Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

Science.gov (United States)

Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

2015-01-01

Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

Solution to urn models of pairwise interaction with application to social, physical, and biological sciences

Science.gov (United States)

Pickering, William; Lim, Chjan

2017-07-01

We investigate a family of urn models that correspond to one-dimensional random walks with quadratic transition probabilities that have highly diverse applications. Well-known instances of these two-urn models are the Ehrenfest model of molecular diffusion, the voter model of social influence, and the Moran model of population genetics. We also provide a generating function method for diagonalizing the corresponding transition matrix that is valid if and only if the underlying mean density satisfies a linear differential equation and express the eigenvector components as terms of ordinary hypergeometric functions. The nature of the models lead to a natural extension to interaction between agents in a general network topology. We analyze the dynamics on uncorrelated heterogeneous degree sequence networks and relate the convergence times to the moments of the degree sequences for various pairwise interaction mechanisms.

Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa

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Mobegi Victor A

2012-07-01

Full Text Available Abstract Background Malaria parasite population genetic structure varies among areas of differing endemicity, but this has not been systematically studied across Plasmodium falciparum populations in Africa where most infections occur. Methods Ten polymorphic P. falciparum microsatellite loci were genotyped in 268 infections from eight locations in four West African countries (Republic of Guinea, Guinea Bissau, The Gambia and Senegal, spanning a highly endemic forested region in the south to a low endemic Sahelian region in the north. Analysis was performed on proportions of mixed genotype infections, genotypic diversity among isolates, multilocus standardized index of association, and inter-population differentiation. Results Each location had similar levels of pairwise genotypic diversity among isolates, although there were many more mixed parasite genotype infections in the south. Apart from a few isolates that were virtually identical, the multilocus index of association was not significant in any population. Genetic differentiation between populations was low (most pairwise FST values  Conclusions Although proportions of mixed genotype infections varied with endemicity as expected, population genetic structure was similar across the diverse sites. Very substantial reduction in transmission would be needed to cause fragmented or epidemic sub-structure in this region.

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

OpenAIRE

Liu, Jian-Bin; Wang, Fan; Lang, Xia; Zha, Xi; Sun, Xiao-Ping; Yue, Yao-Jing; Feng, Rui-Lin; Yang, Bo-Hui; Guo, Jian

2013-01-01

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism i...

Scale-dependent effects of a heterogeneous landscape on genetic differentiation in the Central American squirrel monkey (Saimiri oerstedii.

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Mary E Blair

Full Text Available Landscape genetic studies offer a fine-scale understanding of how habitat heterogeneity influences population genetic structure. We examined population genetic structure and conducted a landscape genetic analysis for the endangered Central American Squirrel Monkey (Saimiri oerstedii that lives in the fragmented, human-modified habitats of the Central Pacific region of Costa Rica. We analyzed non-invasively collected fecal samples from 244 individuals from 14 groups for 16 microsatellite markers. We found two geographically separate genetic clusters in the Central Pacific region with evidence of recent gene flow among them. We also found significant differentiation among groups of S. o. citrinellus using pairwise F(ST comparisons. These groups are in fragments of secondary forest separated by unsuitable "matrix" habitats such as cattle pasture, commercial African oil palm plantations, and human residential areas. We used an individual-based landscape genetic approach to measure spatial patterns of genetic variance while taking into account landscape heterogeneity. We found that large, commercial oil palm plantations represent moderate barriers to gene flow between populations, but cattle pastures, rivers, and residential areas do not. However, the influence of oil palm plantations on genetic variance was diminished when we restricted analyses to within population pairs, suggesting that their effect is scale-dependent and manifests during longer dispersal events among populations. We show that when landscape genetic methods are applied rigorously and at the right scale, they are sensitive enough to track population processes even in species with long, overlapping generations such as primates. Thus landscape genetic approaches are extremely valuable for the conservation management of a diverse array of endangered species in heterogeneous, human-modified habitats. Our results also stress the importance of explicitly considering the heterogeneity of

Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

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C. MAGGI

2015-09-01

Full Text Available Parastichopus regalis (Cuvier, 1817 is the most expensive seafood product on the catalonian market (NE Spain, with prices around 130 €/Kg (fresh weight. Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia. We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST, AMOVA and correspondence analysis (CA based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1 an accurate assessment of the stocks status along the Spanish coasts; 2 the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3 the founding of protected areas (i.e. not take zones to conserve healthy populations and favour the recruitment on the nearby areas.

Pareto optimal pairwise sequence alignment.

Science.gov (United States)

DeRonne, Kevin W; Karypis, George

2013-01-01

Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

Three genetically divergent lineages of the Oryx in eastern Africa: Evidence for an ancient introgressive hybridization

DEFF Research Database (Denmark)

Masembe, Charles; Muwanika, Vincent B.; Nyakaana, Silvester

2006-01-01

Phylogeographic and population genetic studies using sequence information are frequently used to infer species boundaries and history; and to assess hybridization and population level processes. In this study, partial mitochondrial DNA (mtDNA) control region (423 bp) and cytochrome b sequences (666...... bp) of Oryx beisa sampled from five isolated localities in its entire current range in Africa were analyzed to investigate the extent of genetic variation and differentiation between populations. We observed high nucleotide diversity at the control region in the total sample (6.3%) but within...... populations, it varied considerably ranging from 1.6% to 8.1%. Population pairwise genetic differentiation was generally significantly high (ranging from F ST¿=¿0.15, P

Metabolic network prediction through pairwise rational kernels.

Science.gov (United States)

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy

Pseudo inputs for pairwise learning with Gaussian processes

DEFF Research Database (Denmark)

Nielsen, Jens Brehm; Jensen, Bjørn Sand; Larsen, Jan

2012-01-01

We consider learning and prediction of pairwise comparisons between instances. The problem is motivated from a perceptual view point, where pairwise comparisons serve as an effective and extensively used paradigm. A state-of-the-art method for modeling pairwise data in high dimensional domains...... is based on a classical pairwise probit likelihood imposed with a Gaussian process prior. While extremely flexible, this non-parametric method struggles with an inconvenient O(n3) scaling in terms of the n input instances which limits the method only to smaller problems. To overcome this, we derive...... to other similar approximations that have been applied in standard Gaussian process regression and classification problems such as FI(T)C and PI(T)C....

Genetic population structure of muskellunge in the Great Lakes

Science.gov (United States)

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

2013-01-01

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

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

Science.gov (United States)

Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

2017-12-15

Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

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Monika Sharma

Full Text Available The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA. Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes. Further the nucleotide sequences (retrieved from GenBank for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia, indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

Elevation, Not Deforestation, Promotes Genetic Differentiation in a Pioneer Tropical Tree.

Science.gov (United States)

Castilla, Antonio R; Pope, Nathaniel; Jaffé, Rodolfo; Jha, Shalene

2016-01-01

The regeneration of disturbed forest is an essential part of tropical forest ecology, both with respect to natural disturbance regimes and large-scale human-mediated logging, grazing, and agriculture. Pioneer tree species are critical for facilitating the transition from deforested land to secondary forest because they stabilize terrain and enhance connectivity between forest fragments by increasing matrix permeability and initiating disperser community assembly. Despite the ecological importance of early successional species, little is known about their ability to maintain gene flow across deforested landscapes. Utilizing highly polymorphic microsatellite markers, we examined patterns of genetic diversity and differentiation for the pioneer understory tree Miconia affinis across the Isthmus of Panama. Furthermore, we investigated the impact of geographic distance, forest cover, and elevation on genetic differentiation among populations using circuit theory and regression modeling within a landscape genetics framework. We report marked differences in historical and contemporary migration rates and moderately high levels of genetic differentiation in M. affinis populations across the Isthmus of Panama. Genetic differentiation increased significantly with elevation and geographic distance among populations; however, we did not find that forest cover enhanced or reduced genetic differentiation in the study region. Overall, our results reveal strong dispersal for M. affinis across human-altered landscapes, highlighting the potential use of this species for reforestation in tropical regions. Additionally, this study demonstrates the importance of considering topography when designing programs aimed at conserving genetic diversity within degraded tropical landscapes.

Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog (Rana temporaria?

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Patrick P. Lenhardt

2017-07-01

Full Text Available Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity on the genetic population structure of amphibians in agricultural landscapes. We investigated the effects of viniculture on the genetic differentiation of European common frog (Rana temporaria populations in Southern Palatinate (Germany. We analyzed microsatellite data of ten loci from ten breeding pond populations located within viniculture landscape and in the adjacent forest block and compared these results with a previously developed landscape permeability model. We tested for significant correlation of genetic population differentiation and landscape elements, including land use as well as roads and their associated traffic intensity, to explain the genetic structure in the study area. Genetic differentiation among forest populations was significantly lower (median pairwise FST = 0.0041 at 5.39 km to 0.0159 at 9.40 km distance than between viniculture populations (median pairwise FST = 0.0215 at 2.34 km to 0.0987 at 2.39 km distance. Our analyses rejected isolation by distance based on roads and associated traffic intensity as the sole explanation of the genetic differentiation and suggest that the viniculture landscape has to be considered as a limiting barrier for R. temporaria migration, partially confirming the isolation of breeding ponds predicted by the landscape permeability model. Therefore, arable land may act as a sink habitat

Founder effects and genetic population structure of brown trout (Salmo trutta) in a Danish river system

DEFF Research Database (Denmark)

Hansen, Michael Møller; Mensberg, Karen-Lise Dons

1996-01-01

The influence of founder effects on the genetic population structure of brown trout (Salmo trutta) was studied in a small Danish river system. Samples of trout from seven locations were analysed by allozyme electrophoresis and mitochondrial DNA restriction fragment length polymorphism analysis....... For comparison, allozyme data from other Danish trout populations and mtDNA data from two hatchery strains were included. Genetic differentiation among populations was found to be small but significant. Pairwise tests for homogeneity of allele and haplotype frequencies between samples showed that significance...... simulations of the influence of founder effects on mitochondrial DNA differentiation and variability showed that the observed divergence could be due either to natural founder effects or to a genetic contribution by hatchery trout. However, the allozyme results pointed towards natural founder effects...

Statistical physics of pairwise probability models

DEFF Research Database (Denmark)

Roudi, Yasser; Aurell, Erik; Hertz, John

2009-01-01

(dansk abstrakt findes ikke) Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of  data......: knowledge of the means and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying...

Genetic differentiation of watermelon landraces in Mozambique ...

African Journals Online (AJOL)

Ezedom Theresa

2013-09-04

Sep 4, 2013 ... country, were analysed to assess their genetic differentiation. Ninety-six accessions (269 .... In view of developing national and regional strategies ... with fluorescent labelling of the products according to Schuelke. (2000).

Regional Genetic Structuring and Evolutionary History of the Impala Aepyceros melampus

DEFF Research Database (Denmark)

Lorenzen, Eline Deirdre; Arctander, Peter; Siegismund, Hans Redlef

2006-01-01

Samples of 162 impala antelope (Aepyceros melampus) from throughout its distribution range in sub-Saharan Africa were surveyed using eight polymorphic microsatellite loci. Furthermore, 155 previously published mitochondrial DNA (mtDNA) sequences from the same localities were reanalyzed. Two...... subspecies of impala are presently recognized-the isolated black-faced impala (Aepyceros melampus petersi) in southwest Africa and the common impala (Aepyceros melampus melampus) abundant in southern and east Africa. All tests performed indicated significant genetic differentiation at the subspecific level....... Furthermore, individual-based analyses split the common impala subspecies into two distinct genetic groups, conforming with regional geographic affiliation to southern or east Africa. This was supported by assignment tests, genetic distance measures, pairwise values, and analysis of molecular variance. We...

Pairwise Constraint-Guided Sparse Learning for Feature Selection.

Science.gov (United States)

Liu, Mingxia; Zhang, Daoqiang

2016-01-01

Feature selection aims to identify the most informative features for a compact and accurate data representation. As typical supervised feature selection methods, Lasso and its variants using L1-norm-based regularization terms have received much attention in recent studies, most of which use class labels as supervised information. Besides class labels, there are other types of supervised information, e.g., pairwise constraints that specify whether a pair of data samples belong to the same class (must-link constraint) or different classes (cannot-link constraint). However, most of existing L1-norm-based sparse learning methods do not take advantage of the pairwise constraints that provide us weak and more general supervised information. For addressing that problem, we propose a pairwise constraint-guided sparse (CGS) learning method for feature selection, where the must-link and the cannot-link constraints are used as discriminative regularization terms that directly concentrate on the local discriminative structure of data. Furthermore, we develop two variants of CGS, including: 1) semi-supervised CGS that utilizes labeled data, pairwise constraints, and unlabeled data and 2) ensemble CGS that uses the ensemble of pairwise constraint sets. We conduct a series of experiments on a number of data sets from University of California-Irvine machine learning repository, a gene expression data set, two real-world neuroimaging-based classification tasks, and two large-scale attribute classification tasks. Experimental results demonstrate the efficacy of our proposed methods, compared with several established feature selection methods.

Genetic diversity, structure and differentiation in cultivate walnut (Juglans regia L.)

Science.gov (United States)

M. Aradhya; K. Woeste; D. Velasco

2012-01-01

An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of walnut in Eurasia. Despite the narrow genetic...

A scalable pairwise class interaction framework for multidimensional classification

DEFF Research Database (Denmark)

Arias, Jacinto; Gámez, Jose A.; Nielsen, Thomas Dyhre

2016-01-01

We present a general framework for multidimensional classification that cap- tures the pairwise interactions between class variables. The pairwise class inter- actions are encoded using a collection of base classifiers (Phase 1), for which the class predictions are combined in a Markov random fie...

Dynamics of pairwise motions in the Cosmic Web

Science.gov (United States)

Hellwing, Wojciech A.

2016-10-01

We present results of analysis of the dark matter (DM) pairwise velocity statistics in different Cosmic Web environments. We use the DM velocity and density field from the Millennium 2 simulation together with the NEXUS+ algorithm to segment the simulation volume into voxels uniquely identifying one of the four possible environments: nodes, filaments, walls or cosmic voids. We show that the PDFs of the mean infall velocities v 12 as well as its spatial dependence together with the perpendicular and parallel velocity dispersions bear a significant signal of the large-scale structure environment in which DM particle pairs are embedded. The pairwise flows are notably colder and have smaller mean magnitude in wall and voids, when compared to much denser environments of filaments and nodes. We discuss on our results, indicating that they are consistent with a simple theoretical predictions for pairwise motions as induced by gravitational instability mechanism. Our results indicate that the Cosmic Web elements are coherent dynamical entities rather than just temporal geometrical associations. In addition it should be possible to observationally test various Cosmic Web finding algorithms by segmenting available peculiar velocity data and studying resulting pairwise velocity statistics.

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

Science.gov (United States)

Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S.; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P.; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E.

2018-01-01

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

Directory of Open Access Journals (Sweden)

Guillermo Sánchez-de la Vega

2018-03-01

Full Text Available Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma. Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango. We detected low

Clustering and genetic differentiation of the normocyte binding protein (nbpxa) of Plasmodium knowlesi clinical isolates from Peninsular Malaysia and Malaysia Borneo.

Science.gov (United States)

Ahmed, Md Atique; Fong, Mun Yik; Lau, Yee Ling; Yusof, Ruhani

2016-04-26

The zoonotic malaria parasite Plasmodium knowlesi has become an emerging threat to South East Asian countries particular in Malaysia. A recent study from Sarawak (Malaysian Borneo) discovered two distinct normocyte binding protein xa (Pknbpxa) types of P. knowlesi. In the present study, the Pknbpxa of clinical isolates from Peninsular Malaysia and Sabah (Malaysian Borneo) were investigated for the presence of Pknbpxa types and natural selection force acting on the gene. Blood samples were collected from 47 clinical samples from Peninsular Malaysia (n = 35) and Sabah (Malaysian Borneo, n = 12) were used in the study. The Pknbpxa gene was successfully amplified and directly sequenced from 38 of the samples (n = 31, Peninsular Malaysia and n = 7, Sabah, Malaysian Borneo). The Pknbpxa sequences of P. knowlesi isolates from Sarawak (Malaysian Borneo) were retrieved from GenBank and included in the analysis. Polymorphism, genetic diversity and natural selection of Pknbpxa sequences were analysed using DNAsp v 5.10, MEGA5. Phylogentics of Pknbpxa sequences was analysed using MrBayes v3.2 and Splits Tree v4.13.1. The pairwise F ST indices were used to determine the genetic differentiation between the Pknbpxa types and was calculated using Arlequin 3.5.1.3. Analyses of the sequences revealed Pknbpxa dimorphism throughout Malaysia indicating co-existence of the two types (Type-1 and Type-2) of Pknbpxa. More importantly, a third type (Type 3) closely related to Type 2 Pknbpxa was also detected. This third type was found only in the isolates originating from Peninsular Malaysia. Negative natural selection was observed, suggesting functional constrains within the Pknbpxa types. This study revealed the existence of three Pknbpxa types in Malaysia. Types 1 and 2 were found not only in Malaysian Borneo (Sarawak and Sabah) but also in Peninsular Malaysia. A third type which was specific only to samples originating from Peninsular Malaysia was discovered. Further genetic

Development of microsatellite markers to genetically differentiate populations of Octopus minor from Korea and China.

Science.gov (United States)

Kang, Jung-Ha; Kim, Yi-Kyung; Park, Jung-Youn; An, Chel-Min; Jun, Je-Chun

2012-08-01

Of the more than 300 octopus species, Octopus minor is one of the most popular and economically important species in Eastern Asia, including Korea, along with O. vulgaris, O. ocellatus, and O. aegina. We developed 19 microsatellite markers from Octopus minor and eight polymorphic markers were developed to analyze the genetic diversity and relationships among four octopus populations from Korea and three from China. The number of alleles per locus varied from 10 to 49, and allelic richness per locus ranged from 2 to 16.4 across all populations. The average allele number among the populations was 11.1, with a minimum of 8.3 and a maximum of 13.6. The mean allelic richness was 8.7 in all populations. The Hardy-Weinberg equilibrium (HWE) test revealed significant deviation in 19 of the 56 single-locus sites, and null alleles were presumed in five of eight loci. The pairwise F ( ST ) values between populations from Korea and China differed significantly in all pairwise comparisons. The genetic distances between the China and Korea samples ranged from 0.161 to 0.454. The genetic distances among the populations from Korea ranged from 0.033 to 0.090, with an average of 0.062; those among populations from China ranged from 0.191 to 0.316, with an average of 0.254. The populations from Korea and China formed clearly separated into clusters via an unweighted pair group method with arithmetic mean dendrogram. Furthermore, a population from muddy flats on the western coast of the Korean Peninsula and one from a rocky area on Jeju Island formed clearly separated subclusters. An assignment test based on the allele distribution discriminated between the Korean and Chinese origins with 96.9 % accuracy.

Genetic differentiation between sympatric and allopatric wintering populations of Snow Geese

Science.gov (United States)

Humphries, E.M.; Peters, J.L.; Jonsson, J.E.; Stone, R.; Afton, A.D.; Omland, K.E.

2009-01-01

Blackwater National Wildlife Refuge on the Delmarva Peninsula, Maryland, USA has been the wintering area of a small population of Lesser Snow Geese (Chen caerulescens caerulescens; LSGO) since the 1930s. Snow Geese primarily pair in wintering areas and gene flow could be restricted between this and other LSGO wintering populations. Winter pair formation also could facilitate interbreeding with sympatric but morphologically differentiated Greater Snow Geese (C. c. atlantica; GSGO).We sequenced 658 bp of the mitochondrial DNA control region for 68 Snow Geese from East Coast and Louisiana wintering populations to examine the level of genetic differentiation among populations and subspecies. We found no evidence for genetic differentiation between LSGO populations but, consistent with morphological differences, LSGO and GSGO were significantly differentiated. We also found a lack of genetic differentiation between different LSGO morphotypes from Louisiana. We examined available banding data and found the breeding range of Delmarva LSGO overlaps extensively with LSGO that winter in Louisiana, and documented movements between wintering populations. Our results suggest the Delmarva population of LSGO is not a unique population unit apart from Mid-Continent Snow Geese. ?? 2009 by the Wilson Ornithological Society.

Supplier Evaluation Process by Pairwise Comparisons

Directory of Open Access Journals (Sweden)

Arkadiusz Kawa

2015-01-01

Full Text Available We propose to assess suppliers by using consistency-driven pairwise comparisons for tangible and intangible criteria. The tangible criteria are simpler to compare (e.g., the price of a service is lower than that of another service with identical characteristics. Intangible criteria are more difficult to assess. The proposed model combines assessments of both types of criteria. The main contribution of this paper is the presentation of an extension framework for the selection of suppliers in a procurement process. The final weights are computed from relative pairwise comparisons. For the needs of the paper, surveys were conducted among Polish managers dealing with cooperation with suppliers in their enterprises. The Polish practice and restricted bidding are discussed, too.

Spatial distribution of genetic diversity in populations of Hagenia abyssinica (Bruce J.F. Gmel from Ethiopia

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Taye Bekele Ayele

2017-07-01

Full Text Available Genetic variation among 596 individuals from 22 natural and 3 planted populations of Hagenia abyssinica (Rosaceae sampled from the montane forests of Ethiopia was investigated at amplified fragment length polymorphism (AFLP loci. We observed 106 unequivocally scorable AFLP markers out of which 91.5 percent were polymorphic. Populations harbored varying genetic diversities (He = 0.139-0.362, and showed low but significant genetic differentiation among them (FST = 0.077. Significant differentiation was observed even though previous paleoecological studies indicated that Hagenia abyssinica recolonized Ethiopia only after the Last Glacial Maximum, and our earlier analyses of maternally inherited chloroplast DNA revealed low mixing of recolonizing lineages through seeds and rare long distance seed dispersal. Genetic diversity did not decrease along recolonization routes, confirming effective gene flow, most likely through pollen, among populations. The observed variation at putatively neutral AFLPs does not reflect clinal variation patterns. As expected, population differentiation is lower at anonymous, mostly biparentally inherited, AFLPs than at maternally inherited chloroplast haplotypes. Despite presumably efficient seed and pollen dispersal of H. abyssinica by wind, a significant non-random fine-scale spatial genetic structure was observed up to 80 m in some populations. Due to significant pair-wise differentiation observed between populations, as many populations as possible should be considered for conservation, tree improvement and forestation programs.

Doctoral Program Selection Using Pairwise Comparisons.

Science.gov (United States)

Tadisina, Suresh K.; Bhasin, Vijay

1989-01-01

The application of a pairwise comparison methodology (Saaty's Analytic Hierarchy Process) to the doctoral program selection process is illustrated. A hierarchy for structuring and facilitating the doctoral program selection decision is described. (Author/MLW)

Intraspecific morphological and genetic differentiation in Scrophularia grayana (Scrophulariaceae).

Science.gov (United States)

Kamada, Takuro; Yamashiro, Tadashi; Maki, Masayuki

2007-05-01

Scrophularia grayana, which is distributed throughout northern Japan and Sakhalin, and its locally endemic variety var. grayanoides, have been examined morphometrically and genetically. Principal-component analysis using a total of 26 morphological characteristics revealed that these taxa are morphologically differentiated, but that the difference is not distinct. These two taxa have the same number of chromosomes in the somatic cells, 2n = 94, suggesting that ploidal level difference is not relevant to their divergence. The distributions of the taxa are adjoining in the north of Japanese mainland Honshu. Nevertheless, principal-coordinate analysis using putative 112 ISSR loci indicated they are genetically very distinct. Many taxon-specific alleles were found, and many of the alleles were fixed in each taxon. This genetic information suggests that a relatively long time has passed since the taxa became differentiated and that gene flow has rarely occurred between them, although morphological similarity has been maintained, probably because of natural selective forces.

Preference Learning and Ranking by Pairwise Comparison

Science.gov (United States)

Fürnkranz, Johannes; Hüllermeier, Eyke

This chapter provides an overview of recent work on preference learning and ranking via pairwise classification. The learning by pairwise comparison (LPC) paradigm is the natural machine learning counterpart to the relational approach to preference modeling and decision making. From a machine learning point of view, LPC is especially appealing as it decomposes a possibly complex prediction problem into a certain number of learning problems of the simplest type, namely binary classification. We explain how to approach different preference learning problems, such as label and instance ranking, within the framework of LPC. We primarily focus on methodological aspects, but also address theoretical questions as well as algorithmic and complexity issues.

Population Genetic Structure of red mullet (Mullus barbatus L. in Turkish Sea Based on Mitochondrial DNA

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Fevzi Bardakci

2014-06-01

Aegean Sea coupled with the Mediterranean sea and the Black sea. Control region of mtDNA sequence data information of this study showed high genetic diversity and structuring among groups. (Gamma st; 0,140, Nm; 3,05. According to pairwise γSt matrix the highest genetic differentiation was found between Hopa and Ayvalık (γSt: 0.17973 and the lowest genetic differentiation was detected between Bandırma and Zonguldak (γSt: 0,01606. Conclusions: Determination of genetic structures of fish populations and their genetic diversities are very important for perpetuation of fish populations and sustainable fisheries management. In this way, results of the present study are şmportant not only for the continuity of this species, but also would contribute to the sustainability of other fish species under the fishing pressure.

Landscape characteristics influencing the genetic structure of greater sage-grouse within the stronghold of their range: a holistic modeling approach

Science.gov (United States)

Row, Jeff R; Oyler-McCance, Sara J.; Fike, Jennifer; O'Donnell, Michael; Doherty, Kevin E.; Aldridge, Cameron L.; Bowen, Zachary H.; Fedy, Brad C.

2015-01-01

Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new opportunities to disentangle the menagerie of factors behind effective dispersal across a given landscape. Here, we combine these approaches with novel resistance surface parameterization to determine how the distribution of high- and low-quality seasonal habitat and individual landscape components shape patterns of gene flow for the greater sage-grouse (Centrocercus urophasianus) across Wyoming. We found that pairwise resistance derived from the distribution of low-quality nesting and winter, but not summer, seasonal habitat had the strongest correlation with genetic differentiation. Although the patterns were not as strong as with habitat distribution, multivariate models with sagebrush cover and landscape ruggedness or forest cover and ruggedness similarly had a much stronger fit with genetic differentiation than an undifferentiated landscape. In most cases, landscape resistance surfaces transformed with 17.33-km-diameter moving windows were preferred, suggesting small-scale differences in habitat were unimportant at this large spatial extent. Despite the emergence of these overall patterns, there were differences in the selection of top models depending on the model selection criteria, suggesting research into the most appropriate criteria for landscape genetics is required. Overall, our results highlight the importance of differences in seasonal habitat preferences to patterns of gene flow and suggest the combination of habitat suitability modeling and linear mixed models with our resistance parameterization is a powerful approach to discerning the effects of landscape

Hybridizing Differential Evolution with a Genetic Algorithm for Color Image Segmentation

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R. V. V. Krishna

2016-10-01

Full Text Available This paper proposes a hybrid of differential evolution and genetic algorithms to solve the color image segmentation problem. Clustering based color image segmentation algorithms segment an image by clustering the features of color and texture, thereby obtaining accurate prototype cluster centers. In the proposed algorithm, the color features are obtained using the homogeneity model. A new texture feature named Power Law Descriptor (PLD which is a modification of Weber Local Descriptor (WLD is proposed and further used as a texture feature for clustering. Genetic algorithms are competent in handling binary variables, while differential evolution on the other hand is more efficient in handling real parameters. The obtained texture feature is binary in nature and the color feature is a real value, which suits very well the hybrid cluster center optimization problem in image segmentation. Thus in the proposed algorithm, the optimum texture feature centers are evolved using genetic algorithms, whereas the optimum color feature centers are evolved using differential evolution.

Pairwise Choice Markov Chains

OpenAIRE

Ragain, Stephen; Ugander, Johan

2016-01-01

As datasets capturing human choices grow in richness and scale---particularly in online domains---there is an increasing need for choice models that escape traditional choice-theoretic axioms such as regularity, stochastic transitivity, and Luce's choice axiom. In this work we introduce the Pairwise Choice Markov Chain (PCMC) model of discrete choice, an inferentially tractable model that does not assume any of the above axioms while still satisfying the foundational axiom of uniform expansio...

Selecting numerical scales for pairwise comparisons

International Nuclear Information System (INIS)

Elliott, Michael A.

2010-01-01

It is often desirable in decision analysis problems to elicit from an individual the rankings of a population of attributes according to the individual's preference and to understand the degree to which each attribute is preferred to the others. A common method for obtaining this information involves the use of pairwise comparisons, which allows an analyst to convert subjective expressions of preference between two attributes into numerical values indicating preferences across the entire population of attributes. Key to the use of pairwise comparisons is the underlying numerical scale that is used to convert subjective linguistic expressions of preference into numerical values. This scale represents the psychological manner in which individuals perceive increments of preference among abstract attributes and it has important implications about the distribution and consistency of an individual's preferences. Three popular scale types, the traditional integer scales, balanced scales and power scales are examined. Results of a study of 64 individuals responding to a hypothetical decision problem show that none of these scales can accurately capture the preferences of all individuals. A study of three individuals working on an actual engineering decision problem involving the design of a decay heat removal system for a nuclear fission reactor show that the choice of scale can affect the preferred decision. It is concluded that applications of pairwise comparisons would benefit from permitting participants to choose the scale that best models their own particular way of thinking about the relative preference of attributes.

Population genetic structure and genetic diversity of Chinese pomfret at the coast of the East China Sea and the South China Sea.

Science.gov (United States)

Sun, Peng; Tang, Baojun; Yin, Fei

2018-05-01

The Chinese pomfret Pampus chinensis is one of the most economic and ecological important marine fish species in China. In the present study, the population genetic structure and genetic diversity of P. chinensis were evaluated from a total sample size of 180 individuals representing six populations from the East China Sea and the South China Sea using mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 24 variable sites (including 3 singleton sites and 21 parsimony information sites) were observed, and 18 haplotypes were defined. The haplotype diversity (Hd) of the populations ranged from 0.559 to 0.775, and the nucleotide diversity (π) ranged from 0.330 to 1.090%. Analysis of molecular variance (AMOVA) reveals that the main variation (66.02%) was among individuals within populations. The average pairwise differences and ϕ ST values indicated significant genetic differentiation between Dongxing population and the other populations. The results of the present study are helpful for the sustainable management and utilization of this species.

Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L..

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Brad L Smith

Full Text Available Previous genetic studies of Atlantic swordfish (Xiphias gladius L. revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.

Hierarchical genetic structure of the introduced wasp Vespula germanica in Australia.

Science.gov (United States)

Goodisman, M A; Matthews, R W; Crozier, R H

2001-06-01

The wasp Vespula germanica is a highly successful invasive pest. This study examined the population genetic structure of V. germanica in its introduced range in Australia. We sampled 1320 workers and 376 males from 141 nests obtained from three widely separated geographical areas on the Australian mainland and one on the island of Tasmania. The genotypes of all wasps were assayed at three polymorphic DNA microsatellite markers. Our analyses uncovered significant allelic differentiation among all four V. germanica populations. Pairwise estimates of genetic divergence between populations agreed with the results of a model-based clustering algorithm which indicated that the Tasmanian population was particularly distinct from the other populations. Within-population analyses revealed that genetic similarity declined with spatial distance, indicating that wasps from nests separated by more than approximately 25 km belonged to separate mating pools. We suggest that the observed genetic patterns resulted from frequent bottlenecks experienced by the V. germanica populations during their colonization of Australia.

Evidence for genetic differentiation at the microgeographic scale in Phlebotomus papatasi populations from Sudan

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Khalid Noteila M

2012-11-01

Full Text Available Abstract Background Cutaneous Leishmaniasis (CL is endemic in Sudan. It is caused by Leishmania major parasites and transmitted by Phlebotomus papatasi sandflies. Recently, uncommon clinical manifestations of CL have been reported. Moreover, L. donovani parasites that cause Visceral Leishmaniasis (VL have been isolated from CL lesions of some patients who contracted the disease in Khartoum State, Central Sudan with no history of travelling to VL endemic sites on south-eastern Sudan. Because different clinical manifestations and the parasite behaviour could be related to genetic differentiation, or even sub-structuring within sandfly vector populations, a population genetic study was conducted on P. papatasi populations collected from different localities in Khartoum State known for their uncommon CL cases and characterized by contrasting environmental conditions. Methods A set of seven microsatellite loci was used to investigate the population structure of P. papatasi samples collected from different localities in Khartoum State, Central Sudan. Populations from Kassala State, Eastern Sudan and Egypt were also included in the analyses as outgroups. The level of genetic diversity and genetic differentiation among natural populations of P. papatasi was determined using FST statistics and Bayesian assignments. Results Genetic analyses revealed significant genetic differentiation (FST between the Sudanese and the Egyptian populations. Within the Sudanese P. papatasi populations, one population from Gerif West, Khartoum State, exhibited significant genetic differentiation from all other populations including those collected as near as 22 km. Conclusion The significant genetic differentiation of Gerif West P. papatasi population from other Sudanese populations may have important implication for the epidemiology of leishmaniasis in Khartoum State and needs to be further investigated. Primarily, it could be linked to the unique location of Gerif West

Genetic consequences of population decline in the European otter ( Lutra lutra ) : an assessment of microsatellite DNA variation in Danish otters from 1883 to 1993

DEFF Research Database (Denmark)

Pertoldi, C.; Hansen, Michael Møller; Loeschcke, V.

2001-01-01

alleles, suggested that a drastic long-term population decline has taken place, which could have started more than 2000 years ago, possibly due to ancient anthropogenic pressure. Finally, assignment tests and pairwise F-ST values suggested weak but statistically significant genetic differentiation between......The European otter (Lutra lutra) was common in Denmark until the 1960s, but its present distribution encompasses only a minor part of the country. The aim of this study was to assess whether the recent population decline has resulted in loss of genetic variability and to gain further insight...

High degree of genetic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus).

Science.gov (United States)

Defaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Merilä, Juha

2013-09-01

Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene-based genome-scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection-as determined with several outlier detection methods-was low (F(ST) = 0.033 or 0.011, respectively), whereas average FST for directionally selected markers was significantly higher (F(ST) = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes. © 2013 John Wiley & Sons Ltd.

Crater Lake Apoyo Revisited - Population Genetics of an Emerging Species Flock

Science.gov (United States)

Geiger, Matthias F.; McCrary, Jeffrey K.; Schliewen, Ulrich K.

2013-01-01

The polytypic Nicaraguan Midas cichlids ( Amphilophus cf. citrinellus) have been established as a model system for studying the mechanisms of speciation and patterns of diversification in allopatry and sympatry. The species assemblage in Crater Lake Apoyo has been accepted as a textbook example for sympatric speciation. Here, we present a first comprehensive data set of population genetic (mtDNA & AFLPs) proxies of species level differentiation for a representative set of individuals of all six endemic Amphilophus species occurring in Crater Lake Apoyo. AFLP genetic differentiation was partitioned into a neutral and non-neutral component based on outlier-loci detection approaches, and patterns of species divergence were explored with Bayesian clustering methods. Substantial levels of admixture between species were detected, indicating different levels of reproductive isolation between the six species. Analysis of neutral genetic variation revealed several A . zaliosus as being introgressed by an unknown contributor, hereby rendering the sympatrically evolving L. Apoyo flock polyphyletic. This is contrasted by the mtDNA analysis delivering a clear monophyly signal with Crater Lake Apoyo private haplotypes characterising all six described species, but also demonstrating different demographic histories as inferred from pairwise mismatch distributions. PMID:24086393

Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

Science.gov (United States)

Ren, Jing; Chen, Liang; Jin, Xiaoli; Zhang, Miaomiao; You, Frank M; Wang, Jirui; Frenkel, Vladimir; Yin, Xuegui; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2017-01-01

Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ F ST ≤ 0.15) or high genetic differentiation ( F ST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different F ST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.

The Role of Middlemen inEfficient and Strongly Pairwise Stable Networks

NARCIS (Netherlands)

Gilles, R.P.; Chakrabarti, S.; Sarangi, S.; Badasyan, N.

2004-01-01

We examine the strong pairwise stability concept in network formation theory under collective network benefits.Strong pairwise stability considers a pair of players to add a link through mutual consent while permitting them to unilaterally delete any subset of links under their control.We examine

Worldwide genetic differentiation in the common fouling barnacle, Amphibalanus amphitrite

KAUST Repository

Chen, Hsi-Nien

2014-10-21

© 2014, © 2014 Taylor & Francis. Amphibalanus amphitrite is a common fouling barnacle distributed globally in tropical and subtropical waters. In the present study, the genetic (mitochondrial cytochrome oxidase subunit I) and morphological differentiation in A. amphitrite from 25 localities around the world were investigated. The results revealed three clades within A. amphitrite with a genetic divergence of ~ 4% among clades, whereas there were no diagnostic morphological differences among clades. Clade 1 is widely distributed in both temperate and tropical waters, whereas Clade 3 is currently restricted to the tropical region. The deep divergence among clades suggests historical isolation within A. amphitrite; thus, the present geographical overlaps are possibly a result of the combined effects of rising sea level and human-mediated dispersals. This study highlights the genetic differentiation that exists in a common, widely distributed fouling organism with great dispersal potential; future antifouling research should take into account the choice of lineages.

Historical and contemporary population genetics of the invasive western corn rootworm (Coleoptera: Chrysomelidae) in Croatia.

Science.gov (United States)

Lemic, D; Mikac, K M; Bažok, R

2013-08-01

Classical population genetic analyses were used to investigate populations of the western corn rootworm, Diabrotica virgifera virgifera LeConte, in Croatia in 1996 and 2009. The number of alleles was low in both 1996 and 2009; however, more alleles were found in the putative populations surveyed in 2009. Croatia had only 51% of the alleles recorded from the United States and 69% from Europe. However, 10 private (unique) alleles were found in Croatia, which were not found previously in Europe. Most populations were out of Hardy-Weinberg equilibrium, although no linkage disequilibrium was found. Low to no genetic differentiation was found between population pairwise comparisons in 1996, with a greater level of differentiation found between populations sampled in 2009. Using the program STRUCTURE, a single genetic cluster was found for populations sampled in 1996 and 2009. However, two genetic clusters were detected when the 1996 and 2009 data were combined, indicating significant temporal differentiation. Isolation by distance pattern of gene flow characterized populations sampled in 2009 only when the most distant population of Ogulin (the head of the expansion front) was included in the analysis. When Ogluin was excluded from the 2009 analysis no isolation by distance pattern was found. The possible impact that control practices have had on the population genetics of D. v. virgifera in Croatia from 1996 to 2009 are discussed in light of the temporal genetics differences found.

Population Expansion and Genetic Structure in Carcharhinus brevipinna in the Southern Indo-Pacific

Science.gov (United States)

Geraghty, Pascal T.; Williamson, Jane E.; Macbeth, William G.; Wintner, Sabine P.; Harry, Alastair V.; Ovenden, Jennifer R.; Gillings, Michael R.

2013-01-01

Background Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna), a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa. Methods and Findings Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025). While two metrics of genetic divergence (ΦST and F ST) revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717–0.03508, p values ≤ 0.0013; pairwise F ST South Africa vs New South Wales = 0.04056, p = 0.0008). Evidence for fine-scale genetic structuring was also detected along Australia’s east coast (pairwise ΦST = 0.01328, p Indo-Pacific. PMID:24086462

Automatic Camera Calibration Using Multiple Sets of Pairwise Correspondences.

Science.gov (United States)

Vasconcelos, Francisco; Barreto, Joao P; Boyer, Edmond

2018-04-01

We propose a new method to add an uncalibrated node into a network of calibrated cameras using only pairwise point correspondences. While previous methods perform this task using triple correspondences, these are often difficult to establish when there is limited overlap between different views. In such challenging cases we must rely on pairwise correspondences and our solution becomes more advantageous. Our method includes an 11-point minimal solution for the intrinsic and extrinsic calibration of a camera from pairwise correspondences with other two calibrated cameras, and a new inlier selection framework that extends the traditional RANSAC family of algorithms to sampling across multiple datasets. Our method is validated on different application scenarios where a lack of triple correspondences might occur: addition of a new node to a camera network; calibration and motion estimation of a moving camera inside a camera network; and addition of views with limited overlap to a Structure-from-Motion model.

MAINTENANCE OF ECOLOGICALLY SIGNIFICANT GENETIC VARIATION IN THE TIGER SWALLOWTAIL BUTTERFLY THROUGH DIFFERENTIAL SELECTION AND GENE FLOW.

Science.gov (United States)

Bossart, J L; Scriber, J M

1995-12-01

Differential selection in a heterogeneous environment is thought to promote the maintenance of ecologically significant genetic variation. Variation is maintained when selection is counterbalanced by the homogenizing effects of gene flow and random mating. In this study, we examine the relative importance of differential selection and gene flow in maintaining genetic variation in Papilio glaucus. Differential selection on traits contributing to successful use of host plants (oviposition preference and larval performance) was assessed by comparing the responses of southern Ohio, north central Georgia, and southern Florida populations of P. glaucus to three hosts: Liriodendron tulipifera, Magnolia virginiana, and Prunus serotina. Gene flow among populations was estimated using allozyme frequencies from nine polymorphic loci. Significant genetic differentiation was observed among populations for both oviposition preference and larval performance. This differentiation was interpreted to be the result of selection acting on Florida P. glaucus for enhanced use of Magnolia, the prevalent host in Florida. In contrast, no evidence of population differentiation was revealed by allozyme frequencies. F ST -values were very small and Nm, an estimate of the relative strengths of gene flow and genetic drift, was large, indicating that genetic exchange among P. glaucus populations is relatively unrestricted. The contrasting patterns of spatial differentiation for host-use traits and lack of differentiation for electrophoretically detectable variation implies that differential selection among populations will be counterbalanced by gene flow, thereby maintaining genetic variation for host-use traits. © 1995 The Society for the Study of Evolution.

Genetic differentiation and gene flow between the Tunisian ovine ...

African Journals Online (AJOL)

Haifa

Sheep is an important livestock species of Tunisia. They contribute greatly ... Genetic differentiation coefficient (Gst) over all loci was 0.1922, the fixation index [Fst by Analysis of molecular variance ..... their first cross with the D'Man. Anim. Res.

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

Science.gov (United States)

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-01-01

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

[Genetic differentiation of Isaria farinosa populations in Anhui Province of East China].

Science.gov (United States)

Sun, Zhao-Hong; Luan, Feng-Gang; Zhang, Da-Min; Chen, Ming-Jun; Wang, Bin; Li, Zeng-Zhi

2011-11-01

Isaria farinosa is an important entomopathogenic fungus. By using ISSR, this paper studied the genetic heterogeneity of six I. farinosa populations at different localities of Anhui Province, East China. A total of 98.5% polymorphic loci were amplified with ten polymorphic primers, but the polymorphism at population level varied greatly, within the range of 59.6%-93.2%. The genetic differentiation index (G(st)) between the populations based on Nei's genetic heterogenesis analysis was 0.3365, and the gene flow (N(m)) was 0.4931. The genetic differentiation between the populations was lower than that within the populations, suggesting that the genetic variation of I. farinosa mainly come from the interior of the populations. The UPGMA clustering based on the genetic similarities between the isolates revealed that the Xishan population was monophylectic, while the other five populations were polyphylectic, with the Yaoluoping population being the most heterogenic and the Langyashan population being the least heterogenic. No correlations were observed between the geographic distance and the genetic distance of the populations. According to the UPGMA clustering based on the genetic distance between the populations, the six populations were classified into three groups, and this classification was accorded with the clustering based on geographic environment, suggesting the effects of environmental heterogeneity on the population heterogeneity.

Genetic structure of three Croatian horse breeds: implications for their conservation strategy

Directory of Open Access Journals (Sweden)

Miljenko Konjačić

2010-01-01

Full Text Available The genetic variability for a sample of 107 animals from three autochthonous Croatian horse breeds was estimated using 20 microsatellites. The average number of alleles per locus (6.3 and proportion of heterozygosity (0.732 indicated a moderate variability. The expected heterozygosity was similar among all breeds and ranged between 0.724 in the Posavina horse, and 0.737 in the Croatian Coldblood and Murinsulaner horse. The inbreeding coefficient FIS was low and non-significant over the three populations. The genetic differentiation among the three populations was low (FST=0.026, suggesting that only 2.6% of the total genetic variability was due to differences between the breeds, and 97% to individual differences. The results of pairwise genetic differentiation suggest that the Posavina horse and the Croatian Coldblood were the most closely related populations (FST=0.016. These results are confirmed by Nei’s genetic distances with the highest value observed between the Posavina horse and the Murinsulaner (0.082 and the lowest between the Posavina horse and the Croatian Coldblood (0.044. An assignment test correctly assigned 82% of individuals to the correct breed. Strategies for preserving the original native genes in the Croatian native horse breeds should be considered in order to prevent these breeds from becoming extinct and include them in the future breeding programmes.

A predictive model of music preference using pairwise comparisons

DEFF Research Database (Denmark)

Jensen, Bjørn Sand; Gallego, Javier Saez; Larsen, Jan

2012-01-01

Music recommendation is an important aspect of many streaming services and multi-media systems, however, it is typically based on so-called collaborative filtering methods. In this paper we consider the recommendation task from a personal viewpoint and examine to which degree music preference can...... be elicited and predicted using simple and robust queries such as pairwise comparisons. We propose to model - and in turn predict - the pairwise music preference using a very flexible model based on Gaussian Process priors for which we describe the required inference. We further propose a specific covariance...

Revisiting the classification of curtoviruses based on genome-wide pairwise identity

KAUST Repository

Varsani, Arvind; Martin, Darren Patrick; Navas-Castillo, Jesú s; Moriones, Enrique; Herná ndez-Zepeda, Cecilia; Idris, Ali; Murilo Zerbini, F.; Brown, Judith K.

2014-01-01

Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

Revisiting the classification of curtoviruses based on genome-wide pairwise identity

KAUST Repository

Varsani, Arvind

2014-01-25

Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis.

Science.gov (United States)

Wang, Baosheng; Mao, Jian-Feng; Zhao, Wei; Wang, Xiao-Ru

2013-01-01

Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species' range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.

Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape

International Nuclear Information System (INIS)

Andre, J.; King, R.A.; Stuerzenbaum, S.R.; Kille, P.; Hodson, M.E.; Morgan, A.J.

2010-01-01

A Pb-mine site situated on acidic soil, but comprising of Ca-enriched islands around derelict buildings was used to study the spatial pattern of genetic diversity in Lumbricus rubellus. Two distinct genetic lineages ('A' and 'B'), differentiated at both the mitochondrial (mtDNA COII) and nuclear level (AFLPs) were revealed with a mean inter-lineage mtDNA sequence divergence of approximately 13%, indicative of a cryptic species complex. AFLP analysis indicates that lineage A individuals within one central 'ecological island' site are uniquely clustered, with little genetic overlap with lineage A individuals at the two peripheral sites. FTIR microspectroscopy of Pb-sequestering chloragocytes revealed different phosphate profiles in residents of adjacent acidic and calcareous islands. Bioinformatics found over-representation of Ca pathway genes in EST Pb libraries. Subsequent sequencing of a Ca-transport gene, SERCA, revealed mutations in the protein's cytosolic domain. We recommend the mandatory genotyping of all individuals prior to field-based ecotoxicological assays, particularly those using discriminating genomic technologies. - Landscapes punctuated by Pb-polluted islands have engendered local genetic differentiation in resident earthworms.

Facial emotion perception differs in young persons at genetic and clinical high-risk for psychosis.

Science.gov (United States)

Kohler, Christian G; Richard, Jan A; Brensinger, Colleen M; Borgmann-Winter, Karin E; Conroy, Catherine G; Moberg, Paul J; Gur, Ruben C; Gur, Raquel E; Calkins, Monica E

2014-05-15

A large body of literature has documented facial emotion perception impairments in schizophrenia. More recently, emotion perception has been investigated in persons at genetic and clinical high-risk for psychosis. This study compared emotion perception abilities in groups of young persons with schizophrenia, clinical high-risk, genetic risk and healthy controls. Groups, ages 13-25, included 24 persons at clinical high-risk, 52 first-degree relatives at genetic risk, 91 persons with schizophrenia and 90 low risk persons who completed computerized testing of emotion recognition and differentiation. Groups differed by overall emotion recognition abilities and recognition of happy, sad, anger and fear expressions. Pairwise comparisons revealed comparable impairments in recognition of happy, angry, and fearful expressions for persons at clinical high-risk and schizophrenia, while genetic risk participants were less impaired, showing reduced recognition of fearful expressions. Groups also differed for differentiation of happy and sad expressions, but differences were mainly between schizophrenia and control groups. Emotion perception impairments are observable in young persons at-risk for psychosis. Preliminary results with clinical high-risk participants, when considered along findings in genetic risk relatives, suggest social cognition abilities to reflect pathophysiological processes involved in risk of schizophrenia. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Meckel Syndrome: Genetics, Perinatal Findings, and Differential Diagnosis

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Chih-Ping Chen

2007-03-01

Full Text Available Meckel syndrome (MKS is a lethal, autosomal recessive disorder characterized by occipital encephalocele, bilateral renal cystic dysplasia, hepatic ductal proliferation, fibrosis and cysts, and polydactyly. Genetic heterogeneity of MKS has been established by three reported MKS loci, i.e., MKS1 on 17q23, MKS2 on 11q13, and MKS3 on 8q21.13-q22.1. MKS1 encodes a component of flagellar apparatus basal body proteome, which is associated with ciliary function. MKS3 encodes a seven-transmembrane receptor protein, meckelin. The identification of the MKS3 gene as well as the MKS1 gene enables molecular genetic testing for at-risk families, and allows accurate genetic counseling, carrier testing, and prenatal diagnosis. Pregnancies with MKS fetuses may be associated with an elevated maternal serum α-fetoprotein level and an abnormal screening result in the second-trimester maternal serum screening test. The classic MKS triad of occipital encephalocele, postaxial polydactyly, and bilateral enlarged multicystic kidneys can be diagnosed before the 14th gestational weeks by ultrasonography. However, later in pregnancy, severe oligohydramnios may make the diagnosis of polydactyly and encephalocele difficult. Differential diagnosis for MKS includes autosomal recessive polycystic kidney disease, trisomy 13, Smith-Lemli-Opitz syndrome, hydrolethalus syndrome, Senior-Loken syndrome, Joubert syndrome, Bardet-Biedl syndrome, and oral-facial-digital syndrome type 1. This article provides an overview of genetics, perinatal findings, and differential diagnosis of MKS. The ciliopathy underlies the pathogenesis of MKS. Prenatal diagnosis of bilateral enlarged multicystic kidneys should alert MKS and prompt a thorough investigation of central nervous system malformations and polydactyly.

Short tandem repeat (STR based genetic diversity and relationship of indigenous Niger cattle

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M. Grema

2017-11-01

Full Text Available The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 % was consistently higher than Zebu Arabe (59.3 to 70.4 % and Kuri (80.0 to 83.3 % cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu–taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

Genetic differentiation between the ant Myrmica rubra and its microgynous social parasite

DEFF Research Database (Denmark)

Vepsäläinen, K.; Ebsen, J. R.; Savolainen, R.

2009-01-01

Hymenopteran inquiline species have been proposed to originate by sympatric speciation through intraspecific social parasitism. One such parasite, Myrmica microrubra, was recently synonymized with its Myrmica rubra host, because comparisons across Europe indicated insufficient genetic differentia......Hymenopteran inquiline species have been proposed to originate by sympatric speciation through intraspecific social parasitism. One such parasite, Myrmica microrubra, was recently synonymized with its Myrmica rubra host, because comparisons across Europe indicated insufficient genetic...... differentiation. Here, we use microsatellite markers to study genetic differentiation more precisely in a sample of Finnish M. rubra and its inquilines collected at two localities, supplemented with mitochondrial DNA sequences. The parasite had much lower genetic variation than the host at three of the four loci...

Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis

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Rabinowicz Pablo D

2010-01-01

Full Text Available Abstract Background Castor bean (Ricinus communis is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale. We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs at 48 loci. Results Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74% followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕPT values, p Conclusion Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.

Population genetics of the malaria vector Anopheles aconitus in China and Southeast Asia.

Science.gov (United States)

Chen, Bin; Harbach, Ralph E; Walton, Catherine; He, Zhengbo; Zhong, Daibin; Yan, Guiyun; Butlin, Roger K

2012-12-01

Anopheles aconitus is a well-known vector of malaria and is broadly distributed in the Oriental Region, yet there is no information on its population genetic characteristics. In this study, the genetic differentiation among populations was examined using 140 mtDNA COII sequences from 21 sites throughout Southern China, Myanmar, Vietnam, Thailand, Laos and Sri Lanka. The population in Sri Lanka has characteristic rDNA D3 and ITS2, mtDNA COII and ND5 haplotypes, and may be considered a distinct subspecies. Clear genetic structure was observed with highly significant genetic variation present among population groups in Southeast Asia. The greatest genetic diversity exists in Yunnan and Myanmar population groups. All population groups are significantly different from one another in pairwise Fst values, except Northern Thailand with Central Thailand. Mismatch distributions and extremely significant F(s) values suggest that the populations passed through a recent demographic expansion. These patterns are discussed in relation to the likely biogeographic history of the region and compared to other Anopheles species. Copyright © 2012 Elsevier B.V. All rights reserved.

Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia.

Science.gov (United States)

Assaeed, Abdulaziz M; Al-Faifi, Sulieman A; Migdadi, Hussein M; El-Bana, Magdy I; Al Qarawi, Abdulaziz A; Khan, Mohammad Altaf

2018-01-01

The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances ( r  = 0.35, P  < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum . The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.

Worldwide genetic differentiation in the common fouling barnacle, Amphibalanus amphitrite

KAUST Repository

Chen, Hsi-Nien; Tsang, Ling Ming; Chong, Ving Ching; Chan, Benny K.K.

2014-01-01

differentiation in A. amphitrite from 25 localities around the world were investigated. The results revealed three clades within A. amphitrite with a genetic divergence of ~ 4% among clades, whereas there were no diagnostic morphological differences among clades

Unjamming in models with analytic pairwise potentials

Science.gov (United States)

Kooij, Stefan; Lerner, Edan

2017-06-01

Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the coordination number z , which has an unambiguous definition in these cases. Pairwise potentials without a sharp cutoff in the interaction range have not been studied in this context, but should in fact be considered to understand the relevance of the unjamming phenomenology in systems where such a cutoff is not present. In this work we explore two systems with such interactions: an inverse power law and an exponentially decaying pairwise potential, with the control parameters being the exponent (of the inverse power law) for the former and the number density for the latter. Both systems are shown to exhibit the characteristic features of the unjamming transition, among which are the vanishing of the shear-to-bulk modulus ratio and the emergence of an excess of low-frequency vibrational modes. We establish a relation between the pressure-to-bulk modulus ratio and the distance to unjamming in each of our model systems. This allows us to predict the dependence of other key observables on the distance to unjamming. Our results provide the means for a quantitative estimation of the proximity of generic glass-forming models to the unjamming transition in the absence of a clear-cut definition of the coordination number and highlight the general irrelevance of nonaffine contributions to the bulk modulus.

Product differentiation under bounded rationality

NARCIS (Netherlands)

Vermeulen, B.; Poutré, La J.A.; Kok, de A.G.; Pyka, A.; Handa, H.; Ishibuchi, H.; Ong, Y.-S.; Tan, K.-C.

2015-01-01

We study product differentiation equilibria and dynamics on the Salop circle under bounded rationality. Due to bounded rationality, firms tend to agglomerate in pairs. Upon adding a second tier of component suppliers, downstream assemblers may escape pairwise horizontal agglomeration. Moreover, we

Pairwise conjoint analysis of activity engagement choice

NARCIS (Netherlands)

Wang, Donggen; Oppewal, H.; Timmermans, H.J.P.

2000-01-01

Information overload is a well-known problem of conjoint choice models when respondents have to evaluate a large number of attributes and/or attribute levels. In this paper we develop an alternative conjoint modelling approach, called pairwise conjoint analysis. It differs from conventional conjoint

Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape

Energy Technology Data Exchange (ETDEWEB)

Andre, J., E-mail: Andrej@cardiff.ac.u [Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3TL (United Kingdom); Department of Soil Science, School of Human and Environmental Sciences, University of Reading, Whiteknights, Reading RG6 6DW (United Kingdom); King, R.A. [Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3TL (United Kingdom); Stuerzenbaum, S.R. [King' s College London, School of Biomedical and Health Sciences, Pharmaceutical Sciences Division, London SE1 9NH (United Kingdom); Kille, P. [Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3TL (United Kingdom); Hodson, M.E. [Department of Soil Science, School of Human and Environmental Sciences, University of Reading, Whiteknights, Reading RG6 6DW (United Kingdom); Morgan, A.J. [Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3TL (United Kingdom)

2010-03-15

A Pb-mine site situated on acidic soil, but comprising of Ca-enriched islands around derelict buildings was used to study the spatial pattern of genetic diversity in Lumbricus rubellus. Two distinct genetic lineages ('A' and 'B'), differentiated at both the mitochondrial (mtDNA COII) and nuclear level (AFLPs) were revealed with a mean inter-lineage mtDNA sequence divergence of approximately 13%, indicative of a cryptic species complex. AFLP analysis indicates that lineage A individuals within one central 'ecological island' site are uniquely clustered, with little genetic overlap with lineage A individuals at the two peripheral sites. FTIR microspectroscopy of Pb-sequestering chloragocytes revealed different phosphate profiles in residents of adjacent acidic and calcareous islands. Bioinformatics found over-representation of Ca pathway genes in EST{sub Pb} libraries. Subsequent sequencing of a Ca-transport gene, SERCA, revealed mutations in the protein's cytosolic domain. We recommend the mandatory genotyping of all individuals prior to field-based ecotoxicological assays, particularly those using discriminating genomic technologies. - Landscapes punctuated by Pb-polluted islands have engendered local genetic differentiation in resident earthworms.

Biochemical genetic variation between four populations of ...

African Journals Online (AJOL)

system) to 0.093 in the Spekboom River population (Limpopo River system). The genetic distance, FST and NEM values, as well as pair-wise contingency c2 analyses indicate a lack of gene flow between populations, as expected for isolated fish. Evidence of foreign genetic material in one population was also observed.

PAIRWISE BLENDING OF HIGH LEVEL WASTE

International Nuclear Information System (INIS)

CERTA, P.J.

2006-01-01

The primary objective of this study is to demonstrate a mission scenario that uses pairwise and incidental blending of high level waste (HLW) to reduce the total mass of HLW glass. Secondary objectives include understanding how recent refinements to the tank waste inventory and solubility assumptions affect the mass of HLW glass and how logistical constraints may affect the efficacy of HLW blending

Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

Science.gov (United States)

Hand, Brian K.; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P.; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

2016-01-01

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

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.

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.

Genetic variation and local differences in Pacific cod Gadus macrocephalus around Japan.

Science.gov (United States)

Suda, A; Nagata, N; Sato, A; Narimatsu, Y; Nadiatul, H H; Kawata, M

2017-01-01

The population structure of the Pacific cod Gadus macrocephalus was examined using 15 microsatellite loci and mitochondrial DNA (ND2 region). In total, 274 individuals were sampled from 16 locations around Japan to estimate the level of genetic differentiation and effective population size (N e ). Pairwise F ST , analysis of molecular variance and Bayesian clustering analysis suggested the presence of two genetically distinct groups in waters around Japan, with a higher N e value in the eastern group than in the western group. A possible factor that restricts gene flow between groups may be related to the water temperature differences in the south-western part of the Sea of Japan, where the Tsushima Warm Current flows around the area inhabited by the western group, which may limit migration between the west and east. © 2016 The Fisheries Society of the British Isles.

Genetic Diversity and Population Structure of a Threatened African Tree Species, Milicia excelsa, Using Nuclear Micro satellites DNA Markers

International Nuclear Information System (INIS)

Ouinsavi, Ch.; Sokpon, N.; Ouinsavi, Ch.; Khasa, D.P.

2009-01-01

To accurately estimate the genetic diversity and population structure for improved conservation planning of Milicia excelsa tree, 212 individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific micro satellite DNA loci. All loci were variable, with the mean number of alleles per locus ranging from 5.86 to 7.69. Considerable genetic variability was detected for all populations at the seven loci (AR=4.60; HE=0.811). Moderate but statistically significant genetic differentiation was found among populations considering both FST (0.112) and RST (0.342). All of the populations showed heterozygosity deficits in test of Hardy-Weinberg Equilibrium and significantly positive FIS values due to inbreeding occurring in the species. Pairwise FST values were positively and significantly correlated with geographical distances (r=0.432; P=.007, Mantel's test) indicating that populations are differentiated by isolation by distance. Bayesian analysis of population structure showed division of the genetic variation into four clusters revealing the existence of heterogeneity in population genetic structure. Altogether, these results indicate that genetic variation in Milicia excelsa is geographically structured. Information gained from this study also emphasized the need for in situ conservation of the relict populations and establishment of gene flow corridors through agroforestry systems for interconnecting these remnant populations.

Unjamming in models with analytic pairwise potentials

NARCIS (Netherlands)

Kooij, S.; Lerner, E.

Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the

Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

Directory of Open Access Journals (Sweden)

Raphaël Mourad

Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

Population expansion and genetic structure in Carcharhinus brevipinna in the southern Indo-Pacific.

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Pascal T Geraghty

Full Text Available Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna, a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa.Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025. While two metrics of genetic divergence (ΦST and F ST revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717-0.03508, p values ≤ 0.0013; pairwise F ST South Africa vs New South Wales = 0.04056, p = 0.0008. Evidence for fine-scale genetic structuring was also detected along Australia's east coast (pairwise ΦST = 0.01328, p < 0.015, and between south-eastern and northern locations (pairwise ΦST = 0.00669, p < 0.04.The Indian Ocean represents a robust barrier to contemporary gene flow in C. brevipinna between Australia and South Africa. Gene flow also appears restricted along a continuous continental margin in this species, with data tentatively suggesting the delineation of two management units within Australian waters. Further sampling, however, is required for a more robust evaluation of the latter finding. Evidence indicates that all sampled populations were shaped by a substantial demographic expansion event, with the resultant high genetic diversity being cause for optimism when considering conservation of this commercially-targeted species in the southern Indo-Pacific.

A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

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Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

2018-06-12

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

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Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

2015-08-01

The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Serum-free Erythroid Differentiation for Efficient Genetic Modification and High-Level Adult Hemoglobin Production.

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Uchida, Naoya; Demirci, Selami; Haro-Mora, Juan J; Fujita, Atsushi; Raines, Lydia N; Hsieh, Matthew M; Tisdale, John F

2018-06-15

In vitro erythroid differentiation from primary human cells is valuable to develop genetic strategies for hemoglobin disorders. However, current erythroid differentiation methods are encumbered by modest transduction rates and high baseline fetal hemoglobin production. In this study, we sought to improve both genetic modification and hemoglobin production among human erythroid cells in vitro . To model therapeutic strategies, we transduced human CD34 + cells and peripheral blood mononuclear cells (PBMCs) with lentiviral vectors and compared erythropoietin-based erythroid differentiation using fetal-bovine-serum-containing media and serum-free media. We observed more efficient transduction (85%-93%) in serum-free media than serum-containing media (20%-69%), whereas the addition of knockout serum replacement (KSR) was required for serum-free media to promote efficient erythroid differentiation (96%). High-level adult hemoglobin production detectable by electrophoresis was achieved using serum-free media similar to serum-containing media. Importantly, low fetal hemoglobin production was observed in the optimized serum-free media. Using KSR-containing, serum-free erythroid differentiation media, therapeutic adult hemoglobin production was detected at protein levels with β-globin lentiviral transduction in both CD34 + cells and PBMCs from sickle cell disease subjects. Our in vitro erythroid differentiation system provides a practical evaluation platform for adult hemoglobin production among human erythroid cells following genetic manipulation.

Genetic differentiation and population structure of five ethnic groups of Punjab (North-West India).

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Singh, Gagandeep; Talwar, Indu; Sharma, Rubina; Matharoo, Kawaljit; Bhanwer, A J S

2016-12-01

The state of Punjab in the North-West part of India has acted as the main passage for all the major human invasions into the Indian subcontinent. It has resulted in the mixing of foreign gene pool into the local populations, which led to an extensive range of genetic diversity and has influenced the genetic structure of populations in Punjab, North-West India. The present study was conducted to examine the genetic structure, relationships, and extent of genetic differentiation in five Indo-European speaking ethnic groups of Punjab. A total of 1021 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris, and Scheduled castes were analyzed for four human-specific Ins/Del polymorphic loci (ACE, APO, PLAT, and D1) and three restriction fragment length polymorphisms ESR (PvuII), LPL (PvuII), and T2 (MspI) using Polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. The frequency of the Alu insertion at APO locus was observed to exhibit the highest value (82.6-96.3 %), whereas D1 exhibited the lowest (26.5-45.6 %) among all the ethnic groups. The average heterozygosity among the studied populations ranged from 0.3816 in Banias to 0.4163 in Khatris. The F ST values ranged from 0.0418 to 0.0033 for the PLAT and LPL loci, respectively, with an average value being 0.0166. Phylogenetic analysis revealed that Banias and Khatris are genetically closest to each other. The Jat Sikhs are genetically close to Brahmins and are distant from the Banias. The Jat Sikhs, Banias, Brahmins, and Khatris are genetically very distant from the Scheduled castes. Overall, Uniform allele frequency distribution patterns, high average heterozygosity values, and a small degree of genetic differentiation in this study suggest a genetic proximity among the selected populations. A low level of genetic differentiation was observed in the studied population groups indicating that genetic drift might have been small or negligible in shaping

Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia.

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Zhu, Wenbin; Wang, Lanmei; Dong, Zaijie; Chen, Xingting; Song, Feibiao; Liu, Nian; Yang, Hui; Fu, Jianjun

2016-08-11

Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

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FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

2016-01-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

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Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

2016-05-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

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

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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. Copyright © 2015 Elsevier B.V. All rights reserved.

Pairwise Comparison and Distance Measure of Hesitant Fuzzy Linguistic Term Sets

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Han-Chen Huang

2014-01-01

Full Text Available A hesitant fuzzy linguistic term set (HFLTS, allowing experts using several possible linguistic terms to assess a qualitative linguistic variable, is very useful to express people’s hesitancy in practical decision-making problems. Up to now, a little research has been done on the comparison and distance measure of HFLTSs. In this paper, we present a comparison method for HFLTSs based on pairwise comparisons of each linguistic term in the two HFLTSs. Then, a distance measure method based on the pairwise comparison matrix of HFLTSs is proposed, and we prove that this distance is equal to the distance of the average values of HFLTSs, which makes the distance measure much more simple. Finally, the pairwise comparison and distance measure methods are utilized to develop two multicriteria decision-making approaches under hesitant fuzzy linguistic environments. The results analysis shows that our methods in this paper are more reasonable.

Analysis of genetic diversity in Bolivian llama populations using microsatellites.

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Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

2013-08-01

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

Genetic diversity and population genetic analysis of Donax vittatus (Mollusca: Bivalvia) and phylogeny of the genus with mitochondrial and nuclear markers

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Fernández-Pérez, Jenyfer; Froufe, Elsa; Nantón, Ana; Gaspar, Miguel B.; Méndez, Josefina

2017-10-01

In this study, the genetic diversity of Donax vittatus across the Iberian Peninsula was investigated using four mitochondrial (COI, Cytb, 16S F and M types) and three nuclear (H3, 18S and 28S) genes. These same molecular markers were also sequenced in D. semistriatus and D variegatus to address the phylogenetic relationships of the species of the genus Donax common along the European coasts. Our results showed high haplotype diversity in combination with a low nucleotide diversity and a star-shaped network with a predominant haplotype, indicating a recent population expansion for the examined sampling sites of D. vittatus. Furthermore, analyses of population differentiation performed with COI mitochondrial marker, including global FST estimation and pairwise FST values, indicated the non-existence of significant genetic structure in D. vittatus of Northwest Iberian populations. Because these localities show a high genetic similarity, we suggest that D. vittatus could be a potentially alternative exploitable resource, as complement to the D. trunculus fisheries, whose natural stocks have decreased dramatically in some areas. Furthermore, we present for the first time, evidence of DUI in the clams D. vittatus and D. semistriatus.

Genetic diversity and geographic differentiation analysis of duckweed using inter-simple sequence repeat markers.

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Xue, Huiling; Xiao, Yao; Jin, Yanling; Li, Xinbo; Fang, Yang; Zhao, Hai; Zhao, Yun; Guan, Jiafa

2012-01-01

Duckweed, with rapid growth rate and high starch content, is a new alternate feedstock for bioethanol production. The genetic diversity among 27 duckweed populations of seven species in genus Lemna and Spirodela from China and Vietnam was analyzed by ISSR-PCR. Eight ISSR primers generating a reproducible amplification banding pattern had been screened. 89 polymorphic bands were scored out of the 92 banding patterns of 16 Lemna populations, accounting for 96.74% of the polymorphism. 98 polymorphic bands of 11 Spirodela populations were scored out of 99 banding patterns, and the polymorphism was 98.43%. The genetic distance of Lemna varied from 0.127 to 0.784, and from 0.138 to 0.902 for Spirodela, which indicated a high level of genetic variation among the populations studied. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis corresponded well with the genetic distance. Populations from Sichuan China grouped together and so did the populations from Vietnam, which illuminated populations collected from the same region clustered into one group. Especially, the only one population from Tibet was included in subgroup A2 alone. Clustering analysis indicated that the geographic differentiation of collected sites correlated closely with the genetic differentiation of duckweeds. The results suggested that geographic differentiation had great influence on genetic diversity of duckweed in China and Vietnam at the regional scale. This study provided primary guidelines for collection, conservation, characterization of duckweed resources for bioethanol production etc.

Pairwise Trajectory Management (PTM): Concept Overview

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Jones, Kenneth M.; Graff, Thomas J.; Chartrand, Ryan C.; Carreno, Victor; Kibler, Jennifer L.

2017-01-01

Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the precision of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the PTM minimum spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This paper provides an overview of the proposed application, description of a few key scenarios, high level discussion of expected air and ground equipment and procedure changes, overview of a potential flight crew human-machine interface that would support PTM operations and some initial PTM benefits results.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

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Manuel Gil

2014-09-01

Full Text Available Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989 which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

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Gil, Manuel

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus).

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DeFaveri, Jacquelin; Merilä, Juha

2015-01-01

Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus) populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (Ne) of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, Nes were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the Ne estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable - at least over periods of few generations - across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.

Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus.

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Jacquelin DeFaveri

Full Text Available Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (Ne of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, Nes were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the Ne estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable - at least over periods of few generations - across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.

East-west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

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Guay, P.-J.; Chesser, R.T.; Mulder, R.A.; Afton, A.D.; Paton, D.C.; McCracken, K.G.

2010-01-01

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (??ST = 0. 747), one nuclear intron (??ST = 0.193) and eight microsatellite loci (FST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews' (Austral Avian Record 2:83-107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other. ?? 2010 Springer Science+Business Media B.V.

Pattern of genetic differentiation of an incipient speciation process: The case of the high Andean killifish Orestias

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Guerrero-Jiménez, Claudia Jimena; Peña, Fabiola; Morales, Pamela; Méndez, Marco; Sallaberry, Michel; Vila, Irma; Poulin, Elie

2017-01-01

During the Pleistocene and Holocene, the southwest Andean Altiplano (17°-22°S) was affected by repeated fluctuations in water levels, high volcanic activity and major tectonic movements. In the early Holocene the humid Tauca phase shifted to the arid conditions that have lasted until the present, producing endorheic rivers, lakes, lagoons and wetlands. The endemic fish Orestias (Cyprinodontidae) represents a good model to observe the genetic differentiation that characterizes an incipient speciation process in allopatry since the morphospecies described inhabit a restricted geographic area, with present habitat fragmentation. The genetic diversity and population structure of four endemic morphospecies of Orestias (Cyprinodontidae) found in the Lauca National Park (LNP) analyzed with mitochondrial markers (Control Region) and eight microsatellites, revealed the existence of genetic groups that matches the fragmentation of these systems. High values of genetic and phylogeographic differentiation indices were observed between Chungará Lake and Piacota lagoon. The group composed of the Lauca River, Copapujo and Chuviri wetlands sampling sites showed a clear signal of expansion, with a star-like haplotype network. Levels of genetic differentiation were lower than in Chungará and Piacota, suggesting that these localities would have differentiated after the bottlenecks linked to the collapse of Parinacota volcano. The Parinacota sample showed a population signal that differed from the other localities revealing greater genetic diversity and a disperse network, presenting haplotypes shared with other LNP localities. A mixing pattern of the different genetic groups was evident using the microsatellite markers. The chronology of the vicariance events in LNP may indicate that the partition process of the Orestias populations was gradual. Considering this, and in view of the genetic results, we may conclude that the morphospecies from LNP are populations in ongoing

Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

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Jones, Kenneth M.

2014-01-01

This document describes the Pair-wise Trajectory Management-Oceanic (PTM-O) Concept of Operations (ConOps). Pair-wise Trajectory Management (PTM) is a concept that includes airborne and ground-based capabilities designed to enable and to benefit from, airborne pair-wise distance-monitoring capability. PTM includes the capabilities needed for the controller to issue a PTM clearance that resolves a conflict for a specific pair of aircraft. PTM avionics include the capabilities needed for the flight crew to manage their trajectory relative to specific designated aircraft. Pair-wise Trajectory Management PTM-Oceanic (PTM-O) is a regional specific application of the PTM concept. PTM is sponsored by the National Aeronautics and Space Administration (NASA) Concept and Technology Development Project (part of NASA's Airspace Systems Program). The goal of PTM is to use enhanced and distributed communications and surveillance along with airborne tools to permit reduced separation standards for given aircraft pairs, thereby increasing the capacity and efficiency of aircraft operations at a given altitude or volume of airspace.

Genetic differentiation in Elaeocarpus photiniifolia (Elaeocarpaceae) associated with geographic distribution and habitat variation in the Bonin (Ogasawara) Islands.

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Sugai, Kyoko; Setsuko, Suzuki; Nagamitsu, Teruyoshi; Murakami, Noriaki; Kato, Hidetoshi; Yoshimaru, Hiroshi

2013-11-01

Gene flow between populations in different environmental conditions can be limited due to divergent natural selection, thus promoting genetic differentiation. Elaeocarpus photiniifolia, an endemic tree species in the Bonin Islands, is distributed in two types of habitats, dry scrubs and mesic forests. We aim to elucidate the genetic differentiation in E. photiniifolia within and between islands and between the habitat types. We investigated genotypes of 639 individuals from 19 populations of E. photiniifolia and its closely-related E. sylvestris at 24 microsatellite loci derived from expressed sequence tags. The data revealed genetic differentiation (1) between E. photiniifolia and E. sylvestris (0.307 ≤ F ST ≤ 0.470), (2) between the E. photiniifolia populations of the Chichijima and Hahajima Island Groups in the Bonin Islands (0.033 ≤ F ST ≤ 0.121) and (3) between E. photiniifolia populations associated with dry scrubs and mesic forests in the Chichijima Island Group (0.005 ≤ F ST ≤ 0.071). Principal coordinate analysis and Bayesian clustering analysis also showed that genetically distinct groups were associated with the habitat types, and isolation by distance was not responsible for the genetic differentiation. These findings suggest that E. photiniifolia is divided into genetically differentiated groups associated with different environmental conditions in the Bonin Islands.

Robust Subjective Visual Property Prediction from Crowdsourced Pairwise Labels.

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Fu, Yanwei; Hospedales, Timothy M; Xiang, Tao; Xiong, Jiechao; Gong, Shaogang; Wang, Yizhou; Yao, Yuan

2016-03-01

The problem of estimating subjective visual properties from image and video has attracted increasing interest. A subjective visual property is useful either on its own (e.g. image and video interestingness) or as an intermediate representation for visual recognition (e.g. a relative attribute). Due to its ambiguous nature, annotating the value of a subjective visual property for learning a prediction model is challenging. To make the annotation more reliable, recent studies employ crowdsourcing tools to collect pairwise comparison labels. However, using crowdsourced data also introduces outliers. Existing methods rely on majority voting to prune the annotation outliers/errors. They thus require a large amount of pairwise labels to be collected. More importantly as a local outlier detection method, majority voting is ineffective in identifying outliers that can cause global ranking inconsistencies. In this paper, we propose a more principled way to identify annotation outliers by formulating the subjective visual property prediction task as a unified robust learning to rank problem, tackling both the outlier detection and learning to rank jointly. This differs from existing methods in that (1) the proposed method integrates local pairwise comparison labels together to minimise a cost that corresponds to global inconsistency of ranking order, and (2) the outlier detection and learning to rank problems are solved jointly. This not only leads to better detection of annotation outliers but also enables learning with extremely sparse annotations.

Theory of pairwise lesion interaction

International Nuclear Information System (INIS)

Harder, Dietrich; Virsik-Peuckert, Patricia; Bartels, Ernst

1992-01-01

A comparison between repair time constants measured both at the molecular and cellular levels has shown that the DNA double strand break is the molecular change of key importance in the causation of cellular effects such as chromosome aberrations and cell inactivation. Cell fusion experiments provided the evidence that it needs the pairwise interaction between two double strand breaks - or more exactly between the two ''repair sites'' arising from them in the course of enzymatic repair - to provide the faulty chromatin crosslink which leads to cytogenetic and cytolethal effects. These modern experiments have confirmed the classical assumption of pairwise lesion interaction (PLI) on which the models of Lea and Neary were based. It seems worthwhile to continue and complete the mathematical treatment of their proposed mechanism in order to show in quantitative terms that the well-known fractionation, protraction and linear energy transfer (LET) irradiation effects are consequences of or can at least be partly attributed to PLI. Arithmetic treatment of PLI - a second order reaction - has also the advantage of providing a prerequisite for further investigations into the stages of development of misrepair products such as chromatin crosslinks. It has been possible to formulate a completely arithmetic theory of PLI by consequently applying three biophysically permitted approximations - pure first order lesion repair kinetics, dose-independent repair time constants and low yield of the ionization/lesion conversion. The mathematical approach will be summarized here, including several formulae not elaborated at the time of previous publications. We will also study an application which sheds light on the chain of events involved in PLI. (author)

Characterization of type and genetic diversity among soybean cyst nematode differentiators

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Éder Matsuo

2012-04-01

Full Text Available The development of soybean cyst nematode, Heterodera glycines Ichinohe, resistant genotypes with high yields has been one of the objectives of soybean (Glycine max (L. Merrill breeding programs. The objective of this study was to characterize the pathotype of soybean cyst nematodes and analyze the genetic diversity of ten differentiator lines ('Lee 74', Peking, Pickett, PI 88788, PI 90763, PI 437654, PI 209332, PI 89772, PI 548316 and 'Hartwig'. Inoculum was obtained from plants cultivated in field soil in Viçosa, state of Minas Gerais, Brazil. Thirty-four days after inoculating each plant with 4,000 eggs, the number of females, female index, total number of eggs, number of eggs per female, reproduction factor, plant height, number of nodes, fresh and dry matter weights were assessed. The differential lines were first grouped with Scott-Knott test. Subsequently, the genetic diversity was evaluated using dendrograms, graphic analysis and the Tocher grouping method. The inoculum of H. glycines obtained from NBSGBP-UFV was characterized as HG Type 0. The differentiating lines were divergent, and PI 89772, PI 437654, 'Hartwig' and 'Peking' had the greatest potential for use in breeding programs.

Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

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A. A. Maw

2015-01-01

Full Text Available The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels markers. Most of the indels loci were polymorphic (71% to 96%, and the genetic variability was similar in all populations. The average observed heterozygosities (HO and expected heterozygosities (HE ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088 than Myanmar (0.041 and Laotian (0.024 populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ tree, using Nei’s genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3 from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

A decomposition of pairwise continuity via ideals

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Mahes Wari

2016-02-01

Full Text Available In this paper, we introduce and study the notions of (i, j - regular - ℐ -closed sets, (i, j - Aℐ -sets, (i, j - ℐ -locally closed sets, p- Aℐ -continuous functions and p- ℐ -LC-continuous functions in ideal bitopological spaces and investigate some of their properties. Also, a new decomposition of pairwise continuity is obtained using these sets.

Modeling Expressed Emotions in Music using Pairwise Comparisons

DEFF Research Database (Denmark)

Madsen, Jens; Nielsen, Jens Brehm; Jensen, Bjørn Sand

2012-01-01

We introduce a two-alternative forced-choice experimental paradigm to quantify expressed emotions in music using the two wellknown arousal and valence (AV) dimensions. In order to produce AV scores from the pairwise comparisons and to visualize the locations of excerpts in the AV space, we...

Genetic diversity of Hypostomus ancistroides (Teleostei, Loricariidae from an urban stream

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Silvia H. Sofia

2008-01-01

Full Text Available In this study, random amplified polymorphic DNA (RAPD markers were applied to analyze the genetic diversity of samples of the Neotropical catfish Hypostomus ancistroides, collected from four sites (S1, S2, S3 and S4 along an urban stream in Southern Brazil. The 11 primers used in RAPD analysis amplified 147 loci, 76 (51.7% of which were polymorphic. The proportions of polymorphic loci observed in the four samples were: 29.93% (S1, 31.97% (S2, 23.81% (S3 and 38.77% (S4. The average heterozygosity within sampling localities ranged from 0.1230 to 0.1526 and unbiased genetic distances ranged from 0.0253 to 0.0445. AMOVA partitioned 90.85% of the total variation within samples and 9.15% among samples. Excepting for the sample pair S1-S2 (phiST = 0.02784; p > 0.05, all others pairwise phiST values were significantly greater than zero, indicating moderate genetic differentiation among catfish samples from four localities. The relative low levels of genetic variation detected in all groups studied could be related to different factors, including the sedentary habit of these fish, which can be eroding the genetic variation of H. ancistroides from each locality.

Genetic exchange versus genetic differentiation in a medium-sized inversion of Drosophila: the A2/Ast arrangements of Drosophila subobscura.

Science.gov (United States)

Nóbrega, Clévio; Khadem, Mahnaz; Aguadé, Montserrat; Segarra, Carmen

2008-08-01

Chromosomal inversion polymorphism affects nucleotide variation at loci associated with inversions. In Drosophila subobscura, a species with a rich chromosomal inversion polymorphism and the largest recombinational map so far reported in the Drosophila genus, extensive genetic structure of nucleotide variation was detected in the segment affected by the O(3) inversion, a moderately sized inversion at Muller's element E. Indeed, a strong genetic differentiation all over O(3) and no evidence of a higher genetic exchange in the center of the inversion than at breakpoints were detected. In order to ascertain, whether other polymorphic and differently sized inversions of D. subobscura also exhibited a strong genetic structure, nucleotide variation in 5 gene regions (P236, P275, P150, Sxl, and P125) located along the A(2) inversion was analyzed in A(st) and A(2) chromosomes of D. subobscura. A(2) is a medium-sized inversion at Muller's element A and forms a single inversion loop in heterokaryotypes. The lower level of variation in A(2) relative to A(st) and the significant excess of low-frequency variants at polymorphic sites indicate that nucleotide variation at A(2) is not at mutation-drift equilibrium. The closest region to an inversion breakpoint, P236, exhibits the highest level of genetic differentiation (F(ST)) and of linkage disequilibrium (LD) between arrangements and variants at nucleotide polymorphic sites. The remaining 4 regions show a higher level of genetic exchange between A(2) and A(st) chromosomes than P236, as revealed by F(ST) and LD estimates. However, significant genetic differentiation between the A(st) and A(2) arrangements was detected not only at P236 but also in the other 4 regions separated from the nearest breakpoint by 1.2-2.9 Mb. Therefore, the extent of genetic exchange between arrangements has not been high enough to homogenize nucleotide variation in the center of the A(2) inversion. A(2) can be considered a typical successful inversion

Differential network analysis reveals genetic effects on catalepsy modules.

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Ovidiu D Iancu

Full Text Available We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS formed by crossing four inbred strains (HS4 and a heterogeneous stock (HS-CC formed from the inbred strain founders of the Collaborative Cross (CC. All three selections were successful, with large differences in haloperidol response emerging within three generations. Using a custom differential network analysis procedure, we found that gene coexpression patterns changed significantly; importantly, a number of these changes were concordant across genetic backgrounds. In contrast, absolute gene-expression changes were modest and not concordant across genetic backgrounds, in spite of the large and similar phenotypic differences. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

KAUST Repository

Cui, Xuefeng

2015-09-09

To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

Differential diagnosis of genetic disease by DNA restriction fragment length polymorphisms

NARCIS (Netherlands)

Bolhuis, P. A.; Defesche, J. C.; van der Helm, H. J.

1987-01-01

DNA restriction fragment length polymorphisms (RFLPs) are used for diagnosis of genetic disease in families known to be affected by specific disorders, but RFLPs can be also useful for the differential diagnosis of hereditary disease. An RFLP pattern represents the inheritance of chromosomal markers

Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

Science.gov (United States)

Clowers, Katie J; Heilberger, Justin; Piotrowski, Jeff S; Will, Jessica L; Gasch, Audrey P

2015-09-01

How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)

Science.gov (United States)

Talla, Venkat; Kalsoom, Faheema; Shipilina, Daria; Marova, Irina; Backström, Niclas

2017-01-01

Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)—two recently diverged species which differ in morphology, plumage, song, habitat, and migration—to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that postdivergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species. PMID:29054864

Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

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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

Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment

Science.gov (United States)

Heo, Muyoung; Kim, Suhkmann; Moon, Eun-Joung; Cheon, Mookyung; Chung, Kwanghoon; Chang, Iksoo

2005-07-01

Although a coarse-grained description of proteins is a simple and convenient way to attack the protein folding problem, the construction of a global pairwise energy function which can simultaneously recognize the native folds of many proteins has resulted in partial success. We have sought the possibility of a systematic improvement of this pairwise-contact energy function as we extended the parameter space of amino acids, incorporating local environments of amino acids, beyond a 20×20 matrix. We have studied the pairwise contact energy functions of 20×20 , 60×60 , and 180×180 matrices depending on the extent of parameter space, and compared their effect on the learnability of energy parameters in the context of a gapless threading, bearing in mind that a 20×20 pairwise contact matrix has been shown to be too simple to recognize the native folds of many proteins. In this paper, we show that the construction of a global pairwise energy function was achieved using 1006 training proteins of a homology of less than 30%, which include all representatives of different protein classes. After parametrizing the local environments of the amino acids into nine categories depending on three secondary structures and three kinds of hydrophobicity (desolvation), the 16290 pairwise contact energies (scores) of the amino acids could be determined by perceptron learning and protein threading. These could simultaneously recognize all the native folds of the 1006 training proteins. When these energy parameters were tested on the 382 test proteins of a homology of less than 90%, 370 (96.9%) proteins could recognize their native folds. We set up a simple thermodynamic framework in the conformational space of decoys to calculate the unfolded fraction and the specific heat of real proteins. The different thermodynamic stabilities of E.coli ribonuclease H (RNase H) and its mutants were well described in our calculation, agreeing with the experiment.

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.

Geographic differences in patterns of genetic differentiation among bitter and sweet manioc (Manihot esculenta subsp. esculenta; Euphorbiaceae).

Science.gov (United States)

Bradbury, E Jane; Duputié, Anne; Delêtre, Marc; Roullier, Caroline; Narváez-Trujillo, Alexandra; Manu-Aduening, Joseph A; Emshwiller, Eve; McKey, Doyle

2013-05-01

Manioc (Manihot esculenta subsp. esculenta), one of the most important tropical food crops, is commonly divided according to cyanide content into two use-categories, "sweet" and "bitter." While bitter and sweet varieties are genetically differentiated at the local scale, whether this differentiation is consistent across continents is yet unknown. • Using eight microsatellite loci, we genotyped 522 manioc samples (135 bitter and 387 sweet) from Ecuador, French Guiana, Cameroon, Gabon, Ghana, and Vanuatu. Genetic differentiation between use-categories was assessed using double principal coordinate analyses (DPCoA) with multivariate analysis of variance (MANOVA) and Jost's measure of estimated differentiation (D(est)). Genetic structure was analyzed using Bayesian clustering analysis. • Manioc neutral genetic diversity was high in all sampled regions. Sweet and bitter manioc landraces are differentiated in South America but not in Africa. Correspondingly, bitter and sweet manioc samples share a higher proportion of neutral alleles in Africa than in South America. We also found seven clones classified by some farmers as sweet and by others as bitter. • Lack of differentiation in Africa is most likely due to postintroduction hybridization between bitter and sweet manioc. Inconsistent transfer from South America to Africa of ethnobotanical knowledge surrounding use-category management may contribute to increased hybridization in Africa. Investigating this issue requires more data on the variation in cyanogenesis in roots within and among manioc populations and how manioc diversity is managed on the farm.

Local environment but not genetic differentiation influences biparental care in ten plover populations.

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Orsolya Vincze

Full Text Available Social behaviours are highly variable between species, populations and individuals. However, it is contentious whether behavioural variations are primarily moulded by the environment, caused by genetic differences, or a combination of both. Here we establish that biparental care, a complex social behaviour that involves rearing of young by both parents, differs between closely related populations, and then test two potential sources of variation in parental behaviour between populations: ambient environment and genetic differentiation. We use 2904 hours behavioural data from 10 geographically distinct Kentish (Charadrius alexandrinus and snowy plover (C. nivosus populations in America, Europe, the Middle East and North Africa to test these two sources of behavioural variation. We show that local ambient temperature has a significant influence on parental care: with extreme heat (above 40 °C total incubation (i.e. % of time the male or female incubated the nest increased, and female share (% female share of incubation decreased. By contrast, neither genetic differences between populations, nor geographic distances predicted total incubation or female's share of incubation. These results suggest that the local environment has a stronger influence on a social behaviour than genetic differentiation, at least between populations of closely related species.

Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.

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Małgorzata Pilot

Full Text Available Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13C and δ(15N values for Eastern European wolves (Canis lupus as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure, to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores.

Genetic Differentiation in Insular Lowland Rainforests: Insights from Historical Demographic Patterns in Philippine Birds.

Science.gov (United States)

Sánchez-González, Luis Antonio; Hosner, Peter A; Moyle, Robert G

2015-01-01

Phylogeographic studies of Philippine birds support that deep genetic structure occurs across continuous lowland forests within islands, despite the lack of obvious contemporary isolation mechanisms. To examine the pattern and tempo of diversification within Philippine island forests, and test if common mechanisms are responsible for observed differentiation, we focused on three co-distributed lowland bird taxa endemic to Greater Luzon and Greater Negros-Panay: Blue-headed Fantail (Rhipidura cyaniceps), White-browed Shama (Copsychus luzoniensis), and Lemon-throated Leaf-Warbler (Phylloscopus cebuensis). Each species has two described subspecies within Greater Luzon, and a single described subspecies on Greater Negros/Panay. Each of the three focal species showed a common geographic pattern of two monophyletic groups in Greater Luzon sister to a third monophyletic group found in Greater Negros-Panay, suggesting that common or similar biogeographic processes may have produced similar distributions. However, studied species displayed variable levels of mitochondrial DNA differentiation between clades, and genetic differentiation within Luzon was not necessarily concordant with described subspecies boundaries. Population genetic parameters for the three species suggested both rapid population growth from small numbers and geographic expansion across Luzon Island. Estimates of the timing of population expansion further supported that these events occurred asynchronously throughout the Pleistocene in the focal species, demanding particular explanations for differentiation, and support that co-distribution may be secondarily congruent.

Habitat Fragmentation Differentially Affects Genetic Variation, Phenotypic Plasticity and Survival in Populations of a Gypsum Endemic

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Silvia Matesanz

2017-05-01

Full Text Available Habitat fragmentation, i.e., fragment size and isolation, can differentially alter patterns of neutral and quantitative genetic variation, fitness and phenotypic plasticity of plant populations, but their effects have rarely been tested simultaneously. We assessed the combined effects of size and connectivity on these aspects of genetic and phenotypic variation in populations of Centaurea hyssopifolia, a narrow endemic gypsophile that previously showed performance differences associated with fragmentation. We grew 111 maternal families sampled from 10 populations that differed in their fragment size and connectivity in a common garden, and characterized quantitative genetic variation, phenotypic plasticity to drought for key functional traits, and plant survival, as a measure of population fitness. We also assessed neutral genetic variation within and among populations using eight microsatellite markers. Although C. hyssopifolia is a narrow endemic gypsophile, we found substantial neutral genetic variation and quantitative variation for key functional traits. The partition of genetic variance indicated that a higher proportion of variation was found within populations, which is also consistent with low population differentiation in molecular markers, functional traits and their plasticity. This, combined with the generally small effect of habitat fragmentation suggests that gene flow among populations is not restricted, despite large differences in fragment size and isolation. Importantly, population’s similarities in genetic variation and plasticity did not reflect the lower survival observed in isolated populations. Overall, our results indicate that, although the species consists of genetically variable populations able to express functional plasticity, such aspects of adaptive potential may not always reflect populations’ survival. Given the differential effects of habitat connectivity on functional traits, genetic variation and fitness

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

OpenAIRE

Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe

2015-01-01

Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-...

Temporal genetic population structure and interannual variation in migration behavior of Pacific Lamprey Entosphenus tridentatus

Science.gov (United States)

Clemens, Benjamin J.; Wyss, Lance A.; McCoun, Rebecca; Courter, Ian; Schwabe, Lawrence; Peery, Christopher; Schreck, Carl B.; Spice, Erin K.; Docker, Margaret F.

2017-01-01

Studies using neutral loci suggest that Pacific lamprey, Entosphenus tridentatus, lack strong spatial genetic population structure. However, it is unknown whether temporal genetic population structure exists. We tested whether adult Pacific lamprey: (1) show temporal genetic population structure; and (2) migrate different distances between years. We non-lethally sampled lamprey for DNA in 2009 and 2010 and used eight microsatellite loci to test for genetic population structure. We used telemetry to record the migration behaviors of these fish. Lamprey were assignable to three moderately differentiated genetic clusters (FST = 0.16–0.24 for all pairwise comparisons): one cluster was composed of individuals from 2009, and the other two contained individuals from 2010. The FST value between years was 0.13 and between genetic clusters within 2010 was 0.20. A total of 372 (72.5%) fish were detected multiple times during their migrations. Most fish (69.9%) remained in the mainstem Willamette River; the remaining 30.1% migrated into tributaries. Eighty-two lamprey exhibited multiple back-and-forth movements among tributaries and the mainstem, which may indicate searching behaviors. All migration distances were significantly greater in 2010, when the amplitude of river discharge was greater. Our data suggest genetic structuring between and within years that may reflect different cohorts.

Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil

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Almeida Leonardo D

2007-12-01

Full Text Available Abstract Background Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil. Results Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine. For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals. Conclusion This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The

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

Science.gov (United States)

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

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

Pairwise Trajectory Management (PTM): Concept Description and Documentation

Science.gov (United States)

Jones, Kenneth M.; Graff, Thomas J.; Carreno, Victor; Chartrand, Ryan C.; Kibler, Jennifer L.

2018-01-01

Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the accuracy of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the minimum PTM spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This document provides an overview of the proposed application, a description of several key scenarios, a high level discussion of expected air and ground equipment and procedure changes, a description of a NASA human-machine interface (HMI) prototype for the flight crew that would support PTM operations, and initial benefits analysis results. Additionally, included as appendices, are the following documents: the PTM Operational Services and Environment Definition (OSED) document and a companion "Future Considerations for the Pairwise Trajectory Management (PTM) Concept: Potential Future Updates for the PTM OSED" paper, a detailed description of the PTM algorithm and PTM Limit Mach rules, initial PTM safety requirements and safety assessment documents, a detailed description of the design, development, and initial evaluations of the proposed flight crew HMI, an overview of the methodology and results of PTM pilot training

Quantifying population genetic differentiation from next-generation sequencing data

DEFF Research Database (Denmark)

Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

2013-01-01

method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based...... on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled......Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data...

Genetic biomarkers for brain hemisphere differentiation in Parkinson's Disease

Science.gov (United States)

Hourani, Mou'ath; Mendes, Alexandre; Berretta, Regina; Moscato, Pablo

2007-11-01

This work presents a study on the genetic profile of the left and right hemispheres of the brain of a mouse model of Parkinson's disease (PD). The goal is to characterize, in a genetic basis, PD as a disease that affects these two brain regions in different ways. Using the same whole-genome microarray expression data introduced by Brown et al. (2002) [1], we could find significant differences in the expression of some key genes, well-known to be involved in the mechanisms of dopamine production control and PD. The problem of selecting such genes was modeled as the MIN (α,β)—FEATURE SET problem [2]; a similar approach to that employed previously to find biomarkers for different types of cancer using gene expression microarray data [3]. The Feature Selection method produced a series of genetic signatures for PD, with distinct expression profiles in the Parkinson's model and control mice experiments. In addition, a close examination of the genes composing those signatures shows that many of them belong to genetic pathways or have ontology annotations considered to be involved in the onset and development of PD. Such elements could provide new clues on which mechanisms are implicated in hemisphere differentiation in PD.

Revision of Begomovirus taxonomy based on pairwise sequence comparisons

KAUST Repository

Brown, Judith K.; Zerbini, F. Murilo; Navas-Castillo, Jesú s; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé , Elvira; Briddon, Rob W.; Herná ndez-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind

2015-01-01

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Revision of Begomovirus taxonomy based on pairwise sequence comparisons

KAUST Repository

Brown, Judith K.

2015-04-18

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Shallow Population Genetic Structures of Thread-sail Filefish ( Populations from Korean Coastal Waters

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M. Yoon

2012-02-01

Full Text Available Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076 and nucleotide diversities (0.014 to 0.019, and low levels of genetic differentiation among populations inferred from pairwise population FST values (−0.007 to 0.107, support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA revealed weak but significant genetic structures among three groups (FCT = 0.028, p<0.05, and no genetic variation within groups (0.53%; FSC = 0.005, p = 0.23. These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

Genetic effects of air pollution on forest tree species of the Carpathian Mountains

International Nuclear Information System (INIS)

Longauer, Roman; Goemoery, Dusan; Paule, Ladislav; Blada, Ioan; Popescu, Flaviu; Mankovska, Blanka; Mueller-Starck, Gerhard; Schubert, Roland; Percy, Kevin; Szaro, Robert C.; Karnosky, David F.

2004-01-01

The effects of air pollution on the genetic structure of Norway spruce, European silver fir and European beech were studied at four polluted sites in Slovakia, Romania and Czech Republic. In order to reduce potential effects of site heterogeneity on the health condition, pair-wise sampling of pollution-tolerant and sensitive trees was applied. Genotypes of sampled trees were determined at 21 isozyme gene loci of spruce, 18 loci of fir and 15 loci of beech. In comparison with Norway spruce, fewer genetic differences were revealed in beech and almost no differentiation between pollution-tolerant and sensitive trees was observed in fir. In adult stands of Norway spruce, sensitive trees exhibited higher genetic multiplicity and diversity. The decline of pollution-sensitive trees may result thus in a gradual genetic depletion of pollution-exposed populations of Norway spruce through the loss of less frequent alleles with potential adaptive significance to altered stressing regimes in the future. Comparison of the subsets of sensitive and tolerant Norway spruce individuals as determined by presence or absence of discolorations (''spruce yellowing'') revealed different heterozygosity at 3 out of 11 polymorphic loci. - Genetic effects of air pollution on main forest trees of the Carpathians are species- and site-specific

Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis accessions from two ex situ genebanks.

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Eltohamy A A Yousef

Full Text Available Cauliflower (Brassica oleracea var. botrytis is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS. They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1% of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower

Theory of pairwise coupling embedded in more general local dispersion relations

International Nuclear Information System (INIS)

Fuchs, V.; Bers, A.; Harten, L.

1985-01-01

Earlier work on the mode conversion theory by Fuchs, Ko, and Bers is detailed and expanded upon, and its relation to energy conservation is discussed. Given a local dispersion relation, D(ω; k, z) = 0, describing stable waves excited at an externally imposed frequency ω, a pairwise mode-coupling event embedded therein is extracted by expanding D(k, z) around a contour k = k/sub c/(z) given by partialD/partialk = 0. The branch points of D(k, z) = 0 are the turning points of a second-order differential-equation representation. In obtaining the fraction of mode-converted energy, the connection formula and conservation of energy must be used together. Also, proper attention must be given to distinguish cases for which the coupling disappears or persists upon confluence of the branches, a property which is shown to depend on the forward (v/sub g/v/sub ph/>0) or backward (v/sub g/v/sub ph/<0) nature of the waves. Examples occurring in ion-cyclotron and lower-hybrid heating are presented, illustrating the use of the theory

Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

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Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

2011-12-01

Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

Adaptive genetic variability and differentiation of Croatian and Austrian Quercus robur L. populations at a drought prone field trial

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Saša Bogdan

2017-07-01

Full Text Available Provenance trials, where populations of different geographical origin are tested in a common environment (common garden test, are a tool suited to allow the study of intraspecific adaptive genetic variation. Research of pedunculate oak (Quercus robur L. adaptive genetic variability through analyses of populations in common garden tests has a long tradition. However, pedunculated oak populations originating south-eastern from the Alps have been scarcely studied in this way. This study addresses the adaptive genetic variability and differentiation of pedunculate oak populations originating from Austria and Croatia in a provenance/progeny field trial. Studied plants were six years old and were growing at the trial for three years. After two years of unusually low precipitations height and survival were analysed. The total mean height of all plants in the trial was 137.8 cm and ranged from 123.0 cm to 151.8 cm. The overall mean survival rate was rather high (0.85. Mean population survival ranged from 0.64 to 0.94. Individual narrow-sense heritabilities (hi2, family mean heritabilities (hf2, the coefficients of additive genetic variation (CVA and quantitative genetic differentiation coefficients (QST were calculated. A multivariate regression tree (MRT analysis was used to determine the pattern of genetic differentiation of the populations. Individual heritabilities for height ranged between 0.00 and 0.39. Family mean heritabilities for height were rather low in most populations as well (<0.5. Family mean heritabilities for survival were higher than for height (ranging between 0.00 and 0.77. Calculated QST coefficients (0.25 for height and 0.14 for survival indicated between-population genetic differentiation. The populations were separated into two clusters by MRT analysis regarding a climatic variable, namely Hargreaves’ reference evapotranspiration. Populations originating from comparatively more humid habitats were grouped in the first

Recent habitat fragmentation caused by major roads leads to reduction of gene flow and loss of genetic variability in ground beetles.

Science.gov (United States)

Keller, Irene; Largiadèr, Carlo R

2003-02-22

Although habitat fragmentation is suspected to jeopardize the long-term survival of many species, few data are available on its impact on the genetic variability of invertebrates. We assess the genetic population structure of the flightless ground beetle Carabus violaceus L., 1758 in a Swiss forest, which is divided into several fragments by a highway and two main roads. Eight samples were collected from different forest fragments and analysed at six microsatellite loci. The largest genetic differentiation was observed between samples separated by roads and in particular by the highway. The number of roads between sites explained 44% of the variance in pairwise F(ST) estimates, whereas the age of the road and the geographical distance between locations were not significant factors. Furthermore, a comparison of allelic richness showed that the genetic variability in a small forest fragment isolated by the highway was significantly lower than in the rest of the study area. These findings strongly support the hypothesis that large roads are absolute barriers to gene flow in C. violaceus, which may lead to a loss of genetic variability in fragmented populations.

Accelerated Genetic Algorithm Solutions Of Some Parametric Families Of Stochastic Differential Equations

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Eman Ali Hussain

2015-01-01

Full Text Available Absract In this project A new method for solving Stochastic Differential Equations SDEs deriving by Wiener process numerically will be construct and implement using Accelerated Genetic Algorithm AGA. An SDE is a differential equation in which one or more of the terms and hence the solutions itself is a stochastic process. Solving stochastic differential equations requires going away from the recognizable deterministic setting of ordinary and partial differential equations into a world where the evolution of a quantity has an inherent random component and where the expected behavior of this quantity can be described in terms of probability distributions. We applied our method on the Ito formula which is equivalent to the SDE to find approximation solution of the SDEs. Numerical experiments illustrate the behavior of the proposed method.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

Science.gov (United States)

Ruan, Peiying; Hayashida, Morihiro; Akutsu, Tatsuya; Vert, Jean-Philippe

2018-02-19

Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several computational methods have been proposed to predict complexes from the topology and structure of experimental protein-protein interaction (PPI) network. These methods work well to predict complexes involving at least three proteins, but generally fail at identifying complexes involving only two different proteins, called heterodimeric complexes or heterodimers. There is however an urgent need for efficient methods to predict heterodimers, since the majority of known protein complexes are precisely heterodimers. In this paper, we use three promising kernel functions, Min kernel and two pairwise kernels, which are Metric Learning Pairwise Kernel (MLPK) and Tensor Product Pairwise Kernel (TPPK). We also consider the normalization forms of Min kernel. Then, we combine Min kernel or its normalization form and one of the pairwise kernels by plugging. We applied kernels based on PPI, domain, phylogenetic profile, and subcellular localization properties to predicting heterodimers. Then, we evaluate our method by employing C-Support Vector Classification (C-SVC), carrying out 10-fold cross-validation, and calculating the average F-measures. The results suggest that the combination of normalized-Min-kernel and MLPK leads to the best F-measure and improved the performance of our previous work, which had been the best existing method so far. We propose new methods to predict heterodimers, using a machine learning-based approach. We train a support vector machine (SVM) to discriminate interacting vs non-interacting protein pairs, based on informations extracted from PPI, domain, phylogenetic profiles and subcellular localization. We evaluate in detail new kernel functions to encode these data, and report prediction performance that outperforms the state-of-the-art.

Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management.

Science.gov (United States)

Adin, A; Weber, J C; Sotelo Montes, C; Vidaurre, H; Vosman, B; Smulders, M J M

2004-05-01

Peach palm ( Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations ( G(st)) was 0.0377-0.0416 ( Prodents is thought to occur only across relatively short distances (100-200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the 'long-distance' (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers' fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers ( G(st)=0.0249, PPeru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.

Genetic analysis on three South Indian sympatric hipposiderid bats (Chiroptera, Hipposideridae

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Kanagaraj, C

2010-12-01

Full Text Available In mitochondrial DNA, variations in the sequence of 16S rRNA region were analyzed to infer the genetic relationship and population history of three sympatric hipposiderid bats, Hipposideros speoris, H. fulvus and H. ater. Based on the DNA sequence data, we observed relatively lower haplotype and higher nucleotide diversity in H. speoris than in the other two species. The pairwise comparisons of the genetic divergence inferred a genetic relationship between the three hipposiderid bats. We used haplotype sequences to construct a phylogenetic tree. Maximum parsimony and Bayesian inference analysis generated a tree with similar topology. H. fulvus and H. ater formed one cluster and H. speoris formed another cluster. Analysis of the demographic history of populations using Jajima’s D test revealed past changes in populations. Comparison of the observed distribution of pairwise differences in the nucleotides with expected sudden expansion model accepts for H. fulvus and H. ater but not for H. speoris populations.

The effect of alcohol on the differential expression of cluster of differentiation 14 gene, associated pathways, and genetic network.

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Diana X Zhou

Full Text Available Alcohol consumption affects human health in part by compromising the immune system. In this study, we examined the expression of the Cd14 (cluster of differentiation 14 gene, which is involved in the immune system through a proinflammatory cascade. Expression was evaluated in BXD mice treated with saline or acute 1.8 g/kg i.p. ethanol (12.5% v/v. Hippocampal gene expression data were generated to examine differential expression and to perform systems genetics analyses. The Cd14 gene expression showed significant changes among the BXD strains after ethanol treatment, and eQTL mapping revealed that Cd14 is a cis-regulated gene. We also identified eighteen ethanol-related phenotypes correlated with Cd14 expression related to either ethanol responses or ethanol consumption. Pathway analysis was performed to identify possible biological pathways involved in the response to ethanol and Cd14. We also constructed a genetic network for Cd14 using the top 20 correlated genes and present several genes possibly involved in Cd14 and ethanol responses based on differential gene expression. In conclusion, we found Cd14, along with several other genes and pathways, to be involved in ethanol responses in the hippocampus, such as increased susceptibility to lipopolysaccharides and neuroinflammation.

Global genetic differentiation in a cosmopolitan pest of stored beans: effects of geography, host-plant usage and anthropogenic factors.

Science.gov (United States)

Tuda, Midori; Kagoshima, Kumiko; Toquenaga, Yukihiko; Arnqvist, Göran

2014-01-01

Genetic differentiation can be promoted allopatrically by geographic isolation of populations due to limited dispersal ability and diversification over time or sympatrically through, for example, host-race formation. In crop pests, the trading of crops across the world can lead to intermixing of genetically distinct pest populations. However, our understanding of the importance of allopatric and sympatric genetic differentiation in the face of anthropogenic genetic intermixing is limited. Here, we examined global sequence variation in two mitochondrial and one nuclear genes in the seed beetle Callosobruchus maculatus that uses different legumes as hosts. We analyzed 180 samples from 42 populations of this stored bean pest from tropical and subtropical continents and archipelagos: Africa, the Middle East, South and Southeast Asia, Oceania and South America. For the mitochondrial genes, there was weak but significant genetic differentiation across continents/archipelagos. Further, we found pronounced differentiation among subregions within continents/archipelagos both globally and within Africa but not within Asia. We suggest that multiple introductions into Asia and subsequent intermixing within Asia have generated this pattern. The isolation by distance hypothesis was supported globally (with or without continents controlled) but not when host species was restricted to cowpeas Vigna unguiculata, the ancestral host of C. maculatus. We also document significant among-host differentiation both globally and within Asia, but not within Africa. We failed to reject a scenario of a constant population size in the recent past combined with selective neutrality for the mitochondrial genes. We conclude that mitochondrial DNA differentiation is primarily due to geographic isolation within Africa and to multiple invasions by different alleles, followed by host shifts, within Asia. The weak inter-continental differentiation is most likely due to frequent inter-continental gene

Global and local genetic diversity at two microsatellite loci in Plasmodium vivax parasites from Asia, Africa and South America

DEFF Research Database (Denmark)

Schousboe, Mette L; Ranjitkar, Samir; Rajakaruna, Rupika S

2014-01-01

diversity are vital to the evaluation of drug and vaccine efficacy, tracking of P. vivax outbreaks, and assessing geographical differentiation between parasite populations. METHODS: The genetic diversity of eight P. vivax populations (n = 543) was investigated by using two microsatellites (MS), m1501 and m......3502, chosen because of their seven and eight base-pair (bp) repeat lengths, respectively. These were compared with published data of the same loci from six other P. vivax populations. RESULTS: In total, 1,440 P. vivax samples from 14 countries on three continents were compared. There was highest...... heterozygosity within Asian populations, where expected heterozygosity (He) was 0.92-0.98, and alleles with a high repeat number were more common. Pairwise FST revealed significant differentiation between most P. vivax populations, with the highest divergence found between Asian and South American populations...

Molecular and Genetic Analysis of Hormone-Regulated Differential Cell Elongation in Arabidopsis

Energy Technology Data Exchange (ETDEWEB)

Ecker, Joseph R.

2005-09-15

We have utilized the response of Arabidopsis seedlings to the plant hormone ethylene to identify new genes involved in the regulation of ethylene biosynthesis, perception, signal transduction and differential cell growth. In building a genetic framework for the action of these genes, we have developed a molecular model that has facilitated our understanding of the molecular requirements of ethylene for cell elongation processes. The ethylene response pathway in Arabidopsis appears to be primarily linear and is defined by the genes: ETR1, ETR2, ERS1, ERS2, EIN4, CTR1, EIN2, EIN3, EIN5, EIN6, and EIN. Downstream branches identified by the HLS1, EIR1, and AUX1 genes involve interactions with other hormonal (auxin) signals in the process of differential cell elongation in the hypocotyl hook. Cloning and characterization of HLS1 (and three HLL genes) and ETO1 (and ETOL genes) in my laboratory has been supported under this award. HLS1 is required for differential elongation of cells in the hypocotyl and may act in the establishment of hormone gradients. Also during the previous period, we have identified and characterized a gene that genetically acts upstream of the ethylene receptors. ETO1 encodes negative regulators of ethylene biosynthesis.

Genetic differentiation of watermelon landrace types in Mali revealed by microsatellite (SSR) markers

DEFF Research Database (Denmark)

Nantoume, Aminata Dolo; Andersen, Sven Bode; Jensen, Brita Dahl

2013-01-01

This study describes the genetic differentiation of a collection of 134 watermelon landrace accessions from Mali, representing red fleshed dessert and white fleshed seed and cooking type watermelons from five regions, plus three commercial dessert type cultivars with red flesh. The material...... the accessions into use groups (dessert, cooking, seed processing) explained 25 % of the variation. When categorising the accessions further into 10 landrace types, differentiated on the basis of use groups, local accession name, flesh colour and seed phenotype, these landrace types explained 26......-groups. One group included again the red fleshed dessert types with local and commercial origin, while the remaining seven genetic sub-groups comprised the white fleshed landrace types used for seed processing and cooking, as well as white fleshed types of one dessert type. Some of the seed and cooking types...

Genetic and morphological divergence among Cooper's Hawk (Accipiter cooperii) populations breeding in north-central and western North America

Science.gov (United States)

Sonsthagen, Sarah A.; Rosenfield, Robert N.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William C.; Driscoll, Timothy G.; Bozek, Michael A.; Sloss, Brian L.; Talbot, Sandra L.

2012-01-01

Cooper's Hawk (Accipiter cooperii) populations breeding in the northern portion of the species' range exhibit variation in morphological traits that conforms to predictions based on differences in prey size, tree stand density, and migratory behavior. We examined genetic structure and gene flow and compared divergence at morphological traits (PST) and genetic markers (FST) to elucidate mechanisms (selection or genetic drift) that promote morphological diversification among Cooper's Hawk populations. Cooper's Hawks appear to conform to the genetic pattern of an east-west divide. Populations in British Columbia are genetically differentiated from north-central populations (Wisconsin, Minnesota, and North Dakota; pairwise microsatellite FST= 0.031-0.050; mitochondrial DNA ΦST = 0.177-0.204), which suggests that Cooper's Hawks were restricted to at least two Pleistocene glacial refugia. The strength of the Rocky Mountains—Great Plains area as a barrier to dispersal is further supported by restricted gene-flow rates between British Columbia and other sampled breeding populations. Divergence in morphological traits (PST) was also observed across study areas, but with British Columbia and North Dakota differentiated from Wisconsin and Minnesota, a pattern not predicted on the basis of FST and ΦST interpopulation estimates. Comparison of PSTand FSTestimates suggests that heterogeneous selection may be acting on Cooper's Hawks in the northern portion of their distribution, which is consistent with hypotheses that variation in prey mass and migratory behavior among populations may be influencing overall body size and wing chord. We were unable to distinguish between the effects of genetic drift and selection on tail length in the study populations.

Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters.

Science.gov (United States)

Yoon, M; Park, W; Nam, Y K; Kim, D S

2012-02-01

Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

Pioneer study of population genetics of Rhodnius ecuadoriensis (Hemiptera: Reduviidae) from the central coastand southern Andean regions of Ecuador.

Science.gov (United States)

Villacís, Anita G; Marcet, Paula L; Yumiseva, César A; Dotson, Ellen M; Tibayrenc, Michel; Brenière, Simone Frédérique; Grijalva, Mario J

2017-09-01

Effective control of Chagas disease vector populations requires a good understanding of the epidemiological components, including a reliable analysis of the genetic structure of vector populations. Rhodnius ecuadoriensis is the most widespread vector of Chagas disease in Ecuador, occupying domestic, peridomestic and sylvatic habitats. It is widely distributed in the central coast and southern highlands regions of Ecuador, two very different regions in terms of bio-geographical characteristics. To evaluate the genetic relationship among R. ecuadoriensis populations in these two regions, we analyzed genetic variability at two microsatellite loci for 326 specimens (n=122 in Manabí and n=204 in Loja) and the mitochondrial cytochrome b gene (Cyt b) sequences for 174 individuals collected in the two provinces (n=73 and=101 in Manabí and Loja respectively). The individual samples were grouped in populations according to their community of origin. A few populations presented positive F IS, possible due to Wahlund effect. Significant pairwise differentiation was detected between populations within each province for both genetic markers, and the isolation by distance model was significant for these populations. Microsatellite markers showed significant genetic differentiation between the populations of the two provinces. The partial sequences of the Cyt b gene (578bp) identified a total of 34 haplotypes among 174 specimens sequenced, which translated into high haplotype diversity (Hd=0.929). The haplotype distribution differed among provinces (significant Fisher's exact test). Overall, the genetic differentiation of R. ecuadoriensis between provinces detected in this study is consistent with the biological and phenotypic differences previously observed between Manabí and Loja populations. The current phylogenetic analysis evidenced the monophyly of the populations of R. ecuadoriensis within the R. pallescens species complex; R. pallescens and R. colombiensis were more

How to measure genetic heterogeneity

International Nuclear Information System (INIS)

Yamada, Ryo

2009-01-01

Genetic information of organisms is coded as a string of four letters, A, T, G and C, a sequence in macromolecules called deoxyribonucleic acid (DNA). DNA sequence offers blueprint of organisms and its heterogeneity determines identity and variation of species. The quantitation of this genetic heterogeneity is fundamental to understand biology. We compared previously-reported three measures, covariance matrix expression of list of loci (pair-wise r 2 ), the most popular index in genetics, and its multi-dimensional form, Ψ, and entropy-based index, ε. Thereafter we proposed two methods so that we could handle the diplotypic heterogeneity and quantitate the conditions where the number of DNA sequence samples is much smaller than the number of possible variants.

Determinants of sovereign debt yield spreads under EMU: Pairwise approach

NARCIS (Netherlands)

Fazlioglu, S.

2013-01-01

This study aims at providing an empirical analysis of long-term determinants of sovereign debt yield spreads under European EMU (Economic and Monetary Union) through pairwise approach within panel framework. Panel gravity models are increasingly used in the cross-market correlation literature while

Predicting risk in space: Genetic markers for differential vulnerability to sleep restriction

Science.gov (United States)

Goel, Namni; Dinges, David F.

2012-08-01

Several laboratories have found large, highly reliable individual differences in the magnitude of cognitive performance, fatigue and sleepiness, and sleep homeostatic vulnerability to acute total sleep deprivation and to chronic sleep restriction in healthy adults. Such individual differences in neurobehavioral performance are also observed in space flight as a result of sleep loss. The reasons for these stable phenotypic differential vulnerabilities are unknown: such differences are not yet accounted for by demographic factors, IQ or sleep need, and moreover, psychometric scales do not predict those individuals cognitively vulnerable to sleep loss. The stable, trait-like (phenotypic) inter-individual differences observed in response to sleep loss—with intraclass correlation coefficients accounting for 58-92% of the variance in neurobehavioral measures—point to an underlying genetic component. To this end, we utilized multi-day highly controlled laboratory studies to investigate the role of various common candidate gene variants—each independently—in relation to cumulative neurobehavioral and sleep homeostatic responses to sleep restriction. These data suggest that common genetic variations (polymorphisms) involved in sleep-wake, circadian, and cognitive regulation may serve as markers for prediction of inter-individual differences in sleep homeostatic and neurobehavioral vulnerability to sleep restriction in healthy adults. Identification of genetic predictors of differential vulnerability to sleep restriction—as determined from candidate gene studies—will help identify astronauts most in need of fatigue countermeasures in space flight and inform medical standards for obtaining adequate sleep in space. This review summarizes individual differences in neurobehavioral vulnerability to sleep deprivation and ongoing genetic efforts to identify markers of such differences.

Classification between normal and tumor tissues based on the pair-wise gene expression ratio

International Nuclear Information System (INIS)

Yap, YeeLeng; Zhang, XueWu; Ling, MT; Wang, XiangHong; Wong, YC; Danchin, Antoine

2004-01-01

Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking. Using recent datasets on colon and prostate cancer, a data transformation procedure from single gene expression to pair-wise gene expression ratio is proposed. Making use of the internal consistency of each expression profiling dataset this transformation improves the signal to noise ratio of the dataset and uncovers new relevant cancer-related signals (features). The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation) as discriminating axes (single gene expression or pair-wise gene expression ratio). Classification results were compared to the original datasets for up to 10-feature model classifiers. 82 and 262 genes that have high correlation to tissue phenotype were selected from the colon and prostate datasets respectively. Remarkably, data transformation of the highly noisy expression data successfully led to lower the coefficient of variation (CV) for the within-class samples as well as improved the correlation with tissue phenotypes. The transformed dataset exhibited lower CV when compared to that of single gene expression. In the colon cancer set, the minimum CV decreased from 45.3% to 16.5%. In prostate cancer, comparable CV was achieved with and without transformation. This improvement in CV, coupled with the improved correlation between the pair-wise gene expression ratio and tissue phenotypes, yielded higher classification efficiency, especially with the colon dataset – from 87.1% to 93.5%. Over 90% of the top ten discriminating axes in both datasets showed significant improvement after data transformation. The high classification efficiency achieved suggested

Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispersing freshwater zooplankton.

Science.gov (United States)

Xiang, Xian-ling; Xi, Yi-long; Wen, Xin-li; Zhang, Gen; Wang, Jin-xia; Hu, Ke

2011-05-01

Elucidating the evolutionary patterns and processes of extant species is an important objective of any research program that seeks to understand population divergence and, ultimately, speciation. The island-like nature and temporal fluctuation of limnetic habitats create opportunities for genetic differentiation in rotifers through space and time. To gain further understanding of spatio-temporal patterns of genetic differentiation in rotifers other than the well-studied Brachionus plicatilis complex in brackish water, a total of 318 nrDNA ITS sequences from the B. calyciflorus complex in freshwater were analysed using phylogenetic and phylogeographic methods. DNA taxonomy conducted by both the sequence divergence and the GMYC model suggested the occurrence of six potential cryptic species, supported also by reproductive isolation among the tested lineages. The significant genetic differentiation and non-significant correlation between geographic and genetic distances existed in the most abundant cryptic species, BcI-W and Bc-SW. The large proportion of genetic variability for cryptic species Bc-SW was due to differences between sampling localities within seasons, rather than between different seasons. Nested Clade Analysis suggested allopatric or past fragmentation, contiguous range expansion and long-distance colonization possibly coupled with subsequent fragmentation as the probable main forces shaping the present-day phylogeographic structure of the B. calyciflorus species complex. Copyright © 2011 Elsevier Inc. All rights reserved.

Genetic differentiation across multiple spatial scales of the Red Sea of the corals Stylophora pistillata and Pocillopora verrucosa

KAUST Repository

Monroe, Alison

2015-12-01

Observing populations at different spatial scales gives greater insight into the specific processes driving genetic differentiation and population structure. Here we determined population connectivity across multiple spatial scales in the Red Sea to determine the population structures of two reef building corals Stylophora pistillata and Pocillopora verrucosa. The Red sea is a 2,250 km long body of water with extremely variable latitudinal environmental gradients. Mitochondrial and microsatellite markers were used to determine distinct lineages and to look for genetic differentiation among sampling sites. No distinctive population structure across the latitudinal gradient was discovered within this study suggesting a phenotypic plasticity of both these species to various environments. Stylophora pistillata displayed a heterogeneous distribution of three distinct genetic populations on both a fine and large scale. Fst, Gst, and Dest were all significant (p-value<0.05) and showed moderate genetic differentiation between all sampling sites. However this seems to be byproduct of the heterogeneous distribution, as no distinct genetic population breaks were found. Stylophora pistillata showed greater population structure on a fine scale suggesting genetic selection based on fine scale environmental variations. However, further environmental and oceanographic data is needed to make more inferences on this structure at small spatial scales. This study highlights the deficits of knowledge of both the Red Sea and coral plasticity in regards to local environmental conditions.

Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China.

Science.gov (United States)

Zhan, Aibin; Li, Cheng; Fu, Jinzhong

2009-04-09

Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the

Host-associated genetic differentiation in the goldenrod elliptical-gall moth, Gnorimoschema gallaesolidaginis (Lepidoptera: Gelechiidae).

Science.gov (United States)

Nason, John D; Heard, Stephen B; Williams, Frederick R

2002-07-01

Careful study of apparently generalist phytophagous insects often reveals that they instead represent complexes of genetically differentiated host races or cryptic species. The goldenrod elliptical-gall moth, Gnorimoschema gallaesolidaginis, attacks two goldenrods in the Solidago canadensis complex: S. altissima and S. gigantea (Asteraceae). We tested for host-associated genetic differentiation in G. gallaesolidaginis via analysis of variation at 12 allozyme loci among larvae collected at six sites in Iowa, Minnesota, and Nebraska. Gnorimoschema gallaesolidaginis from each host are highly polymorphic (3.6-4.7 alleles/locus and expected heterozygosity 0.28-0.38 within site-host combinations). Although there were no fixed differences between larvae from S. altissima and S. gigantea at any site, these represent well differentiated host forms, with 11 of 12 loci showing significantly different allele frequencies between host-associated collections at one or more sites. Host plant has a larger effect on genetic structure among populations than does location (Wright's FST = 0.16 between host forms vs. F(ST) = 0.061 and 0.026 among altissima and gigantea populations, respectively). The estimated F(ST) between host forms suggests that the historical effective rate of gene flow has been low (N(e)m approximately 1.3). Consistent with this historical estimate is the absence of detectable recombinant (hybrid and introgressant between host form) individuals in contemporary populations (none of 431 genotyped individuals). Upper 95% confidence limits for the frequency of recombinant individuals range from 5% to 9%. Host association is tight, but imperfect, with only one likely example of a host mismatch (a larva galling the wrong host species). Our inferences about hybridization and host association are based on new maximum-likelihood methods for estimating frequencies of genealogical classes (in this case, two parental classes, F1 and F2 hybrids, and backcrosses) in a population

Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China.

Science.gov (United States)

Zhao, Liangjie; Chenoweth, Erica L; Liu, Qigen

2018-03-01

In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise F ST , gene flow (Nm), and genetic distance (Da) indicated that Longquan and Changtan significantly differentiate from other populations. Nested clade phylogeographical analysis (NCPA) showed some clades and total cladogram experienced isolation by distance. In conclusion, the populations from severely fragmented Ou River have the lower diversity and more intense differentiation than that from the mainstream of Ling River, Changtan population present the lowest diversity and were isolated by the dam construction.

Genetic and Morphological Differentiation of the Semiterrestrial Crab Armases angustipes (Brachyura: Sesarmidae) along the Brazilian Coast.

Science.gov (United States)

Marochi, Murilo Zanetti; Masunari, Setuko; Schubart, Christoph D

2017-02-01

The genetic and morphometric population structures of the semiterrestrial crab Armases angustipes from along the Brazilian coast were examined. The influence of the Central South Equatorial Current on larval dispersal of A. angustipes also was evaluated. Six populations were sampled from estuarine areas in São Luis do Maranhão, Maranhão; Natal, Rio Grande do Norte; Maceió, Alagoas; Ilhéus, Bahia; Aracruz, Espírito Santo; and Guaratuba, Paraná. Patterns of genetic differentiation were assessed using DNA sequence data corresponding to parts of the mitochondrial cytochrome c oxidase subunit 1. Geometric morphometric techniques were used to evaluate morphological variation in shape and size of the carapace and right cheliped propodus. Our results revealed low genetic variability and lack of phylogeographic structure; geometric morphometrics showed statistically significant morphological differentiation and geographic structuring. Our data indicate the absence of possible barriers to gene flow for this mobile species, and no clear correlation of morphological or genetic variation with ocean currents and/or geographic distance. Our results also suggest that historical geological and climatological events and/or possible bottleneck effects influenced the current low genetic variability among the populations of A. angustipes.

Brief Communication: Quantitative- and molecular-genetic differentiation in humans and chimpanzees: implications for the evolutionary processes underlying cranial diversification.

Science.gov (United States)

Weaver, Timothy D

2014-08-01

Estimates of the amount of genetic differentiation in humans among major geographic regions (e.g., Eastern Asia vs. Europe) from quantitative-genetic analyses of cranial measurements closely match those from classical- and molecular-genetic markers. Typically, among-region differences account for ∼10% of the total variation. This correspondence is generally interpreted as evidence for the importance of neutral evolutionary processes (e.g., genetic drift) in generating among-region differences in human cranial form, but it was initially surprising because human cranial diversity was frequently assumed to show a strong signature of natural selection. Is the human degree of similarity of cranial and DNA-sequence estimates of among-region genetic differentiation unusual? How do comparisons with other taxa illuminate the evolutionary processes underlying cranial diversification? Chimpanzees provide a useful starting point for placing the human results in a broader comparative context, because common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the extant species most closely related to humans. To address these questions, I used 27 cranial measurements collected on a sample of 861 humans and 263 chimpanzees to estimate the amount of genetic differentiation between pairs of groups (between regions for humans and between species or subspecies for chimpanzees). Consistent with previous results, the human cranial estimates are quite similar to published DNA-sequence estimates. In contrast, the chimpanzee cranial estimates are much smaller than published DNA-sequence estimates. It appears that cranial differentiation has been limited in chimpanzees relative to humans. © 2014 Wiley Periodicals, Inc.

Molecular and Genetic Analysis of Hormone-Regulated Differential Cell Elongation in Arabidopsis

Energy Technology Data Exchange (ETDEWEB)

Ecker, Joseph R.

2002-12-03

The authors have utilized the response of Arabidopsis seedlings to the plant hormone ethylene to identify new genes involved in the regulation of ethylene biosynthesis, perception, signal transduction and differential cell growth. In building a genetic framework for the action of these genes, they developed a molecular model that has facilitated the understanding of the molecular requirements of ethylene for cell elongation processes. The ethylene response pathway in Arabidopsis appears to be primarily linear and is defined by the genes: ETR1, ETR2, ERS1, ERS2, EIN4, CTR1, EIN2, EIN3, EIN5 EIN6, and EIN. Downstream branches identified by the HLS1, EIR1, and AUX1 genes involve interactions with other hormonal (auxin) signals in the process of differential cell elongation in the hypocotyl hook. Cloning and characterization of HLS1 and three HLS1-LIKE genes in the laboratory has been supported under this award. HLS1 is required for differential elongation of cells in the hypocotyl and may act in the establishment of hormone gradients. Also during the award period, they have identified and begun preliminary characterization of two genes that genetically act upstream of the ethylene receptors. ETO1 and RAN1 encode negative regulators of ethylene biosynthesis and signaling respectively. Progress on the analysis of these genes along with HOOKLESS1 is described.

Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

Science.gov (United States)

Lesser, M R; Parchman, T L; Jackson, S T

2013-05-01

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century. © 2013 Blackwell Publishing Ltd.

Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers.

Science.gov (United States)

Ahmed Mohamed, Nadjim; Yu, Qian; Chanfi, Mohamed Ibrahim; Li, Yangping; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin

2016-01-01

Small giant clam, Tridacna maxima , widely distributed from French Polynesia to East Africa, has faced population declines due to over-exploitation. Comoros islands are an important biogeographic region due to potential richness of marine species, but no relevant information is available. In order to facilitate devising effective conservation management plan for T. maxima , nine microsatellite markers were used to survey genetic diversity and population differentiation of 72 specimens collected from three Comoros islands, Grande Comore, Moheli and Anjouan. A total of 51 alleles were detected ranged from 2 to 8 per locus. Observed and expected heterozygosity varied from 0.260 to 0.790 and from 0.542 to 0.830, respectively. All populations have high genetic diversity, especially the population in Moheli, a protected area, has higher genetic diversity than the others. Significant heterozygote deficiencies were recorded, and null alleles were probably the main factor leading to these deficits. F ST value indicated medium genetic differentiation among the populations. Although significant, AMOVA revealed 48.9 % of genetic variation within individuals and only a small variation of 8.9 % was found between populations. Gene flow was high ( Nm  = 12.40) between Grande Comore and Moheli, while lower ( Nm  = 1.80) between Grande Comore and Anjouan, explaining geographic barriers to genetic exchanges might exist in these two islands. Global gene flow analysis ( Nm  = 5.50) showed that larval dispersal is enough to move between the islands. The high genetic diversity and medium population differentiation revealed in the present study offer useful information on genetic conservation of small giant clams.

Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event.

Science.gov (United States)

Plath, Martin; Hermann, Bernd; Schröder, Christiane; Riesch, Rüdiger; Tobler, Michael; García de León, Francisco J; Schlupp, Ingo; Tiedemann, Ralph

2010-08-23

Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations

Pairwise harmonics for shape analysis

KAUST Repository

Zheng, Youyi

2013-07-01

This paper introduces a simple yet effective shape analysis mechanism for geometry processing. Unlike traditional shape analysis techniques which compute descriptors per surface point up to certain neighborhoods, we introduce a shape analysis framework in which the descriptors are based on pairs of surface points. Such a pairwise analysis approach leads to a new class of shape descriptors that are more global, discriminative, and can effectively capture the variations in the underlying geometry. Specifically, we introduce new shape descriptors based on the isocurves of harmonic functions whose global maximum and minimum occur at the point pair. We show that these shape descriptors can infer shape structures and consistently lead to simpler and more efficient algorithms than the state-of-the-art methods for three applications: intrinsic reflectional symmetry axis computation, matching shape extremities, and simultaneous surface segmentation and skeletonization. © 2012 IEEE.

Genetic and morphologic differentiation of the Lusitanian toadfish (Halobatrachus didactylus between estuarine and coastal areas in Portugal

Directory of Open Access Journals (Sweden)

Joana F. Marques

2006-12-01

Full Text Available The Lusitanian toadfish, Halobatrachus didactylus (Bloch and Schneider, 1801, is distributed from the Ghana coast to the Iberian Peninsula, being particularly abundant on the south coast of Portugal. The differentiation of this species along the Portuguese coast was assessed through the analysis of 10 samples, considering morphological characters (20 morphometric and 16 meristic and genetic markers (10 allozymes, 11 loci. Southern samples included estuaries and their adjacent coastal areas, given that this species inhabits both environments, whereas western samples only comprised estuaries. Morphometric and meristic data discriminant analysis evidenced some differentiation between estuarine and coastal populations. This was not entirely corroborated by the genetic analysis, which showed an overall pattern of low FST (0.042 and Nei’s genetic distance, even between geographically distant areas. However, higher values of these parameters were found between estuaries of the south coast and their adjacent coastal areas, suggesting that estuarine systems play a major role in such differentiation. Results are discussed regarding toadfish life-history pattern and Portuguese coast geomorphology, giving an insight into the biological and environmental factors influencing population sub-structuring.

The relationships between chemical and genetic differentiation and environmental factors across the distribution of Erigeron breviscapus (Asteraceae).

Science.gov (United States)

Li, Xiang; Peng, Li-yan; Zhang, Shu-dong; Zhao, Qin-shi; Yi, Ting-shuang

2013-01-01

Erigeron breviscapus (Vant.) Hand.-Mazz. is an important, widely used Chinese herb with scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B being its major active compounds. We aimed to resolve the influence of biotic and abiotic factors on the concentrations of these compounds and to determine appropriate cultivation methods to improve the yields of the four compounds in this herb. In order to detect the major genetic and natural environmental factors affecting the yields of these four compounds, we applied AFLP markers to investigate the population genetic differentiation and HPLC to measure the concentrations of four major active compounds among 23 wild populations which were located across almost the entire distribution of this species in China. The meteorological data including annual average temperature, annual average precipitation and annual average hours of sunshine were collected. The relationships among the concentrations of four compounds and environmental factors and genetic differentiation were studied. Low intraspecific genetic differentiation is detected, and there is no obvious correlation between the genetic differentiation and the contents of the chemical compounds. We investigated the correlation between the concentrationsof four compounds (scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B) and environmental factors. Concentrations of two compounds (1,5-dicaffeoylquinic acid and 3,5-dicaffeoylquinic acid) were correlated with environmental factors. The concentration of 1,5-dicaffeoylquinic acid is positively correlated with latitude, and is negatively correlated with the annual average temperature. The concentration of 3,5-dicaffeoylquinic acid is positively correlated with annual average precipitation. Therefore, changing cultivation conditions may significantly improve the yields of these two compounds. We found the concentration of scutellarin positively correlated with that of

Genetic Characterization of Five Hatchery Populations of the Pacific Abalone (Haliotis discus hannai Using Microsatellite Markers

Directory of Open Access Journals (Sweden)

Jeong-In Myeong

2011-07-01

Full Text Available The Pacific abalone, Haliotis discus hannai, is a popular food in Eastern Asia. Aquacultural production of this species has increased because of recent resource declines, the growing consumption, and ongoing government-operated stock release programs. Therefore, the genetic characterization of hatchery populations is necessary to maintain the genetic diversity of this species and to develop more effective aquaculture practices. We analyzed the genetic structures of five cultured populations in Korea using six microsatellite markers. The number of alleles per locus ranged from 15 to 64, with an average of 23.5. The mean observed and expected heterozygosities were 0.797 and 0.904, respectively. The inbreeding coefficient FIS ranged from 0.054 to 0.184 (mean FIS = 0.121 ± 0.056. The genetic differentiation across all populations was low but significant (overall FST = 0.009, P < 0.01. Pairwise multilocus FST tests, estimates of genetic distance, and phylogenetic and principal component analyses did not show a consistent relationship between geographic and genetic distances. These results could reflect extensive aquaculture, the exchange of breeds and eggs between hatcheries and/or genetic drift due to intensive breeding practices. Thus, for optimal resource management, the genetic variation of hatchery stocks should be monitored and inbreeding controlled within the abalone stocks that are being released every year. This genetic information will be useful for the management of both H. discus hannai fisheries and the aquaculture industry.

RAPID-COMMUNICATION Genetic diversity and differentiation in natural populations of Arapaima gigas from lower Amazon revealed by microsatellites.

Science.gov (United States)

Fazzi-Gomes, P F; Melo, N; Palheta, G; Guerreiro, S; Amador, M; Ribeiro-Dos-Santos, A K; Santos, S; Hamoy, I

2017-02-08

Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A. gigas analyzed had high levels of genetic variability, which were similar to those described in previous studies. These two populations had a significant population differentiation supported by the estimates of F ST and R ST (0.06), by Bayesian analysis (K = 2), and by population assignment tests, which revealed a moderate genetic distance.

Microsatellite data suggest significant population structure and differentiation within the malaria vector Anopheles darlingi in Central and South America

Directory of Open Access Journals (Sweden)

Achee Nicole L

2008-03-01

Full Text Available Abstract Background Anopheles darlingi is the most important malaria vector in the Neotropics. An understanding of A. darlingi's population structure and contemporary gene flow patterns is necessary if vector populations are to be successfully controlled. We assessed population genetic structure and levels of differentiation based on 1,376 samples from 31 localities throughout the Peruvian and Brazilian Amazon and Central America using 5–8 microsatellite loci. Results We found high levels of polymorphism for all of the Amazonian populations (mean RS = 7.62, mean HO = 0.742, and low levels for the Belize and Guatemalan populations (mean RS = 4.3, mean HO = 0.457. The Bayesian clustering analysis revealed five population clusters: northeastern Amazonian Brazil, southeastern and central Amazonian Brazil, western and central Amazonian Brazil, Peruvian Amazon, and the Central American populations. Within Central America there was low non-significant differentiation, except for between the populations separated by the Maya Mountains. Within Amazonia there was a moderate level of significant differentiation attributed to isolation by distance. Within Peru there was no significant population structure and low differentiation, and some evidence of a population expansion. The pairwise estimates of genetic differentiation between Central America and Amazonian populations were all very high and highly significant (FST = 0.1859 – 0.3901, P DA and FST distance-based trees illustrated the main division to be between Central America and Amazonia. Conclusion We detected a large amount of population structure in Amazonia, with three population clusters within Brazil and one including the Peru populations. The considerable differences in Ne among the populations may have contributed to the observed genetic differentiation. All of the data suggest that the primary division within A. darlingi corresponds to two white gene genotypes between Amazonia (genotype 1

Genetic control of differential acetylation in diabetic rats.

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Pamela J Kaisaki

Full Text Available Post-translational protein modifications such as acetylation have significant regulatory roles in metabolic processes, but their relationship to both variation in gene expression and DNA sequence is unclear. We address this question in the Goto-Kakizaki (GK rat inbred strain, a model of polygenic type 2 diabetes. Expression of the NAD-dependent deacetylase Sirtuin-3 is down-regulated in GK rats compared to normoglycemic Brown Norway (BN rats. We show first that a promoter SNP causes down-regulation of Sirtuin-3 expression in GK rats. We then use mass-spectrometry to identify proteome-wide differential lysine acetylation of putative Sirtuin-3 protein targets in livers of GK and BN rats. These include many proteins in pathways connected to diabetes and metabolic syndrome. We finally sequence GK and BN liver transcriptomes and find that mRNA expression of these targets does not differ significantly between GK and BN rats, in contrast to other components of the same pathways. We conclude that physiological differences between GK and BN rats are mediated by a combination of differential protein acetylation and gene transcription and that genetic variation can modulate acetylation independently of expression.

Comparing the genetic structure of codling moth Cydia pomonella (L.) from Greece and France: long distance gene-flow in a sedentary pest species.

Science.gov (United States)

Voudouris, C Ch; Franck, P; Olivares, J; Sauphanor, B; Mamuris, Z; Tsitsipis, J A; Margaritopoulos, J T

2012-04-01

Codling moth Cydia pomonella L. (Lepidoptera: Tortricidae) is the most important insect pest of apple production in Europe. Despite the economic importance of this pest, there is not information about the genetic structure of its population in Greece and the patterns of gene-flow which might affect the success of control programs. In this study, we analysed nine samples from apple, pear and walnut from various regions of mainland Greece using 11 microsatellite loci. Six samples from the aforementioned hosts from southern France were also examined for comparison. Bayesian clustering and genetic distance analyses separated the codling moth samples in two genetic clusters. The first cluster consisted mainly of the individuals from Greece, and the second of those from France, although admixture and miss-classified individuals were also observed. The low genetic differentiation among samples within each country was also revealed by F(ST) statistics (0.009 among Greek samples and 0.0150 among French samples compared to 0.050 global value among all samples and 0.032 the mean of the pair-wise values between the two countries). These F(ST) values suggest little structuring at large geographical scales in agreement with previous published studies. The host species and local factors (climatic conditions, topography, pest control programs) did not affect the genetic structure of codling moth populations within each country. The results are discussed in relation to human-made activities that promote gene-flow even at large geographic distances. Possible factors for the genetic differentiation between the two genetic clusters are also discussed.

Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits.

NARCIS (Netherlands)

Lemoine, M.; Lucek, K.; Perrier, C.; Saladin, V.; Adriaensen, F.; Barba, E.; Belda, E.J.; Charmantier, A.; Cichoń, M.; Eeva, T.; Grégoire, A.; Hinde, C.A.; Johnsen, A.; Komdeur, J.; Mänd, R.; Matthysen, E.; Norte, A.C.; Pitala, N.; Sheldon, B.C.; Slagsvold, T.; Tinbergen, J.M.; Török, J.; Ubels, R.; van Oers, K.; Visser, M.E.; Doligez, Blandine; Richner, Heinz

2016-01-01

Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing

Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures.

Science.gov (United States)

Filippi, Sarah; Holmes, Chris C; Nieto-Barajas, Luis E

2016-11-16

In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a "null model" of pairwise independence. In simulation studies, as well as for a real data analysis, we show that our approach provides a useful tool for the exploratory nonparametric Bayesian analysis of large multivariate data sets.

A gradient approximation for calculating Debye temperatures from pairwise interatomic potentials

International Nuclear Information System (INIS)

Jackson, D.P.

1975-09-01

A simple gradient approximation is given for calculating the effective Debye temperature of a cubic crystal from central pairwise interatomic potentials. For examples of the Morse potential applied to cubic metals the results are in generally good agreement with experiment. (author)

Genetic structure of the threatened Dipterocarpus costatus populations in lowland tropical rainforests of southern Vietnam.

Science.gov (United States)

Duc, N M; Duy, V D; Xuan, B T T; Thang, B V; Ha, N T H; Tam, N M

2016-10-24

Dipterocarpus costatus is an endangered species restricted to the lowland forests of southern Vietnam. Habitat loss and over-exploitation of D. costatus wood are the major threats to this species. We investigated the level of genetic variability within and among populations of D. costatus in order to provide guidelines for the conservation, management, and restoration of this species to the Forest Protection Department, Vietnam. Nine microsatellite markers were used to analyze 114 samples from four populations representing the natural range of D. costatus in southeast Vietnam. We indicated the low allelic diversity (N A = 2.3) and low genetic diversities with an average observed and expected heterozygosity of 0.130 and 0.151, respectively, in the lowland forests of southeast Vietnam. The low genetic diversity might be a consequence of inbreeding within the small and isolated populations of D. costatus owing to its habitat loss and over-exploitation. All populations deviated from Hardy-Weinberg equilibrium showing reduced heterozygosity. Alleles were lost from the populations by genetic drift. Genetic differentiation among populations was high (average pairwise F ST = 0.405), indicating low gene flow (<1) and isolated populations due to its destructed habitat and large geographical distances (P < 0.05) among populations. Heterozygosity excess tests (except of Bu Gia Map only under infinite allele model) were negative. The high genetic variation (62.7%) was found within populations. The STRUCTURE and neighbor joining tree results suggest strong differentiation among D. costatus populations, with the three genetic clusters, Phu Quoc, Tan Phu and Bu Gia Map, and Lo Go-Xa Mat due to habitat fragmentation and isolation. The threatened status of D. costatus was related to a lack of genetic diversity, with all its populations isolated in small forest patches. We recommend the establishment of an ex situ conservation site for D. costatus with a new big population comprising

Genetic differentiation of Solea solea (Linnaeus, 1758 and Solea senegalensis Kaup, 1858, (Pisces: Pleuronectiformes from several estuarine systems of the Portuguese coast

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Henrique N. Cabral

2003-03-01

Full Text Available The genetic differentiation of Solea solea and Solea senegalensis from several estuarine systems along the Portuguese coast was studied. Nine polymorphic isozyme loci (ACP-1*, ACP-2*, GPI-1*, GPI-2*, sMDH*, ME-1*, ME-2*, MPI* and PGM* were analysed using starch gel electrophoresis and isoelectric focusing. Differentiation between the species was high (mean average Nei distance of 0.93. The most efficient loci in the diagnosis of the two species were ACP-1*, ME-2* and GPI-2*. S. solea showed a higher genetic diversity than S. senegalensis. Within each species a low genetic differentiation between the samples analysed was found. Although with a low magnitude the interpopulational genetic differentiation of S. solea was higher than that of S. senegalensis. This could probably be explained by some particularities of the life cycles of these species, namely the more extended period of occurrence of larval stages of S. senegalensis in the plankton. Although no clear evidence about the population structure model emerged from the analysis of several Atlantic and Mediterranean populations of S. solea, the significant correlations obtained between genetic and geographical distances support an isolation by distance model.

Genetic differentiation between 'Araucana' creole and 'Hampshire Down' sheeps in Chile

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Silvana Bravo

2015-03-01

Full Text Available Genetic diversity studies in domestic animals allow evaluating genetic variation within and among breeds mainly for conservation purposes. In Chile exist isolated recovery programs, conservation and characterization of animal genetic resources, a consequence of which the vast majority of them have not been characterized, poorly used, and some of them have become extinct. The aim of this research was to determine genetic diversity and relationship between 'Araucana' creole and 'Hampshire Down' sheeps based on microsatellite markers; sheep breeds with similar phenotypic characteristics, raised in the south of Chile. A total of 64 'Araucana' sheep ('Araucana' from Freire, AF: 27, 'Araucana' from Padre Las Casas, AP: 10, 'Araucana' from Chol Chol, AC: 15, 'Araucana' from Villarrica, AV: 12 and 43 'Hampshire Down' sheep ('Hampshire' from Marchigue, HM: 18, 'Hampshire' from Valdivia, HV: 11, 'Hampshire' from San José, HS: 14 were analyzed using 17 microsatellite markers for determine the genetic diversity and relationship between breeds. A total of 284 alleles were observed with average polymorphic information content equal to 0.76, showing that the microsatellites panel used was highly informative. Estimated heterozygosity ranged from 0.73 in 'Hampshire Down' to 0.85 in 'Araucana'. The low inbreeding or endogamy coefficient (F IS, 0.022 and total inbreeding estimate (F IT, 0.070 indicated low level of inbreeding within and among breeds. The phylogenetic tree showed a separation between HS and HV, and the other sheep populations. The results indicated high genetic variability, low inbreeding, and low genetic differentiation, except for HV and HS, and were in according with geographical location and breeding practices.

ISSR diversity and genetic differentiation of ancient tea (camellia sinensis var. assamica) plantations from China: implications for precious tea germplasm conservation

International Nuclear Information System (INIS)

Huang, X.Q.; Ji, P.Z.; Li, H.; Zhang, J.; Gao, L.Z.; Cheng, Z.Q.

2011-01-01

Over 10 centuries, ancient cultivated tea populations (Camellia sinensis var. assamica) are still planted merely in Yunnan province of China. Genetic diversity and differentiation were examined in 10 ancient tea plantations by using ISSR markers. The average genetic diversity within populations, estimated with Nei's genetic diversity (HE), was approximately 0.2809, while Shannon indices (HO) was 0.4179. The percentage of polymorphic loci (P) of the 10 populations ranged from 56.5% to 90.91%. We found a moderate level of genetic differentiation among population as evidenced by the coefficients of gene differentiation (Gst) of 0.3911 and the analysis of molecular variance (AMOVA) of 39.70%. The result could be explained by the nature of highly out crossing in the tea species as well as serious habitat fragmentation. Finally, conservation strategies were discussed to protect these ancient tea populations, including in situ reserve settings and ex situ germplasm sampling. (author)

Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data.

Science.gov (United States)

Yew, Chee Wei; Hoque, Mohd Zahirul; Pugh-Kitingan, Jacqueline; Minsong, Alexander; Voo, Christopher Lok Yung; Ransangan, Julian; Lau, Sophia Tiek Ying; Wang, Xu; Saw, Woei Yuh; Ong, Rick Twee-Hee; Teo, Yik-Ying; Xu, Shuhua; Hoh, Boon-Peng; Phipps, Maude E; Kumar, S Vijay

2018-07-01

The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (F ST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent

Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models.

Science.gov (United States)

Rostami, Vahid; Porta Mana, PierGianLuca; Grün, Sonja; Helias, Moritz

2017-10-01

Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations, given only the time-averaged correlations of the neuron activities. This paper provides evidence that the pairwise model, applied to experimental recordings, would produce a bimodal distribution for the population-averaged activity, and for some population sizes the second mode would peak at high activities, that experimentally would be equivalent to 90% of the neuron population active within time-windows of few milliseconds. Several problems are connected with this bimodality: 1. The presence of the high-activity mode is unrealistic in view of observed neuronal activity and on neurobiological grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise maximum-entropy distribution cannot be found: in fact, Boltzmann learning would produce an incorrect distribution; similarly, common variants of mean-field approximations also produce an incorrect distribution. 3. The Glauber dynamics associated with the model is unrealistically bistable and cannot be used to generate realistic surrogate data. This bimodality problem is first demonstrated for an experimental dataset from 159 neurons in the motor cortex of macaque monkey. Evidence is then provided that this problem affects typical neural recordings of population sizes of a couple of hundreds or more neurons. The cause of the bimodality problem is identified as the inability of standard maximum-entropy distributions with a uniform reference measure to model neuronal inhibition. To eliminate this problem a modified maximum-entropy model is presented, which reflects a basic effect of inhibition in the form of a simple but non-uniform reference measure. This model does not lead to unrealistic bimodalities, can be found with Boltzmann learning, and has an associated Glauber dynamics which incorporates a minimal asymmetric inhibition.

Extension of Pairwise Broadcast Clock Synchronization for Multicluster Sensor Networks

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Bruce W. Suter

2008-01-01

Full Text Available Time synchronization is crucial for wireless sensor networks (WSNs in performing a number of fundamental operations such as data coordination, power management, security, and localization. The Pairwise Broadcast Synchronization (PBS protocol was recently proposed to minimize the number of timing messages required for global network synchronization, which enables the design of highly energy-efficient WSNs. However, PBS requires all nodes in the network to lie within the communication ranges of two leader nodes, a condition which might not be available in some applications. This paper proposes an extension of PBS to the more general class of sensor networks. Based on the hierarchical structure of the network, an energy-efficient pair selection algorithm is proposed to select the best pairwise synchronization sequence to reduce the overall energy consumption. It is shown that in a multicluster networking environment, PBS requires a far less number of timing messages than other well-known synchronization protocols and incurs no loss in synchronization accuracy. Moreover, the proposed scheme presents significant energy savings for densely deployed WSNs.

Local adaptation and pronounced genetic differentiation in an extremophile fish, Poecilia mexicana, inhabiting a Mexican cave with toxic hydrogen sulphide.

Science.gov (United States)

Plath, M; Hauswaldt, J S; Moll, K; Tobler, M; García De León, F J; Schlupp, I; Tiedemann, R

2007-03-01

We investigated genetic differentiation and migration patterns in a small livebearing fish, Poecilia mexicana, inhabiting a sulfidic Mexican limestone cave (Cueva del Azufre). We examined fish from three different cave chambers, the sulfidic surface creek draining the cave (El Azufre) and a nearby surface creek without the toxic hydrogen sulphide (Arroyo Cristal). Using microsatellite analysis of 10 unlinked loci, we found pronounced genetic differentiation among the three major habitats: Arroyo Cristal, El Azufre and the cave. Genetic differentiation was also found within the cave between different pools. An estimation of first-generation migrants suggests that (i) migration is unidirectional, out of the cave, and (ii) migration among different cave chambers occurs to some extent. We investigated if the pattern of genetic differentiation is also reflected in a morphological trait, eye size. Relatively large eyes were found in surface habitats, small eyes in the anterior cave chambers, and the smallest eyes were detected in the innermost cave chamber (XIII). This pattern shows some congruence with a previously proposed morphocline in eye size. However, our data do not support the proposed mechanism for this morphocline, namely that it would be maintained by migration from both directions into the middle cave chambers. This would have led to an increased variance in eye size in the middle cave chambers, which we did not find. Restricted gene flow between the cave and the surface can be explained by local adaptations to extreme environmental conditions, namely H2S and absence of light. Within the cave system, habitat properties are patchy, and genetic differentiation between cave chambers despite migration could indicate local adaptation at an even smaller scale.

A Relative-Localization Algorithm Using Incomplete Pairwise Distance Measurements for Underwater Applications

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Kae Y. Foo

2010-01-01

Full Text Available The task of localizing underwater assets involves the relative localization of each unit using only pairwise distance measurements, usually obtained from time-of-arrival or time-delay-of-arrival measurements. In the fluctuating underwater environment, a complete set of pair-wise distance measurements can often be difficult to acquire, thus hindering a straightforward closed-form solution in deriving the assets' relative coordinates. An iterative multidimensional scaling approach is presented based upon a weighted-majorization algorithm that tolerates missing or inaccurate distance measurements. Substantial modifications are proposed to optimize the algorithm, while the effects of refractive propagation paths are considered. A parametric study of the algorithm based upon simulation results is shown. An acoustic field-trial was then carried out, presenting field measurements to highlight the practical implementation of this algorithm.

Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea.

Science.gov (United States)

Postaire, Bautisse; Gélin, Pauline; Bruggemann, J Henrich; Pratlong, Marine; Magalon, Hélène

2017-10-01

Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α ( sensu Postaire et al ., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive F IS values (from -0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (11,000 km distance), with significant pairwise F ST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo-Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.

Genetic studies with morphological mutants of Aspergillus niger

International Nuclear Information System (INIS)

Roy, Ponty; Das, Arati

1979-01-01

Three classes of coloured mutations, viz., fawn, yellow and green, occurred recurrently among the population following UV- and γ-radiation from Co 60 of a wild Aspergillus niger strain 350. Ten mutants were picked up and complementation tests were performed by growing them in pairwise combinations. In two cases, allelic mutants of the same colour were observed. All these mutants were again grown in pairwise crosses with a brown A. niger mutant of different lineage. A poor heterokaryotic growth was, however, observed in one combination which later produced a diploid heterozygous nucleus. It segregated spontaneously to develop a large variety of colonies ranging from haploidy to diploidy including aneuploids. These have been analysed genetically and the possible explanations have been given. (auth.)

The spatial genetic differentiation of the legume pod borer, Maruca vitrata F. (Lepidoptera: Crambidae) populations in West Africa

KAUST Repository

Agunbiade, Tolulope A.

2012-04-17

The legume pod borer, Maruca vitrata, is an endemic insect pest that causes significant yield loss to the cowpea crop in West Africa. The application of population genetic tools is important in the management of insect pests but such data on M. vitrata is lacking. We applied a set of six microsatellite markers to assess the population structure of M. vitrata collected at five sites from Burkina Faso, Niger and Nigeria. Observed polymorphisms ranged from one (marker 3393) to eight (marker 32008) alleles per locus. Observed and expected heterozygosities ranged from 0.0 to 0.8 and 0.0 to 0.6, respectively. Three of the loci in samples from Nigeria and Burkina Faso deviated significantly from Hardy-Weinberg Equilibrium (HWE), whereas no loci deviated significantly in samples from Niger. Analysis of molecular variance (AMOVA) indicated that 67.3% level of the genetic variation was within individuals compared to 17.3% among populations. A global estimate of F ST=0.1 (ENA corrected F ST=0.1) was significant (Pa=0.05) and corroborated by pairwise F ST values that were significant among all possible comparisons. A significant correlation was predicted between genetic divergence and geographic distance between subpopulations (R2=0.6, P=0.04), and cluster analysis by the program STRUCTURE predicted that co-ancestry of genotypes were indicative of three distinct populations. The spatial genetic variance among M. vitrata in West Africa may be due to limited gene flow, south-north seasonal movement pattern or other reproductive barriers. This information is important for the cultural, chemical and biological control strategies for managing M. vitrata. Copyright © 2012 Cambridge University Press.

Genetic diversity of sesame (sesamum indicum L.) germplasm from Pakistan using RAPD markers

Energy Technology Data Exchange (ETDEWEB)

Akbar, F; Rabbani, M A; Masood, M S; Shinwari, Z.K., E-mail: shinwari@qau.edu.p

2011-08-15

Genetic diversity among 20 sesame (Sesamum indicum L.) accessions was examined at DNA level by means of random amplified polymorphic DNA (RAPD) analysis. Ten primers used produced a total of 93 RAPD fragments, of which 70 (75%) were polymorphic. Each primer generated 5 to 17 amplified fragments with an average of 9.3 bands per primer. Based on pair-wise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were computed to assess the associations among the accessions. Pair-wise similarity indices varied from 0.65 to 0.91. A UPGMA cluster analysis based on these genetic similarities located most of the accessions far apart from one another, showing a high level of polymorphism. Genetically, all the genotypes were classified into two major groups and six subgroups or clusters. A single accession (22243) was relatively distinct from rest of the accessions and created independent cluster. In conclusion, even with the use of a limited set of primers, RAPD technique revealed a high level of genetic variation among sesame accessions collected from diverse ecologies of Pakistan. This high level of genetic diversity among the genotypes suggested that RAPD technique is valuable for sesame systematic, and can be helpful for the upholding of germplasm banks and the competent choice of parents in breeding programs. (author)

Genetic diversity of sesame (sesamum indicum L.) germplasm from Pakistan using RAPD markers

International Nuclear Information System (INIS)

Akbar, F; Rabbani, M.A.; Masood, M.S.; Shinwari, Z.K.

2011-01-01

Genetic diversity among 20 sesame (Sesamum indicum L.) accessions was examined at DNA level by means of random amplified polymorphic DNA (RAPD) analysis. Ten primers used produced a total of 93 RAPD fragments, of which 70 (75%) were polymorphic. Each primer generated 5 to 17 amplified fragments with an average of 9.3 bands per primer. Based on pair-wise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were computed to assess the associations among the accessions. Pair-wise similarity indices varied from 0.65 to 0.91. A UPGMA cluster analysis based on these genetic similarities located most of the accessions far apart from one another, showing a high level of polymorphism. Genetically, all the genotypes were classified into two major groups and six subgroups or clusters. A single accession (22243) was relatively distinct from rest of the accessions and created independent cluster. In conclusion, even with the use of a limited set of primers, RAPD technique revealed a high level of genetic variation among sesame accessions collected from diverse ecologies of Pakistan. This high level of genetic diversity among the genotypes suggested that RAPD technique is valuable for sesame systematic, and can be helpful for the upholding of germplasm banks and the competent choice of parents in breeding programs. (author)

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

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Lu Hou

2018-04-01

Full Text Available Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548 and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958 were found in this species. Molecular variance analysis suggested that most of the variation (83% existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.

Genetic parameters for different growth scales in GIFT strain of Nile tilapia (Oreochromis niloticus).

Science.gov (United States)

He, J; Gao, H; Xu, P; Yang, R

2015-12-01

Body weight, length, width and depth at two growth stages were observed for a total of 5015 individuals of GIFT strain, along with a pedigree including 5588 individuals from 104 sires and 162 dams was collected. Multivariate animal models and a random regression model were used to genetically analyse absolute and relative growth scales of these growth traits. In absolute growth scale, the observed growth traits had moderate heritabilities ranging from 0.321 to 0.576, while pairwise ratios between body length, width and depth were lowly inherited and maximum heritability was only 0.146 for length/depth. All genetic correlations were above 0.5 between pairwise growth traits and genetic correlation between length/width and length/depth varied between both growth stages. Based on those estimates, selection index of multiple traits of interest can be formulated in future breeding program to improve genetically body weight and morphology of the GIFT strain. In relative growth scale, heritabilities in relative growths of body length, width and depth to body weight were 0.257, 0.412 and 0.066, respectively, while genetic correlations among these allometry scalings were above 0.8. Genetic analysis for joint allometries of body weight to body length, width and depth will contribute to genetically regulate the growth rate between body shape and body weight. © 2015 Blackwell Verlag GmbH.

Measuring pair-wise molecular interactions in a complex mixture

Science.gov (United States)

Chakraborty, Krishnendu; Varma, Manoj M.; Venkatapathi, Murugesan

2016-03-01

Complex biological samples such as serum contain thousands of proteins and other molecules spanning up to 13 orders of magnitude in concentration. Present measurement techniques do not permit the analysis of all pair-wise interactions between the components of such a complex mixture to a given target molecule. In this work we explore the use of nanoparticle tags which encode the identity of the molecule to obtain the statistical distribution of pair-wise interactions using their Localized Surface Plasmon Resonance (LSPR) signals. The nanoparticle tags are chosen such that the binding between two molecules conjugated to the respective nanoparticle tags can be recognized by the coupling of their LSPR signals. This numerical simulation is done by DDA to investigate this approach using a reduced system consisting of three nanoparticles (a gold ellipsoid with aspect ratio 2.5 and short axis 16 nm, and two silver ellipsoids with aspect ratios 3 and 2 and short axes 8 nm and 10 nm respectively) and the set of all possible dimers formed between them. Incident light was circularly polarized and all possible particle and dimer orientations were considered. We observed that minimum peak separation between two spectra is 5 nm while maximum is 184nm.

[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%).

The relationships between chemical and genetic differentiation and environmental factors across the distribution of Erigeron breviscapus (Asteraceae.

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Xiang Li

Full Text Available AIMS: Erigeron breviscapus (Vant. Hand.-Mazz. is an important, widely used Chinese herb with scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B being its major active compounds. We aimed to resolve the influence of biotic and abiotic factors on the concentrations of these compounds and to determine appropriate cultivation methods to improve the yields of the four compounds in this herb. METHODS: In order to detect the major genetic and natural environmental factors affecting the yields of these four compounds, we applied AFLP markers to investigate the population genetic differentiation and HPLC to measure the concentrations of four major active compounds among 23 wild populations which were located across almost the entire distribution of this species in China. The meteorological data including annual average temperature, annual average precipitation and annual average hours of sunshine were collected. The relationships among the concentrations of four compounds and environmental factors and genetic differentiation were studied. IMPORTANT FINDINGS: Low intraspecific genetic differentiation is detected, and there is no obvious correlation between the genetic differentiation and the contents of the chemical compounds. We investigated the correlation between the concentrationsof four compounds (scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B and environmental factors. Concentrations of two compounds (1,5-dicaffeoylquinic acid and 3,5-dicaffeoylquinic acid were correlated with environmental factors. The concentration of 1,5-dicaffeoylquinic acid is positively correlated with latitude, and is negatively correlated with the annual average temperature. The concentration of 3,5-dicaffeoylquinic acid is positively correlated with annual average precipitation. Therefore, changing cultivation conditions may significantly improve the yields of these two compounds. We found the concentration

Significant genetic differentiation within the population of the Island of Corsica (France) revealed by y-chromosome analysis.

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Ghiani, Maria Elena; Varesi, Laurent; Mitchell, Robert John; Vona, Giuseppe

2009-12-01

Using 10 Y-chromosome short tandem repeat allelic and haplotypic frequencies, we examined genetic variation within the population of Corsica and its relationship with other Mediterranean populations. The most significant finding is the high level of genetic differentiation within Corsica, with strong evidence of an effective barrier to male-mediated gene flow between the south and the rest of the island. This internal differentiation most probably results from low exogamy among small isolated populations and also from the orography of the island, with a central mountain chain running the length of the island restricting human movement. This physical barrier is reflected not only in present-day intraisland linguistic and genetic differences but also in the relatedness of Corsican regions to other Mediterranean groups. Northwest and Central Corsica are much closer to West Mediterranean populations, whereas South Corsica is closer to Central-North Sardinia and East Mediterranean populations.

Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches.

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Ai, Lin; Chen, Mu-Xin; Alasaad, Samer; Elsheikha, Hany M; Li, Juan; Li, Hai-Long; Lin, Rui-Qing; Zou, Feng-Cai; Zhu, Xing-Quan; Chen, Jia-Xu

2011-06-10

Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

Genetic and Epigenetic Regulation of Human Cardiac Reprogramming and Differentiation in Regenerative Medicine.

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Burridge, Paul W; Sharma, Arun; Wu, Joseph C

2015-01-01

Regeneration or replacement of lost cardiomyocytes within the heart has the potential to revolutionize cardiovascular medicine. Numerous methodologies have been used to achieve this aim, including the engraftment of bone marrow- and heart-derived cells as well as the identification of modulators of adult cardiomyocyte proliferation. Recently, the conversion of human somatic cells into induced pluripotent stem cells and induced cardiomyocyte-like cells has transformed potential approaches toward this goal, and the engraftment of cardiac progenitors derived from human embryonic stem cells into patients is now feasible. Here we review recent advances in our understanding of the genetic and epigenetic control of human cardiogenesis, cardiac differentiation, and the induced reprogramming of somatic cells to cardiomyocytes. We also cover genetic programs for inducing the proliferation of endogenous cardiomyocytes and discuss the genetic state of cells used in cardiac regenerative medicine.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

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Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae from Malaysian coastal waters

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Nima Khalili Samani

2016-05-01

Full Text Available Plotosus canius (Hamilton, 1822 is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho = 0.79. This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

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Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

2018-01-01

Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing

Historical demography of common carp estimated from individuals collected from various parts of the world using the pairwise sequentially markovian coalescent approach.

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Yuan, Zihao; Huang, Wei; Liu, Shikai; Xu, Peng; Dunham, Rex; Liu, Zhanjiang

2018-04-01

The inference of historical demography of a species is helpful for understanding species' differentiation and its population dynamics. However, such inference has been previously difficult due to the lack of proper analytical methods and availability of genetic data. A recently developed method called Pairwise Sequentially Markovian Coalescent (PSMC) offers the capability for estimation of the trajectories of historical populations over considerable time periods using genomic sequences. In this study, we applied this approach to infer the historical demography of the common carp using samples collected from Europe, Asia and the Americas. Comparison between Asian and European common carp populations showed that the last glacial period starting 100 ka BP likely caused a significant decline in population size of the wild common carp in Europe, while it did not have much of an impact on its counterparts in Asia. This was probably caused by differences in glacial activities in East Asia and Europe, and suggesting a separation of the European and Asian clades before the last glacial maximum. The North American clade which is an invasive population shared a similar demographic history as those from Europe, consistent with the idea that the North American common carp probably had European ancestral origins. Our analysis represents the first reconstruction of the historical population demography of the common carp, which is important to elucidate the separation of European and Asian common carp clades during the Quaternary glaciation, as well as the dispersal of common carp across the world.

Big mountains but small barriers: Population genetic structure of the Chinese wood frog (Rana chensinensis in the Tsinling and Daba Mountain region of northern China

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Li Cheng

2009-04-01

Full Text Available Abstract Background Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Results Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. Conclusion The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high

Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L. as revealed by microsatellite DNA analysis

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D. LOUKOVITIS

2014-10-01

Full Text Available Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.

An animal model of differential genetic risk for methamphetamine intake

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Tamara ePhillips

2015-09-01

Full Text Available The question of whether genetic factors contribute to risk for methamphetamine (MA use and dependence has not been intensively investigated. Compared to human populations, genetic animal models offer the advantages of control over genetic family history and drug exposure. Using selective breeding, we created lines of mice that differ in genetic risk for voluntary MA intake and identified the chromosomal addresses of contributory genes. A quantitative trait locus was identified on chromosome 10 that accounts for more than 50% of the genetic variance in MA intake in the selected mouse lines. In addition, behavioral and physiological screening identified differences corresponding with risk for MA intake that have generated hypotheses that are testable in humans. Heightened sensitivity to aversive and certain physiological effects of MA, such as MA-induced reduction in body temperature, are hallmarks of mice bred for low MA intake. Furthermore, unlike MA-avoiding mice, MA-preferring mice are sensitive to rewarding and reinforcing MA effects, and to MA-induced increases in brain extracellular dopamine levels. Gene expression analyses implicate the importance of a network enriched in transcription factor genes, some of which regulate the mu opioid receptor gene, Oprm1, in risk for MA use. Neuroimmune factors appear to play a role in differential response to MA between the mice bred for high and low intake. In addition, chromosome 10 candidate gene studies provide strong support for a trace amine associated receptor 1 gene, Taar1, polymorphism in risk for MA intake. MA is a trace amine-associated receptor 1 (TAAR1 agonist, and a non-functional Taar1 allele segregates with high MA consumption. Thus, reduced TAAR1 function has the potential to increase risk for MA use. Overall, existing findings support the MA drinking lines as a powerful model for identifying genetic factors involved in determining risk for harmful MA use. Future directions include the

Uniform Selection as a Primary Force Reducing Population Genetic Differentiation of Cavitation Resistance across a Species Range

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Lamy, Jean-Baptiste; Bouffier, Laurent; Burlett, Régis; Plomion, Christophe; Cochard, Hervé; Delzon, Sylvain

2011-01-01

Background Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. Methodology We assessed cavitation resistance (P 50), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F ST) and quantitative genetic differentiation (Q ST), for retrospective identification of the evolutionary forces acting on these traits. Results/Discussion In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h2 ns = 0.43±0.18, CVA = 4.4%). Q ST was significantly lower than F ST, indicating uniform selection for P 50, rather than genetic drift. Putative mechanisms underlying QST

Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences.

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Guo, Guo-Ye; Chen, Fang; Shi, Xiao-Dong; Tian, Yin-Shuai; Yu, Mao-Qun; Han, Xue-Qin; Yuan, Li-Chun; Zhang, Ying

2016-01-01

Genetic variation and phylogenetic relationships among 102 Jatropha curcas accessions from Asia, Africa, and the Americas were assessed using the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS). The average G+C content (65.04%) was considerably higher than the A+T (34.96%) content. The estimated genetic diversity revealed moderate genetic variation. The pairwise genetic divergences (GD) between haplotypes were evaluated and ranged from 0.000 to 0.017, suggesting a higher level of genetic differentiation in Mexican accessions than those of other regions. Phylogenetic relationships and intraspecific divergence were inferred by Bayesian inference (BI), maximum parsimony (MP), and median joining (MJ) network analysis and were generally resolved. The J. curcas accessions were consistently divided into three lineages, groups A, B, and C, which demonstrated distant geographical isolation and genetic divergence between American accessions and those from other regions. The MJ network analysis confirmed that Central America was the possible center of origin. The putative migration route suggested that J. curcas was distributed from Mexico or Brazil, via Cape Verde and then split into two routes. One route was dispersed to Spain, then migrated to China, eventually spreading to southeastern Asia, while the other route was dispersed to Africa, via Madagascar and migrated to China, later spreading to southeastern Asia. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Genetic Structure and Eco-Geographical Differentiation of Wild Sheep Fescue (Festuca ovina L. in Xinjiang, Northwest China

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Chenglin Zhang

2017-08-01

Full Text Available Glaciation and mountain orogeny have generated new ecologic opportunities for plants, favoring an increase in the speciation rate. Moreover, they also act as corridors or barriers for plant lineages and populations. High genetic diversity ensures that species are able to survive and adapt. Gene flow is one of the most important determinants of the genetic diversity and structure of out-crossed species, and it is easily affected by biotic and abiotic factors. The aim of this study was to characterize the genetic diversity and structure of an alpine species, Festuca ovina L., in Xinjiang, China. A total of 100 individuals from 10 populations were analyzed using six amplified fragment length polymorphism (AFLP primer pairs. A total of 583 clear bands were generated, of which 392 were polymorphic; thus, the percentage of polymorphic bands (PPB was 67.24%. The total and average genetic diversities were 0.2722 and 0.2006 (0.1686–0.2225, respectively. The unweighted group method with arithmetic mean (UPGMA tree, principal coordinates analysis (PCoA and Structure analyses revealed that these populations or individuals could be clustered into two groups. The analysis of molecular variance analysis (AMOVA suggested that most of the genetic variance existed within a population, and the genetic differentiation (Fst among populations was 20.71%. The Shannon differentiation coefficient (G’st among populations was 0.2350. Limited gene flow (Nm = 0.9571 was detected across all sampling sites. The Fst and Nm presented at different levels under the genetic barriers due to fragmentation. The population genetic diversity was significant relative to environmental factors such as temperature, altitude and precipitation.

Contrasting geographic patterns of genetic differentiation in body size and development time with reproductive isolation in Dendroctonus ponderosae (Coleoptera: Curculionidae, Scolytinae)

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Ryan R. Bracewell; Michael E. Pfrender; Karen E. Mock; Barbara J. Bentz

2013-01-01

Body size and development time are two critical phenotypic traits that can be highly adaptive in insects. Recent population genetic analyses and crossing experiments with the mountain pine beetle (Dendroctonus ponderosae Hopkins) have described substantial levels of neutral molecular genetic differentiation, genetic differences in phenotypic traits, and reproductive...

Image ranking in video sequences using pairwise image comparisons and temporal smoothing

CSIR Research Space (South Africa)

Burke, Michael

2016-12-01

Full Text Available The ability to predict the importance of an image is highly desirable in computer vision. This work introduces an image ranking scheme suitable for use in video or image sequences. Pairwise image comparisons are used to determine image ‘interest...

Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats.

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Hua, Panyu; Zhang, Libiao; Guo, Tingting; Flanders, Jon; Zhang, Shuyi

2013-01-01

Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus) is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST) estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST) values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.

Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats.

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Panyu Hua

Full Text Available Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.

Dynamics of pairwise entanglement between two Tavis-Cummings atoms

International Nuclear Information System (INIS)

Guo Jinliang; Song Heshan

2008-01-01

We investigate the time evolution of pairwise entanglement between two Tavis-Cummings atoms for various entangled initial states, including pure and mixed states. We find that the phenomenon of entanglement sudden death behaviors is distinct in the evolution of entanglement for different initial states. What deserves mentioning here is that the initial portion of the excited state in the initial state is responsible for the sudden death of entanglement, and the degree of this effect also depends on the initial states

Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

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Li Hai-Long

2011-06-01

Full Text Available Abstract Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

Genetic diversity analysis of the oriental river prawn (Macrobrachium nipponense) in Huaihe River.

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Cui, Feng; Yu, Yanyan; Bao, Fangyin; Wang, Song; Xiao, Ming Song

2018-04-19

The oriental river prawn (Macrobrachium nipponense) is an economically and nutritionally important species of decapod crustaceans in China. Genetic structure and demographic history of Macrobrachium nipponense were examined using sequence data from portions of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Samples of 191 individuals were collected from 10 localities in the upper to middle reaches of the Huaihe River. Variability was detected at a total of 42 nucleotide sites along 684 bp length of homologous sequence (6.14%), and base substitutions occurred mostly at the second codon position. Haplotype diversity (h) and nucleotide diversity (π) of all populations were 0.9136 ± 0.0116 and 0.0078 ± 0.0042, respectively. Phylogenetic tree constructed using the maximum-likelihood (ML) method showed that the 44 haplotypes were assigned to two obvious clades associated with geographic regions. Moreover, the median-joining network was similar to the topology of the phylogenetic tree with 44 haplotypes. The pairwise F ST values between the populations varied from -0.0298 to 0.2994. Generally, moderate genetic differentiation (F ST  = 0.1598, p = .0000) among different geographic populations was detected, with the significant differentiation between the Huaibin (HB) and other Macrobrachium nipponense populations. Both mismatch distribution analyses and neutrality tests suggested the early stage of Late Pleistocene population expansion 85,500 years before present for the species, which was consistent with the palaeoclimatic condition of the Huaihe River Basin.

Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda.

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Zhu, Ying; Wan, Qiu-Hong; Yu, Bin; Ge, Yun-Fa; Fang, Sheng-Guo

2013-10-22

Evaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units. Overall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated. The giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend

Genetic and clinical characteristics of primary and secondary glioblastoma is associated with differential molecular subtype distribution

OpenAIRE

Li, Rui; Li, Hailin; Yan, Wei; Yang, Pei; Bao, Zhaoshi; Zhang, Chuanbao; Jiang, Tao; You, Yongping

2015-01-01

Glioblastoma multiforme (GBM) is classified into primary (pGBM) or secondary (sGBM) based on clinical progression. However, there are some limits to this classification for insight into genetically and clinically distinction between pGBM and sGBM. The aim of this study is to characterize pGBM and sGBM associating with differential molecular subtype distribution. Whole transcriptome sequencing data was used to assess the distribution of molecular subtypes and genetic alterations in 88 pGBM and...

Range expansion, genetic differentiation, and phenotypic adaption of Hippophae neurocarpa (Elaeagnaceae) on the Qinghai- Tibet Plateau

Czech Academy of Sciences Publication Activity Database

Kou, Y.-X.; Wu, Y.-X.; Jia, Dong-Rui; Li, Z.-H.; Wang, Y.-J.

2014-01-01

Roč. 52, č. 3 (2014), s. 303-312 ISSN 1674-4918 Institutional support: RVO:67985939 Keywords : genetic differentiation * phenotyp adaptation * range expansion Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 1.488, year: 2014

Simultaneous-Fault Diagnosis of Gas Turbine Generator Systems Using a Pairwise-Coupled Probabilistic Classifier

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Zhixin Yang

2013-01-01

Full Text Available A reliable fault diagnostic system for gas turbine generator system (GTGS, which is complicated and inherent with many types of component faults, is essential to avoid the interruption of electricity supply. However, the GTGS diagnosis faces challenges in terms of the existence of simultaneous-fault diagnosis and high cost in acquiring the exponentially increased simultaneous-fault vibration signals for constructing the diagnostic system. This research proposes a new diagnostic framework combining feature extraction, pairwise-coupled probabilistic classifier, and decision threshold optimization. The feature extraction module adopts wavelet packet transform and time-domain statistical features to extract vibration signal features. Kernel principal component analysis is then applied to further reduce the redundant features. The features of single faults in a simultaneous-fault pattern are extracted and then detected using a probabilistic classifier, namely, pairwise-coupled relevance vector machine, which is trained with single-fault patterns only. Therefore, the training dataset of simultaneous-fault patterns is unnecessary. To optimize the decision threshold, this research proposes to use grid search method which can ensure a global solution as compared with traditional computational intelligence techniques. Experimental results show that the proposed framework performs well for both single-fault and simultaneous-fault diagnosis and is superior to the frameworks without feature extraction and pairwise coupling.

Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation

NARCIS (Netherlands)

Botta, Filippo; Eriksen, Casper; Fontaine, Michael Christophe; Guillot, Gilles

2015-01-01

In a recent paper, Bradburd et al. (2013) proposed a model to quantify the relative effect ofgeographic and environmental distance on genetic differentiation. Here, we enhance this method in several ways. 1. We modify the covariance model so as to fit better with mainstream geostatistical models and

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.

Science.gov (United States)

Cortázar-Chinarro, Maria; Lattenkamp, Ella Z; Meyer-Lucht, Yvonne; Luquet, Emilien; Laurila, Anssi; Höglund, Jacob

2017-08-14

Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

Genetic Influence on the Peripheral Blood CD4+ T-cell Differentiation Status in CMV Infection

DEFF Research Database (Denmark)

Goldeck, David; Larsen, Lisbeth Aagaard; Christiansen, Lene

2016-01-01

from the Danish Twin Registry for their T-cell differentiation status, assessed by surface expression of CD27, CD28, CD57, and KLRG-1. We observed a significant intraclass correlation between cotwins of MZ, but not DZ pairs for the differentiation status of CD4(+) and CD8(+) subsets. Classical......A latent infection with cytomegalovirus (CMV), a ubiquitous beta herpesvirus, is associated with an accumulation of late-differentiated memory T-cells, often accompanied by a reciprocal reduced frequency of early-differentiated cells (commonly also referred to as "naïve"). However, this impact...... of CMV on T-cell phenotypes is variable between individuals. Our previous findings in a subgroup of participants in the Leiden familial Longevity Study indicated an important role of genetics. For further testing, we have analyzed middle-aged monozygotic (MZ, n = 42) and dizygotic (DZ, n = 39) twin pairs...

GapMis: a tool for pairwise sequence alignment with a single gap.

Science.gov (United States)

Flouri, Tomás; Frousios, Kimon; Iliopoulos, Costas S; Park, Kunsoo; Pissis, Solon P; Tischler, German

2013-08-01

Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.

Locating one pairwise interaction: Three recursive constructions

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Charles J. Colbourn

2016-09-01

Full Text Available In a complex component-based system, choices (levels for components (factors may interact tocause faults in the system behaviour. When faults may be caused by interactions among few factorsat specific levels, covering arrays provide a combinatorial test suite for discovering the presence offaults. While well studied, covering arrays do not enable one to determine the specific levels of factorscausing the faults; locating arrays ensure that the results from test suite execution suffice to determinethe precise levels and factors causing faults, when the number of such causes is small. Constructionsfor locating arrays are at present limited to heuristic computational methods and quite specific directconstructions. In this paper three recursive constructions are developed for locating arrays to locateone pairwise interaction causing a fault.

Genetic variations of ND5 gene of mtDNA in populations of Anopheles sinensis (Diptera: Culicidae) malaria vector in China

Science.gov (United States)

2013-01-01

Background Anopheles sinensis is a principal vector for Plasmodium vivax malaria in most parts of China. Understanding of genetic structure and genetic differentiation of the mosquito should contribute to the vector control and malaria elimination in China. Methods The present study investigated the genetic structure of An. sinensis populations using a 729 bp fragment of mtDNA ND5 among 10 populations collected from seven provinces in China. Results ND5 was polymorphic by single mutations within three groups of An. sinensis that were collected from 10 different geographic populations in China. Out of 140 specimens collected from 10 representative sites, 84 haplotypes and 71 variable positions were determined. The overall level of genetic differentiation of An. sinensis varied from low to moderate across China and with a FST range of 0.00065 – 0.341. Genealogy analysis clustered the populations of An. sinensis into three main clusters. Each cluster shared one main haplotype. Pairwise variations within populations were higher (68.68%) than among populations (31.32%) and with high fixation index (FST = 0.313). The results of the present study support population growth and expansion in the An. sinensis populations from China. Three clusters of An. sinensis populations were detected in this study with each displaying different proportion patterns over seven Chinese provinces. No correlation between genetic and geographic distance was detected in overall populations of An. sinensis (R2 = 0.058; P = 0.301). Conclusions The results indicate that the ND5 gene of mtDNA is highly polymorphic in An. sinensis and has moderate genetic variability in the populations of this mosquito in China. Demographic and spatial results support evidence of expansion in An. sinensis populations. PMID:24192424

Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms.

Science.gov (United States)

Bahri, Raoudha; El Moncer, Wifak; Al-Batayneh, Khalid; Sadiq, May; Esteban, Esther; Moral, Pedro; Chaabani, Hassen

2012-05-01

Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.

Genetic structure of the Caribbean giant barrel sponge Xestospongia muta using the I3-M11 partition of COI

Science.gov (United States)

López-Legentil, S.; Pawlik, J. R.

2009-03-01

In recent years, reports of sponge bleaching, disease, and subsequent mortality have increased alarmingly. Population recovery may depend strongly on colonization capabilities of the affected species. The giant barrel sponge Xestospongia muta is a dominant reef constituent in the Caribbean. However, little is known about its population structure and gene flow. The 5'-end fragment of the mitochondrial gene cytochrome oxidase subunit I is often used to address these kinds of questions, but it presents very low intraspecific nucleotide variability in sponges. In this study, the usefulness of the I3-M11 partition of COI to determine the genetic structure of X. muta was tested for seven populations from Florida, the Bahamas and Belize. A total of 116 sequences of 544 bp were obtained for the I3-M11 partition corresponding to four haplotypes. In order to make a comparison with the 5'-end partition, 10 sequences per haplotype were analyzed for this fragment. The 40 resulting sequences were of 569 bp and corresponded to two haplotypes. The nucleotide diversity of the I3-M11 partition (π = 0.00386) was higher than that of the 5'-end partition (π = 0.00058), indicating better resolution at the intraspecific level. Sponges with the most divergent external morphologies (smooth vs. digitate surface) had different haplotypes, while those with the most common external morphology (rough surface) presented a mixture of haplotypes. Pairwise tests for genetic differentiation among geographic locations based on F ST values showed significant genetic divergence between most populations, but this genetic differentiation was not due to isolation by distance. While limited larval dispersal may have led to differentiation among some of the populations, the patterns of genetic structure appear to be most strongly related to patterns of ocean currents. Therefore, hydrological features may play a major role in sponge colonization and need to be considered in future plans for management and

Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range.

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Jean-Baptiste Lamy

Full Text Available BACKGROUND: Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. METHODOLOGY: We assessed cavitation resistance (P(50, growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F(ST and quantitative genetic differentiation (Q(ST, for retrospective identification of the evolutionary forces acting on these traits. RESULTS/DISCUSSION: In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h(2 (ns = 0.43±0.18, CV(A = 4.4%. Q(ST was significantly lower than F(ST, indicating uniform selection for P(50, rather than genetic drift. Putative mechanisms underlying Q(ST

Multispecies genetic structure and hybridization in the Betula genus across Eurasia.

Science.gov (United States)

Tsuda, Yoshiaki; Semerikov, Vladimir; Sebastiani, Federico; Vendramin, Giovanni Giuseppe; Lascoux, Martin

2017-01-01

Boreal and cool temperate forests are the major land cover of northern Eurasia, and information about continental-scale genetic structure and past demographic history of forest species is important from an evolutionary perspective and has conservation implications. However, although many population genetic studies of forest tree species have been conducted in Europe or Eastern Asia, continental-scale genetic structure and past demographic history remain poorly known. Here, we focus on the birch genus Betula, which is commonly distributed in boreal and cool temperate forests, and examine 129 populations of two tetraploid and four diploid species collected from Iceland to Japan. All individuals were genotyped at seven to 18 nuclear simple sequence repeats (nSSRs). Pairwise FST' among the six species ranged from 0.285 to 0.903, and genetic differentiation among them was clear. structure analysis suggested that Betula pubescens is an allotetraploid and one of the parental species was Betula pendula. In both species pairs of B. pendula and B. plathyphylla, and B. pubescens and B. ermanii, genetic diversity was highest in central Siberia. A hybrid zone was detected around Lake Baikal for eastern and western species pairs regardless of ploidy level. Approximate Bayesian computation suggested that the divergence of B. pendula and B. platyphylla occurred around the beginning of the last ice age (36 300 years BP, 95% CI: 15 330-92 700) and hybridization between them was inferred to have occurred after the last glacial maximum (1614 years BP, 95% CI: 561-4710), with B. pendula providing a higher contribution to hybrids. © 2016 John Wiley & Sons Ltd.

Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

International Nuclear Information System (INIS)

Daoud, M.; Ahl Laamara, R.

2012-01-01

We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl–Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger–Horne–Zeilinger states. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states

Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

Energy Technology Data Exchange (ETDEWEB)

Daoud, M., E-mail: m_daoud@hotmail.com [Department of Physics, Faculty of Sciences, University Ibnou Zohr, Agadir (Morocco); Ahl Laamara, R., E-mail: ahllaamara@gmail.com [LPHE-Modeling and Simulation, Faculty of Sciences, University Mohammed V, Rabat (Morocco); Centre of Physics and Mathematics, CPM, CNESTEN, Rabat (Morocco)

2012-07-16

We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl–Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger–Horne–Zeilinger states. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states.

Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

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Oussama Ahrazem

2012-05-01

Full Text Available Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA and Nei’s genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst was 0.233. Cuenca showed the highest Nei’s genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups—Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco—while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

Genetic divergence between populations of the stingless bee uruçu amarela (Melipona rufiventris group, Hymenoptera, Meliponini: is there a new Melipona species in the Brazilian state of Minas Gerais?

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Mara Garcia Tavares

2007-01-01

Full Text Available Allozyme, microsatellite and random amplified polymorphic DNA (RAPD molecular markers were used to investigate the within and between population genetic variability and between population genetic differentiation of the Brazilian stingless bee uruçu amarela (nominally Melipona rufiventris Lepeletier, 1836 present in savanna and Atlantic forest habitats of the Brazilian state of Minas Gerais (MG. We found low levels of within population variability, although there were a large number of private alleles that specifically characterized these populations. The F ST values indicated a high level of genetic diversity between populations. Analysis of molecular variance (AMOVA showed a high degree of population differentiation between the savanna and Atlantic forest habitats, confirmed by population pairwise F ST data. Principal coordinates analysis and unweighted pair-group method using an arithmetic average (UPGMA dendrograms also confirmed that in Minas Gerais the savanna populations (M. rufiventris were genetically distinct from those present in the Atlantic forest (M. mondury. In addition, populations from locations near the towns of Dom Bosco and Brasilândia de Minas were genetically different from those collected in other localities in the savanna. Our data indicate that populations of uruçu amarela found in the savanna and Atlantic forest habitats of Minas Gerais state should be treated separately for conservation purposes and that special attention should be given to the populations found in the region of Dom Bosco and Brasilândia de Minas until their taxonomic status is clarified.

A Novel Technique for Steganography Method Based on Improved Genetic Algorithm Optimization in Spatial Domain

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M. Soleimanpour-moghadam

2013-06-01

Full Text Available This paper devotes itself to the study of secret message delivery using cover image and introduces a novel steganographic technique based on genetic algorithm to find a near-optimum structure for the pair-wise least-significant-bit (LSB matching scheme. A survey of the related literatures shows that the LSB matching method developed by Mielikainen, employs a binary function to reduce the number of changes of LSB values. This method verifiably reduces the probability of detection and also improves the visual quality of stego images. So, our proposal draws on the Mielikainen's technique to present an enhanced dual-state scoring model, structured upon genetic algorithm which assesses the performance of different orders for LSB matching and searches for a near-optimum solution among all the permutation orders. Experimental results confirm superiority of the new approach compared to the Mielikainen’s pair-wise LSB matching scheme.

Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity.

Science.gov (United States)

De Luca, Daniele; Cennamo, Paola; Del Guacchio, Emanuele; Di Novella, Riccardo; Caputo, Paolo

2018-02-01

Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.

On the calculation of x-ray scattering signals from pairwise radial distribution functions

DEFF Research Database (Denmark)

Dohn, Asmus Ougaard; Biasin, Elisa; Haldrup, Kristoffer

2015-01-01

We derive a formulation for evaluating (time-resolved) x-ray scattering signals of solvated chemical systems, based on pairwise radial distribution functions, with the aim of this formulation to accompany molecular dynamics simulations. The derivation is described in detail to eliminate any possi...

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

Science.gov (United States)

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

2017-11-01

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

Genetic Diversity and Population Structure of Theileria annulata in Oman.

Science.gov (United States)

Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

2015-01-01

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, θ = 0.07) were

Genetic Diversity and Population Structure of Theileria annulata in Oman.

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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, �

Differential effects of genetic - and diet - induced obesity on fertility, spermatogenesis and sperm epigenome in adult male rats

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Sharvari Deshpande

2017-10-01

Full Text Available Obesity is a global health issue affecting millions of people of different age groups. The incidence of male obesity induced infertility is rising in couples undergoing ARTs suggesting that obesity is an established risk factor for male infertility. Recent studies demonstrate that paternal diet induced obesity could induce epigenetic disturbances in offspring. Obesity is a multifactorial disorder with predominantly genetic or environmental causes. No studies have compared the effect of genetic and diet induced obesity on male reproduction. The present study aims to delineate effects of obesity on male fertility, spermatogenesis and sperm epigenome using two rat models: genetically induced obese (GIO – WNIN/OB and diet induced obese (DIO – High fat diet. Body weights were similar in both groups, but, differential effects on hormonal profiles were observed. Fertility assessment showed decreased litter size mainly due to increased pre- and post-implantation loss in DIO group. However, GIO group were infertile due to decrease in libido. We observed a decrease in sperm counts in GIO group but not in DIO group despite the body weights being similar in both the groups. Flow cytometry and cell type specific marker expression studies in testis revealed that both DIO and GIO affect mitosis and differentiation process by increasing spermatogonial proliferation. In DIO group, no effect was observed on meiosis whereas in GIO group, we observed an effect on meiosis. Spermiogenesis process was affected in both the groups. In order to study the effect of genetic and diet induced obesity on different aspects of spermatogenesis, we performed qRT-PCR to study expression of genes involved in spermatocyte progression, spermiogenesis process, reproductive hormone receptors and leptin signaling in testis. Since epigenetic mechanisms are susceptible to environmental and genetic changes, we analyzed the methylation status of Igf2-H19 DMR in spermatozoa of both the

Inferring genetic diversity and differentiation of the endangered chinese endemic plant sauvagesia rhodoleuca (ochnaceae) using microsatelite markers

International Nuclear Information System (INIS)

Chen, Z. Y.; Wei, X.; Jiang, Y. S.; Chai, S. F.

2015-01-01

Sauvagesia rhodoleuca is one of the most endangered species in China. It has a narrow distribution in the evergreen broadleaved forest of southern China. Up to now, only six populations remained in two provinces. In this study, eight microsatellite loci were used to examine genetic diversity in these populations. We found very low levels of genetic diversity within populations of S. rhodoleuca with average observed and expected heterozygosity (HO and HE) of 0.069 and 0.186, respectively. Estimated inbreeding coefficients (FIS) within populations were high suggests the probable selfing in the species.Combination of the UPGMA dendrogram and the INSTRUCT analysis show that six extant populations could be classified into three distinct genetic groups and no pattern of isolation by distance was detected among populations. The low genetic variation within populations and high genetic differentiation among populations indicate that the management for the conservation of genetic diversity in S. rhodoleuca should aim to preserve every population. (author)

A pragmatic pairwise group-decision method for selection of sites for nuclear power plants

International Nuclear Information System (INIS)

Kutbi, I.I.

1987-01-01

A pragmatic pairwise group-decision approach is applied to compare two regions in order to select the more suitable one for construction of nulcear power plants in the Kingdom of Saudi Arabia. The selection methodology is based on pairwise comparison by forced choice. The method facilitates rating of the regions or sites using simple calculations. Two regions, one close to Dhahran on the Arabian Gulf and another close to Jeddah on the Red Sea, are evaluated. No specific site in either region is considered at this stage. The comparison is based on a set of selection criteria which include (i) topography, (ii) geology, (iii) seismology, (iv) meteorology, (v) oceanography, (vi) hydrology and (vii) proximetry to oil and gas fields. The comparison shows that the Jeddah region is more suitable than the Dhahran region. (orig.)

Genetic characterization and phylogenetic analysis of Eimeria arloingi in Iranian native kids.

Science.gov (United States)

Khodakaram-Tafti, A; Hashemnia, M; Razavi, S M; Sharifiyazdi, H; Nazifi, S

2013-09-01

Among the 16 species of Eimeria from goats, Eimeria arloingi and Eimeria ninakohlyakimovae are regarded as the most pathogenic species in the world and cause clinical caprine coccidiosis. E. arloingi is known to be an important cause of coccidiosis in Iranian kids. Molecular analyses of two portions of nuclear ribosomal DNA (internal transcribed spacer1 (ITS1) and 18S rDNA) were used for the genetic characterization of the E. arloingi. Comparison of the sequencing data of E. arloingi obtained in the present study (ITS1: KC507793 and 18S rDNA: KC507792) with other Eimeria species in the GenBank database revealed a particularly close relationship between E. arloingi and Eimeria spp. from the cattle and sheep. The phylogram based on the ITS1 sequences shows that the E. arloingi, Eimeria bovis, and Eimeria zuernii formed a distinct group separate from the other remaining Eimeria spp. in cattle and poultry. In pairwise alignment, 18S rDNA sequence derived from E. arloingi showed 99% similarity to Eimeria ahsata with differences observed at only three nucleotides. This study showed that the ITS1 and 18S rDNA gene are useful genetic markers for the specific identification and differentiation of Eimeria spp. in ruminants.

Document Level Assessment of Document Retrieval Systems in a Pairwise System Evaluation

Science.gov (United States)

Rajagopal, Prabha; Ravana, Sri Devi

2017-01-01

Introduction: The use of averaged topic-level scores can result in the loss of valuable data and can cause misinterpretation of the effectiveness of system performance. This study aims to use the scores of each document to evaluate document retrieval systems in a pairwise system evaluation. Method: The chosen evaluation metrics are document-level…

Genetic characterization of different pakistani date palm varieties

International Nuclear Information System (INIS)

Akhtar, W.; Rashid, A.; Mahmood, T.

2014-01-01

Date palm (Phoenix dactylifera L.) is the oldest cultivated fruit tree and it has a great socioeconomic and nutritional value. Breeding programs and conservation rely on genetic characterization and diversity in gene pool. Its genetic diversity has not been focused more in Pakistan yet, therefore the present study aimed at the evaluation of genetic relationship based on chloroplast ribosomal protein gene (rps14). Rps14 gene was amplified and sequenced from selected varieties. Phylogram illustrated over all genetic distance of 0.001 representing close genetic relationship of selected P. dactylifera varieties. Pairwise distance was calculated for rps14 gene and very low genetic diversity values were observed ranging 0.003-0.017. Estimates of average evolutionary divergence of overall sequence pairs and nucleotide diversity were again found very low with 0.008 and 0.007 respectively. Sequences were analyzed by MEGA6, which revealed Pathri, Dhaddy, Makhi and Khudrawi as recent varieties. On the basis of rps14 genetic makeup, it can be suggested that Pakistani date palm varieties show very high degree of similarity. (author)

If F(ST) does not measure neutral genetic differentiation, then comparing it with Q(ST) is misleading. Or is it?

Science.gov (United States)

Edelaar, Pim; Björklund, Mats

2011-05-01

The comparison between neutral genetic differentiation (F(ST) ) and quantitative genetic differentiation (Q(ST) ) is commonly used to test for signatures of selection in population divergence. However, there is an ongoing discussion about what F(ST) actually measures, even resulting in some alternative metrics to express neutral genetic differentiation. If there is a problem with F(ST) , this could have repercussions for its comparison with Q(ST) as well. We show that as the mutation rate of the neutral marker increases, F(ST) decreases: a higher within-population heterozygosity (He) yields a lower F(ST) value. However, the same is true for Q(ST) : a higher mutation rate for the underlying QTL also results in a lower Q(ST) estimate. The effect of mutation rate is equivalent in Q(ST) and F(ST) . Hence, the comparison between Q(ST) and F(ST) remains valid, if one uses neutral markers whose mutation rates are not too high compared to those of quantitative traits. Usage of highly variable neutral markers such as hypervariable microsatellites can lead to serious biases and the incorrect inference that divergent selection has acted on populations. Much of the discussion on F(ST) seems to stem from the misunderstanding that it measures the differentiation of populations, whereas it actually measures the fixation of alleles. In their capacity as measures of population differentiation, Hedrick's G'(ST) and Jost's D reach their maximum value of 1 when populations do not share alleles even when there remains variation within populations, which invalidates them for comparisons with Q(ST) . © 2011 Blackwell Publishing Ltd.

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...

Genetic differentiation of Agrostis capillaris in a grassland system with stable heterogeneity due to terricolous ants

Czech Academy of Sciences Publication Activity Database

Rothanzl, J.; Kotoučová, M.; Hrabinová, I.; Plačková, Ivana; Herben, Tomáš

2007-01-01

Roč. 95, č. 1 (2007), s. 197-207 ISSN 0022-0477 R&D Projects: GA ČR GA206/06/0098 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal growth * functional differentiation * genetic variation * isozyme markers Subject RIV: EF - Botanics Impact factor: 4.422, year: 2007

Genetic Differentiation, Isolation-by-Distance, and Metapopulation Dynamics of the Arizona Treefrog (Hyla wrightorum in an Isolated Portion of Its Range.

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Meryl C Mims

Full Text Available Population attributes such as diversity, connectivity, and structure are important components of understanding species persistence and vulnerability to extinction. Hyla wrightorum, the Arizona treefrog, is native to the southwestern United States and Mexico, and an isolated group of populations exists in the Huachuca Mountains and Canelo Hills (HMCH of southeastern Arizona, USA. Due to concerns about declining observations of the species within the isolated HMCH portion of its range, the HMCH group is currently a candidate for federal protection under the U.S. Endangered Species Act. We present results of a genetic study examining population diversity, structure, and connectivity within the HMCH region. We sampled DNA from H. wrightorum larvae and adults from ten distinct locations, 8 of which were breeding sites and 4 of which were previously undescribed localities for the species. We developed and genotyped 17 polymorphic microsatellite loci and quantified genetic diversity, population differentiation, and landscape influences on population genetic structure. We found evidence of larger than expected effective population sizes, significant genetic differentiation between populations, and evidence of distance being the primary driver of genetic structure of populations with some influence of slope and canopy cover. We found little evidence of recent genetic bottlenecks, and individual-based analyses indicate admixture between populations despite significant genetic differentiation. These patterns may indicate that the breeding sites within the Huachuca Mountains constitute a metapopulation. We suggest that the HMCH region may contain larger and more connected breeding populations than previously understood, but the dynamics of this system and the limited geographic extent of the HMCH group justify current concern for the persistence of the species in this region. Efforts to ensure availability of high-quality breeding habitats and control for

Genetic Correction and Hepatic Differentiation of Hemophilia B-specific Human Induced Pluripotent Stem Cells.

Science.gov (United States)

He, Qiong; Wang, Hui-Hui; Cheng, Tao; Yuan, Wei-Ping; Ma, Yu-Po; Jiang, Yong-Ping; Ren, Zhi-Hua

2017-09-27

Objective To genetically correct a disease-causing point mutation in human induced pluripotent stem cells (iPSCs) derived from a hemophilia B patient. Methods First, the disease-causing mutation was detected by sequencing the encoding area of human coagulation factor IX (F IX) gene. Genomic DNA was extracted from the iPSCs, and the primers were designed to amplify the eight exons of F IX. Next, the point mutation in those iPSCs was genetically corrected using CRISPR/Cas9 technology in the presence of a 129-nucleotide homologous repair template that contained two synonymous mutations. Then, top 8 potential off-target sites were subsequently analyzed using Sanger sequencing. Finally, the corrected clones were differentiated into hepatocyte-like cells, and the secretion of F IX was validated by immunocytochemistry and ELISA assay. Results The cell line bore a missense mutation in the 6 th coding exon (c.676 C>T) of F IX gene. Correction of the point mutation was achieved via CRISPR/Cas9 technology in situ with a high efficacy at about 22% (10/45) and no off-target effects detected in the corrected iPSC clones. F IX secretion, which was further visualized by immunocytochemistry and quantified by ELISA in vitro, reached about 6 ng/ml on day 21 of differentiation procedure. Conclusions Mutations in human disease-specific iPSCs could be precisely corrected by CRISPR/Cas9 technology, and corrected cells still maintained hepatic differentiation capability. Our findings might throw a light on iPSC-based personalized therapies in the clinical application, especially for hemophilia B.

Genetic, epigenetic, and HPLC fingerprint differentiation between natural and ex situ populations of Rhodiola sachalinensis from Changbai Mountain, China.

Science.gov (United States)

Zhao, Wei; Shi, Xiaozheng; Li, Jiangnan; Guo, Wei; Liu, Chengbai; Chen, Xia

2014-01-01

Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = -0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.

Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal.

Science.gov (United States)

Thomas, Evert; van Zonneveld, Maarten; Loo, Judy; Hodgkin, Toby; Galluzzi, Gea; van Etten, Jacob

2012-01-01

Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao's distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000-13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species' Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao.

Landscape genetics of Schistocephalus solidus parasites in threespine stickleback (Gasterosteus aculeatus) from Alaska.

Science.gov (United States)

Sprehn, C Grace; Blum, Michael J; Quinn, Thomas P; Heins, David C

2015-01-01

The nature of gene flow in parasites with complex life cycles is poorly understood, particularly when intermediate and definitive hosts have contrasting movement potential. We examined whether the fine-scale population genetic structure of the diphyllobothriidean cestode Schistocephalus solidus reflects the habits of intermediate threespine stickleback hosts or those of its definitive hosts, semi-aquatic piscivorous birds, to better understand complex host-parasite interactions. Seventeen lakes in the Cook Inlet region of south-central Alaska were sampled, including ten in the Matanuska-Susitna Valley, five on the Kenai Peninsula, and two in the Bristol Bay drainage. We analyzed sequence variation across a 759 bp region of the mitochondrial DNA (mtDNA) cytochrome oxidase I region for 1,026 S. solidus individuals sampled from 2009-2012. We also analyzed allelic variation at 8 microsatellite loci for 1,243 individuals. Analysis of mtDNA haplotype and microsatellite genotype variation recovered evidence of significant population genetic structure within S. solidus. Host, location, and year were factors in structuring observed genetic variation. Pairwise measures revealed significant differentiation among lakes, including a pattern of isolation-by-distance. Bayesian analysis identified three distinct genotypic clusters in the study region, little admixture within hosts and lakes, and a shift in genotype frequencies over time. Evidence of fine-scale population structure in S. solidus indicates that movement of its vagile, definitive avian hosts has less influence on gene flow than expected based solely on movement potential. Observed patterns of genetic variation may reflect genetic drift, behaviors of definitive hosts that constrain dispersal, life history of intermediate hosts, and adaptive specificity of S. solidus to intermediate host genotype.

Landscape genetics of Schistocephalus solidus parasites in threespine stickleback (Gasterosteus aculeatus from Alaska.

Directory of Open Access Journals (Sweden)

C Grace Sprehn

Full Text Available The nature of gene flow in parasites with complex life cycles is poorly understood, particularly when intermediate and definitive hosts have contrasting movement potential. We examined whether the fine-scale population genetic structure of the diphyllobothriidean cestode Schistocephalus solidus reflects the habits of intermediate threespine stickleback hosts or those of its definitive hosts, semi-aquatic piscivorous birds, to better understand complex host-parasite interactions. Seventeen lakes in the Cook Inlet region of south-central Alaska were sampled, including ten in the Matanuska-Susitna Valley, five on the Kenai Peninsula, and two in the Bristol Bay drainage. We analyzed sequence variation across a 759 bp region of the mitochondrial DNA (mtDNA cytochrome oxidase I region for 1,026 S. solidus individuals sampled from 2009-2012. We also analyzed allelic variation at 8 microsatellite loci for 1,243 individuals. Analysis of mtDNA haplotype and microsatellite genotype variation recovered evidence of significant population genetic structure within S. solidus. Host, location, and year were factors in structuring observed genetic variation. Pairwise measures revealed significant differentiation among lakes, including a pattern of isolation-by-distance. Bayesian analysis identified three distinct genotypic clusters in the study region, little admixture within hosts and lakes, and a shift in genotype frequencies over time. Evidence of fine-scale population structure in S. solidus indicates that movement of its vagile, definitive avian hosts has less influence on gene flow than expected based solely on movement potential. Observed patterns of genetic variation may reflect genetic drift, behaviors of definitive hosts that constrain dispersal, life history of intermediate hosts, and adaptive specificity of S. solidus to intermediate host genotype.

Pairwise contact energy statistical potentials can help to find probability of point mutations.

Science.gov (United States)

Saravanan, K M; Suvaithenamudhan, S; Parthasarathy, S; Selvaraj, S

2017-01-01

To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β) 8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than i Mutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structural profiles of human miRNA families from pairwise clustering

DEFF Research Database (Denmark)

Kaczkowski, Bogumil; Þórarinsson, Elfar; Reiche, Kristin

2009-01-01

secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment...... of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures. Availability: http://genome.ku.dk/resources/mirclust...

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

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Brunner Sylvia

2008-05-01

Full Text Available Abstract Background Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation. Results We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation. Conclusion Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

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.

Genetic diversity and substantial population differentiation in Crassostrea hongkongensis revealed by mitochondrial DNA.

Science.gov (United States)

Li, Lu; Wu, Xiangyun; Yu, Ziniu

2013-09-01

The Hong Kong oyster, Crassostrea hongkongensis, is an important fisheries resource that is cultivated in the coastal waters of the South China Sea. Despite significant advances in understanding biological and taxonomic aspects of this species, no detailed study of its population genetic diversity in regions of extensive cultivation are available. Direct sequencing of the mtDNA cox1 gene region was used to investigate genetic variation within and between eleven C. hongkongensis populations collected from typical habitats. Sixty-two haplotypes were identified; only haplotype 2 (21.74% of total haplotypes) was shared among all the eleven populations, and most of the observed haplotypes were restricted to individual populations. Both AMOVA and FST analyses revealed significant population structure, and the isolation by distance (IBD) was confirmed. The highest local differentiation was observed between the sample pools from Guangxi versus Guangdong and Fujian, which are separated by a geographic barrier, the Leizhou Peninsula. Current knowledge from seed management suggests that seed transfer from Guangxi province has likely reduced the divergence that somewhat naturally exists between these pools. The findings from the present study could be useful for genetic management and may serve as a baseline by which to monitor future changes in genetic diversity, either due to natural or anthropogenic impacts. Copyright © 2013 Elsevier B.V. All rights reserved.

Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

Science.gov (United States)

Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

1984-08-01

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

A water market simulator considering pair-wise trades between agents

Science.gov (United States)

Huskova, I.; Erfani, T.; Harou, J. J.

2012-04-01

In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

Random regression analysis for body weights and main morphological traits in genetically improved farmed tilapia (Oreochromis niloticus).

Science.gov (United States)

He, Jie; Zhao, Yunfeng; Zhao, Jingli; Gao, Jin; Xu, Pao; Yang, Runqing

2018-02-01

To genetically analyse growth traits in genetically improved farmed tilapia (GIFT), the body weight (BWE) and main morphological traits, including body length (BL), body depth (BD), body width (BWI), head length (HL) and length of the caudal peduncle (CPL), were measured six times in growth duration on 1451 fish from 45 mixed families of full and half sibs. A random regression model (RRM) was used to model genetic changes of the growth traits with days of age and estimate the heritability for any growth point and genetic correlations between pairwise growth points. Using the covariance function based on optimal RRMs, the heritabilities were estimated to be from 0.102 to 0.662 for BWE, 0.157 to 0.591 for BL, 0.047 to 0.621 for BD, 0.018 to 0.577 for BWI, 0.075 to 0.597 for HL and 0.032 to 0.610 for CPL between 60 and 140 days of age. All genetic correlations exceeded 0.5 between pairwise growth points. Moreover, the traits at initial days of age showed less correlation with those at later days of age. With phenotypes observed repeatedly, the model choice showed that the optimal RRMs could more precisely predict breeding values at a specific growth time than repeatability models or multiple trait animal models, which enhanced the efficiency of selection for the BWE and main morphological traits.

Phylogeography and genetic diversity of a widespread Old World butterfly, Lampides boeticus (Lepidoptera: Lycaenidae

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Pierce Naomi E

2008-10-01

Full Text Available Abstract Background Evolutionary genetics provides a rich theoretical framework for empirical studies of phylogeography. Investigations of intraspecific genetic variation can uncover new putative species while allowing inference into the evolutionary origin and history of extant populations. With a distribution on four continents ranging throughout most of the Old World, Lampides boeticus (Lepidoptera: Lycaenidae is one of the most widely distributed species of butterfly. It is placed in a monotypic genus with no commonly accepted subspecies. Here, we investigate the demographic history and taxonomic status of this widespread species, and screen for the presence or absence of the bacterial endosymbiont Wolbachia. Results We performed phylogenetic, population genetic, and phylogeographic analyses using 1799 bp of mitochondrial sequence data from 57 specimens collected throughout the species' range. Most of the samples (>90% were nearly genetically identical, with uncorrected pairwise sequence differences of 0 – 0.5% across geographic distances > 9,000 km. However, five samples from central Thailand, Madagascar, northern Australia and the Moluccas formed two divergent clades differing from the majority of samples by uncorrected pairwise distances ranging from 1.79 – 2.21%. Phylogenetic analyses suggest that L. boeticus is almost certainly monophyletic, with all sampled genes coalescing well after the divergence from three closely related taxa included for outgroup comparisons. Analyses of molecular diversity indicate that most L. boeticus individuals in extant populations are descended from one or two relatively recent population bottlenecks. Conclusion The combined analyses suggest a scenario in which the most recent common ancestor of L. boeticus and its sister taxon lived in the African region approximately 7 Mya; extant lineages of L. boeticus began spreading throughout the Old World at least 1.5 Mya. More recently, expansion after

Lifting the differentiation embargo

OpenAIRE

Latif, Anne-Louise; Holyoake, Tessa

2016-01-01

Effective differentiation therapy for acute myeloid leukemia (AML) has been restricted to a small subset of patients with one defined genetic abnormality. Using an unbiased small molecule screen, Sykes et al. now identify a mechanism of de-repression of differentiation in several models of AML driven by distinct genetic drivers.

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

Science.gov (United States)

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

2018-02-28

To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided

Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract

Science.gov (United States)

Debiasse, M. B.; Richards, V. P.; Shivji, M. S.

2010-03-01

The genetic population structure of the common branching vase sponge, Callyspongia vaginalis, was determined along the entire length (465 km) of the Florida reef system from Palm Beach to the Dry Tortugas based on sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Populations of C. vaginalis were highly structured (overall ΦST = 0.33), in some cases over distances as small as tens of kilometers. However, nonsignificant pairwise ΦST values were also found between a few relatively distant sampling sites suggesting that some long distance larval dispersal may occur via ocean currents or transport in sponge fragments along continuous, shallow coastlines. Indeed, sufficient gene flow appears to occur along the Florida reef tract to obscure a signal of isolation by distance, but not to homogenize COI haplotype frequencies. The strong genetic differentiation among most of the sampling locations suggests that recruitment in this species is largely local source-driven, pointing to the importance of further elucidating general connectivity patterns along the Florida reef tract to guide the spatial scale of management efforts.

Pairwise correlations via quantum discord and its geometric measure in a four-qubit spin chain

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Abdel-Baset A. Mohamed

2013-04-01

Full Text Available The dynamic of pairwise correlations, including quantum entanglement (QE and discord (QD with geometric measure of quantum discord (GMQD, are shown in the four-qubit Heisenberg XX spin chain. The results show that the effect of the entanglement degree of the initial state on the pairwise correlations is stronger for alternate qubits than it is for nearest-neighbor qubits. This parameter results in sudden death for QE, but it cannot do so for QD and GMQD. With different values for this entanglement parameter of the initial state, QD and GMQD differ and are sensitive for any change in this parameter. It is found that GMQD is more robust than both QD and QE to describe correlations with nonzero values, which offers a valuable resource for quantum computation.

Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran.

Science.gov (United States)

Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

2016-01-01

Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among

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

Science.gov (United States)

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

2016-10-13

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

Population structure, historical biogeography and demographic history of the alpine toad Scutiger ningshanensis in the Tsinling Mountains of Central China.

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Hongzhe Meng

Full Text Available Population genetic structure, historical biogeography and historical demography of the alpine toad Scutiger ningshanensis were studied using the combined data mtDNA cytochrome b (cyt b and the mtDNA cytochrome c oxidase subunit I (COI as the molecular markers. This species has high genetic variation. There was a significant genetic differentiation among most populations. Three lineages were detected. The phylogenetic relationship analyses and the SAMOVA (spatial analysis of molecular variance results showed significant phylogeographic structure. 82.15% genetic variation occurred among populations whereas differentiation within populations only contributed 17.85% to the total. Mantel test results showed a significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (regression coefficient  = 0.001286, correlation coefficient  = 0.77051, p (rrand≥robs  = 0.0185<0.05, indicating the existence of isolation-by-distance pattern of genetic divergence for cyt b + COI sequence, which suggests that the distribution of genetic variation is due to geographical separation rather than natural selection. The population expansion or contraction and genetic differentiation between populations or lineages could be explained by topography and the repetitive uplifts of the Tsinling Mountains and the climatic cycles during the late Pliocene and Pleistocene. S. ningshanensis experienced a rapid population expansion about 40,000 years before present. The current decline in population size was probably caused by anthropogenic disturbance. Current populations of S. ningshanensis are from different refugia though the location of these refugia could not be determined in our study. Topography, climatic changes and repetitive population expansion/contraction together led to the high level of genetic variation in S. ningshanensis. A total of three management units (MUs was determined

Extraction of tacit knowledge from large ADME data sets via pairwise analysis.

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Keefer, Christopher E; Chang, George; Kauffman, Gregory W

2011-06-15

Pharmaceutical companies routinely collect data across multiple projects for common ADME endpoints. Although at the time of collection the data is intended for use in decision making within a specific project, knowledge can be gained by data mining the entire cross-project data set for patterns of structure-activity relationships (SAR) that may be applied to any project. One such data mining method is pairwise analysis. This method has the advantage of being able to identify small structural changes that lead to significant changes in activity. In this paper, we describe the process for full pairwise analysis of our high-throughput ADME assays routinely used for compound discovery efforts at Pfizer (microsomal clearance, passive membrane permeability, P-gp efflux, and lipophilicity). We also describe multiple strategies for the application of these transforms in a prospective manner during compound design. Finally, a detailed analysis of the activity patterns in pairs of compounds that share the same molecular transformation reveals multiple types of transforms from an SAR perspective. These include bioisosteres, additives, multiplicatives, and a type we call switches as they act to either turn on or turn off an activity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Differential association of family subsystem negativity on siblings' maladjustment: using behavior genetic methods to test process theory.

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Feinberg, Mark E; Reiss, David; Neiderhiser, Jenae M; Hetherington, E Mavis

2005-12-01

This study investigated the family context of adolescent sibling similarity and differentiation in maladjustment (antisocial behavior and depression) by examining negativity in different subsystems. Two hypotheses were proposed: (1) Parental and sibling negativity tends to diffuse through the family system, especially because of the high level of reciprocity in sibling relationships, leading to sibling similarity; and (2) interparental (coparenting) conflict disrupts cohesive functioning and thereby motivates and facilitates sibling differentiation and niche picking. To control for the effects of similar genes between siblings, the authors used behavioral genetic models with a genetically informed sample of 720 two-parent families, each with at least 2 adolescent siblings. Results for the differences in shared environmental influences across groups high and low in each of the domains of family negativity provided partial support for the hypotheses. The results further understanding of influences on individual differences and support a theory of how parent-child and interparental relationships intersect with sibling relationship dynamics. Copyright 2006 APA, all rights reserved).

The power to detect recent fragmentation events using genetic differentiation methods.

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Michael W Lloyd

Full Text Available Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright's F st, Hedrick' G'st , Sherwin's MI, and Jost's D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G'st , MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst , G'st , MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst , G'st , MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G'st , MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.

Genetic, epigenetic, and HPLC fingerprint differentiation between natural and ex situ populations of Rhodiola sachalinensis from Changbai Mountain, China.

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Wei Zhao

Full Text Available Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR and methylation-sensitive amplified polymorphism (MSAP markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88% was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%. UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = -0.95 for HPLC fingerprint and altitude. Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.

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

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Yi, Shaokui; Wang, Weimin; Zhou, Xiaoyun

2018-02-21

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

Microsatellite DNA fingerprinting, differentiation, and genetic relationships of clones, cultivars, and varieties of six poplar species from three sections of the genus Populus.

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Rahman, Muhammad H; Rajora, Om P

2002-12-01

Accurate identification of Populus clones and cultivars is essential for effective selection, breeding, and genetic resource management programs. The unit of cultivation and breeding in poplars is a clone, and individual cultivars are normally represented by a single clone. Microsatellite DNA markers of 10 simple sequence repeat loci were used for genetic fingerprinting and differentiation of 96 clones/cultivars and varieties belonging to six Populus species (P. deltoides, P. nigra, P. balsamifera, P. trichocarpa, P. grandidentata, and P maximowiczii) from three sections of the genus. All 96 clones/cultivars could be uniquely fingerprinted based on their single- or multilocus microsatellite genotypes. The five P. grandidentata clones could be differentiated based on their single-locus genotypes, while six clones of P. trichocarpa and 11 clones of P. maximowiczii could be identified by their two-locus genotypes. Twenty clones of P. deltoides and 25 clones of P. nigra could be differentiated by their multilocus genotypes employing three loci, and 29 clones of P. balsamifera required the use of multilocus genotypes at five loci for their genetic fingerprinting and differentiation. The loci PTR3, PTR5, and PTR7 were found to be the most informative for genetic fingerprinting and differentiation of the clones. The mean number of alleles per locus ranged from 2.9 in P. trichocarpa or P. grandidentata to 6.0 in P. balsamifera and 11.2 in 96 clones of the six species. The mean number of observed genotypes per locus ranged from 2.4 in P. grandidentata to 7.4 in P. balsamifera and 19.6 in 96 clones of the six species. The mean number of unique genotypes per locus ranged from 1.3 in P. grandidentata to 3.9 in P. deltoides and 8.8 in 96 clones of the six species. The power of discrimination of the microsatellite DNA markers in the 96 clones ranged from 0.726 for PTR4 to 0.939 for PTR7, with a mean of 0.832 over the 10 simple sequence repeat loci. Clones/cultivars from the same

Genetic Diversity and Population Differentiation of the Causal Agent of Citrus Black Spot in Brazil

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Ester Wickert

2012-01-01

Full Text Available One of the most important diseases that affect sweet orange orchards in Brazil is the Citrus Black Spot that is caused by the fungus Guignardia citricarpa. This disease causes irreparable losses due to the premature falling of fruit, as well as its severe effects on the epidermis of ripe fruit that renders them unacceptable at the fresh fruit markets. Despite the fact that the fungus and the disease are well studied, little is known about the genetic diversity and the structure of the fungi populations in Brazilian orchards. The objective of this work was study the genetic diversity and population differentiation of G. citricarpa associated with four sweet orange varieties in two geographic locations using DNA sequence of ITS1-5.8S-ITS2 region from fungi isolates. We observed that different populations are closely related and present little genetic structure according to varieties and geographic places with the highest genetic diversity distributed among isolates of the same populations. The same haplotypes were sampled in different populations from the same and different orange varieties and from similar and different origins. If new and pathogenic fungi would become resistant to fungicides, the observed genetic structure could rapidly spread this new form from one population to others.

Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

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Jiang Wei

2008-08-01

Full Text Available Abstract Background With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. Results The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8 (p ≈ 0, desmin (DES (p = 2.71 × 10-6 and enolase 1 (ENO1 (p = 4.19 × 10-5], while two novel hub genes [RNA binding motif protein 9 (RBM9 (p = 1.50 × 10-4 and ribosomal protein L30 (RPL30 (p = 1.50 × 10-4] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO based analysis of the colon cancer-specific gene network and

Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements.

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Jiang, Wei; Li, Xia; Rao, Shaoqi; Wang, Lihong; Du, Lei; Li, Chuanxing; Wu, Chao; Wang, Hongzhi; Wang, Yadong; Yang, Baofeng

2008-08-10

With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8) (p approximately 0), desmin (DES) (p = 2.71 x 10(-6)) and enolase 1 (ENO1) (p = 4.19 x 10(-5))], while two novel hub genes [RNA binding motif protein 9 (RBM9) (p = 1.50 x 10(-4)) and ribosomal protein L30 (RPL30) (p = 1.50 x 10(-4))] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO) based analysis of the colon cancer-specific gene network and the sub-network that

Habitat differentiation vs. isolation-by-distance : the genetic population structure of Elymus athericus in European salt marshes

NARCIS (Netherlands)

Bockelmann, AC; Reusch, TBH; Bijlsma, R; Bakker, JP

We investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt-marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the

Insight into podocyte differentiation from the study of human genetic disease: nail-patella syndrome and transcriptional regulation in podocytes.

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Morello, Roy; Lee, Brendan

2002-05-01

In recent years, our understanding of the molecular basis of kidney development has benefited from the study of rare genetic diseases affecting renal function. This has especially been the case with the differentiation of the highly specialized podocyte in the pathogenesis of human disorders and mouse phenotypes affecting the renal filtration barrier. This filtration barrier represents the end product of a complex series of signaling events that produce a tripartite structure consisting of interdigitating podocyte foot processes with intervening slit diaphragms, the glomerular basement membrane, and the fenestrated endothelial cell. Dysregulation of unique cytoskeletal and extracellular matrix proteins in genetic forms of nephrotic syndrome has shown how specific structural proteins contribute to podocyte function and differentiation. However, much less is known about the transcriptional determinants that both specify and maintain this differentiated cell. Our studies of a skeletal malformation syndrome, nail-patella syndrome, have shown how the LIM homeodomain transcription factor, Lmx1b, contributes to transcriptional regulation of glomerular basement membrane collagen expression by podocytes. Moreover, they raise intriguing questions about more global transcriptional regulation of podocyte morphogenesis.

Hierarchical ordering with partial pairwise hierarchical relationships on the macaque brain data sets.

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Woosang Lim

Full Text Available Hierarchical organizations of information processing in the brain networks have been known to exist and widely studied. To find proper hierarchical structures in the macaque brain, the traditional methods need the entire pairwise hierarchical relationships between cortical areas. In this paper, we present a new method that discovers hierarchical structures of macaque brain networks by using partial information of pairwise hierarchical relationships. Our method uses a graph-based manifold learning to exploit inherent relationship, and computes pseudo distances of hierarchical levels for every pair of cortical areas. Then, we compute hierarchy levels of all cortical areas by minimizing the sum of squared hierarchical distance errors with the hierarchical information of few cortical areas. We evaluate our method on the macaque brain data sets whose true hierarchical levels are known as the FV91 model. The experimental results show that hierarchy levels computed by our method are similar to the FV91 model, and its errors are much smaller than the errors of hierarchical clustering approaches.

Genetic search feature selection for affective modeling

DEFF Research Database (Denmark)

Martínez, Héctor P.; Yannakakis, Georgios N.

2010-01-01

Automatic feature selection is a critical step towards the generation of successful computational models of affect. This paper presents a genetic search-based feature selection method which is developed as a global-search algorithm for improving the accuracy of the affective models built....... The method is tested and compared against sequential forward feature selection and random search in a dataset derived from a game survey experiment which contains bimodal input features (physiological and gameplay) and expressed pairwise preferences of affect. Results suggest that the proposed method...

Genetic Structure and Demographic History Reveal Migration of the Diamondback Moth Plutella xylostella (Lepidoptera: Plutellidae) from the Southern to Northern Regions of China

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Wei, Shu-Jun; Shi, Bao-Cai; Gong, Ya-Jun; Jin, Gui-Hua; Chen, Xue-Xin; Meng, Xiang-Feng

2013-01-01

The diamondback moth Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae) is one of the most destructive insect pests of cruciferous plants worldwide. Biological, ecological and genetic studies have indicated that this moth is migratory in many regions around the world. Although outbreaks of this pest occur annually in China and cause heavy damage, little is known concerning its migration. To better understand its migration pattern, we investigated the population genetic structure and demographic history of the diamondback moth by analyzing 27 geographical populations across China using four mitochondrial genes and nine microsatellite loci. The results showed that high haplotype diversity and low nucleotide diversity occurred in the diamondback moth populations, a finding that is typical for migratory species. No genetic differentiation among all populations and no correlation between genetic and geographical distance were found. However, pairwise analysis of the mitochondrial genes has indicated that populations from the southern region were more differentiated than those from the northern region. Gene flow analysis revealed that the effective number of migrants per generation into populations of the northern region is very high, whereas that into populations of the southern region is quite low. Neutrality testing, mismatch distribution and Bayesian Skyline Plot analyses based on mitochondrial genes all revealed that deviation from Hardy-Weinberg equilibrium and sudden expansion of the effective population size were present in populations from the northern region but not in those from the southern region. In conclusion, all our analyses strongly demonstrated that the diamondback moth migrates within China from the southern to northern regions with rare effective migration in the reverse direction. Our research provides a successful example of using population genetic approaches to resolve the seasonal migration of insects. PMID:23565158

Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks.

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Yousef, Eltohamy A A; Müller, Thomas; Börner, Andreas; Schmid, Karl J

2018-01-01

Cauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (cauliflower genebank material and our results suggest that it may be useful to incorporate routine genotyping into accession management and seed regeneration to monitor the diversity present in ex situ collections and to reduce the loss of genetic diversity during seed regeneration.

Genetic variation and geographical differentiation revealed using ...

Indian Academy of Sciences (India)

there are a few reports on the genetic evaluation of tung tree germplasm. .... bES, Enshi in Hubei province; SN, Suining in Sichuan province. Journal of Genetics Vol. 94, Online Resources e6 ... gene diversity. Journal of Genetics Vol. 94, Online Resources e7 .... Pan Y., Pan L., Chen L., Zhang L. L., Nevo E. and Peng J. H..

Genetics of human body size and shape: pleiotropic and independent genetic determinants of adiposity.

Science.gov (United States)

Livshits, G; Yakovenko, K; Ginsburg, E; Kobyliansky, E

1998-01-01

The present study utilized pedigree data from three ethnically different populations of Kirghizstan, Turkmenia and Chuvasha. Principal component analysis was performed on a matrix of genetic correlations between 22 measures of adiposity, including skinfolds, circumferences and indices. Findings are summarized as follows: (1) All three genetic matrices were not positive definite and the first four factors retained even after exclusion RG > or = 1.0, explained from 88% to 97% of the total additive genetic variation in the 22 trials studied. This clearly emphasizes the massive involvement of pleiotropic gene effects in the variability of adiposity traits. (2) Despite the quite natural differences in pairwise correlations between the adiposity traits in the three ethnically different samples under study, factor analysis revealed a common basic pattern of covariability for the adiposity traits. In each of the three samples, four genetic factors were retained, namely, the amount of subcutaneous fat, the total body obesity, the pattern of distribution of subcutaneous fat and the central adiposity distribution. (3) Genetic correlations between the retained four factors were virtually non-existent, suggesting that several independent genetic sources may be governing the variation of adiposity traits. (4) Variance decomposition analysis on the obtained genetic factors leaves no doubt regarding the substantial familial and (most probably genetic) effects on variation of each factor in each studied population. The similarity of results in the three different samples indicates that the findings may be deemed valid and reliable descriptions of the genetic variation and covariation pattern of adiposity traits in the human species.

Lifting the Differentiation Embargo.

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Latif, Anne-Louise; Holyoake, Tessa L

2016-09-22

Effective differentiation therapy for acute myeloid leukemia (AML) has been restricted to a small subset of patients with one defined genetic abnormality. Using an unbiased small molecule screen, Sykes et al. now identify a mechanism of de-repression of differentiation in several models of AML driven by distinct genetic drivers. Copyright © 2016 Elsevier Inc. All rights reserved.

Population genetic structure and demographic history of the freshwater crab Potamon elbursi (Brachyura: Potamidae from the Alborz Mountains in northern Iran

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Alireza Keikhosravi

2015-04-01

Full Text Available Hydrographically separated populations of the freshwater crab Potamon elbursi Pretzmann, 1976 were genetically investigated to assess their local diversity and to reconstruct the possible role of Quaternary glaciations in shaping current diversity in the Alborz Mountains, northern Iran. A total of 61 specimens from six rivers were collected from the two different drainage systems of the Alborz Mountains, Namak Lake and the South Caspian watershed. A comparative analysis of a partial sequence of the mitochondrial cytochrome oxidase subunit I gene revealed relatively high overall haplotype diversity and low nucleotide diversity. In four populations, there is no association between the haplotype network and the geographical separation between drainages, whereas the remaining two populations consist of private haplotypes. Gene flow among rivers was estimated using pairwise differences of Φst; in almost all cases gene flow was significantly restricted, regardless of association to a particular river system. Surprisingly, the only exception was the pairwise comparison of two distant rivers belonging to different drainages; this lack of differentiation may be attributed to incomplete lineage sorting or secondary introduction events. The mismatch distribution analysis, together with the shape of the haplotype network and the nucleotide and haplotype diversity indices, indicates that the studied metapopulation show the signature of recent population bottlenecks followed by demographic or spatial expansion and dating back to Pleistocene climatic fluctuations. 

Nonparametric predictive pairwise comparison with competing risks

International Nuclear Information System (INIS)

Coolen-Maturi, Tahani

2014-01-01

In reliability, failure data often correspond to competing risks, where several failure modes can cause a unit to fail. This paper presents nonparametric predictive inference (NPI) for pairwise comparison with competing risks data, assuming that the failure modes are independent. These failure modes could be the same or different among the two groups, and these can be both observed and unobserved failure modes. NPI is a statistical approach based on few assumptions, with inferences strongly based on data and with uncertainty quantified via lower and upper probabilities. The focus is on the lower and upper probabilities for the event that the lifetime of a future unit from one group, say Y, is greater than the lifetime of a future unit from the second group, say X. The paper also shows how the two groups can be compared based on particular failure mode(s), and the comparison of the two groups when some of the competing risks are combined is discussed

PairWise Neighbours database: overlaps and spacers among prokaryote genomes

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Garcia-Vallvé Santiago

2009-06-01

Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

[Hereditary colorectal cancer : An update on genetics and entities in terms of differential diagnosis].

Science.gov (United States)

Rau, T T; Dawson, H; Hartmann, A; Rüschoff, J

2017-05-01

The pathologist can contribute to recognizing hereditary causes of colorectal cancer via morphology. By identifying so-called index patients, it is possible to take preventive measures in affected families. The precise definition of the clinical presentation and the histopathological phenotype help to narrow the spectrum of expected genetic alterations. Novelties within Lynch syndrome include the recognition of EPCAM as a fifth gene locus, as well as the newly defined Lynch-like syndrome with evidence of somatic mismatch repair (MMR) mutations. With regard to polyposis-associated syndromes, the spectrum of polyps, whether serrated, hamartomatous or classic adenoma, is of crucial importance. The resulting differential diagnosis includes (attenuated) familial adenomatous polyposis ([a]FAP), MUTYH-associated polyposis (MAP), polymerase proofreading-associated polyposis (PPAP), phosphatase and tensin homolog (PTEN) hamartoma tumor syndrome (PHTS), Peutz-Jeghers syndrome and juvenile polyposis, each with a specific genetic background.

Pairwise comparisons and visual perceptions of equal area polygons.

Science.gov (United States)

Adamic, P; Babiy, V; Janicki, R; Kakiashvili, T; Koczkodaj, W W; Tadeusiewicz, R

2009-02-01

The number of studies related to visual perception has been plentiful in recent years. Participants rated the areas of five randomly generated shapes of equal area, using a reference unit area that was displayed together with the shapes. Respondents were 179 university students from Canada and Poland. The average error estimated by respondents using the unit square was 25.75%. The error was substantially decreased to 5.51% when the shapes were compared to one another in pairs. This gain of 20.24% for this two-dimensional experiment was substantially better than the 11.78% gain reported in the previous one-dimensional experiments. This is the first statistically sound two-dimensional experiment demonstrating that pairwise comparisons improve accuracy.

Predicting community composition from pairwise interactions

Science.gov (United States)

Friedman, Jonathan; Higgins, Logan; Gore, Jeff

The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

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Denman, Daniel J; Contreras, Diego

2014-10-01

Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genetic differentiation in Gammarus fossarum and G. caparti (Crustacea, Amphipoda) with reference to G. pulex pulex in northwestern Europe

NARCIS (Netherlands)

Scheepmaker, Maarten; Dalfsen, van Jan

1989-01-01

Genetic differentiation among G. fossarum Koch, 1835 from different stations in Germany, Switzerland, Belgium and northern France, and the closely related Belgian form G. caparti Pètre-Stroobants, 1980 was investigated by electrophoresis at 20 enzyme loci. Although morphologically variable,

Post-embryonic nerve-associated precursors to adult pigment cells: genetic requirements and dynamics of morphogenesis and differentiation.

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Erine H Budi

2011-05-01

Full Text Available The pigment cells of vertebrates serve a variety of functions and generate a stunning variety of patterns. These cells are also implicated in human pathologies including melanoma. Whereas the events of pigment cell development have been studied extensively in the embryo, much less is known about morphogenesis and differentiation of these cells during post-embryonic stages. Previous studies of zebrafish revealed genetically distinct populations of embryonic and adult melanophores, the ectotherm homologue of amniote melanocytes. Here, we use molecular markers, vital labeling, time-lapse imaging, mutational analyses, and transgenesis to identify peripheral nerves as a niche for precursors to adult melanophores that subsequently migrate to the skin to form the adult pigment pattern. We further identify genetic requirements for establishing, maintaining, and recruiting precursors to the adult melanophore lineage and demonstrate novel compensatory behaviors during pattern regulation in mutant backgrounds. Finally, we show that distinct populations of latent precursors having differential regenerative capabilities persist into the adult. These findings provide a foundation for future studies of post-embryonic pigment cell precursors in development, evolution, and neoplasia.

Genetic differentiation of Mexican Holstein cattle and its relationship with Canadian and U.S. Holsteins

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Felipe De Jesus Ruiz-Lopez

2015-02-01

Full Text Available The Mexican Holstein industry has imported Canadian and US (CAN+USA Holstein germplasm for use in two different production systems, the conventional (Conv and the low income system (Lowi. The objective of this work was to study the genetic composition and differentiation of the Mexican Holstein cattle, considering the production system in which they perform and their relationship with the Canadian and US Holstein populations. The analysis included information from 149, 303 and 173 unrelated or with unknown pedigree Holstein (HO animals from the Conv, Lowi and CAN+USA populations, respectively. Canadian and US Jersey (JE and Brown Swiss (BS genotypes (162 and 86, respectively were used to determine if Mexican Holsteins were hybridized with either of these breeds. After quality control filtering, a total of 6,617 out of 6,836 SNP markers were used. To describe the genetic diversity across the populations, principal component (PC, admixture composition, and linkage disequilibrium (r2 analyses were performed. Through the PC analysis, HOxJE and HOxBS crossbreeding was detected in the Lowi system. The Conv system appeared to be in between Lowi and CAN+USA populations. Admixture analysis differentiated between the genetic composition of the Conv and Lowi systems, and five ancestry groups associated to sire’s country of origin were identified. The minimum distance between markers to estimate a useful LD was found to be 54.5 kb for the Mexican HO populations. At this average distance, the persistence of phase across autosomes of Conv and Lowi systems was 0.94, for Conv and CAN+USA was 0.92 and for the Lowi and CAN+USA was 0.91. Results supported the flow of germplasm among populations being Conv a source for Lowi, and dependent on migration from CAN+USA. Mexican Holstein cattle in Conv and Lowi populations share common ancestry with CAN+USA but have different genetic signatures.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

OpenAIRE

Maréchal Eric; Ortet Philippe; Roy Sylvaine; Bastien Olivier

2005-01-01

Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic recon...

Genetic analysis of basmati and non-basmati Pakistani rice (oryza sativa l.) cultivars using microsatellite markers

International Nuclear Information System (INIS)

Rabbani, M.A.; Masood, M.A.; Shinwari, Z.K.

2010-01-01

Information of genetic variability and relatedness among rice genotypes is essential for future breeding programmes and derivation of superior cultivars. The objective of the present study was to evaluate the genetic relationship among traditional and improved cultivars of Pakistani rice and to determine differences in the patterns of variation between two indica rice groups: basmati and nonbasmati. Forty-one cultivars were evaluated by means of 30 microsatellite markers distributed over the whole rice genome. A total of 104 alleles were detected by 30 markers, all of them (100%) were polymorphic. The number of alleles generated by each marker ranged from 2 to 6 with an average of 3.5 alleles marker-1. Polymorphism information content (PIC) varied from 0.259 to 0.782 with an average of 0.571. A significant positive correlation (r = 0.71) was found between the number of alleles at SSR locus and the PIC values. Pair-wise Nei and Li's similarity coefficients ranged from 0.10 to 0.99. A dendrogram based on cluster analysis by microsatellite polymorphism grouped 41 rice cultivars into 2 major groups effectively differentiating the late maturing, tall and slender-grain basmati and other aromatic rice cultivars from the early, short statured, short bold and long bold grain non-aromatic cultivars. Higher level of genetic diversity between basmati and non-basmati support the concept that former had a long history of independent evolution and diverged from nonbasmati rice a long time ago through human selection and patronage. Present investigation further indicated that genetically basmati rice is different from that of coarse indica and japonica type. The results suggested that microsatellite markers could efficiently be utilized for diversity analysis, and differentiation of basmati and non-basmati rice cultivars. In addition, marker-based identification of traditional basmati rice may help in maintaining the integrity of this high quality product to the benefit of both

Non-genetic heterogeneity, criticality and cell differentiation.

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Pal, Mainak; Ghosh, Sayantari; Bose, Indrani

2014-11-27

The different cell types in a living organism acquire their identity through the process of cell differentiation in which multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of large-scale microarray data establish the key role played by a two-gene motif in cell differentiation in a number of cell systems. The two genes express transcription factors which repress each other's expression and autoactivate their own production. A number of theoretical models have recently been proposed based on the two-gene motif to provide a physical understanding of how cell differentiation occurs. In this paper, we study a simple model of cell differentiation which assumes no cooperativity in the regulation of gene expression by the transcription factors. The latter repress each other's activity directly through DNA binding and indirectly through the formation of heterodimers. We specifically investigate how deterministic processes combined with stochasticity contribute in bringing about cell differentiation. The deterministic dynamics of our model give rise to a supercritical pitchfork bifurcation from an undifferentiated stable steady state to two differentiated stable steady states. The stochastic dynamics of our model are studied using the approaches based on the Langevin equations and the linear noise approximation. The simulation results provide a new physical understanding of recent experimental observations. We further propose experimental measurements of quantities like the variance and the lag-1 autocorrelation function in protein fluctuations as the early signatures of an approaching bifurcation point in the cell differentiation process.

Population genetic structure of the freshwater snail, Bulinus globosus, (Gastropoda: Planorbidae) from selected habitats of KwaZulu-Natal, South Africa.

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Mkize, Lwamkelekile Sitshilelo; Mukaratirwa, Samson; Zishiri, Oliver Tendayi

2016-09-01

The freshwater snail Bulinus globosus is an important intermediate host of Schistosoma haematobium, the causative agent of urinary schistosomiasis. This disease is of major health concern, especially in Africa where the majority of cases have been reported. In this study the inter- and intra-genetic diversity and population genetic structure of B. globosus from nine locations in the KwaZulu-Natal province of South Africa was studied using four polymorphic microsatellite loci (BgZ1-BgZ4). Moderate genetic diversity was detected within populations with a mean diversity (HE) of 0.49±0.09. The majority of populations significantly deviated from Hardy-Weinberg equilibrium (p<0.05), due to a deficit of heterozygotes. Such deviations may be due to founder events that were caused by bottlenecks that occurred as a result of frequent droughts and flooding that these snails' habitats are exposed to. Overall, the populations studied seem to be partially inbreeders/selfers with mean estimates of 0.24/0.38. A discernable genetic structure was elucidated among populations as evident by the mean pairwise FST of 0.58±0.13. There was no significant association between genetic and geographical distance among populations, an indication of limited gene flow. This increases the chances of populations losing alleles due to genetic drift. Populations in close proximity demonstrated high genetic differentiation (58.77% total variation) due to allelic differences between them. The sample populations fell into 12 clusters, however, the populations from uMkhanyakude and uThungulu exhibited no discernable genetic structure. Genetically, the Bhobhoyi site found within the uGu district was equidistant to the two main sampling regions. Copyright © 2016 Elsevier B.V. All rights reserved.

Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures

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Galanter, Joshua M; Gignoux, Christopher R; Oh, Sam S; Torgerson, Dara; Pino-Yanes, Maria; Thakur, Neeta; Eng, Celeste; Hu, Donglei; Huntsman, Scott; Farber, Harold J; Avila, Pedro C; Brigino-Buenaventura, Emerita; LeNoir, Michael A; Meade, Kelly; Serebrisky, Denise; Rodríguez-Cintrón, William; Kumar, Rajesh; Rodríguez-Santana, Jose R; Seibold, Max A; Borrell, Luisa N; Burchard, Esteban G; Zaitlen, Noah

2017-01-01

Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self-identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75.7% (IQR 45.8% to 92%) of the variance in methylation associated with ethnicity. There was a significant enrichment (p=4.2×10-64) of ethnicity-associated sites amongst loci previously associated environmental exposures, particularly maternal smoking during pregnancy. We conclude that differential methylation between ethnic groups is partially explained by the shared genetic ancestry but that environmental factors not captured by ancestry significantly contribute to variation in methylation. DOI: http://dx.doi.org/10.7554/eLife.20532.001 PMID:28044981

Improving pairwise comparison of protein sequences with domain co-occurrence

Science.gov (United States)

Gascuel, Olivier

2018-01-01

Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence PMID:29293498

Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group

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Kong, Tingting; Chen, Yahao; Guo, Yuxin; Wei, Yuanyuan; Jin, Xiaoye; Xie, Tong; Mu, Yuling; Dong, Qian; Wen, Shaoqing; Zhou, Boyan; Zhang, Li; Shen, Chunmei; Zhu, Bofeng

2017-01-01

In the present study, we assessed the genetic diversities of the Chinese Kazak ethnic group on the basis of 30 well-chosen autosomal insertion and deletion loci and explored the genetic relationships between Kazak and 23 reference groups. We detected the level of the expected heterozygosity ranging from 0.3605 at HLD39 locus to 0.5000 at HLD136 locus and the observed heterozygosity ranging from 0.3548 at HLD39 locus to 0.5283 at HLD136 locus. The combined power of discrimination and the combined power of exclusion for all 30 loci in the studied Kazak group were 0.999999999999128 and 0.9945, respectively. The dataset generated in this study indicated the panel of 30 InDels was highly efficient in forensic individual identifcation but may not have enough power in paternity cases. The results of the interpopulation differentiations, PCA plots, phylogenetic trees and STRUCTURE analyses showed a close genetic affiliation between the Kazak and Uigur group. PMID:28915619

Genetic diversity and population structure of Prunus mira (Koehne from the Tibet plateau in China and recommended conservation strategies.

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Wenquan Bao

Full Text Available Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17 within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%, whereas morphological analyses revealed low variation (1.30%-36.17% within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units

[Genetic Variability and Structure of SNP Haplotypes in the DMPK Gene in Yakuts and Other Ethnic Groups of Northern Eurasia in Relation to Myotonic Dystrophy].

Science.gov (United States)

Swarovskaya, M G; Stepanova, S K; Marussin, A V; Sukhomyasova, A L; Maximova, N R; Stepanov, V A

2015-06-01

The genetic variability of the DMPK locus has been studied in relation to six SNP markers (rs2070736, rs572634, rs1799894, rs527221, rs915915, and rs10415988) in Yakuts with myotonic dystrophy (MD) in the Yakut population and in populations of northern Eurasia. Significant differences were observed in the allele frequencies between patients and a population sample of Yakuts for three SNP loci (rs915915, rs1799894, and rs10415988) associated with a high chance of disease manifestation. The odds ratios (OR) of MD development in representatives of the Yakut population for these three loci were 2.59 (95% CI, p = 0,004), 4.99 (95% CI, p = 0.000), and 3.15 (95% CI, p = 0.01), respectively. Haplotype TTTCTC, which is associated with MD, and haplotype GTCCTT, which was observed only in Yakut MD patients (never in MD patients of non-Yakut origin), were revealed. A low level of variability in the locus of DMRK gene in Yakuts (H(e) = 0.283) compared with other examined populations was noted. An analysis of pairwise genetic relationships between populations revealed their significant differentiation for all the examined loci. In addition, a low level of differentiation in territorial groups of Yakut populations (F(ST) = 0.79%), which was related to the high subdivision of the northern Eurasian population (F(ST) = 11.83%), was observed.

Influence of ethnolinguistic diversity on the sorghum genetic patterns in subsistence farming systems in eastern Kenya.

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Vanesse Labeyrie

Full Text Available Understanding the effects of actions undertaken by human societies on crop evolution processes is a major challenge for the conservation of genetic resources. This study investigated the mechanisms whereby social boundaries associated with patterns of ethnolinguistic diversity have influenced the on-farm distribution of sorghum diversity. Social boundaries limit the diffusion of planting material, practices and knowledge, thus shaping crop diversity in situ. To assess the effect of social boundaries, this study was conducted in the contact zone between the Chuka, Mbeere and Tharaka ethnolinguistic groups in eastern Kenya. Sorghum varieties were inventoried and samples collected in 130 households. In all, 297 individual plants derived from seeds collected under sixteen variety names were characterized using a set of 18 SSR molecular markers and 15 morphological descriptors. The genetic structure was investigated using both a Bayesian assignment method and distance-based clustering. Principal Coordinates Analysis was used to describe the structure of the morphological diversity of the panicles. The distribution of the varieties and the main genetic clusters across ethnolinguistic groups was described using a non-parametric MANOVA and pairwise Fisher tests. The spatial distribution of landrace names and the overall genetic spatial patterns were significantly correlated with ethnolinguistic partition. However, the genetic structure inferred from molecular makers did not discriminate the short-cycle landraces despite their morphological distinctness. The cases of two improved varieties highlighted possible fates of improved materials. The most recent one was often given the name of local landraces. The second one, that was introduced a dozen years ago, displays traces of admixture with local landraces with differential intensity among ethnic groups. The patterns of congruence or discordance between the nomenclature of farmers' varieties and the

Probing dark energy models with extreme pairwise velocities of galaxy clusters from the DEUS-FUR simulations

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Bouillot, Vincent R.; Alimi, Jean-Michel; Corasaniti, Pier-Stefano; Rasera, Yann

2015-06-01

Observations of colliding galaxy clusters with high relative velocity probe the tail of the halo pairwise velocity distribution with the potential of providing a powerful test of cosmology. As an example it has been argued that the discovery of the Bullet Cluster challenges standard Λ cold dark matter (ΛCDM) model predictions. Halo catalogues from N-body simulations have been used to estimate the probability of Bullet-like clusters. However, due to simulation volume effects previous studies had to rely on a Gaussian extrapolation of the pairwise velocity distribution to high velocities. Here, we perform a detail analysis using the halo catalogues from the Dark Energy Universe Simulation Full Universe Runs (DEUS-FUR), which enables us to resolve the high-velocity tail of the distribution and study its dependence on the halo mass definition, redshift and cosmology. Building upon these results, we estimate the probability of Bullet-like systems in the framework of Extreme Value Statistics. We show that the tail of extreme pairwise velocities significantly deviates from that of a Gaussian, moreover it carries an imprint of the underlying cosmology. We find the Bullet Cluster probability to be two orders of magnitude larger than previous estimates, thus easing the tension with the ΛCDM model. Finally, the comparison of the inferred probabilities for the different DEUS-FUR cosmologies suggests that observations of extreme interacting clusters can provide constraints on dark energy models complementary to standard cosmological tests.

Population genetic structure of the cotton bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in India as inferred from EPIC-PCR DNA markers.

Science.gov (United States)

Behere, Gajanan Tryambak; Tay, Wee Tek; Russell, Derek Alan; Kranthi, Keshav Raj; Batterham, Philip

2013-01-01

Helicoverpa armigera is an important pest of cotton and other agricultural crops in the Old World. Its wide host range, high mobility and fecundity, and the ability to adapt and develop resistance against all common groups of insecticides used for its management have exacerbated its pest status. An understanding of the population genetic structure in H. armigera under Indian agricultural conditions will help ascertain gene flow patterns across different agricultural zones. This study inferred the population genetic structure of Indian H. armigera using five Exon-Primed Intron-Crossing (EPIC)-PCR markers. Nested alternative EPIC markers detected moderate null allele frequencies (4.3% to 9.4%) in loci used to infer population genetic structure but the apparently genome-wide heterozygote deficit suggests in-breeding or a Wahlund effect rather than a null allele effect. Population genetic analysis of the 26 populations suggested significant genetic differentiation within India but especially in cotton-feeding populations in the 2006-07 cropping season. In contrast, overall pair-wise F(ST) estimates from populations feeding on food crops indicated no significant population substructure irrespective of cropping seasons. A Baysian cluster analysis was used to assign the genetic make-up of individuals to likely membership of population clusters. Some evidence was found for four major clusters with individuals in two populations from cotton in one year (from two populations in northern India) showing especially high homogeneity. Taken as a whole, this study found evidence of population substructure at host crop, temporal and spatial levels in Indian H. armigera, without, however, a clear biological rationale for these structures being evident.

Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers

NARCIS (Netherlands)

Eisinga, R.N.; Heskes, T.M.; Pelzer, B.J.; Grotenhuis, H.F. te

2017-01-01

Background: The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to

A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: easy Bayesian computing for real parameter spaces

NARCIS (Netherlands)

Braak, ter C.J.F.

2006-01-01

Differential Evolution (DE) is a simple genetic algorithm for numerical optimization in real parameter spaces. In a statistical context one would not just want the optimum but also its uncertainty. The uncertainty distribution can be obtained by a Bayesian analysis (after specifying prior and

Significant genetic differentiation between native and introduced silver carp (Hypophthalmichthys molitrix) inferred from mtDNA analysis

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Li, S.-F.; Xu, J.-W.; Yang, Q.-L.; Wang, C.H.; Chapman, D.C.; Lu, G.

2011-01-01

Silver carp Hypophthalmichthys molitrix (Cyprinidae) is native to China and has been introduced to over 80 countries. The extent of genetic diversity in introduced silver carp and the genetic divergence between introduced and native populations remain largely unknown. In this study, 241 silver carp sampled from three major native rivers and two non-native rivers (Mississippi River and Danube River) were analyzed using nucleotide sequences of mitochondrial COI gene and D-loop region. A total of 73 haplotypes were observed, with no haplotype found common to all the five populations and eight haplotypes shared by two to four populations. As compared with introduced populations, all native populations possess both higher haplotype diversity and higher nucleotide diversity, presumably a result of the founder effect. Significant genetic differentiation was revealed between native and introduced populations as well as among five sampled populations, suggesting strong selection pressures might have occurred in introduced populations. Collectively, this study not only provides baseline information for sustainable use of silver carp in their native country (i.e., China), but also offers first-hand genetic data for the control of silver carp in countries (e.g., the United States) where they are considered invasive.

Evidence of genetic differentiation and karyotype evolution of the sedges Cyperus ligularis L. and C. odoratus L. (Cyperaceae

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Geyner Alves dos Santos Cruz

2018-01-01

Full Text Available ABSTRACT The taxonomy of Cyperaceae is complex, with genera like Cyperus harboring species complexes. We analyzed the genetic similarity between Cyperus ligularis L. and C. odoratus L. based on DNA fingerprinting and cytogenetics. Significative genetic differentiation (G ST = 0.363 and low gene flow (N m = 0.877 indicated a clear genetic distinction between the two species. Moreover, the clustering analysis showed two distinct genetic groups, suggesting a lack of evidence for hybridization. The phenogram revealed two different lineages, and although all individuals of C. odoratus were collected from plots close to each other, they possessed greater genetic diversity than that observed among individuals of C. ligularis, which were sampled over a wider geographic range. Variation in chromosome number within the two species exhibited the opposite pattern, indicating greater karyotype stability in C. odoratus with 2n = 72 and 2n = 76, while the diploid number for C. ligularis varied from 2n = 66 to 88. The lower genetic variation in C. ligularis may be a result of the founder effect associated with seed dispersion and clonal reproduction. Field observations and analysis of reproductive biology should enrich the understanding of the genetic structure of the investigated populations and their role in successional processes.

QUANTITATIVE GENETICS OF MORPHOLOGICAL DIFFERENTIATION IN PEROMYSCUS. II. ANALYSIS OF SELECTION AND DRIFT.

Science.gov (United States)

Lofsvold, David

1988-01-01

The hypothesis that the morphological divergence of local populations of Peromyscus is due to random genetic drift was evaluated by testing the proportionality of the among-locality covariance matrix, L, and the additive genetic covariance matrix, G. Overall, significant proportionality of L̂ and Ĝ was not observed, indicating the evolutionary divergence of local populations does not result from random genetic drift. The forces of selection needed to differentiate three taxa of Peromyscus were reconstructed to examine the divergence of species and subspecies. The selection gradients obtained illustrate the inadequacy of univariate analyses of selection by finding that some characters evolve in the direction opposite to the force of selection acting directly on them. A retrospective selection index was constructed using the estimated selection gradients, and truncation selection on this index was used to estimate the minimum selective mortality per generation required to produce the observed change. On any of the time scales used, the proportion of the population that would need to be culled was quite low, the greatest being of the same order of magnitude as the selective intensities observed in extant natural populations. Thus, entirely plausible intensities of directional natural selection can produce species-level differences in a period of time too short to be resolved in the fossil record. © 1988 The Society for the Study of Evolution.

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

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Nobushima Fuyuo

2006-10-01

Full Text Available Abstract Background Morus boninensis, is an endemic plant of the Bonin (Ogasawara Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Results Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. Conclusion The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

Science.gov (United States)

Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

2006-10-11

Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

Genetic differentiation in the populations of red piranha, Pygocentrus nattereri Kner (1860 (Characiformes: Serrasalminae, from the river basins of northeastern Brazil

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L. A. Luz

Full Text Available Abstract The red piranha, Pygocentrus nattereri, is an important resource for artisanal and commercial fisheries. The present study determines the genetic differentiation among P. nattereri populations from the northeastern Brazilian state of Maranhão. The DNA was isolated using a standard phenol-chloroform protocol and the Control Region was amplified by PCR. The PCR products were sequenced using the didesoxyterminal method. A sequence of 1039 bps was obtained from the Control Region of 60 specimens, which presented 33 polymorphic sites, 41 haplotypes, һ =0.978 and π =0.009. The neutrality tests (D and Fs were significant (P < 0.05 for most of the populations analyzed. The AMOVA indicated that most of the molecular variation (72% arises between groups. The fixation index was highly significant (FST = 0.707, P < 0.00001. The phylogenetic analyses indicated that the specimens represented a monophyletic group. Genetic distances between populations varied from 0.8% to 1.9%, and were <0.5% within populations. The degree of genetic differentiation found among the stocks of P. nattereri indicates the need for the development of independent management plans for the different river basins in order to preserve the genetic variability of their populations.

Phenotypic and genetic differentiation among yellow monkeyflower populations from thermal and non-thermal soils in Yellowstone National Park.

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Lekberg, Ylva; Roskilly, Beth; Hendrick, Margaret F; Zabinski, Catherine A; Barr, Camille M; Fishman, Lila

2012-09-01

In flowering plants, soil heterogeneity can generate divergent natural selection over fine spatial scales, and thus promote local adaptation in the absence of geographic barriers to gene flow. Here, we investigate phenotypic and genetic differentiation in one of the few flowering plants that thrives in both geothermal and non-thermal soils in Yellowstone National Park (YNP). Yellow monkeyflowers (Mimulus guttatus) growing at two geothermal ("thermal") sites in YNP were distinct in growth form and phenology from paired populations growing nearby ( 0.34), which were only weakly differentiated from each other (all F (ST) geothermal gradient in Yellowstone.

Prospect of Induced Pluripotent Stem Cell Genetic Repair to Cure Genetic Diseases

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Jeanne Adiwinata Pawitan

2012-01-01

Full Text Available In genetic diseases, where the cells are already damaged, the damaged cells can be replaced by new normal cells, which can be differentiated from iPSC. To avoid immune rejection, iPSC from the patient’s own cell can be developed. However, iPSC from the patients’s cell harbors the same genetic aberration. Therefore, before differentiating the iPSCs into required cells, genetic repair should be done. This review discusses the various technologies to repair the genetic aberration in patient-derived iPSC, or to prevent the genetic aberration to cause further damage in the iPSC-derived cells, such as Zn finger and TALE nuclease genetic editing, RNA interference technology, exon skipping, and gene transfer method. In addition, the challenges in using the iPSC and the strategies to manage the hurdles are addressed.

Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the black fly Simulium tani Takaoka & Davies along an elevational gradient in Malaysia.

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Van Lun Low

Full Text Available The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI and II (COII along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected.

Adaptive divergence in resistance to herbivores in Datura stramonium

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Guillermo Castillo

2015-11-01

Full Text Available Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations of Datura stramonium, we compared the degree of phenotypic differentiation (PST of leaf resistance traits (trichome density, atropine and scopolamine concentration against neutral genetic differentiation (FST at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher than FST across the range of trait heritability values. In contrast, genetic differentiation in trichome density was different from FST only when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits in D. stramonium.

Genetic differentiation in Pyrenophora teres f. teres populations from Syria and Tunisia as assessed by AFLP markers.

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Bouajila, A; Zoghlami, N; Murad, S; Baum, M; Ghorbel, A; Nazari, K

2013-06-01

To investigate the level of genetic differentiation and diversity among Pyrenophora teres isolate populations originating from different agro-ecological areas of Syria and Tunisia and to determine the potential of AFLP profiling in genotyping Pyrenophora teres f. teres. In this study, AFLP markers have been employed to identify patterns of population structure in 20 Pyrenophora teres f. teres populations from Syria and Tunisia. Ninety-four isolates were studied by the use of a protocol that involved stringent PCR amplification of fragments derived from digestion of genomic DNA with restriction enzymes EcoRI and MesI. Based on 401 amplified polymorphic DNA markers (AFLP), variance analyses indicated that most of the variation was partitioned within rather than between populations. Genotypic diversity (GD) was high for populations from Rihane, local landraces and different agro-ecological zones (GD = 0·75-0·86). There was high genetic differentiation among pathogen populations from different host populations in Syria (Gst  = 0·31, ht = 0·190) and Tunisia (Gst  = 0·39, ht = 0·263), which may be partly explained by the low gene flow around the areas sampled. A phenetic tree revealed three groups with high bootstrap values (55, 68, 76) and reflected the grouping of isolates based on host, or agro-ecological areas. AFLP profiling is an effective method for typing the genetically diverse pathogen Pyrenophora teres f. teres. The study represents a comparative analysis of the genetic diversity in P. teres isolates from two countries spanning two continents and also shows that several distinct P. teres genotypes may be found in a given environment. The implications of these findings for Pyrenophora teres f. teres evolutionary potential and net blotch-resistance breeding in Syria and Tunisia were also discussed. © 2012 The Society for Applied Microbiology.

Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation

DEFF Research Database (Denmark)

Botta, Filippo; Eriksen, Casper; Fontaine, Michaël C.

2015-01-01

1. In a recent paper, Bradburd et al. (Evolution, 67, 2013, 3258) proposed a model to quantify the relative effect of geographic and environmental distance on genetic differentiation. Here, we enhance this method in several ways. 2. We modify the covariance model so as to fit better with mainstre...... available as an R package called sunder. It takes as input georeferenced allele counts at the individual or population level for co-dominant markers. Program homepage: http://www2.imm.dtu.dk/~gigu/Sunder/....

Examining maternal effects and genetic differentiation in P. flexilis and P. aristata to improve success of conservation actions

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Erin M. Borgman

2013-01-01

As the climate changes and invasive species continue to spread, proactive management may be needed to conserve native plant populations. Selecting appropriate plant material for restoration or other actions that will sustain populations is an integral part of any such plan and must take into account genetic differentiation to limit maladaptation. Common garden studies...

Psychopathic Personality Traits and Environmental Contexts: Differential Correlates, Gender Differences, and Genetic Mediation

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Hicks, Brian M.; Carlson, Marie D.; Blonigen, Daniel M.; Patrick, Christopher J.; Iacono, William G.; MGue, Matt

2011-01-01

Theorists have speculated that primary psychopathy (or Factor 1 affective-interpersonal features) is prominently heritable whereas secondary psychopathy (or Factor 2 social deviance) is more environmentally determined. We tested this differential heritability hypothesis using a large adolescent twin sample. Trait-based proxies of primary and secondary psychopathic tendencies were assessed using Multidimensional Personality Questionnaire (MPQ; Tellegen & Waller, 2008) estimates of Fearless Dominance and Impulsive Antisociality, respectively (Benning et al., 2005). The environmental contexts of family, school, peers, and stressful life events were assessed using multiple raters and methods. Consistent with prior research, MPQ Impulsive Antisociality was robustly associated with each environmental risk factor, and these associations were significantly greater than those for MPQ Fearless Dominance. However, MPQ Fearless Dominance and Impulsive Antisociality exhibited similar heritability, and genetic effects mediated the associations between MPQ Impulsive Antisociality and the environmental measures. Results were largely consistent across male and female twins. We conclude that gene-environment correlations rather than main effects of genes and environments account for the differential environmental correlates of primary and secondary psychopathy. PMID:22452762

Low genetic diversity and high genetic differentiation among ...

African Journals Online (AJOL)

Of a total of 26 known populations, 14 are now extinct, five during the course of this study. Action to prevent complete extinction of the species is therefore urgent. Keywords: Caesalpinioideae, Fabaceae, Ghana, inbreeding, population differentiation, RAPD, species extinction. Southern Forests 2011, 73(2): 73–80 ...

Genetic structure analysis of Spirometra erinaceieuropaei isolates from central and southern China.

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Xi Zhang

Full Text Available Sparganosis caused by invasion of the plerocercoid larvae (spargana of Spirometra erinaceieuropaei have increased in recent years in China. However, the population genetic structure regarding this parasite is still unclear. In this study, we used the sequences of two mitochondrial genes cytochrome b (cytb and cytochrome c oxidase subunit I (cox1 to analyze genetic variation and phylogeographic structure of the S. erinaceieuropaei populations.A total of 88 S. erinaceieuropaei isolates were collected from naturally infected frogs in 14 geographical locations of China. The complete cytb and cox1 genes of each sample was amplified and sequenced. Total 61 haplotypes were found in these 88 concatenated sequences. Each sampled population and the total population have high haplotype diversity (Hd, accompanied by very low nucleotide diversity (Pi. Phylogenetic analyses of haplotypes revealed two distinct clades (HeN+HuN+GZ-AS clade and GX+HN+GZ-GY clade corresponding two sub-networks yielded by the median-joining network. Pairwise FST values supported great genetic differentiation between S. erinaceieuropaei populations. Both negative Fu's FS value of neutrality tests and unimodal curve of mismatch distribution analyses supported demographic population expansion in the HeN+HuN+GZ-AS clade. The BEAST analysis showed that the divergence time between the two clades took place in the early Pleistocene (1.16 Myr, and by Bayesian skyline plot (BSP an expansion occurred after about 0.3 Myr ago.S. erinaceieuropaei from central and southern China has significant phylogeographic structure, and climatic oscillations during glacial periods in the Quaternary may affect the demography and diversification of this species.

Racial characterization and genetic diversity of sunflower broomrape populations from Northern Spain

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Jebri MALEK

2017-05-01

Full Text Available In Spain, sunflower broomrape (Orobanche cumana Wallr. has been restricted to Cuenca province in Central Spain, and the Guadalquivir Valley in Southern Spain, that represent different gene pools of the species. This pathogenic plant has now spread to other areas such as Castilla y León region in Northern Spain. The racial status and genetic diversity were investigated in six populations of sunflower broomrape collected in several provinces of Castilla y León. Evaluation of virulence to a set of differential host genotypes classified three of the populations as race F, while the other three populations were classified as a race below F, probably race E. Genetic diversity analysis using a set of 20 SSR markers showed that the broomrape populations from new areas of Northern Spain are mainly derived from the Guadalquivir Valley gene pool. Introgression from the Cuenca gene pool was observed in one of the populations, in which the percentage of polymorphic loci was 31%, Shanon´s diversity index was 0.17, and the average number of pairwise differences was 1.69, compared to zero for the three parameters in the other five populations. The absence of race F individuals in the populations classified as race below F indicated that seed migration took place, probably before the generalized expansion of race F in the Guadalquivir Valley area, at the beginning of the 1990s.

Pairwise registration of TLS point clouds using covariance descriptors and a non-cooperative game

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Zai, Dawei; Li, Jonathan; Guo, Yulan; Cheng, Ming; Huang, Pengdi; Cao, Xiaofei; Wang, Cheng

2017-12-01

It is challenging to automatically register TLS point clouds with noise, outliers and varying overlap. In this paper, we propose a new method for pairwise registration of TLS point clouds. We first generate covariance matrix descriptors with an adaptive neighborhood size from point clouds to find candidate correspondences, we then construct a non-cooperative game to isolate mutual compatible correspondences, which are considered as true positives. The method was tested on three models acquired by two different TLS systems. Experimental results demonstrate that our proposed adaptive covariance (ACOV) descriptor is invariant to rigid transformation and robust to noise and varying resolutions. The average registration errors achieved on three models are 0.46 cm, 0.32 cm and 1.73 cm, respectively. The computational times cost on these models are about 288 s, 184 s and 903 s, respectively. Besides, our registration framework using ACOV descriptors and a game theoretic method is superior to the state-of-the-art methods in terms of both registration error and computational time. The experiment on a large outdoor scene further demonstrates the feasibility and effectiveness of our proposed pairwise registration framework.

Genetic variation and differentiation of Gekko gecko from different populations based on mitochondrial cytochrome b gene sequences and karyotypes.

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Qin, Xin-Min; Li, Hui-Min; Zeng, Zhen-Hua; Zeng, De-Long; Guan, Qing-Xin

2012-06-01

Black-spotted and red-spotted tokay geckos are distributed in different regions and have significant differences in morphological appearance, but have been regarded as the same species, Gekko gecko, in taxonomy. To determine whether black-spotted and red-spotted tokay geckos are genetically differentiated, we sequenced the entire mitochondrial cytochrome b gene (1147 bp) from 110 individuals of Gekko gecko collected in 11 areas including Guangxi China, Yunnan China, Vietnam, and Laos. In addition, we performed karyotypic analyses of black-spotted tokay geckos from Guangxi China and red-spotted tokay geckos from Laos. These phylogenetic analyses showed that black-spotted and red-spotted tokay geckos are divided into two branches in molecular phylogenetic trees. The average genetic distances are as follows: 0.12-0.47% among six haplotypes in the black-spotted tokay gecko group, 0.12-1.66% among five haplotypes in the red-spotted tokay gecko group, and 8.76-9.18% between the black-spotted and red-spotted tokay geckos, respectively. The karyotypic analyses showed that the karyotype formula is 2n = 38 = 8m + 2sm + 2st + 26t in red-spotted tokay geckos from Laos compared with 2n = 38 = 8m + 2sm + 28t in black-spotted tokay geckos from Guangxi China. The differences in these two kinds of karyotypes were detected on the 15th chromosome. The clear differences in genetic levels between black-spotted and red-spotted tokay geckos suggest a significant level of genetic differentiation between the two.

Genetic differentiation among species of the genus Thermophis Malnate (Serpentes, Colubridae) and comments on T. shangrila.

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Hofmann, Sylvia; Tillack, Frank; Miehe, Georg

2015-10-07

The genus Thermophis includes the two species, T. baileyi and T. zhaoermii, which differ morphologically, geographically and molecularly. Recently, a third Thermophis species was described from Shangri-La, northern Yunnan Province, China, and named T. shangrila. The new species was based on morphological and genetic data derived from three specimens. However, the morphological features used to delimit this species seem vague, because they may fall within the range of intraspecific variation of T. zhaoermii. Furthermore, the reported genetic differences in nuclear data are questionable. They likely resulted from a misinterpretation probably due to alignment/analytical flaws or sample/sequence mix-up. Here, we used partial sequences of three mitochondrial (CO1, ND4, cytb) genes and one nuclear (c-mos) gene to analyse the genetic variation between and within species of Thermophis. We inferred the phylogeny using Bayesian Inference and Maximum Likelihood approaches and present additional morphological data that contribute to the knowledge on intraspecific variation in the genus. Our results indicate lacking robustness in the distinguishing morphological features and in the genetic differentiation of T. shangrila and highlight the need for more detailed morphological and molecular studies from a substantially larger sample.

Convergent cross-mapping and pairwise asymmetric inference.

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McCracken, James M; Weigel, Robert S

2014-12-01

Convergent cross-mapping (CCM) is a technique for computing specific kinds of correlations between sets of times series. It was introduced by Sugihara et al. [Science 338, 496 (2012).] and is reported to be "a necessary condition for causation" capable of distinguishing causality from standard correlation. We show that the relationships between CCM correlations proposed by Sugihara et al. do not, in general, agree with intuitive concepts of "driving" and as such should not be considered indicative of causality. It is shown that the fact that the CCM algorithm implies causality is a function of system parameters for simple linear and nonlinear systems. For example, in a circuit containing a single resistor and inductor, both voltage and current can be identified as the driver depending on the frequency of the source voltage. It is shown that the CCM algorithm, however, can be modified to identify relationships between pairs of time series that are consistent with intuition for the considered example systems for which CCM causality analysis provided nonintuitive driver identifications. This modification of the CCM algorithm is introduced as "pairwise asymmetric inference" (PAI) and examples of its use are presented.

Small cell and large cell neuroendocrine carcinomas of the pancreas are genetically similar and distinct from well-differentiated pancreatic neuroendocrine tumors.

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Yachida, Shinichi; Vakiani, Efsevia; White, Catherine M; Zhong, Yi; Saunders, Tyler; Morgan, Richard; de Wilde, Roeland F; Maitra, Anirban; Hicks, Jessica; Demarzo, Angelo M; Shi, Chanjuan; Sharma, Rajni; Laheru, Daniel; Edil, Barish H; Wolfgang, Christopher L; Schulick, Richard D; Hruban, Ralph H; Tang, Laura H; Klimstra, David S; Iacobuzio-Donahue, Christine A

2012-02-01

Poorly differentiated neuroendocrine carcinomas (NECs) of the pancreas are rare malignant neoplasms with a poor prognosis. The aim of this study was to determine the clinicopathologic and genetic features of poorly differentiated NECs and compare them with other types of pancreatic neoplasms. We investigated alterations of KRAS, CDKN2A/p16, TP53, SMAD4/DPC4, DAXX, ATRX, PTEN, Bcl2, and RB1 by immunohistochemistry and/or targeted exomic sequencing in surgically resected specimens of 9 small cell NECs, 10 large cell NECs, and 11 well-differentiated neuroendocrine tumors (PanNETs) of the pancreas. Abnormal immunolabeling patterns of p53 and Rb were frequent (p53, 18 of 19, 95%; Rb, 14 of 19, 74%) in both small cell and large cell NECs, whereas Smad4/Dpc4, DAXX, and ATRX labeling was intact in virtually all of these same carcinomas. Abnormal immunolabeling of p53 and Rb proteins correlated with intragenic mutations in the TP53 and RB1 genes. In contrast, DAXX and ATRX labeling was lost in 45% of PanNETs, whereas p53 and Rb immunolabeling was intact in these same cases. Overexpression of Bcl-2 protein was observed in all 9 small cell NECs (100%) and in 5 of 10 (50%) large cell NECs compared with only 2 of 11 (18%) PanNETs. Bcl-2 overexpression was significantly correlated with higher mitotic rate and Ki67 labeling index in neoplasms in which it was present. Small cell NECs are genetically similar to large cell NECs, and these genetic changes are distinct from those reported in PanNETs. The finding of Bcl-2 overexpression in poorly differentiated NECs, particularly small cell NEC, suggests that Bcl-2 antagonists/inhibitors may be a viable treatment option for these patients.

Genetic differentiation in red-bellied piranha populations (Pygocentrus nattereri, Kner, 1858) from the Solimões-Amazonas River.

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Dos Santos, Carlos Henrique Dos A; de Sá Leitão, Carolina S; Paula-Silva, Maria de N; Almeida-Val, Vera Maria F

2016-06-01

Red-bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões-Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red-bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red-bellied piranha populations collected at different locations of Solimões-Amazonas River system. We collected 234 red-bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões-Amazonas River system, with significant genetic differentiation between them. The red-bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing.

A comparative analysis of genetic differentiation across six shared willow host species in leaf- and bud-galling sawflies.

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Sanna A Leppänen

Full Text Available Genetic divergence and speciation in plant-feeding insects could be driven by contrasting selection pressures imposed by different plant species and taxa. While numerous examples of host-associated differentiation (HAD have been found, the overall importance of HAD in insect diversification remains unclear, as few studies have investigated its frequency in relation to all speciation events. One promising way to infer the prevalence and repeatability of HAD is to estimate genetic differentiation in multiple insect taxa that use the same set of hosts. To this end, we measured and compared variation in mitochondrial COI and nuclear ITS2 sequences in population samples of leaf-galling Pontania and bud-galling Euura sawflies (Hymenoptera: Tenthredinidae collected from six Salix species in two replicate locations in northern Fennoscandia. We found evidence of frequent HAD in both species complexes, as individuals from the same willow species tended to cluster together on both mitochondrial and nuclear phylogenetic trees. Although few fixed differences among the putative species were found, hierarchical AMOVAs showed that most of the genetic variation in the samples was explained by host species rather than by sampling location. Nevertheless, the levels of HAD measured across specific pairs of host species were not correlated in the two focal galler groups. Hence, our results support the hypothesis of HAD as a central force in herbivore speciation, but also indicate that evolutionary trajectories are only weakly repeatable even in temporally overlapping radiations of related insect taxa.

Genetic differentiation between marine iguanas from different breeding sites on the island of Santa Fe (Galapagos Archipelago).

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Lanterbecq, Deborah; Glaberman, Scott; Vitousek, Maren Noelani; Steinfartz, Sebastian; Benavides, Edgar; Wikelski, Martin; Caccone, Adalgisa

2010-01-01

We studied patterns of genetic diversity within and among 5 populations (318 individuals) of Galápagos marine iguanas (Amblyrhynchus cristatus) from the island Santa Fé. Populations were separated by distances of 0.2 to 9.9 km. We sequenced 1182 base pairs of the mitochondrial control region and screened 13 microsatellite loci for variability. We also added data from 5 populations (397 individuals) sampled on 4 neighboring islands (Santa Cruz, Floreana, Espanola, and San Cristobal). The 5 Santa Fé populations, revealed as genetically distinct from populations on other islands, present relatively low levels of genetic diversity, which are similar for both microsatellite (average observed heterozygosity from 0.7686 to 0.7773) and mitochondrial DNA (mtDNA) markers (haplotypic and nucleotide diversity from 0.587 to 0.728 and from 0.00079 to 0.00293, respectively), and comparable with those observed in similar-sized sampling sites on other islands. There was frequency-based evidence of genetic structure between northern and southern sites on Santa Fé (F(st) of 0.0027-0.0115 for microsatellite and 0.0447-0.2391 for mtDNA), but the 4 southern sites showed little differentiation. Most of the intra-island genetic variation was allocated within rather than between sites. There was no evidence of sex-biased dispersal or population substructuring due to lek-mating behavior, suggesting that these 2 observed behaviors are not strong enough to leave an evolutionary signal on genetic patterns in this species.

Novel tetra-nucleotide microsatellite DNA markers for assessing the evolutionary genetics and demographics of Northern Snakehead (Channa argus) invading North America

Science.gov (United States)

King, Timothy L.; Johnson, Robin L.

2011-01-01

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy–Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness.

Vorinostat induces apoptosis and differentiation in myeloid malignancies: genetic and molecular mechanisms.

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Gabriela Silva

Full Text Available BACKGROUND: Aberrant epigenetic patterns are central in the pathogenesis of haematopoietic diseases such as myelodysplastic syndromes (MDS and acute myeloid leukaemia (AML. Vorinostat is a HDACi which has produced responses in these disorders. The purpose of this study was to address the functional effects of vorinostat in leukemic cell lines and primary AML and MDS myeloid cells and to dissect the genetic and molecular mechanisms by which it exerts its action. METHODOLOGY/PRINCIPAL FINDINGS: Functional assays showed vorinostat promoted cell cycle arrest, inhibited growth, and induced apoptosis and differentiation of K562, HL60 and THP-1 and of CD33(+ cells from AML and MDS patients. To explore the genetic mechanism for these effects, we quantified gene expression modulation by vorinostat in these cells. Vorinostat increased expression of genes down-regulated in MDS and/or AML (cFOS, COX2, IER3, p15, RAI3 and suppressed expression of genes over-expressed in these malignancies (AXL, c-MYC, Cyclin D1 and modulated cell cycle and apoptosis genes in a manner which would favor cell cycle arrest, differentiation, and apoptosis of neoplastic cells, consistent with the functional assays. Reporter assays showed transcriptional effect of vorinostat on some of these genes was mediated by proximal promoter elements in GC-rich regions. Vorinostat-modulated expression of some genes was potentiated by mithramycin A, a compound that interferes with SP1 binding to GC-rich DNA sequences, and siRNA-mediated SP1 reduction. ChIP assays revealed vorinostat inhibited DNA binding of SP1 to the proximal promoter regions of these genes. These results suggest vorinostat transcriptional action in some genes is regulated by proximal promoter GC-rich DNA sequences and by SP1. CONCLUSION: This study sheds light on the effects of vorinostat in AML and MDS and supports the implementation of clinical trials to explore the use of vorinostat in the treatment of these diseases.

Vorinostat induces apoptosis and differentiation in myeloid malignancies: genetic and molecular mechanisms.

Science.gov (United States)

Silva, Gabriela; Cardoso, Bruno A; Belo, Hélio; Almeida, António Medina

2013-01-01

Aberrant epigenetic patterns are central in the pathogenesis of haematopoietic diseases such as myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML). Vorinostat is a HDACi which has produced responses in these disorders. The purpose of this study was to address the functional effects of vorinostat in leukemic cell lines and primary AML and MDS myeloid cells and to dissect the genetic and molecular mechanisms by which it exerts its action. Functional assays showed vorinostat promoted cell cycle arrest, inhibited growth, and induced apoptosis and differentiation of K562, HL60 and THP-1 and of CD33(+) cells from AML and MDS patients. To explore the genetic mechanism for these effects, we quantified gene expression modulation by vorinostat in these cells. Vorinostat increased expression of genes down-regulated in MDS and/or AML (cFOS, COX2, IER3, p15, RAI3) and suppressed expression of genes over-expressed in these malignancies (AXL, c-MYC, Cyclin D1) and modulated cell cycle and apoptosis genes in a manner which would favor cell cycle arrest, differentiation, and apoptosis of neoplastic cells, consistent with the functional assays. Reporter assays showed transcriptional effect of vorinostat on some of these genes was mediated by proximal promoter elements in GC-rich regions. Vorinostat-modulated expression of some genes was potentiated by mithramycin A, a compound that interferes with SP1 binding to GC-rich DNA sequences, and siRNA-mediated SP1 reduction. ChIP assays revealed vorinostat inhibited DNA binding of SP1 to the proximal promoter regions of these genes. These results suggest vorinostat transcriptional action in some genes is regulated by proximal promoter GC-rich DNA sequences and by SP1. This study sheds light on the effects of vorinostat in AML and MDS and supports the implementation of clinical trials to explore the use of vorinostat in the treatment of these diseases.

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

Energy Technology Data Exchange (ETDEWEB)

Bernardis, F. De; Vavagiakis, E.M.; Niemack, M.D.; Gallardo, P.A. [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Aiola, S. [Department of Physics and Astronomy, University of Pittsburgh, and Pittsburgh Particle Physics, Astrophysics, and Cosmology Center, 3941 O' Hara Street, Pittsburgh, PA 15260 (United States); Battaglia, N. [Department of Astrophysical Sciences, Peyton Hall, Princeton University, Princeton, NJ 08544 (United States); Beall, J.; Becker, D.T.; Cho, H.; Fox, A. [National Institute of Standards and Technology, Boulder, CO 80305 (United States); Bond, J.R. [CITA, University of Toronto, 60 St. George St., Toronto, ON M5S 3H8 (Canada); Calabrese, E.; Dunkley, J. [Sub-Department of Astrophysics, University of Oxford, Keble Road, Oxford, OX1 3RH (United Kingdom); Coughlin, K.; Datta, R. [Department of Physics, University of Michigan Ann Arbor, MI 48109 (United States); Devlin, M. [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Dunner, R. [Instituto de Astrofísica and Centro de Astro-Ingeniería, Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, 7820436 Macul, Santiago (Chile); Ferraro, S. [Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720 (United States); Halpern, M. [University of British Columbia, Department of Physics and Astronomy, 6224 Agricultural Road, Vancouver BC V6T 1Z1 (Canada); Hand, N., E-mail: fdeberna@gmail.com [Astronomy Department, University of California, Berkeley, CA 94720 (United States); and others

2017-03-01

We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

Genetic differentiation in populations of Aedes aegypti (Diptera, Culicidae dengue vector from the Brazilian state of Maranhão

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Andrelina Alves de Sousa

Full Text Available ABSTRACT Aedes (Stegomyia aegypti is the vector responsible for the transmission of the viruses that cause zika, yellow and chikungunya fevers, the four dengue fever serotypes (DENV - 1, 2, 3, 4, and hemorrhagic dengue fever in tropical and subtropical regions around the world. The present study investigated the genetic differentiation of the 15 populations of this vector in the Brazilian state of Maranhão, based on the mitochondrial ND4 marker. A total of 177 sequences were obtained for Aedes aegypti, with a fragment of 337 bps, 15 haplotypes, 15 polymorphics sites, haplotype diversity of h = 0.6938, and nucleotide diversity of π = 0.01486. The neutrality tests (D and Fs were not significant. The AMOVA revealed that most of the variation (58.47% was found within populations, with FST = 0.41533 (p < 0.05. Possible isolation by distance was tested and a significant correlation coefficient (r = 0.3486; p = 0.0040 was found using the Mantel test. The phylogenetic relationships among the 15 haplotypes indicated the existence of two distinct clades. This finding, together with the population parameters, was consistent with a pattern of genetic structuring that underpinned the genetic differentiation of the study populations in Maranhão, and was characterized by the presence of distinct lineages of Aedes aegypti.

Applications of Genetic Programming

DEFF Research Database (Denmark)

Gaunholt, Hans; Toma, Laura

1996-01-01

In this report a study of genetic programming (GP) has been performed with respect to a number of applications such as Symbolic function regression, Solving Symbolic Differential Equations, Image encoding, the ant problem etc.......In this report a study of genetic programming (GP) has been performed with respect to a number of applications such as Symbolic function regression, Solving Symbolic Differential Equations, Image encoding, the ant problem etc....

Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

Science.gov (United States)

Newberg, Lee A

2008-08-15

A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

Benefits of Using Pairwise Trajectory Management in the Central East Pacific

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Chartrand, Ryan; Ballard, Kathryn

2017-01-01

Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in procedural airspace. This concept makes use of updated ground automation, Automatic Dependent Surveillance-Broadcast (ADS-B) and on board avionics generating real time guidance. An experiment was conducted to examine the potential benefits of implementing PTM in the Central East Pacific oceanic region. An explanation of the experiment and some of the results are included in this paper. The PTM concept allowed for an increase in the average time an aircraft is able to spend at its desired flight level and a reduction in fuel burn.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

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Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

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Maréchal Eric

2005-03-01

Full Text Available Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. Conclusion The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

International Nuclear Information System (INIS)

Hardy, David J.; Schulten, Klaus; Wolff, Matthew A.; Skeel, Robert D.; Xia, Jianlin

2016-01-01

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.

Phylogeography and Genetic Differentiation among Populations of the Moon Turban Snail Lunella granulata Gmelin, 1791 (Gastropoda: Turbinidae

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Chuen-Tan Jean

2013-04-01

Full Text Available We examined the genetic variation and phylogeographic relationships among 10 populations of Lunella granulata from mainland China, Penghu Archipelago, Taiwan Island, and Japan using mitochondrial COI and 16S markers. A total of 45 haplotypes were obtained in 112 specimens, and relatively high levels of haplotype diversity (h = 0.903 and low levels of nucleotide diversity (π = 0.0046 were detected. Four major phylogenetic lineage clusters were revealed and were concordant with their geographic distribution, agreeing with the haplotype network. These results suggested that geographic barrier isolating effects were occurring among the populations. This hypothesis was also supported by a significant genetic differentiation index (FST = 0.709 and by a spatial analysis of molecular variance (SAMOVA analysis. A mismatch distribution analysis, neutrality tests and Bayesian skyline plots found a single significant population expansion. This expansion occurred on the coast of mainland China before 20–17 ka. Consequently, although the dispersal ability of the planktonic stage and the circulation of ocean currents generally promote genetic exchanges among populations, L. granulata has tended to maintain distinct genetic groups that reflect the respective geographic origins of the constituent lineages. Although the circulation of ocean currents, in principle, may still play a role in determining the genetic composition of populations, long-distance migration between regions is difficult even at the planktonic stage.

Connecting Palau's marine protected areas: a population genetic approach to conservation

Science.gov (United States)

Cros, Annick; Toonen, Robert J.; Donahue, Megan J.; Karl, Stephen A.

2017-09-01

Bleaching events are becoming more frequent and are projected to become annual in Micronesia by 2040. To prepare for this threat, the Government of Palau is reviewing its marine protected area network to increase the resilience of the reefs by integrating connectivity into the network design. To support their effort, we used high-throughput sequencing of microsatellites to create genotypes of colonies of the coral Acropora hyacinthus to characterize population genetic structure and dispersal patterns that led to the recovery of Palau's reefs from a 1998 bleaching event. We found no evidence of a founder effect or refugium where colonies may have survived to recolonize the reef. Instead, we found significant pairwise F' st values, indicating population structure and low connectivity among most of the 25 sites around Palau. We used kinship to measure genetic differences at the individual level among sites and found that differences were best explained by the degree of exposure to the ocean [ F 1,20 = 3.015, Pr(> F) = 0.01], but with little of the total variation explained. A permutation test of the pairwise kinship coefficients revealed that there was self-seeding within sites. Overall, the data point to the population of A. hyacinthus in Palau recovering from a handful of surviving colonies with population growth primarily from self-seeding and little exchange among sites. This finding has significant implications for the management strategies for the reefs of Palau, and we recommend increasing the number and distribution of management areas around Palau to capture the genetic architecture and increase the chances of protecting potential refuges in the future.

Further investigations of the W-test for pairwise epistasis testing [version 1; referees: 2 approved

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Richard Howey

2017-07-01

Full Text Available Background: In a recent paper, a novel W-test for pairwise epistasis testing was proposed that appeared, in computer simulations, to have higher power than competing alternatives. Application to genome-wide bipolar data detected significant epistasis between SNPs in genes of relevant biological function. Network analysis indicated that the implicated genes formed two separate interaction networks, each containing genes highly related to autism and neurodegenerative disorders. Methods: Here we investigate further the properties and performance of the W-test via theoretical evaluation, computer simulations and application to real data. Results: We demonstrate that, for common variants, the W-test is closely related to several existing tests of association allowing for interaction, including logistic regression on 8 degrees of freedom, although logistic regression can show inflated type I error for low minor allele frequencies,  whereas the W-test shows good/conservative type I error control. Although in some situations the W-test can show higher power, logistic regression is not limited to tests on 8 degrees of freedom but can instead be taylored to impose greater structure on the assumed alternative hypothesis, offering a power advantage when the imposed structure matches the true structure. Conclusions: The W-test is a potentially useful method for testing for association - without necessarily implying interaction - between genetic variants disease, particularly when one or more of the genetic variants are rare. For common variants, the advantages of the W-test are less clear, and, indeed, there are situations where existing methods perform better. In our investigations, we further uncover a number of problems with the practical implementation and application of the W-test (to bipolar disorder previously described, apparently due to inadequate use of standard data quality-control procedures. This observation leads us to urge caution in

Natural selection among Eurasians at genomic regions associated with HIV-1 control

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Allison David B

2011-06-01

Full Text Available Abstract Background HIV susceptibility and pathogenicity exhibit both interindividual and intergroup variability. The etiology of intergroup variability is still poorly understood, and could be partly linked to genetic differences among racial/ethnic groups. These genetic differences may be traceable to different regimes of natural selection in the 60,000 years since the human radiation out of Africa. Here, we examine population differentiation and haplotype patterns at several loci identified through genome-wide association studies on HIV-1 control, as determined by viral-load setpoint, in European and African-American populations. We use genome-wide data from the Human Genome Diversity Project, consisting of 53 world-wide populations, to compare measures of FST and relative extended haplotype homozygosity (REHH at these candidate loci to the rest of the respective chromosome. Results We find that the Europe-Middle East and Europe-South Asia pairwise FST in the most strongly associated region are elevated compared to most pairwise comparisons with the sub-Saharan African group, which exhibit very low FST. We also find genetic signatures of recent positive selection (higher REHH at these associated regions among all groups except for sub-Saharan Africans and Native Americans. This pattern is consistent with one in which genetic differentiation, possibly due to diversifying/positive selection, occurred at these loci among Eurasians. Conclusions These findings are concordant with those from earlier studies suggesting recent evolutionary change at immunity-related genomic regions among Europeans, and shed light on the potential genetic and evolutionary origin of population differences in HIV-1 control.

Genetic evidence for landscape effects on dispersal in the army ant Eciton burchellii.

Science.gov (United States)

Soare, Thomas W; Kumar, Anjali; Naish, Kerry A; O'Donnell, Sean

2014-01-01

Inhibited dispersal, leading to reduced gene flow, threatens populations with inbreeding depression and local extinction. Fragmentation may be especially detrimental to social insects because inhibited gene flow has important consequences for cooperation and competition within and among colonies. Army ants have winged males and permanently wingless queens; these traits imply male-biased dispersal. However, army ant colonies are obligately nomadic and have the potential to traverse landscapes. Eciton burchellii, the most regularly nomadic army ant, is a forest interior species: colony raiding activities are limited in the absence of forest cover. To examine whether nomadism and landscape (forest clearing and elevation) affect population genetic structure in a montane E. burchellii population, we reconstructed queen and male genotypes from 25 colonies at seven polymorphic microsatellite loci. Pairwise genetic distances among individuals were compared to pairwise geographical and resistance distances using regressions with permutations, partial Mantel tests and random forests analyses. Although there was no significant spatial genetic structure in queens or males in montane forest, dispersal may be male-biased. We found significant isolation by landscape resistance for queens based on land cover (forest clearing), but not on elevation. Summed colony emigrations over the lifetime of the queen may contribute to gene flow in this species and forest clearing impedes these movements and subsequent gene dispersal. Further forest cover removal may increasingly inhibit Eciton burchellii colony dispersal. We recommend maintaining habitat connectivity in tropical forests to promote population persistence for this keystone species. © 2013 John Wiley & Sons Ltd.

Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip.

Science.gov (United States)

Zamora, Jane Louie Fresco; Kashihara, Shigeru; Yamaguchi, Suguru

2015-01-01

Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

Genetic differentiation of Octopus minor (Mollusca, Cephalopoda) off the northern coast of China as revealed by amplified fragment length polymorphisms.

Science.gov (United States)

Yang, J M; Sun, G H; Zheng, X D; Ren, L H; Wang, W J; Li, G R; Sun, B C

2015-12-02

Octopus minor (Sasaki, 1920) is an economically important cephalopod that is found in the northern coastal waters of China. In this study, we investigated genetic differentiation in fishery populations using amplified fragment length polymorphisms (AFLPs). A total of 150 individuals were collected from five locations: Dalian (DL), Yan-tai (YT), Qingdao (QD), Lianyungang (LY), and Zhoushan (ZS), and 243 reproducible bands were amplified using five AFLP primer combinations. The percentage of polymorphic bands ranged from 53.33 to 76.08%. Nei's genetic identity ranged from 0.9139 to 0.9713, and the genetic distance ranged from 0.0291 to 0.0900. A phylogenetic tree was constructed using the unweighted pair group method with arithmetic mean, based on the genetic distance. The DL and YT populations originated from one clade, while the QD, LY, and ZS populations originated from another. The results indicate that the O. minor stock consisted of two genetic populations with an overall significantly analogous FST value (0.1088, P octopus fisheries, so that this marine resource can be conserved for its long-term utilization.

Correlation among genetic, Euclidean, temporal, and herd ownership distances of porcine reproductive and respiratory syndrome virus strains in Quebec, Canada

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Lambert Marie-Ève

2012-06-01

Full Text Available Abstract Background Porcine reproductive and respiratory syndrome (PRRS is a viral disease that has a major economic impact for the swine industry. Its control is mostly directed towards preventing its spread which requires a better understanding of the mechanisms of transmission of the virus between herds. The objectives of this study were to describe the genetic diversity and to assess the correlation among genetic, Euclidean and temporal distances and ownership to better understand pathways of transmission. Results A cross-sectional study was conducted on sites located in a high density area of swine production in Quebec. Geographical coordinates (longitude/latitude, date of submission and ownership were obtained for each site. ORF5 sequencing was attempted on PRRSV positive sites. Proportion of pairwise combinations of strains having ≥98% genetic homology were analysed according to Euclidean distances and ownership. Correlations between genetic, Euclidean and temporal distances and ownership were assessed using Mantel tests on continuous and binary matrices. Sensitivity of the correlations between genetic and Euclidean as well as temporal distances was evaluated for different Euclidean and temporal distance thresholds. An ORF5 sequence was identified for 132 of the 176 (75% PRRSV positive sites; 122 were wild-type strains. The mean (min-max genetic, Euclidean and temporal pairwise distances were 11.6% (0–18.7, 15.0 km (0.04-45.7 and 218 days (0–852, respectively. Significant positive correlations were observed between genetic and ownership, genetic and Euclidean and between genetic and temporal binary distances. The relationship between genetic and ownership suggests either common sources of animals or semen, employees, technical services or vehicles, whereas that between genetic and Euclidean binary distances is compatible with area spread of the virus. The latter correlation was observed only up to 5 km. Conclusions This study

Indirect evidence for genetic differentiation in vulnerability to embolism in Pinus halepensis

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Rakefet eDavid-Schwartz

2016-06-01

Full Text Available Climate change is increasing mean temperatures and in the eastern Mediterranean is expected to decrease annual precipitation. The resulting increase in aridity may be too rapid for adaptation of tree species unless their gene pool already possesses variation in drought resistance. Vulnerability to embolism, estimated by the pressure inducing 50% loss of xylem hydraulic conductivity (P50, is strongly associated with drought stress resistance in trees. Yet, previous studies on various tree species reported low intraspecific genetic variation for this trait, and therefore limited adaptive capacities to increasing aridity. Here we quantified differences in hydraulic efficiency (xylem hydraulic conductance and safety (resistance to embolism in four contrasting provenances of Pinus halepensis (Aleppo pine in a provenance trial, which is indirect evidence for genetic differences. Results obtained with three techniques (bench dehydration, centrifugation and X-ray micro-CT evidenced significant differentiation with similar ranking between provenances. Inter-provenance variation in P50 correlated with pit anatomical properties (torus overlap and pit aperture size. These results suggest that adaptation of P. halepensis to xeric habitats has been accompanied by modifications of bordered pit function driven by variation in pit aperture. This study thus provides evidence that appropriate exploitation of provenance differences will allow continued forestry with P. halepensis in future climates of the Eastern Mediterranean.

Variability and genetic differentiation among Anopheles (Ano. intermedius Chagas, 1908 and Anopheles (Ano. mattogrossensis Lutz & Neiva, 1911 (Diptera: Culicidae from the Brazilian Amazon

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Joselita Maria Mendes dos Santos

2005-10-01

Full Text Available Anopheles (Anopheles intermedius and Anopheles (Ano. mattogrossensis are Brazilian anopheline species belonging to the scarcely studied Anopheles subgenus. Few studies have been done on the genetic differentiation of these species. Both species have been found infected by Plasmodium and are sympatric with other anopheline species from the Nyssorhynchus subgenus. Eighteen enzymatic loci were analyzed in larval specimens of An. intermedius and An. mattogrossensis aiming to estimate the variability and genetic differentiation between these species. An. mattogrossensis population showed higher genetic variability (P = 44.4 and Ho = 0.081 ± 0.031 than that of An. intermedius (P = 33.3 and Ho = 0.048 ± 0.021. Most analyzed loci showed genotypic frequencies according to Hardy-Weinberg equilibrium, except for LAP1 and LAP2 in An. intermedius, and EST1 and PGM loci in An. mattogrossensis. The genetic distance between these species (D = 0.683 was consistent with the inter-specific values reported for Anopheles subgenus. We verified that the polymorphism and heterozygosity percentile values found in both species and compared to those in the literature, showed no relation between the level of isozyme variability and geographical distribution. The low variability found in these two species is probably more related to the niche they occupy than to their geographic distribution.

Discordant patterns of genetic and phenotypic differentiation in five grasshopper species codistributed across a microreserve network.

Science.gov (United States)

Ortego, Joaquín; García-Navas, Vicente; Noguerales, Víctor; Cordero, Pedro J

2015-12-01

Conservation plans can be greatly improved when information on the evolutionary and demographic consequences of habitat fragmentation is available for several codistributed species. Here, we study spatial patterns of phenotypic and genetic variation among five grasshopper species that are codistributed across a network of microreserves but show remarkable differences in dispersal-related morphology (body size and wing length), degree of habitat specialization and extent of fragmentation of their respective habitats in the study region. In particular, we tested the hypothesis that species with preferences for highly fragmented microhabitats show stronger genetic and phenotypic structure than codistributed generalist taxa inhabiting a continuous matrix of suitable habitat. We also hypothesized a higher resemblance of spatial patterns of genetic and phenotypic variability among species that have experienced a higher degree of habitat fragmentation due to their more similar responses to the parallel large-scale destruction of their natural habitats. In partial agreement with our first hypothesis, we found that genetic structure, but not phenotypic differentiation, was higher in species linked to highly fragmented habitats. We did not find support for congruent patterns of phenotypic and genetic variability among any studied species, indicating that they show idiosyncratic evolutionary trajectories and distinctive demographic responses to habitat fragmentation across a common landscape. This suggests that conservation practices in networks of protected areas require detailed ecological and evolutionary information on target species to focus management efforts on those taxa that are more sensitive to the effects of habitat fragmentation. © 2015 John Wiley & Sons Ltd.

Genetic diversity revealed by AFLP markers in Albanian goat breeds

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Hoda Anila

2012-01-01

Full Text Available The amplified fragment length polymorphism (AFLP technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei’s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright’s FST index, Nei’s unbiased genetic distance and Reynolds’ genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds’ genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard’s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

Statistical pairwise interaction model of stock market

Science.gov (United States)

Bury, Thomas

2013-03-01

Financial markets are a classical example of complex systems as they are compound by many interacting stocks. As such, we can obtain a surprisingly good description of their structure by making the rough simplification of binary daily returns. Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviors. Here we show that the pairwise model is actually a statistically consistent model with the observed first and second moments of the stocks orientation without making such restrictive assumptions. This is done with an approach only based on empirical data of price returns. Our data analysis of six major indices suggests that the actual interaction structure may be thought as an Ising model on a complex network with interaction strengths scaling as the inverse of the system size. This has potentially important implications since many properties of such a model are already known and some techniques of the spin glass theory can be straightforwardly applied. Typical behaviors, as multiple equilibria or metastable states, different characteristic time scales, spatial patterns, order-disorder, could find an explanation in this picture.

Genetic differentiation in populations of Aedes aegypti (Diptera, Culicidae dengue vector from the Brazilian state of Maranhão

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Andrelina Alves de Sousa

2017-01-01

Full Text Available Aedes (Stegomyia aegypti is the vector responsible for the transmission of the viruses that cause zika, yellow and chikungunya fevers, the four dengue fever serotypes (DENV – 1, 2, 3, 4, and hemorrhagic dengue fever in tropical and subtropical regions around the world. The present study investigated the genetic differentiation of the 15 populations of this vector in the Brazilian state of Maranhão, based on the mitochondrial ND4 marker. A total of 177 sequences were obtained for Aedes aegypti, with a fragment of 337 bps, 15 haplotypes, 15 polymorphics sites, haplotype diversity of h = 0.6938, and nucleotide diversity of π = 0.01486. The neutrality tests (D and Fs were not significant. The AMOVA revealed that most of the variation (58.47% was found within populations, with FST = 0.41533 (p < 0.05. Possible isolation by distance was tested and a significant correlation coefficient (r = 0.3486; p = 0.0040 was found using the Mantel test. The phylogenetic relationships among the 15 haplotypes indicated the existence of two distinct clades. This finding, together with the population parameters, was consistent with a pattern of genetic structuring that underpinned the genetic differentiation of the study populations in Maranhão, and was characterized by the presence of distinct lineages of Aedes aegypti. Keywords: Gene flow, Mitochondrial DNA, ND4

[Genetic variation and differentiation in striped field mouse Apodemus agrarius inferred from RAPD-PCR analysis].

Science.gov (United States)

Atopkin, D M; Bogdanov, A S; Chelomina, G N

2007-06-01

Genetic variation and differentiation of the trans-Palearctic species Apodemus agrarius (striped field mouse), whose range consists of two large isolates-European-Siberian and Far Eastern-Chinese, were examined using RAPD-PCR analysis. The material from the both parts of the range was examined (41 individual of A. agrarius from 18 localities of Russia, Ukraine, Moldova, and Kazakhstan); the Far-Eastern part was represented by samples from the Amur region, Khabarovsk krai, and Primorye (Russia). Differences in frequencies of polymorphic RAPD loci were found between the European-Siberian and the Far Eastern population groups of striped field mouse. No "fixed" differences between them in RAPD spectra were found, and none of the used statistical methods permitted to distinguish with absolute certainty animals from the two range parts. Thus, genetic isolation of the European-Siberian and the Far Eastern population groups of A. agrarius is not strict. These results support the hypothesis on recent dispersal of striped field mouse from East to West Palearctics (during the Holocene climatic optimum, 7000 to 4500 years ago) and subsequent disjunction of the species range (not earlier than 4000-4500 years ago). The Far Eastern population group is more polymorphic than the European-Siberian one, while genetic heterogeneity is more uniformly distributed within it. This is probably explained by both historical events that happened during the species dispersal in the past, and different environmental conditions for the species in different parts of its range. The Far Eastern population group inhabits the area close to the distribution center of A. agrarius. It is likely that this group preserved genetic variation of the formerly integral ancestral form, while some amount of genetic polymorphism could be lost during the species colonization of the Siberian and European areas. To date, the settlement density and population number in general are higher than within the European

The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks

Directory of Open Access Journals (Sweden)

Wingender Edgar

2008-05-01

Full Text Available Abstract Background Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emphasize the global characterization of regulatory systems, the practical approaches focus on the role of distinct molecules and genes in regulation. To bridge the gap between these opposite approaches, one needs to combine 'general' with 'particular' properties and translate abstract topological features of large systems into testable functional characteristics of individual components. Here, we propose a new topological parameter – the pairwise disconnectivity index of a network's element – that is capable of such bridging. Results The pairwise disconnectivity index quantifies how crucial an individual element is for sustaining the communication ability between connected pairs of vertices in a network that is displayed as a directed graph. Such an element might be a vertex (i.e., molecules, genes, an edge (i.e., reactions, interactions, as well as a group of vertices and/or edges. The index can be viewed as a measure of topological redundancy of regulatory paths which connect different parts of a given network and as a measure of sensitivity (robustness of this network to the presence (absence of each individual element. Accordingly, we introduce the notion of a path-degree of a vertex in terms of its corresponding incoming, outgoing and mediated paths, respectively. The pairwise disconnectivity index has been applied to the analysis of several regulatory networks from various organisms. The importance of an individual vertex or edge for the coherence of the network is determined by the particular position of the given element in the whole network. Conclusion Our approach enables to evaluate the effect of removing each element (i.e., vertex, edge, or their combinations from a network. The greatest potential value of

Strong genetic differentiation among east Atlantic populations of the sword razor shell ( Ensis siliqua) assessed with mtDNA and RAPD markers

Science.gov (United States)

Arias, Alberto; Fernández-Moreno, Mercedes; Fernández-Tajes, Juan; Gaspar, Miguel B.; Méndez, Josefina

2011-03-01

The sword razor shell Ensis siliqua (Linnaeus, 1758) is a bivalve with a high commercial value being appreciated in fresh and processed markets. However, the genetic studies carried out in populations of E. siliqua are scarce. In this work, the genetic variability and differentiation of the sword razor shell was assessed using PCR-RFLPs of a fragment of the 16S rRNA mitochondrial gene and random amplified polymorphic loci (RAPD) in nine localities from Ireland, Spain, and Portugal. In the 314 individuals examined for the mitochondrial fragment, 12 composite haplotypes were observed; meanwhile, a unique phenotype was observed for each of the 242 individuals analyzed with 61 RAPD loci. Two of the mitochondrial composite haplotypes accounted for the majority of individuals (89.81%) and showed a remarkably disjoint distribution between Irish and Iberian samples, with the exception of Aveiro which exhibited as the most frequent haplotype the same found in Ireland. The level of variability observed for each sample was generally correlated with both types of markers and the results obtained suggest the existence of a strong population differentiation between Irish and Iberian localities, except for the Portuguese sample from Aveiro which is surprisingly closer to Irish individuals, although it is probably highly differentiated.

Searching for speciation genes: molecular evidence for selection associated with colour morphotypes in the Caribbean reef fish genus Hypoplectrus.

Directory of Open Access Journals (Sweden)

Ben G Holt

Full Text Available Closely related species that show clear phenotypic divergence, but without obvious geographic barriers, can provide opportunities to study how diversification can occur when opportunities for allopatric speciation are limited. We examined genetic divergence in the coral reef fish genus Hypoplectrus (family: Serranidae, which comprises of 10-14 morphotypes that are distinguished solely by their distinct colour patterns, but which show little genetic differentiation. Our goal was to detect loci that show clear disequilibrium between morphotypes and across geographical locations. We conducted Amplified Fragment Length Polymorphism molecular analysis to quantify genetic differentiation among, and selection between, morphotypes. Three loci were consistently divergent beyond neutral expectations in repeated pair-wise morphotype comparisons using two different methods. These loci provide the first evidence for genes that may be associated with colour morphotype in the genus Hypoplectrus.

Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip

Directory of Open Access Journals (Sweden)

Jane Louie Fresco Zamora

2015-01-01

Full Text Available Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

Criteria for the singularity of a pairwise l1-distance matrix and their generalizations

International Nuclear Information System (INIS)

D'yakonov, Alexander G

2012-01-01

We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

Fast evolutionary genetic differentiation during experimental ...

Indian Academy of Sciences (India)

of six foundations, derived from different locations, different years and from two samples in one of the years. We show that ... bottleneck on effective population size (Ne) is expected to .... Here we deepen a previous analysis of the genetic vari-.

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

2005-01-01

FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural RNA...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

Science.gov (United States)

2014-01-01

Background Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas. Results We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy. Conclusions The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle

Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons.

Science.gov (United States)

Curto, M; Puppo, P; Kratschmer, S; Meimberg, H

2017-08-22

Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572-575, 2005; Saunders and Gibson, J Ecol 93: 649-652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168-173, 2004; Silvertown et al., J Ecol 93: 653-657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different

The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland.

Science.gov (United States)

Mullins, Jacinta; McDevitt, Allan D; Kowalczyk, Rafał; Ruczyńska, Iwona; Górny, Marcin; Wójcik, Jan M

2014-01-01

The red fox ( Vulpes vulpes ) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002-2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.

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.

First insights into the genetic diversity of Echinococcus granulosus sensu stricto (s.s.) in Serbia.

Science.gov (United States)

Debeljak, Zoran; Boufana, Belgees; Interisano, Maria; Vidanovic, Dejan; Kulisic, Zoran; Casulli, Adriano

2016-06-15

Cystic echinococcosis (CE) caused by Echinococcus granulosus sensu stricto (s.s.) is a cosmopolitan zoonotic infection which is endemic in Serbia where it is subject to mandatory reporting. However, information on the incidence of the disease in humans and prevalence of hydatid infection in livestock remains limited. We used sequenced data of the cytochrome c oxidase subunit 1 (cox 1) mitochondrial gene to examine the genetic diversity and population structure of E. granulosus (s.s.) from intermediate hosts from Serbia. We also compared our generated nucleotide sequences with those reported for neighbouring European countries. Echinococcus canadensis was molecularly confirmed from pig and human hydatid isolates. E. granulosus (G1) was confirmed from sheep and cattle hydatid isolates as well as the first molecular confirmation in Serbia of E. granulosus G2 in sheep and E. granulosus G3 in sheep and cattle hydatid isolates. The Serbian E. granulosus (s.s.) parsimony network displayed 2 main haplotypes (SB02 and SB05) which together with the neutrality indices were suggestive of bottleneck and/or balancing selection. Haplotype analysis showed the presence of the common E. granulosus haplotype described from other worldwide regions. Investigation of the pairwise fixation (Fst) index suggested that Serbian populations of E. granulosus (s.s.) from sheep and cattle hosts showed moderate genetic differentiation. Six of the Serbian haplotypes (SB02-SB07) were shared with haplotypes from Bulgaria, Hungary and/or Romania. Further studies using a larger number of hydatid isolates from various locations across Serbia will provide more information on the genetic structure of E. granulosus (s.s.) within this region. Copyright © 2016 Elsevier B.V. All rights reserved.

Modeling delay in genetic networks: from delay birth-death processes to delay stochastic differential equations.

Science.gov (United States)

Gupta, Chinmaya; López, José Manuel; Azencott, Robert; Bennett, Matthew R; Josić, Krešimir; Ott, William

2014-05-28

Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemical Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay.

Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations

Energy Technology Data Exchange (ETDEWEB)

Gupta, Chinmaya; López, José Manuel; Azencott, Robert; Ott, William [Department of Mathematics, University of Houston, Houston, Texas 77004 (United States); Bennett, Matthew R. [Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77204, USA and Institute of Biosciences and Bioengineering, Rice University, Houston, Texas 77005 (United States); Josić, Krešimir [Department of Mathematics, University of Houston, Houston, Texas 77004 (United States); Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204 (United States)

2014-05-28

Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemical Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay.

Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations

International Nuclear Information System (INIS)

Gupta, Chinmaya; López, José Manuel; Azencott, Robert; Ott, William; Bennett, Matthew R.; Josić, Krešimir

2014-01-01

Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemical Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay

Effect of pairwise additivity on finite-temperature behavior of classical ideal gas

Science.gov (United States)

Shekaari, Ashkan; Jafari, Mahmoud

2018-05-01

Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.

Atomic pairwise distribution function analysis of the amorphous phase prepared by different manufacturing routes

DEFF Research Database (Denmark)

Boetker, Johan P.; Koradia, Vishal; Rades, Thomas

2012-01-01

was subjected to quench cooling thereby creating an amorphous form of the drug from both starting materials. The milled and quench cooled samples were, together with the crystalline starting materials, analyzed with X-ray powder diffraction (XRPD), Raman spectroscopy and atomic pair-wise distribution function...... (PDF) analysis of the XRPD pattern. When compared to XRPD and Raman spectroscopy, the PDF analysis was superior in displaying the difference between the amorphous samples prepared by milling and quench cooling approaches of the two starting materials....

Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation

International Nuclear Information System (INIS)

Wolf, D.; Keblinski, P.; Phillpot, S.R.; Eggebrecht, J.

1999-01-01

Based on a recent result showing that the net Coulomb potential in condensed ionic systems is rather short ranged, an exact and physically transparent method permitting the evaluation of the Coulomb potential by direct summation over the r -1 Coulomb pair potential is presented. The key observation is that the problems encountered in determining the Coulomb energy by pairwise, spherically truncated r -1 summation are a direct consequence of the fact that the system summed over is practically never neutral. A simple method is developed that achieves charge neutralization wherever the r -1 pair potential is truncated. This enables the extraction of the Coulomb energy, forces, and stresses from a spherically truncated, usually charged environment in a manner that is independent of the grouping of the pair terms. The close connection of our approach with the Ewald method is demonstrated and exploited, providing an efficient method for the simulation of even highly disordered ionic systems by direct, pairwise r -1 summation with spherical truncation at rather short range, i.e., a method which fully exploits the short-ranged nature of the interactions in ionic systems. The method is validated by simulations of crystals, liquids, and interfacial systems, such as free surfaces and grain boundaries. copyright 1999 American Institute of Physics

Limited overwater dispersal and genetic differentiation of the snake-eyed skink (Cryptoblepharus nigropunctatus) in the Oceanic Ogasawara Islands, Japan.

Science.gov (United States)

Hayashi, Fumio; Shima, Akina; Horikoshi, Kazuo; Kawakami, Kazuto; Segawa, Ryoko D; Aotsuka, Tadashi; Suzuki, Tadashi

2009-08-01

The genetic differentiation and speciation of lizards on oceanic islands may be affected by their rate of overwater dispersal. Cryptoblepharus is one of the most geographically widespread scincid lizards throughout the Indo-Pacific and Australian regions. Cryptoblepharus nigropunctatus is the northernmost species of the genus, dwelling on several small Pacific islands. To examine the colonization history of this lizard, mitochondrial 16S rDNA and D-loop sequences were compared among populations of the Ogasawara Islands consisting of four island groups (the Muko-jima, Chichi-jima, Haha-jima, and Kazan groups), and an isolated island, Minamitori-shima (Marcus Island). These four groups and Minamitori-shima have not been connected to each other because each is surrounded by deep sea (>100 m). DNA analyses showed that the lizard populations on individual islands had each representative haplotypes. The ancestors of C. nigropunctatus probably arrived on the islands from the southern Pacific Ocean via wave dispersal and differentiated to produce the present state. They appear to have dispersed from their origin along two independent pathways: one between Kitaiwo-to (Kazan group) and the Muko-jima and Chichi-jima groups, and the other among the Minamitori-shima, Minamiiwo-to (Kazan group), and Haha-jima groups. Limited long-distance overwater dispersal may be responsible for the genetic structure of the C. nigropunctatus populations on these oceanic islands. However, among the small islands within the same island group, D-loop haplotypes were shared and the local genetic diversity was usually high, suggesting frequent gene flow across the same group of islands.

Variation in sclerophylly among Iberian populations of Quercus coccifera L. is associated with genetic differentiation across contrasting environments.

Science.gov (United States)

Rubio de Casas, R; Vargas, P; Pérez-Corona, E; Cano, E; Manrique, E; García-Verdugo, C; Balaguer, L

2009-05-01

Evergreen oaks are an emblematic element of the Mediterranean vegetation and have a leaf phenotype that seems to have remained unchanged since the Miocene. We hypothesise that variation of the sclerophyll phenotype among Iberian populations of Quercus coccifera is partly due to an ulterior process of ecotypic differentiation. We analysed the genetic structure of nine Iberian populations using ISSR fingerprints, and their leaf phenotypes using mean and intracanopy plasticity values of eight morphological (leaf angle, area, spinescence, lobation and specific area) and biochemical traits (VAZ pool, chlorophyll and beta-carotene content). Climate and soil were also characterised at the population sites. Significant genetic and phenotypic differences were found among populations and between NE Iberia and the rest of the populations of the peninsula. Mean phenotypes showed a strong and independent correlation with both genetic and geographic distances. Northeastern plants were smaller, less plastic, with smaller, spinier and thicker leaves, a phenotype consistent with the stressful conditions that prevailed in the steppe environments of the refugia within this geographic area during glaciations. These genetic, phenotypic, geographic and environmental patterns are consistent with previously reported palaeoecological and common evidence. Such consistency leads us to conclude that there has been a Quaternary divergence within the sclerophyllous syndrome that was at least partially driven by ecological factors.

The consistent differential expression of genetic pathways following exposure of an industrial Pseudomonas aeruginosa strain to preservatives and a laundry detergent formulation

Science.gov (United States)

Amézquita, Alejandro; Le Marc, Yvan; Bull, Matthew J; Connor, Thomas R; Mahenthiralingam, Eshwar

2018-01-01

Abstract Pseudomonas aeruginosa is a common contaminant associated with product recalls in the home and personal care industry. Preservation systems are used to prevent spoilage and protect consumers, but greater knowledge is needed of preservative resistance mechanisms used by P. aeruginosa contaminants. We aimed to identify genetic pathways associated with preservative exposure by using an industrial P. aeruginosa strain and implementing RNA-Seq to understand gene expression changes in response to industry relevant conditions. The consistent differential expression of five genetic pathways during exposure to multiple industrial growth conditions associated with benzisothiazolone (BIT) and phenoxyethanol (POE) preservatives, and a laundry detergent (LD) formulation, was observed. A MexPQ-OpmE Resistance Nodulation Division efflux pump system was commonly upregulated in response to POE, a combination of BIT and POE, and LD together with BIT. In response to all industry conditions, a putative sialic acid transporter and isoprenoid biosynthesis gnyRDBHAL operon demonstrated consistent upregulation. Two operons phnBA and pqsEDCBA involved in Pseudomonas quinolone signaling production and quorum-sensing were also consistently downregulated during exposure to all the industry conditions. The ability to identify consistently differentially expressed genetic pathways in P. aeruginosa can inform the development of future targeted preservation systems that maintain product safety and minimise resistance development. PMID:29548026

Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

Energy Technology Data Exchange (ETDEWEB)

Bond, Stephen D.

2014-01-01

The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods whos cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana.

Science.gov (United States)

Luo, Y; Widmer, A; Karrenberg, S

2015-02-01

Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall QST-FST comparisons and correlation analyses among pair-wise QST, FST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana.

Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

Science.gov (United States)

Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

2013-08-13

We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

Reverse genetics with animal viruses. NSV reverse genetics

International Nuclear Information System (INIS)

Mebatsion, T.

2005-01-01

New strategies to genetically manipulate the genomes of several important animal pathogens have been established in recent years. This article focuses on the reverse genetics techniques, which enables genetic manipulation of the genomes of non-segmented negative-sense RNA viruses. Recovery of a negative-sense RNA virus entirely from cDNA was first achieved for rabies virus in 1994. Since then, reverse genetic systems have been established for several pathogens of medical and veterinary importance. Based on the reverse genetics technique, it is now possible to design safe and more effective live attenuated vaccines against important viral agents. In addition, genetically tagged recombinant viruses can be designed to facilitate serological differentiation of vaccinated animals from infected animals. The approach of delivering protective immunogens of different pathogens using a single vector was made possible with the introduction of the reverse genetics system, and these novel broad-spectrum vaccine vectors have potential applications in improving animal health in developing countries. (author)

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

Science.gov (United States)

Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or

Genetic population structure of the desert shrub species lycium ruthenicum inferred from chloroplast dna

International Nuclear Information System (INIS)

Chen, H.; Yonezawa, T.

2014-01-01

Lycium ruthenicum (Solananeae), a spiny shrub mostly distributed in the desert regions of north and northwest China, has been shown to exhibit high tolerance to the extreme environment. In this study, the phylogeography and evolutionary history of L. ruthenicum were examined, on the basis of 80 individuals from eight populations. Using the sequence variations of two spacer regions of chloroplast DNA (trnH-psbA and rps16-trnK) , the absence of a geographic component in the chloroplast DNA genetic structure was identified (GST = 0.351, NST = 0.304, NST< GST), which was consisted with the result of SAMOVA, suggesting weak phylogeographic structure of this species. Phylogenetic and network analyses showed that a total of 10 haplotypes identified in the present study clustered into two clades, in which clade I harbored the ancestral haplotypes that inferred two independent glacial refugia in the middle of Qaidam Basin and the western Inner Mongolia. The existence of regional evolutionary differences was supported by GENETREE, which revealed that one of the population in Qaidam Basin and the two populations in Tarim Basin had experienced rapid expansion, and the other populations retained relatively stable population size during the Pleistocene . Given the results of long-term gene flow and pairwise differences, strong gene flow was insufficient to reduce the genetic differentiation among populations or within populations, probably due to the genetic composition containing a common haplotype and the high number of private haplotypes fixed for most of the population. The divergence times of different lineages were consistent with the rapid uplift phases of the Qinghai-Tibetan Plateau and the initiation and expansion of deserts in northern China, suggesting that the origin and evolution of L. ruthenicum were strongly influenced by Quaternary environment changes. (author)

Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time

DEFF Research Database (Denmark)

Tsirogiannis, Constantinos; Sandel, Brody Steven

2014-01-01

The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree and for a set of species R represented by a subset of the leaf nodes of , the MPD of R is equal...... to the average cost of all possible simple paths in that connect pairs of nodes in R. Among other phylogenetic measures, the MPD is used as a tool for deciding if the species of a given group R are closely related. To do this, it is important to compute not only the value of the MPD for this group but also...

Classification of forest-based ecotourism areas in Pocahontas County of West Virginia using GIS and pairwise comparison method

Science.gov (United States)

Ishwar Dhami; Jinyang. Deng

2012-01-01

Many previous studies have examined ecotourism primarily from the perspective of tourists while largely ignoring ecotourism destinations. This study used geographical information system (GIS) and pairwise comparison to identify forest-based ecotourism areas in Pocahontas County, West Virginia. The study adopted the criteria and scores developed by Boyd and Butler (1994...

PTM Along Track Algorithm to Maintain Spacing During Same Direction Pair-Wise Trajectory Management Operations

Science.gov (United States)

Carreno, Victor A.

2015-01-01

Pair-wise Trajectory Management (PTM) is a cockpit based delegated responsibility separation standard. When an air traffic service provider gives a PTM clearance to an aircraft and the flight crew accepts the clearance, the flight crew will maintain spacing and separation from a designated aircraft. A PTM along track algorithm will receive state information from the designated aircraft and from the own ship to produce speed guidance for the flight crew to maintain spacing and separation

Criteria for the singularity of a pairwise l{sub 1}-distance matrix and their generalizations

Energy Technology Data Exchange (ETDEWEB)

D' yakonov, Alexander G [M. V. Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Moscow (Russian Federation)

2012-06-30

We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

Probing genetic diversity to characterize red rot resistance in sugarcane

Energy Technology Data Exchange (ETDEWEB)

Mumtaz, A S; Dure-e-Nayab,; Iqbal, M J; Shinwari, Z.K., E-mail: asmumtaz@qau.edu.pk

2011-10-15

Genetic diversity was assessed in a set of twelve sugarcane genotypes using Random Amplified Polymorphic DNA (RAPD). A total of thirty-two oligo-primers were employed, sixteen of them revealed amplification at 149 loci, out of which 136 were polymorphic. The genotype SPSG-26 showed the highest number of polymorphic loci, followed by CSSG-668 and HSF-242. Pairwise genetic similarity ranged from 67.2% to 83.3%. The UPGMA cluster analysis resolved most of the accessions in two groups. The clustering pattern did not place all resistant varieties in one or related group which depict diverse resistance source in the present set of sugarcane varieties. Ten primers revealed genotype specific bands among which four primers (K07, H02, K10 and F01) produced multiple genotype specific bands that aid genotype identification especially those with red rot resistance. The present study not only provided information on the genetic diversity among the genotypes but also revealed the potential of RAPD-PCR markers for genotype identification and therefore could be utilized in marker assisted selection for red rot resistance in sugarcane. (author)

Linking Diversity and Differentiation

Directory of Open Access Journals (Sweden)

Hans-Rolf Gregorius

2010-03-01

Full Text Available Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective numbers of trait states (types. Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, β-diversity and fixation (inadvertently called differentiation are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered.

Cytochrome b based genetic differentiation of Indian wild pig (Sus scrofa cristatus) and domestic pig (Sus scrofa domestica) and its use in wildlife forensics.

Science.gov (United States)

Gupta, Sandeep Kumar; Kumar, Ajit; Hussain, Syed Ainul; Vipin; Singh, Lalji

2013-06-01

The Indian wild pig (Sus scrofa cristatus) is a protected species and listed in the Indian Wildlife (Protection) Act, 1972. The wild pig is often hunted illegally and sold in market as meat warranting punishment under law. To avoid confusion in identification of these two subspecies during wildlife forensic examinations, we describe genetic differentiation of Indian wild and domestic pigs using a molecular technique. Analysis of sequence generated from the partial fragment (421bp) of mitochondrial DNA (mtDNA) cytochrome b (Cyt b) gene exhibited unambiguous (>3%) genetic variation between Indian wild and domestic pigs. We observed nine forensically informative nucleotide sequence (FINS) variations between Indian wild and domestic pigs. The overall genetic variation described in this study is helpful in forensic identification of the biological samples of wild and domestic pigs. It also helped in differentiating the Indian wild pig from other wild pig races. This study indicates that domestic pigs in India are not descendent of the Indian wild pig, however; they are closer to the other wild pig races found in Asia and Europe. Copyright © 2012 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

Phylogeography, genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences: A systematic review and meta-analysis.

Science.gov (United States)

Spotin, Adel; Moslemzadeh, Hamid Reza; Mahami-Oskouei, Mahmoud; Ahmadpour, Ehsan; Niyyati, Maryam; Hejazi, Seyed Hossein; Memari, Fatemeh; Noori, Jafar

2017-09-01

To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country. We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran. T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F ST ) was from low to high values (0.02433-0.41892). The statistically F ST points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates. An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first

Paravertebral Well-Differentiated Liposarcoma with Low-Grade Osteosarcomatous Component: Case Report with 11-Year Follow-Up, Radiological, Pathological, and Genetic Data, and Literature Review

Directory of Open Access Journals (Sweden)

Nicolas Macagno

2017-01-01

Full Text Available Despite being one of the most frequent soft-tissue sarcomas, well-differentiated liposarcoma has never been reported near the spine. The authors present the case of a 67-year-old man with progressive history of back pain. Physical examination revealed a mass located within the right paravertebral muscles. MR and CT imaging showed a heavily ossified central mass surrounded by a peripheral fatty component. No connection with the underlying bone was detected on imagery and during surgery. After surgical resection, histopathological examination revealed a tumor harboring combined features of well-differentiated liposarcoma and low-grade osteosarcoma. Tumor cells displayed overexpression of MDM2, CDK4, and P16 by immunohistochemistry and CGH revealed amplification of 12q13-15 as the only genetic imbalance. MDM2 FISH analysis was performed but was inconclusive. The pathological, immunohistochemical, and genetic features, the differential diagnoses, and the therapeutic management of this unusual tumor are discussed. No complementary treatment was performed initially. Following first treatment, two recurrences occurred 6 and 9 years later, both displaying histological features similar to the first occurrence. Radiotherapy was started after the second recurrence. Follow-up shows no evidence of disease 11 years after initial diagnosis. This case was unusual due to the paravertebral location of the tumor and its divergent differentiation.

Differential Genetic Associations for Systemic Lupus Erythematosus Based on Anti–dsDNA Autoantibody Production

Science.gov (United States)

Chung, Sharon A.; Taylor, Kimberly E.; Graham, Robert R.; Nititham, Joanne; Lee, Annette T.; Ortmann, Ward A.; Jacob, Chaim O.; Alarcón-Riquelme, Marta E.; Tsao, Betty P.; Harley, John B.; Gaffney, Patrick M.; Moser, Kathy L.; Petri, Michelle; Demirci, F. Yesim; Kamboh, M. Ilyas; Manzi, Susan; Gregersen, Peter K.; Langefeld, Carl D.; Behrens, Timothy W.; Criswell, Lindsey A.

2011-01-01

Systemic lupus erythematosus (SLE) is a clinically heterogeneous, systemic autoimmune disease characterized by autoantibody formation. Previously published genome-wide association studies (GWAS) have investigated SLE as a single phenotype. Therefore, we conducted a GWAS to identify genetic factors associated with anti–dsDNA autoantibody production, a SLE–related autoantibody with diagnostic and clinical importance. Using two independent datasets, over 400,000 single nucleotide polymorphisms (SNPs) were studied in a total of 1,717 SLE cases and 4,813 healthy controls. Anti–dsDNA autoantibody positive (anti–dsDNA +, n = 811) and anti–dsDNA autoantibody negative (anti–dsDNA –, n = 906) SLE cases were compared to healthy controls and to each other to identify SNPs associated specifically with these SLE subtypes. SNPs in the previously identified SLE susceptibility loci STAT4, IRF5, ITGAM, and the major histocompatibility complex were strongly associated with anti–dsDNA + SLE. Far fewer and weaker associations were observed for anti–dsDNA – SLE. For example, rs7574865 in STAT4 had an OR for anti–dsDNA + SLE of 1.77 (95% CI 1.57–1.99, p = 2.0E-20) compared to an OR for anti–dsDNA – SLE of 1.26 (95% CI 1.12–1.41, p = 2.4E-04), with pheterogeneity<0.0005. SNPs in the SLE susceptibility loci BANK1, KIAA1542, and UBE2L3 showed evidence of association with anti–dsDNA + SLE and were not associated with anti–dsDNA – SLE. In conclusion, we identified differential genetic associations with SLE based on anti–dsDNA autoantibody production. Many previously identified SLE susceptibility loci may confer disease risk through their role in autoantibody production and be more accurately described as autoantibody propensity loci. Lack of strong SNP associations may suggest that other types of genetic variation or non-genetic factors such as environmental exposures have a greater impact on susceptibility to anti–dsDNA – SLE. PMID

Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.

Directory of Open Access Journals (Sweden)

Sharon A Chung

2011-03-01

Full Text Available Systemic lupus erythematosus (SLE is a clinically heterogeneous, systemic autoimmune disease characterized by autoantibody formation. Previously published genome-wide association studies (GWAS have investigated SLE as a single phenotype. Therefore, we conducted a GWAS to identify genetic factors associated with anti-dsDNA autoantibody production, a SLE-related autoantibody with diagnostic and clinical importance. Using two independent datasets, over 400,000 single nucleotide polymorphisms (SNPs were studied in a total of 1,717 SLE cases and 4,813 healthy controls. Anti-dsDNA autoantibody positive (anti-dsDNA +, n = 811 and anti-dsDNA autoantibody negative (anti-dsDNA -, n = 906 SLE cases were compared to healthy controls and to each other to identify SNPs associated specifically with these SLE subtypes. SNPs in the previously identified SLE susceptibility loci STAT4, IRF5, ITGAM, and the major histocompatibility complex were strongly associated with anti-dsDNA + SLE. Far fewer and weaker associations were observed for anti-dsDNA - SLE. For example, rs7574865 in STAT4 had an OR for anti-dsDNA + SLE of 1.77 (95% CI 1.57-1.99, p = 2.0E-20 compared to an OR for anti-dsDNA - SLE of 1.26 (95% CI 1.12-1.41, p = 2.4E-04, with p(heterogeneity<0.0005. SNPs in the SLE susceptibility loci BANK1, KIAA1542, and UBE2L3 showed evidence of association with anti-dsDNA + SLE and were not associated with anti-dsDNA - SLE. In conclusion, we identified differential genetic associations with SLE based on anti-dsDNA autoantibody production. Many previously identified SLE susceptibility loci may confer disease risk through their role in autoantibody production and be more accurately described as autoantibody propensity loci. Lack of strong SNP associations may suggest that other types of genetic variation or non-genetic factors such as environmental exposures have a greater impact on susceptibility to anti-dsDNA - SLE.

Where is the line? Phylogeography and secondary contact of western Palearctic coal tits (Periparus ater: Aves, Passeriformes, Paridae)

DEFF Research Database (Denmark)

Pentzold, Stefan; Tritsch, Christian; Martens, Jochen

2013-01-01

-European delimitation of a postulated secondary contact zone among coal tits from the north-eastern Palearctic ater subspecies group and those from the south-western Palearctic abietum group. Generally, between population differentiation was greatest in the Mediterranean range, which was explained by a greater...... separation in multiple Pleistocene refuge areas compared to the lower differentiation across the northeastern Palearctic range. Genetic diversity indices were lowest on Mediterranean island populations as compared to continental populations. Pairwise ˚ST values were highest among island populations....... At the same time, at least four distinct genetic lineages emerged in eastern Eurasia, the nominate ater subspecies group being one of them. Finally, during the Holocene extant wide-range secondary contact in Europe was established via rapid westward range expansion from an East Asian refuge and via...

Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR

Directory of Open Access Journals (Sweden)

Farshid Mahmodi

2014-03-01

Full Text Available Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3 verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4% and (15.5–19.9, respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

Science.gov (United States)

Daily, Jeff

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

Identifying the Academic Rising Stars via Pairwise Citation Increment Ranking

KAUST Repository

Zhang, Chuxu

2017-08-02

Predicting the fast-rising young researchers (the Academic Rising Stars) in the future provides useful guidance to the research community, e.g., offering competitive candidates to university for young faculty hiring as they are expected to have success academic careers. In this work, given a set of young researchers who have published the first first-author paper recently, we solve the problem of how to effectively predict the top k% researchers who achieve the highest citation increment in Δt years. We explore a series of factors that can drive an author to be fast-rising and design a novel pairwise citation increment ranking (PCIR) method that leverages those factors to predict the academic rising stars. Experimental results on the large ArnetMiner dataset with over 1.7 million authors demonstrate the effectiveness of PCIR. Specifically, it outperforms all given benchmark methods, with over 8% average improvement. Further analysis demonstrates that temporal features are the best indicators for rising stars prediction, while venue features are less relevant.

Genetic Diversity and Phylogenetic Relationships of Cytochrome C Oxidase Subunit I in Cimex hemipterus (Hemiptera: Cimicidae) Populations in Malaysia.

Science.gov (United States)

Seri Masran, Siti Nor Ain; Ab Majid, Abdul Hafiz

2017-07-01

The tropical bed bug is scientifically recognized as a significant public health problem. While there is an increased awareness about their resurgence by medical and life science committees, efficient bed bug management still remains unresolved. The solution may soon arise, as information about bed bugs' infestation dynamics and systematics are becoming more distinguishable. Recent developments in studies about bed bugs are based on molecular intervention by determining their genetic variation and phylogeography. The aim of this study is to assess the phylogenetic relationships and genetic diversity among the populations of tropical bed bugs inhabiting Malaysia. A molecular genotyping study was conducted with 22 tropical bed bug populations composed of three individuals per population. The mitochondrial (COI) gene was used as a marker. The data obtained were analyzed using the T-Coffee, ClustalX, MEGA 6.0, and PAUP software. The results showed one main monophyletic clade that consisted of two groups: Ch01 and Ch02. Ch02 consists of samples from the Bandar Hilir population, differing from the other populations studied by one singleton base. However, as there were no changes in the amino acid, this singleton genetic variation was considered to have no effect on genetic differentiation. Ch01 shows similarity with some sequence of Cimex hemipterus (F.) from Thailand, suggesting an international diversity connection. The disparity index apparently suggests that all isolates are homogeneous populations and are supported by the low value of the mean pairwise distance between isolates. This study will increase the knowledge about phylogeographic diversity of tropical bed bug in Malaysia. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic Differentiation within the Puccinia triticina Population in South America and Comparison with the North American Population Suggests Common Ancestry and Intercontinental Migration

Science.gov (United States)

Leaf rust, caused by Puccinia triticina is the most prevalent and widespread disease of wheat in South America. The objective of this study was to determine the number of genetically differentiated groups of P. triticina that are currently present in South America, and to compare the South American ...

Wetlands explain most in the genetic divergence pattern of Oncomelania hupensis.

Science.gov (United States)

Liang, Lu; Liu, Yang; Liao, Jishan; Gong, Peng

2014-10-01

Understanding the divergence patterns of hosts could shed lights on the prediction of their parasite transmission. No effort has been devoted to understand the drivers of genetic divergence pattern of Oncomelania hupensis, the only intermediate host of Schistosoma japonicum. Based on a compilation of two O. hupensis gene datasets covering a wide geographic range in China and an array of geographical distance and environmental dissimilarity metrics built from earth observation data and ecological niche modeling, we conducted causal modeling analysis via simple, partial Mantel test and local polynomial fitting to understand the interactions among isolation-by-distance, isolation-by-environment, and genetic divergence. We found that geography contributes more to genetic divergence than environmental isolation, and among all variables involved, wetland showed the strongest correlation with the genetic pairwise distances. These results suggested that in China, O. hupensis dispersal is strongly linked to the distribution of wetlands, and the current divergence pattern of both O. hupensis and schistosomiasis might be altered due to the changed wetland pattern with the accomplishment of the Three Gorges Dam and the South-to-North water transfer project. Copyright © 2014 Elsevier B.V. All rights reserved.

The genetic network controlling plasma cell differentiation.

Science.gov (United States)

Nutt, Stephen L; Taubenheim, Nadine; Hasbold, Jhagvaral; Corcoran, Lynn M; Hodgkin, Philip D

2011-10-01

Upon activation by antigen, mature B cells undergo immunoglobulin class switch recombination and differentiate into antibody-secreting plasma cells, the endpoint of the B cell developmental lineage. Careful quantitation of these processes, which are stochastic, independent and strongly linked to the division history of the cell, has revealed that populations of B cells behave in a highly predictable manner. Considerable progress has also been made in the last few years in understanding the gene regulatory network that controls the B cell to plasma cell transition. The mutually exclusive transcriptomes of B cells and plasma cells are maintained by the antagonistic influences of two groups of transcription factors, those that maintain the B cell program, including Pax5, Bach2 and Bcl6, and those that promote and facilitate plasma cell differentiation, notably Irf4, Blimp1 and Xbp1. In this review, we discuss progress in the definition of both the transcriptional and cellular events occurring during late B cell differentiation, as integrating these two approaches is crucial to defining a regulatory network that faithfully reflects the stochastic features and complexity of the humoral immune response. 2011 Elsevier Ltd. All rights reserved.

Microsatellite markers to determine population genetic structure in the golden anchovy, Coilia dussumieri.

Science.gov (United States)

Kathirvelpandian, A; Gopalakrishnan, A; Lakra, W S; Krishna, Gopal; Sharma, Rupam; Musammilu, K K; Basheer, V S; Jena, J K

2014-06-01

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.

Genetic structure of populations and differentiation in forest trees

Science.gov (United States)

Raymond P. Guries; F. Thomas Ledig

1981-01-01

Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus) (Chiroptera: Phyllostomidae) of Mexico.

Science.gov (United States)

Romero-Nava, Claudia; León-Paniagua, Livia; Ortega, Jorge

2014-06-01

A limited number of studies have focused on the population genetic structure of vampire bats (Desmous rotundus) in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting) and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North) to Quintana Roo (Southeast). Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise (ST) and R(ST) detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site.

Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus (Chiroptera: Phyllostomidae of Mexico

Directory of Open Access Journals (Sweden)

Claudia Romero-Nava

2014-08-01

Full Text Available A limited number of studies have focused on the population genetic structure of vampire bats (Desmodus rotundus in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North to Quintana Roo (Southeast. Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise F ST and R ST detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site. Rev. Biol. Trop. 62 (2: 659-669. Epub 2014 June 01.

Genetic susceptibility loci, environmental exposures, and Parkinson's disease: a case-control study of gene-environment interactions.

Science.gov (United States)

Chung, Sun Ju; Armasu, Sebastian M; Anderson, Kari J; Biernacka, Joanna M; Lesnick, Timothy G; Rider, David N; Cunningham, Julie M; Ahlskog, J Eric; Frigerio, Roberta; Maraganore, Demetrius M

2013-06-01

Prior studies causally linked mutations in SNCA, MAPT, and LRRK2 genes with familial Parkinsonism. Genome-wide association studies have demonstrated association of single nucleotide polymorphisms (SNPs) in those three genes with sporadic Parkinson's disease (PD) susceptibility worldwide. Here we investigated the interactions between SNPs in those three susceptibility genes and environmental exposures (pesticides application, tobacco smoking, coffee drinking, and alcohol drinking) also associated with PD susceptibility. Pairwise interactions between environmental exposures and 18 variants (16 SNPs and two variable number tandem repeats, or "VNTRs") in SNCA, MAPT and LRRK2, were investigated using data from 1098 PD cases from the upper Midwest, USA and 1098 matched controls. Environmental exposures were assessed using a validated telephone interview script. Five pairwise interactions had uncorrected P-values coffee drinking × MAPT H1/H2 haplotype or MAPT rs16940806, and alcohol drinking × MAPT rs2435211. None of these interactions remained significant after Bonferroni correction. Secondary analyses in strata defined by type of control (sibling or unrelated), sex, or age at onset of the case also did not identify significant interactions after Bonferroni correction. This study documented limited pairwise interactions between established genetic and environmental risk factors for PD; however, the associations were not significant after correction for multiple testing. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microsatellite markers reveal low genetic differentiation among ...

African Journals Online (AJOL)

Ben

Assignment. 1* Khai Apple Game Reserve, Kathu, Northern Cape ... Previous genetic studies on Camelidae in Dubai, Germany, Australia, Kenya and Ethiopia mainly reporting the ... All the biological samples were deposited in the Bio-Bank at.

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.

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Richard R Stein

2015-07-01

Full Text Available Maximum entropy-based inference methods have been successfully used to infer direct interactions from biological datasets such as gene expression data or sequence ensembles. Here, we review undirected pairwise maximum-entropy probability models in two categories of data types, those with continuous and categorical random variables. As a concrete example, we present recently developed inference methods from the field of protein contact prediction and show that a basic set of assumptions leads to similar solution strategies for inferring the model parameters in both variable types. These parameters reflect interactive couplings between observables, which can be used to predict global properties of the biological system. Such methods are applicable to the important problems of protein 3-D structure prediction and association of gene-gene networks, and they enable potential applications to the analysis of gene alteration patterns and to protein design.

Market Competitiveness Evaluation of Mechanical Equipment with a Pairwise Comparisons Hierarchical Model.

Science.gov (United States)

Hou, Fujun

2016-01-01

This paper provides a description of how market competitiveness evaluations concerning mechanical equipment can be made in the context of multi-criteria decision environments. It is assumed that, when we are evaluating the market competitiveness, there are limited number of candidates with some required qualifications, and the alternatives will be pairwise compared on a ratio scale. The qualifications are depicted as criteria in hierarchical structure. A hierarchical decision model called PCbHDM was used in this study based on an analysis of its desirable traits. Illustration and comparison shows that the PCbHDM provides a convenient and effective tool for evaluating the market competitiveness of mechanical equipment. The researchers and practitioners might use findings of this paper in application of PCbHDM.

Genetic and epigenetic factors: Role in male infertility

Directory of Open Access Journals (Sweden)

M B Shamsi

2011-01-01

Full Text Available Genetic factors contribute upto 15%-30% cases of male infertility. Formation of spermatozoa occurs in a sequential manner with mitotic, meiotic, and postmeiotic differentiation phases each of which is controlled by an intricate genetic program. Genes control a variety of physiologic processes, such as hypothalamus-pituitary-gonadal axis, germ cell development, and differentiation. In the era of assisted reproduction technology, it is important to understand the genetic basis of infertility to provide maximum adapted therapeutics and counseling to the couple.