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Sample records for gene flow evidence

  1. Evidence for gene flow between two sympatric mealybug species (Insecta; Coccoidea; Pseudococcidae).

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    Kol-Maimon, Hofit; Ghanim, Murad; Franco, José Carlos; Mendel, Zvi

    2014-01-01

    Occurrence of inter-species hybrids in natural populations might be evidence of gene flow between species. In the present study we found evidence of gene flow between two sympatric, genetically related scale insect species--the citrus mealybug Planococcus citri (Risso) and the vine mealybug Planococcus ficus (Signoret). These species can be distinguished by morphological, behavioral, and molecular traits. We employed the sex pheromones of the two respective species to study their different patterns of male attraction. We also used nuclear ITS2 (internal transcribed spacer 2) and mitochondrial COI (Cytochrome c oxidase sub unit 1) DNA sequences to characterize populations of the two species, in order to demonstrate the outcome of a possible gene flow between feral populations of the two species. Our results showed attraction to P. ficus pheromones of all tested populations of P. citri males but not vice versa. Furthermore, ITS2 sequences revealed the presence of 'hybrid females' among P. citri populations but not among those of P. ficus. 'hybrid females' from P. citri populations identified as P. citri females according to COI sequences. We offer two hypotheses for these results. 1) The occurrence of phenotypic and genotypic traits of P. ficus in P. citri populations may be attributed to both ancient and contemporary gene flow between their populations; and 2) we cannot rule out that an ancient sympatric speciation by which P. ficus emerged from P. citri might have led to the present situation of shared traits between these species. In light of these findings we also discuss the origin of the studied species and the importance of the pherotype phenomenon as a tool with which to study genetic relationships between congener scale insects.

  2. Evidence for gene flow between two sympatric mealybug species (Insecta; Coccoidea; Pseudococcidae.

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    Hofit Kol-Maimon

    Full Text Available Occurrence of inter-species hybrids in natural populations might be evidence of gene flow between species. In the present study we found evidence of gene flow between two sympatric, genetically related scale insect species--the citrus mealybug Planococcus citri (Risso and the vine mealybug Planococcus ficus (Signoret. These species can be distinguished by morphological, behavioral, and molecular traits. We employed the sex pheromones of the two respective species to study their different patterns of male attraction. We also used nuclear ITS2 (internal transcribed spacer 2 and mitochondrial COI (Cytochrome c oxidase sub unit 1 DNA sequences to characterize populations of the two species, in order to demonstrate the outcome of a possible gene flow between feral populations of the two species. Our results showed attraction to P. ficus pheromones of all tested populations of P. citri males but not vice versa. Furthermore, ITS2 sequences revealed the presence of 'hybrid females' among P. citri populations but not among those of P. ficus. 'hybrid females' from P. citri populations identified as P. citri females according to COI sequences. We offer two hypotheses for these results. 1 The occurrence of phenotypic and genotypic traits of P. ficus in P. citri populations may be attributed to both ancient and contemporary gene flow between their populations; and 2 we cannot rule out that an ancient sympatric speciation by which P. ficus emerged from P. citri might have led to the present situation of shared traits between these species. In light of these findings we also discuss the origin of the studied species and the importance of the pherotype phenomenon as a tool with which to study genetic relationships between congener scale insects.

  3. Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

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    Whittaker, Kerry A.; Rynearson, Tatiana A.

    2017-01-01

    The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations (FST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a. Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a, a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time. PMID:28209775

  4. Gene flow between wheat and wild relatives: empirical evidence from Aegilops geniculata, Ae. neglecta and Ae. triuncialis.

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    Arrigo, Nils; Guadagnuolo, Roberto; Lappe, Sylvain; Pasche, Sophie; Parisod, Christian; Felber, François

    2011-09-01

    Gene flow between domesticated species and their wild relatives is receiving growing attention. This study addressed introgression between wheat and natural populations of its wild relatives (Aegilops species). The sampling included 472 individuals, collected from 32 Mediterranean populations of three widespread Aegilops species (Aegilops geniculata, Ae. neglecta and Ae. triuncialis) and compared wheat field borders to areas isolated from agriculture. Individuals were characterized with amplified fragment length polymorphism fingerprinting, analysed through two computational approaches (i.e. Bayesian estimations of admixture and fuzzy clustering), and sequences marking wheat-specific insertions of transposable elements. With this combined approach, we detected substantial gene flow between wheat and Aegilops species. Specifically, Ae. neglecta and Ae. triuncialis showed significantly more admixed individuals close to wheat fields than in locations isolated from agriculture. In contrast, little evidence of gene flow was found in Ae. geniculata. Our results indicated that reproductive barriers have been regularly bypassed during the long history of sympatry between wheat and Aegilops.

  5. Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations

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    Chi C Vu

    2009-01-01

    Full Text Available Abstract Background Previous studies suggested that multiple domestication events in South and South-East Asia (Yunnan and surrounding areas and India have led to the genesis of modern domestic chickens. Ha Giang province is a northern Vietnamese region, where local chickens, such as the H'mong breed, and wild junglefowl coexist. The assumption was made that hybridisation between wild junglefowl and Ha Giang chickens may have occurred and led to the high genetic diversity previously observed. The objectives of this study were i to clarify the genetic structure of the chicken population within the Ha Giang province and ii to give evidence of admixture with G. gallus. A large survey of the molecular polymorphism for 18 microsatellite markers was conducted on 1082 chickens from 30 communes of the Ha Giang province (HG chickens. This dataset was combined with a previous dataset of Asian breeds, commercial lines and samples of Red junglefowl from Thailand and Vietnam (Ha Noï. Measurements of genetic diversity were estimated both within-population and between populations, and a step-by-step Bayesian approach was performed on the global data set. Results The highest value for expected heterozygosity (> 0.60 was found in HG chickens and in the wild junglefowl populations from Thailand. HG chickens exhibited the highest allelic richness (mean A = 2.9. No significant genetic subdivisions of the chicken population within the Ha Giang province were found. As compared to other breeds, HG chickens clustered with wild populations. Furthermore, the neighbornet tree and the Bayesian clustering analysis showed that chickens from 4 communes were closely related to the wild ones and showed an admixture pattern. Conclusion In the absence of any population structuring within the province, the H'mong chicken, identified from its black phenotype, shared a common gene pool with other chickens from the Ha Giang population. The large number of alleles shared exclusively

  6. Gene flow among different taxonomic units: evidence from nuclear and cytoplasmic markers in Cedrus plantation forests.

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    Fady, B; Lefèvre, F; Reynaud, M; Vendramin, G G; Bou Dagher-Kharrat, M; Anzidei, M; Pastorelli, R; Savouré, A; Bariteau, M

    2003-10-01

    Hybridization and introgression are important natural evolutionary processes that can be successfully investigated using molecular markers and open- and controlled-pollinated progeny. In this study, we collected open-pollinated seeds from Cedrus atlantica, Cedrus libani and C. libani x C. atlantica hybrids from three French-plantation forests. We also used pollen from C. libani and Cedrus brevifolia to pollinate C. atlantica trees. The progeny were analyzed using three different types of molecular markers: RAPDs, AFLPs and cpSSRs. Chloroplast DNA was found to be paternally inherited in Cedrus from the progeny of controlled-crosses. Heteroplasmy, although possible, could not be undoubtedly detected. There was no indication of strong reproductive isolating barriers among the three Mediterranean Cedrus taxa. Gene flow between C. atlantica and C. libani accounted for 67 to 81% of viable open-pollinated seedlings in two plantation forests. We propose that Mediterranean Cedrus taxa should be considered as units of a single collective species comprising two regional groups, North Africa and the Middle East. We recommend the use of cpSSRs for monitoring gene flow between taxa in plantation forests, especially in areas where garden specimens of one species are planted in the vicinity of selected seed-stands and gene-conservation reserves of another species.

  7. Localizing F(ST) outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow.

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    Via, Sara; Conte, Gina; Mason-Foley, Casey; Mills, Kelly

    2012-11-01

    Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing F(ST) outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between-population recombination and gene exchange are reduced over large 'divergence hitchhiking' (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of F(ST) outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation-with-gene-flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence. © 2012 Blackwell Publishing Ltd.

  8. Genomic evidence of rapid, global-scale gene flow in a Sulfolobus species.

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    Mao, Dominic; Grogan, Dennis

    2012-08-01

    Local populations of Sulfolobus islandicus diverge genetically with geographical separation, and this has been attributed to restricted transfer of propagules imposed by the unfavorable spatial distribution of acidic geothermal habitat. We tested the generality of genetic divergence with distance in Sulfolobus species by analyzing genomes of Sulfolobus acidocaldarius drawn from three populations separated by more than 8000 km. In sharp contrast to S. islandicus, the geographically diverse S. acidocaldarius genomes proved to be nearly identical. We could not link the difference in genome conservation between the two species to a corresponding difference in genome stability or ecological factors affecting propagule dispersal. The results provide the first evidence that genetic isolation of local populations does not result primarily from properties intrinsic to Sulfolobus and the severe discontinuity of its geothermal habitat, but varies with species, and thus may reflect biotic interactions that act after propagule dispersal.

  9. Evidence for landscape-level, pollen-mediated gene flow from genetically modified creeping bentgrass with CP4 EPSPS as a marker

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    Watrud, L.S.; Lee, E.H.; Fairbrother, A.; Burdick, C.; Reichman, J.R.; Bollman, M.; Storm, M.; King, G.; Van De Water, Peter K.

    2004-01-01

    Sampling methods and results of a gene flow study are described that will be of interest to plant scientists, evolutionary biologists, ecologists, and stakeholders assessing the environmental safety of transgenic crops. This study documents gene flow on a landscape level from creeping bentgrass (Agrostis stolonifera L.), one of the first wind-pollinated, perennial, and highly outcrossing transgenic crops being developed for commercial use. Most of the gene flow occurred within 2 km in the direction of prevailing winds. The maximal gene flow distances observed were 21 km and 14 km in sentinel and resident plants, respectively, that were located in primarily nonagronomic habitats. The selectable marker used in these studies was the CP4 EPSPS gene derived from Agrobacterium spp. strain CP4 that encodes 5-enol-pyruvylshikimate-3-phosphate synthase and confers resistance to glyphosate herbicide. Evidence for gene flow to 75 of 138 sentinel plants of A. stolonifera and to 29 of 69 resident Agrostis plants was based on seedling progeny survival after spraying with glyphosate in greenhouse assays and positive TraitChek, PCR, and sequencing results. Additional studies are needed to determine whether introgression will occur and whether it will affect the ecological fitness of progeny or the structure of plant communities in which transgenic progeny may become established.

  10. EVIDENCE FOR LANDSCAPE LEVEL, POLLEN-MEDIATED GENE FLOW FROM CREEPING BENTGRASS WITH CP4 EPSPS AS A MARKER

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    In a landscape level study, gene flow via pollen was tracked from multiple source fields of genetically modified (GM) herbicide resistant creeping bentgrass (Agrostis stolonifera L.) to 75 of 138 sentinel plants of A. stolonifera and to 29 of 69 resident populations of Agrostis s...

  11. Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flow.

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    Martin, J; Guryev, V; Blinov, A

    2002-10-01

    Phylogenetic analysis of DNA sequences from mitochondrial (mt) genes (Cytochrome b and Cytochrome oxidase I) and one nuclear gene (globin 2b) was used for the investigation of Nearctic and Palearctic populations representing four Chironomus species of the subgenus Camptochironomus, namely C. biwaprimus, C. pallidivittatus, C. tentans sensu stricto and C. dilutus (the last two species constitute Holarctic C. tentans sensu lato). Phenograms constructed on the basis of mt sequences were not congruent with trees based on nuclear genes, or with morphological and cytological data. The mt tree divided the populations by continental region, rather than by the species groupings recognized by the other data sets. The incongruence is explained by mt gene flow resulting from hybridization between the sympatric species on each continent. Calculation of divergence times, based on the sequence data, suggest that C. tentans (s.l.) and C. pallidivittatus have both been in North America for about 2.5 My.

  12. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.

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    Frantz, Laurent A F; Schraiber, Joshua G; Madsen, Ole; Megens, Hendrik-Jan; Cagan, Alex; Bosse, Mirte; Paudel, Yogesh; Crooijmans, Richard P M A; Larson, Greger; Groenen, Martien A M

    2015-10-01

    Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

  13. Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae

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    von der Heyden Sophie

    2008-12-01

    Full Text Available Abstract Background Oceanography and life-history characteristics are known to influence the genetic structure of marine species, however the relative role that these factors play in shaping phylogeographic patterns remains unresolved. The population genetic structure of the endemic, rocky shore dwelling Caffrogobius caffer was investigated across a known major oceanographic barrier, Cape Agulhas, which has previously been shown to strongly influence genetic structuring of South African rocky shore and intertidal marine organisms. Given the variable and dynamic oceanographical features of the region, we further sought to test how the pattern of gene flow between C. caffer populations is affected by the dominant Agulhas and Benguela current systems of the southern oceans. Results The variable 5' region of the mtDNA control region was amplified for 242 individuals from ten localities spanning the distributional range of C. caffer. Fifty-five haplotypes were recovered and in stark contrast to previous phylogeographic studies of South African marine species, C. caffer showed no significant population genetic structuring along 1300 km of coastline. The parsimony haplotype network, AMOVA and SAMOVA analyses revealed panmixia. Coalescent analyses reveal that gene flow in C. caffer is strongly asymmetrical and predominantly affected by the Agulhas Current. Notably, there was no gene flow between the east coast and all other populations, although all other analyses detect no significant population structure, suggesting a recent divergence. The mismatch distribution suggests that C. caffer underwent a population expansion at least 14 500 years ago. Conclusion We propose several possible life-history adaptations that could have enabled C. caffer to maintain gene flow across its distributional range, including a long pelagic larval stage. We have shown that life-history characteristics can be an important contributing factor to the phylogeography of marine

  14. Evidence for homosexuality gene

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    Pool, R.

    1993-07-16

    A genetic analysis of 40 pairs of homosexual brothers has uncovered a region on the X chromosome that appears to contain a gene or genes for homosexuality. When analyzing the pedigrees of homosexual males, the researcheres found evidence that the trait has a higher likelihood of being passed through maternal genes. This led them to search the X chromosome for genes predisposing to homosexuality. The researchers examined the X chromosomes of pairs of homosexual brothers for regions of DNA that most or all had in common. Of the 40 sets of brothers, 33 shared a set of five markers in the q28 region of the long arm of the X chromosome. The linkage has a LOD score of 4.0, which translates into a 99.5% certainty that there is a gene or genes in this area that predispose males to homosexuality. The chief researcher warns, however, that this one site cannot explain all instances of homosexuality, since there were some cases where the trait seemed to be passed paternally. And even among those brothers where there was no evidence that the trait was passed paternally, seven sets of brothers did not share the Xq28 markers. It seems likely that homosexuality arises from a variety of causes.

  15. Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow.

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    Egan, Scott P; Ragland, Gregory J; Assour, Lauren; Powell, Thomas H Q; Hood, Glen R; Emrich, Scott; Nosil, Patrik; Feder, Jeffrey L

    2015-08-01

    Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence. © 2015 The Authors Ecology Letters published by John Wiley & Sons Ltd and CNRS.

  16. Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers.

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    Ben Romdhane, Meriam; Riahi, Leila; Selmi, Ayet; Zoghlami, Nejia

    2016-01-01

    This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  17. The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions

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    Stoneking Mark

    2010-03-01

    Full Text Available Abstract Background The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12. Results Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe. Conclusions As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.

  18. The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions.

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    Athanasiadis, Georgios; González-Pérez, Emili; Esteban, Esther; Dugoujon, Jean-Michel; Stoneking, Mark; Moral, Pedro

    2010-03-27

    The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12). Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe. As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.

  19. Genomics of local adaptation with gene flow.

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    Tigano, Anna; Friesen, Vicki L

    2016-05-01

    Gene flow is a fundamental evolutionary force in adaptation that is especially important to understand as humans are rapidly changing both the natural environment and natural levels of gene flow. Theory proposes a multifaceted role for gene flow in adaptation, but it focuses mainly on the disruptive effect that gene flow has on adaptation when selection is not strong enough to prevent the loss of locally adapted alleles. The role of gene flow in adaptation is now better understood due to the recent development of both genomic models of adaptive evolution and genomic techniques, which both point to the importance of genetic architecture in the origin and maintenance of adaptation with gene flow. In this review, we discuss three main topics on the genomics of adaptation with gene flow. First, we investigate selection on migration and gene flow. Second, we discuss the three potential sources of adaptive variation in relation to the role of gene flow in the origin of adaptation. Third, we explain how local adaptation is maintained despite gene flow: we provide a synthesis of recent genomic models of adaptation, discuss the genomic mechanisms and review empirical studies on the genomics of adaptation with gene flow. Despite predictions on the disruptive effect of gene flow in adaptation, an increasing number of studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow.

  20. Targeted gene flow for conservation.

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    Kelly, Ella; Phillips, Ben L

    2016-04-01

    Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre-adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species' range there may be long-standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens.

  1. No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola, Violaceae).

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    Migdałek, G; Nowak, J; Saługa, M; Cieślak, E; Szczepaniak, M; Ronikier, M; Marcussen, T; Słomka, A; Kuta, E

    2017-07-01

    Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations. For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH-psbA. Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species-specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among-population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana. The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  2. Gene flow from glyphosate-resistant crops.

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    Mallory-Smith, Carol; Zapiola, Maria

    2008-04-01

    Gene flow from transgenic glyphosate-resistant crops can result in the adventitious presence of the transgene, which may negatively impact markets. Gene flow can also produce glyphosate-resistant plants that may interfere with weed management systems. The objective of this article is to review the gene flow literature as it pertains to glyphosate-resistant crops. Gene flow is a natural phenomenon not unique to transgenic crops and can occur via pollen, seed and, in some cases, vegetative propagules. Gene flow via pollen can occur in all crops, even those that are considered to be self-pollinated, because all have low levels of outcrossing. Gene flow via seed or vegetative propagules occurs when they are moved naturally or by humans during crop production and commercialization. There are many factors that influence gene flow; therefore, it is difficult to prevent or predict. Gene flow via pollen and seed from glyphosate-resistant canola and creeping bentgrass fields has been documented. The adventitious presence of the transgene responsible for glyphosate resistance has been found in commercial seed lots of canola, corn and soybeans. In general, the glyphosate-resistant trait is not considered to provide an ecological advantage. However, regulators should consider the examples of gene flow from glyphosate-resistant crops when formulating rules for the release of crops with traits that could negatively impact the environment or human health.

  3. Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow.

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    Nyakaana, S; Arctander, P

    1999-07-01

    A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.

  4. Mitochondrial population structure and post-glacial dispersal of longnose sucker Catostomus catostomus in Labrador, Canada: evidence for multiple refugial origins and limited ongoing gene flow.

    Science.gov (United States)

    Langille, B L; Perry, R; Keefe, D; Barker, O; Marshall, H D

    2016-08-01

    Two hundred and eighty-seven longnose sucker Catostomus catostomus were collected from 14 lakes in Labrador, 52 from three lakes in Ontario, 43 from two lakes in British Columbia and 32 from a lake in Yukon; a total of 414 in all. The resulting 34 haplotypes (20 in Labrador) contained moderate haplotypic diversity (h = 0·657) and relatively low nucleotide diversity (π = 3·730 × 10(-3) . Mean ϕST (0·453, P < 0·05) over all populations revealed distinct genetic structuring among C. catostomus populations across Canada, based on province, which was validated by the analysis and spatial analysis of molecular variance (c. 80% variation between provinces). These results probably reflect the historical imprint of recolonization from different refugia and possibly indicate limited ongoing gene flow within provinces. A haplotype network revealed one major and two minor clades within Labrador that were assigned to the Atlantic, Beringian and Mississippian refugia, respectively, with tests of neutrality and mismatch distribution indicative of a recent population expansion in Labrador, dated between c. 3500 and 8300 years ago.

  5. Genomic evidence for adaptation by gene duplication.

    Science.gov (United States)

    Qian, Wenfeng; Zhang, Jianzhi

    2014-08-01

    Gene duplication is widely believed to facilitate adaptation, but unambiguous evidence for this hypothesis has been found in only a small number of cases. Although gene duplication may increase the fitness of the involved organisms by doubling gene dosage or neofunctionalization, it may also result in a simple division of ancestral functions into daughter genes, which need not promote adaptation. Hence, the general validity of the adaptation by gene duplication hypothesis remains uncertain. Indeed, a genome-scale experiment found similar fitness effects of deleting pairs of duplicate genes and deleting individual singleton genes from the yeast genome, leading to the conclusion that duplication rarely results in adaptation. Here we contend that the above comparison is unfair because of a known duplication bias among genes with different fitness contributions. To rectify this problem, we compare homologous genes from the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. We discover that simultaneously deleting a duplicate gene pair in S. cerevisiae reduces fitness significantly more than deleting their singleton counterpart in S. pombe, revealing post-duplication adaptation. The duplicates-singleton difference in fitness effect is not attributable to a potential increase in gene dose after duplication, suggesting that the adaptation is owing to neofunctionalization, which we find to be explicable by acquisitions of binary protein-protein interactions rather than gene expression changes. These results provide genomic evidence for the role of gene duplication in organismal adaptation and are important for understanding the genetic mechanisms of evolutionary innovation.

  6. The flow of gene expression.

    Science.gov (United States)

    Misteli, Tom

    2004-03-01

    Gene expression is a highly interconnected multistep process. A recent meeting in Iguazu Falls, Argentina, highlighted the need to uncover both the molecular details of each single step as well as the mechanisms of coordination among processes in order to fully understand the expression of genes.

  7. Polyphyly and gene flow between non-sibling Heliconius species

    Directory of Open Access Journals (Sweden)

    Jiggins Chris D

    2006-04-01

    Full Text Available Abstract Background The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae, whose distributions overlap in Central and Northwestern South America. Results In these taxa, we sequenced 30–45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII, and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi, mannose-6-phosphate isomerase (Mpi and cubitus interruptus (Ci genes. A fifth gene, dopa decarboxylase (Ddc produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. Conclusion Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Müllerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

  8. Chapter 2: Genetic Variability in Nuclear Ribosomal and Chloroplast DNA in Utah (Juniperus Osteosperma) and Western (J. Occidentalis) Juniper (Cupressaceae): Evidence for Interspecific Gene Flow1

    Energy Technology Data Exchange (ETDEWEB)

    Terry, Randall G.; Tausch, Robin J.; Nowak, Robert S.

    1998-02-14

    Early studies of evolutionary change in chloroplast DNA indicated limited variability within species. This finding has been attributed to relatively low rates of sequence evolution and has been maintained as justification for the lack of intraspecific sampling in studies examining, relationships at the species level and above. However, documentation of intraspecific variation in cpDNA has become increasingly common and has been attributed in many cases to ''chloroplast capture'' following genetic exchange across species boundaries. Rleseberg and Wendel (1993) list 37 cases of proposed hybridization in plants that include intraspecific variation in cpDNA, 24 (65%) of which they considered to be probable instances of introgression. Rieseberg (1995) suspected that a review of the literature at that time would reveal over 100 cases of intraspecific variation in CPDNA that could be attributed to hybridization and introgression. That intraspecific variation in cpDNA is potentially indicative of hybridization is founded on the expectation that slowly evolving loci or genomes will produce greater molecular variation between than within species. In cases where a species is polymorphic for CPDNA and at least one of the molecular variants is diagnostic for a second species, interspecific hybridization is a plausible explanation. Incongruence between relationships suggested by cpDNA variation and those supported by other types of data (e.g., morphology or molecular data from an additional locus) provides additional support for introgression. One aspect of hybridization in both animals and plants that has become increasingly evident is incongruence in the phylogenetic and geographic distribution of cytoplasmic and nuclear markers. In most cases cytoplasmic introgression appears to be more pervasive than nuclear exchange. This discordance appears attributable to several factors including differences in the mutation rate, number of effective alleles, and modes

  9. On the relation between gene flow theory and genetic gain

    Directory of Open Access Journals (Sweden)

    Woolliams John A

    2000-01-01

    Full Text Available Abstract In conventional gene flow theory the rate of genetic gain is calculated as the summed products of genetic selection differential and asymptotic proportion of genes deriving from sex-age groups. Recent studies have shown that asymptotic proportions of genes predicted from conventional gene flow theory may deviate considerably from true proportions. However, the rate of genetic gain predicted from conventional gene flow theory was accurate. The current note shows that the connection between asymptotic proportions of genes and rate of genetic gain that is embodied in conventional gene flow theory is invalid, even though genetic gain may be predicted correctly from it.

  10. Less pollen-mediated gene flow for more signatures of glacial lineages: congruent evidence from balsam fir cpDNA and mtDNA for multiple refugia in eastern and central North America.

    Directory of Open Access Journals (Sweden)

    Benjamin Cinget

    Full Text Available The phylogeographic structure and postglacial history of balsam fir (Abies balsamea, a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA and chloroplast DNA (cpDNA markers. Genetic structure among 107 populations (mtDNA data and 75 populations (cpDNA data was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only, but also for cpDNA (dispersed by seeds and pollen, indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.

  11. Less pollen-mediated gene flow for more signatures of glacial lineages: congruent evidence from balsam fir cpDNA and mtDNA for multiple refugia in eastern and central North America.

    Science.gov (United States)

    Cinget, Benjamin; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-01-01

    The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.

  12. Evidence based selection of housekeeping genes.

    Directory of Open Access Journals (Sweden)

    Hendrik J M de Jonge

    Full Text Available For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes (reference or internal control genes is required. It is known that commonly used housekeeping genes (e.g. ACTB, GAPDH, HPRT1, and B2M vary considerably under different experimental conditions and therefore their use for normalization is limited. We performed a meta-analysis of 13,629 human gene array samples in order to identify the most stable expressed genes. Here we show novel candidate housekeeping genes (e.g. RPS13, RPL27, RPS20 and OAZ1 with enhanced stability among a multitude of different cell types and varying experimental conditions. None of the commonly used housekeeping genes were present in the top 50 of the most stable expressed genes. In addition, using 2,543 diverse mouse gene array samples we were able to confirm the enhanced stability of the candidate novel housekeeping genes in another mammalian species. Therefore, the identified novel candidate housekeeping genes seem to be the most appropriate choice for normalizing gene expression data.

  13. Time to get moving: assisted gene flow of forest trees.

    Science.gov (United States)

    Aitken, Sally N; Bemmels, Jordan B

    2016-01-01

    Geographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a 'local is best' seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of clines. The maintenance of local adaptation despite high gene flow suggests selection for local adaptation to climate is strong. Concerns over maladaptation resulting from climate change have motivated many new genecological and population genomics studies; however, few jurisdictions have implemented assisted gene flow (AGF), the translocation of pre-adapted individuals to facilitate adaptation of planted forests to climate change. Here, we provide evidence that temperate tree species show clines along climatic gradients sufficiently similar for average patterns or climate models to guide AGF in the absence of species-specific knowledge. Composite provenancing of multiple seed sources can be used to increase diversity and buffer against future climate uncertainty. New knowledge will continue to refine and improve AGF as climates warm further.

  14. Hidden histories of gene flow in highland birds revealed with genomic markers.

    Science.gov (United States)

    Zarza, Eugenia; Faircloth, Brant C; Tsai, Whitney L E; Bryson, Robert W; Klicka, John; McCormack, John E

    2016-10-01

    Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation.

  15. Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications.

    Science.gov (United States)

    Aketarawong, Nidchaya; Isasawin, Siriwan; Thanaphum, Sujinda

    2014-06-14

    Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia. Basic genetic variations were not significantly different among forms, populations, and geographical areas (P > 0.05). Nonetheless, two sets of microsatellite markers showed significantly different levels of polymorphisms. Genetic differentiation between intra- and inter-specific differences was significant, but low. Seventeen populations revealed three hypothetical genetic clusters (K = 3) regardless of forms and geographical areas. The genetic structure of sympatric populations slightly changed during the different years of collection. Recent gene flow (m ≥ 0.10) was frequently detected whether samples were sympatric or allopatric. Ninety-five of 379 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. As a consequence of substantial migration, no significant correlation between genetic and geographic distances was detected (R2 = 0.056, P = 0.650). According to the 12 microsatellite variations, weak population structure and recent gene flow suggest that there is no status for cryptic species between B. dorsalis s.s. and B

  16. Experimental evidence of conformal invariance in soap film turbulent flows

    CERN Document Server

    Thalabard, S; Artana, G; Mininni, P D; Pouquet, A

    2010-01-01

    We present experimental evidence of statistical conformal invariance in isocontours of fluid thickness in experiments of two-dimensional turbulence using soap films. A Schlieren technique is used to visualize regions of the flow with constant film thickness, and association of isocontours with Schramm-L\\"owner evolution (SLE) is used to identify conformal invariance. In experiments where an inverse energy cascade develops, statistical evidence is consistent with such an association. The diffusivity of the associated one-dimensional Brownian process is close to 8/3, a value previously identified in isocontours of vorticity in high-resolution numerical simulations of two-dimensional turbulence (D. Bernard et al., Nature Phys. 2, 124, 2006). In experiments where the inverse energy cascade is not sufficiently developed, no statistical evidence of conformal invariance is found.

  17. Extensive gene flow over Europe and possible speciation

    Energy Technology Data Exchange (ETDEWEB)

    VINCENOT, Dr. LUCIE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; NARA, Dr. KAZUHIDE [Department of Natural Environmental Studies, The University of Tokyo, Japan; STHULTZ, CHRISTOPHER [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; Labbe, Jessy L [ORNL; DUBOIS, MARIE-PIERRE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; TEDERSOO, LEHO [University of Tartu, Estonia; Martin, Francis [INRA, Nancy, France; SELOSSE, Dr. MARC-ANDRE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France

    2012-01-01

    Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (104 km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average FST = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (FST = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.

  18. Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of

  19. Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-08

    With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  20. Speciation and gene flow between snails of opposite chirality.

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    Angus Davison

    2005-09-01

    Full Text Available Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent "single-gene speciation" or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be

  1. Evidence for mitochondrial genetic control of autosomal gene expression.

    Science.gov (United States)

    Kassam, Irfahan; Qi, Tuan; Lloyd-Jones, Luke; Holloway, Alexander; Jan Bonder, Marc; Henders, Anjali K; Martin, Nicholas G; Powell, Joseph E; Franke, Lude; Montgomery, Grant W; Visscher, Peter M; McRae, Allan F

    2016-10-18

    The mitochondrial and nuclear genomes coordinate and co-evolve in eukaryotes in order to adapt to environmental changes. Variation in the mitochondrial genome is capable of affecting expression of genes on the nuclear genome. Sex-specific mitochondrial genetic control of gene expression has been demonstrated in Drosophila melanogaster, where males were found to drive most of the total variation in gene expression. This has potential implications for male-related health and disease resulting from variation in mtDNA solely inherited from the mother. We used a family-based study comprised of 47,323 gene expression probes and 78 mitochondrial SNPs (mtSNPs) from n = 846 individuals to examine the extent of mitochondrial genetic control of gene expression in humans. This identified 15 significant probe-mtSNP associations (P[Formula: see text]) corresponding to 5 unique genes on the mitochondrial and nuclear genomes, with three of these genes corresponding to mitochondrial genetic control of gene expression in the nuclear genome. The associated mtSNPs for three genes (one cis and two trans associations) were replicated (P expression in any of these five probes. Sex-specific effects were examined by applying our analysis to males and females separately and testing for differences in effect size. The MEST gene was identified as having the most significantly different effect sizes across the sexes (P [Formula: see text]). MEST was similarly expressed in males and females with the G allele; however, males with the C allele are highly expressed for MEST, while females show no expression of the gene. This study provides evidence for the mitochondrial genetic control of expression of several genes in humans, with little evidence found for sex-specific effects.

  2. Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient

    Science.gov (United States)

    Funk, W. C.; Murphy, M.A.; Hoke, K. L.; Muths, Erin L.; Amburgey, Staci M.; Lemmon, Emily M.; Lemmon, A. R.

    2016-01-01

    Evolutionary theory predicts that divergent selection pressures across elevational gradients could cause adaptive divergence and reproductive isolation in the process of ecological speciation. Although there is substantial evidence for adaptive divergence across elevation, there is less evidence that this restricts gene flow. Previous work in the boreal chorus frog (Pseudacris maculata) has demonstrated adaptive divergence in morphological, life history and physiological traits across an elevational gradient from approximately 1500–3000 m in the Colorado Front Range, USA. We tested whether this adaptive divergence is associated with restricted gene flow across elevation – as would be expected if incipient speciation were occurring – and, if so, whether behavioural isolation contributes to reproductive isolation. Our analysis of 12 microsatellite loci in 797 frogs from 53 populations revealed restricted gene flow across elevation, even after controlling for geographic distance and topography. Calls also varied significantly across elevation in dominant frequency, pulse number and pulse duration, which was partly, but not entirely, due to variation in body size and temperature across elevation. However, call variation did not result in strong behavioural isolation: in phonotaxis experiments, low-elevation females tended to prefer an average low-elevation call over a high-elevation call, and vice versa for high-elevation females, but this trend was not statistically significant. In summary, our results show that adaptive divergence across elevation restricts gene flow in P. maculata, but the mechanisms for this potential incipient speciation remain open.

  3. Local evolution of pyrethroid resistance offsets gene flow among Aedes aegypti collections in Yucatan State, Mexico.

    Science.gov (United States)

    Saavedra-Rodriguez, Karla; Beaty, Meaghan; Lozano-Fuentes, Saul; Denham, Steven; Garcia-Rejon, Julian; Reyes-Solis, Guadalupe; Machain-Williams, Carlos; Loroño-Pino, Maria Alba; Flores-Suarez, Adriana; Ponce-Garcia, Gustavo; Beaty, Barry; Eisen, Lars; Black, William C

    2015-01-01

    The mosquito Aedes aegypti is the major vector of the four serotypes of dengue virus (DENV1-4). Previous studies have shown that Ae. aegypti in Mexico have a high effective migration rate and that gene flow occurs among populations that are up to 150 km apart. Since 2000, pyrethroids have been widely used for suppression of Ae. aegypti in cities in Mexico. In Yucatan State in particular, pyrethroids have been applied in and around dengue case households creating an opportunity for local selection and evolution of resistance. Herein, we test for evidence of local adaptation by comparing patterns of variation among 27 Ae. aegypti collections at 13 single nucleotide polymorphisms (SNPs): two in the voltage-gated sodium channel gene para known to confer knockdown resistance, three in detoxification genes previously associated with pyrethroid resistance, and eight in putatively neutral loci. The SNPs in para varied greatly in frequency among collections, whereas SNPs at the remaining 11 loci showed little variation supporting previous evidence for extensive local gene flow. Among Ae. aegypti in Yucatan State, Mexico, local adaptation to pyrethroids appears to offset the homogenizing effects of gene flow.

  4. Local Evolution of Pyrethroid Resistance Offsets Gene Flow Among Aedes aegypti Collections in Yucatan State, Mexico

    Science.gov (United States)

    Saavedra-Rodriguez, Karla; Beaty, Meaghan; Lozano-Fuentes, Saul; Denham, Steven; Garcia-Rejon, Julian; Reyes-Solis, Guadalupe; Machain-Williams, Carlos; Loroño-Pino, Maria Alba; Flores-Suarez, Adriana; Ponce-Garcia, Gustavo; Beaty, Barry; Eisen, Lars; Black, William C.

    2015-01-01

    The mosquito Aedes aegypti is the major vector of the four serotypes of dengue virus (DENV1–4). Previous studies have shown that Ae. aegypti in Mexico have a high effective migration rate and that gene flow occurs among populations that are up to 150 km apart. Since 2000, pyrethroids have been widely used for suppression of Ae. aegypti in cities in Mexico. In Yucatan State in particular, pyrethroids have been applied in and around dengue case households creating an opportunity for local selection and evolution of resistance. Herein, we test for evidence of local adaptation by comparing patterns of variation among 27 Ae. aegypti collections at 13 single nucleotide polymorphisms (SNPs): two in the voltage-gated sodium channel gene para known to confer knockdown resistance, three in detoxification genes previously associated with pyrethroid resistance, and eight in putatively neutral loci. The SNPs in para varied greatly in frequency among collections, whereas SNPs at the remaining 11 loci showed little variation supporting previous evidence for extensive local gene flow. Among Ae. aegypti in Yucatan State, Mexico, local adaptation to pyrethroids appears to offset the homogenizing effects of gene flow. PMID:25371186

  5. Available Evidence on Leber Congenital Amaurosis and Gene Therapy.

    Science.gov (United States)

    Alkharashi, Maan; Fulton, Anne B

    2017-01-01

    Leber congenital amaurosis (LCA) is a group of severe inherited retinal dystrophies that lead to early childhood blindness. In the last decade, interest in LCA has increased as advances in genetics have been applied to better identify, classify, and treat LCA. To date, 23 LCA genes have been identified. Gene replacement in the RPE65 form of LCA represents a major advance in treatment, although limitations have been recognized. In this article, we review the clinical and genetic features of LCA and evaluate the evidence available for gene therapy in RPE65 disease.

  6. Urban land use limits regional bumble bee gene flow.

    Science.gov (United States)

    Jha, Shalene; Kremen, C

    2013-05-01

    Potential declines in native pollinator communities and increased reliance on pollinator-dependent crops have raised concerns about native pollinator conservation and dispersal across human-altered landscapes. Bumble bees are one of the most effective native pollinators and are often the first to be extirpated in human-altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic differentiation and fine-scale relatedness patterns of the yellow-faced bumble bee, Bombus vosnesenskii, to investigate how current and historic habitat composition impact gene flow. We conducted our study across a landscape mosaic of natural, agricultural and urban/suburban habitats, and we show that B. vosnesenskii exhibits low but significant levels of differentiation across the study system (F(ST) = 0.019, D(est) = 0.049). Most importantly, we reveal significant relationships between pairwise F(ST) and resistance models created from contemporary land use maps. Specifically, B. vosnesenskii gene flow is most limited by commercial, industrial and transportation-related impervious cover. Finally, our fine-scale analysis reveals significant but declining relatedness between individuals at the 1-9 km spatial scale, most likely due to local queen dispersal. Overall, our results indicate that B. vosnesenskii exhibits considerable local dispersal and that regional gene flow is significantly limited by impervious cover associated with urbanization.

  7. LONG DISTANCE POLLEN-MEDIATED GENE FLOW FROM CREEPING BENTGRASS

    Science.gov (United States)

    Researchers from USEPA WED have measured gene flow from experimental fields of Roundup? herbicide resistant genetically modified (GM) creeping bentgrass a grass used primarily on golf courses, to compatible non-crop relatives. Using a sampling design based on the estimated time ...

  8. Combining Hierarchical and Associative Gene Ontology Relations with Textual Evidence in Estimating Gene and Gene Product Similarity

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Riensche, Roderick M.; Beagley, Nathaniel; Baddeley, Bob L.; Tratz, Stephen C.; Gregory, Michelle L.

    2007-03-01

    Gene and gene product similarity is a fundamental diagnostic measure in analyzing biological data and constructing predictive models for functional genomics. With the rising influence of the Gene Ontology, two complementary approaches have emerged where the similarity between two genes or gene products is obtained by comparing Gene Ontology (GO) annotations associated with the genes or gene products. One approach captures GO-based similarity in terms of hierarchical relations within each gene subontology. The other approach identifies GO-based similarity in terms of associative relations across the three gene subontologies. We propose a novel methodology where the two approaches can be merged with ensuing benefits in coverage and accuracy, and demonstrate that further improvements can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  9. Increased sensitivity of photosynthesis to antimycin A induced by inactivation of the chloroplast ndhB gene. Evidence for a participation of the NADH-dehydrogenase complex to cyclic electron flow around photosystem I.

    Science.gov (United States)

    Joët, T; Cournac, L; Horvath, E M; Medgyesy, P; Peltier, G

    2001-04-01

    Tobacco (Nicotiana tabacum var Petit Havana) ndhB-inactivated mutants (ndhB-) obtained by plastid transformation (E.M. Horvath, S.O. Peter, T. Joët, D. Rumeau, L. Cournac, G.V. Horvath, T.A. Kavanagh, C. Schäfer, G. Peltier, P. MedgyesyHorvath [2000] Plant Physiol 123: 1337-1350) were used to study the role of the NADH-dehydrogenase complex (NDH) during photosynthesis and particularly the involvement of this complex in cyclic electron flow around photosystem I (PSI). Photosynthetic activity was determined on leaf discs by measuring CO2 exchange and chlorophyll fluorescence quenchings during a dark-to-light transition. In the absence of treatment, both non-photochemical and photochemical fluorescence quenchings were similar in ndhB- and wild type (WT). When leaf discs were treated with 5 microM antimycin A, an inhibitor of cyclic electron flow around PSI, both quenchings were strongly affected. At steady state, maximum photosynthetic electron transport activity was inhibited by 20% in WT and by 50% in ndhB-. Under non-photorespiratory conditions (2% O2, 2,500 microL x L(-1) CO2), antimycin A had no effect on photosynthetic activity of WT, whereas a 30% inhibition was observed both on quantum yield of photosynthesis assayed by chlorophyll fluorescence and on CO2 assimilation in ndhB-. The effect of antimycin A on ndhB- could not be mimicked by myxothiazol, an inhibitor of the mitochondrial cytochrome bc1 complex, therefore showing that it is not related to an inhibition of the mitochondrial electron transport chain but rather to an inhibition of cyclic electron flow around PSI. We conclude to the existence of two different pathways of cyclic electron flow operating around PSI in higher plant chloroplasts. One of these pathways, sensitive to antimycin A, probably involves ferredoxin plastoquinone reductase, whereas the other involves the NDH complex. The absence of visible phenotype in ndhB- plants under normal conditions is explained by the complement of these two

  10. Historical divergence and gene flow: coalescent analyses of mitochondrial, autosomal and sex-linked loci in Passerina buntings.

    Science.gov (United States)

    Carling, Matthew D; Lovette, Irby J; Brumfield, Robb T

    2010-06-01

    Quantifying the role of gene flow during the divergence of closely related species is crucial to understanding the process of speciation. We collected DNA sequence data from 20 loci (one mitochondrial, 13 autosomal, and six sex-linked) for population samples of Lazuli Buntings (Passerina amoena) and Indigo Buntings (Passerina cyanea) (Aves: Cardinalidae) to test explicitly between a strict allopatric speciation model and a model in which divergence occurred despite postdivergence gene flow. Likelihood ratio tests of coalescent-based population genetic parameter estimates indicated a strong signal of postdivergence gene flow and a strict allopatric speciation model was rejected. Analyses of partitioned datasets (mitochondrial, autosomal, and sex-linked) suggest the overall gene flow patterns are driven primarily by autosomal gene flow, as there is no evidence of mitochondrial gene flow and we were unable to reject an allopatric speciation model for the sex-linked data. This pattern is consistent with either a parapatric divergence model or repeated periods of allopatry with gene flow occurring via secondary contact. These results are consistent with the low fitness of female avian hybrids under Haldane's rule and demonstrate that sex-linked loci likely are important in the initial generation of reproductive isolation, not just its maintenance.

  11. No Evidence for Association between Amelogenesis Imperfecta and Candidate Genes

    Directory of Open Access Journals (Sweden)

    M Ghandehari Motlagh

    2009-03-01

    Full Text Available "nBackground: Amelogenesis imperfecta (AI is an inherited tooth disorder. Despite the fact that up to now, several gene muta­tions in MMP20, ENAM, AMELX and KLK4 genes have been reported to be associated with AI, many other genes sug­gested to be involved. The main objective of this study was to find the mutations in three major candidate genes including MMP20, ENAM and KLK4 responsible for AI from three Iranian families with generalized hypoplastic phenotype in all teeth. "nMethods: All exon/intron boundaries of subjected genes were amplified by polymerase chain reaction and subjected to direct sequencing."nResults: One polymorphisms was identified in KLK4 exon 2, in one family a homozygous mutation was found in the third base of codon 22 for serine (TCG>TCT, but not in other families. Although these base substitutions have been occurred in the signaling domain, they do not seem to influence the activity of KLK4 protein."nConclusion: Our results might support the further evidence for genetic heterogeneity; at least, in some AI cases are not caused by a gene in these reported candidate genes.

  12. Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae

    Directory of Open Access Journals (Sweden)

    Jørgensen Marte H

    2011-11-01

    Full Text Available Abstract Background Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. Results Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid A. arenosa to tetraploid A. lyrata and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in A. arenosa and bidirectional in A. lyrata. Conclusions Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus Arabidopsis, we find very different evolutionary fates when it comes to introgression.

  13. Evidence of the role of tick subolesin in gene expression

    Directory of Open Access Journals (Sweden)

    Blouin Edmour F

    2008-08-01

    Full Text Available Abstract Background Subolesin is an evolutionary conserved protein that was discovered recently in Ixodes scapularis as a tick protective antigen and has a role in tick blood digestion, reproduction and development. In other organisms, subolesin orthologs may be involved in the control of developmental processes. Because of the profound effect of subolesin knockdown in ticks and other organisms, we hypothesized that subolesin plays a role in gene expression, and therefore affects multiple cellular processes. The objective of this study was to provide evidence for the role of subolesin in gene expression. Results Two subolesin-interacting proteins were identified and characterized by yeast two-hybrid screen, co-affinity purification and RNA interference (RNAi. The effect of subolesin knockdown on the tick gene expression pattern was characterized by microarray analysis and demonstrated that subolesin RNAi affects the expression of genes involved in multiple cellular pathways. The analysis of subolesin and interacting protein sequences identified regulatory motifs and predicted the presence of conserved protein kinase C (PKC phosphorylation sites. Conclusion Collectively, these results provide evidence that subolesin plays a role in gene expression in ticks.

  14. Interspecific gene flow and maintenance of species integrity in oaks

    Directory of Open Access Journals (Sweden)

    Oliver Gailing

    2014-07-01

    Full Text Available Oak species show a wide variation in morphological and physiological characters, and species boundaries between closely related species are often not clear-cut. Still, despite frequent interspecific gene flow, oaks maintain distinct morphological and physiological adaptations. In sympatric stands, spatial distribution of species with different ecological requirements is not random but constrained by soil and other microenvironmental factors. Pre-zygotic isolation (e.g. cross incompatibilities, asynchrony in flowering, pollen competition and post-zygotic isolation (divergent selection contribute to the maintenance of species integrity in sympatric oak stands. The antagonistic effects of interspecific gene flow and divergent selection are reflected in the low genetic differentiation between hybridizing oak species at most genomic regions interspersed by regions with signatures of divergent selection (outlier regions. In the near future, the availability of high-density genetic linkage maps anchored to scaffolds of a sequenced Q. robur genome will allow to characterize the underlying genes in these outlier regions and their putative role in reproductive isolation between species. Reciprocal transplant experiments of seedlings between parental environments can be used to characterize selection on outlier genes. High transferability of gene-based markers will enable comparative outlier screens in different oak species.

  15. Interspecific gene flow and maintenance of species integrity in oaks

    Directory of Open Access Journals (Sweden)

    Oliver Gailing

    2014-07-01

    Full Text Available Oak species show a wide variation in morphological and physiological characters, and species boundaries between closely related species are often not clear-cut. Still, despite frequent interspecific gene flow, oaks maintain distinct morphological and physiological adaptations. In sympatric stands, spatial distribution of species with different ecological requirements is not random but constrained by soil and other microenvironmental factors. Pre-zygotic isolation (e.g. cross incompatibilities, asynchrony in flowering, pollen competition and post-zygotic isolation (divergent selection contribute to the maintenance of species integrity in sympatric oak stands. The antagonistic effects of interspecific gene flow and divergent selection are reflected in the low genetic differentiation between hybridizing oak species at most genomic regions interspersed by regions with signatures of divergent selection (outlier regions. In the near future, the availability of high-density genetic linkage maps anchored to scaffolds of a sequenced Q. robur genome will allow to characterize the underlying genes in these outlier regions and their putative role in reproductive isolation between species. Reciprocal transplant experiments of seedlings between parental environments can be used to characterize selection on outlier genes. High transferability of gene-based markers will enable comparative outlier screens in different oak species.

  16. Divergence and gene flow in the globally distributed blue-winged ducks

    Science.gov (United States)

    Nelson, Joel; Wilson, Robert E.; McCracken, Kevin G.; Cumming, Graeme; Joseph, Leo; Guay, Patrick-Jean; Peters, Jeffrey

    2016-01-01

    The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence-with-gene-flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue-winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub-lineages, the globally-distributed shoveler group and the New World blue-winged/cinnamon teal group. The blue-winged/cinnamon sub-lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler (A. clypeata) and the more sedentary, African Cape shoveler (A. smithii) into the Australasian shoveler (A. rhynchotis), although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue-winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.

  17. Field evidence for buoyancy-driven water flow in a Sphagnum dominated peat bog

    NARCIS (Netherlands)

    Adema, E.B.; Baaijens, G. J.; van Belle, J.; Rappoldt, C.; Grootjans, A. P.; Smolders, A. J. P.

    2006-01-01

    Nocturnal buoyancy-driven water flow in bogs is proposed as a mechanism to replenish the nutrient availability in the top of the acrotelm. In an earlier paper, we provided evidence for buoyancy-driven water flow on theoretical and experimental grounds. In this paper, field evidence is given for the

  18. Experimental Evidence of Helical Flow in Porous Media

    DEFF Research Database (Denmark)

    Ye, Yu; Chiogna, Gabriele; Cirpka, Olaf A.;

    2015-01-01

    Helical flow leads to deformation of solute plumes and enhances transverse mixing in porous media. We present experiments in which macroscopic helical flow is created by arranging different materials to obtain an anisotropic macroscopic permeability tensor with spatially variable orientation...... mixers, but in porous media....

  19. Gene flow between Atlantic and Pacific Ocean basins in three lineages of deep-sea clams (Bivalvia: Vesicomyidae: Pliocardiinae) and subsequent limited gene flow within the Atlantic

    Science.gov (United States)

    LaBella, Abigail Leavitt; Van Dover, Cindy L.; Jollivet, Didier; Cunningham, Clifford W.

    2017-03-01

    Pliocardiin (vesicomyid) clams rely on microbial symbionts for nutrition and are obligate inhabitants of deep-sea chemosynthetic ecosystems. Unlike many other invertebrate hosts of chemosynthetic microbes, pliocardiin clams are found in every ocean in a variety of reducing habitats, including hydrothermal vents, cold seeps, organic falls and deep-sea fans. The global distribution of pliocardiin clams suggests historical gene flow between ocean basins. We focus on 3 pliocardiin genera-'Pliocardia' I, Calyptogena and Abyssogena-each of which has a pair of sister clades in the Atlantic and Pacific. Our work tests the hypothesis that historical gene flow between the Atlantic and Pacific Oceans within these genera was interrupted by the closure of the Panamanian seaway and tests whether isolation between the ocean basins is the result of vicariance or past colonization. These questions are investigated in the context of fossil evidence, biogeography and phylogenetics. This study revealed a set of substitution rates consistent with other invertebrate studies (μ=0.8%/My/lineage), and a set consistent with much lower rates often attributed to deep-sea organisms (μ=0.3%/My/lineage). Among the Pacific/Atlantic sister pairs, 'Pliocardia' I COI divergence per lineage is intermediate (2.5%), Calyptogena is the highest (6.1%) and Abyssogena the lowest (0.8%). The substitution rates suggest that 'Pliocardia' I and Calyptogena have histories of at least 2.8 My in the Atlantic, with Calyptogena likely older. The slower rate, however, is inconsistent with both the maximum age of the family and several well studied fossils: leaving the faster rate preferred. With the faster rate, the Abyssogena southwardae clade diverged from its Pacific sister clade around 1 Mya, which likely post-dates the closure of the Isthmus of Panama and the opening of the Bering Strait. In light of this recent divergence, we test the previously proposed hypothesis that there is a high level of ongoing gene

  20. The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu.

    Science.gov (United States)

    Clegg, Sonya M; Phillimore, Albert B

    2010-04-12

    Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago.

  1. Sedimentological evidence for debris-flow formation of Martian gullies

    Science.gov (United States)

    de Haas, Tjalling; Hauber, Ernst; Ventra, Dario; Conway, Susan; Kleinhans, Maarten

    2015-04-01

    Gullies are among the youngest landforms formed by liquid water on Mars, and therefore of critical importance in resolving the planet's recent hydrologic and climatic history. The key to estimating the amount of liquid water involved in gully formation is their formative mechanism. Water-free sediment flows, debris flows and fluvial flows, which all require very different amounts of liquid water, contributed to gully formation but their abundance and effectiveness differs greatly between sites. We show that many gullies dominantly formed by debris flows, based on sedimentological analysis of outcrops in gully-fans rather than surficial debris-flow features, which are often degraded beyond recognition by weathering and wind erosion or masked by ice-dust mantling. This resolves the controversy between previously published morphometric analyses implying debris-flow formation and observations of modified fan surfaces often interpreted to have formed by fluvial flows. Furthermore, it shows that deriving formative processes on gullies from surface characteristics can be highly misleading, which should therefore be inferred from multiple approaches, including sedimentological outcrop and morphometric analyses.

  2. Evidence of digenic inheritance in autoinflammation-associated genes

    Indian Academy of Sciences (India)

    VASSOS NEOCLEOUS; STEFANIA BYROU; MEROPI TOUMBA; CONSTANTINA COSTI; CHRISTOS SHAMMAS; CHRISTINA KYRIAKOU; VIOLETTA CHRISTOPHIDOU-ANASTASIADOU; GEORGE A. TANTELES; ADAMOS HADJIPANAYIS; LEONIDAS A. PHYLACTOU

    2016-12-01

    Familial Mediterranean fever (FMF) has traditionally been considered as a monogenic autosomal recessive disorder caused by mutations in the MEFV gene with highest incidence among Mediterranean populations. In a considerable number of patients with typical FMF, only one MEFV mutation was identified and the possibility that more than one autoinflammatory gene may be responsible for their disease was investigated. In the present study, an extensive search for possiblemutations in three hereditary recurrent fever (HRF) genes was performed in 128 MEFV heterozygous Greek–Cypriots clinically diagnosed based on their phenotype with FMF-like disease from a previous study. Sequence analysis was performedfor MVK, TNFRSF1A and NLRP3 genes which is also known to cause HRFs. In total, three patients were identified with heterozygous mutations and a second mutation in an autoinflammatory gene. Two patients carried a MEFVmutation and a NLRP3 mutation, and an additional third carried a MEFV mutation and a TNFRSF1A mutation. Patient 1 carried MEFV p.[Val726Ala] (NM_000243.2:c.2177T>C) and NLRP3 p.[Val198Met] (NM_001243133.1:c.592G>A) variants and patient 2 carried MEFV p.[Glu148Gln] (NM_000243.2:c.442G>C) variant which is of uncertain significance and NLRP3 p.[Arg176Trp] (NM_001243133.1:c.526C>T). Lastly, patient 3 was identified to carry MEFV p.[Met694Val] (NM_000243.2:c.2080A>G) and TNFRSF1A p.[Arg121Gln] (NM_001065.3:c.362G>A) variants. The results from this study indicate that screening of genes known to cause HRFs in patients already identified with a single MEFV mutation, can reveal quite rare but potentially causative mutational combinations at different loci. Such interaction provide further evidence for possible locus–locus interactions and phenotypes resulting from digenic inheritance.

  3. Experimental evidence links volcanic particle characteristics to pyroclastic flow hazard

    Science.gov (United States)

    Dellino, Pierfrancesco; Büttner, Ralf; Dioguardi, Fabio; Doronzo, Domenico M.; La Volpe, Luigi; Mele, Daniela; Sonder, Ingo; Sulpizio, Roberto; Zimanowski, Bernd

    2010-06-01

    Pyroclastic flows represent the most hazardous events of explosive volcanism, one striking example being the famous historical eruption of Vesuvius that destroyed Pompeii (AD 79). Much of our knowledge of the mechanics of pyroclastic flows comes from theoretical models and numerical simulations. Valuable data are also stored in the geological record of past eruptions, including the particles contained in pyroclastic deposits, but the deposit characteristics are rarely used for quantifying the destructive potential of pyroclastic flows. By means of experiments, we validate a model that is based on data from pyroclastic deposits. The model allows the reconstruction of the current's fluid-dynamic behaviour. Model results are consistent with measured values of dynamic pressure in the experiments, and allow the quantification of the damage potential of pyroclastic flows.

  4. Evidence on the dynamics of investment-cash flow sensitivity

    OpenAIRE

    Gautam, Vikash

    2011-01-01

    An important debate in the literature relates to the use of investment-cash flow sensitivity (ICFS) to measure finance constraint faced by firms. This debate is grounded on four prominent issues: a priori sorting of firms, treatment of distressed firms, use of cash flow to represent only internal liquidity of firms and restricting firms to a single regime. In this paper we investigate these issues using a sample of 2676 Indian manufacturing firms over the period 1994 to 2009. We use firm leve...

  5. Contemporary gene flow and mating system of Arabis alpina in a Central European alpine landscape

    OpenAIRE

    Buehler, D.; Graf, R; Holderegger, R; Gugerli, F.

    2017-01-01

    Background and Aims Gene flow is important in counteracting the divergence of populations but also in spreading genes among populations. However, contemporary gene flow is not well understood across alpine landscapes. The aim of this study was to estimate contemporary gene flow through pollen and to examine the realized mating system in the alpine perennial plant, Arabis alpina (Brassicaceae). Methods An entire sub-alpine to alpine landscape of 2 km2 was exhaustively sampled in the Swiss Alps...

  6. Investment, cash flow, and uncertainty : evidence for the Netherlands

    NARCIS (Netherlands)

    Sterken, Elmer; Lensink, Robert; Bo, Hong

    2001-01-01

    Abstract We contribute to the debate on the interpretation of investment-cash flow sensitivities by including uncertainty measures in both a simple theoretical investment model and an empirical illustration for Dutch firm-level data. Using a slightly modified version of the Kaplan-Zingales (1997) mo

  7. Tail dependence and information flow: Evidence from international equity markets

    Science.gov (United States)

    Al Rahahleh, Naseem; Bhatti, M. Ishaq; Adeinat, Iman

    2017-05-01

    Bhatti and Nguyen (2012) used the copula approach to measure the tail dependence between a number of international markets. They observed that some country pairs exhibit only left-tail dependence whereas others show only right-tail. However, the flow of information from uni-dimensional (one-tail) to bi-dimensional (two-tails) between various markets was not accounted for. In this study, we address the flow of information of this nature by using the dynamic conditional correlation (DCC-GARCH) model. More specifically, we use various versions of the DCC models to explain the nexus between the information flow of international equity and to explain the stochastic forward vs. backward dynamics of financial markets based on data for a 15-year period comprising 3,782 observations. We observed that the information flow between the US and Hong Kong markets and between the US and Australian markets are bi-directional. We also observed that the DCC model captures a wider co-movement structure and inter-connectedness compared to the symmetric Joe-Clayton copula.

  8. Sexual selection and magic traits in speciation with gene flow

    Institute of Scientific and Technical Information of China (English)

    Maria R.SERVEDIO; Michael KOPP

    2012-01-01

    The extent to which sexual selection is involved in speciation with gene flow remains an open question and the subject of much research.Here,we propose that some insight can be gained from considering the concept of magic traits (i.e.,traits involved in both reproductive isolation and ecological divergence).Both magic traits and other,“non-magic”,traits can contribute to speciation via a number of specific mechanisms.We argue that many of these mechanisms are likely to differ widely in the extent to which they involve sexual selection.Furthermore,in some cases where sexual selection is present,it may be prone to inhibit rather than drive speciation.Finally,there are a priori reasons to believe that certain categories of traits are much more effective than others in driving speciation.The combination of these points suggests a classification of traits that may shed light on the broader role of sexual selection in speciation with gene flow.In particular,we suggest that sexual selection can act as a driver of speciation in some scenarios,but may play a negligible role in potentially common categories of magic traits,and may be likely to inhibit speeiation in common categories of non-magic traits.

  9. The Himalayas as a directional barrier to gene flow.

    Science.gov (United States)

    Gayden, Tenzin; Cadenas, Alicia M; Regueiro, Maria; Singh, Nanda B; Zhivotovsky, Lev A; Underhill, Peter A; Cavalli-Sforza, Luigi L; Herrera, Rene J

    2007-05-01

    High-resolution Y-chromosome haplogroup analyses coupled with Y-short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal--including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)--as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman-speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134-derived chromosomes, whose Y-STR-based age (+/-SE) was estimated at 8.1+/-2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives--namely, D1-M15 and D3-P47 in Tibet--involved two different demographic events (5.1+/-1.8 and 11.3+/-3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal

  10. Inteins as Indicators of Gene Flow in the Halobacteria

    Directory of Open Access Journals (Sweden)

    Shannon Margaret Soucy

    2014-06-01

    Full Text Available This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed one hundred and eighteen genomes representing twenty-six genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified twenty-four proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein’s life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN; smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena, Bacteriodetes (Salinibacter, Betaproteobacteria (Delftia, Acidovorax, Firmicutes (Halanaerobium, Actinobacteria (Longispora, and Deinococcus-Thermus-group.

  11. Gene Expression by PBMC in Primary Sclerosing Cholangitis: Evidence for Dysregulation of Immune Mediated Genes

    Directory of Open Access Journals (Sweden)

    Christopher A. Aoki

    2006-01-01

    Full Text Available Primary sclerosing cholangitis (PSC is a chronic disease of the bile ducts characterized by an inflammatory infiltrate and obliterative fibrosis. The precise role of the immune system in the pathogenesis of PSC remains unknown. We used RNA microarray analysis to identify immune-related genes and pathways that are differentially expressed in PSC. Messenger RNA (mRNA from peripheral blood mononuclear cells (PBMC was isolated from both patients with PSC and age and sex matched healthy controls. Samples from 5 PSC patients and 5 controls were analyzed by microarray and based upon rigorous statistical analysis of the data, relevant genes were chosen for confirmation by RT-PCR in 10 PSC patients and 10 controls. Using unsupervised hierarchical clustering, gene expression in PSC was statistically different from our control population. Interestingly, genes within the IL-2 receptor beta, IL-6 and MAP Kinase pathways were found to be differently expressed in patients with PSC compared to controls. Further, individual genes, TNF-α induced protein 6 (TNFaip6 and membrane-spanning 4-domains, subfamily A (ms4a were found to be upregulated in PSC while similar to Mothers against decapentaplegic homolog 5 (SMAD 5 was downregulated. In conclusion, several immune-related pathways and genes were differentially expressed in PSC compared to control patients, giving further evidence that this disease is systemic and immune-mediated.

  12. Observations of ebb flows on tidal flats: Evidence of dewatering?

    Science.gov (United States)

    Rinehimer, J. P.; Thomson, J. M.; Chickadel, C.

    2010-12-01

    Incised channels are a common morphological feature of tidal flats. When the flats are inundated, flows are generally forced by the tidally varying sea surface height. During low tide, however, these channels continue to drain throughout flat exposure even without an upstream source of water. While the role of porewater is generally overlooked due to the low permeability of marine muds, it remains the only potential source of flows through the channels during low tide. In situ and remotely sensed observations (Figure 1) at an incised channel on a tidal flat in Willapa Bay from Spring 2010 indicate that dewatering of the flats may be driving these low tide flows. High resolution Aquadopp ADCP velocity profiles are combined with observations from tower-based infrared (IR) video to produce a complete time series of surface velocity measurements throughout low tide. The IR video observations provide a measurement of surface currents even when the channel depth is below the blanking distance of the ADCP (10 cm). As the depth within the channel drops from 50 cm to 10 cm surface velocities increase from 10 cm/s to 60 cm/s even as the tide level drops below the channel flanks and the flats are dry. As the drainage continues, the temperature of the flow rises throughout low tide, mirroring temperatures within the sediment bed on the tidal flat. Drainage salinity falls despite the lack of any freshwater input to the flat indicating that less saline porewater may be the source. The likely source of the drainage water is from the channel flanks where time-lapse video shows slumping and compaction of channel sediments. Velocity profiles, in situ temperatures, and IR observations also are consistent with the presence of fluid muds and a hyperpycnal, density driven outflow at the channel mouth highlighting a possible pathway for sediment delivery from the flats to the main distributary channels of the bay. Figure 1: Time series of tidal flat channel velocities and temperatures

  13. Observations of pockmark flow structure in Belfast Bay, Maine, Part 2: evidence for cavity flow

    Science.gov (United States)

    Fandel, Christina L.; Lippmann, Thomas C.; Foster, Diane L.; Brothers, Laura L.

    2017-01-01

    Pockmark flow circulation patterns were investigated through current measurements along the rim and center of two pockmarks in Belfast Bay, Maine. Observed time-varying current profiles have a complex vertical and directional structure that rotates significantly with depth and is strongly dependent on the phase of the tide. Observations of the vertical profiles of horizontal velocities in relation to relative geometric parameters of the pockmark are consistent with circulation patterns described qualitatively by cavity flow models (Ashcroft and Zhang 2005). The time-mean behavior of the shear layer is typically used to characterize cavity flow, and was estimated using vorticity thickness to quantify the growth rate of the shear layer horizontally across the pockmark. Estimated positive vorticity thickness spreading rates are consistent with cavity flow predictions, and occur at largely different rates between the two pockmarks. Previously modeled flow (Brothers et al. 2011) and laboratory measurements (Pau et al. 2014) over pockmarks of similar geometry to those examined herein are also qualitatively consistent with cavity flow circulation, suggesting that cavity flow may be a good first-order flow model for pockmarks in general.

  14. Observations of pockmark flow structure in Belfast Bay, Maine, Part 2: evidence for cavity flow

    Science.gov (United States)

    Fandel, Christina L.; Lippmann, Thomas C.; Foster, Diane L.; Brothers, Laura L.

    2017-02-01

    Pockmark flow circulation patterns were investigated through current measurements along the rim and center of two pockmarks in Belfast Bay, Maine. Observed time-varying current profiles have a complex vertical and directional structure that rotates significantly with depth and is strongly dependent on the phase of the tide. Observations of the vertical profiles of horizontal velocities in relation to relative geometric parameters of the pockmark are consistent with circulation patterns described qualitatively by cavity flow models (Ashcroft and Zhang 2005). The time-mean behavior of the shear layer is typically used to characterize cavity flow, and was estimated using vorticity thickness to quantify the growth rate of the shear layer horizontally across the pockmark. Estimated positive vorticity thickness spreading rates are consistent with cavity flow predictions, and occur at largely different rates between the two pockmarks. Previously modeled flow (Brothers et al. 2011) and laboratory measurements (Pau et al. 2014) over pockmarks of similar geometry to those examined herein are also qualitatively consistent with cavity flow circulation, suggesting that cavity flow may be a good first-order flow model for pockmarks in general.

  15. The Himalayas: barrier and conduit for gene flow.

    Science.gov (United States)

    Gayden, Tenzin; Perez, Annabel; Persad, Patrice J; Bukhari, Areej; Chennakrishnaiah, Shilpa; Simms, Tanya; Maloney, Trisha; Rodriguez, Kristina; Herrera, Rene J

    2013-06-01

    The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y-chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian-specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep-rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y-chromosome data indicate sex-biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia.

  16. Gene flow between sympatric life history forms of Oncorhynchus mykiss located above and below migratory barriers.

    Directory of Open Access Journals (Sweden)

    Donald M Van Doornik

    Full Text Available Oncorhynchus mykiss have a diverse array of life history types, and understanding the relationship among types is important for management of the species. Patterns of gene flow between sympatric freshwater resident O. mykiss, commonly known as rainbow trout, and anadromous O. mykiss, commonly known as steelhead, populations are complex and poorly understood. In this study, we attempt to determine the occurrence and pathways of gene flow and the degree of genetic similarity between sympatric resident and anadromous O. mykiss in three river systems, and investigate whether resident O. mykiss are producing anadromous offspring in these rivers, two of which have complete barriers to upstream migration. We found that the population structure of the O. mykiss in these rivers appears to be influenced more by the presence of a barrier to upstream migration than by life history type. The sex ratio of resident O. mykiss located above a barrier, and smolts captured in screw traps was significantly skewed in favor of females, whereas the reverse was true below the barriers, suggesting that male resident O. mykiss readily migrate downstream over the barrier, and that precocious male maturation may be occurring in the anadromous populations. Through paternity analyses, we also provide direct confirmation that resident O. mykiss can produce offspring that become anadromous. Most (89% of the resident O. mykiss that produced anadromous offspring were males. Our results add to the growing body of evidence that shows that gene flow does readily occur between sympatric resident and anadromous O. mykiss life history types, and indicates that resident O. mykiss populations may be a potential repository of genes for the anadromous life history type.

  17. An investigation on how to estimate future cash flows: Evidence from Tehran Stock Exchange

    Directory of Open Access Journals (Sweden)

    Roghayeh Ahmdi Panah Banad Koki

    2014-03-01

    Full Text Available This paper presents an empirical investigation to predict future cash flows using present cash flow and accruals using the information of 96 selected firms listed on Tehran Stock Exchange over the period 2007-2011. The proposed study uses linear regression techniques to forecast future cash flow and the results indicate that cash flow and accruals together could provide more power to forecast cash flow. In addition, accrual provides future cash flow better than cash flow. The survey also performs an investigation on discretionary accrual and finds that the firms with higher accruals maintain lower return compared with firms with lower return. This means there is a clear evidence of discretionary accruals on Tehran Stock Exchange.

  18. Observational evidence for matter propagation in accretion flows

    CERN Document Server

    Revnivtsev, M; Kniazev, A; Burenin, R; Buckley, D A H; Churazov, E

    2010-01-01

    We study simultaneous X-ray and optical observations of three intermediate polars EX Hya, V1223 Sgr and TV Col with the aim to understand the propagation of matter in their accretion flows. We show that in all cases the power spectra of flux variability of binary systems in X-rays and in optical band are similar to each other and the majority of X-ray and optical fluxes are correlated with time lag <1 sec. These findings support the idea that optical emission of accretion disks, in these binary systems,largely originates as reprocessing of X-ray luminosity of their white dwarfs. In the best obtained dataset of EX Hya we see that the optical lightcurve unambiguously contains some component, which leads the X-ray emission by ~7 sec. We interpret this in the framework of the model of propagating fluctuations and thus deduce the time of travel of the matter from the innermost part of the truncated accretion disk to the white dwarf surface. This value agrees very well with the time expected for matter threaded ...

  19. Evidence for Rapid Redshift Evolution of Strong Cluster Cooling Flows

    CERN Document Server

    Samuele, R; Vikhlinin, A; Mullis, C R

    2011-01-01

    We present equivalent widths of the [OII] and Ha nebular emission lines for 77 brightest cluster galaxies (BCGs) selected from the 160 Square Degree $ROSAT$ X-ray survey. We find no [OII] or Ha emission stronger than -15 angstroms or -5 angstroms, respectively, in any BCG. The corresponding emission line luminosities lie below 6E40 erg/s, which is a factor of 30 below that of NGC1275 in the Perseus cluster. A comparison to the detection frequency of nebular emission in BCGs lying at redshifts above z = 0.35 drawn from the Brightest Cluster Survey (Crawford et al. 1999) indicates that we should have detected roughly one dozen emission-line galaxies, assuming the two surveys are selecting similar clusters in the X-ray luminosity range 10E42 erg/s to 10E45 erg/s. The absence of luminous nebular emission (ie., Perseus-like systems) in our sample is consistent with an increase in the number density of {\\it strong} cooling flow (cooling core) clusters between $\\rm z=0.5$ and today. The decline in their numbers at h...

  20. Gene flow and genetic diversity in cultivated and wild cacao (Theobroma cacao) in Bolivia.

    Science.gov (United States)

    Chumacero de Schawe, Claudia; Durka, Walter; Tscharntke, Teja; Hensen, Isabell; Kessler, Michael

    2013-11-01

    The role of pollen flow within and between cultivated and wild tropical crop species is little known. To study the pollen flow of cacao, we estimated the degree of self-pollination and pollen dispersal distances as well as gene flow between wild and cultivated cacao (Theobroma cacao L.). We studied pollen flow and genetic diversity of cultivated and wild cacao populations by genotyping 143 wild and 86 cultivated mature plants and 374 seedlings raised from 19 wild and 25 cultivated trees at nine microsatellite loci. A principal component analysis distinguished wild and cultivated cacao trees, supporting the notion that Bolivia harbors truly wild cacao populations. Cultivated cacao had a higher level of genetic diversity than wild cacao, presumably reflecting the varied origin of cultivated plants. Both cacao types had high outcrossing rates, but the paternity analysis revealed 7-14% self-pollination in wild and cultivated cacao. Despite the tiny size of the pollinators, pollen was transported distances up to 3 km; wild cacao showed longer distances (mean = 922 m) than cultivated cacao (826 m). Our data revealed that 16-20% of pollination events occurred between cultivated and wild populations. We found evidence of self-pollination in both wild and cultivated cacao. Pollination distances are larger than those typically reported in tropical understory tree species. The relatively high pollen exchange from cultivated to wild cacao compromises genetic identity of wild populations, calling for the protection of extensive natural forest tracts to protect wild cacao in Bolivia.

  1. Sex-biased gene flow among elk in the greater Yellowstone ecosystem

    Science.gov (United States)

    , Brian K. Hand; , Shanyuan Chen; , N. Anderson; , A. Beja-Pereira; Cross, Paul C.; , M. Ebinger; , H. Edwards; , R.A. Garrott; , M.D. Kardos; Kauffman, Matthew J.; , E.L. Landguth; , A. Middleton; , B. Scurlock; , P.J. White; , P. Zager; , M.K. Schwartz; , G. Luikart

    2014-01-01

    We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf = 46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel’s r = 0.274, P = 0.168). Large mitochondrial DNA genetic distances (e.g., FST > 0.2) between some of the geographically closest populations (<65 km) suggested behavioral factors and/or landscape features might shape female gene flow patterns. Given the strong sex-biased gene flow, future research and conservation efforts should consider the sexes separately when modeling corridors of gene flow or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female gene flow provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased gene flow likely to occur in many species

  2. Evidence of gene conversion in genes encoding the Gal/GalNac lectin complex of Entamoeba.

    Directory of Open Access Journals (Sweden)

    Gareth D Weedall

    2011-06-01

    Full Text Available The human gut parasite Entamoeba histolytica, uses a lectin complex on its cell surface to bind to mucin and to ligands on the intestinal epithelia. Binding to mucin is necessary for colonisation and binding to intestinal epithelia for invasion, therefore blocking this binding may protect against amoebiasis. Acquired protective immunity raised against the lectin complex should create a selection pressure to change the amino acid sequence of lectin genes in order to avoid future detection. We present evidence that gene conversion has occurred in lineages leading to E. histolytica strain HM1:IMSS and E. dispar strain SAW760. This evolutionary mechanism generates diversity and could contribute to immune evasion by the parasites.

  3. Evidence of gene conversion in genes encoding the Gal/GalNac lectin complex of Entamoeba.

    Directory of Open Access Journals (Sweden)

    Gareth D Weedall

    2011-06-01

    Full Text Available The human gut parasite Entamoeba histolytica, uses a lectin complex on its cell surface to bind to mucin and to ligands on the intestinal epithelia. Binding to mucin is necessary for colonisation and binding to intestinal epithelia for invasion, therefore blocking this binding may protect against amoebiasis. Acquired protective immunity raised against the lectin complex should create a selection pressure to change the amino acid sequence of lectin genes in order to avoid future detection. We present evidence that gene conversion has occurred in lineages leading to E. histolytica strain HM1:IMSS and E. dispar strain SAW760. This evolutionary mechanism generates diversity and could contribute to immune evasion by the parasites.

  4. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  5. Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis.

    Directory of Open Access Journals (Sweden)

    René M Malenfant

    Full Text Available Recently, an extensive study of 2,748 polar bears (Ursus maritimus from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago-an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study's main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1 highly unbalanced sample sizes and large amounts of systematically missing data; (2 incorrect calculation of FST and of significance levels; (3 misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and-importantly-we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada's expected last sea-ice refugium. Although polar bears' abundance, distribution, and population structure will certainly be negatively affected by ongoing-and increasingly rapid-loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.

  6. Contemporary human-altered landscapes and oceanic barriers reduce bumble bee gene flow.

    Science.gov (United States)

    Jha, S

    2015-03-01

    Much of the world's terrestrial landscapes are being altered by humans in the form of agriculture, urbanization and pastoral systems, with major implications for biodiversity. Bumble bees are one of the most effective pollinators in both natural and cultivated landscapes, but are often the first to be extirpated in human-altered habitats. Yet, little is known about the role of natural and human-altered habitats in promoting or limiting bumble bee gene flow. In this study, I closely examine the genetic structure of the yellow-faced bumble bee, Bombus vosnesenskii, across the southwestern US coast and find strong evidence that natural oceanic barriers, as well as contemporary human-altered habitats, limit bee gene flow. Heterozygosity and allelic richness were lower in island populations, while private allelic richness was higher in island populations compared to mainland populations. Genetic differentiation, measured for three indices across the 1000 km study region, was significantly greater than the null expectation (F(ST) = 0.041, F'(ST) = 0.044 and D(est) = 0.155) and correlated with geographic distance. Furthermore, genetic differentiation patterns were most strongly correlated with contemporary (2011) not past (2006, 2001) resistance maps calibrated for high dispersal limitation over oceans, impervious habitat and croplands. Despite the incorporation of dramatic elevation gradients, the analyses reveal that oceans and contemporary human land use, not mountains, are the primary dispersal barriers for B. vosnesenskii gene flow. These findings reinforce the importance of maintaining corridors of suitable habitat across the distribution range of native pollinators to promote their persistence and safeguard their ability to provide essential pollination services.

  7. Phenological mismatch and the effectiveness of assisted gene flow.

    Science.gov (United States)

    Wadgymar, Susana M; Weis, Arthur E

    2017-06-01

    The persistence of narrowly adapted species under climate change will depend on their ability to migrate apace with their historical climatic envelope or to adapt in place to maintain fitness. This second path to persistence can only occur if there is sufficient genetic variance for response to new selection regimes. Inadequate levels of genetic variation can be remedied through assisted gene flow (AGF), that is the intentional introduction of individuals genetically adapted to localities with historic climates similar to the current or future climate experienced by the resident population. However, the timing of reproduction is frequently adapted to local conditions. Phenological mismatch between residents and migrants can reduce resident × migrant mating frequencies, slowing the introgression of migrant alleles into the resident genetic background and impeding evolutionary rescue efforts. Focusing on plants, we devised a method to estimate the frequency of resident × migrant matings based on flowering schedules and applied it in an experiment that mimicked the first generation of an AGF program with Chamaecrista fasciculata, a prairie annual, under current and expected future temperature regimes. Phenological mismatch reduced the potential for resident × migrant matings by 40-90%, regardless of thermal treatment. The most successful migrant sires were the most resident like in their flowering time, further biasing the genetic admixture between resident and migrant populations. Other loci contributing to local adaptation-heat-tolerance genes, for instance-may be in linkage disequilibrium with phenology when residents and migrants are combined into a single mating pool. Thus, introgression of potentially adaptive migrant alleles into the resident genetic background is slowed when selection acts against migrant phenology. Successful AGF programs may require sustained high immigration rates or preliminary breeding programs when phenologically matched migrant

  8. FORMULAE FOR AVERAGE VELOCITY OF GROUNDWATER FLOW AND EXPERIMENTAL EVIDENCE OF NON-DARCY'S FLOW THROUGH A SINGLE FRACTURE

    Institute of Scientific and Technical Information of China (English)

    Qian Jia-zhong; Wang Jia-quan; Li Ru-zhong; Liu Yong

    2003-01-01

    The formulae for average velocity of groundwater flow in a single fracture were derived based on the characteristics of fracture properties and hydraulic methods. The results show that the average velocity is proportional to the square root of the hydraulic gradient. In order to verify the results, a laboratory model was established, and the experimental data were analyzed. Experimental results indicate that the relation between the average velocity and hydraulic gradient is nonlinear, and can be fitted with power functions. And for both the unconfined and confined flows, the value of the exponent of power functions are close to 0.5. Thus the experimental results agree well with those from the theoretical analysis. By comparing the calculated and measured values of the average velocity under the same conditions, the formulae presented herein are more effective than the traditional formula based on Darcy's Law. These results provide the evidences of non-Darcy's flow in single fracture.

  9. Direct evidence of recombination in the recA gene of Aeromonas bestiarum.

    Science.gov (United States)

    Sanglas, Ariadna; Albarral, Vicenta; Farfán, Maribel; Lorén, J Gaspar; Fusté, M Carmen

    2016-03-01

    Two hundred and twenty-one strains representative of all Aeromonas species were characterized using the recA gene sequence, assessing its potential as a molecular marker for the genus Aeromonas. The inter-species distance values obtained demonstrated that recA has a high discriminatory power. Phylogenetic analysis, based on full-length gene nucleotide sequences, revealed a robust topology with clearly separated clusters for each species. The maximum likelihood tree showed the Aeromonas bestiarum strains in a well-defined cluster, containing a subset of four strains of different geographical origins in a deep internal branch. Data analysis provided strong evidence of recombination at the end of the recA sequences in these four strains. Intergenomic recombination corresponding to partial regions of the two adjacent genes recA and recX (248 bp) was identified between A. bestiarum (major parent) and Aeromonas eucrenophila (minor parent). The low number of recombinant strains detected (1.8%) suggests that horizontal flow between recA sequences is relatively uncommon in this genus. Moreover, only a few nucleotide differences were detected among these fragments, indicating that recombination has occurred recently. Finally, we also determined if the recombinant fragment could have influenced the structure and basic functions of the RecA protein, comparing models reconstructed from the translated amino acid sequences of our A. bestiarum strains with known Escherichia coli RecA structures.

  10. High rates of gene flow by pollen and seed in oak populations across Europe

    NARCIS (Netherlands)

    Gerber, S.; Chadoeuf, J.; Gugerli, F.; Lascoux, M.; Buiteveld, J.; Cottrell, J.; Dounavi, A.; Fineschi, S.; Forrest, L.; Fogelqvist, J.; Goicoechea, P.G.; Jensen, J.S.; Salvini, D.; Vendramin, G.G.; Kremer, A.

    2014-01-01

    Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult tree

  11. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    DEFF Research Database (Denmark)

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.

    2009-01-01

    and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...

  12. Euglossine bees mediate only limited long-distance gene flow in a tropical vine.

    Science.gov (United States)

    Opedal, Øystein H; Falahati-Anbaran, Mohsen; Albertsen, Elena; Armbruster, W Scott; Pérez-Barrales, Rocío; Stenøien, Hans K; Pélabon, Christophe

    2017-03-01

    Euglossine bees (Apidae: Euglossini) have long been hypothesized to act as long-distance pollinators of many low-density tropical plants. We tested this hypothesis by the analysis of gene flow and genetic structure within and among populations of the euglossine bee-pollinated vine Dalechampia scandens. Using microsatellite markers, we assessed historical gene flow by the quantification of regional-scale genetic structure and isolation by distance among 18 populations, and contemporary gene flow by the estimation of recent migration rates among populations. To assess bee-mediated pollen dispersal on a smaller scale, we conducted paternity analyses within a focal population, and quantified within-population spatial genetic structure in four populations. Gene flow was limited to certain nearby populations within continuous forest blocks, whereas drift appeared to dominate on larger scales. Limited long-distance gene flow was supported by within-population patterns; gene flow was biased towards nearby plants, and significant small-scale spatial genetic structure was detected within populations. These findings suggest that, although female euglossine bees might be effective at moving pollen within populations, and perhaps within forest blocks, their contribution to gene flow on the regional scale seems too limited to counteract genetic drift in patchily distributed tropical plants. Among-population gene flow might have been reduced following habitat fragmentation.

  13. Directional gene flow and ecological separation in Yersinia enterocolitica

    Science.gov (United States)

    Reuter, Sandra; Corander, Jukka; de Been, Mark; Harris, Simon; Cheng, Lu; Hall, Miquette; Thomson, Nicholas R.

    2015-01-01

    Yersinia enterocolitica is a common cause of food-borne gastroenteritis worldwide. Recent work defining the phylogeny of the genus Yersinia subdivided Y. enterocolitica into six distinct phylogroups. Here, we provide detailed analyses of the evolutionary processes leading to the emergence of these phylogroups. The dominant phylogroups isolated from human infections, PG3–5, show very little diversity at the sequence level, but do present marked patterns of gain and loss of functions, including those involved in pathogenicity and metabolism, including the acquisition of phylogroup-specific O-antigen loci. We tracked gene flow across the species in the core and accessory genome, and show that the non-pathogenic PG1 strains act as a reservoir for diversity, frequently acting as donors in recombination events. Analysis of the core and accessory genome also suggested that the different Y. enterocolitica phylogroups may be ecologically separated, in contrast to the long-held belief of common shared ecological niches across the Y. enterocolitica species.

  14. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    DEFF Research Database (Denmark)

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.;

    2009-01-01

    Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from...... and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...... landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North–South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin...

  15. Genome-wide data substantiate Holocene gene flow from India to Australia.

    Science.gov (United States)

    Pugach, Irina; Delfin, Frederick; Gunnarsdóttir, Ellen; Kayser, Manfred; Stoneking, Mark

    2013-01-29

    The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

  16. OncoSearch: cancer gene search engine with literature evidence.

    Science.gov (United States)

    Lee, Hee-Jin; Dang, Tien Cuong; Lee, Hyunju; Park, Jong C

    2014-07-01

    In order to identify genes that are involved in oncogenesis and to understand how such genes affect cancers, abnormal gene expressions in cancers are actively studied. For an efficient access to the results of such studies that are reported in biomedical literature, the relevant information is accumulated via text-mining tools and made available through the Web. However, current Web tools are not yet tailored enough to allow queries that specify how a cancer changes along with the change in gene expression level, which is an important piece of information to understand an involved gene's role in cancer progression or regression. OncoSearch is a Web-based engine that searches Medline abstracts for sentences that mention gene expression changes in cancers, with queries that specify (i) whether a gene expression level is up-regulated or down-regulated, (ii) whether a certain type of cancer progresses or regresses along with such gene expression change and (iii) the expected role of the gene in the cancer. OncoSearch is available through http://oncosearch.biopathway.org.

  17. DNA capture reveals transoceanic gene flow in endangered river sharks.

    Science.gov (United States)

    Li, Chenhong; Corrigan, Shannon; Yang, Lei; Straube, Nicolas; Harris, Mark; Hofreiter, Michael; White, William T; Naylor, Gavin J P

    2015-10-27

    For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.

  18. Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases

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    Khoury Muin J

    2008-12-01

    Full Text Available Abstract Background Millions of single nucleotide polymorphisms have been identified as a result of the human genome project and the rapid advance of high throughput genotyping technology. Genetic association studies, such as recent genome-wide association studies (GWAS, have provided a springboard for exploring the contribution of inherited genetic variation and gene/environment interactions in relation to disease. Given the capacity of such studies to produce a plethora of information that may then be described in a number of publications, selecting possible disease susceptibility genes and identifying related modifiable risk factors is a major challenge. A Web-based application for finding evidence of such relationships is key to the development of follow-up studies and evidence for translational research. We developed a Web-based application that selects and prioritizes potential disease-related genes by using a highly curated and updated literature database of genetic association studies. The application, called Gene Prospector, also provides a comprehensive set of links to additional data sources. Results We compared Gene Prospector results for the query "Parkinson" with a list of 13 leading candidate genes (Top Results from a curated, specialty database for genetic associations with Parkinson disease (PDGene. Nine of the thirteen leading candidate genes from PDGene were in the top 10th percentile of the ranked list from Gene Prospector. In fact, Gene Prospector included more published genetic association studies for the 13 leading candidate genes than PDGene did. Conclusion Gene Prospector provides an online gateway for searching for evidence about human genes in relation to diseases, other phenotypes, and risk factors, and provides links to published literature and other online data sources. Gene Prospector can be accessed via http://www.hugenavigator.net/HuGENavigator/geneProspectorStartPage.do.

  19. Rock magnetic evidence of inflation of a flood basalt lava flow

    Science.gov (United States)

    Cañón-Tapia, Edgardo; Coe, Robert

    2002-07-01

    The anisotropy of magnetic susceptibility (AMS) of lava flows is an innovative method which has been proved to be directly related to the shear history of lava. One of the advantages of this method is that it can be used in the absence of other morphological features commonly employed to study the mechanism of emplacement of lava flows. This feature of the AMS method makes it very attractive to gain insight into the mechanism of emplacement of massive, relatively featureless, long lava flows such as those forming flood basalt provinces. In this work, we report the results of the measurement of AMS as a function of vertical position within the Birkett lava flow, one of the Columbia River Basalt Group flows. The observed variation of AMS allows us to identify at least 16 discrete events of lava injection and to estimate the thickness of individual injection events. The AMS-estimated thickness of each injection event (in the range of 0.5-4.0 m) coincides with the range inferred for injected lava pulses in modern Hawaiian lava flows. Thus, the evidence provided by the AMS method supports the notion that at least some flood basalt lava flows were emplaced by the same mechanism as many present-day inflated pahoehoe flows. Regarding the orientation of the principal susceptibilities, in the central part of the flow they define a preferred orientation along an E-W trend, whereas in the outer parts of the flow they have a NNE-SSW trend. This difference in the orientation of the principal susceptibilities is interpreted as the result of a change of flow direction of the lava as emplacement progressed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00445-002-0203-8.

  20. Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria).

    Science.gov (United States)

    Muir, A P; Biek, R; Thomas, R; Mable, B K

    2014-02-01

    Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether local adaptation occurs in the face of high gene flow and to identify potential environmental selection pressures that drive adaptation. Phenotypic variation in larval traits was quantified in R. temporaria from paired high- and low-altitude sites using three common temperature treatments. Local adaptation was assessed using Q(ST)-F(ST) analyses, and quantitative phenotypic divergence was related to environmental parameters using Mantel tests. Although evidence of local adaptation was found for all traits measured, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites. This variation was correlated with mean summer and winter temperatures, suggesting that temperature parameters are potentially strong selective pressures maintaining local adaptation, despite high gene flow.

  1. The impact of pollination syndrome and habitat on gene flow: a comparative study of two Streptocarpus (Gesneriaceae) species.

    Science.gov (United States)

    Hughes, Mark; Möller, Michael; Edwards, Trevor J; Bellstedt, Dirk U; Villiers, Margaret de

    2007-10-01

    Gene flow through pollen and seed dispersal is important in terms of population differentiation and eventually speciation. Seed and pollen flow are affected in turn by habitats and pollen vectors. We examined the effect of different pollinators and habitats on gene flow by comparing two species of Streptocarpus, using microsatellite and chloroplast RFLP markers. Populations of the forest-dwelling S. primulifolius were highly differentiated according to nuclear microsatellite data and had mutually exclusive chloroplast haplotypes. This result is congruent with infrequent seed dispersal and limited between-population foraging by the long-tongued fly pollinator Stenobasipteron wiedemanni. In contrast, populations of S. dunnii growing in exposed crags had lower levels of population differentiation according to both nuclear and chloroplast data, congruent with a hypothesis of more effective between population seed dispersal and greater pollen-mediated gene flow due to the sunbird pollinator Nectarinia famosa. The population genetic behavior of these species is reflected in their taxonomy and phylogenetic position; S. primulifolius belongs to a taxonomically complex clade in which recent speciation is evident, while the clade containing S. dunnii is characterized by taxonomically well-defined species on longer phylogenetic branches. Our study shows that pollinator movements and seed dispersal patterns are a major determinant of the evolutionary trajectories of these species.

  2. Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

    Directory of Open Access Journals (Sweden)

    Victor Borges Rezende

    2016-10-01

    Full Text Available Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species’ reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index (D¯ of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c, among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.

  3. Estimating exotic gene flow into native pine stands: zygotic vs. gametic components.

    Science.gov (United States)

    Unger, G M; Vendramin, G G; Robledo-Arnuncio, J J

    2014-11-01

    Monitoring contemporary gene flow from widespread exotic plantations is becoming an important problem in forest conservation genetics. In plants, where both seed and pollen disperse, three components of exotic gene flow with potentially unequal consequences should be, but have not been, explicitly distinguished: zygotic, male gametic and female gametic. Building on a previous model for estimating contemporary rates of zygotic and male gametic gene flow among plant populations, we present here an approach that additionally estimates the third (female gametic) gene flow component, based on a combination of uni- and biparentally inherited markers. Using this method and a combined set of chloroplast and nuclear microsatellites, we estimate gene flow rates from exotic plantations into two Iberian relict stands of maritime pine (Pinus pinaster) and Scots pine (Pinus sylvestris). Results show neither zygotic nor female gametic gene flow but moderate (6-8%) male gametic introgression for both species, implying significant dispersal of pollen, but not of seeds, from exotic plantations into native stands shortly after introduced trees reached reproductive maturity. Numerical simulation results suggest that the model yields reasonably accurate estimates for our empirical data sets, especially for larger samples. We discuss conservation management implications of observed levels of exposure to nonlocal genes and identify research needs to determine potentially associated hazards. Our approach should be useful for plant ecologists and ecosystem managers interested in the vectors of contemporary genetic connectivity among discrete plant populations.

  4. Psychiatric gene discoveries shape evidence on ADHD's biology

    Science.gov (United States)

    Thapar, A; Martin, J; Mick, E; Arias Vásquez, A; Langley, K; Scherer, S W; Schachar, R; Crosbie, J; Williams, N; Franke, B; Elia, J; Glessner, J; Hakonarson, H; Owen, M J; Faraone, S V; O'Donovan, M C; Holmans, P

    2016-01-01

    A strong motivation for undertaking psychiatric gene discovery studies is to provide novel insights into unknown biology. Although attention-deficit hyperactivity disorder (ADHD) is highly heritable, and large, rare copy number variants (CNVs) contribute to risk, little is known about its pathogenesis and it remains commonly misunderstood. We assembled and pooled five ADHD and control CNV data sets from the United Kingdom, Ireland, United States of America, Northern Europe and Canada. Our aim was to test for enrichment of neurodevelopmental gene sets, implicated by recent exome-sequencing studies of (a) schizophrenia and (b) autism as a means of testing the hypothesis that common pathogenic mechanisms underlie ADHD and these other neurodevelopmental disorders. We also undertook hypothesis-free testing of all biological pathways. We observed significant enrichment of individual genes previously found to harbour schizophrenia de novo non-synonymous single-nucleotide variants (SNVs; P=5.4 × 10−4) and targets of the Fragile X mental retardation protein (P=0.0018). No enrichment was observed for activity-regulated cytoskeleton-associated protein (P=0.23) or N-methyl-D-aspartate receptor (P=0.74) post-synaptic signalling gene sets previously implicated in schizophrenia. Enrichment of ADHD CNV hits for genes impacted by autism de novo SNVs (P=0.019 for non-synonymous SNV genes) did not survive Bonferroni correction. Hypothesis-free testing yielded several highly significantly enriched biological pathways, including ion channel pathways. Enrichment findings were robust to multiple testing corrections and to sensitivity analyses that excluded the most significant sample. The findings reveal that CNVs in ADHD converge on biologically meaningful gene clusters, including ones now established as conferring risk of other neurodevelopmental disorders. PMID:26573769

  5. Distribution of coalescent histories under the coalescent model with gene flow.

    Science.gov (United States)

    Tian, Yuan; Kubatko, Laura S

    2016-12-01

    We propose a coalescent model for three species that allows gene flow between both pairs of sister populations. The model is designed for multilocus genomic sequence alignments, with one sequence sampled from each of the three species, and is formulated using a Markov chain representation that allows use of matrix exponentiation to compute analytical expressions for the probability density of coalescent histories. The coalescent history distribution as well as the gene tree topology distribution under this coalescent model with gene flow are then calculated via numerical integration. We analyze the model to compare the distributions of gene tree topologies and coalescent histories for species trees with differing effective population sizes and gene flow rates. Our results suggest conditions under which the species tree and associated parameters are not identifiable from the gene tree topology distribution when gene flow is present, but indicate that the coalescent history distribution may identify the species tree and associated parameters. Thus, the coalescent history distribution can be used to infer parameters such as the ancestral effective population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We conduct computer simulations to evaluate the performance of our method in estimating these parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 2015). Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Flux-flow resistivity in UPt3: Evidence for nonsingular vortex-core structure

    Science.gov (United States)

    Lütke-Entrup, N.; Blaauwgeers, R.; Plaçais, B.; Huxley, A.; Kambe, S.; Krusius, M.; Mathieu, P.; Simon, Y.

    2001-07-01

    We have investigated the core structure of B-phase vortex lines in two clean UPt3 crystals, using flux-flow dissipation as the probe. The flux-flow resistivity is determined from the skin depth of the high-frequency oscillations of the vortex lines in the pinned state. With Ĥ⊥ĉ, our data agree with the previously established scaling law of the moderately clean limit with anisotropic gap. When Ĥ||ĉ, the resistivity is three times larger. We interpret this increase as evidence for a vortex-core structure with two length scales, as predicted for UPt3 with a two-component order parameter.

  7. Evidence for debris flow gully formation initiated by shallow subsurface water on Mars

    Science.gov (United States)

    Lanza, N.L.; Meyer, G.A.; Okubo, C.H.; Newsom, Horton E.; Wiens, R.C.

    2010-01-01

    The morphologies of some martian gullies appear similar to terrestrial features associated with debris flow initiation, erosion, and deposition. On Earth, debris flows are often triggered by shallow subsurface throughflow of liquid water in slope-mantling colluvium. This flow causes increased levels of pore pressure and thus decreased shear strength, which can lead to slide failure of slope materials and subsequent debris flow. The threshold for pore pressure-induced failure creates a distinct relationship between the contributing area supplying the subsurface flow and the slope gradient. To provide initial tests of a similar debris flow initiation hypothesis for martian gullies, measurements of the contributing areas and slope gradients were made at the channel heads of martian gullies seen in three HiRISE stereo pairs. These gullies exhibit morphologies suggestive of debris flows such as leveed channels and lobate debris fans, and have well-defined channel heads and limited evidence for multiple flows. Our results show an area-slope relationship for these martian gullies that is consistent with that observed for terrestrial gullies formed by debris flow, supporting the hypothesis that these gullies formed as the result of saturation of near-surface regolith by a liquid. This model favors a source of liquid that is broadly distributed within the source area and shallow; we suggest that such liquid could be generated by melting of broadly distributed icy materials such as snow or permafrost. This interpretation is strengthened by observations of polygonal and mantled terrain in the study areas, which are both suggestive of near-surface ice. ?? 2009 Elsevier Inc.

  8. A multilocus perspective on colonization accompanied by selection and gene flow.

    Science.gov (United States)

    Rosenblum, Erica Bree; Hickerson, Michael J; Moritz, Craig

    2007-12-01

    The colonization of novel habitats involves complex interactions between founder events, selection, and ongoing migration, and can lead to diverse evolutionary outcomes from local extinction to adaptation to speciation. Although there have been several studies of the demography of colonization of remote habitats, less is known about the demographic consequences of colonization of novel habitats within a continuous species range. Populations of the Eastern Fence Lizard, Sceloporus undulatus, are continuously distributed across two dramatic transitions in substrate color in southern New Mexico and have undergone rapid adaptation following colonization of these novel environments. Blanched forms inhabit the gypsum sand dunes of White Sands and melanic forms are found on the black basalt rocks of the Carrizozo lava flow. Each of these habitats formed within the last 10,000 years, allowing comparison of genetic signatures of population history for two independent colonizations from the same source population. We present evidence on phenotypic variation in lizard color, environmental variation in substrate color, and sequence variation for mitochondrial DNA and 19 independent nuclear loci. To confirm the influence of natural selection and gene flow in this system, we show that phenotypic variation is best explained by environmental variation and that neutral genetic variation is related to distance between populations, not partitioned by habitat. The historical demography of colonization was inferred using an Approximate Bayesian Computation (ABC) framework that incorporates known geological information and allows for ongoing migration with the source population. The inferences differed somewhat between mtDNA and nuclear markers, but overall provided strong evidence of historical size reductions in both white sand and black lava populations at the time of colonization. Populations in both novel habitats appear to have undergone partial but incomplete recovery from the

  9. Evidence for horizontal gene transfer of anaerobic carbon monoxide dehydrogenases

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    Stephen eTechtmann

    2012-04-01

    Full Text Available Carbon monoxide (CO is commonly known as a toxic gas, yet it is used by both aerobic and anaerobic bacteria and many archaea. In this study, we determined the prevalence of anaerobic carbon monoxide dehydrogenases (anaerobic CODHs, or [Ni,Fe]-CODHs in currently available genomic sequence databases. More than 6% (185 genomes out of 2887 bacterial and archaeal genome sequences in the IMG database possess at least one gene encoding [Ni,Fe]-CODH, the key enzyme for anaerobic CO utilization. The phylogenetic study of this extended protein family revealed nine distinct clades of [Ni,Fe]-CODHs. These clades consisted of [Ni,Fe]-CODHs that, while apparently monophyletic within the clades, were encoded by microorganisms of disparate phylogeny, based on 16S rRNA sequences, and widely ranging physiology. Following this discovery, it was therefore of interest to examine the extent and possible routes of horizontal gene transfer (HGT affecting [Ni,Fe]-CODH genes and gene clusters that include [Ni,Fe]-CODHs.The genome sequence of the extreme thermophile Thermosinus carboxydivorans was used as a case study for HGT. The [Ni,Fe]-CODH operon of T. carboxydivorans differs from its whole genome in its G+C content by 8.2 mol%. Here, we apply statistical methods to establish acquisition by T. carboxydivorans of the gene cluster including [Ni,Fe]-CODH via HGT. Analysis of tetranucleotide frequency and codon usage with application of the Kullback-Leibler divergence metric showed that the [Ni,Fe]-CODH-1 operon of T. carboxidyvorans is quite dissimilar to the whole genome. Using the same metrics, the T. carboxydivorans [Ni,Fe]-CODH-1 operon is highly similar to the genome of the phylogenetically distant anaerobic carboxydotroph Carboxydothermus hydrogenoformans. These results allow to assume recent HTG of the gene cluster from a relative of C. hydrogenoformans to T. carboxydivorans or a more ancient transfer from a C. hydrogenoformans ancestor to a T. carboxydivorans

  10. Parallel evolution of local adaptation and reproductive isolation in the face of gene flow.

    Science.gov (United States)

    Butlin, Roger K; Saura, Maria; Charrier, Grégory; Jackson, Benjamin; André, Carl; Caballero, Armando; Coyne, Jerry A; Galindo, Juan; Grahame, John W; Hollander, Johan; Kemppainen, Petri; Martínez-Fernández, Mónica; Panova, Marina; Quesada, Humberto; Johannesson, Kerstin; Rolán-Alvarez, Emilio

    2014-04-01

    Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and amplified fragment length polymorphism markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonization of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically driven speciation.

  11. Independent domestication of Asian rice followed by gene flow from japonica to indica.

    Science.gov (United States)

    Yang, Ching-chia; Kawahara, Yoshihiro; Mizuno, Hiroshi; Wu, Jianzhong; Matsumoto, Takashi; Itoh, Takeshi

    2012-05-01

    Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.

  12. VOLUNTARY DISCLOSURE OF CASH FLOWS INFORMATION AND COMPANY'S CHARACTERISTICS: EVIDENCE FROM THE CROATIAN CAPITAL MARKET

    Directory of Open Access Journals (Sweden)

    Željana Aljinović Barać

    2012-12-01

    Full Text Available This paper focuses on the voluntary disclosure of cash flows information of Croatian large companies whose shares are listed on the Zagreb Stock Exchange, with the aim to identify characteristics of companies that provide extensive disclosures. In order to conduct the research and test the likelihood that company publicly announces wealth of information about cash flows, three groups of company’s features are defined as variables: accounting data, capital market information and company’s qualitative characteristics. Verification of empirical evidence was provided through the sample of Croatian listed companies using logistic regression analysis. Obtained results indicate that despite the desire of the regulatory authorities that capital market investors receive all relevant information, companies voluntarily disclose information about cash flows very rarely. Those companies are young (i.e. their shares are listed on an organized securities market for a short time and profitable, with growing net income and growing cash flow from operating activities and usually use indirect method for operating cash flow report. The provision of features of Croatian companies that voluntary disclose cash flow information can be found as contribution of our research, because this topic in a cases of macro-oriented accounting system economies, i.e. bank oriented economies with emerging capital market is still unexplored.

  13. Psychiatric gene discoveries shape evidence on ADHD's biology

    NARCIS (Netherlands)

    Thapar, A.; Martin, J.; Mick, E.; Arias Vasquez, A.; Langley, K.; Scherer, S.W.; Schachar, R.; Crosbie, J.; Williams, N.; Franke, B.; Elia, J.; Glessner, J.; Hakonarson, H.; Owen, M.J.; Faraone, S.V; O'Donovan, M.C.; Holmans, P.

    2016-01-01

    A strong motivation for undertaking psychiatric gene discovery studies is to provide novel insights into unknown biology. Although attention-deficit hyperactivity disorder (ADHD) is highly heritable, and large, rare copy number variants (CNVs) contribute to risk, little is known about its pathogenes

  14. Geographic variation in advertisement calls in a tree frog species: gene flow and selection hypotheses.

    Directory of Open Access Journals (Sweden)

    Yikweon Jang

    Full Text Available BACKGROUND: In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation. METHODOLOGY: We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR, note duration (ND, and dominant frequency (DF, along with snout-to-vent length. RESULTS: The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters. CONCLUSIONS: Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japonica. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with

  15. Geographic Variation in Advertisement Calls in a Tree Frog Species: Gene Flow and Selection Hypotheses

    Science.gov (United States)

    Jang, Yikweon; Hahm, Eun Hye; Lee, Hyun-Jung; Park, Soyeon; Won, Yong-Jin; Choe, Jae C.

    2011-01-01

    Background In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD) or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation. Methodology We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR), note duration (ND), and dominant frequency (DF), along with snout-to-vent length. Results The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters. Conclusions Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japoinca. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with restricted gene

  16. Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape.

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    Rachael V Adams

    Full Text Available Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus, along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart, but also within river systems by large treeless canyons (>100 km. Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic

  17. Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape

    Science.gov (United States)

    2015-01-01

    Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus), along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover) were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart), but also within river systems by large treeless canyons (>100 km). Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar) tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic variation. PMID

  18. Segregation Analysis of 231 Ashkenazi Jewish Families for Evidence of Additional Breast Cancer Susceptibility Genes

    National Research Council Canada - National Science Library

    David J. Kaufman; Terri H. Beaty; Jeffery P. Struewing

    2003-01-01

    .... Using segregation analysis, families of cases without BRCA1/2 mutations were studied for statistical evidence of another major breast cancer gene in a community-based sample of Jewish probands tested...

  19. Capital flows and asset prices: empirical evidence from emerging and developing economies

    OpenAIRE

    Taguchi, Hiroyuki; Sahoo, Pravakar; Nataraj, Geethanjali

    2015-01-01

    This paper aims at providing empirical evidence on the effect of capital flows on asset prices including its channel under different currency regimes, focusing on ten emerging and developing economies in the world with data availability and stationarity for the 2000s, by a generalized impulse response analysis under a vector auto-regression model. The main findings are as  follows. Portfolio capital inflows have a significantly positive effect on stock prices in all sample economies except tw...

  20. Gene Flow and the Measurement of Dispersal in Plant Populations.

    Science.gov (United States)

    Nicholls, Marc S.

    1986-01-01

    Reviews methods of estimating pollen and seed dispersals and discusses the extent and frequency of gene exchange within and between populations. Offers suggestions for designing exercises suitable for estimating dispersal distances in natural plant populations. (ML)

  1. Gene flow and herbicide resistance: Lessons learned from herbicide-resistant rice systems

    Science.gov (United States)

    Gene flow in plants is a process whereby genes are exchanged between members of the same or closely related species via pollen and become established in new populations. This natural process has long been an issue in breeding and the seed industry, but interest has increased since the deployment of ...

  2. Patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in the United States

    Science.gov (United States)

    Studies of gene flow between crops and their wild relatives have implications for both management practices for farming and breeding as well as understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene...

  3. Fetal exposure to teratogens: evidence of genes involved in autism.

    Science.gov (United States)

    Dufour-Rainfray, Diane; Vourc'h, Patrick; Tourlet, Sébastien; Guilloteau, Denis; Chalon, Sylvie; Andres, Christian R

    2011-04-01

    Environmental challenges during the prenatal period can result in behavioral abnormalities and cognitive deficits that appear later in life such as autism. Prenatal exposure to valproic acid, ethanol, thalidomide and misoprostol has been shown to be associated with an increased incidence of autism. In addition, rodents exposed in utero to some of these drugs show autism-like abnormalities, including brain changes and lifelong behavior dysfunction. Our aim is to summarize current understanding of the relationship between in utero exposure to these drugs and autism in humans and in autism-like animal model phenotypes. It also highlights the importance of these models to understanding the neurobiology of autism, particularly in the identification of susceptibility genes. These drugs are able to modulate the expression of many genes involved in processes such as proliferation, apoptosis, neuronal differentiation and migration, synaptogenesis and synaptic activity. It seems essential to focus research on genes expressed during early neurodevelopment which may be the target of mutations or affected by drugs such as those included in this review.

  4. Heritability of insulin sensitivity and lipid profile depend on BMI : evidence for gene-obesity interaction

    NARCIS (Netherlands)

    Wang, X.; Ding, X.; Su, S.; Spector, T. D.; Mangino, M.; Iliadou, A.; Snieder, H.

    2009-01-01

    Evidence from candidate gene studies suggests that obesity may modify genetic susceptibility to type 2 diabetes and dyslipidaemia. On an aggregate level, gene-obesity interactions are expected to result in different heritability estimates at different obesity levels. However, this hypothesis has nev

  5. Heritability of insulin sensitivity and lipid profile depend on BMI : evidence for gene-obesity interaction

    NARCIS (Netherlands)

    Wang, X.; Ding, X.; Su, S.; Spector, T. D.; Mangino, M.; Iliadou, A.; Snieder, H.

    2009-01-01

    Evidence from candidate gene studies suggests that obesity may modify genetic susceptibility to type 2 diabetes and dyslipidaemia. On an aggregate level, gene-obesity interactions are expected to result in different heritability estimates at different obesity levels. However, this hypothesis has

  6. Limited contemporary gene flow and high self-replenishment drives peripheral isolation in an endemic coral reef fish.

    Science.gov (United States)

    van der Meer, Martin H; Horne, John B; Gardner, Michael G; Hobbs, Jean-Paul A; Pratchett, Morgan; van Herwerden, Lynne

    2013-06-01

    Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long-term persistence of these species following local extinction. This study explored population connectivity in the ecologically-specialized endemic three-striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self-replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self-replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self-replenishment (95%), and low contemporary abundance.

  7. Evidence for Horizontal Gene Transfer as Origin of Putrescine Production in Oenococcus oeni RM83▿

    Science.gov (United States)

    Marcobal, Ángela; de las Rivas, Blanca; Moreno-Arribas, M. Victoria; Muñoz, Rosario

    2006-01-01

    The nucleotide sequence of a 17.2-kb chromosomal DNA fragment containing the odc gene encoding ornithine decarboxylase has been determined in the putrescine producer Oenococcus oeni RM83. This DNA fragment contains 13 open reading frames, including genes coding for five transposases and two phage proteins. This description might represent the first evidence of a horizontal gene transfer event as the origin of a biogenic amine biosynthetic locus. PMID:17056681

  8. Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

    Science.gov (United States)

    Cruse-Sanders, Jennifer M; Parker, Kathleen C; Friar, Elizabeth A; Huang, Daisie I; Mashayekhi, Saeideh; Prince, Linda M; Otero-Arnaiz, Adriana; Casas, Alejandro

    2013-01-01

    Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (HE = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear-cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species. PMID:23762520

  9. Paleofluid-flow circulation within a Triassic rift basin: Evidence from oil inclusions and thermal histories

    Science.gov (United States)

    Tseng, H.-Y.; Burruss, R.C.; Onstott, T.C.; Omar, G.

    1999-01-01

    The migration of subsurface fluid flow within continental rift basins has been increasingly recognized to significantly affect the thermal history of sediments and petroleum formation. To gain insight into these paleofluid flow effects, the thermal history of the Taylorsville basin in Virginia was reconstructed from fluid-inclusion studies, apatite fission-track data, and vitrinite reflectance data. Models of thermal history indicate that the basin was buried to the thermal maximum at 200 Ma; a cooling event followed during which the eastern side of the basin cooled earlier and faster than the western side, suggesting that there was a differential uplift and topographically driven fluid flow. This hypothesis is supported by analyses of secondary oil and aqueous inclusions trapped in calcite and quartz veins during the uplift stage. Gas chromatograms of inclusion oils exhibit variable but extensive depletion of light molecular-weight hydrocarbons. The relative abundance of n-alkanes, petrographic observations, and the geological data indicate that the alteration process on these inclusion oils was probably neither phase separation nor biodegradation, but water washing. Water:oil ratios necessary to produce the observed alteration are much greater than 10000:1. These exceedingly high ratios are consistent with the migration of inclusion oils along with fluid flow during the early stages of basin evolution. The results provide significant evidence about the role of a subsurface flow system in modifying the temperature structure of the basin and the composition of petroleum generated within the basin.

  10. Evidence for gene conversion among immunoglobulin heavy chain variable region genes.

    Science.gov (United States)

    Clarke, S H; Rudikoff, S

    1984-03-01

    We have previously reported that the VH region amino acid sequence of a phosphocholine (PC)-binding hybridoma antibody of CBA/J origin, HP101 6G6 (6G6), differs extensively from the VH regions of other PC-binding antibodies. The sequence of 6G6 VH appears to be derived from a gene homologous to the BALB/c V11 gene, a member of the PC VH (T15 VH) gene family not normally used to encode PC-binding antibodies. The 6G6 VH sequence differs from the translated sequence of V11 by six amino acids, four of which occur at the same position in other members of this gene family. This coincidence led to the proposal that the 6G6 VH gene was derived by gene conversion involving three genes of the PC VH gene family. We report here the nucleic acid sequence of the rearranged VH gene of hybridoma 6G6. This sequence supports our previous suggestion of gene conversion by confirming those differences, relative to the BALB/c V11 gene sequence, that are encoded by other members of this gene family, and extends this correlation to include three silent base pair substitutions as well. In addition, 5' noncoding region sequence and Southern blot analysis using probes derived from the coding and 5' noncoding regions confirm that the 6G6 VH gene is likely to be derived from the V11 homologue in CBA/J mice, and suggest that all three genes believed to be involved in the generation of the 6G6 VH gene are present in the CBA/J genome, a prerequisite for their involvement in gene conversion.

  11. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

    Science.gov (United States)

    Huang, Chao-Li; Ho, Chuan-Wen; Chiang, Yu-Chung; Shigemoto, Yasumasa; Hsu, Tsai-Wen; Hwang, Chi-Chuan; Ge, Xue-Jun; Chen, Charles; Wu, Tai-Han; Chou, Chang-Hung; Huang, Hao-Jen; Gojobori, Takashi; Osada, Naoki; Chiang, Tzen-Yuh

    2014-12-01

    Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

  12. Long distance pollen-mediated flow of herbicide resistance genes in Lolium rigidum.

    Science.gov (United States)

    Busi, Roberto; Yu, Qin; Barrett-Lennard, Robert; Powles, Stephen

    2008-11-01

    Gene flow promotes genetic exchange among plant populations mediating evolutionary dynamics; yet, the importance of gene flow at distance via pollen movement is poorly understood. A field experiment at the landscape level was conducted with Lolium rigidum herbicide-susceptible individuals (population VLR1) placed into an otherwise Lolium-free bushland environment at increasing distances from adjacent large commercial crop fields infested with herbicide-resistant L. rigidum. Herbicide resistance was used as a marker to quantify the distance and the rate of pollen-mediated gene flow. About 21,245 seeds were produced on the isolated, susceptible mother plants of which 3,303 seedlings were tested for herbicide resistance and 664 seedlings were found to be resistant. Pollen-mediated gene flow occurred at 3,000 m (maximum tested distance). Both Mendelian and molecular analyses (sequencing and CAPS markers) confirmed the introgression of herbicide resistance genes. This is the first documented case of long-distance gene flow in L. rigidum. The results are important for future modeling simulations of herbicide resistance evolution and subsequent mobility. The adoption of integrated agronomic strategies, the control of potential receptor plants on fields' margins and conservative use of herbicides can be realistic options to minimize herbicide resistance spread.

  13. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

    KAUST Repository

    Huang, Chao-Li

    2014-11-11

    Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

  14. Evidence suggesting possible SCA1 gene involvement in schizophrenia

    Energy Technology Data Exchange (ETDEWEB)

    Diehl, S.R.; Wange, S.; Sun, C. [NIDR, Bethesda, MD (United States)] [and others

    1994-09-01

    Several findings suggest a possible role for the SCA1 gene on chromosome 6p in some cases of schizophrenia. First, linkage analyses in Irish pedigrees provided LOD scores up to 3.0 for one model tested using microsatellites closely linked to SCA1. Reanalysis of these data using affected sibpair methods yielded a significant result (p = 0.01) for one marker. An attempt to replicate this linkage finding was made using 44 NIMH families (206 individuals, 80 affected) and 12 Utah families (120 individuals, 49 affected). LOD scores were negative in these new families, even allowing for heterogeneity, as were results using affected sibpair methods. However, one Utah family provided a LOD score of 1.3. We also screened the SCA1 trinucleotide repeat to search for expansions characteristic of this disorder in these families and in 38 additional unrelated schizophrenics. We found 1 schizophrenic with 41 repeats, which is substantially larger than the maximum size of 36 repeats observed in previous studies of several hundred controls. We are now assessing whether the distribution of SCA1 repeats differs significantly in schizophrenia versus controls. Recent reports suggest possible anticipation in schizophrenia (also characteristic of SCA1) and a few cases of psychiatric symptoms suggesting schizophrenia have been observed in the highly related disorder DRPLA (SCA2), which is also based on trinucleotide repeat expansion. These findings suggest that further investigations of this gene and chromosome region may be a priority.

  15. Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes.

    Science.gov (United States)

    Piotti, A; Leonardi, S; Buiteveld, J; Geburek, T; Gerber, S; Kramer, K; Vettori, C; Vendramin, G G

    2012-03-01

    The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle the possible presence of genotyping errors to obtain robust estimates of pollen flow in four European beech (Fagus sylvatica L.) populations from Austria and France. In each country one of the two plots is located in an unmanaged forest; the other plots are managed with a shelterwood system and inside a colonization area (in Austria and France, respectively). The two paternity analysis approaches provided almost identical estimates of gene flow. In general, we found high pollen immigration (~75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (~50%). In the two unmanaged plots, the average within-population pollen dispersal distances (from 80 to 184 m) were higher than previously estimated for beech. From the comparison between the Austrian managed and unmanaged plots, that are only 500 m apart, we found no evidence that either gene flow or reproductive success distributions were significantly altered by forest management. The investigated phenotypic traits (crown area, height, diameter and flowering phenology) were not significantly related with male reproductive success. Shelterwood seems to have an effect on the distribution of within-population pollen dispersal distances. In the managed plot, pollen dispersal distances were shorter, possibly because adult tree density is three-fold (163 versus 57 trees per hectare) with respect to the unmanaged one.

  16. Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution.

    Science.gov (United States)

    Moyers, Bryan A; Zhang, Jianzhi

    2016-05-01

    The source of genetic novelty is an area of wide interest and intense investigation. Although gene duplication is conventionally thought to dominate the production of new genes, this view was recently challenged by a proposal of widespread de novo gene origination in eukaryotic evolution. Specifically, distributions of various gene properties such as coding sequence length, expression level, codon usage, and probability of being subject to purifying selection among groups of genes with different estimated ages were reported to support a model in which new protein-coding proto-genes arise from noncoding DNA and gradually integrate into cellular networks. Here we show that the genomic patterns asserted to support widespread de novo gene origination are largely attributable to biases in gene age estimation by phylostratigraphy, because such patterns are also observed in phylostratigraphic analysis of simulated genes bearing identical ages. Furthermore, there is no evidence of purifying selection on very young de novo genes previously claimed to show such signals. Together, these findings are consistent with the prevailing view that de novo gene birth is a relatively minor contributor to new genes in genome evolution. They also illustrate the danger of using phylostratigraphy in the study of new gene origination without considering its inherent bias. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. On capital flows and macroeconomic performance: Evidence before and after the financial crisis in Turkey

    Directory of Open Access Journals (Sweden)

    Magda Kandil

    2015-12-01

    Full Text Available The paper sheds light on the Turkish experience of capital account liberalization and its effect on key macroeconomic variables, using quarterly data in a multivariate VAR model. We also take into consideration the crisis breakpoint in 2001 and estimate the effect of shocks attributed to capital flows, using quarterly data during the sub-periods 1989:01–2001:01 and 2001:02–2009:03. The findings indicate that capital flows have varying effects on the Turkish economy before and after the crisis in 2001 and the evidence supports significant effects of liberalizing financial flows on macroeconomic performance, especially during the post-crisis period (2001:02–2009:03. Moreover, this latter period exhibited evidence of sterilization policy that has helped mopping up excess liquidity and containing inflationary pressures. These factors seem to signal deliberate efforts by the Central Bank of Turkey to stem the risk of appreciation of the real exchange rate and preserve export competitiveness during periods of high financial inflows, a trend that has been reversed recently by the surge in outflows and currency depreciation in many emerging markets in anticipation of imminent normalization of monetary policy in the United States.

  18. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.

    Science.gov (United States)

    Poelstra, J W; Vijay, N; Bossu, C M; Lantz, H; Ryll, B; Müller, I; Baglione, V; Unneberg, P; Wikelski, M; Grabherr, M G; Wolf, J B W

    2014-06-20

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence. Copyright © 2014, American Association for the Advancement of Science.

  19. Textural evidence for jamming and dewatering of a sub-surface, fluid-saturated granular flow

    Science.gov (United States)

    Sherry, T. J.; Rowe, C. D.; Kirkpatrick, J. D.; Brodsky, E. E.

    2011-12-01

    Sand injectites are spectacular examples of large-scale granular flows involving migration of hundreds of cubic meters of sand slurry over hundreds of meters to kilometers in the sub-surface. By studying the macro- and microstructural textures of a kilometer-scale sand injectite, we interpret the fluid flow regimes during emplacement and define the timing of formation of specific textures in the injected material. Fluidized sand sourced from the Santa Margarita Fm., was injected upward into the Santa Cruz Mudstone, Santa Cruz County, California. The sand injectite exposed at Yellow Bank Beach records emplacement of both hydrocarbon and aqueous sand slurries. Elongate, angular mudstone clasts were ripped from the wall rock during sand migration, providing evidence for high velocity, turbid flow. However, clast long axis orientations are consistently sub-horizontal suggesting the slurry transitioned to a laminar flow as the flow velocity decreased in the sill-like intrusion. Millimeter to centimeter scale laminations are ubiquitous throughout the sand body and are locally parallel to the mudstone clast long axes. The laminations are distinct in exposure because alternating layers are preferentially cemented with limonite sourced from later groundwater infiltration. Quantitative microstructural analyses show that the laminations are defined by subtle oscillations in grain alignment between limonite and non-limonite stained layers. Grain packing, size and shape distributions do not vary. The presence of limonite in alternating layers results from differential infiltration of groundwater, indicating permeability changes between the layers despite minimal grain scale differences. Convolute dewatering structures deform the laminations. Dolomite-cemented sand, a signature of hydrocarbon saturation, forms irregular bodies that cross-cut the laminations and dewatering structures. Laminations are not formed in the dolomite-cemented sand. The relative viscosity difference

  20. Forest corridors maintain historical gene flow in a tiger metapopulation in the highlands of central India.

    Science.gov (United States)

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2013-09-22

    Understanding the patterns of gene flow of an endangered species metapopulation occupying a fragmented habitat is crucial for landscape-level conservation planning and devising effective conservation strategies. Tigers (Panthera tigris) are globally endangered and their populations are highly fragmented and exist in a few isolated metapopulations across their range. We used multi-locus genotypic data from 273 individual tigers (Panthera tigris tigris) from four tiger populations of the Satpura-Maikal landscape of central India to determine whether the corridors in this landscape are functional. This 45 000 km(2) landscape contains 17% of India's tiger population and 12% of its tiger habitat. We applied Bayesian and coalescent-based analyses to estimate contemporary and historical gene flow among these populations and to infer their evolutionary history. We found that the tiger metapopulation in central India has high rates of historical and contemporary gene flow. The tests for population history reveal that tigers populated central India about 10 000 years ago. Their population subdivision began about 1000 years ago and accelerated about 200 years ago owing to habitat fragmentation, leading to four spatially separated populations. These four populations have been in migration-drift equilibrium maintained by high gene flow. We found the highest rates of contemporary gene flow in populations that are connected by forest corridors. This information is highly relevant to conservation practitioners and policy makers, because deforestation, road widening and mining are imminent threats to these corridors.

  1. Considering spatial and temporal scale in landscape-genetic studies of gene flow.

    Science.gov (United States)

    Anderson, Corey Devin; Epperson, Bryan K; Fortin, Marie-Josée; Holderegger, Rolf; James, Patrick M A; Rosenberg, Michael S; Scribner, Kim T; Spear, Stephen

    2010-09-01

    Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.

  2. COUNTRY RISK EVALUATION IMPACT ON FDI FLOW. MEDIUM RUN EVIDENCE FROM ROMANIA

    Directory of Open Access Journals (Sweden)

    EMILIA UNGUREANU

    2014-10-01

    Full Text Available During the last two decades, Romanian economy suffered numerous changes, with direct impact in the socio-economic and political life. This affected also the investment environment, the degree of attractiveness for investors and the flow of FDIs. As the economic system has a global dimension, the need of evaluating different countries from a risk perspective (that will serve as starting point for investor’s decision has increased the role of rating agencies, especially in the economic crisis context. Therefore, by applying two econometric models, we will determine in which degree the risk rating (using the Euromoney index is influencing the FDI flow in Romania, having as evidence the period 1996-2012.

  3. Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

    Science.gov (United States)

    De Groote, Annelies; Hauquier, Freija; Vanreusel, Ann; Derycke, Sofie

    2017-07-01

    There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

  4. Applying gene flow science to environmental policy needs: a boundary work perspective.

    Science.gov (United States)

    Ridley, Caroline E; Alexander, Laurie C

    2016-08-01

    One application of gene flow science is the policy arena. In this article, we describe two examples in which the topic of gene flow has entered into the U.S. national environmental policymaking process: regulation of genetically engineered crops and clarification of the jurisdictional scope of the Clean Water Act. We summarize both current scientific understanding and the legal context within which gene flow science has relevance. We also discuss the process by which scientific knowledge has been synthesized and communicated to decision-makers in these two contexts utilizing the concept of 'boundary work'. Boundary organizations, the work they engage in to bridge the worlds of science, policy, and practice, and the boundary objects they produce to translate scientific knowledge existed in both examples. However, the specific activities and attributes of the objects produced varied based on the needs of the decision-makers. We close with suggestions for how scientists can contribute to or engage in boundary work with policymakers.

  5. Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide.

    Science.gov (United States)

    Baker, C S; Slade, R W; Bannister, J L; Abernethy, R B; Weinrich, M T; Lien, J; Urban, J; Corkeron, P; Calmabokidis, J; Vasquez, O

    1994-08-01

    The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or 'stocks', world-wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world-wide genetic variation among oceanic populations, among subpopulations or 'stocks' within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south-eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or 'American' stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long-lived, mobile vertebrates in the marine ecosystem.

  6. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua

    Directory of Open Access Journals (Sweden)

    Mittelholzer Christian

    2009-12-01

    Full Text Available Abstract Background Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs for evidence of selection in local populations of Atlantic cod (Gadus morhua L. across the species distribution. Results Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se. Conclusion These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of

  7. Gene flow among populations of two rare co-occurring fern species differing in ploidy level.

    Science.gov (United States)

    Bucharová, Anna; Münzbergová, Zuzana

    2012-01-01

    Differences in ploidy levels among different fern species have a vast influence on their mating system, their colonization ability and on the gene flow among populations. Differences in the colonization abilities of species with different ploidy levels are well known: tetraploids, in contrast to diploids, are able to undergo intra-gametophytic selfing. Because fertilization is a post-dispersal process in ferns, selfing results in better colonization abilities in tetraploids because of single spore colonization. Considerably less is known about the gene flow among populations of different ploidy levels. The present study examines two rare fern species that differ in ploidy. While it has already been confirmed that tetraploid species are better at colonizing, the present study focuses on the gene flow among existing populations. We analyzed the genetic structure of a set of populations in a 10×10 km study region using isoenzymes. Genetic variation in tetraploid species is distributed mainly among populations; the genetic distance between populations is correlated with the geographical distance, and larger populations host more genetic diversity than smaller populations. In the diploid species, most variability is partitioned within populations; the genetic distance is not related to geographic distance, and the genetic diversity of populations is not related to the population size. This suggests that in tetraploid species, which undergo selfing, gene flow is limited. In contrast, in the diploid species, which experience outcrossing, gene flow is extensive and the whole system behaves as one large population. Our results suggest that in ferns, the ability to colonize new habitats and the gene flow among existing populations are affected by the mating system.

  8. Assessment on alien herbicide-resistant gene flow among crucifers by sexual compatibility

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiangxiang; LU Weiping; QI Cunkou; PU Huiming; XIA Qiuxia; LU Dalei; LIU Geshan; WANG Youping

    2005-01-01

    Cross-pollination and high cross-compatibility are frequently found in many cruciferous plants, which implies that there might be potential risk of alien gene flow among crucifers. In this work, the alien glyphosate-resistant gene flow between GM (Genetically modified) rapeseed variety Q3 (Brassica napus) and 6 varieties from 5 cruciferous species was assessed by sexual compatibility through aniline blue fluorescence observation, manual cross, mentor pollination with the mixture pollen and DNA identification. The results indicated that the compatibility indices of two B. napus varieties, B. juncea var. multiceps Tsen et Lee and Chinese cabbage (B. chinensis) (as female) with Q3 (as male) were 16.15, 12.77, 2.345 and 0.85, respectively. F1 plants were examined by PCR and all of these samples were confirmed as positive. Crossing between Orychophragmus violaceus, Descurainia sophia (as female) and Q3 (as male) expressed high cross-incompatibility. Fluorescence microscope observation indicated that growing of pollen tube terminated at the upper 1/3 part of the style of O. violaceus and on the stigma surface of D. sophia. The mentor plants were further analyzed by PCR and all were shown to be negative. Under the neighboring growth and natural pollination conditions, the rates of gene flow to two B. napus varieties were 2.3278% and 2.1487%, respectively, B. juncea var. multiceps Tsen et Lee and Chinese cabbage were 1.0157% and 0.9236%, respectively. No gene flow was observed in O. violaceus and D. sophia. Frequency of gene flow was highly correlated with sexual compatibility. Due to possible alien gene flow among crucifers, special consideration and care should be taken to grow GM rapeseed.

  9. Evidence-based prioritisation and enrichment of genes interacting with metformin in type 2 diabetes.

    Science.gov (United States)

    Dawed, Adem Y; Ali, Ashfaq; Zhou, Kaixin; Pearson, Ewan R; Franks, Paul W

    2017-08-25

    There is an extensive body of literature suggesting the involvement of multiple loci in regulating the action of metformin; most findings lack replication, without which distinguishing true-positive from false-positive findings is difficult. To address this, we undertook evidence-based, multiple data integration to determine the validity of published evidence. We (1) built a database of published data on gene-metformin interactions using an automated text-mining approach (n = 5963 publications), (2) generated evidence scores for each reported locus, (3) from which a rank-ordered gene set was generated, and (4) determined the extent to which this gene set was enriched for glycaemic response through replication analyses in a well-powered independent genome-wide association study (GWAS) dataset from the Genetics of Diabetes and Audit Research Tayside Study (GoDARTS). From the literature search, seven genes were identified that are related to the clinical outcomes of metformin. Fifteen genes were linked with either metformin pharmacokinetics or pharmacodynamics, and the expression profiles of a further 51 genes were found to be responsive to metformin. Gene-set enrichment analysis consisting of the three sets and two more composite sets derived from the above three showed no significant enrichment in four of the gene sets. However, we detected significant enrichment of genes in the least prioritised category (a gene set in which their expression is affected by metformin) with glycaemic response to metformin (p = 0.03). This gene set includes novel candidate genes such as SLC2A4 (p = 3.24 × 10(-04)) and G6PC (p = 4.77 × 10(-04)). We have described a semi-automated text-mining and evidence-scoring algorithm that facilitates the organisation and extraction of useful information about gene-drug interactions. We further validated the output of this algorithm in a drug-response GWAS dataset, providing novel candidate loci for gene-metformin interactions.

  10. Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

    Directory of Open Access Journals (Sweden)

    Burgun Anita

    2006-05-01

    Full Text Available Abstract Background Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by trained biologists (annotation based on evidence or text-mining of the published scientific literature (literature profiling. Results We report an original functional annotation method based on a combination of evidence and literature that overcomes the weaknesses and the limitations of each approach. It relies on the Gene Ontology Annotation database (GOA Human and the PubGene biomedical literature index. We support these annotations with statistically associated GO terms and retrieve associative relations across the three GO hierarchies to emphasise the major pathways involved by a gene cluster. Both annotation methods and associative relations were quantitatively evaluated with a reference set of 7397 genes and a multi-cluster study of 14 clusters. We also validated the biological appropriateness of our hybrid method with the annotation of a single gene (cdc2 and that of a down-regulated cluster of 37 genes identified by a transcriptome study of an in vitro enterocyte differentiation model (CaCo-2 cells. Conclusion The combination of both approaches is more informative than either separate approach: literature mining can enrich an annotation based only on evidence. Text-mining of the literature can also find valuable associated MEDLINE references that confirm the relevance of the annotation. Eventually, GO terms networks can be built with associative relations in order to highlight cooperative and competitive pathways and their connected molecular functions.

  11. Gene flow between sexual and facultatively asexual lineages of an aphid species and the maintenance of reproductive mode variation.

    Science.gov (United States)

    Halkett, F; Plantegenest, M; Bonhomme, J; Simon, J-C

    2008-06-01

    Many organisms considered as strictly clonal may in fact experience some rare events of sexual reproduction with their sexual relatives. However, the rate of sexual-asexual gene flow has rarely been assessed mainly because its evaluation is difficult to achieve in the field. In the cyclically parthenogenetic aphid Rhopalosiphum padi, two main sets of lineages, differing in their investment in sexual reproduction and in their genetic attributes, co-exist even at a very fine scale: the 'sexual' lineages which have a full commitment to the sexual reproduction, and the 'facultatively asexual' lineages, which allocate investment in the sexual and parthenogenetic reproduction. This system offers a unique opportunity to tackle the genetic interactions between two contrasting reproductive modes. Here, we provide evidence that gene flow occurred between sexual and facultatively asexual lineages of R. padi. We carefully examined the shuffling in phenotypic and genotypic variation following a sexual reproduction event that took place in the field. Combining genotypic data and phenotypic measurements showed that this gene mixing led to the production of a wide array of reproductive modes, including strictly asexual lineages. Finally, we discuss the central role played by facultatively asexual lineages on the maintenance of reproductive mode variation.

  12. Comparing direct vs. indirect estimates of gene flow within a population of a scattered tree species.

    Science.gov (United States)

    Oddou-Muratorio, Sylvie; Klein, Etienne K

    2008-06-01

    The comparison between historical estimates of gene flow, using variance in allelic frequencies, and contemporary estimates of gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at six microsatellite loci was used to quantify genetic structure in the insect-pollinated, animal-dispersed, low-density tree Sorbus torminalis L. Crantz, and to derive historical estimates of gene flow. The neighbourhood size and root-mean-squared dispersal distance inferred from seedling genotypes (N(b) = 70 individuals, sigma(e) = 417 m) were similar to those inferred from adult genotypes (N(b) = 114 individuals, sigma(e) = 472 m). We also used parentage analyses and a neighbourhood model approach after an evaluation of the statistical properties of this method on simulated data. From our data, we estimated even contributions of seed- and pollen-mediated dispersal to the genetic composition of established seedlings, with both fat-tailed pollen and seed dispersal kernels, and slightly higher mean distance of pollen dispersal (248 m) as compared to seed dispersal (135 m). The resulting contemporary estimate of gene dispersal distance (sigma(c) = 211 m) was approximately twofold smaller than the historical estimates. Besides different assumptions and statistical nuances of both approaches, this discrepancy is likely to reflect a recent restriction in the scale of gene flow which requires manager's attention in a context of increasing forest fragmentation.

  13. Long distance pollen-mediated gene flow at a landscape level: the weed beet as a case study.

    Science.gov (United States)

    Fénart, Stéphane; Austerlitz, Frédéric; Cuguen, Joël; Arnaud, Jean-François

    2007-09-01

    Gene flow is a crucial parameter that can affect the organization of genetic diversity in plant species. It has important implications in terms of conservation of genetic resources and of gene exchanges between crop to wild relatives and within crop species complex. In the Beta vulgaris complex, hybridization between crop and wild beets in seed production areas is well documented and the role of the ensuing hybrids, weed beets, as bridges towards wild forms in sugar beet production areas have been shown. Indeed, in contrast to cultivated beets that are bi-annual, weed beets can bolt, flower and reproduce in the same crop season. Nonetheless, the extent of pollen gene dispersal through weedy lineages remains unknown. In this study, the focus is directed towards weed-to-weed gene flow, and we report the results of a pollen-dispersal analysis within an agricultural landscape composed of five sugar beet fields with different levels of infestation by weed beets. Our results, based on paternity analysis of 3240 progenies from 135 maternal plants using 10 microsatellite loci, clearly demonstrate that even if weedy plants are mostly pollinated by individuals from the same field, some mating events occur between weed beets situated several kilometres apart (up to 9.6 km), with rates of interfield-detected paternities ranging from 11.3% to 17.5%. Moreover, we show that pollen flow appears to be more restricted when individuals are aggregated as most mating events occurred only for short-distance classes. The best-fit dispersal curves were fat-tailed geometric functions for populations exhibiting low densities of weed beets and thin-tailed Weibull function for fields with weed beet high densities. Thus, weed beet populations characterized by low density with geographically isolated individuals may be difficult to detect but are likely to act as pollen traps for pollen emitted by close and remote fields. Hence, it appears evident that interfield pollen-mediated gene flow

  14. Biophysics and biofluid dynamics of primary cilia: evidence for and against the flow-sensing function.

    Science.gov (United States)

    Nag, Subhra; Resnick, Andrew

    2017-09-01

    Primary cilia have been called "the forgotten organelle" for over 20 yr. As cilia now have their own journal and several books devoted to their study, perhaps it is time to reconsider the moniker "forgotten organelle." In fact, during the drafting of this review, 12 relevant publications have been issued; we therefore apologize in advance for any relevant work we inadvertently omitted. What purpose is yet another ciliary review? The primary goal of this review is to specifically examine the evidence for and against the hypothesized flow-sensing function of primary cilia expressed by differentiated epithelia within a kidney tubule, bringing together differing disciplines and their respective conceptual and experimental approaches. We will show that understanding the biophysics/biomechanics of primary cilia provides essential information for understanding any potential role of ciliary function in disease. We will summarize experimental and mathematical models used to characterize renal fluid flow and incident force on primary cilia and to characterize the mechanical response of cilia to an externally applied force and discuss possible ciliary-mediated cell signaling pathways triggered by flow. Throughout, we stress the importance of separating the effects of fluid shear and stretch from the action of hydrodynamic drag. Copyright © 2017 the American Physiological Society.

  15. Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer.

    Directory of Open Access Journals (Sweden)

    Michael J Bryan

    Full Text Available BACKGROUND: S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage. METHODOLOGY/PRINCIPAL FINDINGS: This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces. CONCLUSIONS/SIGNIFICANCE: This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene.

  16. Post-fire hillslope debris flows: Evidence of a distinct erosion process

    Science.gov (United States)

    Langhans, Christoph; Nyman, Petter; Noske, Philip J.; Van der Sant, Rene E.; Lane, Patrick N. J.; Sheridan, Gary J.

    2017-10-01

    After wildfire a hitherto unexplained erosion process that some authors have called 'miniature debris flows on hillslopes' and that leave behind levee-lined rills has been observed in some regions of the world. Despite the unusual proposition of debris flow on planar hillslopes, the process has not received much attention. The objectives of this study were to (1) accumulate observational evidence of Hillslope Debris Flows (HDF) as we have defined the process, to (2) understand their initiation process by conducting runoff experiments on hillslopes, to (3) propose a conceptual model of HDF, and to (4) contrast and classify HDF relative to other erosion and transport processes in the post-wildfire hillslope domain. HDF have been observed at relatively steep slope gradients (0.4-0.8), on a variety of geologies, and after fire of at least moderate severity and consist of a lobe of gravel- to cobble-sized material 0.2-1 m wide that is pushed by runoff damming up behind it. During initiation, runoff moved individual particles that accumulated a small distance downslope until the accumulation of grains failed and formed the granular lobe of the HDF. HDF are a threshold process, and runoff rates of 0.5 L s- 1 2 L s- 1 were required for their initiation during the experiments. The conceptual model highlights HDF as a geomorphic process distinct from channel debris flows, because they occur on planar, unconfined hillslopes rather than confined channels. HDF can erode very coarse non-cohesive surface soil, which distinguishes them from rill erosion that have suspended and bedload transport. On a matrix of slope and grain size, HDF are enveloped between purely gravity-driven dry ravel, and mostly runoff driven bedload transport in rills.

  17. A study on relationship between earnings management and operating cash flows management: Evidence from Tehran Stock Exchange

    Directory of Open Access Journals (Sweden)

    Bahman Banimahd

    2013-06-01

    Full Text Available This study investigates the impact of earnings management on operating cash flows management over the period 2004-2011 using the information of 119 firms listed on the Tehran Stock Exchange. Results indicate that there is a meaningful relationship between earnings management and operating cash flows management. In other words, earnings management creates and shapes operating cash flows management. In addition, after controlling for the loss reporting, firm size and firm's financial risk, the results show that there was a relationship between loss reporting and firm size with the cash flows management. When firms report loss, then operating cash flows increases. Finally, operating cash flows decreases when firm size increases. However, our survey does not provide any evidence to believe there is any relationship between financial risk and cash flows management.

  18. A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data.

    Science.gov (United States)

    Flores, Kevin B

    2013-07-01

    We formulated a structured population model with distributed parameters to identify mechanisms that contribute to gene expression noise in time-dependent flow cytometry data. The model was validated using cell population-level gene expression data from two experiments with synthetically engineered eukaryotic cells. Our model captures the qualitative noise features of both experiments and accurately fit the data from the first experiment. Our results suggest that cellular switching between high and low expression states and transcriptional re-initiation are important factors needed to accurately describe gene expression noise with a structured population model.

  19. Evidence for widespread adaptive evolution of gene expression in budding yeast.

    Science.gov (United States)

    Fraser, Hunter B; Moses, Alan M; Schadt, Eric E

    2010-02-16

    Changes in gene expression have been proposed to underlie many, or even most, adaptive differences between species. Despite the increasing acceptance of this view, only a handful of cases of adaptive gene expression evolution have been demonstrated. To address this discrepancy, we introduce a simple test for lineage-specific selection on gene expression. Applying the test to genome-wide gene expression data from the budding yeast Saccharomyces cerevisiae, we find that hundreds of gene expression levels have been subject to lineage-specific selection. Comparing these findings with independent population genetic evidence of selective sweeps suggests that this lineage-specific selection has resulted in recent sweeps at over a hundred genes, most of which led to increased transcript levels. Examination of the implicated genes revealed a specific biochemical pathway--ergosterol biosynthesis--where the expression of multiple genes has been subject to selection for reduced levels. In sum, these results suggest that adaptive evolution of gene expression is common in yeast, that regulatory adaptation can occur at the level of entire pathways, and that similar genome-wide scans may be possible in other species, including humans.

  20. Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

    Science.gov (United States)

    Lee, Justin S.; Ruell, Emily W.; Boydston, Erin E.; Lyren, Lisa M.; Alonso, Robert S.; Troyer, Jennifer L.; Crooks, Kevin R.; VandeWoude, Sue

    2012-01-01

    Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured--exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

  1. Gene flow from Sorghum bicolor to its weedy relatives and its ...

    African Journals Online (AJOL)

    computer user

    2015-04-29

    Apr 29, 2015 ... drummondii, has shown natural outcrossing ranging from. 0-100% on individual ... result of artificial and natural selection for more than one level of a particular ...... Possible effects of (trans) gene flow from crops on the genetic ...

  2. Gene flow from Sorghum bicolor to its weedy relatives and its ...

    African Journals Online (AJOL)

    computer user

    2015-02-18

    Feb 18, 2015 ... more quantitative and precise methods of analyzing target DNA ... laboratory located at the College of Agriculture and Veterinary .... emitted fluorescence exceeded the standardized ..... designing effective tools to measure gene flow. .... and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for.

  3. Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock.

    Science.gov (United States)

    Kwit, Charles; Stewart, C Neal

    2012-01-01

    There currently exists a large push for the use, improvement, and expansion via landscape modification of dedicated biofuel crops (feedstocks) in the United States and in many parts of the world. Ecological concerns have been voiced because many biofuel feedstocks exhibit characteristics associated with invasiveness, and due to potential negative consequences of agronomic genes in native wild populations. Seed purity concerns for biofuel feedstock cultivars whose seeds would be harvested in agronomic fields also exist from the agribusiness sector. The common thread underlying these concerns, which have regulatory implications, is gene flow; thus detailed knowledge of gene flow in biofuel crop plants is important in the formulation of environmental risk management plans. Here, we synthesize the current state of knowledge of gene flow in an exemplary biofuel crop, switchgrass (Panicum virgatum L.), which is native to eastern North America and is currently experiencing conventional and technological advances in biomass yields and ethanol production. Surprisingly little is known regarding aspects of switchgrass pollen flow and seed dispersal, and whether native populations of conspecific or congeneric relatives will readily cross with current agronomic switchgrass cultivars. We pose that filling these important gaps will be required to confront the sustainability challenges of widespread planting of biofuel feedstocks.

  4. Pollen and seed mediated gene flow in commercial alfalfa seed production fields

    Science.gov (United States)

    The potential for gene flow has been widely recognized since alfalfa is pollinated by bees. The Western US is a major exporter of alfalfa seed and hay and the organic dairy industry is one of the fastest growing agricultural sectors. Because of this, many alfalfa producers are impacted by market sen...

  5. New evidence for ice shelf flow across the Alaska and Beaufort margins, Arctic Ocean

    Science.gov (United States)

    Engels, Jennifer L.

    The Arctic Ocean may act as a lynchpin for global climate change due to its unique physiography as a mediterranean sea located in polar latitudes. In our modern warming climate, debate over the bounds of natural versus anthropogenically-induced climate variability necessitates a comprehensive understanding of Arctic ice extent and configuration over the last interglacial cycle. Longstanding controversy exists as to the volume, timing, and flow trajectories of ice in the Arctic Ocean during glacial maxima when continental ice sheets mantled circum-arctic landmasses. As a result of the Science Ice Exercise surveys of the Arctic Ocean in 1999, new evidence for ice grounding at depths down to 980 m on the Lomonosov Ridge and 750 m on the Chukchi Borderland indicates the likelihood that large ice shelves flowed into the ocean from both the Barents/Kara Sea and the Canadian Arctic Archipelago or eastern Alaska. Sidescan imagery of ˜14100 km2 of seafloor along the Alaska and Beaufort margins in water depths from 250--2800 m maps a repetitive association of recognizable sub-glacially generated bedforms, ice carved-bathymerry, and ice-marginal turbidite gullies over a 640 km stretch of the margin between Point Barrow and the MacKenzie River delta. Glaciogenic bedforms occur across the surface of a flattened bathymetric bench or 'second shelf break' that is interpreted to have been formed by an ice shelf eroding the continental slope. The glacial geology of surrounding areas suggests that an ice shelf on the Alaska and Beaufort margins likely flowed from the mouths of overdeepened glacial troughs in the Canadian Arctic Archipelago westward and across the Chukchi Borderland due to an obstruction in the central Canadian basin. Evidence for an ice shelf along the Alaska and Beaufort margins supports an expanded interpretation of ice volume and extent during Pleistocene glacial periods. This has far-reaching implications for Arctic climate studies, ocean circulation, sediment

  6. Patients, evidence and genes: an exploration of GPs' perspectives on gene-based personalized nutrition advice

    NARCIS (Netherlands)

    Bouwman, L.I.; Molder, te H.F.M.; Hiddink, G.J.

    2008-01-01

    Background. Nutrigenomics science examines the response of individuals to food compounds using post-genomics technology. It is expected that in the future, personalized nutrition advice can be provided based on information about genetic make-up. Objectives. Gene-based personalized nutrition advice e

  7. Evidence of Reactive Gene-Environment Correlation in Preschoolers' Prosocial Play with Unfamiliar Peers

    Science.gov (United States)

    DiLalla, Lisabeth Fisher; Bersted, Kyle; John, Sufna Gheyara

    2015-01-01

    The development of prosocial behaviors during the preschool years is essential for children's positive interactions with peers in school and other social situations. Although there is some evidence of genetic influences on prosocial behaviors, very little is known about how genes and environment, independently and in concert, affect prosocial…

  8. Evidence of current impact of climate change on life : A walk from genes to the biosphere

    NARCIS (Netherlands)

    Penuelas, Josep; Sardans, Jordi; Estiarte, Marc; Ogaya, Roma; Carnicer, Jofre; Coll, Marta; Barbeta, Adria; Rivas-Ubach, Albert; Llusia, Joan; Garbulsky, Martin; Filella, Iolanda; Jump, Alistair S.

    We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of

  9. Delinquent Peer Group Formation: Evidence of a Gene X Environment Correlation

    Science.gov (United States)

    Beaver, Kevin M.; Wright, John Paul; DeLisi, Matt

    2008-01-01

    Emerging evidence suggests that variants of specific genes may influence some youths to seek out or associate with antisocial peers. Using genotypic data (N = 1,816) from the National Longitudinal Study of Adolescent Health (J. R. Udry, 1998, 2003), the authors tested this possibility. They found that the 10R allele of the dopamine transporter…

  10. Delinquent Peer Group Formation: Evidence of a Gene X Environment Correlation

    Science.gov (United States)

    Beaver, Kevin M.; Wright, John Paul; DeLisi, Matt

    2008-01-01

    Emerging evidence suggests that variants of specific genes may influence some youths to seek out or associate with antisocial peers. Using genotypic data (N = 1,816) from the National Longitudinal Study of Adolescent Health (J. R. Udry, 1998, 2003), the authors tested this possibility. They found that the 10R allele of the dopamine transporter…

  11. [Gene flow and its ecological risks of transgenic oilseed rape ( Brassica napus)].

    Science.gov (United States)

    Tang, Guixiang; Song, Wenjian; Zhou, Weijun

    2005-12-01

    Transgenic oilseed rape Brassica napus, one of the first genetically modified crops, has now been released to commercial use in Canada and Australia. As a cross-pollinating crop, its natural crossing rate is 30%, and it is liable to cross with other Brassica species. The ecological risk of transgenic oilseed rape has been concerned by the scientists all over the world. There are two ways for the pollens flow of transgenic oilseed rape, one takes place between transgenic oilseed rape and other related wild species, and the other occurs between transgenic and nontransgenic oilseed rape. The gene may flow to other related wild species, but it is unlikely to get hybrids in field. Because the gene can really flow to the conventional oilseed rape, it is necessary to have a sufficient isolation distance in cultivating transgenic oilseed rape.

  12. Monitoring gene flow from transgenic sugar beet using cytoplasmic male-sterile bait plants.

    Science.gov (United States)

    Saeglitz, C; Pohl, M; Bartsch, D

    2000-12-01

    One of the most discussed environmental effects associated with the use of transgenic plants is the flow of genes to plants in the environment. The flow of genes may occur through pollen since it is the reproductive system that is designed for gene movement. Pollen-mediated gene escape is hard to control in mating plants. Pollen from a wind pollinator can move over distances of more than 1000 m. To investigate the efficiency of transgenic pollen movement under realistic environmental conditions, the use of bait plants might be an effective tool. In this study, cytoplasmic male-sterile (CMS) sugar beets were tested with regard to their potential for monitoring transgene flow. As the pollen source, transgenic sugar beets were used that express recombinant DNA encoding viral (beet necrotic yellow vein virus) resistance, and antibiotic (kanamycin) and herbicide (glufosinate) tolerance genes. In a field trial, the effectiveness of a hemp (Cannabis sativa) stripe containment strategy was tested by measuring the frequency of pollinated CMS bait plants placed at different distances and directions from a transgenic pollen source. The results demonstrated the ineffectiveness of the containment strategy. Physiological and molecular tests confirmed the escape and production of transgenic offspring more than 200 m behind the hemp containment. Since absolute containment is unlikely to be effective, the CMS-bait plant detection system is a useful tool for other monitoring purposes.

  13. Gene flow in Prunus species in the context of novel trait risk assessment.

    Science.gov (United States)

    Cici, S Zahra H; Van Acker, Rene C

    2010-01-01

    Prunus species are important commercial fruit (plums, apricot, peach and cherries), nut (almond) and ornamental trees cultivated broadly worldwide. This review compiles information from available literature on Prunus species in regard to gene flow and hybridization within this complex of species. The review serves as a resource for environmental risk assessment related to pollen mediated gene flow and the release of transgenic Prunus. It reveals that Prunus species, especially plums and cherries show high potential for transgene flow. A range of characteristics including; genetic diversity, genetic bridging capacity, inter- and intra-specific genetic compatibility, self sterility (in most species), high frequency of open pollination, insect assisted pollination, perennial nature, complex phenotypic architecture (canopy height, heterogeneous crown, number of flowers produced in an individual plant), tendency to escape from cultivation, and the existence of ornamental and road side Prunus species suggest that there is a tremendous and complicated ability for pollen mediated gene movement among Prunus species. Ploidy differences among Prunus species do not necessarily provide genetic segregation. The characteristics of Prunu s species highlight the complexity of maintaining coexistence between GM and non-GM Prunus if there were commercial production of GM Prunus species. The results of this review suggest that the commercialization of one GM Prunus species can create coexistence issues for commercial non-GM Prunus production. Despite advances in molecular markers and genetic analysis in agroecology, there remains limited information on the ecological diversity, metapopulation nature, population dynamics, and direct measures of gene flow among different subgenera represented in the Prunus genus. Robust environmental impact, biosafety and coexistence assessments for GM Prunus species will require better understanding of the mechanisms of gene flow and hybridization

  14. Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus).

    Science.gov (United States)

    Pérez-Espona, S; Pérez-Barbería, F J; McLeod, J E; Jiggins, C D; Gordon, I J; Pemberton, J M

    2008-02-01

    Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 x 87 km), significant population structure was found using F-statistics (F(ST) = 0.019) and the program structure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.

  15. Beekeeping practices and geographic distance, not land use, drive gene flow across tropical bees.

    Science.gov (United States)

    Jaffé, Rodolfo; Pope, Nathaniel; Acosta, André L; Alves, Denise A; Arias, Maria C; De la Rúa, Pilar; Francisco, Flávio O; Giannini, Tereza C; González-Chaves, Adrian; Imperatriz-Fonseca, Vera L; Tavares, Mara G; Jha, Shalene; Carvalheiro, Luísa G

    2016-11-01

    Across the globe, wild bees are threatened by ongoing natural habitat loss, risking the maintenance of plant biodiversity and agricultural production. Despite the ecological and economic importance of wild bees and the fact that several species are now managed for pollination services worldwide, little is known about how land use and beekeeping practices jointly influence gene flow. Using stingless bees as a model system, containing wild and managed species that are presumed to be particularly susceptible to habitat degradation, here we examine the main drivers of tropical bee gene flow. We employ a novel landscape genetic approach to analyse data from 135 populations of 17 stingless bee species distributed across diverse tropical biomes within the Americas. Our work has important methodological implications, as we illustrate how a maximum-likelihood approach can be applied in a meta-analysis framework to account for multiple factors, and weight estimates by sample size. In contrast to previously held beliefs, gene flow was not related to body size or deforestation, and isolation by geographic distance (IBD) was significantly affected by management, with managed species exhibiting a weaker IBD than wild ones. Our study thus reveals the critical importance of beekeeping practices in shaping the patterns of genetic differentiation across bee species. Additionally, our results show that many stingless bee species maintain high gene flow across heterogeneous landscapes. We suggest that future efforts to preserve wild tropical bees should focus on regulating beekeeping practices to maintain natural gene flow and enhancing pollinator-friendly habitats, prioritizing species showing a limited dispersal ability.

  16. Testing the role of meander cutoff in promoting gene flow across a riverine barrier in ground skinks (Scincella lateralis.

    Directory of Open Access Journals (Sweden)

    Nathan D Jackson

    Full Text Available Despite considerable attention, the long-term impact of rivers on species diversification remains uncertain. Meander loop cutoff (MLC is one river phenomenon that may compromise a river's diversifying effects by passively transferring organisms from one side of the river to the other. However, the ability of MLC to promote gene flow across rivers has not been demonstrated empirically. Here, we test several predictions of MLC-mediated gene flow in populations of North American ground skinks (Scincella lateralis separated by a well-established riverine barrier, the Mississippi River: 1 individuals collected from within meander cutoffs should be more closely related to individuals across the river than on the same side, 2 individuals within meander cutoffs should contain more immigrants than individuals away from meander cutoffs, 3 immigration rates estimated across the river should be highest in the direction of the cutoff event, and 4 the distribution of alleles native to one side of the river should be better predicted by the historical rather than current path of the river. To test these predictions we sampled 13 microsatellite loci and mitochondrial DNA from ground skinks collected near three ancient meander loops. These predictions were generally supported by genetic data, although support was stronger for mtDNA than for microsatellite data. Partial support for genetic divergence of samples within ancient meander loops also provides evidence for the MLC hypothesis. Although a role for MLC-mediated gene flow was supported here for ground skinks, the transient nature of river channels and morphologies may limit the long-term importance of MLC in stemming population divergence across major rivers.

  17. Evidence against the energetic cost hypothesis for the short introns in highly expressed genes

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    Niu Deng-Ke

    2008-05-01

    Full Text Available Abstract Background In animals, the moss Physcomitrella patens and the pollen of Arabidopsis thaliana, highly expressed genes have shorter introns than weakly expressed genes. A popular explanation for this is selection for transcription efficiency, which includes two sub-hypotheses: to minimize the energetic cost or to minimize the time cost. Results In an individual human, different organs may differ up to hundreds of times in cell number (for example, a liver versus a hypothalamus. Considered at the individual level, a gene specifically expressed in a large organ is actually transcribed tens or hundreds of times more than a gene with a similar expression level (a measure of mRNA abundance per cell specifically expressed in a small organ. According to the energetic cost hypothesis, the former should have shorter introns than the latter. However, in humans and mice we have not found significant differences in intron length between large-tissue/organ-specific genes and small-tissue/organ-specific genes with similar expression levels. Qualitative estimation shows that the deleterious effect (that is, the energetic burden of long introns in highly expressed genes is too negligible to be efficiently selected against in mammals. Conclusion The short introns in highly expressed genes should not be attributed to energy constraint. We evaluated evidence for the time cost hypothesis and other alternatives.

  18. Functional evolution of ADAMTS genes: Evidence from analyses of phylogeny and gene organization

    Directory of Open Access Journals (Sweden)

    Van Meir Erwin G

    2005-02-01

    Full Text Available Abstract Background The ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs proteins are a family of metalloproteases with sequence similarity to the ADAM proteases, that contain the thrombospondin type 1 sequence repeat motifs (TSRs common to extracellular matrix proteins. ADAMTS proteins have recently gained attention with the discovery of their role in a variety of diseases, including tissue and blood disorders, cancer, osteoarthritis, Alzheimer's and the genetic syndromes Weill-Marchesani syndrome (ADAMTS10, thrombotic thrombocytopenic purpura (ADAMTS13, and Ehlers-Danlos syndrome type VIIC (ADAMTS2 in humans and belted white-spotting mutation in mice (ADAMTS20. Results Phylogenetic analysis and comparison of the exon/intron organization of vertebrate (Homo, Mus, Fugu, chordate (Ciona and invertebrate (Drosophila and Caenorhabditis ADAMTS homologs has elucidated the evolutionary relationships of this important gene family, which comprises 19 members in humans. Conclusions The evolutionary history of ADAMTS genes in vertebrate genomes has been marked by rampant gene duplication, including a retrotransposition that gave rise to a distinct ADAMTS subfamily (ADAMTS1, -4, -5, -8, -15 that may have distinct aggrecanase and angiogenesis functions.

  19. Overestimation of heterotrophic bacteria in the Sargasso Sea: direct evidence by flow and imaging cytometry

    Science.gov (United States)

    Sieracki, Michael E.; Haugen, Elin M.; Cucci, Terry L.

    1995-08-01

    Accurate measurements of bacterial biomass in the ocean are needed for modeling marine microbial food webs and global biogeochemical cycling. We present direct evidence that previous estimates of heterotrophic bacteria biomass in the oligotrophic ocean are confounded by the presence of the abundant photosynthetic procaryote, Prochlorococcus. The chlorophyll autofluorescence of these photosynthetic bacterial cells is very faint and fades rapidly under epifluorescence microscopy. Detection and enumeration of these cells thus far has almost exclusively been by flow cytometry. Using a cooled, charge-coupled device (CCD) camera we were able to image these cells for direct biovolume measurements. A double-exposed image of DAPI-stained Prochlorococcus cells shows that they are indistinguishable from heterotrophic bacteria in standard slide preparations. At two Sargasso Sea stations Prochlorococcus could cause an overestimation of surface (top 150 m) integrated heterotrophic bacterial biovolume (biomass) of 18 and 22% determined by standard microscope methods. At the subsurface chlorophyll maximum Prochlorococcus was 33 and 43% of the heterotrophic bacterial biovolume (biomass) at these stations. Prochlorococcus cell size increased from 0.05 μm 3 in the surface mixed layer to about 0.2 μm 3 below 100 m, confirming previous interpretations of flow cytometric light scatter measurements. Shifting biomass from the heterotrophic bacteria pool to the primary producer compartment has significant implications for ecosystem structure and trophic transfer in marine food webs.

  20. The connectivity of Mytilus galloprovincialis in northern Morocco: A gene flow crossroads between continents

    Science.gov (United States)

    Ouagajjou, Yassine; Presa, Pablo

    2015-01-01

    Previous population genetic studies on the Mediterranean mussel Mytilus galloprovincialis have shown the existence of two well differentiated sets of populations around Southern European coasts, one Atlantic and another Mediterranean. Those two population pools are kept apart by the Almería - Oran Oceanographic Front (AOOF), an oceanographic discontinuity acting either as a cause of such differentiation or simply as a means of maintaining two historically differentiated gene pools. The role of the Gibraltar Strait at shaping mussel larval flow entering the Alboran Sea has been much less addressed, especially regarding mussel swarms inhabiting the northern coast of Morocco. The present study applies seven microsatellite markers to describing the genetic status of northern Moroccan populations of M. galloprovincialis and their relationship with the two well-characterized mussel gene pools from southern Europe. We show that the Atlantic Iberia gene pool extending continuously from the Cantabrian Sea (NE Iberia) to the Alboran Sea (SE Iberia) up to the AOOF is well differentiated from the Atlantic Moroccan mussel. Either an oceanographic barrier or a limited larval dispersal or both, are required to explain this unexpected intercontinental differentiation regarding previous studies on this species. Populations from Atlantic Morocco conformed to a single gene pool (FST ± SD = 0.012 ± 0.007) as opposed to the reported latitudinal barrier to gene flow at Cape Ghir in western Morocco. Additionally, a significant restriction to gene flow was observed between Atlantic Morocco and Alboran Morocco (FST ± SD = 0.038 ± 0.010) in contrast to the reported mussel genetic continuity along the Iberian coast up to AOOF. Three major mussel gene pools appear to meet at this crossroads between continents and between seas, namely, a Mediterranean European subpopulation, an Atlantic Iberia subpopulation including the Alboran Sea, and an Atlantic Morocco subpopulation. Knowledge on

  1. Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina

    Science.gov (United States)

    González-Wevar, Claudio A.; Rosenfeld, Sebastián; Segovia, Nicolás I.; Hüne, Mathias; Gérard, Karin; Ojeda, Jaime; Mansilla, Andrés; Brickle, Paul; Díaz, Angie; Poulin, Elie

    2016-01-01

    recognized an older and more complex demographic history than in PP. Demographic reconstructions along PP suggest a post-LGM expansion process (7.5 ka), also supported by neutrality tests, mismatch distribution and maximum parsimony haplotype genealogies. Migration rate estimations showed evidence of asymmetrical gene flow from PP to FI. The absence of genetic differentiation, the presence of a single dominant haplotype, high estimated migration rates, and marked signal of recent demographic growth, support the hypothesis of rapid post-glacial expansion in N. mytilina along PP. This expansion could have been sustained by larval and rafting-mediated dispersal of adults from northernmost populations following the Cape Horn Current System. Marked genetic differentiation between PP and FI could be explained through differences in their respective glacial histories. During the LGM, Pacific Patagonia (PP) was almost fully covered by the Patagonian Ice Sheet, while sheet coverage in the FI ice was restricted to small cirques and valleys. As previously recorded in the sister-species N. magellanica, the FI rather than represent a classical glacial refugium for N. mytilina, seems to represent a sink area and/or a secondary contact zone. Accordingly, historical and contemporary processes, contrasting glacial histories between the analyzed sectors, as well as life history traits constitute the main factors explaining the current biogeographical patterns of most shallow Patagonian marine benthic organisms. PMID:27598461

  2. DigSee: Disease gene search engine with evidence sentences (version cancer).

    Science.gov (United States)

    Kim, Jeongkyun; So, Seongeun; Lee, Hee-Jin; Park, Jong C; Kim, Jung-Jae; Lee, Hyunju

    2013-07-01

    Biological events such as gene expression, regulation, phosphorylation, localization and protein catabolism play important roles in the development of diseases. Understanding the association between diseases and genes can be enhanced with the identification of involved biological events in this association. Although biological knowledge has been accumulated in several databases and can be accessed through the Web, there is no specialized Web tool yet allowing for a query into the relationship among diseases, genes and biological events. For this task, we developed DigSee to search MEDLINE abstracts for evidence sentences describing that 'genes' are involved in the development of 'cancer' through 'biological events'. DigSee is available through http://gcancer.org/digsee.

  3. Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests - the case of sympatric and parapatric Marantaceae species.

    Science.gov (United States)

    Ley, A C; Hardy, O J

    2014-08-01

    Gene flow within and between species is a fundamental process shaping the evolutionary history of taxa. However, the extent of hybridization and reinforcement is little documented in the tropics. Here we explore the pattern of gene flow between three sister species from the herbaceous genus Marantochloa (Marantaceae), sympatrically distributed in the understorey of the African rainforest, using data from the chloroplast and nuclear genomes (DNA sequences and AFLP). We found highly contrasting patterns: while there was no evidence of gene flow between M. congensis and M. monophylla, species identity between M. monophylla and M. incertifolia was maintained despite considerable gene flow. We hypothesize that M. incertifolia originated from an ancient hybridization event between M. congensis and M. monophylla, considering the current absence of hybridization between the two assumed parent species, the rare presence of shared haplotypes between all three species and the high percentage of haplotypes shared by M. incertifolia with each of the two parent species. This example is contrasted with two parapatrically distributed species from the same family in the genus Haumania forming a hybrid zone restricted to the area of overlap. This work illustrates the diversity of speciation/introgression patterns that can potentially occur in the flora of tropical Africa.

  4. High rates of gene flow by pollen and seed in oak populations across Europe.

    Directory of Open Access Journals (Sweden)

    Sophie Gerber

    Full Text Available Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea distributed across Europe. Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423, mapped, and acorns were collected ([17,147], 51 from several mother trees ([3], [47], 23. Seedlings ([65,387], 178 were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5-8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale. On average, the percentage of the wind-borne pollen from outside the stand was 60%, with large variation among stands (21-88%. Mean seed immigration into the stand was 40%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20-66%. Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation. Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.

  5. Gene-splitting technology: a novel approach for the containment of transgene flow in Nicotiana tabacum.

    Directory of Open Access Journals (Sweden)

    Xu-Jing Wang

    Full Text Available The potential impact of transgene escape on the environment and food safety is a major concern to the scientists and public. This work aimed to assess the effect of intein-mediated gene splitting on containment of transgene flow. Two fusion genes, EPSPSn-In and Ic-EPSPSc, were constructed and integrated into N. tabacum, using Agrobacterium tumefaciens-mediated transformation. EPSPSn-In encodes the first 295 aa of the herbicide resistance gene 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS fused with the first 123 aa of the Ssp DnaE intein (In, whereas Ic-EPSPSc encodes the 36 C-terminal aa of the Ssp DnaE intein (Ic fused to the rest of EPSPS C terminus peptide sequences. Both EPSPSn-In and Ic-EPSPSc constructs were introduced into the same N. tabacum genome by genetic crossing. Hybrids displayed resistance to the herbicide N-(phosphonomethyl-glycine (glyphosate. Western blot analysis of protein extracts from hybrid plants identified full-length EPSPS. Furthermore, all hybrid seeds germinated and grew normally on glyphosate selective medium. The 6-8 leaf hybrid plants showed tolerance of 2000 ppm glyphosate in field spraying. These results indicated that functional EPSPS protein was reassembled in vivo by intein-mediated trans-splicing in 100% of plants. In order to evaluate the effect of the gene splitting technique for containment of transgene flow, backcrossing experiments were carried out between hybrids, in which the foreign genes EPSPSn-In and Ic-EPSPSc were inserted into different chromosomes, and non-transgenic plants NC89. Among the 2812 backcrossing progeny, about 25% (664 plantlets displayed glyphosate resistance. These data indicated that transgene flow could be reduced by 75%. Overall, our findings provide a new and highly effective approach for biological containment of transgene flow.

  6. Direct phylogenetic evidence for lateral transfer of elongation factor-like gene.

    Science.gov (United States)

    Kamikawa, Ryoma; Inagaki, Yuji; Sako, Yoshihiko

    2008-05-13

    Genes encoding elongation factor-like (EFL) proteins, which show high similarity to elongation factor-1alpha (EF-1alpha), have been found in phylogenetically distantly related eukaryotes. The sporadic distribution of "EFL-containing" lineages within "EF-1alpha-containing" lineages indirectly, but strongly, suggests lateral gene transfer as the principal driving force in EFL evolution. However, one of the most critical aspects in the above hypothesis, the donor lineages in any putative cases of lateral EFL gene transfer, remained unclear. In this study, we provide direct evidence for lateral transfer of an EFL gene through the analyses of 10 diatom EFL genes. All diatom EFL homologues tightly clustered in phylogenetic analyses, suggesting acquisition of the exogenous EFL gene early in diatom evolution. Our survey additionally identified Thalassiosira pseudonana as a eukaryote bearing EF-1alpha and EFL genes and secondary EFL gene loss in Phaeodactylum tricornutum, the complete genome of which encodes only the EF-1alpha gene. Most importantly, the EFL phylogeny recovered a robust grouping of homologues from diatoms, the cercozoan Bigelowiella natans, and the foraminifer Planoglabratella opecularis, with the diatoms nested within the Bigelowiella plus Planoglabratella (Rhizaria) grouping. The particular relationships recovered are further consistent with two characteristic sequence motifs. The best explanation of our data analyses is an EFL gene transfer from a foraminifer to a diatom, the first case in which the donor-recipient relationship was clarified. Finally, based on a reverse transcriptase quantitative PCR assay and the genome information of Thalassiosira and Phaeodactylum, we propose the loss of elongation factor function in Thalassiosira EF-1alpha.

  7. Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network.

    Science.gov (United States)

    Jachiet, Pierre-Alain; Colson, Philippe; Lopez, Philippe; Bapteste, Eric

    2014-08-07

    Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.

  8. A new clinical evidence-based gene-environment interaction model of depression.

    Science.gov (United States)

    Bagdy, Gyorgy; Juhasz, Gabriella; Gonda, Xenia

    2012-12-01

    In our current understanding of mood disorders, the role of genes is diverse including the mediation of the effects of provoking and protective factors. Different or partially overlapping gene sets play a major role in the development of personality traits including also affective temperaments, in the mediation of the effects of environmental factors, and in the interaction of these elements in the development of depression. Certain genes are associated with personality traits and temperaments including e.g., neuroticism, impulsivity, openness, rumination and extroversion. Environmental factors consist of external (early and provoking life events, seasonal changes, social support etc.) and internal factors (hormones, biological rhythm generators, comorbid disorders etc). Some of these environmental factors, such as early life events and some prenatal events directly influence the development of personality traits and temperaments. In the NEWMOOD cohort polymorphisms of the genes of the serotonin transporter, 5-HT1A, 5-HT1B and 5-HT2A and endocannabinoid CB1 receptors, tryptophan hydroxylase, CREB1, BDNF and GIRK provide evidence for the involvement of these genes in the development of depression. Based on their role in this process they could be assigned to different gene sets. The role of certain genes, such as promoter polymorphisms of the serotonin transporter (5-HTTLPR) and CB1 receptor has been shown in more than one of the above factors. Furthermore, gene-gene interactions of these promoters associated with anxiety suggest the application of these polymorphisms in personalized medicine. In this review we introduce a new model including environmental factors, genes, trait and temperament markers based on human genetic studies.

  9. Evidence for a critical role of gene occlusion in cell fate restriction

    Institute of Scientific and Technical Information of China (English)

    Jedidiah Gaetz; Wei-Hua Yu; Andy Peng Xiang; Bruce T Lahn; Kayla L Clift; Croydon J Fernandes; Frank Fuxiang Mao; Jae Hyun Lee; Li Zhang; Samuel W Baker; Timothy J Looney; Kara M Foshay

    2012-01-01

    The progressive restriction of cell fate during lineage differentiation is a poorly understood phenomenon despite its ubiquity in multicellular organisms.We recently used a cell fusion assay to define a mode of epigenetic silencing that we termed "occlusion",wherein affected genes are silenced by cis-acting chromatin mechanisms irrespective of whether trans-acting transcriptional activators are present.We hypothesized that occlusion of lineage-inappropriate genes could contribute to cell fate restriction.Here,we test this hypothesis by introducing bacterial artificial chromosomes (BACs),which are devoid of chromatin modifications necessary for occlusion,into mouse fibroblasts.We found that BAC transgenes corresponding to occluded endogenous genes are expressed in most eases,whereas BAC transgenes corresponding to silent but non-occluded endogenous genes are not expressed.This indicates that the cellular milieu in trans supports the expression of most occluded genes in fibroblasts,and that the silent state of these genes is solely the consequence of occlusion in cis.For the BAC corresponding to the occluded myogenic master regulator Myf5,expression of the Myf5 transgene on the BAC triggered fibroblasts to acquire a muscle-like phenotype.These results provide compelling evidence for a critical role of gene occlusion in cell fate restriction.

  10. SCGPred: A Score-based Method for Gene Structure Prediction by Combining Multiple Sources of Evidence

    Institute of Scientific and Technical Information of China (English)

    Xiao Li; Qingan Ren; Yang Weng; Haoyang Cai; Yunmin Zhu; Yizheng Zhang

    2008-01-01

    Predicting protein-coding genes still remains a significant challenge. Although a variety of computational programs that use commonly machine learning methods have emerged, the accuracy of predictions remains a low level when implementing in large genomic sequences. Moreover, computational gene finding in newly sequenced genomes is especially a difficult task due to the absence of a training set of abundant validated genes. Here we present a new gene-finding program, SCGPred,to improve the accuracy of prediction by combining multiple sources of evidence.SCGPred can perform both supervised method in previously well-studied genomes and unsupervised one in novel genomes. By testing with datasets composed of large DNA sequences from human and a novel genome of Ustilago maydi, SCGPred gains a significant improvement in comparison to the popular ab initio gene predictors. We also demonstrate that SCGPred can significantly improve prediction in novel genomes by combining several foreign gene finders with similarity alignments, which is superior to other unsupervised methods. Therefore, SCGPred can serve as an alternative gene-finding tool for newly sequenced eukaryotic genomes. The program is freely available at http://bio.scu.edu.cn/SCGPred/.

  11. Phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas.

    Directory of Open Access Journals (Sweden)

    David M Nelson

    Full Text Available BACKGROUND: Lateral gene transfer (LGT appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52% of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT. CONCLUSION: Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members of the phylum Firmicutes inhabiting the intestinal tract of marine iguanas.

  12. Little evidence for demasculinization of the Drosophila X chromosome among genes expressed in the male germline.

    Science.gov (United States)

    Meiklejohn, Colin D; Presgraves, Daven C

    2012-01-01

    Male-biased genes-those expressed at higher levels in males than in females-are underrepresented on the X chromosome of Drosophila melanogaster. Several evolutionary models have been posited to explain this so-called demasculinization of the X. Here, we show that the apparent paucity of male-biased genes on the X chromosome is attributable to global X-autosome differences in expression in Drosophila testes, owing to a lack of sex chromosome dosage compensation in the male germline, but not to any difference in the density of testis-specific or testis-biased genes on the X chromosome. First, using genome-wide gene expression data from 20 tissues, we find no evidence that genes with testis-specific expression are underrepresented on the X chromosome. Second, using contrasts in gene expression profiles among pairs of tissues, we recover a statistical underrepresentation of testis-biased genes on the X but find that the pattern largely disappears once we account for the lack of dosage compensation in the Drosophila male germline. Third, we find that computationally "demasculinizing" the autosomes is not sufficient to produce an expression profile similar to that of the X chromosome in the testes. Our findings thus show that the lack of sex chromosome dosage compensation in Drosophila testes can explain the apparent signal of demasculinization on the X, whereas evolutionary demasculinization of the X cannot explain its overall reduced expression in the testes.

  13. Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

    Directory of Open Access Journals (Sweden)

    Tian Jing

    2009-10-01

    Full Text Available Abstract Background How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, and two aplastidic sister taxa, Phytophthora ramorum and P. sojae. Results Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to Phytophthora genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes. Conclusion Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by a posteriori

  14. Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome.

    Science.gov (United States)

    Karberg, Katherine A; Olsen, Gary J; Davis, James J

    2011-12-13

    Most bacterial and archaeal genomes contain many genes with little or no similarity to other genes, a property that impedes identification of gene origins. By comparing the codon usage of genes shared among strains (primarily vertically inherited genes) and genes unique to one strain (primarily recently horizontally acquired genes), we found that the plurality of unique genes in Escherichia coli and Salmonella enterica are much more similar to each other than are their vertically inherited genes. We conclude that E. coli and S. enterica derive these unique genes from a common source, a supraspecies phylogenetic group that includes the organisms themselves. The phylogenetic range of the sharing appears to include other (but not all) members of the Enterobacteriaceae. We found evidence of similar gene sharing in other bacterial and archaeal taxa. Thus, we conclude that frequent gene exchange, particularly that of genetic novelties, extends well beyond accepted species boundaries.

  15. In situ gene expression in mixed-culture biofilms: Evidence of metabolic interactions between community members

    DEFF Research Database (Denmark)

    Møller, Søren; Sternberg, Claus; Andersen, Jens Bo;

    1998-01-01

    Microbial communities growing in laboratory-based pow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus,vas in particular on Pseudomonas putida and a strain of an Acinetobacter sp., and the genes studied...... are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida......, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol...

  16. Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis.

    Directory of Open Access Journals (Sweden)

    Le Wang

    Full Text Available The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.

  17. Contrasting demographic history and gene flow patterns of two mangrove species on either side of the Central American Isthmus.

    Science.gov (United States)

    Cerón-Souza, Ivania; Gonzalez, Elena G; Schwarzbach, Andrea E; Salas-Leiva, Dayana E; Rivera-Ocasio, Elsie; Toro-Perea, Nelson; Bermingham, Eldredge; McMillan, W Owen

    2015-08-01

    Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed

  18. Minimally-Invasive Gene Transfection by Chemical and Physical Interaction of Atmospheric Pressure Plasma Flow

    Science.gov (United States)

    Kaneko, Toshiro

    2014-10-01

    Non-equilibrium atmospheric pressure plasma irradiated to the living-cell is investigated for medical applications such as gene transfection, which is expected to play an important role in molecular biology, gene therapy, and creation of induced pluripotent stem (iPS) cells. However, the conventional gene transfection using the plasma has some problems that the cell viability is low and the genes cannot be transferred into some specific lipid cells, which is attributed to the unknown mechanism of the gene transfection using the plasma. Therefore, the time-controlled atmospheric pressure plasma flow is generated and irradiated to the living-cell suspended solution for clarifying the transfection mechanism toward developing highly-efficient and minimally- invasive gene transfection system. In this experiment, fluorescent dye YOYO-1 is used as the simulated gene and LIVE/DEAD Stain is simultaneously used for cell viability assay. By the fluorescence image, the transfection efficiency is calculated as the ratio of the number of transferred and surviving cells to total cell count. It is clarified that the transfection efficiency is significantly increased by the short-time (cell viability (>90%). This result indicates that the physical effects such as the electric field caused by the charged particles arriving at the surface of the cell membrane, and chemical effects associated with plasma-activated products in solution act synergistically to enhance the cell-membrane transport with low-damage. This work was supported by JSPS KAKENHI Grant Number 24108004.

  19. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

    DEFF Research Database (Denmark)

    Worning, Peder; Jensen, Lars Juhl; Nelson, K. E.

    2000-01-01

    The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters......, which brings independent evidence for the lateral gene transfer in the genome of T.maritima, The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms...... of different origin, The typical genomic periodicity for Bacteria is 11 bp whilst it is 10 bp for Archaea, Eukaryotes have more complex spectra but the dominant period in the yeast Saccharomyces cerevisiae is 10.2 bp. These periodicities are most likely reflective of differences in chromatin structure....

  20. Involvement of calcitonin gene-related peptide in migraine: regional cerebral blood flow and blood flow velocity in migraine patients

    DEFF Research Database (Denmark)

    Lassen, L.H.; Jacobsen, V.B.; Haderslev, P.A.

    2008-01-01

    g/min) or placebo for 20 min was studied in 12 patients with migraine without aura outside attacks. Xenon-133 inhalation SPECT-determined regional cerebral blood flow (rCBF) and transcranial Doppler (TCD)-determined blood velocity (V-mean) in the middle cerebral artery (MCA), as well as the heart......Calcitonin gene-related peptide (CGRP)-containing nerves are closely associated with cranial blood vessels. CGRP is the most potent vasodilator known in isolated cerebral blood vessels. CGRP can induce migraine attacks, and two selective CGRP receptor antagonists are effective in the treatment...... of migraine attacks. It is therefore important to investigate its mechanism of action in patients with migraine. We here investigate the effects of intravenous human alpha-CGRP (h alpha CGRP) on intracranial hemodynamics. In a double-blind, cross-over study, the effect of intravenous infusion of haCGRP (2 mu...

  1. Evident?

    DEFF Research Database (Denmark)

    Plant, Peter

    2012-01-01

    Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind......Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind...

  2. Emplacement history and inflation evidence of a long basaltic lava flow located in Southern Payenia Volcanic Province, Argentina

    Science.gov (United States)

    Bernardi, Mauro I.; Bertotto, Gustavo W.; Jalowitzki, Tiago L. R.; Orihashi, Yuji; Ponce, Alexis D.

    2015-02-01

    The El Corcovo lava flow, from the Huanul shield volcano in the southern Mendoza province (central-western Argentina) traveled a distance of 70 km and covered a minimum area of ~ 415 km2. The flow emplacement was controlled both by extrinsic (e.g., topography) and intrinsic (e.g., lava supply rate, lava physicochemical characteristics) factors. The distal portion of the lava flow reached the Colorado River Valley, in La Pampa Province, where it spread and then was confined by earlier river channels. Cross-sections through the flow surveyed at several localities show two vesicular layers surrounding a dense central section, where vesicles are absent or clustered in sheet-shaped and cylindrical-shaped structures. Lavas of the El Corcovo flow are alkaline basalts with low values of viscosity. The morphological and structural characteristics of the flow and the presence of landforms associated with lava accumulation are the evidence of inflation. This process involved the formation of a tabular sheet flow up to 4 m of thick with a large areal extent in the proximal sectors, while at terminal sectors frontal lobes reached inflation values up to 10 m. The numerous swelling structures present at these portions of the flow suggest the movement of lava in lava tubes. We propose that this aspect and the low viscosity of the lava allowed the flow travel to a great distance on a gentle slope relief.

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

    Directory of Open Access Journals (Sweden)

    Prasanna HC

    2010-09-01

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

  4. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.

    Science.gov (United States)

    Boothby, Thomas C; Tenlen, Jennifer R; Smith, Frank W; Wang, Jeremy R; Patanella, Kiera A; Nishimura, Erin Osborne; Tintori, Sophia C; Li, Qing; Jones, Corbin D; Yandell, Mark; Messina, David N; Glasscock, Jarret; Goldstein, Bob

    2015-12-29

    Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.

  5. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

    Science.gov (United States)

    Boothby, Thomas C.; Tenlen, Jennifer R.; Smith, Frank W.; Wang, Jeremy R.; Patanella, Kiera A.; Osborne Nishimura, Erin; Tintori, Sophia C.; Li, Qing; Jones, Corbin D.; Yandell, Mark; Glasscock, Jarret; Goldstein, Bob

    2015-01-01

    Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes. PMID:26598659

  6. Gene flow from genetically modified herbicide-resistant rapeseed to cruciferous weeds

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiangxiang; XIA Qiuxia; LU Dalei; LU Weiping; QI Cunkou; PU Huiming; LIU Geshan; ZHAO Jian; WANG Youping

    2006-01-01

    The sexual compatibility between genetically modified (GM) glyphosate-resistant rapeseed variety Q3 (Brassica napus L. ) and 5 cruciferous weeds is studied through the observation of fluorescence microscopy and cross-fertility after manual pollination. The results indicated that Q3 (as male) was highly incompatible with Thlaspi arvense L., Capsella bursa-pastoris (L.) Medic, Cardamine hirsuta L. and Rorippa palustris (L.) Besser (as female). Fluorescence microscopic observation showed that growing of pollen tubes terminated on the stigma surface or at the upper 1/3 part of the style. However, B. juncea×Q3 was compatible, and the compatibility index was 1.65. Under the neighboring growth and natural pollination conditions, the rates of gene flow from Q3 to T. arvense, C.bursa-pastoris, C. hirsute and R. palustris were all 0, while it was 0.86 % for B. juncea. These results indicate that there is difference in the rate of gene flow between GM rapeseed and cruciferous wild weeds, and frequency of gene flow is highly correlated with sexual compatibility.

  7. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M.; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-01-01

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds. PMID:27966592

  8. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach.

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-12-14

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.

  9. Identification of landscape features influencing gene flow: How useful are habitat selection models?

    Science.gov (United States)

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

    2016-01-01

    Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

  10. Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii).

    Science.gov (United States)

    Ujvari, Beata; Dowton, Mark; Madsen, Thomas

    2008-08-01

    By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

  11. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

    Science.gov (United States)

    Scorza, Ralph; Kriss, Alissa B; Callahan, Ann M; Webb, Kevin; Demuth, Mark; Gottwald, Tim

    2013-01-01

    Pollen flow from a 0.46 ha plot of genetically engineered (GE) Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera) were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree) to 0.033-0.017% at longer distances (384-998 m). Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  12. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

    Directory of Open Access Journals (Sweden)

    Ralph Scorza

    Full Text Available Pollen flow from a 0.46 ha plot of genetically engineered (GE Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree to 0.033-0.017% at longer distances (384-998 m. Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  13. Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models

    Science.gov (United States)

    Marr, Julia; Bock, Gavin; Desbonnet, Lieve; Waddington, John

    2016-01-01

    The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia. PMID:27725886

  14. Possible effects of (trans)gene flow from crops on the genetic diversity from landraces and wild relatives.

    Science.gov (United States)

    Gepts, Paul; Papa, Roberto

    2003-01-01

    Gene flow is a potential concern associated with the use of transgenic crops because it could affect genetic diversity of related landraces and wild relatives. This concern has taken on added importance with the looming introduction of transgenic crops in centers of crop domestication (Mexico, China) and those producing pharmaceutical compounds. For gene flow to take place among cultivars and their wild relatives, several steps have to be fulfilled, including the presence of cultivars or wild relatives within pollen or seed dispersal range, the ability to produce viable and fertile hybrids, at least partial overlap in flowering time, actual gene flow by pollen or seed, and the establishment of crop genes in the domesticated or wild recipient populations. In contrast with domestication genes, which often make crops less adapted to natural ecosystems, transgenes frequently represent gains of function, which might release wild relatives from constraints that limit their fitness. In most sexually reproducing organisms, the chromosomal region affected by selection of a single gene amounts to a small percentage of the total genome size. Because of gene flow, the level of genetic diversity present in the domesticated gene pool becomes a crucial factor affecting the genetic diversity of the wild gene pool. For some crops, such as cotton and maize, the introduction of transgenic technologies has led to a consolidation of the seed industry and a reduction in the diversity of the elite crop gene pool. Thus, diversity in improved varieties grown by farmers needs to be monitored. Several areas deserve further study, such as the actual magnitude of gene flow and its determinants in different agroecosystems, the long-term effects of gene flow on genetic diversity both across gene pools and within genomes, the expression of transgenes in new genetic backgrounds, and the effects of socio-economic factors on genetic diversity.

  15. Does blood flow restriction result in skeletal muscle damage? A critical review of available evidence.

    Science.gov (United States)

    Loenneke, J P; Thiebaud, R S; Abe, T

    2014-12-01

    Blood flow restriction (BFR) alone or in combination with exercise has been shown to result in muscle hypertrophy and strength gain across a variety of populations. Although there are numerous studies in the literature showing beneficial muscular effects following the application of BFR, questions have been raised over whether BFR may lead to or even increase the incidence of muscle damage. The purpose of this review is to examine the proposed mechanisms behind muscle damage and critically review the available BFR literature. The available evidence does not support the hypothesis that BFR in combination with low-intensity exercise increases the incidence of muscle damage. Instead, the available literature suggests that minimal to no muscle damage is occurring with this type of exercise. This conclusion is drawn from the following observations: (a) no prolonged decrements in muscle function; (b) no prolonged muscle swelling; (c) muscle soreness ratings similar to a submaximal low load control; and (d) no elevation in blood biomarkers of muscle damage.

  16. Clinical evidence on high flow oxygen therapy and active humidification in adults.

    Science.gov (United States)

    Gotera, C; Díaz Lobato, S; Pinto, T; Winck, J C

    2013-01-01

    Recently there has been growing interest in an alternative to conventional oxygen therapy: the heated, humidified high flow nasal cannula oxygen therapy (HFNC). A number of physiological effects have been described with HFNC: pharyngeal dead space washout, reduction of nasopharyngeal resistance, a positive expiratory pressure effect, an alveolar recruitment, greater humidification, more comfort and better tolerance by the patient, better control of FiO2 and mucociliary clearance. There is limited experience of HFNC in adults. There are no established guidelines or decision-making pathways to guide use of the HFNC therapy for adults. In this article we review the existing evidence of HFNC oxygen therapy in adult patients, its advantages, limitations and the current literature on clinical applications. Further research is required to determine the long-term effect of this therapy and identify the adult patient population to whom it is most beneficial. Copyright © 2013 Sociedade Portuguesa de Pneumologia. Published by Elsevier España. All rights reserved.

  17. Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow.

    Science.gov (United States)

    van Strien, Maarten J; Keller, Daniela; Holderegger, Rolf; Ghazoul, Jaboury; Kienast, Felix; Bolliger, Janine

    2014-03-01

    For conservation managers, it is important to know whether landscape changes lead to increasing or decreasing gene flow. Although the discipline of landscape genetics assesses the influence of landscape elements on gene flow, no studies have yet used landscape-genetic models to predict gene flow resulting from landscape change. A species that has already been severely affected by landscape change is the large marsh grasshopper (Stethophyma grossum), which inhabits moist areas in fragmented agricultural landscapes in Switzerland. From transects drawn between all population pairs within maximum dispersal distance (landscape planning.

  18. Measuring gene flow from two birdsfoot trefoil (Lotus corniculatus) field trials using transgenes as tracer markers.

    Science.gov (United States)

    De Marchis, F; Bellucci, M; Arcioni, S

    2003-06-01

    Genetic engineering is becoming a useful tool in the improvement of plants but concern has been expressed about the potential environmental risks of releasing genetically modified (GM) organisms into the environment. Attention has focused on pollen dispersal as a major issue in the risk assessment of transgenic crop plants. In this study, pollen-mediated dispersal of transgenes via cross-fertilization was examined. Plants of Lotus corniculatus L. transformed with either the Escherichia coli asparagine synthetase gene asnA or the beta-glucuronidase gene uidA, were used as the pollen donor. Nontransgenic plants belonging to the species L. corniculatus L., L. tenuis Waldst. and Kit. ex Willd, and L. pedunculatus Cav., were utilized as recipients. Two experimental fields were established in two areas of central Italy. Plants carrying the uidA gene were partially sterile, therefore only the asnA gene was used as a tracer marker. No transgene flow between L. corniculatus transformants and the nontransgenic L. tenuis and L. pedunculatus plants was detected. As regards nontransgenic L. corniculatus plants, in one location flow of asnA transgene was detected up to 18 m from the 1.8 m2 donor plot. In the other location, pollen dispersal occurred up to 120 m from the 14 m2 pollinating plot.

  19. Gene flow and geographic variation in natural populations of Alnus acuminata ssp. arguta (Fagales: Betulaceae in Costa Rica and Panama

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    Olman Murillo

    1999-12-01

    Full Text Available Seventeen natural populations in Costa Rica and Panama were used to asses gene flow and geographic patterns of genetic variation in this tree species. Gene flow analysis was based on the methods of rare alleles and FST (Index of genetic similarity M, using the only four polymorphic gene loci among 22 investigated (PGI-B, PGM-A, MNR-A and IDH-A. The geographic variation analysis was based on Pearson`s correlations between four geographic and 14 genetic variables. Some evidence of isolation by distance and a weak gene flow among geographic regions was found. Patterns of clinal variation in relation to altitude (r = -0.62 for genetic diversity and latitude (r= -0.77 for PGI-B3 were also observed, supporting the hypothesis of isolation by distance. No private alleles were found at the single population level.Diecisiete poblaciones naturales de esta especie forestal en Costa Rica y Panamá, fueron investigadas en relación con sus patrones de flujo genético y de variación geográfica. El análisis de flujo genético fue basado en los métodos de los alelos raros y de FST (Indice de similaridad genética M. Los análisis fueron a su vez basados en los únicos cuatro loci genéticos de un total de 22 investigados que mostraron polimorfismo (PGI-B, PGM-A, MNR-A and IDH-A. Los análisis de variación geográfica fueron basados en el desarrollo de correlaciones de Pearson entre 4 variables geográficas y 14 variables genéticas. Alguna evidencia de aislamiento por distancia así como un débil flujo genético entre regiones geográficas fue encontrado. Fueron también observados patrones de variación clinal en relación con la altitud (r = -0.62 para la diversidad genética y latitud (r= -0.77 en PGI-B3, que apoyan la hipotesis de aislamiento por distancia para esta especie. No se encontraron alelos privados en ninguna de las poblaciones investigadas.

  20. Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae).

    Science.gov (United States)

    Li, Xiao-Wei; Wang, Ping; Fail, Jozsef; Shelton, Anthony M

    2015-01-01

    Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction) and thelytoky (asexual reproduction). Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene) allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction.

  1. Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae.

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    Xiao-Wei Li

    Full Text Available Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction and thelytoky (asexual reproduction. Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction.

  2. Dielectrophoresis based continuous-flow nano sorter: fast quality control of gene vaccines.

    Science.gov (United States)

    Viefhues, Martina; Wegener, Sonja; Rischmüller, Anja; Schleef, Martin; Anselmetti, Dario

    2013-08-01

    We present a prototype nanofluidic device, developed for the continuous-flow dielectrophoretic (DEP) fractionation, purification, and quality control of sample suspensions for gene vaccine production. The device consists of a cross injector, two operation regions, and separate outlets where the analytes are collected. In each DEP operation region, an inhomogeneous electric field is generated at a channel spanning insulating ridge. The samples are driven by ac and dc voltages that generate a dielectrophoretic potential at the ridge as well as (linear) electrokinetics. Since the DEP potential differs at the two ridges, probes of three and more species can be iteratively fully fractionated. We demonstrate the fast and efficient separation of parental plasmid, miniplasmid, and minicircle DNA, where the latter is applicable as a gene vaccine. Since the present technique is virtually label-free, it offers a fast purification and in-process quality control with low consumption, in parallel, for the production of gene vaccines.

  3. Do foreign portfolio flows increase risk in emerging stock markets? Evidence from six Latin American countries 1999-2008

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    Diego A. Agudelo

    2011-03-01

    Full Text Available Foreign portfolio flows have been blamed for causing instability in emerging markets, especially during financial crises. This study measured the effect of foreign capital flows on volatility and exposure to world market risk in the six largest Latin American stock markets: Argentina, Brazil, Colombia, Chile, Mexico and Peru, for around 10 years including the 2008 World financial crisis. This will test whether these flows cause instability for those markets and increase their exposure to international stock market returns. A proprietary database, from Emerging Portoflio.com and time series models, both univariate (ARCH-GARCH and multivariate (VAR, are used to estimate the effect foreign portfolio flows on the risk variables and the causality of these effects. We found no strong evidence to support the hypothesis that foreign flows cause instability in the Latin American stock markets, in spite of some evidence of causing price pressure. Instead, the evidence points to a strong dependence of market returns on international stock and foreign exchange markets, both in means and in volatility, instrumental to transmit crisis to those markets.

  4. Pollination between maize and teosinte: an important determinant of gene flow in Mexico.

    Science.gov (United States)

    Baltazar, Baltazar M; de Jesús Sánchez-Gonzalez, José; de la Cruz-Larios, Lino; Schoper, John B

    2005-02-01

    Gene flow between maize [Zea mays (L.)] and its wild relatives does occur, but at very low frequencies. Experiments were undertaken in Tapachula, Nayarit, Mexico to investigate gene flow between a hybrid maize, landraces of maize and teosinte (Z. mays ssp. mexicana, races Chalco and Central Plateau). Hybridization, flowering synchrony, pollen size and longevity, silk elongation rates, silk and trichome lengths and tassel diameter and morphology were measured. Hybrid and open-pollinated maize ears produced a mean of 8 and 11 seeds per ear, respectively, when hand-pollinated with teosinte pollen, which is approximately 1-2% of the ovules normally produced on a hybrid maize ear. Teosinte ears produced a mean of 0.2-0.3 seeds per ear when pollinated with maize pollen, which is more than one-fold fewer seeds than produced on a maize ear pollinated with teosinte pollen. The pollination rate on a per plant basis was similar in the context of a maize plant with 400-500 seeds and a teosinte plant with 30-40 inflorescences and 9-12 fruitcases per inflorescence. A number of other factors also influenced gene-flow direction: (1) between 90% and 95% of the fruitcases produced on teosinte that was fertilized by maize pollen were sterile; (2) teosinte collections were made in an area where incompatibility systems that limit fertilization are present; (3) silk longevity was much shorter for teosinte than for maize (approx. 4 days vs. approx. 11 days); (4) teosinte produced more pollen on a per plant basis than the landraces and commercial hybrid maize; (5) teosinte frequently produced lateral branches with silks close to a terminal tassel producing pollen. Collectively these factors tend to favor crossing in the direction of teosinte to maize. Our results support the hypothesis that gene flow and the subsequent introgression of maize genes into teosinte populations most probably results from crosses where teosinte first pollinates maize. The resultant hybrids then backcross with

  5. Flow-dependent regulation of vascular function and gene expression in rat superior mesenteric artery

    Institute of Scientific and Technical Information of China (English)

    XIA Shang; DENG Chang-sheng

    2009-01-01

    Background Mesenteric artery thrombosis is prone to occur at specific arterial regions with different fluid flow patterns,yet mechanistic links between blood flow and vascular function remain unclear. This study aired to investigate the role of blood flow in regulation of vascular function and gene expression in rats.Methods Isometric tension was recorded in wire myograph to examine vascular function of specific regions (trunk parts and proximal parts from the origin) with different blood flow in superior mesenteric artery (SMA). Endothelial nitric oxide syntheses (eNOS), phosphorylated-eNOS (p-eNOS), serine-threonine kinase Akt and phosphorylated-Akt (p-Akt) protein expressions in SMA were examined by Western blotting. Significance was analyzed using a Student's ttest or analysis of variance (ANOVA) followed by a Dunnett's multiple-comparison post hoc test.Results Compared with trunks, proximal parts exhibited severely impaired relaxant responses to acetylcholine (Ach) (1 nmol/L to 10 pmol/L) (P 0.05).Conclusion Critical components that drive the vascular function and influence the localization of mesenteric artery thrombosis are flow-responsive elements within the vascular endothelium.

  6. STUDY OF GENE FLOW FROM GM COTTON (Gossypium hirsutum VARIETIES IN “EL ESPINAL” (TOLIMA, COLOMBIA.

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    Alejandro Chaparro Giraldo

    2013-10-01

    Full Text Available In 2009, 4088 hectares of genetically modified (GM cotton were planted in Tolima (Colombia, however there is some uncertainty about containment measures needed to prevent the flow of pollen and seed from regulated GM fields into adjacent fields. In this study, the gene flow from GM cotton varieties to conventional or feral cotton plants via seed and pollen was evaluated. ImmunostripTM, PCR and ELISA assays were used to detect gene flow. Fifty six refuges, 27 fields with conventional cotton and four feral individuals of the enterprise “Remolinos Inc.” located in El Espinal (Tolima were analyzed in the first half of 2010. The results indicated seeds mediated gene flow in 45 refuges (80,4 % and 26 fields with conventional cotton (96 %, besides a pollen mediated gene flow in one field with conventional cotton and nine refuges. All fields cultivated with conventional cotton showed gene flow from GM cotton. Two refuges and two feral individuals did not reveal gene flow from GM cotton. 

  7. Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene phylogeography.

    Science.gov (United States)

    Kotlík, Petr; Marková, Silvia; Choleva, Lukás; Bogutskaya, Nina G; Ekmekçi, F Guler; Ivanova, Petya P

    2008-02-01

    The Black and Caspian Seas have experienced alternating periods of isolation and interconnection over many Milankovitch climate oscillations and most recently became separated when the meltwater overflow from the Caspian Sea ceased at the end of the last glaciation. Climate-induced habitat changes have indisputably had profound impacts on distribution and demography of aquatic species, yet uncertainties remain about the relative roles of isolation and dispersal in the response of species shared between the Black and Caspian Sea basins. We examined these issues using phylogeographical analysis of an anadromous cyprinid fish Rutilus frisii. Bayesian coalescence analyses of sequence variation at two nuclear and one mitochondrial genes suggest that the Black and Caspian Seas supported separate populations of R. frisii during the last glaciation. Parameter estimates from the fitted isolation-with-migration model showed that their separation was not complete, however, and that the two populations continued to exchange genes in both directions. These analyses also suggested that majority of migrations occurred during the Pleistocene, showing that the variation shared between the Black and Caspian Seas is the result of ancient dispersal along the temporary natural connections between the basins, rather than of incomplete lineage sorting or recent human-mediated dispersal. Gene flow between the refugial populations was therefore an important source of genetic variation, and we suggest that it facilitated the evolutionary response of the populations to changing climate.

  8. Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey.

    Science.gov (United States)

    Promponas, Vasilis J; Ouzounis, Christos A; Iliopoulos, Ioannis

    2014-05-01

    More than a decade ago, a number of methods were proposed for the inference of protein interactions, using whole-genome information from gene clusters, gene fusions and phylogenetic profiles. This structural and evolutionary view of entire genomes has provided a valuable approach for the functional characterization of proteins, especially those without sequence similarity to proteins of known function. Furthermore, this view has raised the real possibility to detect functional associations of genes and their corresponding proteins for any entire genome sequence. Yet, despite these exciting developments, there have been relatively few cases of real use of these methods outside the computational biology field, as reflected from citation analysis. These methods have the potential to be used in high-throughput experimental settings in functional genomics and proteomics to validate results with very high accuracy and good coverage. In this critical survey, we provide a comprehensive overview of 30 most prominent examples of single pairwise protein interaction cases in small-scale studies, where protein interactions have either been detected by gene fusion or yielded additional, corroborating evidence from biochemical observations. Our conclusion is that with the derivation of a validated gold-standard corpus and better data integration with big experiments, gene fusion detection can truly become a valuable tool for large-scale experimental biology.

  9. Performance of vertical up-flow constructed wetlands on swine wastewater containing tetracyclines and tet genes.

    Science.gov (United States)

    Huang, Xu; Liu, Chaoxiang; Li, Ke; Su, Jianqiang; Zhu, Gefu; Liu, Lin

    2015-03-01

    Antibiotics and antibiotic resistance genes (ARGs) pollution in animal feeding farms received more public attention recently. Livestock wastewater contains large quantities of antibiotics and ARGs even after traditional lagoon treatment. In this study, the performance of vertical up-flow constructed wetlands (VUF-CWs) on swine wastewater containing tetracycline compounds (TCs) and tet genes was evaluated based on three aspects, TCs and tet genes removal efficiencies, residual TCs and tet genes in soils and plants, and the effect of TCs accumulation on nutrients removal and tet genes development. High removal efficiencies (69.0-99.9%) were achieved for oxytetracycline (OTC), tetracycline (TC) and chlortetracycline (CTC) with or without OTC spiked in the influent additionally. TCs concentrations in surface soils increased at first two sampling periods and then decreased after plants were harvested. Satisfactory nutrients removal efficiencies were also obtained, but TN and NH4-N removal efficiencies were significantly negative correlated with total concentration of TCs (∑TCs) in the soils (p < 0.01). The absolute abundances of all the target genes (tetO, tetM, tetW, tetA, tetX and intI1) were greatly reduced with their log units ranging from 0.26 to 3.3. However, the relative abundances of tetO, tetM and tetX in some effluent samples were significantly higher than those in the influent (p < 0.05). The relative abundances of tet genes except for tetO were significantly correlated with ∑TCs in the soils (p < 0.05). In summary, the proposed VUF-CWs are effective alternative for the removal of TCs and tet genes. But it is of great importance to prevent large accumulation of TCs in the soils. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Diversification of Lupine Bradyrhizobium Strains: Evidence from Nodulation Gene Trees▿ †

    Science.gov (United States)

    Stępkowski, Tomasz; Hughes, Colin E.; Law, Ian J.; Markiewicz, Łukasz; Gurda, Dorota; Chlebicka, Agnieszka; Moulin, Lionel

    2007-01-01

    Bradyrhizobium strains isolated in Europe from Genisteae and serradella legumes form a distinct lineage, designated clade II, on nodulation gene trees. Clade II bradyrhizobia appear to prevail also in the soils of Western Australia and South Africa following probably accidental introduction with seeds of their lupine and serradella hosts. Given this potential for dispersal, we investigated Bradyrhizobium isolates originating from a range of native New World lupines, based on phylogenetic analyses of nodulation (nodA, nodZ, noeI) and housekeeping (atpD, dnaK, glnII, recA) genes. The housekeeping gene trees revealed considerable diversity among lupine bradyrhizobia, with most isolates placed in the Bradyrhizobium japonicum lineage, while some European strains were closely related to Bradyrhizobium canariense. The nodA gene tree resolved seven strongly supported groups (clades I to VII) that correlated with strain geographical origins and to some extent with major Lupinus clades. All European strains were placed in clade II, whereas only a minority of New World strains was placed in this clade. This work, as well as our previous studies, suggests that clade II diversified predominately in the Old World, possibly in the Mediterranean. Most New World isolates formed subclade III.2, nested in a large “pantropical” clade III, which appears to be New World in origin, although it also includes strains originating from nonlupine legumes. Trees generated using nodZ and noeI gene sequences accorded well with the nodA tree, but evidence is presented that the noeI gene may not be required for nodulation of lupine and that loss of this gene is occurring. PMID:17400786

  11. Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria.

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    Roxane Chiori

    Full Text Available BACKGROUND: The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. CONCLUSIONS/SIGNIFICANCE: Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.

  12. Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever.

    Science.gov (United States)

    Andersen, Kristian G; Shylakhter, Ilya; Tabrizi, Shervin; Grossman, Sharon R; Happi, Christian T; Sabeti, Pardis C

    2012-03-19

    Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 (IL21), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21. Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit.

  13. UNDERSTANDING THE POPULATION GENETIC STRUCTURE OF GLEDITSIA TRIACANTHOS L.: THE SCALE AND PATTERN OF POLLEN GENE FLOW.

    Science.gov (United States)

    Schnabel, Andrew; Hamrick, J L

    1995-10-01

    Spatial and temporal patterns of gene flow determine the extent to which populations can differentiate from one another as a result of natural selection or genetic drift. In this study, we investigated pollen-mediated gene flow in two eastern Kansas populations of the subdioecious tree species, Gleditsia triacanthos L. (Leguminosae), or honeylocust. In 2 yr at each site, we used paternity-exclusion analysis to estimate the proportion of seeds sired by immigrant pollen. We also used a single-parent and parent-pair exclusion analysis on naturally established seedlings and saplings to estimate gene flow into one site over a 12-yr period and into the second site over a 22-yr period. Results of both analyses showed high minimum estimates of pollen gene flow into each site (17%-30%). In each population, we found significantly less gene flow in years of high fruit production than in years of low fruit production, but in one population, we observed little variation in gene-flow rates among age classes of seedlings and saplings. The level of pollen gene flow showed weak negative dependence on the relative isolation distances of the maternal trees sampled (140-240 m at one site vs. 85-120 m at the second site), and gene-flow estimates from naturally established juveniles were very similar at the two sites. Within populations, a multiple regression model showed that maximum-likelihood estimates of male fertility were negatively associated with distances between mates and positively associated with male size as measured by stem diameter. In neither population, however, did the regression explain more than 16% of the total variation in male fertilities. © 1995 The Society for the Study of Evolution.

  14. Gene flow from transgenic oilseed rape (Brassica napus L.) to cruciferous weeds under mentor pollen inducement

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The alien gene flow between genetically modified glyphosate-resistant rapeseed variety Q3 ( Brassica napus L. ) and four cruciferous weeds was studied under mentor pollen inducement. The results showed that when Thlaspi arvense L., Capsella bursapastoris (L.) Medic, Cardamine hirsuta L. and Rorippa palustris (L.) Besser were pollinated with mentor pollen, the mixed Q3 and the weed, pollen grains aggregated largely and germinated quickly, and the numbers of pollen tubes penetrating into the style and the ovary were greatly increased as compared with corresponding self-pollination groups. Twenty four to forty eight hours after pollination, several pollen tubes were observed to penetrate into the ovule via micropyle in each mentor combination. However, when the mentor progenies were analyzed by PCR, all of them showed negative for the Q3 herbicide-resistant gene. Collectively, these results indicated that crossing between T. arvense, C. bursa-pastoris, C. hirsuta, R. palustris (as female) and Q3 (as male) was highly incompatible and the herbicide-resistant gene could not flow from Q3 to these four weeds.

  15. Is the Gibraltar strait a barrier to gene flow for the bat Myotis myotis (Chiroptera: Vespertilionidae)?

    Science.gov (United States)

    Castella, V; Ruedi, M; Excoffier, L; Ibáñez, C; Arlettaz, R; Hausser, J

    2000-11-01

    Because of their role in limiting gene flow, geographical barriers like mountains or seas often coincide with intraspecific genetic discontinuities. Although the Strait of Gibraltar represents such a potential barrier for both plants and animals, few studies have been conducted on its impact on gene flow. Here we test this effect on a bat species (Myotis myotis) which is apparently distributed on both sides of the strait. Six colonies of 20 Myotis myotis each were sampled in southern Spain and northern Morocco along a linear transect of 1350 km. Results based on six nuclear microsatellite loci reveal no significant population structure within regions, but a complete isolation between bats sampled on each side of the strait. Variability at 600 bp of a mitochondrial gene (cytochrome b) confirms the existence of two genetically distinct and perfectly segregating clades, which diverged several million years ago. Despite the narrowness of the Gibraltar Strait (14 km), these molecular data suggest that neither males, nor females from either region have ever reproduced on the opposite side of the strait. Comparisons of molecular divergence with bats from a closely related species (M. blythii) suggest that the North African clade is possibly a distinct taxon warranting full species rank. We provisionally refer to it as Myotis cf punicus Felten 1977, but a definitive systematic understanding of the whole Mouse-eared bat species complex awaits further genetic sampling, especially in the Eastern Mediterranean areas.

  16. A Study on the Relationship of Earnings and Cash Flows: Evidence of Finance Sector in Iran

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    Mahdi Salehi

    2013-08-01

    Full Text Available The present study is investigating the quality of annual accounting earnings in banking firms that have been listed in Tehran Stock Exchange (TSE and it evaluates the most important information of accounting that is earnings and cash flows. The study also intends to investigate the relationship between earnings and cash flows regarding their relationship with the expected return of stocks and the extent of informing in the analysis of the inevitable return of stocks. The analyses of data during 6 years revealed that the earnings in comparison to the cash flows are very important as they have positive effects on the stock. Moreover, in the case of the relations of earnings and earnings changes with the expected return of stocks and the relation of cash flows and cash flow changes with the expected return of stock, it was found that there is only a meaningful relationship between earning changes and the expected return of stock in banking groups. However, there is no meaningful relationship between earning and cash flows with the expected return of stock. The result was that the informational content test didn’t support the value relation of earning and cash flows. Furthermore, the classifying of information through banking group indicated that the changes of earning was in the first rank and next were earning, the changes of cash flow and cash flows.Keywords: Earnings; Cash flows; expected return; Value relevance; Banking risks

  17. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment.

    Science.gov (United States)

    Ford, Antonia G P; Dasmahapatra, Kanchon K; Rüber, Lukas; Gharbi, Karim; Cezard, Timothee; Day, Julia J

    2015-07-01

    Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.

  18. A multiscale analysis of gene flow for the New England cottontail, an imperiled habitat specialist in a fragmented landscape.

    Science.gov (United States)

    Fenderson, Lindsey E; Kovach, Adrienne I; Litvaitis, John A; O'Brien, Kathleen M; Boland, Kelly M; Jakubas, Walter J

    2014-05-01

    Landscape features of anthropogenic or natural origin can influence organisms' dispersal patterns and the connectivity of populations. Understanding these relationships is of broad interest in ecology and evolutionary biology and provides key insights for habitat conservation planning at the landscape scale. This knowledge is germane to restoration efforts for the New England cottontail (Sylvilagus transitionalis), an early successional habitat specialist of conservation concern. We evaluated local population structure and measures of genetic diversity of a geographically isolated population of cottontails in the northeastern United States. We also conducted a multiscale landscape genetic analysis, in which we assessed genetic discontinuities relative to the landscape and developed several resistance models to test hypotheses about landscape features that promote or inhibit cottontail dispersal within and across the local populations. Bayesian clustering identified four genetically distinct populations, with very little migration among them, and additional substructure within one of those populations. These populations had private alleles, low genetic diversity, critically low effective population sizes (3.2-36.7), and evidence of recent genetic bottlenecks. Major highways and a river were found to limit cottontail dispersal and to separate populations. The habitat along roadsides, railroad beds, and utility corridors, on the other hand, was found to facilitate cottontail movement among patches. The relative importance of dispersal barriers and facilitators on gene flow varied among populations in relation to landscape composition, demonstrating the complexity and context dependency of factors influencing gene flow and highlighting the importance of replication and scale in landscape genetic studies. Our findings provide information for the design of restoration landscapes for the New England cottontail and also highlight the dual influence of roads, as both

  19. Evidence of a bigenomic regulation of mitochondrial gene expression by thyroid hormone during rat brain development

    Energy Technology Data Exchange (ETDEWEB)

    Sinha, Rohit Anthony; Pathak, Amrita; Mohan, Vishwa; Babu, Satish; Pal, Amit; Khare, Drirh [Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014 (India); Godbole, Madan M., E-mail: madangodbole@yahoo.co.in [Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014 (India)

    2010-07-02

    Hypothyroidism during early mammalian brain development is associated with decreased expression of various mitochondrial encoded genes along with evidence for mitochondrial dysfunction. However, in-spite of the similarities between neurological disorders caused by perinatal hypothyroidism and those caused by various genetic mitochondrial defects we still do not know as to how thyroid hormone (TH) regulates mitochondrial transcription during development and whether this regulation by TH is nuclear mediated or through mitochondrial TH receptors? We here in rat cerebellum show that hypothyroidism causes reduction in expression of nuclear encoded genes controlling mitochondrial biogenesis like PGC-1{alpha}, NRF-1{alpha} and Tfam. Also, we for the first time demonstrate a mitochondrial localization of thyroid hormone receptor (mTR) isoform in developing brain capable of binding a TH response element (DR2) present in D-loop region of mitochondrial DNA. These results thus indicate an integrated nuclear-mitochondrial cross talk in regulation of mitochondrial transcription by TH during brain development.

  20. The myostatin gene of Mytilus chilensis evidences a high level of polymorphism and ubiquitous transcript expression.

    Science.gov (United States)

    Núñez-Acuña, Gustavo; Gallardo-Escárate, Cristian

    2014-02-15

    Myostatin (MSTN) is a protein of the Transforming Growth Factor-β (TGF-β) superfamily and plays a crucial role in muscular development for higher vertebrates. However, its biological function in marine invertebrates remains undiscovered. This study characterizes the full-length sequence of the Mytilus chilensis myostatin gene (Mc-MSTN). Furthermore, tissue transcription patterns and putative single nucleotide polymorphisms (SNPs) were also identified. The Mc-MSTN cDNA sequence showed 3528 base pairs (bp), consisting of 161 bp of 5' UTR, 2,110 bp of 3' UTR, and an open reading frame of 1,257 bp encoding for 418 amino acids and with an RXXR proteolytic site and nine cysteine-conserved residues. Gene transcription analysis revealed that the Mc-MSTN has ubiquitous expression among several tissues, with higher expression in the gonads and mantle than in the digestive gland, gills, and hemolymph. Furthermore, high levels of polymorphisms were detected (28 SNPs in 3'-UTR and 9 SNPs in the coding region). Two SNPs were non-synonymous and involved amino acid changes between Glu/Asp and Thr/Ile. Until now, the MSTN gene has been mainly related to muscle growth in marine bivalves. However, the present study suggests a putative biological function not entirely associated to muscle tissue and contributes molecular evidence to the current debate about the function of the MSTN gene in marine invertebrates.

  1. Do foreign portfolio flows increase risk in emerging stock markets? Evidence from six Latin American countries

    OpenAIRE

    Agudelo, Diego A.; Castaño, Milena M.

    2011-01-01

    Foreign portfolio flows have been blamed for causing instability in emerging markets, especially during financial crises. This study measured the effect of foreign capital flows on volatility and exposure to world market risk in the six largest Latin American stock markets: Argentina, Brazil, Colombia, Chile, Mexico and Peru, for around 10 years including the 2008 World financial crisis. This will test whether these flows cause instability for those markets and increase their exposure to inte...

  2. Further evidence of an Amerindian contribution to the Polynesian gene pool on Easter Island.

    Science.gov (United States)

    Thorsby, E; Flåm, S T; Woldseth, B; Dupuy, B M; Sanchez-Mazas, A; Fernandez-Vina, M A

    2009-06-01

    Available evidence suggests a Polynesian origin of the Easter Island population. We recently found that some native Easter Islanders also carried some common American Indian (Amerindian) human leukocyte antigen (HLA) alleles, which probably were introduced before Europeans discovered the island in 1722. In this study, we report molecular genetic investigations of 21 other selected native Easter Islanders. Analysis of mitochondrial DNA and Y chromosome markers showed no traces of an Amerindian contribution. However, high-resolution genomic HLA typing showed that two individuals carried some other common Amerindian HLA alleles, different from those found in our previous investigations. The new data support our previous evidence of an Amerindian contribution to the gene pool on Easter Island.

  3. Field dipolarization in Saturn's magnetotail with planetward ion flows and energetic particle flow bursts: Evidence of quasi-steady reconnection

    Science.gov (United States)

    Jackman, C. M.; Thomsen, M. F.; Mitchell, D. G.; Sergis, N.; Arridge, C. S.; Felici, M.; Badman, S. V.; Paranicas, C.; Jia, X.; Hospodarksy, G. B.; Andriopoulou, M.; Khurana, K. K.; Smith, A. W.; Dougherty, M. K.

    2015-05-01

    We present a case study of an event from 20 August (day 232) of 2006, when the Cassini spacecraft was sampling the region near 32 RS and 22 h LT in Saturn's magnetotail. Cassini observed a strong northward-to-southward turning of the magnetic field, which is interpreted as the signature of dipolarization of the field as seen by the spacecraft planetward of the reconnection X line. This event was accompanied by very rapid (up to ~1500 km s-1) thermal plasma flow toward the planet. At energies above 28 keV, energetic hydrogen and oxygen ion flow bursts were observed to stream planetward from a reconnection site downtail of the spacecraft. Meanwhile, a strong field-aligned beam of energetic hydrogen was also observed to stream tailward, likely from an ionospheric source. Saturn kilometric radiation emissions were stimulated shortly after the observation of the dipolarization. We discuss the field, plasma, energetic particle, and radio observations in the context of the impact this reconnection event had on global magnetospheric dynamics.

  4. Evidence for siphon flows with shocks in solar magnetic flux tubes

    Science.gov (United States)

    Degenhardt, D.; Solanki, S. K.; Montesinos, B.; Thomas, J. H.

    1993-01-01

    We synthesize profiles of the infrared line Fe I 15648.5 A (g = 3) for a recently developed theoretical model of siphon flows along photospheric magnetic loops. The synthesized line profiles are compared with the observations from which Rueedi et al. (1992) deduced the presence of such flows across the neutral line of an active region plage. This comparison supports the interpretation of Rueedi et al. (1992). It also suggests that the average footpoint separation of the observed loops carrying the siphon flow is 8-15 sec and that the siphon flow experiences a standing tube shock in the downstream leg near the top of the arch.

  5. Retrieving geomagnetic secular variations from lava flows: evidence from Mounts Arso, Etna and Vesuvius (southern Italy)

    Science.gov (United States)

    Incoronato, Alberto; Angelino, Antimo; Romano, Romolo; Ferrante, Agostino; Sauna, Renata; Vanacore, Gianpio; Vecchione, Claudio

    2002-06-01

    Mean directions of magnetization from Mounts Arso (Ischia Island, Gulf of Naples), Etna and Vesuvius lava flows have been determined based on very stringent linearity criteria. These indicate that, regardless of the source volcano, the lava flow mean directions of magnetization form a common path, the SISVC (Southern Italy Secular Variation Curve). This curve enables a reassessment of the age of eruption of several lavas. A date of AD 1169 is demonstrated to be the only possible time of emplacement for one Etna lava flow previously assigned an age of AD 812/1169. It is also demonstrated that two Etna lava flows, which, according to the literature, were emplaced in AD 1536 and 1595 respectively, were actually both emplaced around AD 1037. Three other Etna lava flows, one ascribed to AD 1566 and two to AD 1595, were actually emplaced between AD 1169 and 1284/85. The same time window also holds for a Vesuvius lava flow for which only an upper time threshold was previously available. Only one of the studied flows needs further sampling and analysis to verify whether this flow has been affected by a complete remagnetization or has an erroneous historical dating. The applied procedure seems to be the most appropriate one in carrying out palaeomagnetic surveys of lava flows, as also suggested by the broad agreement with some 17th and 19th century measurements of the geomagnetic field in Rome, relocated to Etna, and is likely to improve knowledge of past history of a volcano significantly.

  6. Parentage versus two-generation analyses for estimating pollen-mediated gene flow in plant populations.

    Science.gov (United States)

    Burczyk, Jaroslaw; Koralewski, Tomasz E

    2005-07-01

    Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the NEIGHBORHOOD model--a representative of parentage analyses, and (ii) the recently developed TWOGENER analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (N(ep)) and the mean pollen dispersal distance (delta). We demonstrate that both methods provide very congruent estimates of N(ep) and delta, when the methods' assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the NEIGHBORHOOD model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of N(ep). The NEIGHBORHOOD model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the TWOGENER method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of TWOGENER it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied.

  7. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

    Directory of Open Access Journals (Sweden)

    Wall Jeffrey D

    2008-11-01

    Full Text Available Abstract Background Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions. Results Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000 than non-African populations (300–3,300. We estimate mean rates of bidirectional gene flow at 4.8 × 10-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10-3 than among African populations (2.7 × 10-4. Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4. Conclusion We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

  8. Biofluids, cell mechanics and epigenetics: Flow-induced epigenetic mechanisms of endothelial gene expression.

    Science.gov (United States)

    Davies, Peter F; Manduchi, Elisabetta; Jiménez, Juan M; Jiang, Yi-Zhou

    2017-01-04

    Epigenetics is the regulation of gene expression (transcription) in response to changes in the cell environment through genomic modifications that largely involve the non-coding fraction of the human genome and that cannot be attributed to modification of the primary DNA sequence. Epigenetics is dominant in establishing cell fate and positioning during programmed embryonic development. However the same pathways are used by mature postnatal and adult mammalian cells during normal physiology and are implicated in disease mechanisms. Recent research demonstrates that blood flow and pressure are cell environments that can influence transcription via epigenetic pathways. The principal epigenetic pathways are chemical modification of cytosine residues of DNA (DNA methylation) and of the amino tails of histone proteins associated with DNA in nucleosomes. They also encompass the post-transcriptional degradation of mRNA transcripts by non-coding RNAs (ncRNA). In vascular endothelium, epigenetic pathways respond to temporal and spatial variations of flow and pressure, particularly hemodynamic disturbed blood flow, with important consequences for gene expression. The biofluid environment is linked by mechanotransduction and solute transport to cardiovascular cell phenotypes via signaling pathways and epigenetic regulation for which there is an adequate interdisciplinary infrastructure with robust tools and methods available. Epigenetic mechanisms may be less familiar than acute genomic signaling to Investigators at the interface of biofluids, biomechanics and cardiovascular biology. Here we introduce a biofluids / cellular biomechanics readership to the principal epigenetic pathways and provide a contextual overview of endothelial epigenetic plasticity in the regulation of flow-responsive transcription. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Modelling Gene Flow between Fields of White Clover with Honeybees as Pollen Vectors

    DEFF Research Database (Denmark)

    Løjtnant, Christina; Boelt, Birte; Clausen, Sabine Karin

    2012-01-01

    % with an estimated 95% percentile of 70%. The results show that the European Union threshold limit of 0.9% GM admixture for food and feed will likely be exceeded at times and especially organic farmers that do not accept GM admixture and often have clover and clover–grass fields might face challenges with admixture.......7%, but subjected to large uncertainty. In a worst case scenario with adjacent fields—one with a genetically modified (GM) T. repens cultivar and the other with a conventional T. repens cultivar—and where all arriving bees were expected to transfer GM pollen, the median gene flow was modelled to be 7...

  10. Asymmetrical gene flow in a hybrid zone of Hawaiian Schiedea (Caryophyllaceae species with contrasting mating systems.

    Directory of Open Access Journals (Sweden)

    Lisa E Wallace

    Full Text Available Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1 putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2 gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3 in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s of S. menziesii.

  11. Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

    Science.gov (United States)

    Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

    2014-10-01

    Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.

  12. Evidence of a major gene influencing hair length and heat tolerance in Bos taurus cattle.

    Science.gov (United States)

    Olson, T A; Lucena, C; Chase, C C; Hammond, A C

    2003-01-01

    Evidence was found that supports the existence of a major gene (designated as the slick hair gene), dominant in mode of inheritance, that is responsible for producing a very short, sleek hair coat. Cattle with slick hair were observed to maintain lower rectal temperatures (RT). The gene is found in Senepol cattle and criollo (Spanish origin) breeds in Central and South America. This gene is also found in a Venezuelan composite breed, the Carora, formed from the Brown Swiss and a Venezuelan criollo breed. Two sets of backcross matings of normal-haired sire breeds to Senepol crossbred dams assumed to be heterozygous for the slick hair gene resulted in ratios of slick to normal-haired progeny that did not significantly differ from 1:1. Data from Carora x Holstein crossbred cows in Venezuela also support the concept of a major gene that is responsible for the slick hair coat of the Carora breed. Cows that were 75% Holstein: 25% Carora in breed composition segregated with a ratio that did not differ from 1:1, as would be expected from a backcross matinginvolving a dominant gene. The effect of the slick hair gene on RT depended on the degree of heat stress and appeared to be affected by age and/or lactation status. The decreased RT observed for slick-haired crossbred calves compared to normal-haired contemporaries ranged from 0.18 to 0.4 degrees C. An even larger decrease in RT (0.61 degrees C; P heat stress. The improved thermotolerance of crossbred calves due to their slick hair coats did not result in increased weaning weights, possibly because both the slick and normal-haired calves were being nursed by slick-haired dams. There were indications that the slick-haired calves grew faster immediately following weaning and that their growth during the cooler months of the year was not compromised significantly by their reduced quantity of hair. In the Carora x Holstein crossbred cows there was a positive effect of slick hair on milk yield under dry, tropical conditions.

  13. Evidence of population resistance to extreme low flows in a fluvial-dependent fish species

    Science.gov (United States)

    Katz, Rachel A.; Freeman, Mary C.

    2015-01-01

    Extreme low streamflows are natural disturbances to aquatic populations. Species in naturally intermittent streams display adaptations that enhance persistence during extreme events; however, the fate of populations in perennial streams during unprecedented low-flow periods is not well-understood. Biota requiring swift-flowing habitats may be especially vulnerable to flow reductions. We estimated the abundance and local survival of a native fluvial-dependent fish species (Etheostoma inscriptum) across 5 years encompassing historic low flows in a sixth-order southeastern USA perennial river. Based on capturemark-recapture data, the study shoal may have acted as a refuge during severe drought, with increased young-of-the-year (YOY) recruitment and occasionally high adult immigration. Contrary to expectations, summer and autumn survival rates (30 days) were not strongly depressed during low-flow periods, despite 25%-80% reductions in monthly discharge. Instead, YOY survival increased with lower minimum discharge and in response to small rain events that increased low-flow variability. Age-1+ fish showed the opposite pattern, with survival decreasing in response to increasing low-flow variability. Results from this population dynamics study of a small fish in a perennial river suggest that fluvial-dependent species can be resistant to extreme flow reductions through enhanced YOY recruitment and high survival

  14. Investment - Cash Flow Sensitivity and Financing Constraints: New Evidence from Indian Business Group Firms

    NARCIS (Netherlands)

    Pallathitta, Rejie; Kabir, Rezaul; Qian, Jing

    2010-01-01

    A controversy exists on the use of the investment – cash flow sensitivity as a measure of financing constraints of firms. We re-examine this controversy by analyzing firms affiliated to Indian business groups. We find a strong investment – cash flow sensitivity for both group-affiliated and independ

  15. Investment–cash flow sensitivity and financing constraints: new evidence from Indian business group firms

    NARCIS (Netherlands)

    George, R.; Kabir, M.R.; Qian, J.

    2011-01-01

    A controversy exists on the use of the investment–cash flow sensitivity as a measure of financing constraints of firms.Were-examine this controversy by analyzing firms affiliated to Indian business groups. We find a strong investment–cash flow sensitivity for both group-affiliated and independent fi

  16. The flow structure of pyroclastic density currents: evidence from particle models and large-scale experiments

    Science.gov (United States)

    Dellino, Pierfrancesco; Büttner, Ralf; Dioguardi, Fabio; Doronzo, Domenico Maria; La Volpe, Luigi; Mele, Daniela; Sonder, Ingo; Sulpizio, Roberto; Zimanowski, Bernd

    2010-05-01

    Pyroclastic flows are ground hugging, hot, gas-particle flows. They represent the most hazardous events of explosive volcanism, one striking example being the famous historical eruption of Pompeii (AD 79) at Vesuvius. Much of our knowledge on the mechanics of pyroclastic flows comes from theoretical models and numerical simulations. Valuable data are also stored in the geological record of past eruptions, i.e. the particles contained in pyroclastic deposits, but they are rarely used for quantifying the destructive potential of pyroclastic flows. In this paper, by means of experiments, we validate a model that is based on data from pyroclastic deposits. It allows the reconstruction of the current's fluid-dynamic behaviour. We show that our model results in likely values of dynamic pressure and particle volumetric concentration, and allows quantifying the hazard potential of pyroclastic flows.

  17. Genetic Variation, Structure, and Gene Flow in a Sloth Bear (Melursus ursinus Meta-Population in the Satpura-Maikal Landscape of Central India.

    Directory of Open Access Journals (Sweden)

    Trishna Dutta

    Full Text Available Sloth bears (Melursus ursinus are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately.

  18. Genetic Variation, Structure, and Gene Flow in a Sloth Bear (Melursus ursinus) Meta-Population in the Satpura-Maikal Landscape of Central India.

    Science.gov (United States)

    Dutta, Trishna; Sharma, Sandeep; Maldonado, Jesús E; Panwar, Hemendra Singh; Seidensticker, John

    2015-01-01

    Sloth bears (Melursus ursinus) are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately.

  19. Segregation analysis of 231 Ashkenazi Jewish families for evidence of additional breast cancer susceptibility genes.

    Science.gov (United States)

    Kaufman, David J; Beaty, Terri H; Struewing, Jeffery P

    2003-10-01

    Between 5 and 10% of breast cancer is attributable to inherited cancer susceptibility genes. Mutations in the genes BRCA1 and BRCA2 account for two-thirds of hereditary breast cancer cases. Using segregation analysis, families of cases without BRCA1/2 mutations were studied for statistical evidence of another major breast cancer gene in a community-based sample of Jewish probands tested previously for the presence of three BRCA founder mutations. A total of 231 probands with breast cancer, who do not carry a founder mutation, reported complete data on 602 female first-degree relatives of probands over age 20; 78 of these relatives had breast cancer. Segregation analysis was used to evaluate the likelihood of various genetic and nongenetic models. Sporadic, environmental, and general Mendelian genetic models fit the family data poorly and were rejected. A Mendelian recessive model fit better than dominant and codominant models, although none of these could be rejected. Cumulative incidence curves predicted by the recessive and codominant models fit observed incidence among first-degree relatives well. The assumption of Mendelian transmission of a major recessive gene(s) is compatible with the data. The recessive model predicts that 4% of women would carry the high-risk genotype, with 85% of them developing breast cancer by age 70. There was significant heterogeneity between these families and the 114 BRCA1/2 mutation-positive families from the same study population, implying that this apparent recessive effect is not because of undetected BRCA1/2 mutations. The study adds support for a major autosomal recessive component to breast cancer susceptibility.

  20. Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis

    Directory of Open Access Journals (Sweden)

    Butler Geraldine

    2008-06-01

    Full Text Available Abstract Background To date very few incidences of interdomain gene transfer into fungi have been identified. Here, we used the emerging genome sequences of Candida albicans WO-1, Candida tropicalis, Candida parapsilosis, Clavispora lusitaniae, Pichia guilliermondii, and Lodderomyces elongisporus to identify recent interdomain HGT events. We refer to these as CTG species because they translate the CTG codon as serine rather than leucine, and share a recent common ancestor. Results Phylogenetic and syntenic information infer that two C. parapsilosis genes originate from bacterial sources. One encodes a putative proline racemase (PR. Phylogenetic analysis also infers that there were independent transfers of bacterial PR enzymes into members of the Pezizomycotina, and protists. The second HGT gene in C. parapsilosis belongs to the phenazine F (PhzF superfamily. Most CTG species also contain a fungal PhzF homolog. Our phylogeny suggests that the CTG homolog originated from an ancient HGT event, from a member of the proteobacteria. An analysis of synteny suggests that C. parapsilosis has lost the endogenous fungal form of PhzF, and subsequently reacquired it from a proteobacterial source. There is evidence that Schizosaccharomyces pombe and Basidiomycotina also obtained a PhzF homolog through HGT. Conclusion Our search revealed two instances of well-supported HGT from bacteria into the CTG clade, both specific to C. parapsilosis. Therefore, while recent interkingdom gene transfer has taken place in the CTG lineage, its occurrence is rare. However, our analysis will not detect ancient gene transfers, and we may have underestimated the global extent of HGT into CTG species.

  1. The Need to Support of Data Flow Graph Visualization of Forensic Lucid Programs, Forensic Evidence, and their Evaluation by GIPSY

    CERN Document Server

    Mokhov, Serguei A; Debbabi, Mourad

    2010-01-01

    Lucid programs are data-flow programs and can be visually represented as data flow graphs (DFGs) and composed visually. Forensic Lucid, a Lucid dialect, is a language to specify and reason about cyberforensics cases. It includes the encoding of the evidence (representing the context of evaluation) and the crime scene modeling in order to validate claims against the model and perform event reconstruction, potentially within large swaths of digital evidence. To aid investigators to model the scene and evaluate it, instead of typing a Forensic Lucid program, we propose to expand the design and implementation of the Lucid DFG programming onto Forensic Lucid case modeling and specification to enhance the usability of the language and the system.

  2. Model-based calculating tool for pollen-mediated gene flow frequencies in plants.

    Science.gov (United States)

    Lei, Wang; Bao-Rong, Lu

    2016-12-30

    The potential social-economic and environmental impacts caused by transgene flow from genetically engineered (GE) crops have stimulated worldwide biosafety concerns. To determine transgene flow frequencies resulted from pollination is the first critical step for assessing such impacts, in addition to the determination of transgene expression and fitness in crop-wild hybrid descendants. Two methods are commonly used to estimate pollen-mediated gene flow (PMGF) frequencies: field experimenting and mathematical modeling. Field experiments can provide relatively accurate results but are time/resource consuming. Modeling offers an effective complement for PMGF experimental assessment. However, many published models describe PMGF by mathematical equations and are practically not easy to use. To increase the application of PMGF modeling for the estimation of transgene flow, we established a tool to calculate PMGF frequencies based on a quasi-mechanistic PMGF model for wind-pollination species. This tool includes a calculating program displayed by an easy-operating interface. PMGF frequencies of different plant species can be quickly calculated under different environmental conditions by including a number of biological and wind speed parameters that can be measured in the fields/laboratories or obtained from published data. The tool is freely available in the public domain (http://ecology.fudan.edu.cn/userfiles/cn/files/Tool_Manual.zip). Case studies including rice, wheat, and maize demonstrated similar results between the calculated frequencies based on this tool and those from published PMGF data. This PMGF calculating tool will provide useful information for assessing and monitoring social-economic and environmental impacts caused by transgene flow from GE crops. This tool can also be applied to determine the isolation distances between GE and non-GE crops in a coexistence agro-ecosystem, and to ensure the purity of certified seeds by setting proper isolation distances

  3. Genetic evidence for the association between the early growth response 3 (EGR3 gene and schizophrenia.

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    Rui Zhang

    Full Text Available Recently, two genome scan meta-analysis studies have found strong evidence for the association of loci on chromosome 8p with schizophrenia. The early growth response 3 (EGR3 gene located in chromosome 8p21.3 was also found to be involved in the etiology of schizophrenia. However, subsequent studies failed to replicate this finding. To investigate the genetic role of EGR3 in Chinese patients, we genotyped four SNPs (average interval ∼2.3 kb in the chromosome region of EGR3 in 470 Chinese schizophrenia patients and 480 healthy control subjects. The SNP rs35201266 (located in intron 1 of EGR3 showed significant differences between cases and controls in both genotype frequency distribution (P = 0.016 and allele frequency distribution (P = 0.009. Analysis of the haplotype rs35201266-rs3750192 provided significant evidence for association with schizophrenia (P = 0.0012; a significant difference was found for the common haplotype AG (P = 0.0005. Furthermore, significant associations were also found in several other two-, and three-SNP tests of haplotype analyses. The meta-analysis revealed a statistically significant association between rs35201266 and schizophrenia (P = 0.0001. In summary, our study supports the association of EGR3 with schizophrenia in our Han Chinese sample, and further functional exploration of the EGR3 gene will contribute to the molecular basis for the complex network underlying schizophrenia pathogenesis.

  4. Pollen-mediated gene flow from glyphosate-resistant common waterhemp (Amaranthus rudis Sauer): consequences for the dispersal of resistance genes

    Science.gov (United States)

    Sarangi, Debalin; Tyre, Andrew J.; Patterson, Eric L.; Gaines, Todd A.; Irmak, Suat; Knezevic, Stevan Z.; Lindquist, John L.; Jhala, Amit J.

    2017-01-01

    Gene flow is an important component in evolutionary biology; however, the role of gene flow in dispersal of herbicide-resistant alleles among weed populations is poorly understood. Field experiments were conducted at the University of Nebraska-Lincoln to quantify pollen-mediated gene flow (PMGF) from glyphosate-resistant (GR) to -susceptible (GS) common waterhemp using a concentric donor-receptor design. More than 130,000 common waterhemp plants were screened and 26,199 plants were confirmed resistant to glyphosate. Frequency of gene flow from all distances, directions, and years was estimated with a double exponential decay model using Generalized Nonlinear Model (package gnm) in R. PMGF declined by 50% at pollen source, whereas 90% reduction was found at 88 m (maximum) depending on the direction of the pollen-receptor blocks. Amplification of the target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), was identified as the mechanism of glyphosate resistance in parent biotype. The EPSPS gene amplification was heritable in common waterhemp and can be transferred via PMGF, and also correlated with glyphosate resistance in pseudo-F2 progeny. This is the first report of PMGF in GR common waterhemp and the results are critical in explaining the rapid dispersal of GR common waterhemp in Midwestern United States. PMID:28327669

  5. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean.

    Science.gov (United States)

    Sá-Pinto, Alexandra; Branco, Madalena S; Alexandrino, Paulo B; Fontaine, Michaël C; Baird, Stuart J E

    2012-01-01

    Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.

  6. Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae.

    Science.gov (United States)

    Jenkins, Paul A; Song, Yun S; Brem, Rachel B

    2012-01-01

    Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.

  7. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean.

    Directory of Open Access Journals (Sweden)

    Alexandra Sá-Pinto

    Full Text Available Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.

  8. The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome.

    Science.gov (United States)

    Hu, Xin-Sheng; Filatov, Dmitry A

    2016-06-01

    The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7)  years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.

  9. Gas Flow Dynamics in Inlet Capillaries: Evidence for non Laminar Conditions

    Science.gov (United States)

    Wißdorf, Walter; Müller, David; Brachthäuser, Yessica; Langner, Markus; Derpmann, Valerie; Klopotowski, Sebastian; Polaczek, Christine; Kersten, Hendrik; Brockmann, Klaus; Benter, Thorsten

    2016-09-01

    In this work, the characteristics of gas flow in inlet capillaries are examined. Such inlet capillaries are widely used as a first flow restriction stage in commercial atmospheric pressure ionization mass spectrometers. Contrary to the common assumption, we consider the gas flow in typical glass inlet capillaries with 0.5 to 0.6 mm inner diameters and lengths about 20 cm as transitional or turbulent. The measured volume flow of the choked turbulent gas stream in such capillaries is 0.8 L·min-1 to 1.6 L·min-1 under typical operation conditions, which is in good agreement to theoretically calculated values. Likewise, the change of the volume flow in dependence of the pressure difference along the capillary agrees well with a theoretical model for turbulent conditions as well as with exemplary measurements of the static pressure inside the capillary channel. However, the results for the volume flow of heated glass and metal inlet capillaries are neither in agreement with turbulent nor with laminar models. The velocity profile of the neutral gas in a quartz capillary with an inner diameter similar to commercial inlet capillaries was experimentally determined with spatially resolved ion transfer time measurements. The determined gas velocity profiles do not contradict the turbulent character of the flow. Finally, inducing disturbances of the gas flow by placing obstacles in the capillary channel is found to not change the flow characteristics significantly. In combination the findings suggest that laminar conditions inside inlet capillaries are not a valid primary explanation for the observed high ion transparency of inlet capillaries under common operation conditions.

  10. Tocantins river as an effective barrier to gene flow in Saguinus niger populations

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    Marcelo Vallinoto

    2006-01-01

    Full Text Available The Saguinus represent the basal genus of the Callitrichinae subfamily. Traditionally this genus is divided into three groups: Hairy, Mottled and Bare-face, however, molecular data failed to validate these groups as monophyletic units, as well as raised some subspecies to the species status. This is the case of the former subspecies Saguinus midas midas and S. midas niger, which are now considered as different species. In the present study, we sequenced a portion of the D-loop mtDNA region in populations from the East bank of the Xingu and from both banks of the Tocantins river, in order to test the effectiveness of large rivers as barriers to the gene flow in Saguinus. According to our results, the populations from the East and West banks of the Tocantins river are more divergent than true species like S. mystax and S. imperator. The Tocantins river may be acting as a barrier to gene flow, and consequently these very divergent populations may represent distinct taxonomic entities (species?.

  11. Y-STR diversity and sex-biased gene flow among Caribbean populations.

    Science.gov (United States)

    Simms, Tanya M; Wright, Marisil R; Martinez, Emanuel; Regueiro, Maria; McCartney, Quinn; Herrera, Rene J

    2013-03-01

    In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Conservation, spillover and gene flow within a network of Northern European marine protected areas.

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    Mats Brockstedt Olsen Huserbråten

    Full Text Available To ensure that marine protected areas (MPAs benefit conservation and fisheries, the effectiveness of MPA designs has to be evaluated in field studies. Using an interdisciplinary approach, we empirically assessed the design of a network of northern MPAs where fishing for European lobster (Homarusgammarus is prohibited. First, we demonstrate a high level of residency and survival (50% for almost a year (363 days within MPAs, despite small MPA sizes (0.5-1 km(2. Second, we demonstrate limited export (4.7% of lobsters tagged within MPAs (N = 1810 to neighbouring fished areas, over a median distance of 1.6 km out to maximum 21 km away from MPA centres. In comparison, median movement distance of lobsters recaptured within MPAs was 164 m, and recapture rate was high (40%. Third, we demonstrate a high level of gene flow within the study region, with an estimated F ST of less than 0.0001 over a ≈ 400 km coastline. Thus, the restricted movement of older life stages, combined with a high level of gene flow suggests that connectivity is primarily driven by larval drift. Larval export from the MPAs can most likely affect areas far beyond their borders. Our findings are of high importance for the design of MPA networks for sedentary species with pelagic early life stages.

  13. Gene flow in a Yersinia pestis vector, Oropsylla hirsuta, during a plague epizootic

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    Philip H. Jones , Leigh R. Washburn & Hugh B. Britten

    2011-09-01

    Full Text Available Background & objectives: Appreciating how Yersinia pestis, the etiological agent of plague, spreads amongblack-tailed prairie dog (Cynomys ludovicianus colonies (BTPD, is vital to wildlife conservation programsin North American grasslands. A little-studied aspect of the system is the role of Y. pestis vectors, i.e. fleas,play in the spreading of plague in natural settings. We investigated the genetic structure and variability of acommon prairie dog flea (Oropsylla hirsuta in BTPD colonies in order to examine dispersal patterns. Giventhat this research took place during a widespread plague epizootic, there was the added advantage of gaininginformation on the dynamics of sylvatic plague.Methods & Results: Oropsylla hirsuta were collected from BTPD burrows in nine colonies from May 2005 toJuly 2005, and eight polymorphic microsatellite markers were used to generate genotypic data from them.Gene flow estimates revealed low genetic differentiation among fleas sampled from different colonies. NestedPCR plague assays confirmed the presence of Y. pestis with the average Y. pestis prevalence across all ninecolonies at 12%. No significant correlations were found between the genetic variability and gene flow of O.hirsuta and Y. pestis prevalence on a per-colony basis.Conclusion: Oropsylla hirsuta dispersal among BTPD colonies was high, potentially explaining the rapidspread of Y. pestis in our study area in 2005 and 2006.

  14. Gene flow in a Yersinia pestis vector, Oropsylla hirsuta, during a plague epizootic.

    Science.gov (United States)

    Jones, Philip H; Washburn, Leigh R; Britten, Hugh B

    2011-09-01

    Appreciating how Yersinia pestis, the etiological agent of plague, spreads among black - tailed prairie dog (Cynomys ludovicianus) colonies (BTPD), is vital to wildlife conservation programs in North American grasslands. A little - studied aspect of the system is the role of Y. pestis vectors, i.e. fleas, play in the spreading of plague in natural settings. We investigated the genetic structure and variability of a common prairie dog flea (Oropsylla hirsuta) in BTPD colonies in order to examine dispersal patterns. Given that this research took place during a widespread plague epizootic, there was the added advantage of gaining information on the dynamics of sylvatic plague. Oropsylla hirsuta were collected from BTPD burrows in nine colonies from May 2005 to July 2005, and eight polymorphic microsatellite markers were used to generate genotypic data from them. Gene flow estimates revealed low genetic differentiation among fleas sampled from different colonies. NestedPCR plague assays confirmed the presence of Y. pestis with the average Y. pestis prevalence across all nine colonies at 12%. No significant correlations were found between the genetic variability and gene flow of O. hirsuta and Y. pestis prevalence on a per -colony basis. Oropsylla hirsuta dispersal among BTPD colonies was high, potentially explaining the rapid spread of Y. pestis in our study area in 2005 and 2006.

  15. Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus).

    Science.gov (United States)

    Chavez, Andreas S; Maher, Sean P; Arbogast, Brian S; Kenagy, G J

    2014-04-01

    Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow. Sequence data have been archived in GenBank—accession numbers: KF882736–KF885216.

  16. Gene flow and mode of pollination in a dry-grassland species, Filipendula vulgaris (Rosaceae).

    Science.gov (United States)

    Weidema, I R; Magnussen, L S; Philipp, M

    2000-03-01

    Filipendula vulgaris is a characteristic species of dry nonacidic grasslands in Denmark. This habitat type occurs only on marginal areas not suitable for agriculture or urbanization and that are by their nature fragmented. The population genetic structure of F. vulgaris was investigated in 17 populations within two regions of Denmark, using isozyme electrophoresis. Small populations were found to have significantly fewer polymorphic loci than larger populations, but all populations maintained the same common allelic variants. The degree of isolation of individual populations did not affect the amount of genetic variation. Offspring arrays revealed a very high outcrossing rate (0.96). The field study demonstrated a very high level of gene flow between populations considering that small insects are thought to be the main pollinators of this species. An experiment to verify whether pollen transport by wind could explain the results from the field study demonstrated long-distance transport from isolated plants to bagged plants. Filipendula vulgaris pollen grains are very small and this explains why outcrossed progeny were found using pollination bags with small pore sizes. We conclude that wind pollination is indeed possible and together with insect pollination is causing the observed patterns of genetic variation. The substantial gene flow between populations may be reducing the effects of genetic drift in the small fragmented populations of F. vulgaris.

  17. Converging evidence for epistasis between ANK3 and potassium channel gene KCNQ2 in bipolar disorder

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    Jennifer Toolan Judy

    2013-05-01

    Full Text Available Genome-wide association studies (GWAS have implicated ANK3 as a susceptibility gene for bipolar disorder (BP. We examined whether epistasis with ANK3 may contribute to the missing heritability in BP. We first identified via the STRING database 14 genes encoding proteins with prior biological evidence that they interact molecularly with ANK3. We then tested for statistical evidence of interactions between SNPs in these genes in association with BP in a discovery GWAS dataset and two replication GWAS datasets. The most significant interaction in the discovery GWAS was between SNPs in ANK3 and KCNQ2 (p = 3.18 x 10-8. A total of 31 pairwise interactions involving combinations between two SNPs from KCNQ2 and 16 different SNPs in ANK3 were significant after permutation. Of these, 28 pairwise interactions were significant in the first replication GWAS. None were significant in the second replication GWAS, but the two SNPs from KCNQ2 were found to significantly interact with 5 other SNPs in ANK3, suggesting possible allelic heterogeneity. KCNQ2 forms homo- and hetero-meric complexes with KCNQ3 that constitute voltage-gated potassium channels in neurons. ANK3 is an adaptor protein that, through its interaction with KCNQ2 and KCNQ3, directs the localization of this channel in the axon initial segment (AIS. At the AIS, the KCNQ2/3 complex gives rise to the M-current, which stabilizes the neuronal resting potential and inhibits repetitive firing of action potentials. Thus, these channels act as dampening components and prevent neuronal hyperactivity. The interactions between ANK3 and KCNQ2 merit further investigation, and, if confirmed, may motivate a new line of research into a novel therapeutic target for BP.

  18. Lack of evidence of WNT3A as a candidate gene for congenital vertebral malformations

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    Jacobsen F Stig

    2007-09-01

    Full Text Available Abstract Background Prior investigations have not identified a major locus for vertebral malformations, providing evidence that there is genetic heterogeneity for this condition. WNT3A has recently been identified as a negative regulator of Notch signaling and somitogenesis. Mice with mutations in Wnt3a develop caudal vertebral malformations. Because congenital vertebral malformations represent a sporadic occurrence, linkage approaches to identify genes associated with human vertebral development are not feasible. We hypothesized that WNT3A mutations might account for a subset of congenital vertebral malformations. Methods A pilot study was performed using a cohort of patients with congenital vertebral malformations spanning the entire vertebral column was characterized. DNA sequence analysis of the WNT3A gene in these 50 patients with congenital vertebral malformations was performed. Results A female patient of African ancestry with congenital scoliosis and a T12-L1 hemivertebrae was found to be heterozygous for a missense variant resulting in the substitution of alanine by threonine at codon 134 in highly conserved exon 3 of the WNT3A gene. This variant was found at a very low prevalence (0.35% in a control population of 443 anonymized subjects and 1.1% in an African population. Conclusion These data suggest that WNT3A does not contribute towards the development of congenital vertebral malformations. Factors such as phenotypic and genetic heterogeneity may underlie our inability to detect mutations in WNT3A in our patient sample.

  19. Evidence for positive selection on the Osteogenin (BMP3 gene in human populations.

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    Dong-Dong Wu

    Full Text Available BACKGROUND: Human skeletal system has evolved rapidly since the dispersal of modern humans from Africa, potentially driven by selection and adaptation. Osteogenin (BMP3 plays an important role in skeletal development and bone osteogenesis as an antagonist of the osteogenic bone morphogenetic proteins, and negatively regulates bone mineral density. METHODOLOGY/PRINCIPAL FINDINGS: Here, we resequenced the BMP3 gene from individuals in four geographically separated modern human populations. Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality. The prevalent haplotypes of the first exon region in Europeans demonstrated features of long-range haplotype homogeneity. In contrast with findings in European, the derived allele SNP Arg192Gln shows higher extended haplotype homozygosity in East Asian. The worldwide allele frequency distribution of SNP shows not only a high-derived allele frequency in Asians, but also in Americans, which is suggestive of functional adaptation. CONCLUSIONS/SIGNIFICANCE: In conclusion, we provide evidence for recent positive selection operating upon a crucial gene in skeletal development, which may provide new insight into the evolution of the skeletal system and bone development.

  20. In situ gene expression in mixed-culture biofilms: Evidence of metabolic interactions between community members

    DEFF Research Database (Denmark)

    Møller, Søren; Sternberg, Claus; Andersen, Jens Bo

    1998-01-01

    in both community and pure-culture biofilms, while the Pm promoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction of Pm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida...... are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida......, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol...

  1. Investment cash flow sensitivity under managerial optimism: new evidence from NYSE panel data firms

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    Ezzeddine Ben Mohamed

    2014-06-01

    Full Text Available Investment cash flow sensitivity constitutes one important block of the corporate financial literature. While it is well documented in standard corporate finance, it is still young under behavioral corporate finance. In this paper, we test the investment cash flow sensitivity among panel data of American industrial firms during 1999-2010. Using Q-model of investment (Tobin, 1969, we construct and introduce a proxy of managerial optimism following Malmendier and Tate (2005a to show the impact of CEOs’ optimism in the relationship between investment and internal cash flow. Our results report a positive and significant coefficient of investment to cash flow for the full sample. While, on estimations of our model using sub-sample of more and less constrained firms, we find that the sensitivity exists stronger only for totally constrained group. We find also that board characteristics can reduce investment policy’s distortions.

  2. Capital flows and economic growth across spectral frequencies: Evidence from Turkey

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    Yildirim Nuri

    2012-01-01

    Full Text Available This paper examines interactions and feedbacks between categories of capital flows and economic growth in Turkey for the 1992:01-2009:08 period. Our empirical analysis is based on a new version of the causality test of John Geweke (1982, p. 77 and Yuzo Hosoya (1991, p. 88 in the frequency domain proposed recently by Jörg Breitung and Bertrand Candelon (2006, p. 132. In addition, using standard methods in spectral analysis, we decompose the total covariance between capital flows and growth across main frequency bands and capture lead/lag interactions between them. Some of our findings are as follows: Variance decompositions over frequency bands reveal that variations in individual capital flow categories are largely concentrated over high (seasonal frequencies. The nature of the interaction/feedback between growth and capital flows varies significantly over frequency bands and subcategories of flows. Over business cycle frequencies, two out of four subcategories of inflows, short-term external borrowings and portfolio investments on government bonds, drive growth whereas the other two components, long-term borrowings and portfolio investments on shares, are driven by growth. Furthermore, for the post-2001 financial crisis period we found significant bidirectional causality between long-term external borrowings and growth whereas portfolio investments, bond flows and short-term external borrowings do not affect growth in the long run.

  3. Gene expression based evidence of innate immune response activation in the epithelium with oral lichen planus.

    Science.gov (United States)

    Adami, Guy R; Yeung, Alexander C F; Stucki, Grant; Kolokythas, Antonia; Sroussi, Herve Y; Cabay, Robert J; Kuzin, Igor; Schwartz, Joel L

    2014-03-01

    Oral lichen planus (OLP) is a disease of the oral mucosa of unknown cause producing lesions with an intense band-like inflammatory infiltrate of T cells to the subepithelium and keratinocyte cell death. We performed gene expression analysis of the oral epithelium of lesions in subjects with OLP and its sister disease, oral lichenoid reaction (OLR), in order to better understand the role of the keratinocytes in these diseases. Fourteen patients with OLP or OLR were included in the study, along with a control group of 23 subjects with a variety of oral diseases and a normal group of 17 subjects with no clinically visible mucosal abnormalities. Various proteins have been associated with OLP, based on detection of secreted proteins or changes in RNA levels in tissue samples consisting of epithelium, stroma, and immune cells. The mRNA level of twelve of these genes expressed in the epithelium was tested in the three groups. Four genes showed increased expression in the epithelium of OLP patients: CD14, CXCL1, IL8, and TLR1, and at least two of these proteins, TLR1 and CXCL1, were expressed at substantial levels in oral keratinocytes. Because of the large accumulation of T cells in lesions of OLP it has long been thought to be an adaptive immunity malfunction. We provide evidence that there is increased expression of innate immune genes in the epithelium with this illness, suggesting a role for this process in the disease and a possible target for treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Evidence for positive selection in the gene fruitless in Anastrepha fruit flies

    Science.gov (United States)

    2010-01-01

    Background Many genes involved in the sex determining cascade have indicated signals of positive selection and rapid evolution across different species. Even though fruitless is an important gene involved mostly in several aspects of male courtship behavior, the few studies so far have explained its high rates of evolution by relaxed selective constraints. This would indicate that a large portion of this gene has evolved neutrally, contrary to what has been observed for other genes in the sex cascade. Results Here we test whether the fruitless gene has evolved neutrally or under positive selection in species of Anastrepha (Tephritidae: Diptera) using two different approaches, a long-term evolutionary analysis and a populational genetic data analysis. The first analysis was performed by using sequences of three species of Anastrepha and sequences from several species of Drosophila using the ratio of nonsynonymous to synonymous rates of evolution in PAML, which revealed that the fru region here studied has evolved by positive selection. Using Bayes Empirical Bayes we estimated that 16 sites located in the connecting region of the fruitless gene were evolving under positive selection. We also investigated for signs of this positive selection using populational data from 50 specimens from three species of Anastrepha from different localities in Brazil. The use of standard tests of selection and a new test that compares patterns of differential survival between synonymous and nonsynonymous in evolutionary time also provide evidence of positive selection across species and of a selective sweep for one of the species investigated. Conclusions Our data indicate that the high diversification of fru connecting region in Anastrepha flies is due at least in part to positive selection, not merely as a consequence of relaxed selective constraint. These conclusions are based not only on the comparison of distantly related taxa that show long-term divergence time, but also on

  5. Evidence for positive selection in the gene fruitless in Anastrepha fruit flies

    Directory of Open Access Journals (Sweden)

    de Brito Reinaldo A

    2010-09-01

    Full Text Available Abstract Background Many genes involved in the sex determining cascade have indicated signals of positive selection and rapid evolution across different species. Even though fruitless is an important gene involved mostly in several aspects of male courtship behavior, the few studies so far have explained its high rates of evolution by relaxed selective constraints. This would indicate that a large portion of this gene has evolved neutrally, contrary to what has been observed for other genes in the sex cascade. Results Here we test whether the fruitless gene has evolved neutrally or under positive selection in species of Anastrepha (Tephritidae: Diptera using two different approaches, a long-term evolutionary analysis and a populational genetic data analysis. The first analysis was performed by using sequences of three species of Anastrepha and sequences from several species of Drosophila using the ratio of nonsynonymous to synonymous rates of evolution in PAML, which revealed that the fru region here studied has evolved by positive selection. Using Bayes Empirical Bayes we estimated that 16 sites located in the connecting region of the fruitless gene were evolving under positive selection. We also investigated for signs of this positive selection using populational data from 50 specimens from three species of Anastrepha from different localities in Brazil. The use of standard tests of selection and a new test that compares patterns of differential survival between synonymous and nonsynonymous in evolutionary time also provide evidence of positive selection across species and of a selective sweep for one of the species investigated. Conclusions Our data indicate that the high diversification of fru connecting region in Anastrepha flies is due at least in part to positive selection, not merely as a consequence of relaxed selective constraint. These conclusions are based not only on the comparison of distantly related taxa that show long

  6. Removal of antibiotics and antibiotic resistance genes from domestic sewage by constructed wetlands: Effect of flow configuration and plant species.

    Science.gov (United States)

    Chen, Jun; Ying, Guang-Guo; Wei, Xiao-Dong; Liu, You-Sheng; Liu, Shuang-Shuang; Hu, Li-Xin; He, Liang-Ying; Chen, Zhi-Feng; Chen, Fan-Rong; Yang, Yong-Qiang

    2016-11-15

    This study aims to investigate the removal of antibiotics and antibiotic resistance genes (ARGs) in raw domestic wastewater by various mesocosm-scale constructed wetlands (CWs) with different flow configurations or plant species including the constructed wetland with or without plant. Six mesocosm-scale CWs with three flow types (surface flow, horizontal subsurface flow and vertical subsurface flow) and two plant species (Thaliadealbata Fraser and Iris tectorum Maxim) were set up in the outdoor. 8 antibiotics including erythromycin-H2O (ETM-H2O), monensin (MON), clarithromycin (CTM), leucomycin (LCM), sulfamethoxazole (SMX), trimethoprim (TMP), sulfamethazine (SMZ) and sulfapyridine (SPD) and 12 genes including three sulfonamide resistance genes (sul1, sul2 and sul3), four tetracycline resistance genes (tetG, tetM, tetO and tetX), two macrolide resistance genes (ermB and ermC), two chloramphenicol resistance genes (cmlA and floR) and 16S rRNA (bacteria) were determined in different matrices (water, particle, substrate and plant phases) from the mesocosm-scale systems. The aqueous removal efficiencies of total antibiotics ranged from 75.8 to 98.6%, while those of total ARGs varied between 63.9 and 84.0% by the mesocosm-scale CWs. The presence of plants was beneficial to the removal of pollutants, and the subsurface flow CWs had higher pollutant removal than the surface flow CWs, especially for antibiotics. According to the mass balance analysis, the masses of all detected antibiotics during the operation period were 247,000, 4920-10,600, 0.05-0.41 and 3500-60,000μg in influent, substrate, plant and effluent of the mesocosm-scale CWs. In the CWs, biodegradation, substrate adsorption and plant uptake all played certain roles in reducing the loadings of nutrients, antibiotics and ARGs, but biodegradation was the most important process in the removal of these pollutants.

  7. Using seed purity data to estimate an average pollen mediated gene flow from crops to wild relatives.

    Science.gov (United States)

    Lavigne, C; Klein, E K; Couvet, D

    2002-01-01

    Gene flow from crops to wild related species has been recently under focus in risk-assessment studies of the ecological consequences of growing transgenic crops. However, experimental studies addressing this question are usually temporally or spatially limited. Indirect population-structure approaches can provide more global estimates of gene flow, but their assumptions appear inappropriate in an agricultural context. In an attempt to help the committees providing advice on the release of transgenic crops, we present a new method to estimate the quantity of genes migrating from crops to populations of related wild plants by way of pollen dispersal. This method provides an average estimate at a landscape level. Its originality is based on the measure of the inverse gene flow, i.e. gene flow from the wild plants to the crop. Such gene flow results in an observed level of impurities from wild plants in crop seeds. This level of impurity is usually known by the seed producers and, in any case, its measure is easier than a direct screen of wild populations because crop seeds are abundant and their genetic profile is known. By assuming that wild and cultivated plants have a similar individual pollen dispersal function, we infer the level of pollen-mediated gene flow from a crop to the surrounding wild populations from this observed level of impurity. We present an example for sugar beet data. Results suggest that under conditions of seed production in France (isolation distance of 1,000 m) wild beets produce high numbers of seeds fathered by cultivated plants.

  8. The Origin of Ina: Evidence for Inflated Lava Flows on the Moon

    Science.gov (United States)

    Garry, W. B.; Robinson, M. S.; Zimbelman, J. R.; Bleacher, J. E.; Hawke, B. R.; Crumpler, L. S.; Braden, S. E.; Sato, H.

    2012-01-01

    Ina is an enigmatic volcanic feature on the Moon known for its irregularly shaped mounds, the origin of which has been debated since the Apollo Missions. Three main units are observed on the floor of the depression (2.9 km across, lava flows. Comparison of these unusual lunar mounds and possible terrestrial analogs leads us to hypothesize that features in Ina were formed through lava flow inflation processes. While the source of the lava remains unclear, this new model suggests that as the mounds inflated, breakouts along their margins served as sources for surface flows that created the lower morphologic unit. Over time, mass wasting of both morphologic units has exposed fresh surfaces observed in the blocky unit. Ina is different than the terrestrial analogs presented in this study in that the lunar features formed within a depression, no vent sources are observed, and no cracks are observed on the mounds. However, lava flow inflation processes explain many of the morphologic relationships observed in Ina and are proposed to be analogous with inflated lava flows on Earth.

  9. Duplication and Divergence of Floral MADS-Box Genes in Grasses: Evidence for the Generation and Modification of Novel Regulators

    Institute of Scientific and Technical Information of China (English)

    Guixia Xu; Hongzhi Kong

    2007-01-01

    The process of flowering is controlled by a hierarchy of floral genes that act as flowering time genes, inflorescence/floral meristem identity genes, and/or floral organ-identity genes. The most important and well-characterized floral genes are those that belong to the MADS-box family of transcription factors. Compelling evidence suggests that floral MADS-box genes have experienced a few large-scale duplication events. In particular, the pre-core eudicot duplication events have been considered to correlate with the emergence and diversification of core eudicots. Duplication of floral MADS-box genes has also been documented in monocots, particularly in grasses, although a systematic study is lacking. In the present study, by conducting extensive phylogenetic analyses, we identified pre-Poaceae gene duplication events in each of the AP1, PI, AG, AGL11, AGL2/3/4, and AGL9gene lineages. Comparative genomic studies further indicated that some of these duplications actually resulted from the genome doubling event that occurred 66-70 million years ago (MYA). In addition, we found that after gene duplication, exonization (of intron sequences) and pseudoexonization (of exon sequences) have contributed to the divergence of duplicate genes in sequence structure and, possibly, gene function.

  10. Experimental evidence of a helical, supercritical instability in pipe flow of shear thinning fluids

    Science.gov (United States)

    Picaut, L.; Ronsin, O.; Caroli, C.; Baumberger, T.

    2017-08-01

    We study experimentally the flow stability of entangled polymer solutions extruded through glass capillaries. We show that the pipe flow becomes linearly unstable beyond a critical value (Wic≃5 ) of the Weissenberg number, via a supercritical bifurcation which results in a helical distortion of the extrudate. We find that the amplitude of the undulation vanishes as the aspect ratio L /R of the capillary tends to zero, and saturates for large L /R , indicating that the instability affects the whole pipe flow, rather than the contraction or exit regions. These results, when compared to previous theoretical and experimental works, lead us to argue that the nature of the instability is controlled by the level of shear thinning of the fluids. In addition, we provide strong hints that the nonlinear development of the instabiilty is mitigated, in our system, by the gradual emergence of gross wall slip.

  11. Self-transcendence facilitates meaning-making and flow: Evidence from a pilot experimental study

    Directory of Open Access Journals (Sweden)

    Osin, Evgeny N.

    2016-06-01

    Full Text Available We review the psychological theory of flow and focus on the notion of the autotelic personality, arguing that self-transcendence (understood within the existential tradition of Frankl and Längle as the individual’s ability to establish inner relationships with values can be viewed as a personality disposition conducive to flow experience. The study aimed to investigate the effects of situational task meaning and dispositional self-transcendence on productivity and flow experience. We present a pilot quasi-experimental study conducted in a student sample (N = 82 Students were asked to work in small-group settings on a creative task, which consisted in finding solutions to a social problem. Each group was randomly assigned to an instruction presenting the problem as happening either in a distant country (low-meaning or in their home country (high-meaning condition. The outcome variables were measures of flow, perceived meaning of the task, and satisfaction with time spent working. The solutions generated by the students were rated by three experts. The experimental manipulation had a main effect on the quality of the resulting solutions, but not on the subjective experience of the participants. A number of significant interaction effects were found, indicating that the associations of self-transcendence with experiential outcomes tended to be linear under the low-meaning condition, but curvilinear under the high-meaning condition. The findings suggest that self-transcendence is particularly beneficial to flow in situations with unclear meaning, but very high levels of self-transcendence may hinder flow in highly meaningful situations. Overall, the findings suggest that self-transcendence can be considered as a disposition of the autotelic personality.

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

    Science.gov (United States)

    Bellucci, Elisa; Bitocchi, Elena; Rau, Domenico; Nanni, Laura; Ferradini, Nicoletta; Giardini, Alessandro; Rodriguez, Monica; Attene, Giovanna; Papa, Roberto

    2013-01-01

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

  13. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940.

    Science.gov (United States)

    Knapp, Charles W; Dolfing, Jan; Ehlert, Phillip A I; Graham, David W

    2010-01-15

    Mass production and use of antibiotics and antimicrobials in medicine and agriculture have existed for over 60 years, and has substantially benefited public health and agricultural productivity throughout the world. However, there is growing evidence that resistance to antibiotics (AR) is increasing both in benign and pathogenic bacteria, posing an emerging threat to public and environmental health in the future. Although evidence has existed for years from clinical data of increasing AR, almost no quantitative environmental data exist that span increased industrial antibiotic production in the 1950s to the present; i.e., data that might delineate trends in AR potentially valuable for epidemiological studies. To address this critical knowledge gap, we speculated that AR levels might be apparent in historic soil archives as evidenced by antibiotic resistance gene (ARG) abundances over time. Accordingly, DNA was extracted from five long-term soil-series from different locations in The Netherlands that spanned 1940 to 2008, and 16S rRNA gene and 18 ARG abundances from different major antibiotic classes were quantified. Results show that ARG from all classes of antibiotics tested have significantly increased since 1940, but especially within the tetracyclines, with some individual ARG being >15 times more abundant now than in the 1970s. This is noteworthy because waste management procedures have broadly improved and stricter rules on nontherapeutic antibiotic use in agriculture are being promulgated. Although these data are local to The Netherlands, they suggest basal environmental levels of ARG still might be increasing, which has implications to similar locations around the world.

  14. Benzodiazepines use and breast cancer risk: A population-based study and gene expression profiling evidence.

    Science.gov (United States)

    Iqbal, Usman; Chang, Tzu-Hao; Nguyen, Phung-Anh; Syed-Abdul, Shabbir; Yang, Hsuan-Chia; Huang, Chih-Wei; Atique, Suleman; Yang, Wei-Chung; Moldovan, Max; Jian, Wen-Shan; Hsu, Min-Huei; Yen, Yun; Jack Li, Yu-Chuan

    2017-08-26

    The aim of this study was to investigate whether long-term use of Benzodiazepines (BZDs) is associated with breast cancer risk through the combination of population-based observational and gene expression profiling evidence. We conducted a population-based case-control study by using 1998 to 2009 year Taiwan National Health Insurance Research Database and investigated the association between BZDs use and breast cancer risk. We selected subjects age of > 20 years old and six eligible controls matched for age, sex and the index date (i.e., free of any cancer at the case diagnosis date) by using propensity scores. A bioinformatics analysis approach was also performed for the identification of oncogenesis effects of BZDs on breast cancer. We used breast cancer gene expression data from the Cancer Genome Atlas and perturbagen signatures of BZDs from the Library of Integrated Cellular Signatures database in order to identify the oncogenesis effects of BZDs on breast cancer. We found evidence of increased breast cancer risk for diazepam (OR, 1.16; 95%CI, 0.95-1.42; connectivity score [CS], 0.3016), zolpidem (OR, 1.11; 95%CI, 0.95-1.30; CS, 0.2738), but not for lorazepam (OR, 1.04; 95%CI, 0.89-1.23; CS, -0.2952) consistently in both methods. The finding for alparazolam was contradictory from the two methods. Diazepam and zolpidem trends showed association, although not statistically significant, with breast cancer risk in both epidemiological and bioinformatics analyses outcomes. The methodological value of our study is in introducing the way of combining epidemiological and bioinformatics approaches in order to answer a common scientific question. Combining the two approaches would be a substantial step towards uncovering, validation and further application of previously unknown scientific knowledge to the emerging field of precision medicine informatics. Copyright © 2017. Published by Elsevier Inc.

  15. Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow in Ridgeia piscesae.

    Science.gov (United States)

    Young, C R; Fujio, S; Vrijenhoek, R C

    2008-04-01

    This study examined relationships between bathymetrically induced deep-ocean currents and the dispersal of the hydrothermal vent tubeworm Ridgeia piscesae along the northeast Pacific ridge system. A robust diagnostic model of deep-ocean circulation in this region predicted strong southeasterly currents following contours of the Blanco Transform Fault, a 450-km lateral offset that separates the Gorda and Juan de Fuca ridge systems. Such currents should facilitate the southward dispersal of R. piscesae larvae. Immigration rates for populations north and south of the Blanco Transform Fault were estimated from molecular population genetic data. Mitochondrial DNA evidence revealed population subdivision across the Blanco Transform Fault, and a strong directional bias in gene flow that was consistent with predictions of the circulation model. The distribution of mitochondrial diversity between the northern and southern populations of R. piscesae suggests that the Gorda Ridge tubeworms have maintained larger effective population sizes than the northern populations, a pattern that also exists in co-occurring limpets. Together, these data suggest that the northern vent fields may experience a higher frequency of habitat turnover and consequently more rapid losses of genetic diversity.

  16. Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves).

    Science.gov (United States)

    Wang, Ning; Liang, Bin; Wang, Jichao; Yeh, Chia-Fen; Liu, Yang; Liu, Yanlin; Liang, Wei; Yao, Cheng-Te; Li, Shou-Hsien

    2016-09-01

    Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process.

  17. Estimating dispersal and gene flow in the neotropical freshwater turtle Hydromedusa maximiliani (Chelidae by combining ecological and genetic methods

    Directory of Open Access Journals (Sweden)

    Souza Franco L.

    2002-01-01

    Full Text Available Hydromedusa maximiliani is a vulnerable neotropical freshwater turtle endemic to mountainous regions of the Atlantic rainforest in southeastern Brazil. Random amplified polymorphic DNA (RAPD was used to estimate the gene flow and dispersal for individuals inhabiting rivers and streams within a drainage. Nine primers generated 27 scoreable bands, of which 9 (33% were polymorphic and produced 12 RAPD phenotypes. The gene flow estimates (Nm among turtles inhabiting different rivers and streams were variable, ranging from 0.09 to 3.00 (mean: 0.60. For some loci, the rates of gene flow could offset population differentiation (Nm > 1, whereas for others random genetic drift could result in population divergence (Nm < 1. Since the genetic variation of this turtle seems to be structured according to the natural hierarchical system of rivers and streams within drainages, management programs involving translocations between different regions across the geographical range of H. maximiliani should be viewed with caution.

  18. Preliminary evidence of association between EFHC2, a gene implicated in fear recognition, and harm avoidance.

    Science.gov (United States)

    Blaya, Carolina; Moorjani, Priya; Salum, Giovanni Abrahão; Gonçalves, Leonardo; Weiss, Lauren A; Leistner-Segal, Sandra; Manfro, Gisele G; Smoller, Jordan W

    2009-03-06

    Genetic variation at the EF-hand domain containing 2 gene (EFHC2) locus has been associated with fear recognition in Turner syndrome. The aim of this study was to examine whether EFHC2 variants are associated with non-syndromic anxiety-related traits [harm avoidance (HA) and behavioral inhibition (BI)] and with panic disorder (PD). Our sample comprised 127 PD patients and 132 controls without psychiatric disorder. We genotyped nine SNPs within the EFHC2 locus and used PLINK to perform association analyses. An intronic SNP (rs1562875) was associated with HA (permuted p=0.031) accounting alone for over 3% of variance in this trait. This same SNP was nominally, but not empirically, associated with BI (r(2)=0.022; nominal p=0.022) and PD (OR=2.64; nominal p=0.009). The same association was found in a subsample of only females. In sum, we observed evidence of association between a variant in EFHC2, a gene previously associated with the processing of fear and social threat, and HA. Larger studies are warranted to confirm this association.

  19. The color of a Dalmatian's spots: Linkage evidence to support the TYRP1 gene

    Directory of Open Access Journals (Sweden)

    Strain George M

    2005-07-01

    Full Text Available Abstract Background The distinctive coat pattern of a Dalmatian is the result of the interaction of several loci. While the encoded function of these genes is not fully understood, it is known the Piebald, Ticking, and Flecking loci interact to produce the Dalmatian's classic pigmented spots on a white background. The color of the pigmented spots in purebred Dalmatians can either be black or liver, but the locus responsible for color determination is unknown. Studies have been conducted to determine the underlying genes involved in coat color determination in the dog, e.g., in the Labrador Retriever, but none to date have addressed black versus liver in the Dalmatian. Results A genome scan was conducted in a multi-generational kindred of Dalmatians segregating black and liver spot color. Linkage analysis was performed using a total of 113 polymorphic microsatellite markers from the kindred. Linkage was found between spot color and a single microsatellite marker, FH2319 (LOD = 12.5 on chromosome 11. Conclusion The TYRP1 (Brown locus is located at position 50.1 Mb on chromosome 11, which is approximately 0.4 Mb from marker FH2319. Given the recent characterization of TYRP1 genetic variations in the dog and the linkage evidence reported here, TYRP1 is likely responsible for the spot color variation of black versus liver seen in the Dalmatian.

  20. Evidence that genetic variation in the oxytocin receptor (OXTR) gene influences social cognition in ADHD.

    Science.gov (United States)

    Park, J; Willmott, M; Vetuz, G; Toye, C; Kirley, A; Hawi, Z; Brookes, K J; Gill, M; Kent, L

    2010-05-30

    Some children with ADHD also have social and communication difficulties similar to those seen in children with autistic spectrum disorders and this may be due to shared genetic liability. As the oxytocin receptor (OXTR) gene has been implicated in social cognition and autistic spectrum disorders, this study investigated whether OXTR polymorphisms previously implicated in autism were associated with ADHD and whether they influenced OXTR mRNA expression in 27 normal human amygdala brain samples. The family-based association sample consisted of 450 DSM-IV diagnosed ADHD probands and their parents. Although there was no association with the ADHD phenotype, an association with social cognitive impairments in a subset of the ADHD probands (N=112) was found for SNP rs53576 (F=5.24, p=0.007) with post-hoc tests demonstrating that the AA genotype was associated with better social ability compared to the AG genotype. Additionally, significant association was also found for rs13316193 (F=3.09, p=0.05) with post-hoc tests demonstrating that the CC genotype was significantly associated with poorer social ability than the TT genotype. No significant association between genotype and OXTR mRNA expression was found. This study supports previous evidence that the OXTR gene is implicated in social cognition.

  1. Molecular phylogeny of rodents, with special emphasis on murids: evidence from nuclear gene LCAT.

    Science.gov (United States)

    Robinson, M; Catzeflis, F; Briolay, J; Mouchiroud, D

    1997-12-01

    Phylogenetic relationships among 19 extant species of rodents, with special emphasis on rats, mice, and allied Muroidea, were studied using sequences of the nuclear protein-coding gene LCAT (lecithin:cholesterol acyltransferase), an enzyme of cholesterol metabolism. Analysis of 705 base pairs from the exonic regions of LCAT confirmed known groupings in and around Muroidea. Strong support was found for the families Sciuridae (squirrel and marmot) and Gliridae (dormice) and for suprafamilial taxa Muroidea and Caviomorpha (guinea pig and allies). Within Muroidea, the first branching leads to the fossorial mole rats Spalacinae and bamboo rats Rhizomyinae. The other Muroidea appear as a polytomy from which are issued Gerbillinae (gerbils), Murinae (rats and mice), Sigmodontinae (New World cricetids), Cricetinae (hamsters), and Arvicolinae (voles). Evidence from LCAT sequences agrees with that from a number of previous molecular and morphological studies, both concerning branching orders inside Muroidea and the bush-like radiation of rodent suprafamilial taxa (caviomorphs, sciurids, glirids, muroids), thus suggesting that this nuclear gene is an appropriate candidate for addressing questions of rodents relationships.

  2. Revisiting the Diego Blood Group System in Amerindians: Evidence for Gene-Culture Comigration.

    Science.gov (United States)

    Bégat, Christophe; Bailly, Pascal; Chiaroni, Jacques; Mazières, Stéphane

    2015-01-01

    Six decades ago the DI*A allele of the Diego blood group system was instrumental in proving Native American populations originated from Siberia. Since then, it has received scant attention. The present study was undertaken to reappraise distribution of the DI*A allele in 144 Native American populations based on current knowledge. Using analysis of variance tests, frequency distribution was studied according to geographical, environmental, and cultural parameters. Frequencies were highest in Amazonian populations. In contrast, DI*A was undetectable in subarctic, Fuegian, Panamanian, Chaco and Yanomama populations. Closer study revealed a correlation that this unequal distribution was correlated with language, suggesting that linguistic divergence was a driving force in the expansion of DI*A among Native Americans. The absence of DI*A in circumpolar Eskimo-Aleut and Na-Dene speakers was consistent with a late migratory event confined to North America. Distribution of DI*A in subtropical areas indicated that gene and culture exchanges were more intense within than between ecozones. Bolstering the utility of classical genetic markers in biological anthropology, the present study of the expansion of Diego blood group genetic polymorphism in Native Americans shows strong evidence of gene-culture comigration.

  3. Revisiting the Diego Blood Group System in Amerindians: Evidence for Gene-Culture Comigration

    Science.gov (United States)

    Bégat, Christophe; Bailly, Pascal; Chiaroni, Jacques; Mazières, Stéphane

    2015-01-01

    Six decades ago the DI*A allele of the Diego blood group system was instrumental in proving Native American populations originated from Siberia. Since then, it has received scant attention. The present study was undertaken to reappraise distribution of the DI*A allele in 144 Native American populations based on current knowledge. Using analysis of variance tests, frequency distribution was studied according to geographical, environmental, and cultural parameters. Frequencies were highest in Amazonian populations. In contrast, DI*A was undetectable in subarctic, Fuegian, Panamanian, Chaco and Yanomama populations. Closer study revealed a correlation that this unequal distribution was correlated with language, suggesting that linguistic divergence was a driving force in the expansion of DI*A among Native Americans. The absence of DI*A in circumpolar Eskimo-Aleut and Na-Dene speakers was consistent with a late migratory event confined to North America. Distribution of DI*A in subtropical areas indicated that gene and culture exchanges were more intense within than between ecozones. Bolstering the utility of classical genetic markers in biological anthropology, the present study of the expansion of Diego blood group genetic polymorphism in Native Americans shows strong evidence of gene-culture comigration. PMID:26148209

  4. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication

    Science.gov (United States)

    Wood, Dustin A.; Fisher, Robert N.; Vandergast, Amy G.

    2014-01-01

    Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

  5. Fine scale gene flow and individual movements among subpopulations of Centrolene prosoblepon (Anura: Centrolenidae

    Directory of Open Access Journals (Sweden)

    Jeanne M Robertson

    2008-03-01

    Full Text Available Dispersal capabilities determine and maintain local gene flow, and this has implications for population persistence and/or recolonization following environmental perturbations (natural or anthropogenic, disease outbreaks, or other demographic collapses. To predict recolonization and understand dispersal capacity in a stream-breeding frog, we examined individual movement patterns and gene flow among four subpopulations of the Neotropical glassfrog, Centrolene prosoblepon, at a mid-elevation cloud forest site at El Copé, Panama. We measured male movement directly during a two year mark-recapture study, and indirectly with gene flow estimates from mitochondrial DNA sequences (mtDNA. Individuals of this species showed strong site fidelity: over two years, male frogs in all four headwater streams moved very little (mean = 2.33 m; mode = 0 m. Nine individuals changed streams within one or two years, moving 675-1 108 m. For those males moving more than 10 m, movement was biased upstream (p ST = 0.007, p = 0.325 but gene flow was more limited across greater distances (CT = 0.322, p = 0.065, even within the same drainage network. Lowland populations of C. prosoblepon potentially act as an important source of colonists for upland populations in this watershed. Rev. Biol. Trop. 56 (1: 13-26. Epub 2008 March 31.La capacidad de dispersión determina y mantiene el flujo genético local, y esto tiene implicaciones para la persistencia poblacional y/o la recolonización que sigue a perturbaciones ambientales. Examinamos patrones individuales de movimiento y flujo genético entre subpoblaciones de Centrolene prosoblepon (Anura: Centrolenidae en un sitio de elevación media en El Copé, Panamá. Medimos directamente el movimiento de los machos durante un estudio de marcado-recaptura, e indirectamente con estimaciones de flujo genético a partir de secuencias de ADN mitocondrial (mtDNA. Los individuos mostraron fuerte fidelidad a su lugar: por más de dos a

  6. Constraining Eruptive Conditions From Lava Flow Morphometry: A Case Study With Field Evidence

    Science.gov (United States)

    Bowles, Z. R.; Clarke, A.; Greeley, R.

    2007-12-01

    Volcanism is widely recognized as one of the primary factors affecting the surfaces of solid planets and satellites throughout the solar system. Basaltic lava is thought to be the most common composition based on observed features typical of basaltic eruptions found on Earth. Lava flows are one of the most easily recognizable landforms on planetary surfaces and their features may provide information about eruption dynamics, lava rheology, and potential hazards. More recently, researchers have taken a multi-faceted approach to combine remote sensing, field observations and quantitative modeling to constrain volcanic activity on Earth and other planets. Here we test a number of published models, including empirically derived relationships from Mt. Etna and Kilauea, models derived from laboratory experiments, and theoretical models previously applied to remote sensing of planetary surfaces, against well-documented eruptions from the literature and field observations. We find that the Graetz (Hulme and Felder, 1977, Phil.Trans., 285, 227 - 234) method for estimating effusion rates compares favorably with published eruption data, while, on the other hand, inverting lava flow length prediction models to estimate effusion rates leads to several orders of magnitude in error. The Graetz method also better constrains eruption duration. Simple radial spreading laws predict Hawaiian lava flow lengths quite well, as do using the thickness of the lava flow front and chilled crust. There was no observed difference between results from models thought to be exclusive to aa or pahoehoe flow fields. Interpreting historic conditions should therefore follow simple relationships to observable morphologies no matter the composition or surface texture. We have applied the most robust models to understand the eruptive conditions and lava rheology of the Batamote Mountains near Ajo, AZ, an eroded shield volcano in southern Arizona. We find effusion rates on the order of 100 - 200 cubic

  7. Evidence of lateral gene transfer among strains of Streptococcus zooepidemicus in weanling horses with respiratory disease.

    Science.gov (United States)

    Velineni, Sridhar; Breathnach, Cormac C; Timoney, John F

    2014-01-01

    Streptococcus zooepidemicus (Sz) is a tonsillar commensal of healthy horses but with potential to opportunistically invade the lower respiratory tract. Sz is genetically variable and recombinogenic based on analysis of gene sequences including szp, szm and MLST data. Although a variety of serovars of the protective SzP are commonly harbored in the tonsils of the same horse, lower respiratory infections usually involve a single clone. Nevertheless, isolation of specific clones from epizootics of respiratory disease has been recently reported in horses and dogs in N. America, Europe and Asia. In this report, we provide evidence suggestive of lateral gene exchange and recombination between strains of Sz from cases of respiratory disease secondary to experimental equine herpes 1 virus infection in an isolated group of weanling horses and ponies. Nasal swabs of 13 of 18 weanlings with respiratory disease yielded mucoid colonies of Sz following culture. Comparison of arcC, nrdE, proS, spi, tdk, tpi and yqiL of these Sz revealed 3 Clades. Clade-1 (ST-212) and 2 (ST-24) were composed of 7 and 3 isolates, respectively. ST-24 and 212 differed in all 7 housekeeping as well as szp and szm alleles. Two isolates of Clade-1 were assigned to ST-308, a single locus variant of ST-212 that contained the proS-16 allele sequenced in ST-24. One isolate of ST-308 contained szm-2, the same allele sequenced in Clade 2 isolates; the other was positive for the szp-N2HV2 allele of Clade 2. These observations are consistent with gene transfer between Sz in the natural host and may explain formation of novel clones that invade the lower respiratory tract or cause epizootics of respiratory disease in dogs and horses.

  8. Evidence for polymorphism in the cytochrome P450 2D50 gene in horses.

    Science.gov (United States)

    Corado, C R; McKemie, D S; Young, A; Knych, H K

    2016-06-01

    Metabolism is an essential factor in the clearance of many drugs and as such plays a major role in the establishment of dosage regimens and withdrawal times. CYP2D6, the human orthologue to equine CYP2D50, is a drug-metabolizing enzyme that is highly polymorphic in humans leading to widely differing levels of metabolic activity. As CYP2D6 is highly polymorphic, in this study it was hypothesized that the gene coding for the equine orthologue, CYP2D50, may also be prone to polymorphism. Blood samples were collected from 150 horses, the CYP2D50 gene was cloned and sequenced; and full-length sequences were analyzed for single nucleotide polymorphisms (SNPs), deletions, or insertions. Pharmacokinetic data were collected from a subset of horses following the administration of a single oral dose of tramadol and probit analysis used to calculate metabolic ratios. Prior to drug administration, the ability of recombinant CYP2D50 to metabolize tramadol to O-desmethyltramadol was confirmed. Sequencing of CYP2D50 identified 126 exonic SNPs, with 31 of those appearing in multiple horses. Oral administration of tramadol to a subset of these horses revealed variable metabolic ratios (tramadol: O-desmethyltramadol) in individual horses and separation into three metabolic groups. While a limited number of horses of primarily a single breed were studied, the variability in tramadol metabolism to O-desmethyltramadol between horses and preliminary evidence of what appears to be poor, extensive, and ultra-rapid metabolizers supports further study of the potential for genetic polymorphisms in the CYP2D50 gene in horses.

  9. Evidence of current impact of climate change on life: a walk from genes to the biosphere.

    Science.gov (United States)

    Peñuelas, Josep; Sardans, Jordi; Estiarte, Marc; Ogaya, Romà; Carnicer, Jofre; Coll, Marta; Barbeta, Adria; Rivas-Ubach, Albert; Llusià, Joan; Garbulsky, Martin; Filella, Iolanda; Jump, Alistair S

    2013-08-01

    We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade-offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.

  10. The Dopamine D2 Receptor Gene, Perceived Parental Support, and Adolescent Loneliness: Longitudinal Evidence for Gene-Environment Interactions

    Science.gov (United States)

    van Roekel, Eeske; Goossens, Luc; Scholte, Ron H. J.; Engels, Rutger C. M. E.; Verhagen, Maaike

    2011-01-01

    Background: Loneliness is a common problem in adolescence. Earlier research focused on genes within the serotonin and oxytocin systems, but no studies have examined the role of dopamine-related genes in loneliness. In the present study, we focused on the dopamine D2 receptor gene (DRD2). Methods: Associations among the DRD2, sex, parental support,…

  11. The Dopamine D2 Receptor Gene, Perceived Parental Support, and Adolescent Loneliness: Longitudinal Evidence for Gene-Environment Interactions

    Science.gov (United States)

    van Roekel, Eeske; Goossens, Luc; Scholte, Ron H. J.; Engels, Rutger C. M. E.; Verhagen, Maaike

    2011-01-01

    Background: Loneliness is a common problem in adolescence. Earlier research focused on genes within the serotonin and oxytocin systems, but no studies have examined the role of dopamine-related genes in loneliness. In the present study, we focused on the dopamine D2 receptor gene (DRD2). Methods: Associations among the DRD2, sex, parental support,…

  12. Hybridizing Daphnia communities from ten neighbouring lakes: spatio-temporal dynamics, local processes, gene flow and invasiveness.

    Science.gov (United States)

    Yin, Mingbo; Gießler, Sabine; Griebel, Johanna; Wolinska, Justyna

    2014-04-12

    In natural communities of cyclical parthenogens, rapid response to environmental change is enabled by switching between two reproduction modes. While long periods of asexual reproduction allow some clones to outcompete others, and may result in "clonal erosion", sexual reproduction restores genetic variation in such systems. Moreover, sexual reproduction may result in the formation of interspecific hybrids. These hybrids can then reach high abundances, through asexual clonal reproduction. In the present study, we explored genetic variation in water fleas of the genus Daphnia. The focus was on the short-term dynamics within several clonal assemblages from the hybridizing Daphnia longispina complex and the impact of gene flow at small spatial scales. Daphnia individuals belonged either to the parental species D. galeata and D. longispina, or to different hybrid classes, as identified by 15 microsatellite markers. The distribution and genotypic structure of parental species, but not hybrids, corresponded well with the geographical positions of the lakes. Within parental species, the genetic distance among populations of D. galeata was lower than among populations of D. longispina. Moreover, D. galeata dominance was associated with higher phosphorous load. Finally, there was no evidence for clonal erosion. Our results suggest that the contemporary structure of hybridizing Daphnia communities from ten nearby lakes is influenced by colonization events from neighbouring habitats as well as by environmental factors. Unlike the parental species, however, there was little evidence for successful dispersal of hybrids, which seem to be produced locally. Finally, in contrast to temporary Daphnia populations, in which a decrease in clonal diversity was sometimes detectable over a single growing season, the high clonal diversity and lack of clonal erosion observed here might result from repeated hatching of sexually produced offspring. Overall, our study provides insights into

  13. Glyphosate drift promotes changes in fitness and transgene gene flow in canola (Brassica napus) and hybrids

    Science.gov (United States)

    Londo, Jason P.; Bautista, Nonnatus S.; Sagers, Cynthia L.; Lee, E. Henry; Watrud, Lidia S.

    2010-01-01

    Background and Aims With the advent of transgenic crops, genetically modified, herbicide-resistant Brassica napus has become a model system for examining the risks and potential ecological consequences of escape of transgenes from cultivation into wild compatible species. Escaped transgenic feral B. napus and hybrids with compatible weedy species have been identified outside of agriculture and without the apparent selection for herbicide resistance. However, herbicide (glyphosate) exposure can extend beyond crop field boundaries, and a drift-level of herbicide could function as a selective agent contributing to increased persistence of transgenes in the environment. Methods The effects of a drift level (0·1 × the field application rate) of glyphosate herbicide and varied levels of plant competition were examined on plant fitness-associated traits and gene flow in a simulated field plot, common garden experiment. Plants included transgenic, glyphosate-resistant B. napus, its weedy ancestor B. rapa, and hybrid and advanced generations derived from them. Key Results The results of this experiment demonstrate reductions in reproductive fitness for non-transgenic genotypes and a contrasting increase in plant fitness for transgenic genotypes as a result of glyphosate-drift treatments. Results also suggest that a drift level of glyphosate spray may influence the movement of transgenes among transgenic crops and weeds and alter the processes of hybridization and introgression in non-agronomic habitats by impacting flowering phenology and pollen availability within the community. Conclusions The results of this study demonstrate the potential for persistence of glyphosate resistance transgenes in weedy plant communities due to the effect of glyphosate spray drift on plant fitness. Additionally, glyphosate drift has the potential to change the gene-flow dynamics between compatible transgenic crops and weeds, simultaneously reducing direct introgression into weedy species

  14. Geographically weighted regression as a generalized Wombling to detect barriers to gene flow.

    Science.gov (United States)

    Diniz-Filho, José Alexandre Felizola; Soares, Thannya Nascimento; de Campos Telles, Mariana Pires

    2016-08-01

    Barriers to gene flow play an important role in structuring populations, especially in human-modified landscapes, and several methods have been proposed to detect such barriers. However, most applications of these methods require a relative large number of individuals or populations distributed in space, connected by vertices from Delaunay or Gabriel networks. Here we show, using both simulated and empirical data, a new application of geographically weighted regression (GWR) to detect such barriers, modeling the genetic variation as a "local" linear function of geographic coordinates (latitude and longitude). In the GWR, standard regression statistics, such as R(2) and slopes, are estimated for each sampling unit and thus are mapped. Peaks in these local statistics are then expected close to the barriers if genetic discontinuities exist, capturing a higher rate of population differentiation among neighboring populations. Isolation-by-Distance simulations on a longitudinally warped lattice revealed that higher local slopes from GWR coincide with the barrier detected with Monmonier algorithm. Even with a relatively small effect of the barrier, the power of local GWR in detecting the east-west barriers was higher than 95 %. We also analyzed empirical data of genetic differentiation among tree populations of Dipteryx alata and Eugenia dysenterica Brazilian Cerrado. GWR was applied to the principal coordinate of the pairwise FST matrix based on microsatellite loci. In both simulated and empirical data, the GWR results were consistent with discontinuities detected by Monmonier algorithm, as well as with previous explanations for the spatial patterns of genetic differentiation for the two species. Our analyses reveal how this new application of GWR can viewed as a generalized Wombling in a continuous space and be a useful approach to detect barriers and discontinuities to gene flow.

  15. Human-aided and natural dispersal drive gene flow across the range of an invasive mosquito.

    Science.gov (United States)

    Medley, Kim A; Jenkins, David G; Hoffman, Eric A

    2015-01-01

    Human-aided transport is responsible for many contemporary species introductions, yet the contribution of human-aided transport to dispersal within non-native regions is less clear. Understanding dispersal dynamics for invasive species can streamline mitigation efforts by targeting routes that contribute disproportionally to spread. Because of its limited natural dispersal ability, rapid spread of the Asian tiger mosquito (Aedes albopictus) has been attributed to human-aided transport, but until now, the relative roles of human-aided and natural movement have not been rigorously evaluated. Here, we use landscape genetics and information-theoretic model selection to evaluate 52 models representing 9240 pairwise dispersal paths among sites across the US range for Ae. albopictus and show that recent gene flow reflects a combination of natural and human-aided dispersal. Highways and water availability facilitate dispersal at a broad spatial scale, but gene flow is hindered by forests at the current distributional limit (range edge) and by agriculture among sites within the mosquito's native climatic niche (range core). Our results show that highways are important to genetic structure between range-edge and range-core pairs, suggesting a role for human-aided mosquito transport to the range edge. In contrast, natural dispersal is dominant at smaller spatial scales, reflecting a shifting dominance to natural movement two decades after introduction. These conclusions highlight the importance of (i) early intervention for species introductions, particularly those with readily dispersed dormant stages and short generation times, and (ii) strict monitoring of commercial shipments for transported immature stages of Ae. albopictus, particularly towards the northern edge of the US range.

  16. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus

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    Bradic Martina

    2012-01-01

    Full Text Available Abstract Background Cave animals converge evolutionarily on a suite of troglomorphic traits, the best known of which are eyelessness and depigmentation. We studied 11 cave and 10 surface populations of Astyanax mexicanus in order to better understand the evolutionary origins of the cave forms, the basic genetic structuring of both cave and surface populations, and the degree to which present day migration among them affects their genetic divergence. Results To assess the genetic structure within populations and the relationships among them we genotyped individuals at 26 microsatellite loci. We found that surface populations are similar to one another, despite their relatively large geographic separation, whereas the cave populations are better differentiated. The cave populations we studied span the full range of the cave forms in three separate geographic regions and have at least five separate evolutionary origins. Cave populations had lower genetic diversity than surface populations, correlated with their smaller effective population sizes, probably the result of food and space limitations. Some of the cave populations receive migrants from the surface and exchange migrants with one another, especially when geographically close. This admixture results in significant heterozygote deficiencies at numerous loci due to Wahlund effects. Cave populations receiving migrants from the surface contain small numbers of individuals that are intermediate in both phenotype and genotype, affirming at least limited gene flow from the surface. Conclusions Cave populations of this species are derived from two different surface stocks denoted "old" and "new." The old stock colonized caves at least three times independently while the new stock colonized caves at least twice independently. Thus, the similar cave phenotypes found in these caves are the result of repeated convergences. These phenotypic convergences have occurred in spite of gene flow from surface

  17. Population divergence and gene flow in an endangered and highly mobile seabird

    Science.gov (United States)

    Welch, A. J.; Fleischer, R. C.; James, H. F.; Wiley, A. E.; Ostrom, P. H.; Adams, J.; Duvall, F.; Holmes, N.; Hu, D.; Penniman, J.; Swindle, K. A.

    2012-01-01

    Seabirds are highly vagile and can disperse up to thousands of kilometers, making it difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given the great dispersal potential of these petrels, it remains unclear if populations are genetically distinct and which factors may contribute to isolation between them. We sampled petrels from across their range, including individuals from the presumably extirpated Molokai population. We sequenced 524 bp of mitochondrial DNA, 741 bp from three nuclear introns, and genotyped 18 microsatellite loci in order to examine the patterns of divergence in this species and to investigate the potential underlying mechanisms. Both mitochondrial and nuclear data sets indicated significant genetic differentiation among all modern populations, but no differentiation was found between historic samples from Molokai and modern birds from Lanai. Population-specific nonbreeding distribution and strong natal philopatry may reduce gene flow between populations. However, the lack of population structure between extirpated Molokai birds and modern birds on Lanai indicates that there was substantial gene flow between these populations and that petrels may be able to overcome barriers to dispersal prior to complete extirpation. Hawaiian petrel populations could be considered distinct management units, however, the dwindling population on Hawaii may require translocation to prevent extirpation in the near future.

  18. Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets.

    Science.gov (United States)

    Lange, Rebecca; Durka, Walter; Holzhauer, Stephanie I J; Wolters, Volkmar; Diekötter, Tim

    2010-11-01

    Effects of habitat fragmentation on genetic diversity vary among species. This may be attributed to the interacting effects of species traits and landscape structure. While widely distributed and abundant species are often considered less susceptible to fragmentation, this may be different if they are small sized and show limited dispersal. Under intensive land use, habitat fragmentation may reach thresholds at which gene flow among populations of small-sized and dispersal-limited species becomes disrupted. Here, we studied the genetic diversity of two abundant and widespread bush crickets along a gradient of habitat fragmentation in an agricultural landscape. We applied traditional (G(ST), θ) and recently developed (G'ST', D) estimators of genetic differentiation on microsatellite data from each of twelve populations of the grassland species Metrioptera roeselii and the forest-edge species Pholidoptera griseoaptera to identify thresholds of habitat fragmentation below which genetic population structure is affected. Whereas the grassland species exhibited a uniform genetic structuring (G(ST) = 0.020-0.033; D = 0.085-0.149) along the whole fragmentation gradient, the forest-edge species' genetic differentiation increased significantly from D habitat dropped below a threshold of 20% and its proximity decreased substantially at the landscape scale. The influence of fragmentation on genetic differentiation was qualitatively unaffected by the choice of estimators of genetic differentiation but quantitatively underestimated by the traditional estimators. These results indicate that even for widespread species in modern agricultural landscapes fragmentation thresholds exist at which gene flow among suitable habitat patches becomes restricted. © 2010 Blackwell Publishing Ltd.

  19. Fat-tailed gene flow in the dioecious canopy tree species Fraxinus mandshurica var. japonica revealed by microsatellites.

    Science.gov (United States)

    Goto, S; Shimatani, K; Yoshimaru, H; Takahashi, Y

    2006-09-01

    Pollen flow, seed dispersal and individual reproductive success can be simultaneously estimated from the genotypes of adults and offspring using stochastic models. Using four polymorphic microsatellite loci, gene flow of the wind-pollinated and wind-seed-dispersed dioecious tree species, Fraxinus mandshurica var. japonica, was quantified in a riparian forest, in northern Japan. In a 10.5-ha plot, 74 female adults, 76 male adults and 292 current-year seedlings were mapped and genotyped, together with 200 seeds. To estimate dispersal kernels of pollen and seeds, we applied normal, exponential power, Weibull, bivariate t-distribution kernels, and two-component models consisting of two normal distribution functions, one with a small and one with a large variance. A two-component pollen flow model with a small contribution (26.1%) from short-distance dispersal (sigma = 7.2 m), and the rest from long-distance flow (sigma = 209.9 m), was chosen for the best-fitting model. The average distance that integrated pollen flows inside and outside the study plot was estimated to be 196.8 m. Tree size and flowering intensity affected reproduction, and there appeared to be critical values that distinguished reproductively successful and unsuccessful adults. In contrast, the gene flow model that estimated both pollen and seed dispersal from established seedlings resulted in extensive seed dispersal, and the expected spatial genetic structures did not satisfactorily fit with the observations, even for the selected model. Our results advanced small-scale individual-based parentage analysis for quantifying fat-tailed gene flow in wind-mediated species, but also clarified its limitations and suggested future possibilities for gene flow studies.

  20. Migration and population genetics of the grain aphid Macrosiphum miscanti (Takahashi) in relation to the geographic distance and gene flow

    Institute of Scientific and Technical Information of China (English)

    GUO Wei; SHEN Zuorui; LI Zhihong; GAO Lingwang

    2005-01-01

    The population genetics of the grain aphid Macrosiphum miscanti (Takahashi) is analyzed by microsatellite markers.Samples collected from 15 locations in China have been examined at 5 polymorphic microsatellite loci. Overall, genetic diversity displays a relation between the migration and gene flow in the grain aphid: a free and frequent gene flow is found in the eastern populations, and gene isolation occurs in the two western populations, especially Datong population and Guiyang population. The natural barriers may present an insurmountable obstacle preventing gene flow and aphid migration. However, a spatial genetic differentiation between populations is correlated with their geographical separation, indicating the geographic differentiation may play an important role in shaping the genetic structure of M. miscanti populations. In addition, most populations of grain aphids are out of Hardy-Weinberg equilibrium and there is heterozygote deficit. Based on F statistics, the average genetic differentiation among different geographical populations is relatively low. It seems that the long distance migration of the grain aphid may enhance gene flow and decrease genetic differentiation among different populations.

  1. Afghan Hindu Kush: where Eurasian sub-continent gene flows converge.

    Directory of Open Access Journals (Sweden)

    Julie Di Cristofaro

    Full Text Available Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH. The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

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

    Science.gov (United States)

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

    2012-01-01

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

  3. Continuous gene flow contributes to low global species abundance and distribution of a marine model diatom

    KAUST Repository

    Rastogi, Achal

    2017-08-15

    Unlike terrestrial ecosystems where geographical isolation often leads to a restricted gene flow between species, genetic admixing in aquatic micro-eukaryotes is likely to be frequent. Diatoms inhabit marine ecosystems since the Mesozoic period and presently constitute one of the major primary producers in the world ocean. They are a highly diversified group of eukaryotic phytoplankton with estimates of up to 200,000 species. Since decades, Phaeodactylum tricornutum is used as a model diatom species to characterize the functional pathways, physiology and evolution of diatoms in general. In the current study, using whole genome sequencing of ten P. tricornutum strains, sampled at broad geospatial and temporal scales, we show a continuous dispersal and genetic admixing between geographically isolated strains. We also describe a very high level of heterozygosity and propose it to be a consequence of frequent ancestral admixture. Our finding that P. tricornutum sequences are plausibly detectable at low but broadly distributed levels in the world ocean further suggests that high admixing between geographically isolated strains may create a significant bottleneck, thus influencing their global abundance and distribution in nature. Finally, in an attempt to understand the functional implications of genetic diversity between different P. tricornutum ecotypes, we show the effects of domestication in inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success.

  4. Magnetic, structural and geochronologic evidence bearing on volcanic sources and Oligocene Deformation of Ash Flow Tuffs, northeast Nevada

    Science.gov (United States)

    Palmer, H. C.; MacDonald, W. D.; Hayatsu, A.

    1991-02-01

    Magnetic properties of mid-Tertiary volcanic rocks west of Jiggs in northeast Nevada were investigated for the purposes of interpreting igneous, structural, and tectonic processes in this part of the Basin and Range province. Anisotropy of magnetic susceptibility (AMS) patterns reflect flow fabrics and suggest previously unknown sources for these ash flow tuffs. Paleomagnetic and structural evidence suggest counterclockwise relative rotation of the southern part of the area with respect to the north. New stratigraphic, chemical and K-Ar isotopic data support these interpretations. Dacite to rhyolite ash flow tuffs of the Indian Well Formation were subdivided into two main units: the lower and predominant tuff of Jiggs (35.8-37.0 Ma) and the unconformably overlying but areally restricted tuff of Hackwood (30.8 Ma). The Jiggs unit has two polarities whereas the Hackwood has only a reversed polarity remanence. Together these units with tilt correction define a pole (92°E, 87°N, dp = 6°, dm = 8°) for approximately 30-37 Ma. This pole is concordant with coeval North American reference poles, indicating that this zone of approximately 30 km NS extent has not undergone significant vertical axis rotation relative to the North American reference. Andesite lavas of normal magnetic polarity and of 32.5-Ma age characterize the Diamond Hills immediately to the south. We interpret this region, from both structural evidence and discordant paleomagnetic direction, to have rotated approximately 25° counterclockwise relative to the Indian Well volcanic units to the north. The apparent rotation of the Diamond Hills is possibly the result of drag on the left-lateral Garcia fault which limits the Diamond Hills on the southwest. Analysis of AMS data suggests, by patterns of the K1 axes, two distinct sources for the Jiggs unit: a northern buried source and a central partially buried source. Lithologic evidence consistent with proximal vent facies is found near the latter source. An

  5. Are Cirripedia hopeful monsters? Cytogenetic approach and evidence for a Hox gene cluster in the cirripede crustacean Sacculina carcini.

    Science.gov (United States)

    Géant, Elodie; Mouchel-Vielh, Emmanuèle; Coutanceau, Jean-Pierre; Ozouf-Costaz, Catherine; Deutsch, Jean S

    2006-01-01

    The "hopeful monster" has haunted evolutionary thinking since Richard Goldschmidt coined the phrase in 1933. The phrase is directly related to genetic mechanisms in development and evolution. Cirripedes are peculiar crustaceans in that they all lack abdomens as adults. In a previous study aimed at describing the repertoire of Hox genes of the Cirripedia, we failed to isolate the abdominal-A gene in three species representative of all three cirripede orders. To address the question of whether the cirripede ancestor could have been a "hopeful monster" arising from a rearrangement of the Hox complex, we have performed a cytogenetic analysis of the Hox complex of the cirripede Sacculina carcini. We present here molecular and cytogenetic evidence for the grouping of the Hox genes on a single chromosome. This is the first direct evidence reported for the grouping of Hox genes on the same chromosome in a non-insect arthropod species.

  6. Isotopic evidence of complex ground-water flow at Yucca mountain, Nevada, USA

    Science.gov (United States)

    Peterman, Zell E.; Stuckless, John S.

    1993-01-01

    Strontium isotopes (expressed as per mill deviation from mean sea water, ??87Sr) reflect interaction between ground water and the aquifer through which it is flowing. In the Cenozoic aquifer of the Yucca Mountain region, ??87Sr values increase from north to south downgradient in the flow system. The largest ??87Sr values occur in the Amargosa Desert where ground water probably encounters alluvial basin fill derived from Precambrian rocks in the Funeral Range. Similarly, large ??87Sr values for ground water in the Paleozoic aquifer at the western end of the Spring Mountains also probably reflect an encounter with Precambrian rocks. In several wells into the volcanic rocks, apparent isotopic disequilibrium between ground water and the producing units suggests that the ground water probably integrates over a substantial part of the saturated section in attaining its strontium isotope signature.

  7. Evidence of recent interspecies horizontal gene transfer regarding nucleopolyhedrovirus infection of Spodoptera frugiperda.

    Science.gov (United States)

    Barrera, Gloria Patricia; Belaich, Mariano Nicolás; Patarroyo, Manuel Alfonso; Villamizar, Laura Fernanda; Ghiringhelli, Pablo Daniel

    2015-11-25

    Baculoviruses are insect-associated viruses carrying large, circular double-stranded-DNA genomes with significant biotechnological applications such as biological pest control, recombinant protein production, gene delivery in mammals and as a model of DNA genome evolution. These pathogens infect insects from the orders Lepidoptera, Hymenoptera and Diptera, and have high species diversity which is expressed in their diverse biological properties including morphology, virulence or pathogenicity. Spodoptera frugiperda (Lepidoptera: Noctuidae), the fall armyworm, represents a significant pest for agriculture in America; it is a host for baculoviruses such as the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) (Colombia strain, genotype A) having been classified as a Group II alphabaculovirus making it a very attractive target for bioinsecticidal use. Genome analysis by pyrosequencing revealed that SfMNPV ColA has 145 ORFs, 2 of which were not present in the other sequenced genotypes of the virus (SfMNPV-NicB, SfMNPV-NicG, SfMNPV-19 and SfMNPV-3AP2). An in-depth bioinformatics study showed that ORF023 and ORF024 were acquired by a recent homologous recombination process between Spodoptera frugiperda and Spodoptera litura (the Oriental leafworm moth) nucleopolyhedroviruses. Auxiliary genes are numerous in the affected locus which has a homologous region (hr3), a repetitive sequence associated with genome replication which became lost in SfColA along with 1 ORF. Besides, the mRNAs associated with two acquired genes appeared in the virus' life-cycle during the larval stage. Predictive studies concerning the theoretical proteins identified that ORF023 protein would be a phosphatase involved in DNA repair and that the ORF024 protein would be a membrane polypeptide associated with cell transport. The SfColA genome was thus revealed to be a natural recombinant virus showing evidence of recent horizontal gene transfer between different baculovirus species occurring

  8. Evidence of non-Darcy flow and non-Fickian transport in fractured media at laboratory scale

    Directory of Open Access Journals (Sweden)

    C. Cherubini

    2013-07-01

    Full Text Available During a risk assessment procedure as well as when dealing with cleanup and monitoring strategies, accurate predictions of solute propagation in fractured rocks are of particular importance when assessing exposure pathways through which contaminants reach receptors. Experimental data obtained under controlled conditions such as in a laboratory allow to increase the understanding of the fundamental physics of fluid flow and solute transport in fractures. In this study, laboratory hydraulic and tracer tests have been carried out on an artificially created fractured rock sample. The tests regard the analysis of the hydraulic loss and the measurement of breakthrough curves for saline tracer pulse inside a rock sample of parallelepiped shape (0.60 × 0.40 × 0.08 m. The convolution theory has been applied in order to remove the effect of the acquisition apparatus on tracer experiments. The experimental results have shown evidence of a non-Darcy relationship between flow rate and hydraulic loss that is best described by Forchheimer's law. Furthermore, in the flow experiments both inertial and viscous flow terms are not negligible. The observed experimental breakthrough curves of solute transport have been modeled by the classical one-dimensional analytical solution for the advection–dispersion equation (ADE and the single rate mobile–immobile model (MIM. The former model does not properly fit the first arrival and the tail while the latter, which recognizes the existence of mobile and immobile domains for transport, provides a very decent fit. The carried out experiments show that there exists a pronounced mobile–immobile zone interaction that cannot be neglected and that leads to a non-equilibrium behavior of solute transport. The existence of a non-Darcian flow regime has showed to influence the velocity field in that it gives rise to a delay in solute migration with respect to the predicted value assuming linear flow. Furthermore, the

  9. There is no evident correlation between interleukin-10 gene polymorphisms and periportal fibrosis regression after specific treatment.

    Science.gov (United States)

    Silva, Paula Carolina Valença; Silva, Aline Vieira da; Silva, Taysa Nascimento; Vasconcelos, Letícia Moura de; Gomes, Adriana Vieira; Coêlho, Maria Rosângela Cunha Duarte; Muniz, Maria Tereza Cartaxo; Domingues, Ana Lúcia Coutinho

    2016-01-01

    We evaluated the associations between interleukin-10 (IL-10) gene polymorphisms -G1082A/-C819T/-C592A and periportal fibrosis regression after specific treatment for schistosomiasis. This retrospective cohort study involved 125 Brazilian patients infected with Schistosomiasis mansoni, who were followed up for 2 years after specific treatment to estimate the probability of periportal fibrosis regression. There was no evidence of associations between IL-10 polymorphisms and periportal fibrosis regression after treatment. There was no evidence of associations between gene promoter polymorphisms of IL-10 and the regression of periportal fibrosis in this Brazilian population.

  10. Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles.

    Science.gov (United States)

    Zhong, Huaming; Shang, Shuai; Wu, Xiaoyang; Chen, Jun; Zhu, Wanchao; Yan, Jiakuo; Li, Haotian; Zhang, Honghai

    2017-01-01

    As nontraditional model organisms with extreme physiological and morphological phenotypes, snakes are believed to possess an inferior taste system. However, the bitter taste sensation is essential to distinguish the nutritious and poisonous food resources and the genomic evidence of bitter taste in snakes is largely scarce. To explore the genetic basis of the bitter taste of snakes and characterize the evolution of bitter taste receptor genes (Tas2rs) in reptiles, we identified Tas2r genes in 19 genomes (species) corresponding to three orders of non-avian reptiles. Our results indicated contractions of Tas2r gene repertoires in snakes, however dramatic gene expansions have occurred in lizards. Phylogenetic analysis of the Tas2rs with NJ and BI methods revealed that Tas2r genes of snake species formed two clades, whereas in lizards the Tas2r genes clustered into two monophyletic clades and four large clades. Evolutionary changes (birth and death) of intact Tas2r genes in reptiles were determined by reconciliation analysis. Additionally, the taste signaling pathway calcium homeostasis modulator 1 (Calhm1) gene of snakes was putatively functional, suggesting that snakes still possess bitter taste sensation. Furthermore, Phylogenetically Independent Contrasts (PIC) analyses reviewed a significant correlation between the number of Tas2r genes and the amount of potential toxins in reptilian diets, suggesting that insectivores such as some lizards may require more Tas2rs genes than omnivorous and carnivorous reptiles.

  11. Evidence from lava flows for complex polarity transitions: The new composite Steens Mountain reversal record

    Science.gov (United States)

    Jarboe, N.A.; Coe, R.S.; Glen, J.M.

    2011-01-01

    Geomagnetic polarity transitions may be significantly more complex than are currently depicted in many sedimentary and lava-flow records. By splicing together paleomagnetic results from earlier studies at Steens Mountain with those from three newly studied sections of Oregon Plateau flood basalts at Catlow Peak and Poker Jim Ridge 70-90 km to the southeast and west, respectively, we provide support for this interpretation with the most detailed account of a magnetic field reversal yet observed in volcanic rocks. Forty-five new distinguishable transitional (T) directions together with 30 earlier ones reveal a much more complex and detailed record of the 16.7 Ma reversed (R)-to-normal (N) polarity transition that marks the end of Chron C5Cr. Compared to the earlier R-T-N-T-N reversal record, the new record can be described as R-T-N-T-N-T-R-T-N. The composite record confirms earlier features, adds new west and up directions and an entire large N-T-R-T segment to the path, and fills in directions on the path between earlier directional jumps. Persistent virtual geomagnetic pole (VGP) clusters and separate VGPs have a preference for previously described longitudinal bands from transition study compilations, which suggests the presence of features at the core-mantle boundary that influence the flow of core fluid and distribution of magnetic flux. Overall the record is consistent with the generalization that VGP paths vary greatly from reversal to reversal and depend on the location of the observer. Rates of secular variation confirm that the flows comprising these sections were erupted rapidly, with maximum rates estimated to be 85-120 m ka-1 at Catlow and 130-195 m ka-1 at Poker Jim South. Paleomagnetic poles from other studies are combined with 32 non-transitional poles found here to give a clockwise rotation of the Oregon Plateau of 11.4???? 5.6?? with respect to the younger Columbia River Basalt Group flows to the north and 14.5???? 4.6?? with respect to cratonic

  12. Karyological and flow cytometric evidence of triploid specimens in Bufo viridis (Amphibia Anura

    Directory of Open Access Journals (Sweden)

    D Cavallo

    2010-01-01

    Full Text Available Karyological and flow cytometric (FCM analyses were performed on a group of 14 green toads of the Bufo viridis species from seven Eurasian populations. Both approaches gave concordant results concerning the DNA ploidy level. All the populations examined were represented exclusively by diploid or tetraploid specimens, except one, where triploids were found. Results evidenced an interpopulation variability in DNA content against the same ploidy level, as well as an unusually high number of triploids in a particular reproductive place. The origin of polyploidy and the presence and persistence of a high number of triploids in a particular population are discussed.

  13. TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders

    Directory of Open Access Journals (Sweden)

    Tarr D Ellen K

    2009-09-01

    Full Text Available Abstract Background Plant resistance (R gene products recognize pathogen effector molecules. Many R genes code for proteins containing nucleotide binding site (NBS and C-terminal leucine-rich repeat (LRR domains. NBS-LRR proteins can be divided into two groups, TIR-NBS-LRR and non-TIR-NBS-LRR, based on the structure of the N-terminal domain. Although both classes are clearly present in gymnosperms and eudicots, only non-TIR sequences have been found consistently in monocots. Since most studies in monocots have been limited to agriculturally important grasses, it is difficult to draw conclusions. The purpose of our study was to look for evidence of these sequences in additional monocot orders. Findings Using degenerate PCR, we amplified NBS sequences from four monocot species (C. blanda, D. marginata, S. trifasciata, and Spathiphyllum sp., a gymnosperm (C. revoluta and a eudicot (C. canephora. We successfully amplified TIR-NBS-LRR sequences from dicot and gymnosperm DNA, but not from monocot DNA. Using databases, we obtained NBS sequences from additional monocots, magnoliids and basal angiosperms. TIR-type sequences were not present in monocot or magnoliid sequences, but were present in the basal angiosperms. Phylogenetic analysis supported a single TIR clade and multiple non-TIR clades. Conclusion We were unable to find monocot TIR-NBS-LRR sequences by PCR amplification or database searches. In contrast to previous studies, our results represent five monocot orders (Poales, Zingiberales, Arecales, Asparagales, and Alismatales. Our results establish the presence of TIR-NBS-LRR sequences in basal angiosperms and suggest that although these sequences were present in early land plants, they have been reduced significantly in monocots and magnoliids.

  14. A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens.

    Science.gov (United States)

    Worthington, Margaret; Heffelfinger, Christopher; Bernal, Diana; Quintero, Constanza; Zapata, Yeny Patricia; Perez, Juan Guillermo; De Vega, Jose; Miles, John; Dellaporta, Stephen; Tohme, Joe

    2016-07-01

    Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR-BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR-BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR-BBML as candidate genes for the apomictic function of parthenogenesis.

  15. Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain.

    Science.gov (United States)

    Ueno, Ryohei; Huss, Volker A R; Urano, Naoto; Watabe, Shugo

    2007-11-01

    Informational genes such as those encoding rRNAs are related to transcription and translation, and are thus considered to be rarely subject to lateral gene transfer (LGT) between different organisms, compared to operational genes having metabolic functions. However, several lines of evidence have suggested or confirmed the occurrence of LGT of DNA segments encoding evolutionarily variable regions of rRNA genes between different organisms. In the present paper, we show, for the first time to our knowledge, that variable regions of the 18S rRNA gene are segmentally replaced by multiple copies of different sequences in a single strain of the green microalga Prototheca wickerhamii, resulting in at least 17 genotypes, nine of which were actually transcribed. Recombination between different 18S rRNA genes occurred in seven out of eight variable regions (V1-V5 and V7-V9) of eukaryotic small subunit (SSU) rRNAs. While no recombination was observed in V1, one to three different recombination loci were demonstrated for the other regions. Such segmental replacement was also implicated for helix H37, which is defined as V6 of prokaryotic SSU rRNAs. Our observations provide direct evidence for redundant recombination of an informational gene, which encodes a component of mature ribosomes, in a single strain of one organism.

  16. Evidence for negative selection on the gene encoding rhoptry-associated protein 1 (RAP-1) in Plasmodium spp.

    Science.gov (United States)

    Pacheco, M Andreína; Ryan, Elizabeth M; Poe, Amanda C; Basco, Leonardo; Udhayakumar, Venkatachalam; Collins, Williams E; Escalante, Ananias A

    2010-07-01

    Assessing how natural selection, negative or positive, operates on genes with low polymorphism is challenging. We investigated the genetic diversity of orthologous genes encoding the rhoptry-associated protein 1 (RAP-1), a low polymorphic protein of malarial parasites that is involved in erythrocyte invasion. We applied evolutionary genetic methods to study the polymorphism in RAP-1 from Plasmodium falciparum (n=32) and Plasmodium vivax (n=6), the two parasites responsible for most human malaria morbidity and mortality, as well as RAP-1 orthologous in closely related malarial species found in non-human primates (NHPs). Overall, genes encoding RAP-1 are highly conserved in all Plasmodium spp. included in this investigation. We found no evidence for natural selection, positive or negative, acting on the gene encoding RAP-1 in P. falciparum or P. vivax. However, we found evidence that the orthologous genes in non-human primate parasites (Plasmodium cynomolgi, Plasmodium inui, and Plasmodium knowlesi) are under purifying (negative) selection. We discuss the importance of considering negative selection while studying genes encoding proteins with low polymorphism and how selective pressures may differ among orthologous genes in closely related malarial parasites species. Copyright 2010 Elsevier B.V. All rights reserved.

  17. Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus.

    Science.gov (United States)

    Tremblay, Yannick D N; Deslandes, Vincent; Jacques, Mario

    2013-05-31

    Actinobacillus pleuropneumoniae is the Gram-negative bacterium responsible for porcine pleuropneumonia. This respiratory infection is highly contagious and characterized by high morbidity and mortality. The objectives of our study were to study the transcriptome of A. pleuropneumoniae biofilms at different stages and to develop a protocol to grow an A. pleuropneumoniae biofilm in a drip-flow apparatus. This biofilm reactor is a system with an air-liquid interface modeling lung-like environment. Bacteria attached to a surface (biofilm) and free floating bacteria (plankton) were harvested for RNA isolation. Labelled cDNA was hybridized to a microarray to compare the expression profiles of planktonic cells and biofilm cells. It was observed that 47 genes were differentially expressed (22 up, 25 down) in a 4 h-static growing/maturing biofilm and 117 genes were differentially expressed (49 up, 68 down) in a 6h-static dispersing biofilm. The transcriptomes of a 4 h biofilm and a 6 h biofilm were also compared and 456 genes (235 up, 221 down) were identified as differently expressed. Among the genes identified in the 4 h vs 6h biofilm experiment, several regulators of stress response were down-regulated and energy metabolism associated genes were up-regulated. Biofilm bacteria cultured using the drip-flow apparatus differentially expressed 161 genes (68 up, 93 down) compared to the effluent bacteria. Cross-referencing of differentially transcribed genes in the different assays revealed that drip-flow biofilms shared few differentially expressed genes with static biofilms (4 h or 6 h) but shared several differentially expressed genes with natural or experimental infections in pigs. The formation of a static biofilm by A. pleuropneumoniae strain S4074 is a rapid process and transcriptional analysis indicated that dispersal observed at 6 h is driven by nutritional stresses. Furthermore, A. pleuropneumoniae can form a biofilm under low-shear force in a drip-flow apparatus and

  18. Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

    NARCIS (Netherlands)

    Piotti, A.; Leonardi, S.; Buiteveld, J.; Geburek, T.; Gerber, S.; Kramer, K.; Vettori, C.; Vendramin, G.G.

    2012-01-01

    The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of fac

  19. Dispersal and gene flow in the rare, parasitic Large Blue butterfly Maculinea arion

    DEFF Research Database (Denmark)

    Ugelvig, Line Vej; Andersen, Anne; Boomsma, Jacobus Jan

    2012-01-01

    decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark...

  20. Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape

    NARCIS (Netherlands)

    Mix, C.; Arens, P.F.P.; Rengelink, R.; Smulders, M.J.M.; Groenendael, van J.M.; Ouburg, J.

    2006-01-01

    Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in

  1. Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

    KAUST Repository

    Bonnet-Lebrun, Anne-Sophie

    2017-03-17

    Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions. This article is protected by copyright. All rights reserved.

  2. Pollen-mediated gene flow and seed exchange in small-scale Zambian maize farming, implications for biosafety assessment

    Science.gov (United States)

    Bøhn, Thomas; Aheto, Denis W.; Mwangala, Felix S.; Fischer, Klara; Bones, Inger Louise; Simoloka, Christopher; Mbeule, Ireen; Schmidt, Gunther; Breckling, Broder

    2016-10-01

    Gene flow in agricultural crops is important for risk assessment of genetically modified (GM) crops, particularly in countries with a large informal agricultural sector of subsistence cultivation. We present a pollen flow model for maize (Zea mays), a major staple crop in Africa. We use spatial properties of fields (size, position) in three small-scale maize farming communities in Zambia and estimate rates of cross-fertilisation between fields sown with different maize varieties (e.g. conventional and transgene). As an additional factor contributing to gene flow, we present data on seed saving and sharing among farmers that live in the same communities. Our results show that: i) maize fields were small and located in immediate vicinity of neighboring fields; ii) a majority of farmers saved and shared seed; iii) modeled rates of pollen-mediated gene flow showed extensive mixing of germplasm between fields and farms and iv) as a result, segregation of GM and non-GM varieties is not likely to be an option in these systems. We conclude that the overall genetic composition of maize, in this and similar agricultural contexts, will be strongly influenced both by self-organised ecological factors (pollen flow), and by socially mediated intervention (seed recycling and sharing).

  3. Heat flow evolution of the Earth from paleomantle temperatures: Evidence for increasing heat loss since ∼2.5 Ga

    Science.gov (United States)

    Ruiz, Javier

    2017-08-01

    Earth currently loses two to five times as much heat through its surface as it is internally produced by radioactivity. This proportion cannot be extrapolated into the past, because it would imply high interior temperatures and catastrophic melting of the planet in ancient times. The heat loss evolution of the Earth cannot therefore be described by a constant heat flow decreasing. This is consistent with previous work finding that the mantle heated up until ∼2.5-3.0 Ga and then progressively cooled down. The present work derives a first-order heat loss evolution of the Earth by comparing the evolution of the total heat content of the silicate Earth (as described by mantle potential temperatures deduced from the melting conditions of ancient non-arc basalts) with the total radioactive heat production. The results show that the heat flow was declining, and the mantle heating-up, until ∼2.5 Ga, but that after this time the heat flow has been slowly (but constantly) increasing, and the mantle cooling-down, until the present-day. The change in heat loss trend is roughly coeval with other major geological, geochemical and environmental changes, and could indicate the starting of the modern-style of plate tectonics. This work provides therefore the first quantitative evidence of change in terrestrial heat loss regime, and suggests that substantial variations in the internal heat budget occurred during Earth's history.

  4. Environmental implications of gene flow from sugar beet to wild beet--current status and future research needs.

    Science.gov (United States)

    Bartsch, Detlef; Cuguen, Joel; Biancardi, Enrico; Sweet, Jeremy

    2003-01-01

    Gene flow via seed or pollen is a basic biological process in plant evolution. The ecological and genetic consequences of gene flow depend on the amount and direction of gene flow as well as on the fitness of hybrids. The assessment of potential risks of transgenic plants should take into account the fact that conventional crops can often cross with wild plants. The precautionary approach in risk management of genetically modified plants (GMPs) may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Gene flow is hard to control in wind-pollinated plants like beet (Beta vulgaris). In addition, wild beet populations potentially can undergo evolutionary changes which might expand their geographical distribution. Unintended products of cultivated beets pollinated by wild beets are weed beets that bolt and flower during their first year of planting. Weed beets cause yield losses and can delay harvest. Wild beets are important plant genetic resources and the preservation of wild beet diversity in Europe has been considered in biosafety research. We present here the methodology and research approaches that can be used for monitoring the geographical distribution and diversity of Beta populations. It has recently been shown that a century of gene flow from Beta vulgaris ssp. vulgaris has not altered the genetic diversity of wild Beta vulgaris L. ssp. maritima (L.) Arcang. in the Italian sugar beet seed production area. Future research should focus on the potential evolution of transgenic wild beet populations in comparison to these baseline data. Two monitoring models are presented describing how endpoints can be measured: (1) "Pre-post" crop commercialization against today's baseline and (2) "Parallel" to crop commercialization against GMP free reference areas/ populations. Model 2 has the advantage of taking ongoing changes in genetic diversity and population dynamics into account. Model 1 is more applicable if

  5. Evidence for the multicentric origin of the sickle cell hemoglobin gene in Africa.

    OpenAIRE

    Pagnier, J.; Mears, J G; Dunda-Belkhodja, O; Schaefer-Rego, K E; Beldjord, C; Nagel, R L; Labie, D

    1984-01-01

    Previous studies of the Hpa I cleavage site-sickle cell hemoglobin gene linkage in various African populations suggested that the sickle gene arose independently more than once. In the present study we have performed restriction endonuclease haplotype analysis for the beta-globin-like gene cluster from four separate geographic areas in Africa, all of which possess the sickle gene. In Benin (Central West Africa) and Algeria (Arab North Africa) all chromosomes carrying the sickle gene possess a...

  6. Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor

    Directory of Open Access Journals (Sweden)

    Chan Jeannie

    2008-02-01

    Full Text Available Abstract Background Carboxylesterases (CES perform diverse metabolic roles in mammalian organisms in the detoxification of a broad range of drugs and xenobiotics and may also serve in specific roles in lipid, cholesterol, pheromone and lung surfactant metabolism. Five CES families have been reported in mammals with human CES1 and CES2 the most extensively studied. Here we describe the genetics, expression and phylogeny of CES isozymes in the opossum and report on the sequences and locations of CES1, CES2 and CES6 'like' genes within two gene clusters on chromosome one. We also discuss the likely sequence of gene duplication events generating multiple CES genes during vertebrate evolution. Results We report a cDNA sequence for an opossum CES and present evidence for CES1 and CES2 like genes expressed in opossum liver and intestine and for distinct gene locations of five opossum CES genes,CES1, CES2.1, CES2.2, CES2.3 and CES6, on chromosome 1. Phylogenetic and sequence alignment studies compared the predicted amino acid sequences for opossum CES with those for human, mouse, chicken, frog, salmon and Drosophila CES gene products. Phylogenetic analyses produced congruent phylogenetic trees depicting a rapid early diversification into at least five distinct CES gene family clusters: CES2, CES1, CES7, CES3, and CES6. Molecular divergence estimates based on a Bayesian relaxed clock approach revealed an origin for the five mammalian CES gene families between 328–378 MYA. Conclusion The deduced amino acid sequence for an opossum cDNA was consistent with its identity as a mammalian CES2 gene product (designated CES2.1. Distinct gene locations for opossum CES1 (1: 446,222,550–446,274,850, three CES2 genes (1: 677,773,395–677,927,030 and a CES6 gene (1: 677,585,520–677,730,419 were observed on chromosome 1. Opossum CES1 and multiple CES2 genes were expressed in liver and intestine. Amino acid sequences for opossum CES1 and three CES2 gene products

  7. Molecular evidence for ongoing complementarity and horizontal gene transfer in endosymbiotic systems of mealybugs

    Directory of Open Access Journals (Sweden)

    Sergio eLópez-Madrigal

    2014-08-01

    Full Text Available Intracellular bacterial supply of essential amino acids is common among sap-feeding insects, thus complementing the scarcity of nitrogenous compounds in plant phloem. This is also the role of the two mealybug endosymbiotic systems whose genomes have been sequenced. In the nested endosymbiotic system from Planococcus citri (Pseudococcinae, Candidatus Tremblaya princeps and Candidatus Moranella endobia cooperate to synthesize essential amino acids, while in Phenacoccus avenae (Phenacoccinae this function is performed by its single endosymbiont Candidatus Tremblaya phenacola. However, little is known regarding the evolution of essential amino acid supplementation strategies in other mealybug systems. To address this knowledge gap, we screened for the presence of six selected loci involved in essential amino acid biosynthesis in five additional mealybug species. We found evidence of ongoing complementarity among endosymbionts from insects of subfamily Pseudococcinae, as well as horizontal gene transfer affecting endosymbionts from insects of family Phenacoccinae, providing a more comprehensive picture of the evolutionary history of these endosymbiotic systems. Additionally, we report two diagnostic motifs to help identify invasive mealybug species.

  8. Evidence for the Role of Proteoglycans in Cation-Mediated Gene Transfer

    Science.gov (United States)

    Mislick, Kimberly A.; Baldeschwieler, John D.

    1996-10-01

    We report evidence that gene complexes, consisting of polycations and plasmid DNA enter cells via binding to membrane-associated proteoglycans. Treatment of HeLa cells with sodium chlorate, a potent inhibitor of proteoglycan sulfation, reduced luciferase expression by 69%. Cellular treatment with heparinase and chondroitinase ABC inhibited expression by 78% and 20% with respect to control cells. Transfection was dramatically inhibited by heparin and heparan sulfate and to a smaller extent by chondroitan sulfate B. Transfection of mutant, proteoglycan deficient Chinese hamster ovary cells was 53× lower than of wild-type cells. For each of these assays, the intracellular uptake of DNA at 37 degrees C and the binding of DNA to the cell membrane at 4 degrees C was impaired. Preliminary transfection experiments conducted in mutant and wild-type Chinese hamster ovary cells suggest that transfection by some cationic lipids is also proteoglycan dependent. The variable distribution of proteoglycans among tissues may explain why some cell types are more susceptible to transfection than others.

  9. Spectropolarimetric evidence for a siphon flow along an emerging magnetic flux tube

    CERN Document Server

    Requerey, Iker S; Iniesta, J C Del Toro; Suárez, D Orozco; Rodríguez, J Blanco; Solanki, S K; Barthol, P; Gandorfer, A; Gizon, L; Hirzberger, J; Riethmüller, T L; van Noort, M; Schmidt, W; Pillet, V Martínez; Knölker, M

    2016-01-01

    We study the dynamics and topology of an emerging magnetic flux concentration using high spatial resolution spectropolarimetric data acquired with the Imaging Magnetograph eXperiment on board the Sunrise balloon-borne solar observatory. We obtain the full vector magnetic field and the line-of-sight (LOS) velocity through inversions of the Fe I line at 525.02 nm with the SPINOR code. The derived vector magnetic field is used to trace magnetic field lines. Two magnetic flux concentrations with different polarity and LOS velocities are found to be connected by a group of arch-shaped magnetic field lines. The positive polarity footpoint is weaker (1100 G) and displays an upflow, while the negative polarity footpoint is stronger (2200 G) and shows a downflow. This configuration is naturally interpreted as a siphon flow along an arched magnetic flux tube.

  10. Evidence for a heated gas bubble inside the "cooling flow" region of MKW3s

    CERN Document Server

    Mazzotta, P; Paerels, F B S; Ferrigno, C; Colafrancesco, Sergio; Mewe, R; Forman, W R

    2002-01-01

    We report on the deep Chandra observation of central r=200kpc region of the cluster of galaxies MKW3s which was previously identified as a moderate cooling flow cluster. The Chandra image reveals two striking features -- a 100kpc long and 21kpc wide filament, extending from the center to the south-west and a nearly circular, 50kpc diameter depression 90 kpc south of the X-ray peak. The temperature map shows that the filamentary structure is colder while the surface brightness depression is hotter than the average cluster temperature at any radius. The hot and the cold regions indicate that both cooling and heating processes are taking place in the center of MKW3s. We argue that the surface brightness depression is produced by a heated, low-density gas bubble along the line of sight. We suggest that the heated bubble is produced by short-lived nuclear outbursts from the central galaxy.

  11. Inferred vs realized patterns of gene flow: an analysis of population structure in the Andros Island Rock Iguana.

    Directory of Open Access Journals (Sweden)

    Giuliano Colosimo

    Full Text Available Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst =  0.117, p<<0.01. These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes.

  12. Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

    Directory of Open Access Journals (Sweden)

    Christine Dubreuil-Tranchant

    2011-01-01

    Full Text Available Miniature Inverted-repeat Transposable Elements (MITEs are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.

  13. Spectral Evidence for Hydrated Salts in Seasonal Brine Flows on Mars

    Science.gov (United States)

    Ojha, L.

    2015-12-01

    Recurring Slope Lineae (RSL) are narrow, low-reflectance features forming on present-day Mars that have been hypothesized to be due to the transient flow of liquid water. RSL extend incrementally downslope on steep, warm slopes, fade when inactive, and reappear annually over multiple Mars years as monitored by the HiRISE camera on board the Mars Reconnaissance Orbiter (MRO). In the southern mid-latitudes of Mars, RSL are observed to form most commonly on equator facing slopes, but in equatorial regions RSL often "follow the sun", forming and growing on slopes that receive the greatest insolation during a particular season. The temperature on slopes where RSL are active typically exceeds 250 K and often but not always exceeds 273 K, although sub-surface temperatures would be colder. These characteristics suggest a possible role of salts in lowering the freezing point of water, allowing briny solutions to flow. Confirmation of this wet origin hypothesis for RSL would require either (i) detection of liquid water absorptions on the surface, or (ii) detection of hydrated salts precipitated from that water. The mineralogical composition of RSL and their surroundings can be investigated using orbital data acquired by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) also on board MRO, which acquires spectral cubes with 544 spectral channels in the visible to near-infrared range of ~0.36 μm to 3.92 μm [13], within which both liquid water and hydrated salts have diagnostic absorption bands at ~1.4 μm, ~1.9 μm, ~3.0 μm. Additionally, hydrated salts may have combination of overtones at other wavelengths from 1.7 μm to 2.4 μm. We present results from examination of individual pixels containing RSL at four different sites that confirm the hypothesis that RSL are due to present-day activity of briny water.

  14. Temporal Variability from the Two-Component Advective Flow Solution and Its Observational Evidence

    Science.gov (United States)

    Dutta, Broja G.; Chakrabarti, Sandip K.

    2016-09-01

    In the propagating oscillatory shock model, the oscillation of the post-shock region, i.e., the Compton cloud, causes the observed low-frequency quasi-periodic oscillations (QPOs). The evolution of QPO frequency is explained by the systematic variation of the Compton cloud size, i.e., the steady radial movement of the shock front, which is triggered by the cooling of the post-shock region. Thus, analysis of the energy-dependent temporal properties in different variability timescales can diagnose the dynamics and geometry of accretion flows around black holes. We study these properties for the high-inclination black hole source XTE J1550-564 during its 1998 outburst and the low-inclination black hole source GX 339-4 during its 2006-07 outburst using RXTE/PCA data, and we find that they can satisfactorily explain the time lags associated with the QPOs from these systems. We find a smooth decrease of the time lag as a function of time in the rising phase of both sources. In the declining phase, the time lag increases with time. We find a systematic evolution of QPO frequency and hard lags in these outbursts. In XTE J1550-564, the lag changes from hard to soft (i.e., from a positive to a negative value) at a crossing frequency (ν c) of ˜3.4 Hz. We present possible mechanisms to explain the lag behavior of high and low-inclination sources within the framework of a single two-component advective flow model.

  15. Molecular evidence of lateral gene transfer in rpoB gene of Mycobacterium yongonense strains via multilocus sequence analysis.

    Directory of Open Access Journals (Sweden)

    Byoung-Jun Kim

    Full Text Available Recently, a novel species, Mycobacterium yongonense (DSM 45126(T, was introduced and while it is phylogenetically related to Mycobacterium intracellulare, it has a distinct RNA polymerase β-subunit gene (rpoB sequence that is identical to that of Mycobacterium parascrofulaceum, which is a distantly related scotochromogen, which suggests the acquisition of the rpoB gene via a potential lateral gene transfer (LGT event. The aims of this study are to prove the presence of the LGT event in the rpoB gene of the M. yongonense strains via multilocus sequence analysis (MLSA. In order to determine the potential of an LGT event in the rpoB gene of the M. yongonense, the MLSA based on full rpoB sequences (3447 or 3450 bp and on partial sequences of five other targets [16S rRNA (1383 or 1395 bp, hsp65 (603 bp, dnaJ (192 bp, recA (1053 bp, and sodA (501 bp] were conducted. Incongruences between the phylogenetic analysis of the full rpoB and the five other genes in a total of three M. yongonense strains [two clinical strains (MOTT-12 and MOTT-27 and one type strain (DSM 45126(T] were observed, suggesting that rpoB gene of three M. yongonense strains may have been acquired very recently via an LGT event from M. parascrofulaceum, which is a distantly related scotochromogen.

  16. Relating diseases by integrating gene associations and information flow through protein interaction network.

    Science.gov (United States)

    Hamaneh, Mehdi Bagheri; Yu, Yi-Kuo

    2014-01-01

    Identifying similar diseases could potentially provide deeper understanding of their underlying causes, and may even hint at possible treatments. For this purpose, it is necessary to have a similarity measure that reflects the underpinning molecular interactions and biological pathways. We have thus devised a network-based measure that can partially fulfill this goal. Our method assigns weights to all proteins (and consequently their encoding genes) by using information flow from a disease to the protein interaction network and back. Similarity between two diseases is then defined as the cosine of the angle between their corresponding weight vectors. The proposed method also provides a way to suggest disease-pathway associations by using the weights assigned to the genes to perform enrichment analysis for each disease. By calculating pairwise similarities between 2534 diseases, we show that our disease similarity measure is strongly correlated with the probability of finding the diseases in the same disease family and, more importantly, sharing biological pathways. We have also compared our results to those of MimMiner, a text-mining method that assigns pairwise similarity scores to diseases. We find the results of the two methods to be complementary. It is also shown that clustering diseases based on their similarities and performing enrichment analysis for the cluster centers significantly increases the term association rate, suggesting that the cluster centers are better representatives for biological pathways than the diseases themselves. This lends support to the view that our similarity measure is a good indicator of relatedness of biological processes involved in causing the diseases. Although not needed for understanding this paper, the raw results are available for download for further study at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/DiseaseRelations/.

  17. Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations

    OpenAIRE

    Wang, Shuoguo; Lachance, Joseph; Tishkoff, Sarah A.; Hey, Jody; Xing, Jinchuan

    2013-01-01

    Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and modern humans descended from the Out-of-Africa (OOA) migration. Here, we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African mod...

  18. Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations

    NARCIS (Netherlands)

    Palsboll, PJ; Berube, M; Aguilar, A; Notarbartolo-Di-Sciara, G; Nielsen, R

    2004-01-01

    Genetic divergence among conspecific subpopulations can be due to either low recurrent gene flow or recent divergence and no gene flow. Here we present a modification of an earlier method developed by Nielsen and Wakeley (2001), which accommodates a finite-site mutation model, to assess which of the

  19. Investigating Pollen and Gene Flow of WYMV-Resistant Transgenic Wheat N12-1 Using a Dwarf Male-Sterile Line as the Pollen Receptor.

    Directory of Open Access Journals (Sweden)

    Shanshan Dong

    Full Text Available Pollen-mediated gene flow (PMGF is the main mode of transgene flow in flowering plants. The study of pollen and gene flow of transgenic wheat can help to establish the corresponding strategy for preventing transgene escape and contamination between compatible genotypes in wheat. To investigate the pollen dispersal and gene flow frequency in various directions and distances around the pollen source and detect the association between frequency of transgene flow and pollen density from transgenic wheat, a concentric circle design was adopted to conduct a field experiment using transgenic wheat with resistance to wheat yellow mosaic virus (WYMV as the pollen donor and dwarf male-sterile wheat as the pollen receptor. The results showed that the pollen and gene flow of transgenic wheat varied significantly among the different compass sectors. A higher pollen density and gene flow frequency was observed in the downwind SW and W sectors, with average frequencies of transgene flow of 26.37 and 23.69% respectively. The pollen and gene flow of transgenic wheat declined dramatically with increasing distance from its source. Most of the pollen grains concentrated within 5 m and only a few pollen grains were detected beyond 30 m. The percentage of transgene flow was the highest where adjacent to the pollen source, with an average of 48.24% for all eight compass directions at 0 m distance. Transgene flow was reduced to 50% and 95% between 1.61 to 3.15 m, and 10.71 to 20.93 m, respectively. Our results suggest that climate conditions, especially wind direction, may significantly affect pollen dispersal and gene flow of wheat. The isolation-by-distance model is one of the most effective methods for achieving stringent transgene confinement in wheat. The frequency of transgene flow is directly correlated with the relative density of GM pollen grains in air currents, and pollen competition may be a major factor influencing transgene flow.

  20. Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects

    Directory of Open Access Journals (Sweden)

    Cia-Hin Lau

    2012-01-01

    Full Text Available Epistasis (gene-gene interaction is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions between ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G and RETN (SNP-420C > G and SNP+299G > A gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM and metabolic syndrome (MS were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation.

  1. Self-recruitment and sweepstakes reproduction amid extensive gene flow in a coral-reef fish.

    Science.gov (United States)

    Christie, Mark R; Johnson, Darren W; Stallings, Christopher D; Hixon, Mark A

    2010-03-01

    Identifying patterns of larval dispersal within marine metapopulations is vital for effective fisheries management, appropriate marine reserve design, and conservation efforts. We employed genetic markers (microsatellites) to determine dispersal patterns in bicolour damselfish (Pomacentridae: Stegastes partitus). Tissue samples of 751 fish were collected in 2004 and 2005 from 11 sites encompassing the Exuma Sound, Bahamas. Bayesian parentage analysis identified two parent-offspring pairs, which is remarkable given the large population sizes and 28 day pelagic larval duration of bicolour damselfish. The two parent-offspring pairs directly documented self-recruitment at the two northern-most sites, one of which is a long-established marine reserve. Principal coordinates analyses of pair-wise relatedness values further indicated that self-recruitment was common in all sampled populations. Nevertheless, measures of genetic differentiation (F(ST)) and results from assignment methods suggested high levels of gene flow among populations. Comparisons of heterozygosity and relatedness among samples of adults and recruits indicated spatially and temporally independent sweepstakes events, whereby only a subset of adults successfully contribute to subsequent generations. These results indicate that self-recruitment and sweepstakes reproduction are the predominant, ecologically-relevant processes that shape patterns of larval dispersal in this system.

  2. Gene flow and maintenance of genetic diversity in invasive mosquitofish (Gambusia holbrooki.

    Directory of Open Access Journals (Sweden)

    David Díez-del-Molino

    Full Text Available Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations.

  3. Spatial genetic structure and restricted gene flow in bed bugs (Cimex lectularius) populations in France.

    Science.gov (United States)

    Akhoundi, Mohammad; Kengne, Pierre; Cannet, Arnaud; Brengues, Cécile; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Simard, Frederic; Fontenille, Didier; Delaunay, Pascal

    2015-08-01

    Bed bugs (Cimex lectularius) are resurgent blood-sucking ectoparasites that are currently increasing at a rapid rate, particularly in industrialized countries, such as France. Despite the rapid spread of bed bugs, there is a lack of knowledge concerning the population structure and gene flow among C. lectularius populations in France. To fill this gap, a genetic study was conducted using 183 C. lectularius from 14 populations of bed bugs collected in a hotel and in individual apartments in the French Riviera and in the Saint Ouen suburb of Paris. The samples were genotyped using an isolated set of six polymorphic microsatellite loci, including five new loci which were newly isolated and chosen based on prior successful amplification, and one previously described loci (bb15b). The low genetic diversity observed in the samples (of one to five alleles) suggested that most of prospected populations were established by only a few individuals, possibly from a single mated female. The overall genetic differentiation was high and statistically significant (FST=0.556, plectularius populations in France; however, the available information should be expanded in further studies.

  4. Adaptation with gene flow across the landscape in a dune sunflower.

    Science.gov (United States)

    Andrew, Rose L; Ostevik, Katherine L; Ebert, Daniel P; Rieseberg, Loren H

    2012-05-01

    Isolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance (IBD) and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We have studied the divergence of Helianthus petiolaris ecotypes living in active sand dunes and adjacent non-dune habitat, using landscape genetics approaches, such as circuit theory and multiple regression of distance matrices, in addition to coalescent modelling. Divergence between habitats was significant, but not strong, and was shaped by IBD. We expected that increased resistance owing to patchy and unfavourable habitat in the dunes would contribute to divergence. Instead, we found that landscape resistance models with lower resistance in the dunes performed well as predictors of genetic distances among subpopulations. Nevertheless, habitat class remained a strong predictor of genetic distance when controlling for isolation by resistance and IBD. We also measured environmental variables at each site and confirmed that specific variables, especially soil nitrogen and vegetation cover, explained a greater proportion of variance in genetic distance than did landscape or the habitat classification alone. Asymmetry in effective population sizes and numbers of migrants per generation was detected using coalescent modelling with Bayesian inference, which is consistent with incipient ecological speciation being driven by the dune habitat.

  5. Matching genetics with oceanography: directional gene flow in a Mediterranean fish species.

    Science.gov (United States)

    Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M

    2011-12-01

    Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. © 2011 Blackwell Publishing Ltd.

  6. Gene flow between insular, coastal and interior populations of brown bears in Alaska.

    Science.gov (United States)

    Paetkau, D; Shields, G F; Strobeck, C

    1998-10-01

    The brown bears of coastal Alaska have been recently regarded as comprising from one to three distinct genetic groups. We sampled brown bears from each of the regions for which hypotheses of genetic uniqueness have been made, including the bears of the Kodiak Archipelago and the bears of Admiralty, Baranof and Chichagof (ABC) Islands in southeast Alaska. These samples were analysed with a suite of nuclear microsatellite markers. The 'big brown bears' of coastal Alaska were found to be part of the continuous continental distribution of brown bears, and not genetically isolated from the physically smaller 'grizzly bears' of the interior. By contrast, Kodiak brown bears appear to have experienced little or no genetic exchange with continental populations in recent generations. The bears of the ABC Islands, which have previously been shown to undergo little or no female-mediated gene flow with mainland populations, were found not to be genetically isolated from mainland bears. The data from the four insular populations indicate that female and male dispersal can be reduced or eliminated by water barriers of 2-4 km and 7 km in width, respectively.

  7. Seismic evidence for flow in the hydrated mantle wedge of the Ryukyu subduction zone

    Science.gov (United States)

    Nagaya, Takayoshi; Walker, Andrew M.; Wookey, James; Wallis, Simon R.; Ishii, Kazuhiko; Kendall, J.-Michael

    2016-07-01

    It is widely accepted that water-rich serpentinite domains are commonly present in the mantle above shallow subducting slabs and play key roles in controlling the geochemical cycling and physical properties of subduction zones. Thermal and petrological models show the dominant serpentine mineral is antigorite. However, there is no good consensus on the amount, distribution and alignment of this mineral. Seismic velocities are commonly used to identify antigorite-rich domains, but antigorite is highly-anisotropic and depending on the seismic ray path, its properties can be very difficult to distinguish from non-hydrated olivine-rich mantle. Here, we utilize this anisotropy and show how an analysis of seismic anisotropy that incorporates measured ray path geometries in the Ryukyu arc can constrain the distribution, orientation and amount of antigorite. We find more than 54% of the wedge must consist of antigorite and the alignment must change from vertically aligned to parallel to the slab. This orientation change suggests convective flow in the hydrated forearc mantle. Shear wave splitting analysis in other subduction zones indicates large-scale serpentinization and forearc mantle convection are likely to be more widespread than generally recognized. The view that the forearc mantle of cold subduction zones is dry needs to be reassessed.

  8. Evidence for P-Glycoprotein Involvement in Cell Volume Regulation Using Coulter Sizing in Flow Cytometry.

    Science.gov (United States)

    Pasquier, Jennifer; Rioult, Damien; Abu-Kaoud, Nadine; Hoarau-Véchot, Jessica; Marin, Matthieu; Le Foll, Frank

    2015-06-24

    The regulation of cell volume is an essential function that is coupled to a variety of physiological processes such as receptor recycling, excitability and contraction, cell proliferation, migration, and programmed cell death. Under stress, cells undergo emergency swelling and respond to such a phenomenon with a regulatory volume decrease (RVD) where they release cellular ions, and other osmolytes as well as a concomitant loss of water. The link between P-glycoprotein, a transmembrane transporter, and cell volume regulation is controversial, and changes in cells volume are measured using microscopy or electrophysiology. For instance, by using the patch-clamp method, our team demonstrated that chloride currents activated in the RVD were more intense and rapid in a breast cancer cell line overexpressing the P-glycoprotein (P-gp). The Cell Lab Quanta SC is a flow cytometry system that simultaneously measures electronic volume, side scatter and three fluorescent colors; altogether this provides unsurpassed population resolution and accurate cell counting. Therefore, here we propose a novel method to follow cellular volume. By using the Coulter-type channel of the cytometer Cell Lab Quanta SC MPL (multi-platform loading), we demonstrated a role for the P-gp during different osmotic treatments, but also a differential activity of the P-gp through the cell cycle. Altogether, our data strongly suggests a role of P-gp in cell volume regulation.

  9. Temporal variability from the two-component advective flow solution and its observational evidence

    CERN Document Server

    Dutta, Broja G

    2016-01-01

    In the propagating oscillatory shock model, the oscillation of the post-shock region, i.e., the Compton cloud, causes the observed low-frequency quasi-periodic oscillations (QPOs). The evolution of QPO frequency is explained by the systematic variation of the Compton cloud size, i.e., the steady radial movement of the shock front, which is triggered by the cooling of the post-shock region. Thus, analysis of energy-dependent temporal properties in different variability time scales can diagnose the dynamics and geometry of accretion flows around black holes. We study these properties for the high inclination black hole source XTE J1550-564 during its 1998 outburst and the low-inclination black hole source GX 339-4 during its 2006-07 outburst using RXTE/PCA data, and we find that they can satisfactorily explain the time lags associated with the QPOs from these systems. We find a smooth decrease of the time lag as a function of time in the rising phase of both sources. In the declining phase the time lag increase...

  10. Evidence for P-Glycoprotein Involvement in Cell Volume Regulation Using Coulter Sizing in Flow Cytometry

    Directory of Open Access Journals (Sweden)

    Jennifer Pasquier

    2015-06-01

    Full Text Available The regulation of cell volume is an essential function that is coupled to a variety of physiological processes such as receptor recycling, excitability and contraction, cell proliferation, migration, and programmed cell death. Under stress, cells undergo emergency swelling and respond to such a phenomenon with a regulatory volume decrease (RVD where they release cellular ions, and other osmolytes as well as a concomitant loss of water. The link between P-glycoprotein, a transmembrane transporter, and cell volume regulation is controversial, and changes in cells volume are measured using microscopy or electrophysiology. For instance, by using the patch-clamp method, our team demonstrated that chloride currents activated in the RVD were more intense and rapid in a breast cancer cell line overexpressing the P-glycoprotein (P-gp. The Cell Lab Quanta SC is a flow cytometry system that simultaneously measures electronic volume, side scatter and three fluorescent colors; altogether this provides unsurpassed population resolution and accurate cell counting. Therefore, here we propose a novel method to follow cellular volume. By using the Coulter-type channel of the cytometer Cell Lab Quanta SC MPL (multi-platform loading, we demonstrated a role for the P-gp during different osmotic treatments, but also a differential activity of the P-gp through the cell cycle. Altogether, our data strongly suggests a role of P-gp in cell volume regulation.

  11. Strait of Gibraltar: an effective gene-flow barrier for wind-pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation.

    Science.gov (United States)

    Escudero, Marcial; Vargas, Pablo; Valcárcel, Virginia; Luceño, Modesto

    2008-06-01

    The Strait of Gibraltar is the most important barrier disconnecting the landmasses of Europe and Africa on the western Mediterranean extreme. Carex helodes is a wind-pollinated species endemic to the western Mediterranean. Because molecular and cytogenetic data allow the inference of its evolutionary history, we analyzed variations in chromosome number, including meiotic chromosome behavior, amplified fragment length polymorphism (AFLP) fingerprints, and nucleotide substitutions in plastid and nuclear DNA sequences. Cytogeographic results showed that the African populations have stabilized at a single chromosome number of 2n = 74, whereas the most frequent cytotype in Iberia is 2n = 72. Phylogenetic reconstructions of 17 sequences from nine closely related species revealed that C. helodes is monophyletic and that the Moroccan populations are embedded in the Iberian lineages. The haplotype network is also consistent with a European origin of the northern African haplotype. AFLP analysis also revealed hierarchical levels of genetic variation compatible with a founder effect process responsible for the African populations. All sources of evidence support the hypothesis that the Strait of Gibraltar has been an effective gene-flow barrier, generating two isolated evolutionary lineages after their dispersal. Recent connections between the two lineages appear unlikely, whereas active gene flow occurs among populations within the two lineages.

  12. Association between BHMT gene rs3733890 polymorphism and cancer risk: evidence from a meta-analysis

    Directory of Open Access Journals (Sweden)

    Xu Y

    2016-08-01

    : Our results have shown no obvious evidence that rs3733890 polymorphism in BHMT gene affected the susceptibility of head and neck squamous cell carcinoma, breast cancer, ovarian cancer, colorectal adenoma, and liver cancer. In contrast, we found the protective role of BHMT–742G>A polymorphism in uterine cervical cancer incidence. Future well-designed studies comprising larger sample size are warranted to verify our findings. Keywords: BHMT, polymorphism, cancer risk, susceptibility, meta-analysis

  13. Hydrothermal dolomites in SW Sardinia (Italy): evidence for a widespread late-Variscan fluid flow event

    Science.gov (United States)

    Boni, M.; Parente, G.; Bechstädt, T.; De Vivo, B.; Iannace, A.

    2000-03-01

    Epigenetic replacive and saddle dolomite, frequently forming zebra structures (Geodic dolomite), affected Cambrian limestones and early diagenetic dolomites across large areas of the Iglesiente-Sulcis mining district (SW Sardinia, Italy). The dolomite crops out in an area of more than 500 km 2 and reaches a thickness of up to 600 m (or even more). This rock represents one of the most extensive dolomites of epigenetic origin yet documented. Prior to dolomitization, the Cambrian carbonates underwent ductile deformation and greenschist facies metamorphism. The same is true for the overlying tectonic nappes. Fluid inclusion analysis combined with O- and Sr-isotope data indicate that the dolomitizing fluid can be categorized as a "basinal brine". The spread in homogenization temperatures shows a gradient with values decreasing from east to west. The higher temperatures (mean of around 100°C) have been measured in eastern parts of the Iglesiente area, whereas the lowermost temperatures (mean of about 85°C) have been found along the western coast of Iglesiente. This fluid certainly can neither have come directly from the low-grade metamorphic lithotypes undergoing dolomitization, nor from the low-temperature metamorphic rocks within the overlying nappes. It is assumed that a late-Variscan hydrothermal event, which coincided with extensional tectonics, set brine circulation into motion. Dolomitization may have occurred within circulation cells, which were driven by high heat flow. Fluids originated in the underlying rocks and circulated upward to affect the overlying Cambrian carbonates. An alternative model is that the dolomitization was caused by hydrothermal brines that originated within basinal areas of the Variscan orogenic pile circulating deep within the crust, and ascended in the External Zone (Iglesiente-Sulcis). Whatever the origin, these reducing saline fluids, which carried radiogenic Sr, dolomitized a large volume of Early Paleozoic rocks. The many

  14. Evidence for the role of cyclic electron flow in photoprotection for oxygen-evolving complex.

    Science.gov (United States)

    Huang, Wei; Yang, Ying-Jie; Hu, Hong; Zhang, Shi-Bao; Cao, Kun-Fang

    2016-05-01

    Cyclic electron flow (CEF) alleviates PSII photo-inhibition under high light by at least two different mechanisms: one is liked to thermal energy dissipation (qE) and the other one is independent of qE. However, the latter mechanism is unclear. Because the photodamage to PSII primarily occurred at the oxygen-evolving complex (OEC), and the stability of OEC is dependent on proton gradient across thylakoid membrane (ΔpH), we hypothesize that the CEF-dependent generation of ΔpH can alleviate photodamage to OEC. To test this hypothesis, we determined the effects of antimycin A (AA), methyl viologen (MV), chloramphenicol (CM), nigericin (Nig) on PSII activity and the stability of OEC for leaves of a light-demanding tropical tree species Erythrophleum guineense by the analysis of OKJIP chlorophyll a fluorescence transient. After high light treatment, the stronger decrease in Fv/Fm in the AA-, CM-, MV-, and Nig-treated samples was accompanied with larger photo damage of OEC. The AA-treated samples significantly showed lower CEF activity than the H2O-treated samples. Although the AA-treated leaves significantly showed stronger PSII photo-inhibition and photo-damage of OEC compared to the H2O-treated leaves, the value of non-photochemical quenching did not differ between them. Therefore, CEF activity was partly inhibited in the AA-treated samples, and the stronger PSII photo-inhibition in the AA-treated leaves was independent of qE. Taking together, we propose a hypothesis that CEF-dependent generation of ΔpH under high light plays an important role in photoprotection for the OEC activity.

  15. Evidence of low dimensional chaos in renal blood flow control in genetic and experimental hypertension

    Science.gov (United States)

    Yip, K.-P.; Marsh, D. J.; Holstein-Rathlou, N.-H.

    1995-01-01

    We applied a surrogate data technique to test for nonlinear structure in spontaneous fluctuations of hydrostatic pressure in renal tubules of hypertensive rats. Tubular pressure oscillates at 0.03-0.05 Hz in animals with normal blood pressure, but the fluctuations become irregular with chronic hypertension. Using time series from rats with hypertension we produced surrogate data sets to test whether they represent linearly correlated noise or ‘static’ nonlinear transforms of a linear stochastic process. The correlation dimension and the forecasting error were used as discriminating statistics to compare surrogate with experimental data. The results show that the original experimental time series can be distinguished from both linearly and static nonlinearly correlated noise, indicating that the nonlinear behavior is due to the intrinsic dynamics of the system. Together with other evidence this strongly suggests that a low dimensional chaotic attractor governs renal hemodynamics in hypertension. This appears to be the first demonstration of a transition to chaotic dynamics in an integrated physiological control system occurring in association with a pathological condition.

  16. Migration between continents: geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota).

    Science.gov (United States)

    Buschbom, Jutta

    2007-05-01

    Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.

  17. The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.

    Science.gov (United States)

    Ferchaud, Anne-Laure; Hansen, Michael M

    2016-01-01

    Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three-spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the

  18. Amoebozoans Are Secretly but Ancestrally Sexual: Evidence for Sex Genes and Potential Novel Crossover Pathways in Diverse Groups of Amoebae

    Science.gov (United States)

    Wood, Fiona C.; Katz, Laura A.; Cerón-Romero, Mario A.; Gorfu, Lydia A.

    2017-01-01

    Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study, we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade. We analyzed genomic and transcriptomic data of 39 amoebozoans representing all major subclades of Amoebozoa. Our results show that Amoebozoa possess most of the genes exclusive to meiosis but lack genes encoding synaptonemal complex (SC). The absence of SC genes is discussed in the context of earlier studies that reported ultrastructural evidence of SC in some amoebae. We also find interclade and intrageneric variation in sex gene distribution, indicating diversity in sexual pathways in the group. Particularly, members of Mycetozoa engage in a novel sexual pathway independent of the universally conserved meiosis initiator gene, SPO11. Our findings strongly suggest that not only do amoebozoans possess sex genes in their genomes, but also, based on the transcriptome evidence, the present sex genes are functional. We conclude that Amoebozoa is ancestrally sexual, contrary to the long held belief that most of its members are asexual. Thus, asexuality in Amoebozoa, if confirmed to be present, is a derived-trait that appeared later in their evolution. PMID:28087686

  19. Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes.

    OpenAIRE

    Kejnovský, E; Vrána, J; Matsunaga, S.; Soucek, P.; Siroký, J; Dolezel, J; Vyskot, B

    2001-01-01

    The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that ...

  20. Mapping of the Sca1 and pcd genes on mouse chromosome 13 provides evidence that they are different genes

    Energy Technology Data Exchange (ETDEWEB)

    Servadio, A.; McCall, A.; Zoghbi, H. [Baylor College of Medicine, Houston, TX (United States); Eicher, E.M. [Jackson Laboratory, Bar Harbor, ME (United States)

    1995-10-10

    It is well established that large chromosomal segments have remained intact during the evolution of different mammalian species. Thus, mapping information for a gene in mammalian species facilitates mapping the same gene in another mammalian species. In addition, phenotypically similar diseases that map to linkage conserved regions in two species may be caused by mutations in the same gene. Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited human disorder characterized by progressive ataxia, dysarthria, and dysmetria. SCA1 maps to the short arm of human chromosome (Chr) 6 in the 6p23-p22 region. SCA1 is caused by the expansion of an unstable CAG repeat located within the coding region of a novel protein, ataxin-1, Purkinje cell degeneration (pcd) is a recessively inherited mouse disorder characterized by a moderate ataxia, usually noted by 3-4 weeks of age. Progressive degeneration of Purkinje cells is the underlying pathogenesis in this disorder. The pcd gene was assigned to mouse Chr 13 because it showed linkage to extra toes (Xt) and pearl (pe). Some doubt about this assignment existed, however, because the calculated genetic distance between pcd and Xt was 32 cM and that between pcd and pe was 18 cM. If pcd is located in Chr 13, its placement relative to Xt and pe suggests that it would be located in the region that shares linkage homology with the region that shares linkage homology with the region of human Chr 6 that contains SCA1. Here, we present data that confirm the assignment of pcd to Chr 13, map the mouse Sca1 gene to Chr 13, and eliminate Sca1 as a candidate gene for pcd. 11 refs., 1 tab.

  1. Antigen stimulation of peripheral blood mononuclear cells from Mycobacterium bovis infected cattle yields evidence for a novel gene expression program

    Directory of Open Access Journals (Sweden)

    Zhao Yingdong

    2008-09-01

    Full Text Available Abstract Background Bovine tuberculosis (BTB caused by Mycobacterium bovis continues to cause substantial losses to global agriculture and has significant repercussions for human health. The advent of high throughput genomics has facilitated large scale gene expression analyses that present a novel opportunity for revealing the molecular mechanisms underlying mycobacterial infection. Using this approach, we have previously shown that innate immune genes in peripheral blood mononuclear cells (PBMC from BTB-infected animals are repressed in vivo in the absence of exogenous antigen stimulation. In the present study, we hypothesized that the PBMC from BTB-infected cattle would display a distinct gene expression program resulting from exposure to M. bovis. A functional genomics approach was used to examine the immune response of BTB-infected (n = 6 and healthy control (n = 6 cattle to stimulation with bovine tuberculin (purified protein derivative – PPD-b in vitro. PBMC were harvested before, and at 3 h and 12 h post in vitro stimulation with bovine tuberculin. Gene expression changes were catalogued within each group using a reference hybridization design and a targeted immunospecific cDNA microarray platform (BOTL-5 with 4,800 spot features representing 1,391 genes. Results 250 gene spot features were significantly differentially expressed in BTB-infected animals at 3 h post-stimulation contrasting with only 88 gene spot features in the non-infected control animals (P ≤ 0.05. At 12 h post-stimulation, 56 and 80 gene spot features were differentially expressed in both groups respectively. The results provided evidence of a proinflammatory gene expression profile in PBMC from BTB-infected animals in response to antigen stimulation. Furthermore, a common panel of eighteen genes, including transcription factors were significantly expressed in opposite directions in both groups. Real-time quantitative reverse transcription PCR (qRT-PCR demonstrated

  2. Information flow in networks and the law of diminishing marginal returns: evidence from modeling and human electroencephalographic recordings.

    Directory of Open Access Journals (Sweden)

    Daniele Marinazzo

    Full Text Available We analyze simple dynamical network models which describe the limited capacity of nodes to process the input information. For a proper range of their parameters, the information flow pattern in these models is characterized by exponential distribution of the incoming information and a fat-tailed distribution of the outgoing information, as a signature of the law of diminishing marginal returns. We apply this analysis to effective connectivity networks from human EEG signals, obtained by Granger Causality, which has recently been given an interpretation in the framework of information theory. From the distributions of the incoming versus the outgoing values of the information flow it is evident that the incoming information is exponentially distributed whilst the outgoing information shows a fat tail. This suggests that overall brain effective connectivity networks may also be considered in the light of the law of diminishing marginal returns. Interestingly, this pattern is reproduced locally but with a clear modulation: a topographic analysis has also been made considering the distribution of incoming and outgoing values at each electrode, suggesting a functional role for this phenomenon.

  3. Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems.

    Science.gov (United States)

    Pitta, Dipti W; Dou, Zhengxia; Kumar, Sanjay; Indugu, Nagaraju; Toth, John Daniel; Vecchiarelli, Bonnie; Bhukya, Bhima

    2016-06-01

    Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms, but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment through manure, and to this end, we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm. Broadly, the identified AR genes were associated with 18 antibiotic resistances classes across all samples; however, the most abundant genes were classified under multidrug transporters (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%), and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms. Farm 09 was categorized as a high risk farm, as a greater proportion of AR genes were common to at least three sectors, suggesting possible horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.

  4. Characterization of genes encoding poly(A polymerases in plants: evidence for duplication and functional specialization.

    Directory of Open Access Journals (Sweden)

    Lisa R Meeks

    Full Text Available BACKGROUND: Poly(A polymerase is a key enzyme in the machinery that mediates mRNA 3' end formation in eukaryotes. In plants, poly(A polymerases are encoded by modest gene families. To better understand this multiplicity of genes, poly(A polymerase-encoding genes from several other plants, as well as from Selaginella, Physcomitrella, and Chlamydomonas, were studied. METHODOLOGY/PRINCIPAL FINDINGS: Using bioinformatics tools, poly(A polymerase-encoding genes were identified in the genomes of eight species in the plant lineage. Whereas Chlamydomonas reinhardtii was found to possess a single poly(A polymerase gene, other species possessed between two and six possible poly(A polymerase genes. With the exception of four intron-lacking genes, all of the plant poly(A polymerase genes (but not the C. reinhardtii gene possessed almost identical intron positions within the poly(A polymerase coding sequences, suggesting that all plant poly(A polymerase genes derive from a single ancestral gene. The four Arabidopsis poly(A polymerase genes were found to be essential, based on genetic analysis of T-DNA insertion mutants. GFP fusion proteins containing three of the four Arabidopsis poly(A polymerases localized to the nucleus, while one such fusion protein was localized in the cytoplasm. The fact that this latter protein is largely pollen-specific suggests that it has important roles in male gametogenesis. CONCLUSIONS/SIGNIFICANCE: Our results indicate that poly(A polymerase genes have expanded from a single ancestral gene by a series of duplication events during the evolution of higher plants, and that individual members have undergone sorts of functional specialization so as to render them essential for plant growth and development. Perhaps the most interesting of the plant poly(A polymerases is a novel cytoplasmic poly(A polymerase that is expressed in pollen in Arabidopsis; this is reminiscent of spermatocyte-specific cytoplasmic poly(A polymerases in

  5. Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene

    NARCIS (Netherlands)

    L.M. 't Hart (Leen); H.A.P. Pols (Huib); T. Hansen (Torben); I. Rietveld (Ingrid); J.M. Dekker (Jacqueline); J.A. Maassen (Johannes); M.G.A.A.M. Nijpels (Giel); G.M.C. Janssen (George); P.P. Arp (Pascal); R.J. Heine (Robert); A.G. Uitterlinden (André); T. Jorgensen (Torben); C.M. van Duijn (Cock); K. Borch-Johnsen; O. Pedersen (Oluf)

    2005-01-01

    textabstractPreviously, we have shown that a mutation in the mitochondrial DNA-encoded tRNA(Leu(UUR)) gene is associated with type 2 diabetes. One of the consequences of this mutation is a reduced aminoacylation of tRNA(Leu(UUR)). In this study, we have examined whether variants in the leucyl tRNA s

  6. Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene

    DEFF Research Database (Denmark)

    hart, Leen M; Hansen, Torben; Rietveld, Ingrid

    2005-01-01

    Previously, we have shown that a mutation in the mitochondrial DNA-encoded tRNA(Leu(UUR)) gene is associated with type 2 diabetes. One of the consequences of this mutation is a reduced aminoacylation of tRNA(Leu(UUR)). In this study, we have examined whether variants in the leucyl tRNA synthetase...

  7. Gene flow, subspecies composition, and dengue virus-2 susceptibility among Aedes aegypti collections in Senegal.

    Directory of Open Access Journals (Sweden)

    Massamba Sylla

    Full Text Available BACKGROUND: Aedes aegypti, the "yellow fever mosquito", is the primary vector to humans of the four serotypes of dengue viruses (DENV1-4 and yellow fever virus (YFV and is a known vector of Chikungunya virus. There are two recognized subspecies of Ae. aegypti sensu latu (s.l.: the presumed ancestral form, Ae. aegypti formosus (Aaf, a primarily sylvan mosquito in sub-Saharan Africa, and Ae. aegypti aegypti (Aaa, found globally in tropical and subtropical regions typically in association with humans. The designation of Ae. aegypti s.l. subspecies arose from observations made in East Africa in the late 1950s that the frequency of pale "forms" of Ae. aegypti was higher in populations in and around human dwellings than in those of the nearby bush. But few studies have been made of Ae. aegypti s.l. in West Africa. To address this deficiency we have been studying the population genetics, subspecies composition and vector competence for DENV-2 of Ae. aegypti s.l. in Senegal. METHODS AND FINDINGS: A population genetic analysis of gene flow was conducted among 1,040 Aedes aegypti s.l. from 19 collections distributed across the five phytogeographic regions of Senegal. Adults lacking pale scales on their first abdominal tergite were classified as Aedes aegypti formosus (Aaf following the original description of the subspecies and the remainder were classified as Aedes aegypti aegypti (Aaa. There was a clear northwest-southeast cline in the abundance of Aaa and Aaf. Collections from the northern Sahelian region contained only Aaa while southern Forest gallery collections contained only Aaf. The two subspecies occurred in sympatry in four collections north of the Gambia in the central Savannah region and Aaa was a minor component of two collections from the Forest gallery area. Mosquitoes from 11 collections were orally challenged with DENV-2 virus. In agreement with the early literature, Aaf had significantly lower vector competence than Aaa. Among pure Aaa

  8. Bacterial characterization of Beijing drinking water by flow cytometry and MiSeq sequencing of the 16S rRNA gene.

    Science.gov (United States)

    Liu, Tingting; Kong, Weiwen; Chen, Nan; Zhu, Jing; Wang, Jingqi; He, Xiaoqing; Jin, Yi

    2016-02-01

    Flow cytometry (FCM) and 16S rRNA gene sequencing data are commonly used to monitor and characterize microbial differences in drinking water distribution systems. In this study, to assess microbial differences in drinking water distribution systems, 12 water samples from different sources water (groundwater, GW; surface water, SW) were analyzed by FCM, heterotrophic plate count (HPC), and 16S rRNA gene sequencing. FCM intact cell concentrations varied from 2.2 × 10(3) cells/mL to 1.6 × 10(4) cells/mL in the network. Characteristics of each water sample were also observed by FCM fluorescence fingerprint analysis. 16S rRNA gene sequencing showed that Proteobacteria (76.9-42.3%) or Cyanobacteria (42.0-3.1%) was most abundant among samples. Proteobacteria were abundant in samples containing chlorine, indicating resistance to disinfection. Interestingly, Mycobacterium, Corynebacterium, and Pseudomonas, were detected in drinking water distribution systems. There was no evidence that these microorganisms represented a health concern through water consumption by the general population. However, they provided a health risk for special crowd, such as the elderly or infants, patients with burns and immune-compromised people exposed by drinking. The combined use of FCM to detect total bacteria concentrations and sequencing to determine the relative abundance of pathogenic bacteria resulted in the quantitative evaluation of drinking water distribution systems. Knowledge regarding the concentration of opportunistic pathogenic bacteria will be particularly useful for epidemiological studies.

  9. Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance.

    Science.gov (United States)

    Beesley, Nicola J; Williams, Diana J L; Paterson, Steve; Hodgkinson, Jane

    2017-01-01

    Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.

  10. Gene flow rise with habitat fragmentation in the bog fritillary butterfly (Lepidoptera: Nymphalidae

    Directory of Open Access Journals (Sweden)

    Descimon Henri

    2008-03-01

    Full Text Available Abstract Background The main components of the spatial genetic structure of the populations are neighbourhood size and isolation by distance. These may be inferred from the allele frequencies across a series of populations within a region. Here, the spatial population structure of Proclossiana eunomia was investigated in two mountainous areas of southern Europe (Asturias, Spain and Pyrenees, France and in two areas of intermediate elevation (Morvan, France and Ardennes, Belgium. Results A total of eight polymorphic loci were scored by allozyme electrophoresis, revealing a higher polymorphism in the populations of southern Europe than in those of central Europe. Isolation by distance effect was much stronger in the two mountain ranges (Pyrenees and Asturias than in the two areas of lower elevation (Ardennes and Morvan. By contrast, the neighbourhood size estimates were smaller in the Ardennes and in the Morvan than in the two high mountain areas, indicating more common movements between neighbouring patches in the mountains than in plains. Conclusion Short and long dispersal events are two phenomena with distinct consequences in the population genetics of natural populations. The differences in level of population differentiation within each the four regions may be explained by change in dispersal in lowland recently fragmented landscapes: on average, butterflies disperse to a shorter distance but the few ones which disperse long distance do so more efficiently. Habitat fragmentation has evolutionary consequences exceeding by far the selection of dispersal related traits: the balance between local specialisation and gene flow would be perturbed, which would modify the extent to which populations are adapted to heterogeneous environments.

  11. Differentiation and Gene Flow among European Populations of Leishmania infantum MON-1

    Science.gov (United States)

    Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A.; Schönian, Gabriele

    2008-01-01

    Background Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. Methodology/Principal Findings We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups—MON-1 and non-MON-1—could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands–Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. Conclusion In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological

  12. How much gene flow is needed to avoid inbreeding depression in wild tiger populations?

    Science.gov (United States)

    Kenney, John; Allendorf, Fred W; McDougal, Charles; Smith, James L D

    2014-08-22

    The number and size of tiger populations continue to decline owing to habitat loss, habitat fragmentation and poaching of tigers and their prey. As a result, tiger populations have become small and highly structured. Current populations have been isolated since the early 1970s or for approximately seven generations. The objective of this study is to explore how inbreeding may be affecting the persistence of remaining tiger populations and how dispersal, either natural or artificial, may reduce the potentially detrimental effect of inbreeding depression. We developed a tiger simulation model and used published levels of genetic load in mammals to simulate inbreeding depression. Following a 50 year period of population isolation, we introduced one to four dispersing male tigers per generation to explore how gene flow from nearby populations may reduce the negative impact of inbreeding depression. For the smallest populations, even four dispersing male tigers per generation did not increase population viability, and the likelihood of extinction is more than 90% within 30 years. Unless habitat connectivity is restored or animals are artificially introduced in the next 70 years, medium size wild populations are also likely to go extinct, with only four to five of the largest wild tiger populations likely to remain extant in this same period without intervention. To reduce the risk of local extinction, habitat connectivity must be pursued concurrently with efforts to increase population size (e.g. enhance habitat quality, increase habitat availability). It is critical that infrastructure development, dam construction and other similar projects are planned appropriately so that they do not erode the extent or quality of habitat for these populations so that they can truly serve as future source populations. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  13. Prezygotic barriers to gene flow between Taraxacum ceratophorum and the invasive Taraxacum officinale (Asteraceae).

    Science.gov (United States)

    Brock, Marcus T

    2009-08-01

    Prezygotic reproductive barriers limit interspecific gene flow between congeners. Here, I examine the strength of floral isolation and interspecific pollen-pistil barriers between an invasive apomictic, Taraxacum officinale, and the indigenous sexual alpine dandelion, Taraxacum ceratophorum. Experimental arrays of either native inflorescences or a mixture of native and exotic inflorescences were used to examine insect preference and to track movement of a pollen analog. Using hand-pollinations, conspecific and heterospecific pollen germination success on native stigmas was compared. To additionally test for interspecific pollen competition, T. ceratophorum plants received one of three possible hand-pollinations: control conspecific pollination, concomitant conspecific and heterospecific pollination (mixed), or conspecific pollen followed by heterospecific pollen 15 min later (staggered). Floral isolation was negligible as no insect preference was detected. On a presence/absence basis, florets on native inflorescences received slightly less pollen analog from heterospecific donors than from conspecific donors; however, the amount of dye particles transferred from either Taraxacum species to stigmas on recipient T. ceratophorum inflorescences was equivalent. In contrast to weak floral isolation, strong pollen germination and pollen competition barriers should reduce the potential for hybridization. Heterospecific T. officinale pollen exhibited reduced germination success on T. ceratophorum stigmas in comparison to conspecific pollen. Furthermore, a significant pollen-competition effect on the percentage of hybrid offspring was detected only when T. officinale preceded T. ceratophorum pollen by 15 min. This result indicates that conspecific pollen out-competes heterospecific pollen but further suggests that biotic and abiotic factors reducing pollen accrual rates may partially remove barriers to natural hybridization.

  14. Genetic differentiation and gene flow among six sheep breeds of Mongolian group in China

    Institute of Scientific and Technical Information of China (English)

    Yan GENG; Zhangping YANG; Hong CHANG; Yongjiang MAO; Wei SUN; Xiaoya GUO; Dongyan QU

    2008-01-01

    The level of genetic differentiation,gene flow and the relationship between geographical distance and genetic differentiation among six sheep populations of Mongolian group in China (Tong sheep,small-tailed Han sheep,Hu sheep,Tan sheep,Ujumuqin sheep and Bayinbuluk sheep) were analyzed using seven microsatellites.The trees were constructed from diversity coefficient (DC) distances among the six sheep populations.The overall heterozygote deficit across all the populations (Fit) was between 0.167 (OarAE101) and 0.044 (MAF33).The overall significant deficit of heterozygote,because of inbreeding within breeds,(Fis) was between 0.089 (OarFCB304) and 0.005 (MAF33).The coefficient of genetic differentiation (Fst) was between 0.100 (OarAE101) and 0.022 (Oar-FCB48).It indicated that 3.9% of the total genetic variation could be explained by breed differences and the remaining 96.1% by differences among individuals for each population.This illustrated that most variations existed within breeds and genetic differentiation level were very low among sheep breeds of the Mongolian Group in China.The average number of effective migrants exchanged per generation (Nem) ranged from 2.7369 (Tan sheep and Bayinbuluk sheep) to 44.3928 (Tong sheep and Hu sheep),and the mean value was 11.25213.Significantly positive relationships between the level of genetic differentiation and geographical distance and genetic distances were detected.It is concluded that genetic differentiation of sheep breeds of Mongolian group in China is mainly the result of natural selection (different living conditions).

  15. Divergence with gene flow across a speciation continuum of Heliconius butterflies.

    Science.gov (United States)

    Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

    2015-09-24

    A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

  16. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Science.gov (United States)

    Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A; Schönian, Gabriele

    2008-07-09

    Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands-Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological investigations.

  17. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Directory of Open Access Journals (Sweden)

    Katrin Kuhls

    Full Text Available BACKGROUND: Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. METHODOLOGY/PRINCIPAL FINDINGS: We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1 Greece; (2 Spain islands-Majorca/Ibiza; (3 mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. CONCLUSION: In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further

  18. Crossing the threshold: gene flow, dominance and the critical level of standing genetic variation required for adaptation to novel environments.

    Science.gov (United States)

    Nuismer, S L; MacPherson, A; Rosenblum, E B

    2012-12-01

    Genetic architecture plays an important role in the process of adaptation to novel environments. One example is the role of allelic dominance, where advantageous recessive mutations have a lower probability of fixation than advantageous dominant mutations. This classic observation, termed 'Haldane's sieve', has been well explored theoretically for single isolated populations adapting to new selective regimes. However, the role of dominance is less well understood for peripheral populations adapting to novel environments in the face of recurrent and maladaptive gene flow. Here, we use a combination of analytical approximations and individual-based simulations to explore how dominance influences the likelihood of adaptation to novel peripheral environments. We demonstrate that in the face of recurrent maladaptive gene flow, recessive alleles can fuel adaptation only when their frequency exceeds a critical threshold within the ancestral range.

  19. Gene flow among Anopheles albimanus populations in Central America, South America, and the Caribbean assessed by microsatellites and mitochondrial DNA.

    Science.gov (United States)

    Molina-Cruz, Alvaro; de Mérida, Ana María P; Mills, Katherine; Rodríguez, Fernando; Schoua, Carolina; Yurrita, María Marta; Molina, Eduviges; Palmieri, Margarita; Black, William C

    2004-09-01

    Gene flow was examined among Anopheles albimanus populations from Cuba, Mexico, Guatemala, El Salvador, Nicaragua, Costa Rica, Panama, Colombia, and Venezuela by examining variation at four microsatellite (MS) loci and a mitochondrial DNA (mtDNA) marker. There was little variation among Central American populations and weak isolation by distance was only observed with the MS loci. There was moderate to large variation between Central and South American populations, suggesting a barrier to gene flow between Central and South America. However, Panamanian and Pacific Costa Rican populations differed with respect to western Central America, suggesting that there may be another barrier within Central America. There was small to moderate variation among Caribbean and continental populations. Phylogenetic and diversity analyses of mtDNA indicate that more ancestral and diverse haplotypes were present in the Caribbean population, suggesting that current continental An. albimanus populations may have originated from the Caribbean.

  20. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

      FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute...... for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  1. Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds

    Science.gov (United States)

    Lam, T. T. -Y.; Ip, H. S.; Ghedin, E.; Wentworth, D. E.; Halpin, R. A.; Stockwell, T. B.; Spiro, D. J.; Dusek, R. J.; Bortner, J. B.; Hoskins, J.; Bales, B. D.; Yparraguirre, D. R.; Holmes, E. C.

    2012-01-01

    Despite the importance of migratory birds in the ecology and evolution of avian influenza virus (AIV), there is a lack of information on the patterns of AIV spread at the intra-continental scale. We applied a variety of statistical phylogeographic techniques to a plethora of viral genome sequence data to determine the strength, pattern and determinants of gene flow in AIV sampled from wild birds in North America. These analyses revealed a clear isolation-by-distance of AIV among sampling localities. In addition, we show that phylogeographic models incorporating information on the avian flyway of sampling proved a better fit to the observed sequence data than those specifying homogeneous or random rates of gene flow among localities. In sum, these data strongly suggest that the intra-continental spread of AIV by migratory birds is subject to major ecological barriers, including spatial distance and avian flyway. ?? 2011 Blackwell Publishing Ltd/CNRS.

  2. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

    OpenAIRE

    Boothby, Thomas C; Tenlen, Jennifer R.; Smith, Frank W.; Wang, Jeremy R; Patanella, Kiera A.; Osborne Nishimura, Erin; Tintori, Sophia C.; Li, Qing; Jones, Corbin D.; Yandell, Mark; Messina, David N.; Glasscock, Jarret; Goldstein, Bob

    2015-01-01

    Despite fascinating scientists for over 200 years, little at the molecular level is known about tardigrades, microscopic animals resistant to extreme stresses. We present the genome of a tardigrade. Approximately one-sixth of the genes in the tardigrade genome were found to have been acquired through horizontal transfer, a proportion nearly double the proportion of previous known cases of extreme horizontal gene transfer (HGT) in animals. Foreign genes have impacted the composition of the tar...

  3. Isolation of two novel ras genes in Dictyostelium discoideum; evidence for a complex, developmentally regulated ras gene subfamily.

    Science.gov (United States)

    Daniel, J; Bush, J; Cardelli, J; Spiegelman, G B; Weeks, G

    1994-02-01

    In Dictyostelium discoideum, three ras genes (rasD, rasG and rasB) and one ras-related gene (rap1) have been previously isolated and characterized, and the deduced amino acid sequence of their predicted protein products share at least 50% sequence identity with the human H-Ras protein. We have now cloned and characterized two additional members of the ras gene subfamily in Dictyostelium, rasC and rasS. These genes are developmentally regulated and unlike the previously isolated Dictyostelium ras genes, maximum levels of their transcripts were detected during aggregation, suggesting that the encoded proteins have distinct functions during aggregation. The rasC cDNA encodes a 189 amino acid protein that is 65% identical to the Dictyostelium RasD and RasG proteins and 56% identical to the human H-Ras protein. The predicted 194 amino acid gene product encoded by rasS is 60% identical to the Dictyostelium RasD and RasG proteins and 54% identical to the human H-Ras protein. Whereas RasD, RasG, RasB and Rap1 are totally conserved in their putative effector domains relative to H-Ras, RasC and RasS have single amino acid substitutions in their effector domains, consistent with the idea that they have unique functions. In RasC, aspartic acid-38 has been replaced by asparagine (D38N), and in RasS, isoleucine-36 has been replaced by leucine (I36L). In addition, both proteins have several differences in the effector-proximal domain, a domain which is believed to play a role in Ras target activation. In RasC, there is a single conservative amino acid change in the canonical sequence of the binding site for the Ras-specific monoclonal antibody Y13-259, and consequently, RasC is less immunoreactive with the antibody than either of the Dictyostelium RasD or RasG proteins. In contrast, RasS, which has three substitutions in the Y13-259 binding site, does not react with the Y13-259 antibody.

  4. Oxytocin receptor gene methylation: converging multilevel evidence for a role in social anxiety

    National Research Council Canada - National Science Library

    Ziegler, Christiane; Dannlowski, Udo; Bräuer, David; Stevens, Stephan; Laeger, Inga; Wittmann, Hannah; Kugel, Harald; Dobel, Christian; Hurlemann, René; Reif, Andreas; Lesch, Klaus-Peter; Heindel, Walter; Kirschbaum, Clemens; Arolt, Volker; Gerlach, Alexander L; Hoyer, Jürgen; Deckert, Jürgen; Zwanzger, Peter; Domschke, Katharina

    2015-01-01

    .... This study-for the first time applying a multilevel epigenetic approach-investigates the role of OXTR gene methylation in categorical, dimensional, and intermediate neuroendocrinological/neural...

  5. Adaptive traits are maintained on steep selective gradients despite gene flow and hybridization in the intertidal zone.

    Directory of Open Access Journals (Sweden)

    Gerardo I Zardi

    Full Text Available Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients

  6. Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

    OpenAIRE

    2014-01-01

    Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. ...

  7. Adaptive Traits Are Maintained on Steep Selective Gradients despite Gene Flow and Hybridization in the Intertidal Zone

    Science.gov (United States)

    Canovas, Fernando; Ferreira Costa, Joana; Serrão, Ester A.; Pearson, Gareth A.

    2011-01-01

    Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia) population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal) was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients acts to maintain

  8. Adaptive traits are maintained on steep selective gradients despite gene flow and hybridization in the intertidal zone.

    Science.gov (United States)

    Zardi, Gerardo I; Nicastro, Katy R; Canovas, Fernando; Costa, Joana Ferreira; Serrão, Ester A; Pearson, Gareth A

    2011-01-01

    Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia) population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal) was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients acts to maintain

  9. Methylenetetrahydrofolate reductase gene C677T polymorphism and breast cancer risk: Evidence for genetic susceptibility.

    Science.gov (United States)

    Kumar, Pradeep; Yadav, Upendra; Rai, Vandana

    2015-12-01

    There are several evidences supporting the role of 5-10 methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms in breast cancer (BC). Case control association studies on breast cancer have been repeatedly performed over the last two decades, but results are inconsistent. We performed a meta-analysis to confirm the association between MTHFR C677T polymorphism and BC risk. The articles were retrieved by searching the PubMed, Google Scholar, and Springer Link databases. Crude odds ratios (OR) with 95% confidence intervals (CIs) was used to assess the strength of association between C677T polymorphism and BC. Publication bias was assessed by Egger's and Begg-Mazumdar tests. Meta-analysis was performed with Open Meta Analyst. Total 75 studies with 31,315 cases and 35, 608 controls were found suitable for the inclusion in the present meta-analysis. The results of meta-analysis suggested that there were moderate significant association between C677T polymorphism and BC risk using overall comparisons in five genetic models (T vs. C: OR = 1.08, 95% CI = 1.03-1.13, p = < 0.001; TT + CT vs. CC: OR = 1.06, 95% CI = 1.02-1.09, p = < 0.001; TT vs. CC: OR = 1.17, 95% CI = 1.06-1.28, p = 0.001; CT vs. CC OR = 1.05, 95% CI = 1.01-1.08, p = 0.005; TT vs. CT + CC: OR = 1.12, 95% CI = 1.03-1.22, p = 0.005). In conclusion, results of present meta-analysis showed modest association between MTHFR C677T polymorphism with breast cancer in total studies. However, sub-group analysis results based on ethnicity showed strong significant association between TT genotype and breast cancer (TT vs. CC; OR°=°1.26; 95% CI: 1.06-1.51; p = 0.009) in Asian population but in Caucasian population such association was not observed (TT vs. CC; OR°=°1.08; 95% CI: 0.99-1.14; p = 0.05).

  10. Gene Flow Results in High Genetic Similarity Between Sibiraea (Rosaceae species in the Qinghai-Tibetan Plateau

    Directory of Open Access Journals (Sweden)

    Peng-Cheng Fu

    2016-10-01

    Full Text Available Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of S. laevigata and S. angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45% rather than between species (4.39%. We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of these 2 species resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures between the species occurred.

  11. Genetic structure, mating system, and long-distance gene flow in heart of palm (Euterpe edulis Mart.).

    Science.gov (United States)

    Gaiotto, F A; Grattapaglia, D; Vencovsky, R

    2003-01-01

    We report a detailed analysis of the population genetic structure, mating system, and gene flow of heart of palm (Euterpe edulis Mart.-Arecaceae) in central Brazil. This palm is considered a keystone species because it supplies fruits for birds and rodents all year and is intensively harvested for culinary purposes. Two populations of this palm tree were examined, using 18 microsatellite loci. The species displays a predominantly outcrossed mating system (tm = 0.94), with a probability of full sibship greater than 70% within open-pollinated families. The following estimates of interpopulation genetic variation were calculated and found significant: FIT = 0.17, FIS = 0.12, FST = 0.06, and RST = 0.07. This low but significant level of interpopulation genetic variation indicates high levels of gene flow. Two adult trees were identified as likely seed parents (P > 99.9%) of juveniles located at a distance of 22 km. Gene flow over such distances has not been reported before for tropical tree species. The establishment and management of in situ genetic reserves or ex situ conservation and breeding populations for E. edulis should contemplate the collection of several hundreds open-pollinated maternal families from relatively few distant populations to maximize the genetic sampling of a larger number of pollen parents.

  12. A search theory model of patch-to-patch forager movement with application to pollinator-mediated gene flow.

    Science.gov (United States)

    Hoyle, Martin; Cresswell, James E

    2007-09-07

    We present a spatially implicit analytical model of forager movement, designed to address a simple scenario common in nature. We assume minimal depression of patch resources, and discrete foraging bouts, during which foragers fill to capacity. The model is particularly suitable for foragers that search systematically, foragers that deplete resources in a patch only incrementally, and for sit-and-wait foragers, where harvesting does not affect the rate of arrival of forage. Drawing on the theory of job search from microeconomics, we estimate the expected number of patches visited as a function of just two variables: the coefficient of variation of the rate of energy gain among patches, and the ratio of the expected time exploiting a randomly chosen patch and the expected time travelling between patches. We then consider the forager as a pollinator and apply our model to estimate gene flow. Under model assumptions, an upper bound for animal-mediated gene flow between natural plant populations is approximately proportional to the probability that the animal rejects a plant population. In addition, an upper bound for animal-mediated gene flow in any animal-pollinated agricultural crop from a genetically modified (GM) to a non-GM field is approximately proportional to the proportion of fields that are GM and the probability that the animal rejects a field.

  13. Landscape-scale deforestation decreases gene flow distance of a keystone tropical palm, Euterpe edulis Mart (Arecaceae).

    Science.gov (United States)

    Santos, Alesandro S; Cazetta, Eliana; Dodonov, Pavel; Faria, Deborah; Gaiotto, Fernanda A

    2016-09-01

    Habitat loss represents one of the main threats to tropical forests, which have reached extremely high rates of species extinction. Forest loss negatively impacts biodiversity, affecting ecological (e.g., seed dispersal) and genetic (e.g., genetic diversity and structure) processes. Therefore, understanding how deforestation influences genetic resources is strategic for conservation. Our aim was to empirically evaluate the effects of landscape-scale forest reduction on the spatial genetic structure and gene flow of Euterpe edulis Mart (Arecaceae), a palm tree considered a keystone resource for many vertebrate species. This study was carried out in nine forest remnants in the Atlantic Forest, northeastern Brazil, located in landscapes within a gradient of forest cover (19-83%). We collected leaves of 246 adults and 271 seedlings and performed genotyping using microsatellite markers. Our results showed that the palm populations had low spatial genetic structure, indicating that forest reduction did not influence this genetic parameter for neither seedlings nor adults. However, forest loss decreased the gene flow distance, which may negatively affect the genetic diversity of future generations by increasing the risk of local extinction of this keystone palm. For efficient strategies of genetic variability conservation and maintenance of gene flow in E. edulis, we recommend the maintenance of landscapes with intermediary to high levels of forest cover, that is, forest cover above 40%.

  14. Risk assessment of gene flow from genetically engineered virus resistant cassava to wild relatives in Africa: an expert panel report.

    Science.gov (United States)

    Hokanson, Karen E; Ellstrand, Norman C; Dixon, Alfred G O; Kulembeka, Heneriko P; Olsen, Kenneth M; Raybould, Alan

    2016-02-01

    The probability and consequences of gene flow to wild relatives is typically considered in the environmental risk assessment of genetically engineered crops. This is a report from a discussion by a group of experts who used a problem formulation approach to consider existing information for risk assessment of gene flow from cassava (Manihot esculenta) genetically engineered for virus resistance to the 'wild' (naturalized) relative M. glaziovii in East Africa. Two environmental harms were considered in this case: (1) loss of genetic diversity in the germplasm pool, and (2) loss of valued species, ecosystem resources, or crop yield and quality due to weediness or invasiveness of wild relatives. Based on existing information, it was concluded that gene flow will occur, but it is not likely that this will reduce the genetic diversity in the germplasm pool. There is little existing information about the impact of the virus in natural populations that could be used to inform a prediction about whether virus resistance would lead to an increase in reproduction or survival, hence abundance of M. glaziovii. However, an increase in the abundance of M. glaziovii should be manageable, and would not necessarily lead to the identified environmental harms.

  15. Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice.

    Science.gov (United States)

    Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E; Qiang, Sheng

    2015-05-27

    Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely related to cultivated rice. There is suspicion that the outbreak of weedy rice in China may be related to widely grown hybrid rice due to its heterosis and the diversity of its progeny, but this notion remains unsupported by direct evidence. We screened weedy rice accessions by both genetic and molecular marker tests for the cytoplasmic male sterility (CMS) genes (Wild abortive, WA, and Boro type, BT) most widely used in the production of indica and japonica three-line hybrid rice as a diagnostic trait of direct parenthood. Sixteen weedy rice accessions of the 358 tested (4.5%) contained the CMS-WA gene; none contained the CMS-BT gene. These 16 accessions represent weedy rices recently evolved from maternal hybrid rice derivatives, given the primarily maternal inheritance of this trait. Our results provide key direct evidence that hybrid rice can be involved in the evolution of some weedy rice accessions, but is not a primary factor in the recent outbreak of weedy rice in China.

  16. Child dopamine active transporter 1 genotype and parenting: evidence for evocative gene-environment correlations.

    Science.gov (United States)

    Hayden, Elizabeth P; Hanna, Brigitte; Sheikh, Haroon I; Laptook, Rebecca S; Kim, Jiyon; Singh, Shiva M; Klein, Daniel N

    2013-02-01

    The dopamine active transporter 1 (DAT1) gene is implicated in psychopathology risk. Although the processes by which this gene exerts its effects on risk are poorly understood, a small body of research suggests that the DAT1 gene influences early emerging negative emotionality, a marker of children's psychopathology risk. As child negative emotionality evokes negative parenting practices, the DAT1 gene may also play a role in gene-environment correlations. To test this model, children (N = 365) were genotyped for the DAT1 gene and participated in standardized parent-child interaction tasks with their primary caregiver. The DAT1 gene 9-repeat variant was associated with child negative affect expressed toward the parent during parent-child interactions, and parents of children with a 9-repeat allele exhibited more hostility and lower guidance/engagement than parents of children without a 9-repeat allele. These gene-environment associations were partially mediated by child negative affect toward the parent. The findings implicate a specific polymorphism in eliciting negative parenting, suggesting that evocative associations play a role in elevating children's risk for emotional trajectories toward psychopathology risk.

  17. Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

    DEFF Research Database (Denmark)

    Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben

    2013-01-01

    evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae...

  18. Evidence-based gene models for structural and functional annotations of the oil palm genome.

    Science.gov (United States)

    Chan, Kuang-Lim; Tatarinova, Tatiana V; Rosli, Rozana; Amiruddin, Nadzirah; Azizi, Norazah; Halim, Mohd Amin Ab; Sanusi, Nik Shazana Nik Mohd; Jayanthi, Nagappan; Ponomarenko, Petr; Triska, Martin; Solovyev, Victor; Firdaus-Raih, Mohd; Sambanthamurthi, Ravigadevi; Murphy, Denis; Low, Eng-Ti Leslie

    2017-09-08

    Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA

  19. Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba.

    Directory of Open Access Journals (Sweden)

    Watcharee Saisongkorh

    Full Text Available BACKGROUND: Bartonella species cospeciate with mammals and live within erythrocytes. Even in these specific niches, it has been recently suggested by bioinformatic analysis of full genome sequences that Lateral Gene Transfer (LGT may occur but this has never been demonstrated biologically. Here we describe the sequence of the B. rattaustraliani (AUST/NH4(T circular plasmid (pNH4 that encodes the tra cluster of the Type IV secretion system (T4SS and we eventually provide evidence that Bartonella species may conjugate and exchange this plasmid inside amoeba. PRINCIPAL FINDINGS: The T4SS of pNH4 is critical for intracellular viability of bacterial pathogens, exhibits bioinformatic evidence of LGT among bacteria living in phagocytic protists. For instance, 3 out of 4 T4SS encoding genes from pNH4 appear to be closely related to Rhizobiales, suggesting that gene exchange occurs between intracellular bacteria from mammals (bartonellae and plants (Rhizobiales. We show that B. rattaustraliani and Rhizobium radiobacter both survived within the amoeba Acanthamoeba polyphaga and can conjugate together. Our findings further support the hypothesis that tra genes might also move into and out of bacterial communities by conjugation, which might be the primary means of genomic evolution for intracellular adaptation by cross-talk of interchangeable genes between Bartonella species and plant pathogens. CONCLUSIONS: Based on this, we speculate that amoeba favor the transfer of genes as phagocytic protists, which allows for intraphagocytic survival and, as a consequence, promotes the creation of potential pathogenic organisms.

  20. Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

    DEFF Research Database (Denmark)

    Limborg, Morten; Helyar, S.J.; de Bruyn, M.;

    2012-01-01

    High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel...... of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic......, including two temperature clines (5–12 C) and two salinity clines (5–35&). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic–North Sea transition area, North Sea ⁄ British Isles and North Atlantic; notably, samples...

  1. Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

    LENUS (Irish Health Repository)

    2011-10-05

    Abstract Background We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals. Results Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns. Conclusions Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.

  2. Preliminary evidence of phenytoin-induced alterations in embryonic gene expression in a mouse model.

    Science.gov (United States)

    Musselman, A C; Bennett, G D; Greer, K A; Eberwine, J H; Finnell, R H

    1994-01-01

    SWV mouse embryos collected on gestational days (GD) 9:12 and 10:00 following chronic in utero exposure to teratogenic concentrations of phenytoin were utilized for in situ transcription studies of gene expression. The substrate cDNA obtained from the frozen embryo sections was amplified into radiolabelled antisense RNA (RT/aRNA) and used as a probe to screen a panel of 20 cDNA clones representing genes that are important regulators of craniofacial and neural development. The magnitude of alteration in gene expression following phenytoin treatment was determined densitometrically by changes in the hybridization intensity of the aRNA probes to the cDNA clones immobilized to the slot blots. We found that both Wnt-1 and the calcium channel gene were developmentally regulated, as their level of expression decreased significantly between the two collection times. Phenytoin treatment produced a significant downregulation in the level of expression for 25% of the genes examined in the GD 9:12 embryos, including the growth factors TGF-beta and NT3, the proto-oncogene Wnt-1, the nicotinic receptor, and the voltage sensitive calcium channel gene. Additional changes in the coordinate expression of several of the growth and transcription factors were observed at both gestational timepoints. The application of RT/aRNA technology has extended our appreciation of the normal patterns of gene expression during craniofacial and neural development, and provided the first demonstration of multiple coordinate changes in transcription patterns following teratogenic insult.

  3. Evidence of duplicated Hox genes in the most recent common ancestor of extant scorpions.

    Science.gov (United States)

    Sharma, Prashant P; Santiago, Marc A; González-Santillán, Edmundo; Monod, Lionel; Wheeler, Ward C

    2015-01-01

    Scorpions (order Scorpiones) are unusual among arthropods, both for the extreme heteronomy of their bauplan and for the high gene family turnover exhibited in their genomes. These phenomena appear to be correlated, as two scorpion species have been shown to possess nearly twice the number of Hox genes present in most arthropods. Segmentally offset anterior expression boundaries of a subset of Hox paralogs have been shown to correspond to transitions in segmental identities in the scorpion posterior tagmata, suggesting that posterior heteronomy in scorpions may have been achieved by neofunctionalization of Hox paralogs. However, both the first scorpion genome sequenced and the developmental genetic data are based on exemplars of Buthidae, one of 19 families of scorpions. It is therefore not known whether Hox paralogy is limited to Buthidae or widespread among scorpions. We surveyed 24 high throughput transcriptomes and the single whole genome available for scorpions, in order to test the prediction that Hox gene duplications are common to the order. We used gene tree parsimony to infer whether the paralogy was consistent with a duplication event in the scorpion common ancestor. Here we show that duplicated Hox genes in non-buthid scorpions occur in six of the ten Hox classes. Gene tree topologies and parsimony-based reconciliation of the gene trees are consistent with a duplication event in the most recent common ancestor of scorpions. These results suggest that a Hox paralogy, and by extension the model of posterior patterning established in a buthid, can be extended to non-Buthidae scorpions.

  4. Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

    Directory of Open Access Journals (Sweden)

    Korir Paul K

    2011-10-01

    Full Text Available Abstract Background We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals. Results Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns. Conclusions Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.

  5. Soluble epoxide hydrolase gene deletion improves blood flow and reduces infarct size after cerebral ischemia in reproductively senescent female mice

    Directory of Open Access Journals (Sweden)

    Kristen L Zuloaga

    2015-01-01

    Full Text Available Soluble epoxide hydrolase (sEH, a key enzyme in the metabolism of vasodilatory epoxyeicosatrienoic acids (EETs, is sexually dimorphic, suppressed by estrogen, and contributes to underlying sex differences in cerebral blood flow and injury after cerebral ischemia. We tested the hypothesis that sEH inhibition or gene deletion in reproductively senescent (RS female mice would increase cerebral perfusion and decrease infarct size following stroke. RS (15-18 month old and young (3-4 month old female sEH knockout (sEHKO mice and wild type (WT mice were subjected to 45 min middle cerebral artery occlusion (MCAO with laser Doppler perfusion monitoring. WT mice were treated with vehicle or a sEH inhibitor t-AUCB at the time of reperfusion and every 24hrs thereafter for 3 days. Differences in regional cerebral blood flow were measured in vivo using optical microangiography. Infarct size was measured 3 days after reperfusion. Infarct size and cerebral perfusion 24h after MCAO were not altered by age. Both sEH gene deletion and sEH inhibition increased cortical perfusion 24h after MCAO. Neither sEH gene deletion nor sEH inhibition reduced infarct size in young mice. However, sEH gene deletion, but not sEH inhibition of the hydrolase domain of the enzyme, decreased infarct size in RS mice. Results of these studies show that sEH gene deletion and sEH inhibition enhance cortical perfusion following MCAO and sEH gene deletion reduces damage after ischemia in RS female mice; however this neuroprotection in absent is young mice.

  6. Interaction between γ-aminobutyric acid A receptor genes: new evidence in migraine susceptibility.

    Directory of Open Access Journals (Sweden)

    Marlene Quintas

    Full Text Available Migraine is a common neurological episodic disorder with a female-to-male prevalence 3- to 4-fold higher, suggesting a possible X-linked genetic component. Our aims were to assess the role of common variants of gamma-aminobutyric acid A receptor (GABAAR genes, located in the X-chromosome, in migraine susceptibility and the possible interaction between them. An association study with 188 unrelated cases and 286 migraine-free controls age- and ethnic matched was performed. Twenty-three tagging SNPs were selected in three genes (GABRE, GABRA3 and GABRQ. Allelic, genotypic and haplotypic frequencies were compared between cases and controls. We also focused on gene-gene interactions. The AT genotype of rs3810651 of GABRQ gene was associated with an increased risk for migraine (OR: 4.07; 95% CI: 1.71-9.73, p=0.002, while the CT genotype of rs3902802 (OR: 0.41; 95% CI: 0.21-0.78, p=0.006 and GA genotype of rs2131190 of GABRA3 gene (OR: 0.53; 95% CI: 0.32-0.88, p=0.013 seem to be protective factors. All associations were found in the female group and maintained significance after Bonferroni correction. We also found three nominal associations in the allelic analyses although there were no significant results in the haplotypic analyses. Strikingly, we found strong interactions between six SNPs encoding for different subunits of GABAAR, all significant after permutation correction. To our knowledge, we show for the first time, the putative involvement of polymorphisms in GABAAR genes in migraine susceptibility and more importantly we unraveled a role for novel gene-gene interactions opening new perspectives for the development of more effective treatments.

  7. Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region

    Directory of Open Access Journals (Sweden)

    van Pittius Nicolaas

    2009-09-01

    Full Text Available Abstract Background PPE38 (Rv2352c is a member of the large PPE gene family of Mycobacterium tuberculosis and related mycobacteria. The function of PPE proteins is unknown but evidence suggests that many are cell-surface associated and recognised by the host immune system. Previous studies targeting other PPE gene members suggest that some display high levels of polymorphism and it is thought that this might represent a means of providing antigenic variation. We have analysed the genetic variability of the PPE38 genomic region on a cohort of M. tuberculosis clinical isolates representing all of the major phylogenetic lineages, along with the ancestral M. tuberculosis complex (MTBC member M. canettii, and supplemented this with analysis of publicly available whole genome sequences representing additional M. tuberculosis clinical isolates, other MTBC members and non tuberculous mycobacteria (NTM. Where possible we have extended this analysis to include the adjacent plcABC and PPE39/40 genomic regions. Results We show that the ancestral MTBC PPE38 region comprises 2 homologous PPE genes (PPE38 and PPE71, separated by 2 esat-6 (esx-like genes and that this structure derives from an esx/esx/PPE duplication in the common ancestor of M. tuberculosis and M. marinum. We also demonstrate that this region of the genome is hypervariable due to frequent IS6110 integration, IS6110-associated recombination, and homologous recombination and gene conversion events between PPE38 and PPE71. These mutations result in combinations of gene deletion, gene truncation and gene disruption in the majority of clinical isolates. These mutations were generally found to be IS6110 strain lineage-specific, although examples of additional within-lineage and even within-cluster mutations were observed. Furthermore, we provide evidence that the published M. tuberculosis H37Rv whole genome sequence is inaccurate regarding this region. Conclusion Our results show that this antigen

  8. Arete - candidate gene prioritization using biological network topology with additional evidence types

    National Research Council Canada - National Science Library

    Artem Lysenko; Keith Anthony Boroevich; Tatsuhiko Tsunoda

    2017-01-01

    ... of the largest possible fraction of all available data. Results We have developed an easily accessible framework that links two established network-based gene prioritization approaches with a supporting isolation forest-based integrative ranking method...

  9. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

    OpenAIRE

    Koutsovoulos, Georgios; Kumar, Sujai; Laetsch, Dominik R.; Stevens, Lewis; Daub, Jennifer; Conlon, Claire; Maroon, Habib; Thomas, Fran; Aboobaker, Aziz A.; Blaxter, Mark

    2016-01-01

    Tardigrades, also known as moss piglets or water bears, are renowned for their ability to withstand extreme environmental challenges. A recently published analysis of the genome of the tardigrade Hypsibius dujardini by Boothby et al. concluded that horizontal acquisition of genes from bacterial and other sources might be key to cryptobiosis in tardigrades. We independently sequenced the genome of H. dujardini and detected a low level of horizontal gene transfer. We show that the extensive hor...

  10. Fluoroquinolone resistance in atypical pneumococci and oral streptococci: evidence of horizontal gene transfer of fluoroquinolone resistance determinants from Streptococcus pneumoniae.

    Science.gov (United States)

    Ip, Margaret; Chau, Shirley S L; Chi, Fang; Tang, Julian; Chan, Paul K

    2007-08-01

    Atypical strains, presumed to be pneumococcus, with ciprofloxacin MICs of > or =4.0 microg/ml and unique sequence variations within the quinolone resistance-determining regions (QRDRs) of the gyrase and topoisomerase genes in comparison with the Streptococcus pneumoniae R6 strain, were examined. These strains were reidentified using phenotypic methods, including detection of optochin susceptibility, bile solubility, and agglutination by serotype-specific antisera, and genotypic methods, including detection of pneumolysin and autolysin genes by PCR, 16S rRNA sequencing, and multilocus sequence typing (MLST). The analysis based on concatenated sequences of the six MLST loci distinguished the "atypical" strains from pneumococci, and these strains clustered closely with S. mitis. However, all these strains and five of nine strains from the viridans streptococcal group possessed one to three gyrA, gyrB, parC, and parE genes whose QRDR sequences clustered with those of S. pneumoniae, providing evidence of horizontal transfer of the QRDRs of the gyrase and topoisomerase genes from pneumococci into viridans streptococci. These genes also conferred fluoroquinolone resistance to viridans streptococci. In addition, the fluoroquinolone resistance determinants of 32 well-characterized Streptococcus mitis and Streptococcus oralis strains from bacteremic patients were also compared. These strains have unique amino acid substitutions in GyrA and ParC that were distinguishable from those in fluoroquinolone-resistant pneumococci and the "atypical" isolates. Both recombinational events and de novo mutations play an important role in the development of fluoroquinolone resistance.

  11. Informal "seed" systems and the management of gene flow in traditional agroecosystems: the case of cassava in Cauca, Colombia.

    Science.gov (United States)

    Dyer, George A; González, Carolina; Lopera, Diana Carolina

    2011-01-01

    Our ability to manage gene flow within traditional agroecosystems and their repercussions requires understanding the biology of crops, including farming practices' role in crop ecology. That these practices' effects on crop population genetics have not been quantified bespeaks lack of an appropriate analytical framework. We use a model that construes seed-management practices as part of a crop's demography to describe the dynamics of cassava (Manihot esculenta Crantz) in Cauca, Colombia. We quantify several management practices for cassava--the first estimates of their kind for a vegetatively-propagated crop--describe their demographic repercussions, and compare them to those of maize, a sexually-reproduced grain crop. We discuss the implications for gene flow, the conservation of cassava diversity, and the biosafety of vegetatively-propagated crops in centers of diversity. Cassava populations are surprisingly open and dynamic: farmers exchange germplasm across localities, particularly improved varieties, and distribute it among neighbors at extremely high rates vis-à-vis maize. This implies that a large portion of cassava populations consists of non-local germplasm, often grown in mixed stands with local varieties. Gene flow from this germplasm into local seed banks and gene pools via pollen has been documented, but its extent remains uncertain. In sum, cassava's biology and vegetative propagation might facilitate pre-release confinement of genetically-modified varieties, as expected, but simultaneously contribute to their diffusion across traditional agroecosystems if released. Genetically-modified cassava is unlikely to displace landraces or compromise their diversity; but rapid diffusion of improved germplasm and subsequent incorporation into cassava landraces, seed banks or wild populations could obstruct the tracking and eradication of deleterious transgenes. Attempts to regulate traditional farming practices to reduce the risks could compromise cassava

  12. Informal "seed" systems and the management of gene flow in traditional agroecosystems: the case of cassava in Cauca, Colombia.

    Directory of Open Access Journals (Sweden)

    George A Dyer

    Full Text Available Our ability to manage gene flow within traditional agroecosystems and their repercussions requires understanding the biology of crops, including farming practices' role in crop ecology. That these practices' effects on crop population genetics have not been quantified bespeaks lack of an appropriate analytical framework. We use a model that construes seed-management practices as part of a crop's demography to describe the dynamics of cassava (Manihot esculenta Crantz in Cauca, Colombia. We quantify several management practices for cassava--the first estimates of their kind for a vegetatively-propagated crop--describe their demographic repercussions, and compare them to those of maize, a sexually-reproduced grain crop. We discuss the implications for gene flow, the conservation of cassava diversity, and the biosafety of vegetatively-propagated crops in centers of diversity. Cassava populations are surprisingly open and dynamic: farmers exchange germplasm across localities, particularly improved varieties, and distribute it among neighbors at extremely high rates vis-à-vis maize. This implies that a large portion of cassava populations consists of non-local germplasm, often grown in mixed stands with local varieties. Gene flow from this germplasm into local seed banks and gene pools via pollen has been documented, but its extent remains uncertain. In sum, cassava's biology and vegetative propagation might facilitate pre-release confinement of genetically-modified varieties, as expected, but simultaneously contribute to their diffusion across traditional agroecosystems if released. Genetically-modified cassava is unlikely to displace landraces or compromise their diversity; but rapid diffusion of improved germplasm and subsequent incorporation into cassava landraces, seed banks or wild populations could obstruct the tracking and eradication of deleterious transgenes. Attempts to regulate traditional farming practices to reduce the risks could

  13. Suggestive evidence for association of two potassium channel genes with different idiopathic generalised epilepsy syndromes.

    Science.gov (United States)

    Chioza, B; Osei-Lah, A; Wilkie, H; Nashef, L; McCormick, D; Asherson, P; Makoff, A J

    2002-12-01

    Several potassium channel genes have been implicated in epilepsy. We have investigated three such genes, KCNJ3, KCNJ6 and KCNQ2, by association studies using a broad sample of idiopathic generalised epilepsy (IGE) unselected by syndrome. One of the two single nucleotide polymorphisms (SNPs) examined in one of the inward rectifying potassium channel genes, KCNJ3, was associated with IGE by genotype (P=0.0097), while its association by allele was of borderline significance (P=0.051). Analysis of the different clinical subgroups within the IGE sample showed more significant association with the presence of absence seizures (P=0.0041) and which is still significant after correction for multiple testing. Neither SNP in the other rectifying potassium channel gene, KCNJ6, was associated with IGE or any subgroup. None of the three SNPs in the voltage-gated potassium channel gene, KCNQ2, was associated with IGE. However, one SNP was associated with epilepsy with generalised tonic clonic seizures only (P=0.016), as was an SNP approximately 56 kb distant in the closely linked nicotinic acetylcholine gene CHRNA4 (P=0.014). These two SNPs were not in linkage disequilibrium with each other, suggesting that if they are not true associations they have independently occurred by chance. Neither association remains significant after correcting for multiple testing.

  14. 'Obesity' is healthy for cetaceans? Evidence from pervasive positive selection in genes related to triacylglycerol metabolism.

    Science.gov (United States)

    Wang, Zhengfei; Chen, Zhuo; Xu, Shixia; Ren, Wenhua; Zhou, Kaiya; Yang, Guang

    2015-09-18

    Cetaceans are a group of secondarily adapted marine mammals with an enigmatic history of transition from terrestrial to fully aquatic habitat and subsequent adaptive radiation in waters around the world. Numerous physiological and morphological cetacean characteristics have been acquired in response to this drastic habitat transition; for example, the thickened blubber is one of the most striking changes that increases their buoyancy, supports locomotion, and provides thermal insulation. However, the genetic basis underlying the blubber thickening in cetaceans remains poorly explored. Here, 88 candidate genes associated with triacylglycerol metabolism were investigated in representative cetaceans and other mammals to test whether the thickened blubber matched adaptive evolution of triacylglycerol metabolism-related genes. Positive selection was detected in 41 of the 88 candidate genes, and functional characterization of these genes indicated that these are involved mainly in triacylglycerol synthesis and lipolysis processes. In addition, some essential regulatory genes underwent significant positive selection in cetacean-specific lineages, whereas no selection signal was detected in the counterpart terrestrial mammals. The extensive occurrence of positive selection in triacylglycerol metabolism-related genes is suggestive of their essential role in secondary adaptation to an aquatic life, and further implying that 'obesity' might be an indicator of good health for cetaceans.

  15. Bap-dependent biofilm formation by pathogenic species of Staphylococcus: evidence of horizontal gene transfer?

    Science.gov (United States)

    Tormo, M Angeles; Knecht, Erwin; Götz, Friedrich; Lasa, Iñigo; Penadés, José R

    2005-07-01

    The biofilm-associated protein (Bap) is a surface protein implicated in biofilm formation by Staphylococcus aureus isolated from chronic mastitis infections. The bap gene is carried in a putative composite transposon inserted in SaPIbov2, a mobile staphylococcal pathogenicity island. In this study, bap orthologue genes from several staphylococcal species, including Staphylococcus epidermidis, Staphylococcus chromogenes, Staphylococcus xylosus, Staphylococcus simulans and Staphylococcus hyicus, were identified, cloned and sequenced. Sequence analysis comparison of the bap gene from these species revealed a very high sequence similarity, suggesting the horizontal gene transfer of SaPIbov2 amongst them. However, sequence analyses of the flanking region revealed that the bap gene of these species was not contained in the SaPIbov2 pathogenicity island. Although they did not contain the icaADBC operon, all the coagulase-negative staphylococcal isolates harbouring bap were strong biofilm producers. Disruption of the bap gene in S. epidermidis abolished its capacity to form a biofilm, whereas heterologous complementation of a biofilm-negative strain of S. aureus with the Bap protein from S. epidermidis bestowed the capacity to form a biofilm on a polystyrene surface. Altogether, these results demonstrate that Bap orthologues from coagulase-negative staphylococci induce an alternative mechanism of biofilm formation that is independent of the PIA/PNAG exopolysaccharide.

  16. Fluid flow on centimeter-scale in deep paleosubduction zones in western Tianshan, China: Evidence from high-pressure veins

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jin-fu; HUANG De-zhi; HUANG Shi-qi; LI Guo-ming; GAO Jun; SHI Yong-hong

    2008-01-01

    High-pressure(HP) veins were extensively developed in western Tianshan high-pressure(HP) metamorphic belt. The HP vein and host-rocks were analyzed by electronic microprobe to trace the origin of vein-forming fluids. Analytical data show that the immediately adjacent host-rocks of the studied HP vein are eclogites and gradually turned into blueschist as the distance from the veins increases, which indicates that the vein-forming fluid was derived from adjacent host-rocks; the boundaries between the vein and the host-rocks are sharp, which indicates that the fracture of the host-rocks is brittle during the vein-forming process. It is suggested that this type of HP veins is precipitated from the liquid formed by the dehydration of the host-rocks during the prograde metamorphism from blueschist to eclogite facies, which results in hydrofracturing of the rocks and provides the space for the vein to precipitate. The width of the eclogite-facies host-rocks is usually 1-2 cm, which provides the direct evidence that the fluid flow is on centimeter-scale.

  17. Evidence that local land use practices influence regional climate, vegetation, and stream flow patterns in adjacent natural areas

    Science.gov (United States)

    Stohlgren, T.J.; Chase, T.N.; Pielke, R.A.; Kittel, T.G.F.; Baron, J.S.

    1998-01-01

    We present evidence that land use practices in the plains of Colorado influence regional climate and vegetation in adjacent natural areas in the Rocky Mountains in predictable ways. Mesoscale climate model simulations using the Colorado State University Regional Atmospheric Modelling System (RAMS) projected that modifications to natural vegetation in the plains, primarily due to agriculture and urbanization, could produce lower summer temperatures in the mountains. We corroborate the RAMS simulations with three independent sets of data: (i) climate records from 16 weather stations, which showed significant trends of decreasing July temperatures in recent decades; (ii) the distribution of seedlings of five dominant conifer species in Rocky Mountain National Park, Colorado, which suggested that cooler, wetter conditions occurred over roughly the same time period; and (iii) increased stream flow, normalized for changes in precipitation, during the summer months in four river basins, which also indicates cooler summer temperatures and lower transpiration at landscape scales. Combined, the mesoscale atmospheric/land-surface model, short-term in regional temperatures, forest distribution changes, and hydrology data indicate that the effects of land use practices on regional climate may overshadow larger-scale temperature changes commonly associated with observed increases in CO2 and other greenhouse gases.

  18. Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene

    Directory of Open Access Journals (Sweden)

    Rodriguez Jose M

    2002-03-01

    Full Text Available Abstract Background The potential adaptive significance of transposable elements (TEs to the host genomes in which they reside is a topic that has been hotly debated by molecular evolutionists for more than two decades. Recent genomic analyses have demonstrated that TE fragments are associated with functional genes in plants and animals. These findings suggest that TEs may contribute significantly to gene evolution. Results We have analyzed two transposable elements associated with genes in the sequenced Drosophila melanogaster y; cn bw sp strain. A fragment of the Antonia long terminal repeat (LTR retrotransposon is present in the intron of Chitinase 3 (Cht3, a gene located within the constitutive heterochromatin of chromosome 2L. Within the euchromatin of chromosome 2R a full-length Burdock LTR retrotransposon is located immediately 3' to cathD, a gene encoding cathepsin D. We tested for the presence of these two TE/gene associations in strains representing 12 geographically diverse populations of D. melanogaster. While the cathD insertion variant was detected only in the sequenced y; cn bw sp strain, the insertion variant present in the heterochromatic Cht3 gene was found to be fixed throughout twelve D. melanogaster populations and in a D. mauritiana strain suggesting that it maybe of adaptive significance. To further test this hypothesis, we sequenced a 685bp region spanning the LTR fragment in the intron of Cht3 in strains representative of the two sibling species D. melanogaster and D. mauritiana (~2.7 million years divergent. The level of sequence divergence between the two species within this region was significantly lower than expected from the neutral substitution rate and lower than the divergence observed between a randomly selected intron of the Drosophila Alcohol dehydrogenase gene (Adh. Conclusions Our results suggest that a 359 bp fragment of an Antonia retrotransposon (complete LTR is 659 bp located within the intron of the

  19. STUDY OF GENE FLOW FROM GM COTTON (Gossypium hirsutum VARIETIES IN “EL ESPINAL” (TOLIMA, COLOMBIA

    Directory of Open Access Journals (Sweden)

    LEIDY YANIRA RACHE CARDENAL

    2013-01-01

    Full Text Available En el 2009 se plantaron 4088 hectáreas de algodón genéticamente modificado en el departamento de Tolima (Colombia, sin embargo, hay ciertas incertidumbres acerca de las medidas de contención necesarias para impedir el movimiento de polen y semillas desde los campos GM regulados, hacia los campos adyacentes de cultivos convencionales. En este estudio se evaluó el flujo de genes mediado por polen y semillas desde variedades GM hacia variedades convencionales o individuos ferales, en el cultivo del algodón. Para detectar el flujo de genes se utilizaron ImmunostripTM, PCR y ELISA. Cincuenta y seis refugios, 27 campos con algodón convencional y cuatro individuos ferales de la empresa “Remolinos S.A.” localizada en El Espinal (Tolima fueron analizados en el primer semestre de 2010. Los resultados indicaron presencia de plantas GM en 45 refugios (80,4 % y 26 campos de algodón convencional (96 %, además de un flujo génico mediado por polen en un campo de algodón convencional y nueve refugios. En todos los campos cultivados con algodón convencional se evidenció flujo de genes desde algodón GM. Solo en dos refugios y en dos individuos ferales no se evidenció flujo de genes desde algodón GM.

  20. Gene expression responses of HeLa cells to chemical species generated by an atmospheric plasma flow

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Mayo, E-mail: yokoyama@plasma.ifs.tohoku.ac.jp [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Johkura, Kohei, E-mail: kohei@shinshu-u.ac.jp [Department of Histology and Embryology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621 (Japan); Sato, Takehiko, E-mail: sato@ifs.tohoku.ac.jp [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan)

    2014-08-08

    Highlights: • Response of HeLa cells to a plasma-irradiated medium was revealed by DNA microarray. • Gene expression pattern was basically different from that in a H{sub 2}O{sub 2}-added medium. • Prominently up-/down-regulated genes were partly shared by the two media. • Gene ontology analysis showed both similar and different responses in the two media. • Candidate genes involved in response to ROS were detected in each medium. - Abstract: Plasma irradiation generates many factors able to affect the cellular condition, and this feature has been studied for its application in the field of medicine. We previously reported that hydrogen peroxide (H{sub 2}O{sub 2}) was the major cause of HeLa cell death among the chemical species generated by high level irradiation of a culture medium by atmospheric plasma. To assess the effect of plasma-induced factors on the response of live cells, HeLa cells were exposed to a medium irradiated by a non-lethal plasma flow level, and their gene expression was broadly analyzed by DNA microarray in comparison with that in a corresponding concentration of 51 μM H{sub 2}O{sub 2}. As a result, though the cell viability was sufficiently maintained at more than 90% in both cases, the plasma-medium had a greater impact on it than the H{sub 2}O{sub 2}-medium. Hierarchical clustering analysis revealed fundamentally different cellular responses between these two media. A larger population of genes was upregulated in the plasma-medium, whereas genes were downregulated in the H{sub 2}O{sub 2}-medium. However, a part of the genes that showed prominent differential expression was shared by them, including an immediate early gene ID2. In gene ontology analysis of upregulated genes, the plasma-medium showed more diverse ontologies than the H{sub 2}O{sub 2}-medium, whereas ontologies such as “response to stimulus” were common, and several genes corresponded to “response to reactive oxygen species.” Genes of AP-1 proteins, e.g., JUN

  1. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini.

    Science.gov (United States)

    Koutsovoulos, Georgios; Kumar, Sujai; Laetsch, Dominik R; Stevens, Lewis; Daub, Jennifer; Conlon, Claire; Maroon, Habib; Thomas, Fran; Aboobaker, Aziz A; Blaxter, Mark

    2016-05-03

    Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme condit