invasion routes remain undetermined. There are no efficient control methods for the HLB despite the intensive management tools currently in use. We investigated the genetic variability and structure of populations of D. citri to aid in the decision making processes toward sustainable management of this species/disease. We employed different methods to quantify and compare the genetic diversity and structure of D. citri populations among 36 localities in Brazil, using an almost complete sequence of the cytochrome oxidase I (COI gene. Our analyses led to the identification of two geographically and genetically structured groups. The indices of molecular diversity pointed to a recent population expansion, and we discuss the role of multiple invasion events in this scenario. We also argue that such genetic diversity and population structure may have implications for the best management strategies to be adopted for controlling this psyllid and/or the disease it vectors in Brazil.

  20. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  1. Comparative assessment of genetic diversity in cytoplasmic and nuclear genome of upland cotton.

    Science.gov (United States)

    Egamberdiev, Sharof S; Saha, Sukumar; Salakhutdinov, Ilkhom; Jenkins, Johnie N; Deng, Dewayne; Y Abdurakhmonov, Ibrokhim

    2016-06-01

    The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively. Our results revealed that low to moderate level of genetic diversity existed in both nuclear and cytoplasm genome among this set of cotton lines. However, the specific estimation suggested that genetic diversity is lower in cytoplasmic genome compared to the nuclear genome among this set of Upland cotton lines. In summary, this research is important from several perspectives. We detected a set of cytoplasm genome specific SSR primer pairs by using a cost-effective data mining strategy. We reported for the first time the genetic diversity in the cytoplasmic genome within a set of improved Upland cotton accessions. Results revealed that the genetic diversity in cytoplasmic genome is narrow, compared to the nuclear genome within this set of Upland cotton accessions. Our results suggested that most of these polymorphic chloroplast SSRs would be a valuable complementary tool in addition to the nuclear SSR in the study of evolution, gene flow and genetic diversity in Upland cotton.

  2. Genetic structure in insular and mainland populations of house sparrows (Passer domesticus) and their hemosporidian parasites

    Science.gov (United States)

    Bichet, Coraline; Moodley, Yoshan; Penn, Dustin J; Sorci, Gabriele; Garnier, Stéphane

    2015-01-01

    Small and isolated populations usually exhibit low levels of genetic variability, and thus, they are expected to have a lower capacity to adapt to changes in environmental conditions, such as exposure to pathogens and parasites. Comparing the genetic variability of selectively neutral versus functional loci allows one to assess the evolutionary history of populations and their future evolutionary potential. The genes of the major histocompatibility complex (MHC) control immune recognition of parasites, and their unusually high diversity is genes which is likely driven by parasite-mediated balancing selection. Here, we examined diversity and differentiation of neutral microsatellite loci and functional MHC class I genes in house sparrows (Passer domesticus), living in six insular and six mainland populations, and we aimed to determine whether their diversity or differentiation correlates with the diversity and the prevalence of infection of hemosporidian parasites. We found that island bird populations tended to have lower neutral genetic variability, whereas MHC variability gene was similar between island and mainland populations. Similarly, island populations tended to show greater genetic differentiation than mainland populations, especially at microsatellite markers. The maintenance of MHC genetic diversity and its less marked structure in the island populations could be attributed to balancing-selection. The greater MHC differentiation among populations was negatively correlated with similarity in blood parasites (prevalence and diversity of parasite strains) between populations. Even at low prevalence and small geographical scale, haemosporidian parasites might contribute to structure the variability of immune genes among populations of hosts. PMID:25937907

  3. 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.

  4. Application of Modified Genetic Algorithm to Optimal Design of Supporting Structure

    Institute of Scientific and Technical Information of China (English)

    ZHOU Rui-zhong; PAN Shi-wei

    2003-01-01

    The modified genetic algorithm was used for the optimal design of supporting structure in deep pits.Based on the common genetic algorithm, using niche technique and reserving the optimum individual the modified genetic algorithm was presented. By means of the practical engineering, the modified genetic algorithm not only has more expedient convergence, but also can enhance security and operation efficiency.

  5. Learning directed acyclic graphical structures with genetical genomics data.

    Science.gov (United States)

    Gao, Bin; Cui, Yuehua

    2015-12-15

    Large amount of research efforts have been focused on estimating gene networks based on gene expression data to understand the functional basis of a living organism. Such networks are often obtained by considering pairwise correlations between genes, thus may not reflect the true connectivity between genes. By treating gene expressions as quantitative traits while considering genetic markers, genetical genomics analysis has shown its power in enhancing the understanding of gene regulations. Previous works have shown the improved performance on estimating the undirected network graphical structure by incorporating genetic markers as covariates. Knowing that gene expressions are often due to directed regulations, it is more meaningful to estimate the directed graphical network. In this article, we introduce a covariate-adjusted Gaussian graphical model to estimate the Markov equivalence class of the directed acyclic graphs (DAGs) in a genetical genomics analysis framework. We develop a two-stage estimation procedure to first estimate the regression coefficient matrix by [Formula: see text] penalization. The estimated coefficient matrix is then used to estimate the mean values in our multi-response Gaussian model to estimate the regulatory networks of gene expressions using PC-algorithm. The estimation consistency for high dimensional sparse DAGs is established. Simulations are conducted to demonstrate our theoretical results. The method is applied to a human Alzheimer's disease dataset in which differential DAGs are identified between cases and controls. R code for implementing the method can be downloaded at http://www.stt.msu.edu/∼cui. R code for implementing the method is freely available at http://www.stt.msu.edu/∼cui/software.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Genetic and ontogenetic variation in an endangered tree structures dependent arthropod and fungal communities.

    Directory of Open Access Journals (Sweden)

    Benjamin J Gosney

    Full Text Available Plant genetic and ontogenetic variation can significantly impact dependent fungal and arthropod communities. However, little is known of the relative importance of these extended genetic and ontogenetic effects within a species. Using a common garden trial, we compared the dependent arthropod and fungal community on 222 progeny from two highly differentiated populations of the endangered heteroblastic tree species, Eucalyptus morrisbyi. We assessed arthropod and fungal communities on both juvenile and adult foliage. The community variation was related to previous levels of marsupial browsing, as well as the variation in the physicochemical properties of leaves using near-infrared spectroscopy. We found highly significant differences in community composition, abundance and diversity parameters between eucalypt source populations in the common garden, and these were comparable to differences between the distinctive juvenile and adult foliage. The physicochemical properties assessed accounted for a significant percentage of the community variation but did not explain fully the community differences between populations and foliage types. Similarly, while differences in population susceptibility to a major marsupial herbivore may result in diffuse genetic effects on the dependent community, this still did not account for the large genetic-based differences in dependent communities between populations. Our results emphasize the importance of maintaining the populations of this rare species as separate management units, as not only are the populations highly genetically structured, this variation may alter the trajectory of biotic colonization of conservation plantings.

  7. Detection of unbalanced chromosome segregations in preimplantation genetic diagnosis of translocations by short comparative genomic hibridization.

    Science.gov (United States)

    Rius, Mariona; Obradors, Albert; Daina, Gemma; Ramos, Laia; Pujol, Aïda; Martínez-Passarell, Olga; Marquès, Laura; Oliver-Bonet, Maria; Benet, Jordi; Navarro, Joaquima

    2011-07-01

    To apply a comprehensive chromosomal screening through short comparative genomic hybridization (CGH) in the preimplantation genetic diagnosis (PGD) of translocations. Clinical research study. A PGD laboratory and two IVF clinics. Three Robertsonian translocation carriers, two reciprocal translocation carriers, and a double-translocation carrier. After using the short-CGH approach in the reanalysis of two unbalanced embryos, discarded from a PGD for a reciprocal translocation carrier, the same method was applied in the PGD of day-3 embryos of translocation carriers. Ability of short CGH to detect partial chromosomal abnormalities in unbalanced embryos, translocation segregation proportions, and proportion of embryos carrying chromosomal abnormalities not related to the translocations. The short-CGH technique detected errors resulting from the meiotic segregation of the chromosomes involved in the translocations and other abnormalities affecting the remaining chromosomes. Alternate segregation was detected most frequently among Robertsonian translocation cases, whereas unbalanced chromosome segregations were found predominantly in reciprocal ones. Aneuploidy and structural chromosome errors were found more frequently in Robertsonian than in reciprocal translocation carriers. Application of short-CGH PGD achieved pregnancy in two cases. Short CGH is a reliable approach for PGD of translocations, as it is capable of detecting partial chromosome errors caused by unbalanced segregations simultaneously to the screening of all chromosomes, and it may improve the results after PGD for translocation carriers. Copyright © 2011 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  8. The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae).

    Science.gov (United States)

    Fant, J B; Havens, K; Keller, J M; Radosavljevic, A; Yates, E D

    2014-05-01

    Narrow endemics are at risk from climate change because of their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (Fst=0.14), and a north-south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest that populations in the center of the range represent the point of entry to the Lake Michigan and a refugium of diversity for this species. A strong association between genetic distances and lake-level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explains local patterns of movement.

  9. 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

  10. Analysis of a genetically structured variance heterogeneity model using the Box-Cox transformation

    DEFF Research Database (Denmark)

    Yang, Ye; Christensen, Ole Fredslund; Sorensen, Daniel

    2011-01-01

    of the marginal distribution of the data. To investigate how the scale of measurement affects inferences, the genetically structured heterogeneous variance model is extended to accommodate the family of Box–Cox transformations. Litter size data in rabbits and pigs that had previously been analysed...... in the untransformed scale were reanalysed in a scale equal to the mode of the marginal posterior distribution of the Box–Cox parameter. In the rabbit data, the statistical evidence for a genetic component at the level of the environmental variance is considerably weaker than that resulting from an analysis...... in the original metric. In the pig data, the statistical evidence is stronger, but the coefficient of correlation between additive genetic effects affecting mean and variance changes sign, compared to the results in the untransformed scale. The study confirms that inferences on variances can be strongly affected...

  11. CMap3D: a 3D visualization tool for comparative genetic maps.

    Science.gov (United States)

    Duran, Chris; Boskovic, Zoran; Imelfort, Michael; Batley, Jacqueline; Hamilton, Nicholas A; Edwards, David

    2010-01-15

    Genetic linkage mapping enables the study of genome organization and the association of heritable traits with regions of sequenced genomes. Comparative genetic mapping is particularly powerful as it allows translation of information between related genomes and gives an insight into genome evolution. A common tool for the storage, comparison and visualization of genetic maps is CMap. However, current visualization in CMap is limited to the comparison of adjacent aligned maps. To overcome this limitation, we have developed CMap3D, a tool to compare multiple genetic maps in three-dimensional space. CMap3D is based on a client/server model ensuring operability with current CMap data repositories. This tool can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps. The software is a stand-alone application written in Processing and Java. Binaries are available for Windows, OSX and Linux, and require Sun Microsystems Java Runtime Environment 1.6 or later. The software is freely available for non-commercial use from http://flora.acpfg.com.au/.

  12. Genetic structure of drone congregation areas of Africanized honeybees in southern Brazil

    Directory of Open Access Journals (Sweden)

    Thais Collet

    2009-01-01

    Full Text Available As yet, certain aspects of the Africanization process are not well understood, for example, the reproductive behavior of African and European honeybees and how the first Africanized swarms were formed and spread. Drone congregation areas (DCAs are the ideal place to study honeybee reproduction under natural conditions since hundreds of drones from various colonies gather together in the same geographical area for mating. In the present study, we assessed the genetic structure of seven drone congregations and four commercial European-derived and Africanized apiaries in southern Brazil, employing seven microsatellite loci for this purpose. We also estimated the number of mother-colonies that drones of a specific DCA originated from. Pairwise comparison failed to reveal any population sub-structuring among the DCAs, thus indicating low mutual genetic differentiation. We also observed high genetic similarity between colonies of commercial apiaries and DCAs, besides a slight contribution from a European-derived apiary to a DCA formed nearby. Africanized DCAs seem to have a somewhat different genetic structure when compared to the European.

  13. Genetic structure of drone congregation areas of Africanized honeybees in southern Brazil.

    Science.gov (United States)

    Collet, Thais; Cristino, Alexandre Santos; Quiroga, Carlos Fernando Prada; Soares, Ademilson Espencer Egea; Del Lama, Marco Antônio

    2009-10-01

    As yet, certain aspects of the Africanization process are not well understood, for example, the reproductive behavior of African and European honeybees and how the first Africanized swarms were formed and spread. Drone congregation areas (DCAs) are the ideal place to study honeybee reproduction under natural conditions since hundreds of drones from various colonies gather together in the same geographical area for mating. In the present study, we assessed the genetic structure of seven drone congregations and four commercial European-derived and Africanized apiaries in southern Brazil, employing seven microsatellite loci for this purpose. We also estimated the number of mother-colonies that drones of a specific DCA originated from. Pairwise comparison failed to reveal any population sub-structuring among the DCAs, thus indicating low mutual genetic differentiation. We also observed high genetic similarity between colonies of commercial apiaries and DCAs, besides a slight contribution from a European-derived apiary to a DCA formed nearby. Africanized DCAs seem to have a somewhat different genetic structure when compared to the European.

  14. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline

    2017-02-15

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  15. MICRONEEDLE STRUCTURE DESIGN AND OPTIMIZATION USING GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    N. A. ISMAIL

    2015-07-01

    Full Text Available This paper presents a Genetic Algorithm (GA based microneedle design and analysis. GA is an evolutionary optimization technique that mimics the natural biological evolution. The design of microneedle structure considers the shape of microneedle, material used, size of the array, the base of microneedle, the lumen base, the height of microneedle, the height of the lumen, and the height of the drug container or reservoir. The GA is executed in conjunction with ANSYS simulation system to assess the design specifications. The GA uses three operators which are reproduction, crossover and mutation to manipulate the genetic composition of the population. In this research, the microneedle is designed to meet a number of significant specifications such as nodal displacement, strain energy, equivalent stress and flow rate of the fluid / drug that flow through its channel / lumen. A comparison study is conducted to investigate the design of microneedle structure with and without the implementation of GA model. The results showed that GA is able to optimize the design parameters of microneedle and is capable to achieve the required specifications with better performance.

  16. Characterization of large structural genetic mosaicism in human autosomes.

    Science.gov (United States)

    Machiela, Mitchell J; Zhou, Weiyin; Sampson, Joshua N; Dean, Michael C; Jacobs, Kevin B; Black, Amanda; Brinton, Louise A; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M; Gaudet, Mia M; Haiman, Christopher A; Hankinson, Susan E; Hartge, Patricia; Henderson, Brian E; Hong, Yun-Chul; Hosgood, H Dean; Hsiung, Chao A; Hu, Wei; Hunter, David J; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M; Matsuo, Keitaro; Olson, Sara H; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C; Albanes, Demetrius; Aldrich, Melinda C; Amos, Christopher; Amundadottir, Laufey T; Berndt, Sonja I; Blot, William J; Bock, Cathryn H; Bracci, Paige M; Burdett, Laurie; Buring, Julie E; Butler, Mary A; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C; Cook, Michael B; Cullen, Michael; Davis, Faith G; Ding, Ti; Duell, Eric J; Epstein, Caroline G; Fan, Jin-Hu; Figueroa, Jonine D; Fraumeni, Joseph F; Freedman, Neal D; Fuchs, Charles S; Gao, Yu-Tang; Gapstur, Susan M; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J Michael; Giles, Graham G; Gillanders, Elizabeth M; Giovannucci, Edward L; Goldin, Lynn; Goldstein, Alisa M; Greene, Mark H; Hallmans, Goran; Harris, Curtis C; Henriksson, Roger; Holly, Elizabeth A; Hoover, Robert N; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M; Malats, Nuria; McGlynn, Katherine A; McNeill, Lorna H; McWilliams, Robert R; Melin, Beatrice S; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G; Rajaraman, Preetha; Real, Francisco X; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M; Savage, Sharon A; Schwartz, Ann G; Schwartz, Kendra L; Sesso, Howard D; Severi, Gianluca; Silverman, Debra T; Spitz, Margaret R; Stevens, Victoria L; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R; Teras, Lauren R; Tobias, Geoffrey S; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J; Wheeler, William; White, Emily; Wiencke, John K; Wolpin, Brian M; Wu, Xifeng; Wunder, Jay S; Yu, Kai; Zanetti, Krista A; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G; de Andrade, Mariza; Barnes, Kathleen C; Beaty, Terri H; Bierut, Laura J; Desch, Karl C; Doheny, Kimberly F; Feenstra, Bjarke; Ginsburg, David; Heit, John A; Kang, Jae H; Laurie, Cecilia A; Li, Jun Z; Lowe, William L; Marazita, Mary L; Melbye, Mads; Mirel, Daniel B; Murray, Jeffrey C; Nelson, Sarah C; Pasquale, Louis R; Rice, Kenneth; Wiggs, Janey L; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A; Laurie, Cathy C; Caporaso, Neil E; Yeager, Meredith; Chanock, Stephen J

    2015-03-05

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.

  17. 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

  18. Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation.

    Science.gov (United States)

    Holmes, Christopher J; Pantel, Jelena H; Schulz, Kimberly L; Cáceres, Carla E

    2016-07-01

    When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination ('high' clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher-quality and lower-quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with 'high' clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.

  19. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure.

    Directory of Open Access Journals (Sweden)

    Wolfram Möbius

    2015-12-01

    Full Text Available As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the

  20. Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox.

    Directory of Open Access Journals (Sweden)

    Mafalda P Basto

    Full Text Available The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina and red foxes (Vulpes vulpes share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS, a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA. Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive

  1. Range-wide population genetic structure of the Caribbean sea fan coral, Gorgonia ventalina.

    Science.gov (United States)

    Andras, Jason P; Rypien, Krystal L; Harvell, Catherine D

    2013-01-01

    The population structure of benthic marine organisms is of central relevance to the conservation and management of these often threatened species, as well as to the accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow for strong general inferences. Here, we describe the range-wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically modelled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometres, estimated dispersal was low, and populations were differentiated across distances <2 km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks found in other taxa (e.g. an east/west divide near Puerto Rico), and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally.

  2. Genetic resources of teak (Tectona grandis Linn. f.)—strong genetic structure among natural populations

    DEFF Research Database (Denmark)

    Hansen, Ole Kim; Changtragoon, Suchitra; Ponoy, Bundit

    2015-01-01

    Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India ...

  3. A comprehensive comparison of comparative RNA structure prediction approaches

    DEFF Research Database (Denmark)

    Gardner, P. P.; Giegerich, R.

    2004-01-01

    Background An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene-finding...

  4. Comparing Structural Brain Connectivity by the Infinite Relational Model

    DEFF Research Database (Denmark)

    Ambrosen, Karen Marie Sandø; Herlau, Tue; Dyrby, Tim;

    2013-01-01

    The growing focus in neuroimaging on analyzing brain connectivity calls for powerful and reliable statistical modeling tools. We examine the Infinite Relational Model (IRM) as a tool to identify and compare structure in brain connectivity graphs by contrasting its performance on graphs from...... modeling tool for the identification of structure and quantification of similarity in graphs of brain connectivity in general....

  5. Are ethnic minorities synonymous for genetic isolates? Comparing Walser and Romance populations in the Upper Lys Valley (Western Alps).

    Science.gov (United States)

    Boattini, Alessio; Griso, Clio; Pettener, Davide

    2011-01-01

    Cultural differences between neighbouring populations are often said to give rise to reproductive barriers. For ethnic minorities, these barriers can easily result in genetic isolation. In this study, we analyse the surname structure of the Walser of the upper Lys Valley, a German-speaking ethnic minority in the Italian Western Alps, to better understand the relationships between linguistic and genetic isolation. Analyses were based on 1713 marriages registered from 1838 to 1938 in four villages of the valley: three Walser communities (Issime, Gressoney-Saint-Jean, Gressoney-La-Trinité) and the Romance community of Gaby. The results show that endogamy and inbreeding are lower than in other Italian linguistic minorities, with the exception of Gaby, whose values rank among the highest ever found in Italy. Compared to the Walser communities' Gaby behaves as an outgroup and has an almost exclusively autochthonous surname set. The latter aspect is also true, but to a lesser extent, for the Walser villages, in particular for Issime on the one hand and Gressoney-Saint-Jean and Gressoney-La-Trinité on the other. These findings strongly suggest that the Walser communities' ethnic minority status is not associated with genetic isolation, whereas genetic isolation was found in the linguistically non-isolated Gaby. Finally, our results are consistent with two independent late medieval migration events at the origin of these Walser settlements.

  6. Economic governance of property rights: comparative analysis on the collection of royalties in genetically modified soybean seeds

    Directory of Open Access Journals (Sweden)

    Guilherme Fowler de Avila Monteiro

    2013-03-01

    Full Text Available This paper examines the governance of property rights on genetically modified (GM soybean seeds. Specifically, the article undertakes a comparative analysis on the collection of royalties in GM soybean seeds in the U.S. and Brazil. For each country, the authors describe the regulatory framework governing the protection of biotechnology innovations in agriculture and investigate the mechanisms of royalty collection in GM soybean seeds. The paper also offers econometric evidence linking the capture of value on biotech innovations and the protection mechanisms deployed by biotech firms. The results suggest that, subject to the institutional environment, firms may choose to transact a GM attribute separated from the seed, building specialized governance structures framed around the genetic attribute and not around the seed as a whole.

  7. Structural health monitoring feature design by genetic programming

    Science.gov (United States)

    Harvey, Dustin Y.; Todd, Michael D.

    2014-09-01

    Structural health monitoring (SHM) systems provide real-time damage and performance information for civil, aerospace, and other high-capital or life-safety critical structures. Conventional data processing involves pre-processing and extraction of low-dimensional features from in situ time series measurements. The features are then input to a statistical pattern recognition algorithm to perform the relevant classification or regression task necessary to facilitate decisions by the SHM system. Traditional design of signal processing and feature extraction algorithms can be an expensive and time-consuming process requiring extensive system knowledge and domain expertise. Genetic programming, a heuristic program search method from evolutionary computation, was recently adapted by the authors to perform automated, data-driven design of signal processing and feature extraction algorithms for statistical pattern recognition applications. The proposed method, called Autofead, is particularly suitable to handle the challenges inherent in algorithm design for SHM problems where the manifestation of damage in structural response measurements is often unclear or unknown. Autofead mines a training database of response measurements to discover information-rich features specific to the problem at hand. This study provides experimental validation on three SHM applications including ultrasonic damage detection, bearing damage classification for rotating machinery, and vibration-based structural health monitoring. Performance comparisons with common feature choices for each problem area are provided demonstrating the versatility of Autofead to produce significant algorithm improvements on a wide range of problems.

  8. Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification.

    Science.gov (United States)

    Cleary, Katherine A; Waits, Lisette P; Finegan, Bryan

    2017-07-03

    Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy. © 2017 John Wiley & Sons Ltd.

  9. How often do they have sex? A comparative analysis of the population structure of seven eukaryotic microbial pathogens.

    Directory of Open Access Journals (Sweden)

    Nicolás Tomasini

    Full Text Available The model of predominant clonal evolution (PCE proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this "residual" genetic exchange should be evaluated. Multilocus Sequence Typing (MLST is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the

  10. A genetic linkage map and comparative mapping of the prairie vole (Microtus ochrogaster genome

    Directory of Open Access Journals (Sweden)

    Young Larry J

    2011-07-01

    Full Text Available Abstract Background The prairie vole (Microtus ochrogaster is an emerging rodent model for investigating the genetics, evolution and molecular mechanisms of social behavior. Though a karyotype for the prairie vole has been reported and low-resolution comparative cytogenetic analyses have been done in this species, other basic genetic resources for this species, such as a genetic linkage map, are lacking. Results Here we report the construction of a genome-wide linkage map of the prairie vole. The linkage map consists of 406 markers that are spaced on average every 7 Mb and span an estimated ~90% of the genome. The sex average length of the linkage map is 1707 cM, which, like other Muroid rodent linkage maps, is on the lower end of the length distribution of linkage maps reported to date for placental mammals. Linkage groups were assigned to 19 out of the 26 prairie vole autosomes as well as the X chromosome. Comparative analyses of the prairie vole linkage map based on the location of 387 Type I markers identified 61 large blocks of synteny with the mouse genome. In addition, the results of the comparative analyses revealed a potential elevated rate of inversions in the prairie vole lineage compared to the laboratory mouse and rat. Conclusions A genetic linkage map of the prairie vole has been constructed and represents the fourth genome-wide high-resolution linkage map reported for Muroid rodents and the first for a member of the Arvicolinae sub-family. This resource will advance studies designed to dissect the genetic basis of a variety of social behaviors and other traits in the prairie vole as well as our understanding of genome evolution in the genus Microtus.

  11. [Genetic structure, subdivision, and population differentiation in Stankewiczii pine Pinus stankewiczii (Sukacz.) Fomin from Mountain Crimea].

    Science.gov (United States)

    Korshikov, I I; Gorlova, E M

    2006-06-01

    In order to analyze the genetic structure, subdivision and differentiation within and between two small isolated populations of the Crimea relict endemic, Pinus stankewiczii (Sukacz.) Fomin, electrophoretic analysis of the isozyme variation at nine enzymatic systems was carried out using 183 oldest trees. It was demonstrated that in populations of P. stankewiczii, 80% of the genes were in polymorphic state. Each tree was heterozygous at 19.1% loci, and at 21.6% loci in artificial 50-year-old plantation. The genetic structure of two populations was less differentiated (DN = 0.006), compared to their individual localities (DN = 0.008-0.009). Within-population subdivision of the diffusely dispersed populations was higher (FST-GST = 1.8-2.0%) than that of the populations themselves (0.8%).

  12. Genetic structure in the coral, Montastraea cavernosa: assessing genetic differentiation among and within Mesophotic reefs.

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    Daniel A Brazeau

    Full Text Available Mesophotic coral reefs (30-150 m have recently received increased attention as a potential source of larvae (e.g., the refugia hypothesis to repopulate a select subset of the shallow water (<30 m coral fauna. To test the refugia hypothesis we used highly polymorphic Amplified Fragment Length Polymorphism (AFLP markers as a means to assess small-scale genetic heterogeneity between geographic locations and across depth clines in the Caribbean coral, Montastraea cavernosa. Zooxanthellae-free DNA extracts of coral samples (N = 105 were analyzed from four depths, shallow (3-10 m, medium (15-25 m, deep (30-50 m and very deep (60-90 m from Little Cayman Island (LCI, Lee Stocking Island (LSI, Bahamas and San Salvador (SS, Bahamas which range in distance from 170 to 1,600 km apart. Using AMOVA analysis there were significant differences in ΦST values in pair wise comparisons between LCI and LSI. Among depths at LCI, there was significant genetic differentiation between shallow and medium versus deep and very deep depths in contrast there were no significant differences in ΦST values among depths at LSI. The assignment program AFLPOP, however, correctly assigned 95.7% of the LCI and LSI samples to the depths from which they were collected, differentiating among populations as little as 10 to 20 m in depth from one another. Discriminant function analysis of the data showed significant differentiation among samples when categorized by collection site as well as collection depth. FST outlier analyses identified 2 loci under positive selection and 3 under balancing selection at LCI. At LSI 2 loci were identified, both showing balancing selection. This data shows that adult populations of M. cavernosa separated by depths of tens of meters exhibits significant genetic structure, indicative of low population connectivity among and within sites and are not supplying successful recruits to adjacent coral reefs less than 30 m in depth.

  13. Demographic Genetic Structure of Cryptomeria japonica var.sinensis in Tianmushan Nature Reserve,China

    Institute of Scientific and Technical Information of China (English)

    Yan Chen; Shu-Zhen Yang; Ming-Shui Zhao; Bi-Ye Ni; Liang Liu; Xiao-Yong Chen

    2008-01-01

    Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations.However,compared with spatial genetic structure,few studies have been conducted on genetic changes over time.In this study,we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan,Cryptomeria japonica var.sinensis,in the Tianmushan National Nature Reserve,whose origin was debatable.The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively,lower than other conifers with the same life history characteristics.FST was 0.002 4- 0.003,and the pairwise test revealed no significant differentiation in any pair of size classes.Significant heterozygosity excesses were detected in five size classes except the oldest one,indicating bottleneck event(s).The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.

  14. Population genetic structure in the paddyfield warbler (Acrocephalus agricola Jerd.

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    Pavel ZEHTINDJIEV, Mihaela ILIEVA, Bengt HANSSON, Olga OPARINA,Mihail OPARIN, Staffan BENSCH

    2011-02-01

    Full Text Available Population genetic structure was studied in paddyfield warblers Acrocephalus agricola breeding in NE Bulgaria, SE Russia and S Kazakhstan. We were particularly interested in the degree of genetic differentiation and gene flow of the Bulgarian population due to its geographical isolation, recent origin and unique migratory strategy. Analyses of mitochondrial DNA (mtDNA showed that there was no divergence between Bulgarian and Russian populations (FST = 0.007, whereas those in Kazakhstan differed significantly from the European breeding populations (Russia: FST = 0.058; Bulgaria: FST = 0.114. The degree of differentiation between populations at nuclear markers (five microsatellite loci; FST ≈ 0 was weaker than for mtDNA. We suggest that this relatively weak differentiation over the range of this species reflects a recent postglacial expansion, and results from mismatch distribution analyses and Fu’s FS tests are in agreement. Preservation of small and geographically isolated populations which may contain individuals with unique adaptive traits, such as the studied Bulgarian population of paddyfield warbler, is valuable for the long-term conservation of expanding migratory bird species [Current Zoology 57 (1: 63–71, 2011].

  15. 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.

  16. Phylogeography and genetic structure of two Patagonian shag species (Aves: Phalacrocoracidae).

    Science.gov (United States)

    Calderón, Luciano; Quintana, Flavio; Cabanne, Gustavo S; Lougheed, Stephen C; Tubaro, Pablo L

    2014-03-01

    We compared the phylogeographic and genetic structure of two sympatric shag species, Phalacrocorax magellanicus (rock shag) and Phalacrocorax atriceps (imperial shag), from Patagonia (southern South America). We used multilocus genotypes of nuclear DNA (microsatellite loci) from 324 individuals and mitochondrial DNA sequences (ATPase) from 177 individuals, to evaluate hypotheses related to the effect of physical and non-physical barriers on seabird evolution. Despite sharing many ecological traits, the focal species strongly differ in two key aspects: P. magellanicus has a strong tendency to remain at/near their breeding colonies during foraging trips and the non-breeding season, while P. atriceps exhibits the converse pattern. Both species showed similar mtDNA genetic structure, where colonies from the Atlantic Coast, Pacific Coast and Fuegian region were genetically divergent. We also found similarities in the results of Bayesian clustering analysis of microsatellites, with both species having four clusters. However population differentiation (e.g. Fst, Φst) was higher in P. magellanicus compared to P. atriceps, and average membership probabilities of individuals to specific clusters (Q-values) were also higher in the former. Phalacrocorax magellanicus has strong phylogeographic structure, consistent with the impact of Pleistocene glaciations, with diagnostic haplotypes associated with each of the three mentioned regions. The same pattern was not as evident for P. atriceps. Migration rate estimators were higher for P. atriceps than for P. magellanicus; however both species followed an n-island-like model of gene flow, this implies that dispersal occurs across the continental land mass that separates Atlantic and Pacific Oceans. Our results supported the hypothesis that non-physical barriers are important drivers of the genetic and phylogeographic structure in seabirds, and also that physical barriers constitute effective but not absolute impediments to gene flow.

  17. Unexpectedly low rangewide population genetic structure of the imperiled eastern box turtle Terrapene c. carolina.

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    Steven J A Kimble

    Full Text Available Rangewide studies of genetic parameters can elucidate patterns and processes that operate only over large geographic scales. Herein, we present a rangewide population genetic assessment of the eastern box turtle Terrapene c. carolina, a species that is in steep decline across its range. To inform conservation planning for this species, we address the hypothesis that disruptions to demographic and movement parameters associated with the decline of the eastern box turtle has resulted in distinctive genetic signatures in the form of low genetic diversity, high population structuring, and decreased gene flow. We used microsatellite genotype data from (n = 799 individuals from across the species range to perform two Bayesian population assignment approaches, two methods for comparing historical and contemporary migration among populations, an evaluation of isolation by distance, and a method for detecting barriers to gene flow. Both Bayesian methods of population assignment indicated that there are two populations rangewide, both of which have maintained high levels of genetic diversity (HO = 0.756. Evidence of isolation by distance was detected in this species at a spatial scale of 300-500 km, and the Appalachian Mountains were identified as the primary barrier to gene flow across the species range. We also found evidence for historical but not contemporary migration between populations. Our prediction of many, highly structured populations across the range was not supported. This may point to cryptic contemporary gene flow, which might in turn be explained by the presence of rare transients in populations. However these data may be influenced by historical signatures of genetic connectivity because individuals of this species can be long-lived.

  18. Comparative genetics of hybrid incompatibility: sterility in two Solanum species crosses.

    Science.gov (United States)

    Moyle, Leonie C; Nakazato, Takuya

    2008-07-01

    The genetic basis of hybrid sterility can provide insight into the genetic and evolutionary origins of species barriers. We examine the genetics of hybrid incompatibility between two diploid plant species in the plant clade Solanum sect. Lycopersicon. Using a set of near-isogenic lines (NILs) representing the wild species Solanum pennellii (formerly Lycopersicon pennellii) in the genetic background of the cultivated tomato S. lycopersicum (formerly L. esculentum), we found that hybrid pollen and seed infertility are each based on a modest number of loci, male (pollen) and other (seed) incompatibility factors are roughly comparable in number, and seed-infertility QTL act additively or recessively. These findings are remarkably consistent with our previous analysis in a different species pair, S. lycopersicum x S. habrochaites. Data from both studies contrast strongly with data from Drosophila. Finally, QTL for pollen and seed sterility from the two Solanum studies were chromosomally colocalized, indicating a shared evolutionary history for these QTL, a nonrandom genomic distribution of loci causing sterility, and/or a proclivity of certain genes to be involved in hybrid sterility. We show that comparative mapping data can delimit the probable timing of evolution of detected QTL and discern which sterility loci likely evolved earliest among species.

  19. Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure.

    Science.gov (United States)

    Barrès, Benoît; Dutech, Cyril; Andrieux, Axelle; Halkett, Fabien; Frey, Pascal

    2012-10-01

    Fungal plant pathogens, especially rust fungi (Pucciniales), are well known for their complex life cycles, which include phases of sexual and asexual reproduction. The effect of asexual multiplication on population genetic diversity has been investigated in the poplar rust fungus Melampsora larici-populina using a nested hierarchical sampling scheme. Four hierarchical levels were considered: leaf, twig, tree and site. Both cultivated and wild poplar stands were sampled at two time points at the start and end of rust epidemics. A total of 641 fungal isolates was analysed using nine microsatellite markers. This study revealed that the genetic signature of asexual multiplication in the wild poplar stand was seen only at lower hierarchical levels (leaf and twig). Moreover, we observed an erosion of clonal structure through time, with an increase in both gene and genotypic diversity. New genotypes contributed to host infection over time, which demonstrates the importance of allo-infection in the epidemic process in this host-pathogen system. Compared with the wild stands, the nearly lack of detection of clonal structure in the cultivated stands reflects the higher infection level on cultivated poplars. More generally, this genetic analysis illustrates the utility of population genetics approach for elucidating the proportion of asexual reproduction in the multiplication of isolates during an epidemic, and for proper quantification of asexual dispersal in plant pathogens.

  20. Contrasting genetic structure in two co-distributed species of old world fruit bat.

    Science.gov (United States)

    Chen, Jinping; Rossiter, Stephen J; Flanders, Jonathan R; Sun, Yanhong; Hua, Panyu; Miller-Butterworth, Cassandra; Liu, Xusheng; Rajan, Koilmani E; Zhang, Shuyi

    2010-01-01

    The fulvous fruit bat (Rousettus leschenaulti) and the greater short-nosed fruit bat (Cynopterus sphinx) are two abundant and widely co-distributed Old World fruit bats in Southeast and East Asia. The former species forms large colonies in caves while the latter roots in small groups in trees. To test whether these differences in social organization and roosting ecology are associated with contrasting patterns of gene flow, we used mtDNA and nuclear loci to characterize population genetic subdivision and phylogeographic histories in both species sampled from China, Vietnam and India. Our analyses from R. leschenaulti using both types of marker revealed little evidence of genetic structure across the study region. On the other hand, C. sphinx showed significant genetic mtDNA differentiation between the samples from India compared with China and Vietnam, as well as greater structuring of microsatellite genotypes within China. Demographic analyses indicated signatures of past rapid population expansion in both taxa, with more recent demographic growth in C. sphinx. Therefore, the relative genetic homogeneity in R. leschenaulti is unlikely to reflect past events. Instead we suggest that the absence of substructure in R. leschenaulti is a consequence of higher levels of gene flow among colonies, and that greater vagility in this species is an adaptation associated with cave roosting.

  1. Contrasting genetic structure in two co-distributed species of old world fruit bat.

    Directory of Open Access Journals (Sweden)

    Jinping Chen

    Full Text Available The fulvous fruit bat (Rousettus leschenaulti and the greater short-nosed fruit bat (Cynopterus sphinx are two abundant and widely co-distributed Old World fruit bats in Southeast and East Asia. The former species forms large colonies in caves while the latter roots in small groups in trees. To test whether these differences in social organization and roosting ecology are associated with contrasting patterns of gene flow, we used mtDNA and nuclear loci to characterize population genetic subdivision and phylogeographic histories in both species sampled from China, Vietnam and India. Our analyses from R. leschenaulti using both types of marker revealed little evidence of genetic structure across the study region. On the other hand, C. sphinx showed significant genetic mtDNA differentiation between the samples from India compared with China and Vietnam, as well as greater structuring of microsatellite genotypes within China. Demographic analyses indicated signatures of past rapid population expansion in both taxa, with more recent demographic growth in C. sphinx. Therefore, the relative genetic homogeneity in R. leschenaulti is unlikely to reflect past events. Instead we suggest that the absence of substructure in R. leschenaulti is a consequence of higher levels of gene flow among colonies, and that greater vagility in this species is an adaptation associated with cave roosting.

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

    Science.gov (United States)

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

    2016-02-01

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

  3. Population genetic structure of Ascaridia galli re-emerging in non-caged laying hens

    Directory of Open Access Journals (Sweden)

    Höglund Johan

    2012-05-01

    Full Text Available Abstract Background The poultry roundworm Ascaridia galli has reappeared in hens kept for egg production in Sweden after having been almost absent a decade ago. Today this is a frequent intestinal nematode parasite in non-caged laying hens. The aim of this study was to investigate the genetic diversity (Fst in A. galli collected from different poultry production sites in southern Sweden, to identify possible common routes of colonization. Methods Adult parasites (n = 153 from 10 farms, including both broiler breeder parents and laying hens, were investigated by amplified restriction fragment length polymorphism analysis (AFLP. Worms from a Danish laying hen farm were also included for comparison. Most of the farms were represented by worms from a single host, but on two farms multiple samples from different hosts were assessed in order to study flock variation. Results A total of 97 fragments (loci were amplified among which 81% were variable alleles. The average genetic diversity was 0.13 (range = 0.09-0.38, which is comparable to other AFLP studies on nematodes of human and veterinary importance. Within-farm variation showed that worms harboured by a single hen in a flock covered most of the A. galli genetic variation within the same flock (Fst = 0.01 and 0.03 for two farms. Between-farm analysis showed a moderate population genetic structure (Fst = 0.13, along with a low mutational rate but high gene flow between different farms, and absence of strong genetic selection. Network analysis showed repeated genetic patterns among the farms, with most worms on each farm clustering together as supported by high re-allocation rates. Conclusions The investigated A. galli populations were not strongly differentiated, indicating that they have undergone a genetic bottlenecking and subsequent drift. This supports the view that the investigated farms have been recently colonized, and that new flocks are reinfected upon arrival with a

  4. Genetic admixture, relatedness, and structure patterns among Mexican populations revealed by the Y-chromosome.

    Science.gov (United States)

    Rangel-Villalobos, H; Muñoz-Valle, J F; González-Martín, A; Gorostiza, A; Magaña, M T; Páez-Riberos, L A

    2008-04-01

    Y-linked markers are suitable loci to analyze genetic diversity of human populations, offering knowledge of medical, forensic, and anthropological interest. In a population sample of 206 Mestizo males from western Mexico, we analyzed two binary loci (M3 and YAP) and six Y-STRs, adding to the analysis data of Mexican Mestizos and Amerindians, and relevant worldwide populations. The paternal ancestry estimated in western Mexican-Mestizos was mainly European (60-64%), followed by Amerindian (25-21%), and African ( approximately 15%). Significant genetic heterogeneity was established between Mestizos from western (Jalisco State) and northern Mexico (Chihuahua State) compared with Mexicans from the center of the Mexican Republic (Mexico City), this attributable to higher European ancestry in western and northern than in central and southeast populations, where higher Amerindian ancestry was inferred. This genetic structure has important implications for medical and forensic purposes. Two different Pre-Hispanic evolutionary processes were evident. In Mesoamerican region, populations presented higher migration rate (N(m) = 24.76), promoting genetic homogeneity. Conversely, isolated groups from the mountains and canyons of the Western and Northern Sierra Madre (Huichols and Tarahumaras, respectively) presented a lower migration rate (N(m) = 10.27) and stronger genetic differentiation processes (founder effect and/or genetic drift), constituting a Pre-Hispanic population substructure. Additionally, Tarahumaras presented a higher frequency of Y-chromosomes without Q3 that was explained by paternal European admixture (15%) and, more interestingly, by a distinctive Native-American ancestry. In Purepechas, a special admixture process involving preferential integration of non-Purepecha women in their communities could explain contrary genetic evidences (autosomal vs. Y-chromosome) for this tribe.

  5. Exploring the structure of attitudes toward genetically modified food.

    Science.gov (United States)

    Poortinga, Wouter; Pidgeon, Nick F

    2006-12-01

    Although it is often thought that the British public is opposed to genetically modified (GM) food, recent qualitative work suggests that most people are ambivalent about GM food and crops. In this article we explore the structure of attitudes in order to examine whether attitudinal ambivalence can be captured by more quantitative methods. Based on the finding that the perceived risks and benefits of GM food can be treated as independent dimensions, we propose a four-way typology of attitudes, consisting of a positive, negative, indifferent, and ambivalent group. This study showed that the differences between the four groups could best be described by three main dimensions: (1) a general evaluative dimension, (2) an involvement dimension, and (3) an attitudinal certainty dimension. While these different attitudinal dimensions have generally been studied in isolation, we argue that they should be studied collectively.

  6. Alkaline detergent enzymes from alkaliphiles: enzymatic properties, genetics, and structures.

    Science.gov (United States)

    Ito, S; Kobayashi, T; Ara, K; Ozaki, K; Kawai, S; Hatada, Y

    1998-08-01

    The cleaning power of detergents seems to have peaked; all detergents contain similar ingredients and are based on similar detergency mechanisms. To improve detergency, modern types of heavy-duty powder detergents and automatic dishwasher detergents usually contain one or more enzymes, such as protease, amylase, cellulase, and lipase. Alkaliphilic Bacillus strains are often good sources of alkaline extracellular enzymes, the properties of which fulfil the essential requirements for enzymes to be used in detergents. We have isolated numbers of alkaliphilic Bacillus that produce such alkaline detergent enzymes, including cellulase (CMCase), protease, alpha-amylase, and debranching enzymes, and have succeeded in large-scale industrial production of some of these enzymes. Here, we describe the enzymatic properties, genetics, and structures of the detergent enzymes that we have developed.

  7. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

    Science.gov (United States)

    Machiela, Mitchell J.; Zhou, Weiyin; Sampson, Joshua N.; Dean, Michael C.; Jacobs, Kevin B.; Black, Amanda; Brinton, Louise A.; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S.; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M.; Gaudet, Mia M.; Haiman, Christopher A.; Hankinson, Susan E.; Hartge, Patricia; Henderson, Brian E.; Hong, Yun-Chul; Hosgood, H. Dean; Hsiung, Chao A.; Hu, Wei; Hunter, David J.; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M.; Matsuo, Keitaro; Olson, Sara H.; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A.; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P.; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C.; Albanes, Demetrius; Aldrich, Melinda C.; Amos, Christopher; Amundadottir, Laufey T.; Berndt, Sonja I.; Blot, William J.; Bock, Cathryn H.; Bracci, Paige M.; Burdett, Laurie; Buring, Julie E.; Butler, Mary A.; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C.; Cook, Michael B.; Cullen, Michael; Davis, Faith G.; Ding, Ti; Duell, Eric J.; Epstein, Caroline G.; Fan, Jin-Hu; Figueroa, Jonine D.; Fraumeni, Joseph F.; Freedman, Neal D.; Fuchs, Charles S.; Gao, Yu-Tang; Gapstur, Susan M.; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J. Michael; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goldin, Lynn; Goldstein, Alisa M.; Greene, Mark H.; Hallmans, Goran; Harris, Curtis C.; Henriksson, Roger; Holly, Elizabeth A.; Hoover, Robert N.; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N.; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C.; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M.; Malats, Nuria; McGlynn, Katherine A.; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G.; Rajaraman, Preetha; Real, Francisco X.; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M.; Savage, Sharon A.; Schwartz, Ann G.; Schwartz, Kendra L.; Sesso, Howard D.; Severi, Gianluca; Silverman, Debra T.; Spitz, Margaret R.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R.; Teras, Lauren R.; Tobias, Geoffrey S.; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J.; Wheeler, William; White, Emily; Wiencke, John K.; Wolpin, Brian M.; Wu, Xifeng; Wunder, Jay S.; Yu, Kai; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G.; de Andrade, Mariza; Barnes, Kathleen C.; Beaty, Terri H.; Bierut, Laura J.; Desch, Karl C.; Doheny, Kimberly F.; Feenstra, Bjarke; Ginsburg, David; Heit, John A.; Kang, Jae H.; Laurie, Cecilia A.; Li, Jun Z.; Lowe, William L.; Marazita, Mary L.; Melbye, Mads; Mirel, Daniel B.; Murray, Jeffrey C.; Nelson, Sarah C.; Pasquale, Louis R.; Rice, Kenneth; Wiggs, Janey L.; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A.; Laurie, Cathy C.; Caporaso, Neil E.; Yeager, Meredith; Chanock, Stephen J.

    2015-01-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10−31) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  8. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    Melissa D Conrad

    Full Text Available Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  9. Different patterns of genetic structure of relict and isolated populations of endangered peat-bog pine (Pinus uliginosa Neumann).

    Science.gov (United States)

    Wachowiak, W; Prus-Glowacki, W

    2009-01-01

    Recent changes in environmental conditions in populations of peat-bog pine (Pinus uliginosa Neumann) caused rapid decline or even extinction of the species in several stands in Central Europe. Conservation strategies for P. uliginosa require information about the evolutionary history and genetic structure of its populations. Using isozymes we assessed the genetic structure of P. uliginosa from four isolated stands in Poland and compared the results to genetic structures of other closely related pine species including eight populations of Pinus mugo, ten of Pinus sylvestris and one of Pinus uncinata. The level of genetic variability of P. uliginosa measured by the mean number of alleles per locus and average heterozygosity was similar to others related to P. uliginosa taxa from the reference group but it differs among populations. High genetic similarity was found between two populations of P. uliginosa from Low Silesian Pinewood. The populations were genetically distinct as compared to other populations including locus classicus of the species from the peat bog at Batorów Reserve. Very low genetic distance (DN = 0.002) and small genetic differentiation (GST = 0.003) were found between P. uliginosa and P. mugo in the sympatric populations of the species from Zieleniec peat bog suggesting the ongoing natural hybridisation and genetic contamination of peat-bog pine from this area. Some evidence for skew in allele frequency distribution potentially due to recent bottleneck was found in population from Low Silesian Pinewood. The analysed open pollinated progeny derived from two P. uliginosa stands from Low Silesian Pinewood showed the excess of homozygotes as compared to the maternal trees indicating high level of inbreeding (F = 0.105, F = 0.081). The results are discussed in the context of evolution of P. uliginosa populations, taxonomic relationships between the analysed species and conservation strategies for active protection of peat-bog pine.

  10. Comparative testing of nondestructive examination techniques for concrete structures

    Science.gov (United States)

    Clayton, Dwight A.; Smith, Cyrus M.

    2014-03-01

    A multitude of concrete-based structures are typically part of a light water reactor (LWR) plant to provide foundation, support, shielding, and containment functions. Concrete has been used in the construction of nuclear power plants (NPPs) because of three primary properties, its inexpensiveness, its structural strength, and its ability to shield radiation. Examples of concrete structures important to the safety of LWR plants include containment building, spent fuel pool, and cooling towers. Comparative testing of the various NDE concrete measurement techniques requires concrete samples with known material properties, voids, internal microstructure flaws, and reinforcement locations. These samples can be artificially created under laboratory conditions where the various properties can be controlled. Other than NPPs, there are not many applications where critical concrete structures are as thick and reinforced. Therefore, there are not many industries other than the nuclear power plant or power plant industry that are interested in performing NDE on thick and reinforced concrete structures. This leads to the lack of readily available samples of thick and heavily reinforced concrete for performing NDE evaluations, research, and training. The industry that typically performs the most NDE on concrete structures is the bridge and roadway industry. While bridge and roadway structures are thinner and less reinforced, they have a good base of NDE research to support their field NDE programs to detect, identify, and repair concrete failures. This paper will summarize the initial comparative testing of two concrete samples with an emphasis on how these techniques could perform on NPP concrete structures.

  11. Comparative genetics of longevity and cancer: insights from long-lived rodents

    Science.gov (United States)

    Gorbunova, Vera; Seluanov, Andrei; Zhang, Zhengdong; Gladyshev, Vadim N.; Vijg, Jan

    2015-01-01

    Mammals have evolved a dramatic diversity of aging rates. Within the single order of Rodentia maximum lifespans differ from four years in mice to 32 years in naked mole rats. Cancer rates also differ significantly, from cancer-prone mice to virtually cancer-proof naked and blind mole rats. Recent progress in rodent comparative biology, in combination with the emergence of whole genome sequence information, has opened opportunities for the discovery of genetic factors controlling longevity and cancer susceptibility. PMID:24981598

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

    African Journals Online (AJOL)

    STORAGESEVER

    2008-11-05

    Nov 5, 2008 ... Key words: Tanakius kitaharai, mitochondrial DNA control region, genetic variability, genetic .... geneity among sites and nucleotide sequence evolution models ..... Application to human mitochondrial DNA restriction data.

  13. Comparative proteomic analysis of genetically modified maize grown under different agroecosystems conditions in Brazil.

    Science.gov (United States)

    Agapito-Tenfen, Sarah Zanon; Guerra, Miguel Pedro; Wikmark, Odd-Gunnar; Nodari, Rubens Onofre

    2013-12-04

    Profiling technologies allow the simultaneous measurement and comparison of thousands of cell components without prior knowledge of their identity. In the present study, we used two-dimensional gel electrophoresis combined with mass spectrometry to evaluate protein expression of Brazilian genetically modified maize hybrid grown under different agroecosystems conditions. To this effect, leaf samples were subjected to comparative analysis using the near-isogenic non-GM hybrid as the comparator. In the first stage of the analysis, the main sources of variation in the dataset were identified by using Principal Components Analysis which correlated most of the variation to the different agroecosystems conditions. Comparative analysis within each field revealed a total of thirty two differentially expressed proteins between GM and non-GM samples that were identified and their molecular functions were mainly assigned to carbohydrate and energy metabolism, genetic information processing and stress response. To the best of our knowledge this study represents the first evidence of protein identities with differentially expressed isoforms in Brazilian MON810 genetic background hybrid grown under field conditions. As global databases on outputs from "omics" analysis become available, these could provide a highly desirable benchmark for safety assessments.

  14. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  15. Comparative Estimation of Genetic Diversity in Population Studies using Molecular Sampling and Traditional Sampling Methods.

    Science.gov (United States)

    Saeb, Amr Tm; David, Satish Kumar

    2014-01-01

    Entomopathogenic nematodes (EPN) are efficient biological pest control agents. Population genetics studies on EPN are seldom known. Therefore, it is of interest to evaluate the significance of molecular sampling method (MSM) for accuracy, time needed, and cost effectiveness over traditional sampling method (TSM). The study was conducted at the Mohican Hills golf course at the state of Ohio where the EPN H. bacteriophora has been monitored for 18 years. The nematode population occupies an area of approximately 3700 m(2) with density range from 0.25-2 per gram soil. Genetic diversity of EPN was studied by molecular sampling method (MSM) and traditional sampling method (TSM) using the mitochondrial gene pcox1. The MSM picked 88% in compared to TSM with only 30% of sequenced cox 1 gene. All studied genetic polymorphism measures (sequence and haplotype) showed high levels of genetic diversity of MSM over TSM. MSM minimizes the chance of mitochondrial genes amplification from non target organisms (insect or other contaminating microorganisms). Moreover, it allows the sampling of more individuals with a reliable and credible representative sample size. Thus, we show that MSM supersedes TSM in labour intensity, time consumption and requirement of no special experience and efficiency.

  16. Genetic structure of wild emmer wheat populations as reflected by transcribed versus anonymous SSR markers.

    Science.gov (United States)

    Peleg, Zvi; Fahima, Tzion; Abbo, Shahal; Krugman, Tamar; Saranga, Yehoshua

    2008-03-01

    Simple sequence repeat (SSR) markers have become a major tool in population genetic analyses. The anonymous genomic SSRs (gSSRs) have been recently supplemented with expressed sequence tag (EST) derived SSRs (eSSRs), which represent the transcribed regions of the genome. In the present study, we used 8 populations of wild emmer wheat (Triticum turgidum subsp. dicoccoides) to compare the usefulness of the two types of SSR markers in assessing allelic diversity and population structure. gSSRs revealed significantly higher diversity than eSSRs in terms of average number of alleles (14.92 vs. 7.4, respectively), polymorphic information content (0.87 vs. 0.68, respectively), and gene diversity (He; 0.55 vs. 0.38, respectively). Despite the overall differences in the level of diversity, Mantel tests for correlations between eSSR and gSSR pairwise genetic distances were found to be significant for each population as well as for all accessions jointly (RM=0.54, p=0.01). Various genetic structure analyses (AMOVA, PCoA, STRUCTURE, unrooted UPGMA tree) revealed a better capacity of eSSRs to distinguish between populations, while gSSRs showed a higher proportion of intrapopulation (among accessions) diversity. We conclude that eSSR and gSSR markers should be employed in conjunction to obtain a high inter- and intra-specific (or inter- and intra-varietal) distinctness.

  17. Living in isolation - population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink).

    Science.gov (United States)

    Putz, Christina M; Schmid, Christoph; Reisch, Christoph

    2015-09-01

    The endangered plant species Dianthus gratianopolitanus exhibits a highly fragmented distribution range comprising many isolated populations. Based upon this pattern of distribution, we selected a study region in Switzerland with a lower magnitude of isolation (Swiss Jura) and another study region in Germany with a higher degree of isolation (Franconian Jura). In each region, we chose ten populations to analyze population structure, reproduction, and genetic variation in a comparative approach. Therefore, we determined population density, cushion size, and cushion density to analyze population structure, investigated reproductive traits, including number of flowers, capsules, and germination rate, and analyzed amplified fragment length polymorphisms to study genetic variation. Population and cushion density were credibly higher in German than in Swiss populations, whereas reproductive traits and genetic variation within populations were similar in both study regions. However, genetic variation among populations and isolation by distance were stronger in Germany than in Switzerland. Generally, cushion size and density as well as flower and capsule production increased with population size and density, whereas genetic variation decreased with population density. In contrast to our assumptions, we observed denser populations and cushions in the region with the higher magnitude of isolation, whereas reproductive traits and genetic variation within populations were comparable in both regions. This corroborates the assumption that stronger isolation must not necessarily result in the loss of fitness and genetic variation. Furthermore, it supports our conclusion that the protection of strongly isolated populations contributes essentially to the conservation of a species' full evolutionary potential.

  18. Structural modification of polysaccharides: A biochemical-genetic approach

    Science.gov (United States)

    Kern, Roger G.; Petersen, Gene R.

    1991-01-01

    Polysaccharides have a wide range of industrial and biomedical applications. An industry trend is underway towards the increased use of bacteria to produce polysaccharides. Long term goals of this work are the adaptation and enhancement of saccharide properties for electronic and optic applications. In this report we illustrate the application of enzyme-bearing bacteriophage on strains of the enteric bacterium Klebsiella pneumoniae, which produces a polysaccharide with the relatively rare rheological property of drag-reduction. This has resulted in the production of new polysaccharides with enhanced rheological properties. Our laboratory is developing techniques for processing and structurally modifying bacterial polysaccharides and oligosaccharides which comprise their basic polymeric repeat units. Our research has focused on bacteriophage which produce specific polysaccharide degrading enzymes. This has lead to the development of enzymes generated by bacteriophage as tools for polysaccharide modification and purification. These enzymes were used to efficiently convert the native material to uniform-sized high molecular weight polymers, or alternatively into high-purity oligosaccharides. Enzyme-bearing bacteriophage also serve as genetic selection tools for bacteria that produce new families of polysaccharides with modified structures.

  19. A Non-Symmetrical Solution Applying a Genetic Algorithm with Natural Crossover for the Structural Optimization of Truss Structures

    Directory of Open Access Journals (Sweden)

    Alvarado-Cárdenas R.

    2012-07-01

    Full Text Available In this research it is proposed a genetic algorithm with “natural crossover” that was applied to a continuous-discrete representation in order to optimize truss structures. The objective is to reduce the weight by restraining node displacement and limiting the cross sections to use. The solutions are combined applying two types of crossovers to the same representation, thus allowing to effectively explore the search space. The results are validated by comparing those found herein against those found in current literature for the case of the design of a 70 m span bridge truss structure. Solutions obtained are lighter and with different topology. Additionally, a case study is proposed, a greenhouse roof truss structure, in order to generate an actual application that is built in a practical scale and it is loaded afterwards to verify its strength.

  20. Genetic diversity and population structure of different varieties of Morada Nova hair sheep from Brazil.

    Science.gov (United States)

    Ferreira, J S B; Paiva, S R; Silva, E C; McManus, C M; Caetano, A R; Façanha, D A E; de Sousa, M A N

    2014-01-01

    The aim of this study was to analyze genetic diversity and population structure among varieties of White (N = 40), Red (N = 32), and Black (N = 31) Morada Nova hair sheep from flocks in the northeastern Brazilian semiarid region. Fifteen nuclear microsatellite markers and two regions of mitochondrial DNA were used. The intra-population analysis demonstrated that the White variety had higher diversity, while the Red variety had the lowest values. The Bayesian analysis to assess the genetic population structure allowed differentiation between White, Red, and Black varieties, and revealed a tendency towards sub-structuring in the White variety flocks from the States of Ceará and Paraíba. The results of analyses of molecular variance showed that the greatest genetic structure was found when comparing flocks rather than varieties (8.59 vs 6.64% of the total variation, P Dtl, both the dendrogram analysis and the principal coordinate analysis showed the formation of two main groups: one composed of White and another of Black and Red individuals. Five and two haplotypes were found for the D-loop region and the ND5 gene, respectively. A haplotype unique to the Red variety was found in the D-loop region and a variety haplotype unique to the Black variety was found in the ND5 gene; however, these frequencies were low and therefore require further validation. These results support the existence of substantial differences between the Red and White varieties and should be used as separate genetic resources and to improve conservation programs.

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

    Science.gov (United States)

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

    2015-08-01

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

  2. Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand

    Directory of Open Access Journals (Sweden)

    Seielstad Mark

    2011-06-01

    Full Text Available Abstract Background The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. Results A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively. The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2% of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. Conclusions The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them.

  3. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology.

    Science.gov (United States)

    Pennell, Matthew W; Harmon, Luke J

    2013-06-01

    Recent innovations in phylogenetic comparative methods (PCMs) have spurred a renaissance of research into the causes and consequences of large-scale patterns of biodiversity. In this paper, we review these advances. We also highlight the potential of comparative methods to integrate across fields and focus on three examples where such integration might be particularly valuable: quantitative genetics, community ecology, and paleobiology. We argue that PCMs will continue to be a key set of tools in evolutionary biology, shedding new light on how evolutionary processes have shaped patterns of biodiversity through deep time.

  4. Isolation by oceanic distance and spatial genetic structure in an overharvested international fishery

    NARCIS (Netherlands)

    Truelove, Nathan K.; Box, Stephen J.; Aiken, Karl A.; Blythe-Mallett, Azra; Boman, Erik M.; Booker, Catherine J.; Byfield, Tamsen T.; Cox, Courtney E.; Davis, Martha H.; Delgado, Gabriel A.; Glazer, Bob A.; Griffiths, Sarah M.; Kitson-Walters, Kimani; Kough, Andy S.; Pérez Enríquez, Ricardo; Preziosi, Richard F.; Roy, Marcia E.; Segura-García, Iris; Webber, Mona K.; Stoner, Allan W.

    2017-01-01

    Aim: A detailed understanding of spatial genetic structure (SGS) and the factors driving contemporary patterns of gene flow and genetic diversity are fundamental for developing conservation and management plans for marine fisheries. We performed a detailed study of SGS and genetic diversity

  5. Genetic structure of coexisting wild and managed agave populations: implications for the evolution of plants under domestication.

    Science.gov (United States)

    Figueredo, Carmen Julia; Casas, Alejandro; González-Rodríguez, Antonio; Nassar, Jafet M; Colunga-GarcíaMarín, Patricia; Rocha-Ramírez, Víctor

    2015-10-03

    Domestication is a continuous evolutionary process guided by humans. This process leads to divergence in characteristics such as behaviour, morphology or genetics, between wild and managed populations. Agaves have been important resources for Mesoamerican peoples since prehistory. Some species are domesticated and others vary in degree of domestication. Agave inaequidens Koch is used in central Mexico to produce mescal, and a management gradient from gathered wild and silvicultural populations, as well as cultivated plantations, has been documented. Significant morphological differences were reported among wild and managed populations, and a high phenotypic variation in cultivated populations composed of plants from different populations. We evaluated levels of genetic diversity and structure associated with management, hypothesizing that high morphological variation would be accompanied by high genetic diversity in populations with high gene flow and low genetic structure among managed and unmanaged populations. Wild, silvicultural and cultivated populations were studied, collecting tissue of 19-30 plants per population. Through 10 nuclear microsatellite loci, we compared population genetic parameters. We analysed partition of variation associated with management categories to estimate gene flow among populations. Agave inaequidens exhibits high levels of genetic diversity (He = 0.707) and moderate genetic structure (FST = 0.112). No differences were found in levels of genetic diversity among wild (He = 0.704), silviculturally managed (He = 0.733) and cultivated (He = 0.698) populations. Bayesian analysis indicated that five genetic clusters best fit the data, with genetic groups corresponding to habitats where populations grow rather than to management. Migration rates ranged from zero between two populations to markedly high among others (M = 0.73-35.25). Natural mechanisms of gene flow and the dynamic management of agave propagules among populations favour gene

  6. Non-structural carbohydrates in woody plants compared among laboratories

    Science.gov (United States)

    Audrey G. Quentin; Elizabeth A. Pinkard; Michael G. Ryan; David T. Tissue; L. Scott Baggett; Henry D. Adams; Pascale Maillard; Jacqueline Marchand; Simon M. Landhausser; Andre Lacointe; Yves Gibon; William R. L. Anderegg; Shinichi Asao; Owen K. Atkin; Marc Bonhomme; Caroline Claye; Pak S. Chow; Anne Clement-Vidal; Noel W. Davies; L. Turin Dickman; Rita Dumbur; David S. Ellsworth; Kristen Falk; Lucía Galiano; Jose M. Grunzweig; Henrik Hartmann; Gunter Hoch; Sharon Hood; Joanna E. Jones; Takayoshi Koike; Iris Kuhlmann; Francisco Lloret; Melchor Maestro; Shawn D. Mansfield; Jordi Martinez-Vilalta; Mickael Maucourt; Nathan G. McDowell; Annick Moing; Bertrand Muller; Sergio G. Nebauer; Ulo Niinemets; Sara Palacio; Frida Piper; Eran Raveh; Andreas Richter; Gaelle Rolland; Teresa Rosas; Brigitte Saint Joanis; Anna Sala; Renee A. Smith; Frank Sterck; Joseph R. Stinziano; Mari Tobias; Faride Unda; Makoto Watanabe; Danielle A. Way; Lasantha K. Weerasinghe; Birgit Wild; Erin Wiley; David R. Woodruff

    2016-01-01

    Non-structural carbohydrates (NSC) in plant tissue are frequently quantified to make inferences about plant responses to environmental conditions. Laboratories publishing estimates of NSC of woody plants use many different methods to evaluate NSC. We asked whether NSC estimates in the recent literature could be quantitatively compared among studies. We also...

  7. Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

    Science.gov (United States)

    Wang, Linhai; Yu, Jingyin; Li, Donghua; Zhang, Xiurong

    2015-01-01

    Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/.

  8. Diversity and genetic structure analysis of three Amazonian Amerindian populations of Colombia.

    Science.gov (United States)

    Braga, Yamid; Arias B, Leonardo; Barreto, Guillermo

    2012-04-01

    In the departments of the Vaupés and Guaviare, in southeastern Colombia, in a transitional area between Amazonia and the eastern plains, inhabit indigenous groups belonging to the Tukanoan (East) and Guahiban linguistic families. Although some studies have dealt with the culture and the cosmology description of these groups, little research has been done on the biological diversity and genetic relationships of such groups. To estimate the diversity, the structure, and the genetic relationships of one Guahiban and two Tukanoan groups of the Colombian Amazonian region. Samples were collected (n = 106) from unrelated individuals belonging to the Vaupés native indigenous communities. The DNA was extracted and nine autosomal microsatellites were typed. Several measures of diversity, FST, pairwise FST, and population differentiation between groups were calculated. Finally, it was estimated the genetic distances of the groups studied in relation with other Amazonian, Andean and Central American indigenous people. 1. The genetic diversity found stands within the range of other Amazonian populations, whereas compared to the mestizo and afro-descendant Colombian populations, such diversity showed to be lower. 2. The structure and population differentiation tests showed two clusters; one consisting of the Vaupés Tukanoan and Guaviare Tukanoan groups, and a second one formed by the Guayabero. 3. Tukanoan groups are found to be closer related to the Brazilian Amazonian populations than to the Guayabero. The results of this study suggest that the Guayabero group from Guaviare, are genetically differentiated from those Tukanoan groups of the Vaupés and Guaviare.

  9. Comparing High-latitude Ionospheric and Thermospheric Lagrangian Coherent Structures

    Science.gov (United States)

    Wang, N.; Ramirez, U.; Flores, F.; Okic, D.; Datta-Barua, S.

    2015-12-01

    Lagrangian Coherent Structures (LCSs) are invisible boundaries in time varying flow fields that may be subject to mixing and turbulence. The LCS is defined by the local maxima of the finite time Lyapunov exponent (FTLE), a scalar field quantifying the degree of stretching of fluid elements over the flow domain. Although the thermosphere is dominated by neutral wind processes and the ionosphere is governed by plasma electrodynamics, we can compare the LCS in the two modeled flow fields to yield insight into transport and interaction processes in the high-latitude IT system. For obtaining thermospheric LCS, we use the Horizontal Wind Model 2014 (HWM14) [1] at a single altitude to generate the two-dimensional velocity field. The FTLE computation is applied to study the flow field of the neutral wind, and to visualize the forward-time Lagrangian Coherent Structures in the flow domain. The time-varying structures indicate a possible thermospheric LCS ridge in the auroral oval area. The results of a two-day run during a geomagnetically quiet period show that the structures are diurnally quasi-periodic, thus that solar radiation influences the neutral wind flow field. To find the LCS in the high-latitude ionospheric drifts, the Weimer 2001 [2] polar electric potential model and the International Geomagnetic Reference Field 11 [3] are used to compute the ExB drift flow field in ionosphere. As with the neutral winds, the Lagrangian Coherent Structures are obtained by applying the FTLE computation. The relationship between the thermospheric and ionospheric LCS is analyzed by comparing overlapping FTLE maps. Both a publicly available FTLE solver [4] and a custom-built FTLE computation are used and compared for validation [5]. Comparing the modeled IT LCSs on a quiet day with the modeled IT LCSs on a storm day indicates important factors on the structure and time evolution of the LCS.

  10. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  11. Comparison of population-genetic structuring in congeneric kelp- versus rock-associated snails: a test of a dispersal-by-rafting hypothesis

    National Research Council Canada - National Science Library

    Nikula, Raisa; Spencer, Hamish G; Waters, Jonathan M

    2011-01-01

    .... We tested this hypothesis by comparing nuclear multilocus population-genetic structuring in two sister topshell species, which both have a planktonic larval phase but are fairly well segregated...

  12. A preliminary investigation into the genetic variation and population structure of Taenia hydatigena from Sardinia, Italy.

    Science.gov (United States)

    Boufana, Belgees; Scala, Antonio; Lahmar, Samia; Pointing, Steve; Craig, Philip S; Dessì, Giorgia; Zidda, Antonella; Pipia, Anna Paola; Varcasia, Antonio

    2015-11-30

    Cysticercosis caused by the metacestode stage of Taenia hydatigena is endemic in Sardinia. Information on the genetic variation of this parasite is important for epidemiological studies and implementation of control programs. Using two mitochondrial genes, the cytochrome c oxidase subunit 1 (cox1) and the NADH dehydrogenase subunit 1 (ND1) we investigated the genetic variation and population structure of Cysticercus tenuicollis from Sardinian intermediate hosts and compared it to that from other hosts from various geographical regions. The parsimony cox1 network analysis indicated the existence of a common lineage for T. hydatigena and the overall diversity and neutrality indices indicated demographic expansion. Using the cox1 sequences, low pairwise fixation index (Fst) values were recorded for Sardinian, Iranian and Palestinian sheep C. tenuicollis which suggested the absence of genetic differentiation. Using the ND1 sequences, C. tenuicollis from Sardinian sheep appeared to be differentiated from those of goat and pig origin. In addition, goat C. tenuicollis were genetically different from adult T. hydatigena as indicated by the statistically significant Fst value. Our results are consistent with biochemical and morphological studies that suggest the existence of variants of T. hydatigena.

  13. IQ heritability estimation: analyzing genetically-informative data with structural equation models.

    Science.gov (United States)

    Gallardo Pujol, David; García-Forero, Carlos; Kramp, Uwe; Maydeu-Olivares, Albert; Andrés-Pueyo, Antonio

    2007-02-01

    When analyzing genetic data, Structural Equations Modeling (SEM) provides a straightforward methodology to decompose phenotypic variance using a model-based approach. Furthermore, several models can be easily implemented, tested, and compared using SEM, allowing the researcher to obtain valuable information about the sources of variability. This methodology is briefly described and applied to re-analyze a Spanish set of IQ data using the biometric ACE model. In summary, we report heritability estimates that are consistent with those of previous studies and support substantial genetic contribution to phenotypic IQ; around 40% of the variance can be attributable to it. With regard to the environmental contribution, shared environment accounts for 50% of the variance, and non-shared environment accounts for the remaining 10%. These results are discussed in the text.

  14. Evolution and genetic population structure of prickly lettuce (Lactuca serriola) and its RGC2 resistance gene cluster

    NARCIS (Netherlands)

    Kuang, H.; Eck, van H.J.; Sicard, D.; Michelmore, R.; Nevo, E.

    2008-01-01

    Genetic structure and diversity of natural populations of prickly lettuce (Lactuca serriola) were studied using AFLP markers and then compared with the diversity of the RGC2 disease resistance gene cluster. Screening of 696 accessions from 41 populations using 319 AFLP markers showed that eastern Tu

  15. Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor).

    Science.gov (United States)

    Burridge, Christopher P; Peucker, Amanda J; Valautham, Sureen K; Styan, Craig A; Dann, Peter

    2015-01-01

    Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. © The American Genetic Association 2015.

  16. Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations.

    Directory of Open Access Journals (Sweden)

    Rachael Y Dudaniec

    Full Text Available With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus in two core regions (Washington State, United States versus the species' northern peripheral region (British Columbia, Canada where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a 'flat' landscape, but at the periphery, topography (slope and elevation had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.

  17. Plant genetics predicts intra-annual variation in phytochemistry and arthropod community structure.

    Science.gov (United States)

    Wimp, G M; Wooley, S; Bangert, R K; Young, W P; Martinsen, G D; Keim, P; Rehill, B; Lindroth, R L; Whitham, T G

    2007-12-01

    With the emerging field of community genetics, it is important to quantify the key mechanisms that link genetics and community structure. We studied cottonwoods in common gardens and in natural stands and examined the potential for plant chemistry to be a primary mechanism linking plant genetics and arthropod communities. If plant chemistry drives the relationship between plant genetics and arthropod community structure, then several predictions followed. We would find (i) the strongest correlation between plant genetic composition and chemical composition; (ii) an intermediate correlation between plant chemical composition and arthropod community composition; and (iii) the weakest relationship between plant genetic composition and arthropod community composition. Our results supported our first prediction: plant genetics and chemistry had the strongest correlation in the common garden and the wild. Our results largely supported our second prediction, but varied across space, seasonally, and according to arthropod feeding group. Plant chemistry played a larger role in structuring common garden arthropod communities relative to wild communities, free-living arthropods relative to leaf and stem modifiers, and early-season relative to late-season arthropods. Our results did not support our last prediction, as host plant genetics was at least as tightly linked to arthropod community structure as plant chemistry, if not more so. Our results demonstrate the consistency of the relationship between plant genetics and biodiversity. Additionally, plant chemistry can be an important mechanism by which plant genetics affects arthropod community composition, but other genetic-based factors are likely involved that remain to be measured.

  18. Comparative study of codes for the seismic design of structures

    Directory of Open Access Journals (Sweden)

    S. H. C. Santos

    Full Text Available A general evaluation of some points of the South American seismic codes is presented herein, comparing them among themselves and with the American Standard ASCE/SEI 7/10 and with the European Standard Eurocode 8. The study is focused in design criteria for buildings. The Western border of South America is one of the most seismically active regions of the World. It corresponds to the confluence of the South American and Nazca plates. This region corresponds roughly to the vicinity of the Andes Mountains. This seismicity diminishes in the direction of the comparatively seismically quieter Eastern South American areas. The South American countries located in its Western Border possess standards for seismic design since some decades ago, being the Brazilian Standard for seismic design only recently published. This study is focused in some critical topics: definition of the recurrence periods for establishing the seismic input; definition of the seismic zonation and design ground motion values; definition of the shape of the design response spectra; consideration of soil amplification, soil liquefaction and soil-structure interaction; classification of the structures in different importance levels; definition of the seismic force-resisting systems and respective response modification coefficients; consideration of structural irregularities and definition of the allowable procedures for the seismic analyses. A simple building structure is analyzed considering the criteria of the several standards and obtained results are compared.

  19. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    Science.gov (United States)

    Pailles, Yveline; Ho, Shwen; Pires, Inês S.; Tester, Mark; Negrão, Sónia; Schmöckel, Sandra M.

    2017-01-01

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance. PMID:28261227

  20. Transferrin variation and genetic structure of reindeer populations in Scandinavia

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    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

  1. Real-coded genetic algorithm for optimal vibration control of flexible structure

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Presents the study on the optimum location of actuators/sensors for active vibration control in aerospace flexible structures with the performance function first built by maximization of dissipation energy due to control action and a real-coded genetic algorithm then proposed to produce a global-optimum solution, and proves the feasibility and advantages of this algorithm with the example of a standard test function and a two-collocated actuators/sensors cantilever, and comparing the results with those given in the literatures.

  2. Population genetic structure in the paddyfield warbler (Acrocephalus agricola Jerd.)

    Institute of Scientific and Technical Information of China (English)

    Pavel ZEHTINDJIEV; Mihaela ILIEVA; Bengt HANSSON; Olga OPARINA; Mihail OPARIN; Staffan BENSCH

    2011-01-01

    Population genefc structure was studied in paddyfield warblers Acrocephalus agricola breeding in NE Bulgaria, SE Russia and S Kazakhstan. We were particularly interested in the degree of genetic differentiation and gene flow of the Bulgarian population due to its geographical isolation, recent origin and unique migratory strategy. Analyses of mitochondrial DNA (mtDNA) showed that there was no divergence between Bulgarian and Russian populations (FST = 0.007), whereas those in Kazakhstan differed significantly from the European breeding populations (Russia: FST = 0.058; Bulgaria: Fsr = 0.114). The degree of differentiation between populations at nuclear markers (five microsatellite loci; FsT ≈ 0) was weaker than for mtDNA. We suggest that this relatively weak differentiation over the range of this species reflects a recent postglacial expansion, and results from mismatch distribution analyses and Fu's Fs tests are in agreement. Preservation of small and geographically isolated populations which may contain individuals with unique adaptive traits, such as the studied Bulgarian population of paddyfield warbler,is valuable for the long-term conservation of expanding migratory bird species.

  3. Tackling intraspecific genetic structure in distribution models better reflects species geographical range.

    Science.gov (United States)

    Marcer, Arnald; Méndez-Vigo, Belén; Alonso-Blanco, Carlos; Picó, F Xavier

    2016-04-01

    Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms' distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.

  4. THE GENETIC STRUCTURE OF DIFFERENT AGE GROUPS OF SILVER (HYPOPHTHALMICHTHYS MOLITRIX AND BIGHEAD (ARISTICHTHYS NOBILIS CARPS FROM FISH FARM LIMANSKE

    Directory of Open Access Journals (Sweden)

    Т. Nagorniuk

    2015-09-01

    Full Text Available Purpose. Studying the peculiarities of the genetic structure of different age groups of silver and bighead carps from fish farm Limanske with the use of genetic-biochemical markers. Methodology. The methods of vertical polyacrylamide and horizontal starch electrophoresis with our own modifications have been used for the study. Sampling of the biological material and histochemical staining of gel plates were carried out using the generally accepted methods. Statistical analysis of the obtained data were performed in "Biosys-I". Findings. We analyzed the genetic structure of age-1, age-1+ and age-2 of silver and bighead carps with the use of genetic-biochemical markers - Рralb, EST, MDH, МЕ, СА. We demonstrated the peculiarities of allele frequencies and genotypic composition of protein system loci. A high level of heterozygosity in the examined was detected loci for age-1 silver carp – 66.7-88.9% and age-1 bighead carp – 65.4-77.8%. A significantly higher level of the observed average heterozygosity compared to the expected heterozygosity of age-1 as silver carp (Ho = 75.9%, He = 49,6%, and bighead carp (Ho = 73,6%, He = 47,9% was observed. This fact indicated on the necessity for performing a stabilization of their genetic structure. The calculated Wright's F index in different age groups showed a predominance of the observed level of the average heterozygosity over the expected one for 22.7–53% in silver carp and 24.5-53.7% in bighead carp. A stabilization of the genetic structure in age-2 silver carp (Ho = 57.8%; He = 47.1% by the heterogeneity level was observed. Originality. For the first time we analyzed the genetic structure and the level of heterogeneity of the breeding groups of age-1, age-1+, age-2 silver and bighead carps from fish farm Limanske with the use of genetic-biochemical markers. Practical value. The results of the study can be used in selection and breeding works aimed at creating the breeding stocks of silver and

  5. Molecular and structural analysis of genetic variations in congenital cataract

    Science.gov (United States)

    Kumar, Manoj; Agarwal, Tushar; Kaur, Punit; Kumar, Manoj; Khokhar,, Sudarshan

    2013-01-01

    Objective To determine the relative contributions of mutations in congenital cataract cases in an Indian population by systematic screening of genes associated with cataract. Methods We enrolled 100 congenital cataract cases presenting at the Dr. R. P. Centre for Ophthalmic Sciences, a tertiary research and referral hospital (AIIMS, New Delhi, India). Crystallin, alpha A (CRYAA), CRYAB, CRYGs, CRYBA1, CRYBA4, CRYBB1, CRYBB2, CRYBB3, beaded filament structural protein 1 (BFSP1), gap function protein, alpha 3 (GJA3), GJA8, and heat shock transcription factor 4 gene genes were amplified. Protein structure differences analysis was performed using Discovery Studio (DS) 2.0. Results The mean age of the patients was 17.45±16.51 months, and the age of onset was 1.618±0.7181 months. Sequencing analysis of 14 genes identified 18 nucleotide variations. Fourteen variations were found in the crystallin genes, one in Cx-46 (GJA3), and three in BFSP1. Conclusions Congenital cataract shows marked clinical and genetic heterogeneity. Five nucleotide variations (CRYBA4:p.Y67N, CRYBB1:p.D85N, CRYBB1:p.E75K, CRYBB1:p.E155K, and GJA3:p.M1V) were predicted to be pathogenic. Variants in other genes might also be involved in maintaining lens development, growth, and transparency. The study confirms that the crystallin beta cluster on chromosome 22, Cx-46, and BFSP1 plays a major role in maintaining lens transparency. This study also expands the mutation spectrum of the genes associated with congenital cataract. PMID:24319337

  6. Informational structure of genetic sequences and nature of gene splicing

    Science.gov (United States)

    Trifonov, E. N.

    1991-10-01

    Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

  7. Society, demography and genetic structure in the spotted hyena.

    Science.gov (United States)

    Holekamp, Kay E; Smith, Jennifer E; Strelioff, Christopher C; Van Horn, Russell C; Watts, Heather E

    2012-02-01

    Spotted hyenas (Crocuta crocuta) are large mammalian carnivores, but their societies, called 'clans', resemble those of such cercopithecine primates as baboons and macaques with respect to their size, hierarchical structure, and frequency of social interaction among both kin and unrelated group-mates. However, in contrast to cercopithecine primates, spotted hyenas regularly hunt antelope and compete with group-mates for access to kills, which are extremely rich food sources, but also rare and ephemeral. This unique occurrence of baboon-like sociality among top-level predators has favoured the evolution of many unusual traits in this species. We briefly review the relevant socio-ecology of spotted hyenas, document great demographic variation but little variation in social structure across the species' range, and describe the long-term fitness consequences of rank-related variation in resource access among clan-mates. We then summarize patterns of genetic relatedness within and between clans, including some from a population that had recently gone through a population bottleneck, and consider the roles of sexually dimorphic dispersal and female mate choice in the generation of these patterns. Finally, we apply social network theory under varying regimes of resource availability to analyse the effects of kinship on the stability of social relationships among members of one large hyena clan in Kenya. Although social bonds among both kin and non-kin are weakest when resource competition is most intense, hyenas sustain strong social relationships with kin year-round, despite constraints imposed by resource limitation. Our analyses suggest that selection might act on both individuals and matrilineal kin groups within clans containing multiple matrilines. © 2011 Blackwell Publishing Ltd.

  8. Comparing Structural Perspectives on Medical Informatics: EMBASE vs. MEDLINE

    Science.gov (United States)

    Morris, Theodore Allan

    2003-01-01

    Previous bibliometric analyses of Medical Informatics’ internal structure used MEDLINE records as the unit of study. EMBASE, a product of Excerpta Medica, carries a wider international scope and offers complementary retrieval results to MEDLINE. Since much medical informatics critical thinking originated abroad and migrated to North America, this difference in coverage may also indicate a different perspective of “what constitutes medical informatics.” Using traditional bibliometric and multivariate data analysis techniques, the present work examines EMBASE indexing records for the same 1995–1999 time frame as earlier MEDLINE studies to identify and compare structural features of the field.. PMID:14728448

  9. COMPARATIVE ANALYSIS OF THE ORGANIZATIONAL STRUCTURES IN SOME EU COUNTRIES

    Directory of Open Access Journals (Sweden)

    Ioana Raluca Goldbach

    2016-03-01

    Full Text Available The comparative analysis of organizational structures highlights similarities and differences between different factors influencing a company in its way of operation with the internal and/or external environment. The paper analyzes the organizational structures of some top companies from England, France and Romania that influence/determine the cultural organizational values and the norms elaborated and implemented, which, in time, become moral values and norms that acquire a social meaning, which means that they have been accepted by all the members of the organization.

  10. Comparing structural perspectives on Medical Informatics: EMBASE vs. MEDLINE.

    Science.gov (United States)

    Morris, Theodore Allan

    2003-01-01

    Previous bibliometric analyses of Medical Informatics' internal structure used MEDLINE records as the unit of study. EMBASE, a product of Excerpta Medica, carries a wider international scope and offers complementary retrieval results to MEDLINE. Since much medical informatics critical thinking originated abroad and migrated to North America, this difference in coverage may also indicate a different perspective of "what constitutes medical informatics." Using traditional bibliometric and multivariate data analysis techniques, the present work examines EMBASE indexing records for the same 1995-1999 time frame as earlier MEDLINE studies to identify and compare structural features of the field.

  11. Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.

    Science.gov (United States)

    Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R

    2012-04-22

    Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.

  12. Genetic diversity and population structure of genes encoding vaccine candidate antigens of Plasmodium vivax

    Directory of Open Access Journals (Sweden)

    Chenet Stella M

    2012-03-01

    Full Text Available Abstract Background A major concern in malaria vaccine development is genetic polymorphisms typically observed among Plasmodium isolates in different geographical areas across the world. Highly polymorphic regions have been observed in Plasmodium falciparum and Plasmodium vivax antigenic surface proteins such as Circumsporozoite protein (CSP, Duffy-binding protein (DBP, Merozoite surface protein-1 (MSP-1, Apical membrane antigen-1 (AMA-1 and Thrombospondin related anonymous protein (TRAP. Methods Genetic variability was assessed in important polymorphic regions of various vaccine candidate antigens in P. vivax among 106 isolates from the Amazon Region of Loreto, Peru. In addition, genetic diversity determined in Peruvian isolates was compared to population studies from various geographical locations worldwide. Results The structured diversity found in P. vivax populations did not show a geographic pattern and haplotypes from all gene candidates were distributed worldwide. In addition, evidence of balancing selection was found in polymorphic regions of the trap, dbp and ama-1 genes. Conclusions It is important to have a good representation of the haplotypes circulating worldwide when implementing a vaccine, regardless of the geographic region of deployment since selective pressure plays an important role in structuring antigen diversity.

  13. Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm.

    Science.gov (United States)

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

    The protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing the energy function. The protein folding structure prediction is computationally challenging and has been shown to be NP-hard problem when the 3D off-lattice AB model is employed. In this paper, the local adjustment genetic-annealing (LAGA) algorithm was used to search the ground state of 3D offlattice AB model for protein folding structure. The algorithm included an improved crossover strategy and an improved mutation strategy, where a local adjustment strategy was also used to enhance the searching ability. The experiments were carried out with the Fibonacci sequences. The experimental results demonstrate that the LAGA algorithm appears to have better performance and accuracy compared to the previous methods.

  14. Comparative analysis of antimicrobial resistance and genetic diversity of Campylobacter from broilers slaughtered in Poland.

    Science.gov (United States)

    Wieczorek, Kinga; Denis, Edyta; Osek, Jacek

    2015-10-01

    In the current study, the relationship of Campylobacter jejuni and Campylobacter coli strains isolated at slaughter was investigated using comparative analysis of antimicrobial resistance (AMR), virulence gene (VG) and PFGE profiling. A total of 254 Campylobacter isolates from poultry caeca and corresponding carcasses, including 139 C. jejuni and 115 C. coli strains were tested. The most prevalent resistance profiles observed in C. jejuni were ciprofloxacin, nalidixic acid and tetracycline (46 out of 139, 33.1% isolates) as well as ciprofloxacin, nalidixic acid, tetracycline and streptomycin among C. coli strains (34 out of 115, 29.6%). Multi-resistance was found more frequently among C. coli than C. jejuni (PCampylobacter isolates tested. All Campylobacter strains were classified into 154 different PFGE types. Among them, 56 profiles (28 C. jejuni and 28 C. coli) were common for at least two isolates including 9 clusters covering from 4 to 9 strains. Campylobacter composite types generated by a combination of 154 PFGE types, 10 AMR profiles and 19 VG patterns divided 178 distinct types with 95% similarity. The majority of the composite profiles (76 for C. jejuni and 58 for C. coli; 75.3% in total) included only one bacterial isolate. Furthermore, 11 pairs of C. jejuni and 12 pairs of C. coli from caeca and the corresponding carcasses isolated from the same places possessed the identical PFGE, AMR and VG patterns. This study demonstrated that C. jejuni and C. coli isolated from poultry in Poland showed to have a high genetic diversity and a weak clonal population structure. However, the composite analysis revealed a strong evidence for cross-contamination of chicken carcasses during the slaughter process. Additionally, our results confirm that Campylobacter may easily contaminate poultry carcasses at slaughter process and spread around country. More than half of Campylobacter strains tested (50.4%) were resistant to at least two classes of antimicrobials, i

  15. The 'Out of Africa' Hypothesis, Human Genetic Diversity, and Comparative Economic Development

    Science.gov (United States)

    Ashraf, Quamrul; Galor, Oded

    2013-01-01

    This research argues that deep-rooted factors, determined tens of thousands of years ago, had a significant effect on the course of economic development from the dawn of human civilization to the contemporary era. It advances and empirically establishes the hypothesis that, in the course of the exodus of Homo sapiens out of Africa, variation in migratory distance from the cradle of humankind to various settlements across the globe affected genetic diversity and has had a long-lasting effect on the pattern of comparative economic development that is not captured by geographical, institutional, and cultural factors. In particular, the level of genetic diversity within a society is found to have a hump-shaped effect on development outcomes in both the pre-colonial and the modern era, reflecting the trade-off between the beneficial and the detrimental effects of diversity on productivity. While the intermediate level of genetic diversity prevalent among Asian and European populations has been conducive for development, the high degree of diversity among African populations and the low degree of diversity among Native American populations have been a detrimental force in the development of these regions. PMID:25506083

  16. A Comparative Analysis of Genetic and Epigenetic Events of Breast and Ovarian Cancer Related to Tumorigenesis

    Directory of Open Access Journals (Sweden)

    Mckenna Longacre

    2016-05-01

    Full Text Available Breast cancer persists as the most common cause of cancer death in women worldwide. Ovarian cancer is also a significant source of morbidity and mortality, as the fifth leading cause of cancer death among women. This reflects the continued need for further understanding and innovation in cancer treatment. Though breast and ovarian cancer usually present as distinct clinical entities, the recent explosion of large-scale -omics research has uncovered many overlaps, particularly with respect to genetic and epigenetic alterations. We compared genetic, microenvironmental, stromal, and epigenetic changes common between breast and ovarian cancer cells, as well as the clinical relevance of these changes. Some of the most striking commonalities include genetic alterations of BRCA1 and 2, TP53, RB1, NF1, FAT3, MYC, PTEN, and PIK3CA; down regulation of miRNAs 9, 100, 125a, 125b, and 214; and epigenetic alterations such as H3K27me3, H3K9me2, H3K9me3, H4K20me3, and H3K4me. These parallels suggest shared features of pathogenesis. Furthermore, preliminary evidence suggests a shared epigenetic mechanism of oncogenesis. These similarities, warrant further investigation in order to ultimately inform development of more effective chemotherapeutics, as well as strategies to circumvent drug resistance.

  17. Genetic diversity and structure found in samples of Eritrean bread wheat

    DEFF Research Database (Denmark)

    Desta, Zeratsion Abera; Orabi, Jihad; Jahoor, Ahmed

    2014-01-01

    Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple ...

  18. Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks

    Science.gov (United States)

    Lindy B. Mullen; H. Arthur Woods; Michael K. Schwartz; Adam J. Sepulveda; Winsor H. Lowe

    2010-01-01

    The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho...

  19. Genetic and logic networks with the signal-inhibitor-activator structure are dynamically robust

    Institute of Scientific and Technical Information of China (English)

    LI Fangting; TAN Ning

    2006-01-01

    The proteins, DNA and RNA interaction networks govern various biological functions in living cells, these networks should be dynamically robust in the intracellular and environmental fluctuations. Here, we use Boolean network to study the robust structure of both genetic and logic networks. First, SOS network in bacteria E. coli, which regulates cell survival and repair after DNA damage, is shown to be dynamically robust. Comparing with cell cycle network in budding yeast and flagella network in E. coli, we find the signal-inhibitor-activator (SIA) structure in transcription regulatory networks. Second, under the dynamical rule that inhibition is much stronger than activation, we have searched 3-node non-self-loop logical networks that are dynamically robust, and that if the attractive basin of a final attractor is as large as seven, and the final attractor has only one active node, then the active node acts as inhibitor, and the SIA and signal-inhibitor (SI) structures are fundamental architectures of robust networks. SIA and SI networks with dynamic robustness against environment uncertainties may be selected and maintained over the course of evolution, rather than blind trial-error testing and be ing an accidental consequence of particular evolutionary history. SIA network can perform a more complex process than SI network, andSIA might be used to design robust artificial genetic network. Our results provide dynamical support for why the inhibitors and SIA/SI structures are frequently employed in cellular regulatory networks.

  20. Comparative genetics of the central nervous system in epigean and hypogean Astyanax mexicanus.

    Science.gov (United States)

    Strickler, Allen G; Soares, Daphne

    2011-03-01

    The extreme environment of subterranean caves presents an adaptive challenge to troglobitic organisms. The mechanisms by which natural selection modify an ancestral surface neural circuit to produce a novel subterranean behavior remain a mystery. To address this question, we performed cross species microarray experiments to compare differences in gene expression levels in the adult brain of the teleost Astyanax mexicanus. This species provides a unique opportunity for comparative genetic studies as it consists of extant epigean (surface) and hypogean (cave) conspecifics. Microarray experiments herein revealed significant changes in transcription levels of seventeen genes, several of which are important for behaviors involved in metabolic management. We focused on genes central to three neurotransmission and neuromodulation networks: the endocannabinoid system (Cannabinoid receptor CB1), the dopaminergic system (Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein) and the glutamatergic system (glutamate receptor AMPA 2a). All three genes were upregulated in the hypogean form of A. mexicanus compared to the epigean form, indicating that behavioral differences in the hypogean form of the species could be due to alterations in expression levels of several key genes. This information provides insights into the complex relationships among environmental factors, genetics, nervous systems and adaptive behavior, and can subsequently help us understand how these interactions affect behavior in other biological systems.

  1. [Human origin and evolution. A review of advances in paleoanthropology, comparative genetics, and evolutionary psychology].

    Science.gov (United States)

    Markov, A V

    2009-01-01

    In his main work, "On the origin of species", Darwin has refrained from discusion of the origin of man; be only mentioned that his theory would "throw light" on this problem. This famous Darwin's phrase turned out to be one of the most succesful scientific predictions. In the present paper some of the most important recent adavnces in paleoanthroplogy, comparative genetics and evolutionary psychology are reviewed. These three disciplines currently contribute most to our knowledge of anthropogenesis. The review demonstrates that Darwin's ideas not only "threw light" on human origin and evolution; they provided a comprehensive framework for a great variety of studies concerning different aspects of anthropogenesis.

  2. Comparative genetic approaches to the evolution of human brain and behavior.

    Science.gov (United States)

    Vallender, Eric J

    2011-01-01

    With advances in genomic technologies, the amount of genetic data available to scientists today is vast. Genomes are now available or planned for 14 different primate species and complete resequencing of numerous human individuals from numerous populations is underway. Moreover, high-throughput deep sequencing is quickly making whole genome efforts within the reach of single laboratories allowing for unprecedented studies. Comparative genetic approaches to the identification of the underlying basis of human brain, behavior, and cognitive ability are moving to the forefront. Two approaches predominate: inter-species divergence comparisons and intra-species polymorphism studies. These methodological differences are useful for different time scales of evolution and necessarily focus on different evolutionary events in the history of primate and hominin evolution. Inter-species divergence is more useful in studying large scale primate, or hominoid, evolution whereas intra-species polymorphism can be more illuminating of recent hominin evolution. These differences in methodological utility also extend to studies of differing genetic substrates; current divergence studies focus primarily on protein evolution whereas polymorphism studies are substrate ambivalent. Some of the issues inherent in these studies can be ameliorated by current sequencing capabilities whereas others remain intractable. New avenues are also being opened that allow for the incorporation of novel substrates and approaches. In the post-genomic era, the study of human evolution, specifically as it relates to the brain, is becoming more complete focusing increasingly on the totality of the system and better conceptualizing the entirety of the genetic changes that have lead to the human phenotype today.

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

    African Journals Online (AJOL)

    fire7-

    2016-12-28

    Dec 28, 2016 ... markers to assess the genetic diversity within and between common bean landraces, classifying them based on ... since the 1980's from continuous introduction of new ... control genotypes for the Andean and Mesoamerican gene pools, ... http://biology.anu.edu.au/GenAlEx/) was used to calculate genetic.

  4. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... positive correlation between molecular genetic variation and actual population size. ... Key words: Capparis decidua, Tandhab, Assos, Population size, RAPD markers, Genetic diversity. .... polymorphism in some population, and were monomorphic ... highly informative and produced 152 bands with an ...

  5. Comparative Traffic Performance Analysis of Urban Transportation Network Structures

    CERN Document Server

    Amini, Behnam; Mojarradi, Morteza; Derrible, Sybil

    2015-01-01

    The network structure of an urban transportation system has a significant impact on its traffic performance. This study uses network indicators along with several traffic performance measures including speed, trip length, travel time, and traffic volume, to compare a selection of seven transportation networks with a variety of structures and under different travel demand conditions. The selected network structures are: modified linear, branch, grid, 3-directional grid, 1-ring web, 2-ring web, and radial. For the analysis, a base origin-destination matrix is chosen, to which different growth factors are applied in order to simulate various travel demand conditions. Results show that overall the 2-ring web network offers the most efficient traffic performance, followed by the grid and the 1-ring networks. A policy application of this study is that the branch, 3-directional grid, and radial networks are mostly suited for small cities with uncongested traffic conditions. In contrast, the 2-ring web, grid, and 1-r...

  6. The genetic diversity and spatial genetic structure of the Corso-Sardinian endemic Ferula arrigonii Bocchieri (Apiaceae).

    Science.gov (United States)

    Dettori, C A; Sergi, S; Tamburini, E; Bacchetta, G

    2014-09-01

    Corsica and Sardinia represent major hotspots of plant diversity in the Mediterranean area and are priority regions for conservation due to their high number of endemic plant species. However, information supporting human decision-making on the conservation of these species is still scarce, especially at the genetic level. In this work, the first assessment is reported of the species-wide spatial genetic structure and diversity of Ferula arrigonii Bocchieri, a Corso-Sardinian endemic located in a few coastal sites and on small islands. Nine populations covering the entire natural range of the species were investigated by means of AFLP (amplified fragment length polymorphism) markers. Results indicate that this species is characterised by high levels of genetic polymorphism (92% polymorphic fragments) and of genetic diversity (H(w) = 0.317) and by relatively low differentiation among populations (F(st) = 0.057). PCoA, Bayesian analysis and neighbour-joining clustering were also employed to investigate the genetic structure of this species. Three genetically distinct groups were detected, although with considerable overlap between populations.

  7. A Comparative Study on Optimal Structural Dynamics Using Wavelet Functions

    Directory of Open Access Journals (Sweden)

    Seyed Hossein Mahdavi

    2015-01-01

    Full Text Available Wavelet solution techniques have become the focus of interest among researchers in different disciplines of science and technology. In this paper, implementation of two different wavelet basis functions has been comparatively considered for dynamic analysis of structures. For this aim, computational technique is developed by using free scale of simple Haar wavelet, initially. Later, complex and continuous Chebyshev wavelet basis functions are presented to improve the time history analysis of structures. Free-scaled Chebyshev coefficient matrix and operation of integration are derived to directly approximate displacements of the corresponding system. In addition, stability of responses has been investigated for the proposed algorithm of discrete Haar wavelet compared against continuous Chebyshev wavelet. To demonstrate the validity of the wavelet-based algorithms, aforesaid schemes have been extended to the linear and nonlinear structural dynamics. The effectiveness of free-scaled Chebyshev wavelet has been compared with simple Haar wavelet and two common integration methods. It is deduced that either indirect method proposed for discrete Haar wavelet or direct approach for continuous Chebyshev wavelet is unconditionally stable. Finally, it is concluded that numerical solution is highly benefited by the least computation time involved and high accuracy of response, particularly using low scale of complex Chebyshev wavelet.

  8. Genetic structure and diversity of Oryza sativa L.in Guizhou, China

    Institute of Scientific and Technical Information of China (English)

    ZHANG DongLing; CAO YongSheng; WANG XiangKun; LI ZiChao; ZHANG HongLiang; WEI XingHua; QI YongWen; WANG MeiXing; SUN JunLi; DING Li; TANG ShengXiang; QIU Zong'En

    2007-01-01

    Preserving many kinds of rice resources and rich variations, Guizhou Province is one of the districts with the highest genetic diversity of cultivated rice (Oryza sativa L.) in China. In the current research, genetic diversity and structure of 537 accessions of cultivated rice from Guizhou were studied using 36 microsatellite markers and 39 phenotypic characters. The results showed that the model-based genetic structure was the same as genetic-distance-based one using SSRs but somewhat different from the documented classification (mainly based on phenotype) of two subspecies. The accessions being classified into indica by phenotype but japonica by genetic structure were much more than that being classified into japonica by phenotype but indica by genetic structure. Like Ding Ying's taxonomic system of cultivated rice, the subspecific differentiation was the most distinct differentiation within cultivated rice. But the differentiation within indica or japonica population was different: japonica presented clearer differentiation between soil-watery ecotypes than indica, and indica presented clearer differentiation between seasonal ecotypes than japonica. Cultivated rices in Guizhou revealed high genetic diversity at both DNA and phenotypic levels. Possessing the highest genetic diversity and all the necessary conditions as a center of genetic diversity, region Southwestern of Guizhou was suggested as the center of genetic diversity of O. sativa L. from Guizhou.

  9. Low genetic diversity and intrapopulation spatial genetic structure of the Atlantic Forest tree, Esenbeckia leiocarpa Engl. (Rutaceae

    Directory of Open Access Journals (Sweden)

    G. Forti

    2014-12-01

    Full Text Available Studies on population genetics are the key to designing effective in situ management plans for tree species, in particular, those subjected to pressure from anthropogenic processes, such as forest fragmentation and logging. To investigate genetic diversity, inbreeding and intrapopulation spatial genetic structure (SGS in a fragmented population of the insect-pollinated tropical tree, Esenbeckia leiocarpa, we developed specific microsatellite markers for this species and mapped and sampled 100 individuals in a forest plot. Two issues were addressed in particular: (i the level of genetic diversity, inbreeding and effective population size, (ii whether intrapopulation spatial genetic structure exists. Among the 14 loci developed, we only used the three that presented polymorphism to estimate the genetic parameters. Genetic diversity was low, whereby the average number of alleles per locus (A was 3.3 and observed (H0 and expected heterozygosities (He were 0.336 and 0.298, respectively. The average fixation index was significantly higher than zero (F = 0.112, suggesting inbreeding. Significant SGS was found up to 7 m and between 31 to 38 m, indicating that trees growing within these distances may be related. Estimates of the effective population size indicated that the 100 sampled trees correspond to 14 individuals that are neither related nor inbred. Our results suggest that the microsatellite markers developed in this study are suitable for studies on geneticdiversity and structure, mating systems, gene flow and SGS in this species.

  10. Low genetic diversity and intrapopulation spatial genetic structure of the Atlantic Forest tree, Esenbeckia leiocarpa Engl. (Rutaceae

    Directory of Open Access Journals (Sweden)

    G. Forti

    2014-12-01

    Full Text Available Studies on population genetics are the key to designing effective in situ management plans for tree species, in particular, those subjected to pressure from anthropogenic processes, such as forest fragmentation and logging. To investigate genetic diversity, inbreeding and intrapopulation spatial genetic structure (SGS in a fragmented population of the insect-pollinated tropical tree, Esenbeckia leiocarpa, we developed specific microsatellite markers for this species and mapped and sampled 100 individuals in a forest plot. Two issues were addressed in particular: (i the level of genetic diversity, inbreeding and effective population size, (ii whether intrapopulation spatial genetic structure exists. Among the 14 loci developed, we only used the three that presented polymorphism to estimate the genetic parameters. Genetic diversity was low, whereby the average number of alleles per locus (A was 3.3 and observed (H0 and expected heterozygosities (He were 0.336 and 0.298, respectively. The average fixation index was significantly higher than zero (F = 0.112, suggesting inbreeding. Significant SGS was found up to 7 m and between 31 to 38 m, indicating that trees growing within these distances may be related. Estimates of the effective population size indicated that the 100 sampled trees correspond to 14 individuals that are neither related nor inbred. Our results suggest that the microsatellite markers developed in this study are suitable for studies on geneticdiversity and structure, mating systems, gene flow and SGS in this species.

  11. Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci.

    Science.gov (United States)

    Buonaccorsi, Vincent P; Kimbrell, Carol A; Lynn, Eric A; Hyde, John R

    2012-01-01

    Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high gene-flow marine species off the west coast of North America that experienced strong population decline over the past 3 decades. We used 18 anonymous and 13 gene-associated simple sequence repeat (SSR) loci (expressed sequence tag [EST]-SSRs) to characterize range-wide population structure with temporal replicates. No F(ST)-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between F(ST) and variation or marker class was observed. General linear model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates but did not affect the observed pattern of population structure.

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

    Science.gov (United States)

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

    1997-01-01

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

  13. A Comparative Study of Probability Collectives Based Multi-agent Systems and Genetic Algorithms

    Science.gov (United States)

    Huang, Chien-Feng; Wolpert, David H.; Bieniawski, Stefan; Strauss, Charles E. M.

    2005-01-01

    We compare Genetic Algorithms (GA's) with Probability Collectives (PC), a new framework for distributed optimization and control. In contrast to GA's, PC-based methods do not update populations of solutions. Instead they update an explicitly parameterized probability distribution p over the space of solutions. That updating of p arises as the optimization of a functional of p. The functional is chosen so that any p that optimizes it should be p peaked about good solutions. The PC approach works in both continuous and discrete problems. It does not suffer from the resolution limitation of the finite bit length encoding of parameters into GA alleles. It also has deep connections with both game theory and statistical physics. We review the PC approach using its motivation as the information theoretic formulation of bounded rationality for multi-agent systems. It is then compared with GA's on a diverse set of problems. To handle high dimensional surfaces, in the PC method investigated here p is restricted to a product distribution. Each distribution in that product is controlled by a separate agent. The test functions were selected for their difficulty using either traditional gradient descent or genetic algorithms. On those functions the PC-based approach significantly outperforms traditional GA's in both rate of descent, trapping in false minima, and long term optimization.

  14. Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

    Science.gov (United States)

    Cooper, Dawn; Cory, Jenny S; Myers, Judith H

    2003-04-01

    The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

  15. Genetic Identification and Population Structure of Juvenile Mullet ...

    African Journals Online (AJOL)

    then genetically identified using direct sequencing of the CO1 gene with cross- referencing to a recent ..... probabilities were lacking modal distribution, so the optimum number of .... different scenarios with no correspondence between them.

  16. Peripheral genetic structure of Helicoverpa zea indicates asymmetrical panmixia

    Science.gov (United States)

    Seasonal climatic shifts create peripheral habitats that alternate between habitable and uninhabitable for migratory species. Such dynamic peripheral habitats are potential sites where migratory species could evolve high genetic diversity resulting from convergence of immigrants from multiple region...

  17. 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.

  18. Hydraulic Self Servo Swing Cylinder Structure Optimization and Dynamic Characteristics Analysis Based on Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    Lin Jiang; Ruolin Wu∗and Zhichao Zhu

    2015-01-01

    The dynamic characteristics of hydraulic self servo swing cylinder were analyzed according to the hydraulic system natural frequency formula. Based on that, a method of the hydraulic self servo swing cylinder structure optimization based on genetic algorithm was proposed in this paper. By analyzing the four parameters that affect the dynamic characteristics, we had to optimize the structure to obtain as larger the Dm ( displacement) as possible under the condition with the purpose of improving the dynamic characteristics of hydraulic self servo swing cylinder. So three state equations were established in this paper. The paper analyzed the effect of the four parameters in hydraulic self servo swing cylinder natural frequency equation and used the genetic algorithm to obtain the optimal solution of structure parameters. The model was simulated by substituting the parameters and initial value to the simulink model. Simulation results show that: using self servo hydraulic swing cylinder natural frequency equation to study its dynamic response characteristics is very effective. Compared with no optimization, the overall system dynamic response speed is significantly improved.

  19. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839

    Directory of Open Access Journals (Sweden)

    Beerli Peter

    2008-09-01

    Full Text Available Abstract Background Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour and physical (e.g. present-day ocean currents, past changes in sea temperature and levels factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II, which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. Results We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Conclusion Lack of congruence between mt and nuclear evidences, which

  20. A search for lowest energy structures of ZnS quantum dots: Genetic algorithm tight-binding study.

    Science.gov (United States)

    Pal, Sougata; Sharma, Rahul; Goswami, Biplab; Sarkar, Pranab; Bhattacharyya, S P

    2009-06-07

    The lowest energy structures of ZnS quantum dots of different sizes have been determined by an unbiased search using genetic algorithm (GA) coupled with the density-functional tight-binding method. The GA search converges to a rather new ringlike configurations of ZnS quantum dots. We have studied the structural, electronic, and optical properties of these ringlike clusters and compared these properties with those of other reported structures of ZnS quantum dots, namely, hollow, zinc-blende, wurtzite, and rocksalt structures.

  1. Comparing molecules and solids across structural and alchemical space.

    Science.gov (United States)

    De, Sandip; Bartók, Albert P; Csányi, Gábor; Ceriotti, Michele

    2016-05-18

    Evaluating the (dis)similarity of crystalline, disordered and molecular compounds is a critical step in the development of algorithms to navigate automatically the configuration space of complex materials. For instance, a structural similarity metric is crucial for classifying structures, searching chemical space for better compounds and materials, and driving the next generation of machine-learning techniques for predicting the stability and properties of molecules and materials. In the last few years several strategies have been designed to compare atomic coordination environments. In particular, the smooth overlap of atomic positions (SOAPs) has emerged as an elegant framework to obtain translation, rotation and permutation-invariant descriptors of groups of atoms, underlying the development of various classes of machine-learned inter-atomic potentials. Here we discuss how one can combine such local descriptors using a regularized entropy match (REMatch) approach to describe the similarity of both whole molecular and bulk periodic structures, introducing powerful metrics that enable the navigation of alchemical and structural complexities within a unified framework. Furthermore, using this kernel and a ridge regression method we can predict atomization energies for a database of small organic molecules with a mean absolute error below 1 kcal mol(-1), reaching an important milestone in the application of machine-learning techniques for the evaluation of molecular properties.

  2. Genetic Structure of Acetobacter diazotrophicus Populations and Identification of a New Genetically Distant Group

    OpenAIRE

    Caballero-Mellado, J.; Fuentes-Ramirez, L. E.; Reis, V. M.; Martinez-Romero, E.

    1995-01-01

    A total of 55 isolates of Acetobacter diazotrophicus recovered from diverse sucrose-rich host plants and from mealybugs associated with sugarcane plants were characterized by the electrophoretic mobilities of 12 metabolic enzymes. We identified seven different electrophoretic types (ETs), six of which are closely related within a genetic distance of 0.195 and exhibit high DNA-DNA homology. The seventh ET was largely divergent, separated at a genetic distance of 0.53, and had only 54% DNA homo...

  3. Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus

    Directory of Open Access Journals (Sweden)

    Zardoya Rafael

    2007-10-01

    Full Text Available Abstract Background Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multi-locus analyses based on both nuclear and mitochondrial genetic markers are probably the most efficient and informative approach to discerning the relative role of historical events and life-history traits in shaping genetic heterogeneity. The European sardine (Sardina pilchardus is a small pelagic fish with a relatively high migratory capability that is expected to show low levels of genetic differentiation among populations. Previous genetic studies based on meristic and mitochondrial control region haplotype frequency data supported the existence of two sardine subspecies (S. p. pilchardus and S. p. sardina. Results We investigated genetic structure of sardine among nine locations in the Atlantic Ocean and Mediterranean Sea using allelic size variation of eight specific microsatellite loci. Bayesian clustering and assignment tests, maximum likelihood estimates of migration rates, as well as classical genetic-variance-based methods (hierarchical AMOVA test and RST pairwise comparisons supported a single evolutionary unit for sardines. These analyses only detected weak but significant genetic differentiation, which followed an isolation-by-distance pattern according to Mantel test. Conclusion We suggest that the discordant genetic structuring patterns inferred based on mitochondrial and microsatellite data might indicate that the two different classes of molecular markers may be reflecting different and complementary aspects of the evolutionary history of sardine. Mitochondrial data might be reflecting past isolation of sardine populations into two distinct groupings during Pleistocene whereas microsatellite data reveal the existence of present day gene flow among populations, and a pattern of isolation by distance.

  4. Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure

    Institute of Scientific and Technical Information of China (English)

    ZHU Weiyue; ZHOU Taoying; ZHONG Ming; LU Baorong

    2007-01-01

    A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated.Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples),in addition to investigating the fine-scale spatial genetic structure within the population.The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88,expected heterozygosity (He) 0.431,Shannon diversity index (/) 0.699,and percentage of polymorphic loci (P) 100%.Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation.The regression model of the four diversity indexes with the change of sample sizes was computed.As a result,27-52 individuals can reach 95% of total genetic variability of the population.Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m.The study provided a scientific basis for the sampling strategy of wild soybean populations.

  5. COMPARATIVE MOLECULAR GENETIC ANALYSIS BETWEEN UKRAINIAN AND EU REGISTERED GLYPHOSATE-TOLERANT RAPESEED TRANSGENIC PLANTS

    Directory of Open Access Journals (Sweden)

    A. M. Taranenko

    2015-04-01

    Full Text Available The purpose of research was to analyze 10 developed at the Institute of Cell Biology and Genetic Engineering lines of rapeseed to confirm the presence and functionality of the transferred transgene CP4 epsps, as well as the differences among those lines from registered transformation events GT73 and GT200 (Monsanto. During the study extraction of total rapeseed DNA, PCR analysis, electrophoretic separation and visualization of amplicons in agarose gel were conducted, as well as testing of green plants for resistance to glyphosate in greenhouse. The structural difference among 7 transgenic lines from registered transformation events GT73 and GT200 was revealed. Plants showing the presence of synthetic CP4 epsps sequence were resistant to the herbicide in a closed soil. The uniqueness of the obtained transformation events was confirmed, as well as the prospect of using them in breeding.

  6. Adaptive and maladaptive functioning in Kleefstra syndrome compared to other rare genetic disorders with intellectual disabilities.

    Science.gov (United States)

    Vermeulen, Karlijn; de Boer, Anneke; Janzing, Joost G E; Koolen, David A; Ockeloen, Charlotte W; Willemsen, Marjolein H; Verhoef, Floor M; van Deurzen, Patricia A M; van Dongen, Linde; van Bokhoven, Hans; Egger, Jos I M; Staal, Wouter G; Kleefstra, Tjitske

    2017-05-12

    Detailed neurobehavioural profiles are of major value for specific clinical management, but have remained underexposed in the population with intellectual disabilities (ID). This was traditionally classified based on IQ level only. Rapid advances in genetics enable etiology based stratification in the majority of patients, which reduces clinical heterogeneity. This paper illustrates that specific profiles can be obtained for rare syndromes with ID. Our main aim was to study (mal)adaptive functioning in Kleefstra Syndrome (KS) by comparing and contrasting our findings to three other subgroups: Koolen-de Vries Syndrome, GATAD2B-related syndrome, and a mixed control group of individuals with ID. In total, we studied 58 individuals (28 males, 30 females) with ID; 24 were diagnosed with KS, 13 with Koolen-de Vries Syndrome, 6 with the GATAD2B-related syndrome, and 15 individuals with undefined neurodevelopmental disorders. All individuals were examined with a Vineland Adaptive Behavior Scale, mini PAS-ADD interview, and an Autism Diagnostic Observation Schedule to obtain measures of adaptive and maladaptive functioning. Each of the three distinctive genetic disorders showed its own specific profile of adaptive and maladaptive functioning, while being contrasted mutually. However, when data of the subgroups altogether are contrasted to the data of KS, such differences could not be demonstrated. Based on our findings, specific management recommendations were discussed for each of the three syndromes. It is strongly suggested to consider the genetic origin in individuals with congenital neurodevelopmental disorders for individual based psychiatric and behavioral management. © 2017 Wiley Periodicals, Inc.

  7. Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice.

    Science.gov (United States)

    Jakse, Jernej; Telgmann, Alexa; Jung, Christian; Khar, Anil; Melgar, Sergio; Cheung, Foo; Town, Christopher D; Havey, Michael J

    2006-12-01

    The Poales (includes the grasses) and Asparagales [includes onion (Allium cepa L.) and asparagus (Asparagus officinalis L.)] are the two most economically important monocot orders. The Poales are a member of the commelinoid monocots, a group of orders sister to the Asparagales. Comparative genomic analyses have revealed a high degree of synteny among the grasses; however, it is not known if this synteny extends to other major monocot groups such as the Asparagales. Although we previously reported no evidence for synteny at the recombinational level between onion and rice, microsynteny may exist across shorter genomic regions in the grasses and Asparagales. We sequenced nine asparagus BACs to reveal physically linked genic-like sequences and determined their most similar positions in the onion and rice genomes. Four of the asparagus BACs were selected using molecular markers tightly linked to the sex-determining M locus on chromosome 5 of asparagus. These BACs possessed only two putative coding regions and had long tracts of degenerated retroviral elements and transposons. Five asparagus BACs were selected after hybridization of three onion cDNAs that mapped to three different onion chromosomes. Genic-like sequences that were physically linked on the cDNA-selected BACs or genetically linked on the M-linked BACs showed significant similarities (e < -20) to expressed sequences on different rice chromosomes, revealing no evidence for microsynteny between asparagus and rice across these regions. Genic-like sequences that were linked in asparagus were used to identify highly similar (e < -20) expressed sequence tags (ESTs) of onion. These onion ESTs mapped to different onion chromosomes and no relationship was observed between physical or genetic linkages in asparagus and genetic linkages in onion. These results further indicate that synteny among grass genomes does not extend to a sister order in the monocots and that asparagus may not be an appropriate smaller genome

  8. DNA extraction methods for detecting genetically modified foods: A comparative study.

    Science.gov (United States)

    Elsanhoty, Rafaat M; Ramadan, Mohamed Fawzy; Jany, Klaus Dieter

    2011-06-15

    The work presented in this manuscript was achieved to compare six different methods for extracting DNA from raw maize and its derived products. The methods that gave higher yield and quality of DNA were chosen to detect the genetic modification in the samples collected from the Egyptian market. The different methods used were evaluated for extracting DNA from maize kernels (without treatment), maize flour (mechanical treatment), canned maize (sweet corn), frozen maize (sweet corn), maize starch, extruded maize, popcorn, corn flacks, maize snacks, and bread made from corn flour (mechanical and thermal treatments). The quality and quantity of the DNA extracted from the standards, containing known percentages of GMO material and from the different food products were evaluated. For qualitative detection of the GMO varieties in foods, the GMOScreen 35S/NOS test kit was used, to screen the genetic modification in the samples. The positive samples for the 35S promoter and/or the NOS terminator were identified by the standard methods adopted by EU. All of the used methods extracted yielded good DNA quality. However, we noted that the purest DNA extract were obtained using the DNA extraction kit (Roche) and this generally was the best method for extracting DNA from most of the maize-derived foods. We have noted that the yield of DNA extracted from maize-derived foods was generally lower in the processed products. The results indicated that 17 samples were positive for the presence of 35S promoter, while 34% from the samples were positive for the genetically modified maize line Bt-176.

  9. Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords.

    Science.gov (United States)

    Canales-Aguirre, Cristian B; Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Hernández, Cristián E

    2016-01-01

    Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords), but no spatial isolation by distance (IBD) pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf) are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone), and the local geographical configuration (i.e. embayment area, islands, archipelagos). We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA) of continental Chile, which is the Tic-Toc MPA.

  10. Genetic structure, spatial organization, and dispersal in two populations of bat-eared foxes.

    Science.gov (United States)

    Kamler, Jan F; Gray, Melissa M; Oh, Annie; Macdonald, David W

    2013-09-01

    We incorporated radio-telemetry data with genetic analysis of bat-eared foxes (Otocyon megalotis) from individuals in 32 different groups to examine relatedness and spatial organization in two populations in South Africa that differed in density, home-range sizes, and group sizes. Kin clustering occurred only for female dyads in the high-density population. Relatedness was negatively correlated with distance only for female dyads in the high-density population, and for male and mixed-sex dyads in the low-density population. Home-range overlap of neighboring female dyads was significantly greater in the high compared to low-density population, whereas overlap within other dyads was similar between populations. Amount of home-range overlap between neighbors was positively correlated with genetic relatedness for all dyad-site combinations, except for female and male dyads in the low-density population. Foxes from all age and sex classes dispersed, although females (mostly adults) dispersed farther than males. Yearlings dispersed later in the high-density population, and overall exhibited a male-biased dispersal pattern. Our results indicated that genetic structure within populations of bat-eared foxes was sex-biased, and was interrelated to density and group sizes, as well as sex-biases in philopatry and dispersal distances. We conclude that a combination of male-biased dispersal rates, adult dispersals, and sex-biased dispersal distances likely helped to facilitate inbreeding avoidance in this evolutionarily unique species of Canidae.

  11. Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation.

    Science.gov (United States)

    Kuroda, Y; Kaga, A; Tomooka, N; Vaughan, D A

    2006-04-01

    The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size ( 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.

  12. Population genetic structure of Anopheles arabiensis (Diptera: Culicidae) in a rice growing area of central Kenya.

    Science.gov (United States)

    Muturi, Ephantus J; Kim, Chang-Hyun; Baliraine, Frederick N; Musani, Solomon; Jacob, Benjamin; Githure, John; Novak, Robert J

    2010-03-01

    Studies were conducted to examine the population genetic structure of Anopheles arabiensis (Patton) in Mwea Rice Irrigation Scheme and surrounding areas in Central Kenya, under different agricultural systems. This study was motivated by observed differences in malaria transmission indices of An. arabiensis within the scheme compared with adjacent nonirrigated areas. Agricultural practices can modify local microclimate and influence the number and diversity of larval habitats and in so doing may occasion subpopulation differentiation. Thirty samples from each of the three study sites were genotyped at eight microsatellite loci. Seven microsatellite loci showed high polymorphism but revealed no genetic differentiation (FST = 0.006, P = 0.312) and high gene flow (Nm = 29-101) among the three populations. Genetic bottleneck analysis showed no indication of excess heterozygosity in any of the populations. There was high frequency of rare alleles, suggesting that An. arabiensis in the study area has a high potential of responding to selective pressures from environmental changes and vector control efforts. These findings imply that An. arabiensis in the study area occurs as a single, continuous panmictic population with great ability to adapt to human-imposed selective pressures.

  13. Biomimetic self-templating optical structures fabricated by genetically engineered M13 bacteriophage.

    Science.gov (United States)

    Kim, Won-Geun; Song, Hyerin; Kim, Chuntae; Moon, Jong-Sik; Kim, Kyujung; Lee, Seung-Wuk; Oh, Jin-Woo

    2016-11-15

    Here, we describe a highly sensitive and selective surface plasmon resonance sensor system by utilizing self-assembly of genetically engineered M13 bacteriophage. About 2700 copies of genetically expressed peptide copies give superior selectivity and sensitivity to M13 phage-based SPR sensor. Furthermore, the sensitivity of the M13 phage-based SPR sensor was enhanced due to the aligning of receptor matrix in specific direction. Incorporation of specific binding peptide (His Pro Gln: HPQ) gives M13 bacteriophage high selectivity for the streptavidin. Our M13 phage-based SPR sensor takes advantage of simplicity of self-assembly compared with relatively complex photolithography techniques or chemical conjugations. Additionally, designed structure which is composed of functionalized M13 bacteriophage can simultaneously improve the sensitivity and selectivity of SPR sensor evidently. By taking advantages of the genetic engineering and self-assembly, we propose the simple method for fabricating novel M13 phage-based SPR sensor system which has a high sensitivity and high selectivity. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Genetic and lifestyle causal beliefs about obesity and associated diseases among ethnically diverse patients: a structured interview study

    Science.gov (United States)

    Diefenbach, Michael A.; Streicher, Samantha A.; Jabs, Ethylin Wang; Smirnoff, Margaret; Horowitz, Carol R.; Zinberg, Randi; Clesca, Cindy; Richardson, Lynne D.

    2015-01-01

    Background New genetic associations with obesity are rapidly being discovered. People’s causal beliefs about obesity may influence their obesity-related behaviors. Little is known about genetic compared to lifestyle causal beliefs regarding obesity, and obesity-related diseases, among minority populations. This study examined genetic and lifestyle causal beliefs about obesity and three obesity-related diseases among a low-income, ethnically diverse patient sample. Methods Structured interviews were conducted with patients attending an inner-city hospital outpatient clinic. Participants (n=205) were asked how much they agreed that genetics influence risk of obesity, type 2 diabetes, heart disease and cancer. Similar questions were asked regarding lifestyle causal beliefs (overeating, eating certain types of food, chemicals in food, not exercising, smoking). Forty-eight percent of participants were Non-Hispanic Black, 29% Hispanic, and 10% Non-Hispanic White. Results Over two thirds (69%) of participants believed genetics cause obesity ‘some’ or ‘a lot’, compared to 82% for type 2 diabetes, 79% for heart disease, and 75% for cancer. Participants who held genetic causal beliefs about obesity held more lifestyle causal beliefs in total than those who did not hold genetic causal beliefs about obesity (4.4 vs. 3.7 lifestyle causal beliefs respectively, possible range 0 to 5, p=0.025). There were few associations between causal beliefs and socio-demographic characteristics. Conclusions Higher beliefs in genetic causation of obesity and related diseases are not automatically associated with decreased lifestyle beliefs. Future research efforts are needed to determine whether public health messages aimed at reducing obesity and its consequences in racially and ethnically diverse urban communities may benefit from incorporating an acknowledgement of the role of genetics in these conditions. PMID:23235350

  15. Tridimensional Regression for Comparing and Mapping 3D Anatomical Structures

    Directory of Open Access Journals (Sweden)

    Kendra K. Schmid

    2012-01-01

    Full Text Available Shape analysis is useful for a wide variety of disciplines and has many applications. There are many approaches to shape analysis, one of which focuses on the analysis of shapes that are represented by the coordinates of predefined landmarks on the object. This paper discusses Tridimensional Regression, a technique that can be used for mapping images and shapes that are represented by sets of three-dimensional landmark coordinates, for comparing and mapping 3D anatomical structures. The degree of similarity between shapes can be quantified using the tridimensional coefficient of determination (2. An experiment was conducted to evaluate the effectiveness of this technique to correctly match the image of a face with another image of the same face. These results were compared to the 2 values obtained when only two dimensions are used and show that using three dimensions increases the ability to correctly match and discriminate between faces.

  16. Analysis of genetic diversity and population structure of Bellamya quadrata from lakes of middle and lower Yangtze River.

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    Gu, Qianhong; Zhang, Man; Zhou, Chuanjiang; Zhu, Guorong; Dong, Jing; Gao, Yunni; Chen, Jie; Chen, Peng

    2015-10-01

    As an endemic species of freshwater gastropods in China, Bellamya quadrata plays an important role in ecosystem service provision and commercial importance. However, the species is overharvested and its natural habitats are under severe threat due to fragmentation and loss. To estimate the genetic diversity and population structure of B. quadrata, 285 individuals from eight lake populations across middle and lower Yangtze River were sampled. Seven microsatellite loci were genotyped. Our results showed that (i) the genetic diversity of B. quadrata was high in most of the studied populations, yet effective population sizes appear to be rather small in some populations; (ii) low levels of genetic differentiation exists among populations but gene flow was generally high; (iii) no clear geographic or genetic structure was observed in the studied region, implying mechanisms (zoochoric dispersal and anthropogenic translocations) that enhance dispersal and gene flow have promoted population connectivity. However, the comparatively high genetic diversity of B. quadrata could be attributed to a lag phase, suggesting that the genetic diversity of this species may be lost in the future and the priorities for conservation of B. quadrata are necessary.

  17. Genetic structure of avian influenza viruses from ducks of the Atlantic flyway of North America.

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    Yanyan Huang

    Full Text Available Wild birds, including waterfowl such as ducks, are reservoir hosts of influenza A viruses. Despite the increased number of avian influenza virus (AIV genome sequences available, our understanding of AIV genetic structure and transmission through space and time in waterfowl in North America is still limited. In particular, AIVs in ducks of the Atlantic flyway of North America have not been thoroughly investigated. To begin to address this gap, we analyzed 109 AIV genome sequences from ducks in the Atlantic flyway to determine their genetic structure and to document the extent of gene flow in the context of sequences from other locations and other avian and mammalian host groups. The analyses included 25 AIVs from ducks from Newfoundland, Canada, from 2008-2011 and 84 available reference duck AIVs from the Atlantic flyway from 2006-2011. A vast diversity of viral genes and genomes was identified in the 109 viruses. The genetic structure differed amongst the 8 viral segments with predominant single lineages found for the PB2, PB1 and M segments, increased diversity found for the PA, NP and NS segments (2, 3 and 3 lineages, respectively, and the highest diversity found for the HA and NA segments (12 and 9 lineages, respectively. Identification of inter-hemispheric transmissions was rare with only 2% of the genes of Eurasian origin. Virus transmission between ducks and other bird groups was investigated, with 57.3% of the genes having highly similar (≥99% nucleotide identity genes detected in birds other than ducks. Transmission between North American flyways has been frequent and 75.8% of the genes were highly similar to genes found in other North American flyways. However, the duck AIV genes did display spatial distribution bias, which was demonstrated by the different population sizes of specific viral genes in one or two neighbouring flyways compared to more distant flyways.

  18. Genetic variation and structure in the Mediterranean shrubs Myrtus communis and Pistacia lentiscus in different landscape contexts.

    Science.gov (United States)

    Nora, S; Albaladejo, R G; Aparicio, A

    2015-03-01

    Studies concerning different habitat configurations can provide insights into the complex interactions between species' life-history traits and the environment and can help to predict patterns in population genetics. In this study, we compared patterns of genetic variation in two Mediterranean shrub species (Myrtus communis and Pistacia lentiscus) that co-occur in populations within three contrasting landscape contexts: continuous, fragmented-connected and fragmented-isolated populations. Analysing variation at microsatellites loci, our results revealed weak responses to the landscape contexts. We rather found a population-specific response in both study species. However, despite both study species sharing similar levels of genetic diversity, Myrtus displayed higher levels of homozygosity and genetic differentiation among populations, stronger patterns of within-population spatial genetic structure, lower values of mutation-scaled effective population size and stronger evidence for recent genetic bottlenecks than Pistacia. This result highlights the influence of past events (e.g. historical connectivity, fluctuations in population size) and local factors (e.g. microhabitat availability for recruitment, habitat quality, plant density, native fauna) and that the landscape configuration per se (i.e. fragment size and/or isolation) might not completely determine the species' genetic patterns.

  19. 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

  20. Genetic and perinatal determinants of structural brain deficits in schizophrenia.

    Science.gov (United States)

    Cannon, T D; Mednick, S A; Parnas, J

    1989-10-01

    Using a subsample from the Copenhagen schizophrenia high-risk project, we examined the contributions of schizophrenic genetic liability and perinatal complications to computed tomographic (CT) measurements of ventricular enlargement and cortical and cerebellar abnormalities. A factor analysis of six CT measurements yielded two significant factors. One factor reflected multisite neural deficits as evidenced by abnormality of the cerebellar vermis and widening of the sylvian and interhemispheric fissures and cortical sulci. The other factor reflected periventricular damage as evidenced by enlargement of the third and lateral ventricles. Because all of the subjects had schizophrenic mothers, the major source of genetic variation is contributed by the diagnostic status of their fathers. In a stepwise multiple-regression analysis, it was determined that the multisite neural deficits factor was significantly related to genetic risk for schizophrenia (as measured by schizophrenia spectrum illness in the subjects' fathers) but was unrelated to pregnancy or delivery complications or to weight at birth. Periventricular damage was highly and significantly correlated with the number of complications suffered at delivery, but only among subjects with an elevated genetic risk. Although limited by a small sample size, these results suggest that the two types of CT abnormalities in schizophrenia may reflect partially independent processes based on different combinations of genetic and perinatal influences.

  1. Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments.

    Science.gov (United States)

    Bowen, Jennifer L; Weisman, David; Yasuda, Michie; Jayakumar, Amal; Morrison, Hilary G; Ward, Bess B

    2015-08-01

    Denitrification is a critically important biogeochemical pathway that removes fixed nitrogen from ecosystems and thus ultimately controls the rate of primary production in nitrogen-limited systems. We examined the community structure of bacteria containing the nirS gene, a signature gene in the denitrification pathway, from estuarine and salt marsh sediments and from the water column of two of the world's largest marine oxygen-deficient zones (ODZs). We generated over 125,000 nirS gene sequences, revealing a large degree of genetic diversity including 1,815 unique taxa, the vast majority of which formed clades that contain no cultured representatives. These results underscore how little we know about the genetic diversity of metabolisms underlying this critical biogeochemical pathway. Marine sediments yielded 1,776 unique taxa when clustered at 95 % sequence identity, and there was no single nirS denitrifier that was a competitive dominant; different samples had different highly abundant taxa. By contrast, there were only 39 unique taxa identified in samples from the two ODZs, and 99 % of the sequences belonged to 5 or fewer taxa. The ODZ samples were often dominated by nirS sequences that shared a 92 % sequence identity to a nirS found in the anaerobic ammonium-oxidizing (anammox) genus Scalindua. This sequence was abundant in both ODZs, accounting for 38 and 59 % of all sequences, but it was virtually absent in marine sediments. Our data indicate that ODZs are remarkably depauperate in nirS genes compared to the remarkable genetic richness found in coastal sediments.

  2. Improving the structural quality of UML class diagrams with the genetic algorithm

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    Deryugina Olga

    2016-01-01

    Full Text Available The problem of improving the structural quality of UML class diagrams can be formulated as an optimization problem. The Genetic algorithm is concerned to be able to solve such problems. This paper focuses on the ways in which the Genetic algorithm can be applied to the problem of improving structural quality of UML class diagrams. It develops the theme of semantically equivalent transformations of UML class diagrams during the evolutionary search. This paper suggests the structural semantics of the UML class diagrams. It also formulates the problem of improving the structural quality of a UML class diagram during the evolutionary search and proposes a solution of the problem based on the Genetic algorithm. The paper presents the results of the computational experiment aimed at improving of the structural quality of the UML class diagram with the help of the Genetic algorithm and identifies issues for future work.

  3. Genetic structure in dwarf bamboo (Bashania fangiana clonal populations with different genet ages.

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    Qing-qing Ma

    Full Text Available Amplified fragment length polymorphism (AFLP fingerprints were used to reveal genotypic diversity of dwarf bamboo (Bashania fangiana clonal populations with two different genet ages (≤30 years versus >70 years at Wolong National Natural Reserve, Sichuan province, China. We generated AFLP fingerprints for 96 leaf samples, collected at 30 m intervals in the two populations, using ten selective primer pairs. A total of 92 genotypes were identified from the both populations. The mean proportion of distinguishable genotypes (G/N was 0.9583 (0.9375 to 0.9792 and Simpson's index of diversity (D was 0.9982 (0.9973 to 0.9991. So, two B. fangiana populations were multiclonal and highly diverse. The largest single clone may occur over a distance of about 30 m. Our results demonstrated that the genotypic diversity and genet density of B. fangiana clonal population did not change significantly (47 versus 45 with genet aging and low partitioned genetic differentiation was between the two populations (Gst = 0.0571. The analysis of molecular variance consistently showed that a large proportion of the genetic variation (87.79% existed among the individuals within populations, whereas only 12.21% were found among populations. In addition, the high level of genotypic diversity in the two populations implies that the further works were needed to investigate the reasons for the poor seed set in B. fangiana after flowering.

  4. Partial least squares modeling and genetic algorithm optimization in quantitative structure-activity relationships.

    Science.gov (United States)

    Hasegawa, K; Funatsu, K

    2000-01-01

    Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel optimization technique which can be used as a search engine in variable selection. A novel hybrid approach comprising GA and PLS for variable selection developed in our group (GAPLS) is described. The more advanced method for comparative molecular field analysis (CoMFA) modeling called GA-based region selection (GARGS) is described as well. Applications of GAPLS and GARGS to QSAR and 3D-QSAR problems are shown with some representative examples. GA can be hybridized with nonlinear modeling methods such as artificial neural networks (ANN) for providing useful tools in chemometric and QSAR.

  5. Fine-scale population genetic structure of a wildlife disease vector: The southern house mosquito on the island of Hawaii

    Science.gov (United States)

    Keyghobadi, N.; LaPointe, D.; Fleischer, R.C.; Fonseca, D.M.

    2006-01-01

    The southern house mosquito, Culex quinquefasciatus, is a widespread tropical and subtropical disease vector. In the Hawaiian Islands, where it was introduced accidentally almost two centuries ago, it is considered the primary vector of avian malaria and pox. Avian malaria in particular has contributed to the extinction and endangerment of Hawaii's native avifauna, and has altered the altitudinal distribution of native bird populations. We examined the population genetic structure of Cx. quinquefasciatus on the island of Hawaii at a smaller spatial scale than has previously been attempted, with particular emphasis on the effects of elevation on population genetic structure. We found significant genetic differentiation among populations and patterns of isolation by distance within the island. Elevation per se did not have a limiting effect on gene flow; however, there was significantly lower genetic diversity among populations at mid elevations compared to those at low elevations. A recent sample taken from just above the predicted upper altitudinal distribution of Cx. quinquefasciatus on the island of Hawaii was confirmed as being a temporary summer population and appeared to consist of individuals from more than one source population. Our results indicate effects of elevation gradients on genetic structure that are consistent with known effects of elevation on population dynamics of this disease vector. ?? 2006 The Authors.

  6. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  7. Effect of domestication on the genetic diversity and structure of Saccharina japonica populations in China

    Science.gov (United States)

    Zhang, Jie; Wang, Xiuliang; Yao, Jianting; Li, Qiuying; Liu, Fuli; Yotsukura, Norishige; Krupnova, Tatiana N.; Duan, Delin

    2017-01-01

    Saccharina japonica is a commercially and ecologically important seaweed and is an excellent system for understanding the effects of domestication on marine crops. In this study, we used 19 selected simple sequence repeat (SSR) markers to investigate the influence of domestication on the genetic diversity and structure of S. japonica populations. Wild kelp populations exhibited higher genetic diversity than cultivated populations based on total NA, HE, HO, NP and AR. Discriminant analysis of principal components (DAPC), a neighbour-joining (NJ) tree and STRUCTURE analyses indicated that S. japonica populations could be divided into two groups (a cultivated/introduced group and a wild indigenous group) with significant genetic differentiation (P < 0.0001). Divergent selection, continuous inbreeding and inter-specific hybridization have caused the divergence of these two genetically separate gene pools. The significant genetic differentiation between northern and southern cultivated populations appears to be due to inter-specific hybridization and wild germplasm introduction during the domestication process. In addition, the cultivation of S. japonica has not resulted in any serious genetic disturbance of wild introduced S. japonica populations. An understanding of the genetic diversity and genetic structure of domesticated S. japonica will be necessary for further genetic improvement and effective use of germplasm. PMID:28176848

  8. Variation and Genetic Structure in Platanus mexicana (Platanaceae along Riparian Altitudinal Gradient

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    Dulce M. Galván-Hernández

    2015-01-01

    Full Text Available Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian species are scarce. In Mexico, the population of P. mexicana along the Colipa River (Veracruz State grows below its reported minimum altitude range, possibly the lowest where this tree grows. This suggests that altitude might be an important factor in population genetics differentiation. We examined the genetic variation and population structuring at four sites with different altitudes (70, 200, 600 and 1700 m a.s.l. using ten inter-simple sequence repeats (ISSR markers. The highest value for Shannon index and Nei’s gene diversity was obtained at 1700 m a.s.l. (He = 0.27, Ne = 1.47, I = 0.42 and polymorphism reached the top value at the middle altitude (% p = 88.57. Analysis of molecular variance (AMOVA and STRUCTURE analysis indicated intrapopulation genetic differentiation. The arithmetic average (UPGMA dendrogram identified 70 m a.s.l. as the most genetically distant site. The genetic structuring resulted from limited gene flow and genetic drift. This is the first report of genetic variation in populations of P. mexicana in Mexico. This research highlights its importance as a dominant species, and its ecological and evolutionary implications in altitudinal gradients of riparian ecosystems.

  9. FPGA Implementation of Parallel Particle Swarm Optimization Algorithm and Compared with Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    BEN AMEUR Mohamed sadek

    2016-08-01

    Full Text Available In this paper, a digital implementation of Particle Swarm Optimization algorithm (PSO is developed for implementation on Field Programmable Gate Array (FPGA. PSO is a recent intelligent heuristic search method in which the mechanism of algorithm is inspired by the swarming of biological populations. PSO is similar to the Genetic Algorithm (GA. In fact, both of them use a combination of deterministic and probabilistic rules. The experimental results of this algorithm are effective to evaluate the performance of the PSO compared to GA and other PSO algorithm. New digital solutions are available to generate a hardware implementation of PSO Algorithms. Thus, we developed a hardware architecture based on Finite state machine (FSM and implemented into FPGA to solve some dispatch computing problems over other circuits based on swarm intelligence. Moreover, the inherent parallelism of these new hardware solutions with a large computational capacity makes the running time negligible regardless the complexity of the processing.

  10. Monitoring low benzene exposure: comparative evaluation of urinary biomarkers, influence of cigarette smoking, and genetic polymorphisms.

    Science.gov (United States)

    Fustinoni, Silvia; Consonni, Dario; Campo, Laura; Buratti, Marina; Colombi, Antonio; Pesatori, Angela C; Bonzini, Matteo; Bertazzi, Pier A; Foà, Vito; Garte, Seymour; Farmer, Peter B; Levy, Leonard S; Pala, Mauro; Valerio, Federico; Fontana, Vincenzo; Desideri, Arianna; Merlo, Domenico F

    2005-09-01

    Benzene is a human carcinogen and an ubiquitous environmental pollutant. Identification of specific and sensitive biological markers is critical for the definition of exposure to low benzene level and the evaluation of the health risk posed by this exposure. This investigation compared urinary trans,trans-muconic acid (t,t-MA), S-phenylmercapturic acid, and benzene (U-benzene) as biomarkers to assess benzene exposure and evaluated the influence of smoking and the genetic polymorphisms CYP2E1 (RsaI and DraI) and NADPH quinone oxidoreductase-1 on these indices. Gas station attendants, urban policemen, bus drivers, and two groups of controls were studied (415 subjects). Median benzene exposure was 61, 22, 21, 9 and 6 microg/m(3), respectively, with higher levels in workers than in controls. U-benzene, but not t,t-MA and S-phenylmercapturic acid, showed an exposure-related increase. All the biomarkers were strongly influenced by cigarette smoking, with values up to 8-fold higher in smokers compared with nonsmokers. Significant correlations of the biomarkers with each other and with urinary cotinine were found. A possible influence of genetic polymorphism of CYP2E1 (RsaI and/or DraI) on t,t-MA and U-benzene in subjects with a variant allele was found. Multiple linear regression analysis correlated the urinary markers with exposure, smoking status, and CYP2E1 (RsaI; R(2) up to 0.55 for U-benzene). In conclusion, in the range of investigated benzene levels (<478 micro/m(3) or <0.15 ppm), smoking may be regarded as the major source of benzene intake; among the study indices, U-benzene is the marker of choice for biomonitoring low-level occupational and environmental benzene exposure.

  11. Genetic structure in a dynamic baboon hybrid zone corroborates behavioural observations in a hybrid population

    NARCIS (Netherlands)

    Charpentier, M J E; Fontaine, M C; Cherel, E; Renoult, J P; Jenkins, T; Benoit, L; Barthès, N; Alberts, S C; Tung, J

    2012-01-01

    Behaviour and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behaviour of the hybridizing taxa can also impact

  12. Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.

    NARCIS (Netherlands)

    Marle-Koster, van E.; Hefer, C.A.; Nel, L.H.; Groenen, M.A.M.

    2008-01-01

    In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource.

  13. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

    Directory of Open Access Journals (Sweden)

    James W Kijas

    Full Text Available The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

  14. Genetic structure associated with diversity and geographic distribution in the USDA rice world collection

    Science.gov (United States)

    Asian cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, AUS, tropical japonica, temperate japonica and aromatic. Genetic characterization of a global rice collection could help better serve the global research community. Collecting worldwide rice germplasm started in ...

  15. Quantitative genetics of shape in cricket wings: developmental integration in a functional structure.

    Science.gov (United States)

    Klingenberg, Christian Peter; Debat, Vincent; Roff, Derek A

    2010-10-01

    The role of developmental and genetic integration for evolution is contentious. One hypothesis states that integration acts as a constraint on evolution, whereas an alternative is that developmental and genetic systems evolve to match the functional modularity of organisms. This study examined a morphological structure, the cricket wing, where developmental and functional modules are discordant, making it possible to distinguish the two alternatives. Wing shape was characterized with geometric morphometrics, quantitative genetic information was extracted using a full-sibling breeding design, and patterns of developmental integration were inferred from fluctuating asymmetry of wing shape. The patterns of genetic, phenotypic, and developmental integration were clearly similar, but not identical. Heritabilities for different shape variables varied widely, but no shape variables were devoid of genetic variation. Simulated selection for specific shape changes produced predicted responses with marked deflections due to the genetic covariance structure. Three hypotheses of modularity according to the wing structures involved in sound production were inconsistent with the genetic, phenotypic, or developmental covariance structure. Instead, there appears to be strong integration throughout the wing. The hypothesis that genetic and developmental integration evolve to match functional modularity can therefore be rejected for this example.

  16. The effect of a population bottleneck on the evolution of genetic variance/covariance structure.

    Science.gov (United States)

    Jarvis, J P; Cropp, S N; Vaughn, T T; Pletscher, L S; King-Ellison, K; Adams-Hunt, E; Erickson, C; Cheverud, J M

    2011-10-01

    It is well known that standard population genetic theory predicts decreased additive genetic variance (V(a) ) following a population bottleneck and that theoretical models including interallelic and intergenic interactions indicate such loss may be avoided. However, few empirical data from multicellular model systems are available, especially regarding variance/covariance (V/CV) relationships. Here, we compare the V/CV structure of seventeen traits related to body size and composition between control (60 mating pairs/generation) and bottlenecked (2 mating pairs/generation; average F = 0.39) strains of mice. Although results for individual traits vary considerably, multivariate analysis indicates that V(a) in the bottlenecked populations is greater than expected. Traits with patterns and amounts of epistasis predictive of enhanced V(a) also show the largest deviations from additive expectations. Finally, the correlation structure of weekly weights is not significantly different between control and experimental lines but correlations between necropsy traits do differ, especially those involving the heart, kidney and tail length. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  17. Genetic Covariance Structure of Reading, Intelligence and Memory in Children

    NARCIS (Netherlands)

    van Leeuwen, Marieke; van den Berg, Stephanie M.; Peper, Jiska S.; Pol, Hilleke E. Hulshoff; Boomsma, Dorret I.

    2009-01-01

    This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained

  18. Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

    African Journals Online (AJOL)

    Administrator

    between populations in the eastern and the coastal regions with 21.1%, (P < 0.0002) of the total variation attributed to differences ... especially in the highly settled areas. ... to rapidly estimate the patterns and distribution of genetic variation for ... Altitude (m) Region .... application to human mitochondrial DNA restriction data.

  19. Somatic structural rearrangements in genetically engineered mouse mammary tumors

    NARCIS (Netherlands)

    Varela, I.; Klijn, C.N.; Stephens, P.J.; Mudie, L.J.; Stebbings, L.; Galappaththige, D.; Van der Gulden, H.; Schut, E.; Klarenbeek, S.; Campbell, P.J.; Wessels, L.F.A.; Stratton, M.R.; Jonkers, J.; Futreal, P.A.; Adams, D.J.

    2010-01-01

    Background: Here we present the first paired-end sequencing of tumors from genetically engineered mouse models of cancer to determine how faithfully these models recapitulate the landscape of somatic rearrangements found in human tumors. These were models of Trp53-mutated breast cancer, Brca1- and B

  20. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... variation and, hence, restricting the amount of adapted genetic diversity ... the phenotypic diversity of common bean in Uganda. The selection ... The place of collection/origin was also consi- dered in ..... Bean Research and Development Programs at NaCRRI and CIAT .... Evolution 92:1101-1104. Kami JA ...

  1. Genetic structure and domestication history of the grape

    Science.gov (United States)

    The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wi...

  2. The impact of clonality on parasite population genetic structure

    Directory of Open Access Journals (Sweden)

    Prugnolle F.

    2008-09-01

    Full Text Available In this paper, we briefly review the consequences of clonal reproduction on the apportionment of genetic diversity in parasite populations. We distinguish three kinds of parasite life-cycle where clonal reproduction occurs. The consequences of this mode of reproduction for the different kinds of parasite life-cycles are described. We here particularly focus on clonal diploids.

  3. Genetic diversity and population structure of begomoviruses infecting sweet potato

    Science.gov (United States)

    Begomoviruses infecting sweet potatoes (Ipomoea batatas) exhibit high genetic diversity, and approximately eight species including Sweet potato leaf curl virus (SPLCV) have been described from different regions around the world. In this study, the complete genomic sequences of 17 geographically dist...

  4. Genetic Covariance Structure of Reading, Intelligence and Memory in Children

    NARCIS (Netherlands)

    van Leeuwen, Marieke; van den Berg, Stephanie M.; Peper, Jiska S.; Pol, Hilleke E. Hulshoff; Boomsma, Dorret I.

    This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained

  5. Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction

    Directory of Open Access Journals (Sweden)

    Mahmood A. Rashid

    2013-01-01

    Full Text Available Protein structure prediction (PSP is computationally a very challenging problem. The challenge largely comes from the fact that the energy function that needs to be minimised in order to obtain the native structure of a given protein is not clearly known. A high resolution 20×20 energy model could better capture the behaviour of the actual energy function than a low resolution energy model such as hydrophobic polar. However, the fine grained details of the high resolution interaction energy matrix are often not very informative for guiding the search. In contrast, a low resolution energy model could effectively bias the search towards certain promising directions. In this paper, we develop a genetic algorithm that mainly uses a high resolution energy model for protein structure evaluation but uses a low resolution HP energy model in focussing the search towards exploring structures that have hydrophobic cores. We experimentally show that this mixing of energy models leads to significant lower energy structures compared to the state-of-the-art results.

  6. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    Science.gov (United States)

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape

  7. Subpopulation genetic structure of a plant panmictic population of Castanea sequinii as revealed by microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    WANG Ying; KANG Ming; HUANG Hongwen

    2007-01-01

    Castanea squinii Dode,an endemic tree widely distributed in China,plays an important role both in chestnut breeding and forest ecosystem function.The spatial genetic structure within and among populations is an important part of the evolutionary and ecological genetic dynamics of natural populations,and can provide insights into effective conservation of genetic resources.In the present study,the spatial genetic structure of a panmictic natural population of C.sequinii in the Dabie Mountain region was investigated using microsatellite markers.Nine prescreened microsatellite loci generated 29-33 alleles each,and were used for spatial autocorrelation analysis.Based on Moran's I coefficient,a panmictic population of C.sequinii in the Dabie Mountain region was found to be lacking a spatial genetic structure.These results suggest that a high pollen-mediated gene flow among subpopulations counteract genetic drift and/or genetic differentiation and plays an important role in maintaining a random and panmictic population structure in C.sequinii populations.Further,a spatial genetic structure was detected in each subpopulation's scale (0.228 km),with all three subpopulations showing significant fine-scale structure.The genetic variation was found to be nonrandomly distributed within 61 m in each subpopulation (Moran's I positive values).Although Moran's I values varied among the different subpopulations,Moran's I in all the three subpopulations reached the expected values with an increase in distances,suggesting a generally patchy distribution in the subpopulations.The fine-scale structure seems to reflect restricted seed dispersal and microenvironment selection in C.sequinii.These results have important implications for understanding the evolutionary history and ecological process of the natural population of C.sequinii and provide baseline data for formulating a conservation strategy of Castanea species.

  8. Genetic structure from the oldest Jatropha germplasm bank of Brazil and contribution for the genetic improvement

    Directory of Open Access Journals (Sweden)

    DALILHIA N. DOS SANTOS

    Full Text Available ABSTRACT Jatropha is a potential oilseed crop, which requires mitigating factors such as the low genetic variability of the species. The solution runs through the research of Brazilian germplasm. Attention should be given to the germplasm of jatropha the north of Minas Gerais, because this is the oldest national collection and because this region may be a regions of jatropha diversity due to selection pressure arising from environmental adversities. Therefore, the objective of this study was to investigate the genetic diversity of 48 accessions of collection from Empresa de Pesquisa Agropecuária de Minas Gerais (EPAMIG, using SSR and ISSR markers. The results showed low genetic diversity, but some individuals stood out as J. mollissima (48, J. podagrica (47, Mexican accessions (42, 43, 44 and 45 and some national accessions (28, 29, 41 and 46. Therefore, aiming to increase the genetic variability and improve the effectiveness of jatropha breeding programs, it is suggested to explore such as parental accessions to generate commercial hybrids. This fact implies the possibility to support future production of jatropha, since this culture may be an important source of income, especially for small farmers living in semiarid regions of Brazil.

  9. Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

    Directory of Open Access Journals (Sweden)

    Stephen D Bentley

    2007-02-01

    Full Text Available The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an

  10. Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

    Directory of Open Access Journals (Sweden)

    Stephen D Bentley

    2007-02-01

    Full Text Available The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an

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

    Science.gov (United States)

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

    2015-09-25

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

  12. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.

    Science.gov (United States)

    Du, Hongying; Brender, Jeffrey R; Zhang, Jian; Zhang, Yang

    2015-01-01

    Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures.

  13. Contrasting genetic structure of rear edge and continuous range populations of a parasitic butterfly infected by Wolbachia

    Directory of Open Access Journals (Sweden)

    Patricelli Dario

    2013-01-01

    Full Text Available Abstract Background Climatic oscillations are among the long-term factors shaping the molecular features of animals and plants and it is generally supposed that the rear edges (i.e., the low-latitude limits of distribution of any given specialised species situated closer to glacial refugia are vital long-term stores of genetic diversity. In the present study, we compared the genetic structure of several populations of an endangered and obligate myrmecophilous butterfly (Maculinea arion from two distinct and geographically distant parts of its European distribution (i.e., Italy and Poland, which fully represent the ecological and morphological variation occurring across the continent. Results We sequenced the COI mitochondrial DNA gene (the ‘barcoding gene’ and the EF-1α nuclear gene and found substantial genetic differentiation among M. arion Italian populations in both markers. Eleven mtDNA haplotypes were present in Italy. In contrast, almost no mtDNA polymorphisms was found in the Polish M. arion populations, where genetic differentiation at the nuclear gene was low to moderate. Interestingly, the within-population diversity levels in the EF-1α gene observed in Italy and in Poland were comparable. The genetic data did not support any subspecies divisions or any ecological specialisations. All of the populations studied were infected with a single strain of Wolbachia and our screening suggested 100% prevalence of the bacterium. Conclusions Differences in the genetic structure of M. arion observed in Italy and in Poland may be explained by the rear edge theory. Although we were not able to pinpoint any specific evolutionarily significant units, we suggest that the Italian peninsula should be considered as a region of special conservation concern and one that is important for maintaining the genetic diversity of M. arion in Europe. The observed pattern of mtDNA differentiation among the populations could not be explained by an

  14. Within-population genetic structure in beech (Fagus sylvatica L. stands characterized by different disturbance histories: does forest management simplify population substructure?

    Directory of Open Access Journals (Sweden)

    Andrea Piotti

    Full Text Available The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L. plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs. Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot θ ST ranged from 0.025 to 0.124. The proportion of within-population genetic variation due to genetic substructuring (F CluPlot = 0.067 was higher than the differentiation among the 10 plots (F PlotTot = 0.045. Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.

  15. Within-population genetic structure in beech (Fagus sylvatica L.) stands characterized by different disturbance histories: does forest management simplify population substructure?

    Science.gov (United States)

    Piotti, Andrea; Leonardi, Stefano; Heuertz, Myriam; Buiteveld, Joukje; Geburek, Thomas; Gerber, Sophie; Kramer, Koen; Vettori, Cristina; Vendramin, Giovanni Giuseppe

    2013-01-01

    The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L.) plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs). Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot θ ST ranged from 0.025 to 0.124). The proportion of within-population genetic variation due to genetic substructuring (F CluPlot = 0.067) was higher than the differentiation among the 10 plots (F PlotTot = 0.045). Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i) genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii) indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.

  16. Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 complex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.

  17. Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 com-plex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.

  18. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia.

    Science.gov (United States)

    Menegon, Michela; Durand, Patrick; Menard, Didier; Legrand, Eric; Picot, Stéphane; Nour, Bakri; Davidyants, Vladimir; Santi, Flavia; Severini, Carlo

    2014-10-01

    Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed.

  19. Genetic Diversity and Structure of Brazilian Populations of Diatraea saccharalis (Lepidoptera: Crambidae): Implications for Pest Management.

    Science.gov (United States)

    Silva-Brandão, Karina L; Santos, Thiago V; Cônsoli, Fernando L; Omoto, Celso

    2015-02-01

    The sugarcane borer, Diatraea saccharalis (F.), is the main pest of sugarcane in Brazil. Genetic variability and gene flow among 13 Brazilian populations of the species were evaluated based on mitochondrial DNA sequences to estimate the exchange of genetic information within and among populations. We found high genetic structure among sampled localities (ΦST=0.50923), and pairwise genetic distances were significantly correlated to geographic distances. Demographic analysis and genealogical network of mitochondrial sequences indicate population growth and admixture of D. saccharalis populations, events likely related to the sequential expansion of the corn and sugarcane crops in Brazil. The implications of these findings for pest management are discussed.

  20. Public reaction to direct-to-consumer online genetic tests: Comparing attitudes, trust and intentions across commercial and conventional providers.

    Science.gov (United States)

    Critchley, Christine; Nicol, Dianne; Otlowski, Margaret; Chalmers, Don

    2015-08-01

    The success of personalised medicine depends upon the public's embracing genetic tests. Tests that claim to predict an individual's future health can now be accessed via online companies outside of conventional health regulations. This research assessed the extent to which the public embrace direct-to-consumer (DTC) genetic tests relative to those obtained by a conventional medical practitioner (MP). It also examined the reasons for differences across providers using a randomised experimental telephone survey of 1000 Australians. Results suggest that people were significantly less likely to approve of, and order a DTC genetic test administered by a company compared to a MP because they were less trusting of companies' being able to protect their privacy and provide them with access to genetic expertise and counselling. Markets for DTC genetic tests provided by companies would therefore significantly increase if trust in privacy protection and access to expertise are enhanced through regulation.

  1. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    Science.gov (United States)

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pmalaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya. Copyright

  2. Comparison of genetic population structure of the large blue butterflies Maculinea nausithous and M. teleius

    DEFF Research Database (Denmark)

    Figurny-Puchalska, Edyta; Gadeberg, Rebekka M.E.; Boomsma, Jacobus Jan

    2000-01-01

    We investigated the genetic population structure of two rare myrmecophilous lycaenid butterflies, Maculinea nausithous and M. teleius, which often live sympatrically and have similar biology. In Europe, both species occur in highly fragmented populations and are vulnerable to local extinction...

  3. Genetic structure of Leptopilina boulardi populations from different climatic zones of Iran

    NARCIS (Netherlands)

    Seyahooei, M.A.; van Alphen, J.J.M.; Kraaijeveld, K.

    2011-01-01

    Background The genetic structure of populations can be influenced by geographic isolation (including physical distance) and ecology. We examined these effects in Leptopilina boulardi, a parasitoid of Drosophila of African origin and widely distributed over temperate and (sub) tropical climates.

  4. General asymmetric neutral networks and structure design by genetic algorithms: A learning rule for temporal patterns

    Energy Technology Data Exchange (ETDEWEB)

    Bornholdt, S. [Heidelberg Univ., (Germany). Inst., fuer Theoretische Physik; Graudenz, D. [Lawrence Berkeley Lab., CA (United States)

    1993-07-01

    A learning algorithm based on genetic algorithms for asymmetric neural networks with an arbitrary structure is presented. It is suited for the learning of temporal patterns and leads to stable neural networks with feedback.

  5. Genetic structure of the fungal grapevine pathogen Eutypa lata from four continents

    Science.gov (United States)

    The generalist ascomycete fungus Eutypa lata causes Eutypa dieback of grapevine (Vitis vinifera) worldwide. To decipher the cosmopolitan distribution of this fungus, the population genetic structure of 17 geographic samples was investigated from four continental regions (Australia, California, Europ...

  6. Genetic structure of Camellia japonica L. in an old-growth evergreen forest, Tsushima, Japan.

    Science.gov (United States)

    Ueno, S; Tomaru, N; Yoshimaru, H; Manabe, T; Yamamoto, S

    2000-06-01

    The spatial genetic structure of Camellia japonica was investigated, using microsatellite markers, in a 4-ha permanent plot within an old-growth forest. Spatial distribution of individuals was also assessed to obtain an insight into spatial relationships between individuals and alleles. Morisita's index of dispersion showed that 518 C. japonica individuals in the plot were clumped, and Moran's I spatial autocorrelation coefficient revealed weak genetic structure, indicating a low level of allele clustering. Average I correlograms showed that there was stronger genetic structure over short-distance classes. The clumped distribution of individuals and the positive autocorrelation over short-distance classes may result from the limited seed dispersal and microsite heterogeneity of the stand, while the genetic structure may be weakened by overlapping seed shadow and extensive pollen flow, mediated by animal vectors, and the high outcrossing rate found in C. japonica.

  7. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  8. COMPARATIVE DESIGN OF REGULAR STRUCTURED MODIFIED BOOTH MULTIPLIER

    Directory of Open Access Journals (Sweden)

    Ram RackshaTripathi

    2016-04-01

    Full Text Available Multiplication is a crucial function and plays a vital role for practically any DSP system. Several DSP algorithms require different types of multiplications, specifically modified booth multiplication algorithm. In this paper, a simple approach is proposed for generating last partial product row for reducing extra sign (negative bit bit to achieve more regular structure. As compared to the conventional multipliers these proposed modified Booth’s multipliers can achieve improved reduction in area 5.9%, power 3.2%, and delay 0.5% for 8 x 8 multipliers. We can also observe that achievable improvement for 16 x 16 multiplier in area, power, delay are 4.0%, 2.3%, 0.3% respectively. These multipliers are implemented using verilog HDL and synthesized by using synopsis design compiler with an Artisan TSMC 90nm Technology

  9. Microgeographic socio-genetic structure of an African cooperative breeding passerine revealed: integrating behavioural and genetic data.

    Science.gov (United States)

    Ribeiro, A M; Lloyd, P; Feldheim, K A; Bowie, Rauri C K

    2012-02-01

    Dispersal can be motivated by multiple factors including sociality. Dispersal behaviour affects population genetic structure that in turn reinforces social organization. We combined observational information with individual-based genetic data in the Karoo scrub-robin, a facultative cooperatively breeding bird, to understand how social bonds within familial groups affect mating patterns, cause sex asymmetry in dispersal behaviour and ultimately influence the evolution of dispersal. Our results revealed that males and females do not have symmetrical roles in structuring the population. Males are extremely philopatric and tend to delay dispersal until they gain a breeding position within a radius of two territories around the natal site. By contrast, females dispersed over larger distances, as soon as they reach independence. This resulted in male neighbourhoods characterized by high genetic relatedness. The long-distance dispersal strategy of females ensured that Karoo scrub-robins do not pair with relatives thereby compensating for male philopatry caused by cooperation. The observed female-biased strategy seems to be the most prominent mechanism to reduce the risk of inbreeding that characterizes social breeding system. This study demonstrates that tying together ecological data, such as breeding status, determining social relationships with genetic data, such as kinship, provides valuable insights into the proximate causes of dispersal, which are central to any evolutionary interpretation. © 2011 Blackwell Publishing Ltd.

  10. Genetic structure of the Azores Islands: a study using 15 autosomal short tandem repeat loci.

    Science.gov (United States)

    Santos, Cristina; Alvarez, Luis; Aluja, Maria Pilar; Bruges-Armas, Jacome; Lima, Manuela

    2009-12-01

    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes.

  11. 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.

  12. Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam

    Directory of Open Access Journals (Sweden)

    Sergio Tusso

    2016-05-01

    Full Text Available Population outbreaks of the corallivorous crown-of-thorns seastar (COTS, Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1 all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2 Japan, Philippines, GBR and Vanuatu; and (3 Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.

  13. Phenetic and genetic structure of tsetse fly populations (Glossina palpalis palpalis) in southern Ivory Coast.

    Science.gov (United States)

    Kaba, Dramane; Ravel, Sophie; Acapovi-Yao, Geneviève; Solano, Philippe; Allou, Koffi; Bosson-Vanga, Henriette; Gardes, Laetitia; N'Goran, Eliezer Kouakou; Schofield, Christopher John; Koné, Moussa; Dujardin, Jean-Pierre

    2012-07-30

    Sleeping sickness, transmitted by G. p. palpalis, is known to be present in the Ivory Coast. G. p. palpalis has recently been reported to occur in several places within the town of Abidjan, including: (i) the Banco forest, (ii) the Abobo Adjamé University campus and (iii) the zoological park. Could these three places be treated sequentially, as separate tsetse populations, or should they be taken as one area comprising a single, panmictic population? The amount of gene flow between these places provides strategic information for vector control. It was estimated by the use of both microsatellite DNA and morphometric markers. The idea was to assess the interest of the faster and much less expensive morphometric approach in providing relevant information about population structure. Thus, to detect possible lack of insect exchange between these neighbouring areas of Abidjan, we used both genetic (microsatellite DNA) and phenetic (geometric morphometrics) markers on the same specimens.Using these same markers, we also compared these samples with specimens from a more distant area of south Ivory Coast, the region of Aniassué (186 km north from Abidjan). Neither genetic nor phenetic markers detected significant differentiation between the three Abidjan G. p. palpalis samples. Thus, the null hypothesis of a single panmictic population within the city of Abidjan could not be rejected, suggesting the control strategy should not consider them separately. The markers were also in agreement when comparing G. p. palpalis from Abidjan with those of Aniassué, showing significant divergence between the two sites. Both markers suggested that a successful control of tsetse in Abidjan would require the three Abidjan sites to be considered together, either by deploying control measures simultaneously in all three sites, or by a continuous progression of interventions following for instance the "rolling carpet" principle. To compare the geometry of wing venation of tsetse flies is a

  14. Processes affecting genetic structure and conservation: a case study of wild and cultivated Brassica rapa

    DEFF Research Database (Denmark)

    Andersen, Naja Steen; Poulsen, Gert; Andersen, Bente Anni;

    2009-01-01

    a clear distinction of B. rapa and B. napus individuals except for three individuals that seemed to be backcrosses. The backcrossed hybrids descended from two Swedish populations, one wild and one escaped. The overall pattern of genetic variation and structure in B. rapa showed that cultivated and wild B...... cultivar. The study point to that many processes, e.g. spontaneous introgression, naturalisation, breeding and agricultural practise affected the genetic structure of wild and cultivated B. rapa populations....

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

    Science.gov (United States)

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

    2016-01-01

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

  16. Correlation of Klebsiella pneumoniae comparative genetic analyses with virulence profiles in a murine respiratory disease model.

    Directory of Open Access Journals (Sweden)

    Ramy A Fodah

    Full Text Available Klebsiella pneumoniae is a bacterial pathogen of worldwide importance and a significant contributor to multiple disease presentations associated with both nosocomial and community acquired disease. ATCC 43816 is a well-studied K. pneumoniae strain which is capable of causing an acute respiratory disease in surrogate animal models. In this study, we performed sequencing of the ATCC 43816 genome to support future efforts characterizing genetic elements required for disease. Furthermore, we performed comparative genetic analyses to the previously sequenced genomes from NTUH-K2044 and MGH 78578 to gain an understanding of the conservation of known virulence determinants amongst the three strains. We found that ATCC 43816 and NTUH-K2044 both possess the known virulence determinant for yersiniabactin, as well as a Type 4 secretion system (T4SS, CRISPR system, and an acetonin catabolism locus, all absent from MGH 78578. While both NTUH-K2044 and MGH 78578 are clinical isolates, little is known about the disease potential of these strains in cell culture and animal models. Thus, we also performed functional analyses in the murine macrophage cell lines RAW264.7 and J774A.1 and found that MGH 78578 (K52 serotype was internalized at higher levels than ATCC 43816 (K2 and NTUH-K2044 (K1, consistent with previous characterization of the antiphagocytic properties of K1 and K2 serotype capsules. We also examined the three K. pneumoniae strains in a novel BALB/c respiratory disease model and found that ATCC 43816 and NTUH-K2044 are highly virulent (LD50<100 CFU while MGH 78578 is relatively avirulent.

  17. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

    Directory of Open Access Journals (Sweden)

    Yanliang Jiang

    Full Text Available The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

  18. Comparative Transcriptome Analysis Reveals the Genetic Basis of Skin Color Variation in Common Carp

    Science.gov (United States)

    Jiang, Yanliang; Zhang, Songhao; Xu, Jian; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A.; Sun, Xiaowen; Xu, Peng

    2014-01-01

    Background The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied. Methodology/Principal Findings In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains. Conclusions In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values. PMID:25255374

  19. Genetic diversity of Streptococcus suis isolates as determined by comparative genome hybridization

    Directory of Open Access Journals (Sweden)

    Thi Hoa

    2011-07-01

    Full Text Available Abstract Background Streptococcus suis is a zoonotic pathogen that causes infections in young piglets. S. suis is a heterogeneous species. Thirty-three different capsular serotypes have been described, that differ in virulence between as well as within serotypes. Results In this study, the correlation between gene content, serotype, phenotype and virulence among 55 S. suis strains was studied using Comparative Genome Hybridization (CGH. Clustering of CGH data divided S. suis isolates into two clusters, A and B. Cluster A isolates could be discriminated from cluster B isolates based on the protein expression of extracellular factor (EF. Cluster A contained serotype 1 and 2 isolates that were correlated with virulence. Cluster B mainly contained serotype 7 and 9 isolates. Genetic similarity was observed between serotype 7 and serotype 2 isolates that do not express muramidase released protein (MRP and EF (MRP-EF-, suggesting these isolates originated from a common founder. Profiles of 25 putative virulence-associated genes of S. suis were determined among the 55 isolates. Presence of all 25 genes was shown for cluster A isolates, whereas cluster B isolates lacked one or more putative virulence genes. Divergence of S. suis isolates was further studied based on the presence of 39 regions of difference. Conservation of genes was evaluated by the definition of a core genome that contained 78% of all ORFs in P1/7. Conclusions In conclusion, we show that CGH is a valuable method to study distribution of genes or gene clusters among isolates in detail, yielding information on genetic similarity, and virulence traits of S. suis isolates.

  20. Peer Observed Interaction and Structured Evaluation (POISE): a Canadian experience with peer supervision for genetic counselors.

    Science.gov (United States)

    Goldsmith, Claire; Honeywell, Christina; Mettler, Gabrielle

    2011-04-01

    Peer observation, while often used in other professions, has not been formally applied in genetic counseling. The objective of this study was to pilot a method of peer evaluation whereby genetic counselors observed, and were observed by, each other during patient interaction. All of the available genetic counselors participated in both rounds of the pilot study (six in round one, seven in round two). The genetic counselors that observed the session used an observation room. Most participants reported learning a new skill. Sensitivity to, and comfort with, the feedback process improved. We conclude that Peer-Observed Interaction and Structured Evaluation (POISE) provides an opportunity to refresh counseling approaches and develop feedback skills without causing undue team discord. This new approach to peer supervision in genetic counselling offers a live observation approach for genetic counsellor supervision.

  1. Comparing Two Strategies to Model Uncertainties in Structural Dynamics

    Directory of Open Access Journals (Sweden)

    Rubens Sampaio

    2010-01-01

    Full Text Available In the modeling of dynamical systems, uncertainties are present and they must be taken into account to improve the prediction of the models. Some strategies have been used to model uncertainties and the aim of this work is to discuss two of those strategies and to compare them. This will be done using the simplest model possible: a two d.o.f. (degrees of freedom dynamical system. A simple system is used because it is very helpful to assure a better understanding and, consequently, comparison of the strategies. The first strategy (called parametric strategy consists in taking each spring stiffness as uncertain and a random variable is associated to each one of them. The second strategy (called nonparametric strategy is more general and considers the whole stiffness matrix as uncertain, and associates a random matrix to it. In both cases, the probability density functions either of the random parameters or of the random matrix are deduced from the Maximum Entropy Principle using only the available information. With this example, some important results can be discussed, which cannot be assessed when complex structures are used, as it has been done so far in the literature. One important element for the comparison of the two strategies is the analysis of the samples spaces and the how to compare them.

  2. Genetic structure of the carnivorous plant Pinguicula moranensis (Lentibulariaceae) on the transvolcanic Mexican belt.

    Science.gov (United States)

    Alcalá, Raúl E; Domínguez, César A

    2012-06-01

    Most species of Pinguicula present a montane distribution with populations located at high altitudes. In this context, we proposed that populations of Pinguicula species could be genetically differentiated even at a local scale. This study supported that prediction, as a RAPD-based analysis of molecular variance revealed a high degree of genetic structure (Φ (st) = 0.157, P = 0.001) and low gene flow (Nm = 1.0) among four central populations of Pinguicula moranensis in Mexico, with a maximum geographic separation of about 140 km. The four populations also exhibited high levels of genetic diversity (mean Nei's genetic diversity = 0.3716; % polymorphism = 95.45%). The evolutionary implications of the genetic structure found in P. moranensis for other species in the genus are discussed in the context of the naturally fragmented distribution and a set of life history traits shared by most Pinguicula species that could promote geographic isolation and limited gene flow.

  3. Genetic and environmental influences on the longitudinal structure of neuroticism: a trait-state approach.

    Science.gov (United States)

    Laceulle, Odilia M; Ormel, Johan; Aggen, Steven H; Neale, Michael C; Kendler, Kenneth S

    2013-09-01

    In this study, we sought to elucidate both stable and changing factors in the longitudinal structure of neuroticism using a behavioral genetic twin design. We tested whether this structure is best accounted for by a trait-state, a trait-only, or a state-only model. In line with classic views on personality, our results revealed substantial trait and state components. The contributions of genetic and environmental influences on the trait component were nearly equal, whereas environmental influences on the state component were much stronger than genetic influences. Although the overall findings were similar for older and younger twins, genetic influences on the trait component were stronger than environmental influences in younger twins, whereas the opposite was found for older twins. The current findings help to elucidate how the complex interplay between genetic and environmental factors contributes to both stability and change in neuroticism.

  4. Non-structural carbohydrates in woody plants compared among laboratories.

    Science.gov (United States)

    Quentin, Audrey G; Pinkard, Elizabeth A; Ryan, Michael G; Tissue, David T; Baggett, L Scott; Adams, Henry D; Maillard, Pascale; Marchand, Jacqueline; Landhäusser, Simon M; Lacointe, André; Gibon, Yves; Anderegg, William R L; Asao, Shinichi; Atkin, Owen K; Bonhomme, Marc; Claye, Caroline; Chow, Pak S; Clément-Vidal, Anne; Davies, Noel W; Dickman, L Turin; Dumbur, Rita; Ellsworth, David S; Falk, Kristen; Galiano, Lucía; Grünzweig, José M; Hartmann, Henrik; Hoch, Günter; Hood, Sharon; Jones, Joanna E; Koike, Takayoshi; Kuhlmann, Iris; Lloret, Francisco; Maestro, Melchor; Mansfield, Shawn D; Martínez-Vilalta, Jordi; Maucourt, Mickael; McDowell, Nathan G; Moing, Annick; Muller, Bertrand; Nebauer, Sergio G; Niinemets, Ülo; Palacio, Sara; Piper, Frida; Raveh, Eran; Richter, Andreas; Rolland, Gaëlle; Rosas, Teresa; Saint Joanis, Brigitte; Sala, Anna; Smith, Renee A; Sterck, Frank; Stinziano, Joseph R; Tobias, Mari; Unda, Faride; Watanabe, Makoto; Way, Danielle A; Weerasinghe, Lasantha K; Wild, Birgit; Wiley, Erin; Woodruff, David R

    2015-11-01

    Non-structural carbohydrates (NSC) in plant tissue are frequently quantified to make inferences about plant responses to environmental conditions. Laboratories publishing estimates of NSC of woody plants use many different methods to evaluate NSC. We asked whether NSC estimates in the recent literature could be quantitatively compared among studies. We also asked whether any differences among laboratories were related to the extraction and quantification methods used to determine starch and sugar concentrations. These questions were addressed by sending sub-samples collected from five woody plant tissues, which varied in NSC content and chemical composition, to 29 laboratories. Each laboratory analyzed the samples with their laboratory-specific protocols, based on recent publications, to determine concentrations of soluble sugars, starch and their sum, total NSC. Laboratory estimates differed substantially for all samples. For example, estimates for Eucalyptus globulus leaves (EGL) varied from 23 to 116 (mean = 56) mg g(-1) for soluble sugars, 6-533 (mean = 94) mg g(-1) for starch and 53-649 (mean = 153) mg g(-1) for total NSC. Mixed model analysis of variance showed that much of the variability among laboratories was unrelated to the categories we used for extraction and quantification methods (method category R(2) = 0.05-0.12 for soluble sugars, 0.10-0.33 for starch and 0.01-0.09 for total NSC). For EGL, the difference between the highest and lowest least squares means for categories in the mixed model analysis was 33 mg g(-1) for total NSC, compared with the range of laboratory estimates of 596 mg g(-1). Laboratories were reasonably consistent in their ranks of estimates among tissues for starch (r = 0.41-0.91), but less so for total NSC (r = 0.45-0.84) and soluble sugars (r = 0.11-0.83). Our results show that NSC estimates for woody plant tissues cannot be compared among laboratories. The relative changes in NSC between treatments measured within a laboratory

  5. The impact of selection on population genetic structure in the clam Meretrix petechialis revealed by microsatellite markers.

    Science.gov (United States)

    Lu, Xia; Wang, Hongxia; Li, Yan; Liu, Baozhong

    2016-02-01

    The aim of our work is to evaluate the impact of mass selection on genetic structure in artificially closed populations of the clam Meretrix petechialis. In the present study, we performed mass selection over four generations (from 2004 to 2010) on two clam populations [shell features of purple lines (SP) and black dots (SB)] and analyzed their temporal genetic variation and structure using microsatellite makers. The two closed populations originated from the natural Shandong population (SD); thus, a natural SD population (10SD) was used to detect the current genetic structure after 6 years of natural selection. The results showed that the genetic diversity of the four generations of SB and SP was gradually reduced but remained at relatively high levels (SB, A = 18.9.4-16.8, Ho = 0.7389-0.6971, and He = 0.8897-0.8591; SP, A = 20.0-17.8, Ho = 0.7512-0.7043, and He = 0.8938-0.8625), which has not been reduced compared with that of the 10SD population (A = 17.8, Ho = 0.6803, and He = 0.8302). The Ne estimates for the two populations were almost at the same levels as the actual numbers of parental individuals. In addition, a low inbreeding coefficient was detected in the two populations (SB, 0.00201-0.00639; SP, 0.00176-0.00541). Based on the results, the present mass selection has not made a large impact on the population genetic structure of the closed populations. The present investigation provides important information for the development of management strategies for genetic breeding of the clam.

  6. Aphid–parasitoid community structure on genetically modified wheat

    OpenAIRE

    2011-01-01

    Since the introduction of genetically modified (GM) plants, one of the main concerns has been their potential effect on non-target insects. Many studies have looked at GM plant effects on single non-target herbivore species or on simple herbivore–natural enemy food chains. Agro-ecosystems, however, are characterized by numerous insect species which are involved in complex interactions, forming food webs. In this study, we looked at transgenic disease-resistant wheat (Triticum aestivum) and it...

  7. Demography and genetic structure of a recovering grizzly bear population

    Science.gov (United States)

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  8. Population genetic structure of a three-host tick, Amblyomma dissimile, in eastern Venezuela.

    Science.gov (United States)

    Lampo, M; Rangel, Y; Mata, A

    1998-12-01

    Patterns of genetic variation for the tick Amblyomma dissimile were analyzed from a total of 200 ticks collected on 12 toads (Bufo marinus), 14 snakes (Boa constrictor), and 8 lizards (Iguana iguana) at 11 localities. The analyses were performed on electrophoretic data from 8 isozyme loci. Mean heterozygosity per locus was 6% (+/-3.1) per population. Differences in allelic frequencies among ticks from different individual hosts were the major source of genetic variability in this study. Host species was a smaller source of genetic variation. Genetic distances between localities varied according to which host species was present in each locality, and these appeared to be related to the extent of habitat overlap between host species. The smallest genetic distances between samples from different host species were recorded for I. iguana and B. constrictor. In contrast, the genetic distances between tick samples from B. marinus and either of the reptile species were significantly larger than between tick samples from this amphibian species. Ecological variables or the geographic distance did not explain the local patterns of differentiation observed in A. dissimile. Major genetic differences between island and mainland sites (0.03702) suggested an association between genetic distances and geographic isolation. The consistency between patterns of genetic variation and those of host home range overlap suggests that host dispersion is the main force structuring the genetic variation within this tick species.

  9. Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences.

    Science.gov (United States)

    Zhang, D; Ding, Ge; Ge, B; Zhang, H; Tang, B

    2012-12-01

    Genetic diversity, population genetic structure and molecular phylogeographic pattern of mantis shrimp Oratosquilla oratoria in Bohai Sea and South China Sea were analyzed by mitochondrial DNA sequences. Nucleotide and haplotype diversities were 0.00409-0.00669 and 0.894-0.953 respectively. Neighbor-Joining phylogenetic tree clustered two distinct lineages. Both phylogenetic tree and median-joining network showed the consistent genetic structure corresponding to geographical distribution. Mismatch distributions, negative neutral test and "star-like" network supported a sudden population expansion event. And the time was estimated about 44000 and 50000 years ago.

  10. 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

    geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels...... of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic...

  11. Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer.

    Science.gov (United States)

    Sunday, J M; Popovic, I; Palen, W J; Foreman, M G G; Hart, M W

    2014-10-01

    Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50 km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks. © 2014 John Wiley & Sons Ltd.

  12. Predicting brain structure in population-based samples with biologically informed genetic scores for schizophrenia.

    Science.gov (United States)

    Van der Auwera, Sandra; Wittfeld, Katharina; Shumskaya, Elena; Bralten, Janita; Zwiers, Marcel P; Onnink, A Marten H; Usberti, Niccolo; Hertel, Johannes; Völzke, Henry; Völker, Uwe; Hosten, Norbert; Franke, Barbara; Grabe, Hans J

    2017-04-01

    Schizophrenia is associated with brain structural abnormalities including gray and white matter volume reductions. Whether these alterations are caused by genetic risk variants for schizophrenia is unclear. Previous attempts to detect associations between polygenic factors for schizophrenia and structural brain phenotypes in healthy subjects have been negative or remain non-replicated. In this study, we used genetic risk scores that were based on the accumulated effect of selected risk variants for schizophrenia belonging to specific biological systems like synaptic function, neurodevelopment, calcium signaling, and glutamatergic neurotransmission. We hypothesized that this "biologically informed" approach would provide the missing link between genetic risk for schizophrenia and brain structural phenotypes. We applied whole-brain voxel-based morphometry (VBM) analyses in two population-based target samples and subsequent regions of interest (ROIs) analyses in an independent replication sample (total N = 2725). No consistent association between the genetic scores and brain volumes were observed in the investigated samples. These results suggest that in healthy subjects with a higher genetic risk for schizophrenia additional factors apart from common genetic variants (e.g., infection, trauma, rare genetic variants, or gene-gene interactions) are required to induce structural abnormalities of the brain. Further studies are recommended to test for possible gene-gene or gene-environment effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

    Science.gov (United States)

    Odong, T L; van Heerwaarden, J; Jansen, J; van Hintum, T J L; van Eeuwijk, F A

    2011-07-01

    Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.

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

    Science.gov (United States)

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

    2008-01-01

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

  15. Agroecosystems shape population genetic structure of the greenhouse whitefly in Northern and Southern Europe.

    Science.gov (United States)

    Ovčarenko, Irina; Kapantaidaki, Despoina Evripidis; Lindström, Leena; Gauthier, Nathalie; Tsagkarakou, Anastasia; Knott, Karelyn Emily; Vänninen, Irene

    2014-07-29

    To predict further invasions of pests it is important to understand what factors contribute to the genetic structure of their populations. Cosmopolitan pest species are ideal for studying how different agroecosystems affect population genetic structure within a species at different climatic extremes. We undertook the first population genetic study of the greenhouse whitefly (Trialeurodes vaporariorum), a cosmopolitan invasive herbivore, and examined the genetic structure of this species in Northern and Southern Europe. In Finland, cold temperatures limit whiteflies to greenhouses and prevent them from overwintering in nature, and in Greece, milder temperatures allow whiteflies to inhabit both fields and greenhouses year round, providing a greater potential for connectivity among populations. Using nine microsatellite markers, we genotyped 1274 T. vaporariorum females collected from 18 greenhouses in Finland and eight greenhouses as well as eight fields in Greece. Populations from Finland were less diverse than those from Greece, suggesting that Greek populations are larger and subjected to fewer bottlenecks. Moreover, there was significant population genetic structure in both countries that was explained by different factors. Habitat (field vs. greenhouse) together with longitude explained genetic structure in Greece, whereas in Finland, genetic structure was explained by host plant species. Furthermore, there was no temporal genetic structure among populations in Finland, suggesting that year-round populations are able to persist in greenhouses. Taken together our results show that greenhouse agroecosystems can limit gene flow among populations in both climate zones. Fragmented populations in greenhouses could allow for efficient pest management. However, pest persistence in both climate zones, coupled with increasing opportunities for naturalization in temperate latitudes due to climate change, highlight challenges for the management of cosmopolitan pests in

  16. Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; O'Sullivan, Donal; Brown, Anthony H D; Papa, Roberto; Attene, Giovanna

    2012-06-01

    Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F(ST) = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13% of locus pairs, with P landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.

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

    Data.gov (United States)

    U.S. Environmental Protection Agency — Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus...

  18. Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion.

    Science.gov (United States)

    Hoban, Sean; Arntzen, Jan A; Bruford, Michael W; Godoy, José A; Rus Hoelzel, A; Segelbacher, Gernot; Vilà, Carles; Bertorelle, Giorgio

    2014-11-01

    Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

  19. Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India.

    Science.gov (United States)

    Choudhury, Baharul; Khan, Mohamed Latif; Dayanandan, Selvadurai

    2013-12-01

    The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the

  20. The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis.

    Science.gov (United States)

    Rodríguez-Ramilo, Silvia T; Wang, Jinliang

    2012-09-01

    The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Under this assumption, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.

  1. Genetic structure of the paternal lineage of the Roma people.

    Science.gov (United States)

    Pamjav, Horolma; Zalán, Andrea; Béres, Judit; Nagy, Melinda; Chang, Yuet Meng

    2011-05-01

    According to written sources, Roma (Romanies, Gypsies) arrived in the Balkans around 1,000 years ago from India and have subsequently spread through several parts of Europe. Genetic data, particularly from the Y chromosome, have supported this model, and can potentially refine it. We now provide an analysis of Y-chromosomal markers from five Roma and two non-Roma populations (N = 787) in order to investigate the genetic relatedness of the Roma population groups to one another, and to gain further understanding of their likely Indian origins, the genetic contribution of non-Roma males to the Roma populations, and the early history of their splits and migrations in Europe. The two main sources of the Roma paternal gene pool were identified as South Asian and European. The reduced diversity and expansion of H1a-M82 lineages in all Roma groups imply shared descent from a single paternal ancestor in the Indian subcontinent. The Roma paternal gene pool also contains a specific subset of E1b1b1a-M78 and J2a2-M67 lineages, implying admixture during early settlement in the Balkans and the subsequent influx into the Carpathian Basin. Additional admixture, evident in the low and moderate frequencies of typical European haplogroups I1-M253, I2a-P37.2, I2b-M223, R1b1-P25, and R1a1-M198, has occurred in a more population-specific manner.

  2. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation.

    Science.gov (United States)

    Singh, Pradeep; Nag, Akshay; Parmar, Rajni; Ghosh, Sneha; Bhau, Brijmohan Singh; Sharma, Ram Kumar

    2015-12-01

    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. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (Nm: 3.37), low genetic differentiation (FST: 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  3. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation

    Indian Academy of Sciences (India)

    Pradeep Singh; Akshay Nag; Rajni Parmar; Sneha Ghosh; Brijmohan Singh Bhau; Ram Kumar Sharma

    2015-12-01

    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. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (m : 3.37), low genetic differentiation (ST : 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  4. The subtle role of climate change on population genetic structure in Canada lynx.

    Science.gov (United States)

    Row, Jeffrey R; Wilson, Paul J; Gomez, Celine; Koen, Erin L; Bowman, Jeff; Thornton, Daniel; Murray, Dennis L

    2014-07-01

    Anthropogenically driven climatic change is expected to reshape global patterns of species distribution and abundance. Given recent links between genetic variation and environmental patterns, climate change may similarly impact genetic population structure, but we lack information on the spatial and mechanistic underpinnings of genetic-climate associations. Here, we show that current genetic variability of Canada lynx (Lynx canadensis) is strongly correlated with a winter climate gradient (i.e. increasing snow depth and winter precipitation from west-to-east) across the Pacific-North American (PNO) to North Atlantic Oscillation (NAO) climatic systems. This relationship was stronger than isolation by distance and not explained by landscape variables or changes in abundance. Thus, these patterns suggest that individuals restricted dispersal across the climate boundary, likely in the absence of changes in habitat quality. We propose habitat imprinting on snow conditions as one possible explanation for this unusual phenomenon. Coupling historical climate data with future projections, we also found increasingly diverging snow conditions between the two climate systems. Based on genetic simulations using projected climate data (2041-2070), we predicted that this divergence could lead to a threefold increase in genetic differentiation, potentially leading to isolated east-west populations of lynx in North America. Our results imply that subtle genetic structure can be governed by current climate and that substantive genetic differentiation and related ecological divergence may arise from changing climate patterns. © 2014 John Wiley & Sons Ltd.

  5. Temporal analysis of genetic structure to assess population dynamics of reintroduced swift foxes.

    Science.gov (United States)

    Cullingham, Catherine I; Moehrenschlager, Axel

    2013-12-01

    Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos.

  6. Comparing Entrepreneurship Intention: A Multigroup Structural Equation Modeling Approach

    Directory of Open Access Journals (Sweden)

    Sabrina O. Sihombing

    2012-04-01

    Full Text Available Unemployment is one of the main social and economic problems that many countries face nowadays. One strategic way to overcome this problem is by fostering entrepreneurship spirit especially for unem-ployment graduates. Entrepreneurship is becoming an alternative Job for students after they graduate. This is because entrepreneurship of fers major benefits, such as setting up one’s own business and the pos sibility of having significant financial rewards than working for others. Entrepreneurship is then offered by many universities. This research applies the theory of planned behavior (TPB by incorporating attitude toward success as an antecedent variable of the attitude to examine students’ intention to become an entrepreneur. The objective of this research is to compare entrepreneurship intention between business students and non-business students. A self-administered questionnaire was used to collect data for this study. Questionnaires were distributed to respondents by applying the drop-off/pick-up method. A number of 294 by questionnaires were used in the analysis. Data were analyzed by using structural equation modeling. Two out of four hypotheses were confirmed. These hypotheses are the relationship between the attitude toward becoming an entrepreneur and the intention to try becoming an entrepreneur, and the relationship perceived behavioral control and intention to try becoming an entrepreneur. This paper also provides a discussion and offers directions for future research.

  7. The structure of risk perception. A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Martinez-Arias, R. [Universidad Complutense, Madrid (Spain); Prades, A. [Ciemat, Madrid (Spain); Arranz, L. [Hospital Ramon y Cajal, Madrid (Spain); Macias, M.T. [CSIC, Madrid (Spain)

    2000-05-01

    Research by cognitive and social psychologists has demonstrated that when lay persons make estimates of risks they do not merely calculate in terms of probabilistic information. People tend to construe the risk in accordance with other schemata. The Psychometric Paradigm (Slovic et. al., 1980), found out two main dimensions in the perception of risk: the Dread and the Familiarity-Voluntariness factors. This paper presents some of the key findings of a comparative Latin-American study on radiological risk perception in the health area. The main objective is to check whether or not the Dread and the Familiarity-Voluntariness dimensions explain the perception of risk in this specific context. A questionnaire was distributed to outpatient samples from ten countries: Argentine, Brazil, Colombia, Cuba, Ecuador, Mexico, Panama, Peru, Uruguay, and Spain, thanks to the collaboration of the different National Radioprotection Societies of the above mentioned countries, and of other concerned professionals (in case they didn't have any association at the time). A list of 22 risks, including both radiological and non-radiological ones, were evaluated on two rating scales: possibility and seriousness. Factor analysis, both exploratory and confirmatory, as well as Multidimensional Scaling will be used for the data analysis. The paper will discuss the main cross-cultural differences with regard to the structure of risk perception. The peculiarities of the health related risks will be emphasised. (author)

  8. Comparing Entrepreneurship Intention: A Multigroup Structural Equation Modeling Approach

    Directory of Open Access Journals (Sweden)

    Sabrina O. Sihombing

    2012-04-01

    Full Text Available Unemployment is one of the main social and economic problems that many countries face nowadays. One strategic way to overcome this problem is by fostering entrepreneurship spirit especially for unem ployment graduates. Entrepreneurship is becoming an alternative Job for students after they graduate. This is because entrepreneurship of-fers major benefits, such as setting up one’s own business and the pos-sibility of having significant financial rewards than working for others. Entrepreneurship is then offered by many universities. This research applies the theory of planned behavior (TPB by incorporating attitude toward success as an antecedent variable of the attitude to examine students’ intention to become an entrepreneur. The objective of this research is to compare entrepreneurship intention between business students and non-business students. A self-administered questionnaire was used to collect data for this study. Questionnaires were distributed to respondents by applying the drop-off/pick-up method. A number of 294 by questionnaires were used in the analysis. Data were analyzed by using structural equation modeling. Two out of four hypotheses were confirmed. These hypotheses are the relationship between the attitude toward becoming an entrepreneur and the intention to try becoming an entrepreneur, and the relationship perceived behavioral control and intention to try becoming an entrepreneur. This paper also provides a discussion and offers directions for future research.

  9. Population Genetic Structure of the Magnificent Frigatebird Fregata magnificens (Aves, Suliformes) Breeding Colonies in the Western Atlantic Ocean.

    Science.gov (United States)

    Nuss, Andressa; Carlos, Caio J; Moreno, Ignacio B; Fagundes, Nelson J R

    2016-01-01

    The Magnificent Frigatebird Fregata magnificens has a pantropical distribution, nesting on islands along the Atlantic and Pacific coasts. In the Caribbean, there is little genetic structure among colonies; however, the genetic structure among the colonies off Brazil and its relationship with those in the Caribbean are unknown. In this study, we used mtDNA and microsatellite markers to infer population structure and evolutionary history in a sample of F. magnificens individuals collected in Brazil, Grand Connétable (French Guyana), and Barbuda. Virtually all Brazilian individuals had the same mtDNA haplotype. There was no haplotype sharing between Brazil and the Caribbean, though Grand Connétable shared haplotypes with both regions. A Bayesian clustering analysis using microsatellite data found two genetic clusters: one associated with Barbuda and the other with the Brazilian populations. Grand Connétable was more similar to Barbuda but had ancestry from both clusters, corroborating its "intermediate" position. The Caribbean and Grand Connétable populations showed higher genetic diversity and effective population size compared to the Brazilian population. Overall, our results are in good agreement with an effect of marine winds in isolating the Brazilian meta-population.

  10. Comparative evaluation of genetic assays to identify oral pre-cancerous fields

    NARCIS (Netherlands)

    Bremmer, J.F.; Braakhuis, B.J.; Brink, A.; Broeckaert, M.A.; Beliën, J.A.M.; Meijer, G.A.; Kuik, D.J.; Leemans, C.R.; Bloemena, E.; van der Waal, I.; Brakenhoff, R.H.

    2008-01-01

    Background: Oral squamous cell carcinomas often develop in a pre-cancerous field, defined as mucosal epithelium with cancer-related genetic alterations, and which may appear as a clinically visible lesion. The test characteristics of three genetic assays that were developed to detect pre-cancerous f

  11. Genetic Determinism in School Textbooks: A Comparative Study Conducted among Sixteen Countries

    Science.gov (United States)

    Castera, Jeremy; Clement, Pierre; Abrougui, Mondher; Nisiforou, Olympia; Valanides, Nicos; Turcinaviciene, Jurga; Sarapuu, Tago; Agorram, Boujemaa; Calado, Florbela; Bogner, Franz; Carvalho, Graca

    2008-01-01

    Genetic concepts have significantly evolved over the last ten years, and are now less connected to innate ideas and reductionism. Unique reference to genetic determinism has been replaced by the interaction between the genes and their environment (epigenetics). Our analyses relate to how current school biology textbooks present this new paradigm…

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

    Science.gov (United States)

    Sloan, Chantel D; Andrew, Angeline D; Duell, Eric J; Williams, Scott M; K