myPhyloDB: a local web server for the storage and analysis of metagenomics data

Science.gov (United States)

myPhyloDB is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all availab...

The space of ultrametric phylogenetic trees.

Science.gov (United States)

Gavryushkin, Alex; Drummond, Alexei J

2016-08-21

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evaluating realized genetic gains from tree improvement.

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J.B. St. Clair

1993-01-01

Tree improvement has become an essential part of the management of forest lands for wood production, and predicting yields and realized gains from forests planted with genetically-improved trees will become increasingly important. This paper discusses concepts of tree improvement and genetic gain important to growth and yield modeling, and reviews previous studies of...

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

Directory of Open Access Journals (Sweden)

Ivan Gregor

2016-02-01

Full Text Available Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S software. The new (+ component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

Science.gov (United States)

Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher; McHardy, Alice C

2016-01-01

Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into 'bins' representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies 'training' sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4-6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.

Genetic transformation of forest trees | Diouf | African Journal of ...

African Journals Online (AJOL)

In this review, the recent progress on genetic transformation of forest trees were discussed. Its described also, different applications of genetic engineering for improving forest trees or understanding the mechanisms governing genes expression in woody plants. Key words: Genetic transformation, transgenic forest trees, ...

GRFT – Genetic records family tree web applet

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Samuel ePimentel

2011-03-01

Full Text Available Current software for storing and displaying records of genetic crosses does not provide an easy way to determine the lineage of an individual. The genetic records family tree (GRFT applet processes records of genetic crosses and allows researchers to quickly visualize lineages using a family tree construct and to access other information from these records using any Internet browser. Users select from three display features: 1 a family tree view which displays a color-coded family tree for an individual, 2 a sequential list of crosses, and 3 a list of crosses matching user-defined search criteria. Each feature contains options to specify the number of records shown and the latter two contain an option to filter results by the owner of the cross. The family tree feature is interactive, displaying a popup box with genetic information when the user mouses over an individual and allowing the user to draw a new tree by clicking on any individual in the current tree. The applet is written in Javascript and reads genetic records from a tab-delimited text file on the server, so it is cross-platform, can be accessed by anyone with an Internet connection, and supports almost instantaneous generation of new trees and table lists. Researchers can use the tool with their own genetic cross records for any sexually-reproducing organism. No additional software is required and with only minor modifications to the script, researchers can add their own custom columns. GRFT's speed, versatility, and low overhead make it an effective and innovative visualization method for genetic records. A sample tool is available at http://stanford.edu/~walbot/grft-sample.html.

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

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Massingham Tim

2011-04-01

Full Text Available Abstract Background The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity. Results PhyloSim is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, PhyloSim can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing PhyloSim to be adapted to specific needs. Conclusions Close integration with R and the wide range of features implemented offer unmatched flexibility, making it possible to simulate sequence evolution under a wide range of realistic settings. We believe that PhyloSim will be useful to future studies involving simulated alignments.

Tree-space statistics and approximations for large-scale analysis of anatomical trees

DEFF Research Database (Denmark)

Feragen, Aasa; Owen, Megan; Petersen, Jens

2013-01-01

parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than...

Isozymes and the genetic resources of forest trees

Science.gov (United States)

A. H. D. Brown; G. F. Moran

1981-01-01

Genetic data are an essential prerequisite for analysing the genetic structure of tree populations. The isozyme technique is the best currently available method for obtaining such data. Despite several shortcomings, isozyme data directly evaluate the genetic resources of forest trees, and can thus be used to monitor and manipulate these resources. For example,...

Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

DEFF Research Database (Denmark)

Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

2014-01-01

-monitoring schemes. Here, we provide a review and an assessment of the different attempts made to provide such indicators for tree genetic diversity from the global level down to the level of the management unit. So far, no generally accepted indicators have been provided as international standards, nor tested...... for their possible use in practice. We suggest that indicators for monitoring genetic diversity and dynamics should be based on ecological and demographic surrogates of adaptive diversity as well as genetic markers capable of identifying genetic erosion and gene flow. A comparison of past and present genecological...... distributions (patterns of genetic variation of key adaptive traits in the ecological space) of selected species is a realistic way of assessing the trend of intra-specific variation, and thus provides a state indicator of tree genetic diversity also able to reflect possible pressures threatening genetic...

Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling.

Science.gov (United States)

Sferra, Gabriella; Fratini, Federica; Ponzi, Marta; Pizzi, Elisabetta

2017-09-05

Elaboration of powerful methods to predict functional and/or physical protein-protein interactions from genome sequence is one of the main tasks in the post-genomic era. Phylogenetic profiling allows the prediction of protein-protein interactions at a whole genome level in both Prokaryotes and Eukaryotes. For this reason it is considered one of the most promising methods. Here, we propose an improvement of phylogenetic profiling that enables handling of large genomic datasets and infer global protein-protein interactions. This method uses the distance correlation as a new measure of phylogenetic profile similarity. We constructed robust reference sets and developed Phylo-dCor, a parallelized version of the algorithm for calculating the distance correlation that makes it applicable to large genomic data. Using Saccharomyces cerevisiae and Escherichia coli genome datasets, we showed that Phylo-dCor outperforms phylogenetic profiling methods previously described based on the mutual information and Pearson's correlation as measures of profile similarity. In this work, we constructed and assessed robust reference sets and propose the distance correlation as a measure for comparing phylogenetic profiles. To make it applicable to large genomic data, we developed Phylo-dCor, a parallelized version of the algorithm for calculating the distance correlation. Two R scripts that can be run on a wide range of machines are available upon request.

PhyloSift: phylogenetic analysis of genomes and metagenomes.

Science.gov (United States)

Darling, Aaron E; Jospin, Guillaume; Lowe, Eric; Matsen, Frederick A; Bik, Holly M; Eisen, Jonathan A

2014-01-01

Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).

PhyloSift: phylogenetic analysis of genomes and metagenomes

Directory of Open Access Journals (Sweden)

Aaron E. Darling

2014-01-01

Full Text Available Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection.In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata.These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454.

Prediction of direct and indirect genetic gains and genotypic correlations in rubber tree progenies

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Cecília Khusala Verardi

2011-09-01

Full Text Available The objective of this work was to estimate the genetic parameters, genotypic and phenotypic correlations, and direct and indirect genetic gains among and within rubber tree (Hevea brasiliensis progenies. The experiment was set up at the Municipality of Jaú, SP, Brazil. A randomized complete block design was used, with 22 treatments (progenies, 6 replicates, and 10 plants per plot at a spacing of 3x3 m. Three‑year‑old progenies were assessed for girth, rubber yield, and bark thickness by direct and indirect gains and genotypic correlations. The number of latex vessel rings showed the best correlations, correlating positively and significantly with girth and bark thickness. Selection gains among progenies were greater than within progeny for all the variables analyzed. Total gains obtained were high, especially for girth increase and rubber yield, which were 93.38 and 105.95%, respectively. Young progeny selection can maximize the expected genetic gains, reducing the rubber tree selection cycle.

Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip and 16S rRNA gene clone library sequencing

Energy Technology Data Exchange (ETDEWEB)

Shankar Sagaram, U.; DeAngelis, K.M.; Trivedi, P.; Andersen, G.L.; Lu, S.-E.; Wang, N.

2009-03-01

between the relative abundance, species richness and phylogenetic diversity of the microbial communities associated with the leaf midribs of HLB symptomatic and asymptomatic citrus trees were investigated using high-density 16S rDNA microarray PhyloChip and 16S rRNA gene clone library methods.

Fine scale population genetic structure and within tree distribution of mating types of Venturia effusa, cause of pecan scab in the USA

Science.gov (United States)

Scab (caused by Venturia effusa) is the major disease of pecan in the southeastern USA. There is no information available on the fine scale population genetic diversity. Four cv. Wichita trees (populations) were sampled hierarchically. Within each tree canopy, 4 approximately evenly spaced terminals...

Visualising very large phylogenetic trees in three dimensional hyperbolic space

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Liberles David A

2004-04-01

Full Text Available Abstract Background Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. Results We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Walrus graph visualisation tool and have developed a conversion tool that enables the conversion of standard phylogenetic tree formats to Walrus' format. With Walrus, it becomes possible to visualise and navigate phylogenetic trees with more than 100,000 nodes. Conclusion Walrus enables desktop visualisation of very large phylogenetic trees in 3 dimensional hyperbolic space. This application is potentially useful for visualisation of the tree of life and for functional genomics derivatives, like The Adaptive Evolution Database (TAED.

Genetic parameters and estimated genetic gains in young rubber tree progenies

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Cecília Khusala Verardi

2013-04-01

Full Text Available The objective of this work was to assess the genetic parameters and to estimate genetic gains in young rubber tree progenies. The experiments were carried out during three years, in a randomized block design, with six replicates and ten plants per plot, in three representative Hevea crop regions of the state of São Paulo, Brazil. Twenty-two progenies were evaluated, from three to five years old, for rubber yield and annual girth growth. Genetic gain was estimated with the multi-effect index (MEI. Selection by progenies means provided greater estimated genetic gain than selection based on individuals, since heritability values of progeny means were greater than the ones of individual heritability, for both evaluated variables, in all the assessment years. The selection of the three best progenies for rubber yield provided a selection gain of 1.28 g per plant. The genetic gains estimated with MEI using data from early assessments (from 3 to 5-year-old were generally high for annual girth growth and rubber yield. The high genetic gains for annual girth growth in the first year of assessment indicate that progenies can be selected at the beginning of the breeding program. Population effective size was consistent with the three progenies selected, showing that they were not related and that the population genetic variability is ensured. Early selection with the genetic gains estimated by MEI can be made on rubber tree progenies.

Genetic improvement of forest tree species

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Teotônio Francisco Assis

2011-01-01

Full Text Available Brazilian forestry sector is considered one of the most developed in the world, being the base for important industrialsegments which use wood as raw material. Tree breeding has played an important role on improving the competitiveness ofBrazilian forestry-based companies, especially for its positive reflexes on increasing adaptation, forestry productivity and woodquality. In spite of the importance of other forest trees for the economy, such as Schizolobium, Araucaria, Populus and Hevea, themain genera under genetic improvement in the country are Eucalyptus, Pinus, Acacia and Tectona. They are used by industries likepulp and paper, siderurgy, tannin, chips for exportation and lumber, constituting an important source of revenues for the Brazilian’seconomy, besides their positive social and environmental impacts. This paper presents a generic approach to genetic improvementaspects of these four major genera currently undergoing breeding in Brazil.

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

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Deshwar, Amit G; Vembu, Shankar; Morris, Quaid

2015-01-01

Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the phylogeny and genotype of major subclonal lineages represented in the population of cancer cells. We also propose new split-merge updates tailored to the subclonal reconstruction problem that improve the mixing time of Markov chains. In comparisons with the tree-structured stick breaking prior used in PhyloSub, we demonstrate superior mixing and running time using the treeCRP with our new split-merge procedures. We also show that given the same number of samples, TSSB and treeCRP have similar ability to recover the subclonal structure of a tumor…

Context trees for privacy-preserving modeling of genetic data

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.

2016-01-01

In this work, we use context trees for privacypreserving modeling of genetic sequences. The resulting estimated models are applied for functional comparison of genetic sequences in a privacy preserving way. Here we define privacy as uncertainty about the genetic source sequence given its model and

Genetic diversity and conservation of Mexican forest trees

Science.gov (United States)

C. Wehenkel; S. Mariscal-Lucero; J.P. Jaramillo-Correa; C.A. López-Sánchez; J.J. Vargas Hernández; C. Sáenz-Romero

2017-01-01

Over the last 200 years, humans have impacted the genetic diversity of forest trees. Because of widespread deforestation and over-exploitation, about 9,000 tree species are listed worldwide as threatened with extinction, including more than half of the ~600 known conifer taxa. A comprehensive review of the floristic-taxonomic literature compiled a list of 4,331...

Genetic transformation of fruit trees: current status and remaining challenges.

Science.gov (United States)

Gambino, Giorgio; Gribaudo, Ivana

2012-12-01

Genetic transformation has emerged as a powerful tool for genetic improvement of fruit trees hindered by their reproductive biology and their high levels of heterozygosity. For years, genetic engineering of fruit trees has focussed principally on enhancing disease resistance (against viruses, fungi, and bacteria), although there are few examples of field cultivation and commercial application of these transgenic plants. In addition, over the years much work has been performed to enhance abiotic stress tolerance, to induce modifications of plant growth and habit, to produce marker-free transgenic plants and to improve fruit quality by modification of genes that are crucially important in the production of specific plant components. Recently, with the release of several genome sequences, studies of functional genomics are becoming increasingly important: by modification (overexpression or silencing) of genes involved in the production of specific plant components is possible to uncover regulatory mechanisms associated with the biosynthesis and catabolism of metabolites in plants. This review focuses on the main advances, in recent years, in genetic transformation of the most important species of fruit trees, devoting particular attention to functional genomics approaches and possible future challenges of genetic engineering for these species in the post-genomic era.

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

International Nuclear Information System (INIS)

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

2004-01-01

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

Translating conservation genetics into management: Pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity

OpenAIRE

Koskela, Jarkko; Lefèvre, François; Schueler, Silvio; Kraigher, Hojka; Olrik, Ditte C.; Hubert, Jason; Longauer, Roman; Bozzano, Michele; Yrjänä, Leena; Alizoti, Paraskevi; Rotach, Peter; Vietto, Lorenzo; Bordács, Sándor; Myking, Tor; Eysteinsson, Thröstur

2013-01-01

This paper provides a review of theoretical and practical aspects related to genetic management of forest trees. The implementation of international commitments on forest genetic diversity has been slow and partly neglected. Conservation of forest genetic diversity is still riddled with problems, and complexities of national legal and administrative structures. Europe is an example of a complex region where the dis- tribution ranges of tree species extend across large geographical areas with ...

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

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G. Forti

2014-12-01

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

Genetic consequences of seed dispersal to sleeping trees by white-bellied spider monkeys

Science.gov (United States)

Karubian, Jordan; Ottewell, Kym; Link, Andres; Di Fiore, Anthony

2015-10-01

Frugivorous animals frequently generate clumped distributions of seeds away from source trees via 'destination-based' dispersal processes. For example, use of traditional sleeping trees by white-bellied spider monkeys Ateles belzebuth generates high densities of seeds of a preferred food source, the palm Oenocarpus bataua, at these sites. Little is known about the maternal seed source diversity and population genetic metrics of seed pools encountered at these sites. Given the repeated use of sleeping trees over time, and the fluid social organization and wide ranging movements exhibited by spider monkeys, we predicted that O. bataua seed pools beneath sleeping trees would be characterized by relatively high values of maternal seed source diversity and standard metrics of genetic diversity. Contrary to these expectations, we found relatively low average maternal seed source diversity beneath each of 6 sleeping trees we studied (weighted mean α = 3.74), but considerable variation in diversity of maternal seed sources between sleeping trees (range = 1.75-10.1) and high heterogeneity in standard genetic diversity measures between sleeping trees. There was no evidence for overlap in maternal seed sources between sleeping tree sites (δ = 1.0), resulting in significant genetic differentiation (Fst = 0.055-0.319) between these sites. Observed variation between sleeping trees could not be explained by the number of individual spider monkeys whose core home ranges included a given tree, nor by distance to a central mineral lick, a focal point of spider monkey activity. These findings suggest that spider monkey seed dispersal to sleeping trees is spatially restricted, perhaps because the animals visit sleeping trees at the end of the day and therefore only disperse O. bataua fruits that they ingest late in the day. These results add to our growing appreciation of the ways frugivore behavior mechanistically shapes seed dispersal outcomes.

USING GENETIC ALGORTIHM TO SOLVE STEINER MINIMUM SPANNING TREE PROBLEM

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Öznur İŞÇİ

2006-03-01

Full Text Available Genetic algorithms (GA are a stochastic research methods, and they produce solutions that are close to optimum or near optimum. In addition to GA's successful application to traveling salesman problem, square designation, allocation, workshop table, preparation of lesson/examination schedules, planning of communication networks, assembling line balanced, minimum spanning tree type many combinatorial optimization problems it would be applicable to make the best comparison in optimization. In this study a Java program is developed to solve Steiner minimum spanning tree problem by genetic algorithm and its performance is examined. According to the tests carried out on the problems that were given before in the literature, results that are close to optimum are obtained in by GA approach that is recommended in this study. For the predetermined points in the study, length and gain are calculated for Steiner minimum spanning tree problem and minimum spanning tree problem.

Genetically modified trees: State and perspectives

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Nonić Marina

2012-01-01

Full Text Available Genetically modified trees are the result of modern plant breeding. Its introduction into the environment for experimental purposes or wider cultivation is defined differently from country to country. Public opinion is divided! Conducted research are part of the activities within the COST Action FP0905 „Biosafety of forest transgenic trees”, which aims to collect information and define the scientific attitude on genetically modified trees as a basis for future European Union (EU policy in this field. The collected information refer to eight countries: four EU member states (Italy, Slovenia, Romania and Bulgaria and four countries in the process of pre-accession (Croatia, Montenegro, Serbia and Bosnia and Herzegovina. A comparative analysis involved the state of forest resources (area of forest land and forest cover, forestry legislation, legislation relating to genetically modified organisms and the general public attitude on this issue. The collected information provide a good basis for understanding this issue in order to define a clear scientific attitude as a recommendation. [Acknowledgements. The authors wish to acknowledge the support of the COST Action FP0905 „Biosafety of forest transgenic trees” for assigned STSM and financial support, also special thanks to the Host institution (Tuscany Region - Directorate General in Florence for kind cooperation. The performed research was partially conducted within the Project „Establishment of Wood Plantations Intended for Afforestation of Serbia“ TP 31041

Genetic structure of two pseudoscorpion species living in tree hollows in Sweden

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Ranius, T.

2002-12-01

Full Text Available Two saproxylic pseudoscorpions, Larca lata and Allochernes wideri, were compared in an analysis of genetic structure in southern Sweden. Allochernes wideri is a relatively widely distributed species that occurs in single-standing trees and in small tree hollows, while L. lata is on the Swedish red list and confined to larger assemblages of very old trees with hollows containing large amounts of wood mould. In A. wideri, the polymorphism of PGM was used, whereas in L. lata the variation for PGI was studied. The genetic differentiation between trees within a site was low for both species, indicating that the migration between nearby trees is considerable despite the fact that phoretic dispersal has only been occasionally observed in these species. Between sites, situated four to 900 km from each other, the genetic differentiation was small both in A. wideri and L. lata with no difference between the species, when considered on the mainland only. The small differentiation suggests the habitat was fragmented recently (100-170 years ago. The relation between the rate of migration and long-term population survival and the risk of mis-interpretation due to selection for alleles is discussed

CosmoBon, tree research team, for studying utilization of woody plant in space environment

Science.gov (United States)

Tomita-Yokotani, Kaori; Yamashita, Masamichi; Hashimoto, Hirofumi; Sato, Seigo; Baba, Keiichi; Chida, Yukari

2012-07-01

We are proposing to raise woody plants in space for several applications and plant science, as Tree research team, TRT. Trees produce excess oxygen, wooden materials for living cabin, and provide biomass for cultivating mushroom and insect as for the space agriculture. Excellent tree shapes which would be deeply related to wood formation improve quality of life under stressful environment in outer space. We have the serious problem about their size. Bonsai is one of the Japanese traditional arts. We have been investigating the tension wood formation under exotic gravitational environment using Bonsai. CosmoBon is the small tree Bonsai for our space experiment. The tension wood formation in CosmoBon was confirmed as the same as that in the natural trees. Our goal is to examine feasibility to grow various species of trees in space as bioresource for space agriculture.

A support vector machine based test for incongruence between sets of trees in tree space

Science.gov (United States)

2012-01-01

Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The

Transforming phylogenetic networks: Moving beyond tree space.

Science.gov (United States)

Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

2016-09-07

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

Science.gov (United States)

Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

2014-01-01

Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

Do Farmers reduce genetic diversity when they domesticate tropical trees? a case study from Amazonia.

NARCIS (Netherlands)

Hollingsworth, P.M.; Dawson, I.K.; Goodall-Copestake, W.P.; Richardson, J.E.; Weber, J.C.; Sotelo Montes, C.; Pennington, R.T.

2005-01-01

Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity

Challenges and advances in genetically improving trees for the plantation forestry sector

CSIR Research Space (South Africa)

Verryn, SD

2010-08-30

Full Text Available This presentation outlines the South African plantation forestry sector and its contributions and improvement in productivity, acquiring genetic diversity, challenges and advances in genetically improving trees as well as transforming the value...

Epigenetic variability in the genetically uniform forest tree species Pinus pinea L.

Science.gov (United States)

Sáez-Laguna, Enrique; Guevara, María-Ángeles; Díaz, Luis-Manuel; Sánchez-Gómez, David; Collada, Carmen; Aranda, Ismael; Cervera, María-Teresa

2014-01-01

There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

Epigenetic variability in the genetically uniform forest tree species Pinus pinea L.

Directory of Open Access Journals (Sweden)

Enrique Sáez-Laguna

Full Text Available There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments. Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

Sparse suffix tree construction in small space

DEFF Research Database (Denmark)

Bille, Philip; Fischer, Johannes; Gørtz, Inge Li

2013-01-01

the correct tree with high probability. We then give a Las-Vegas algorithm which also uses O(b) space and runs in the same time bounds with high probability when b = O(√n). Furthermore, additional tradeoffs between the space usage and the construction time for the Monte-Carlo algorithm are given......., which may be of independent interest, that allows to efficiently answer b longest common prefix queries on suffixes of T, using only O(b) space. We expect that this technique will prove useful in many other applications in which space usage is a concern. Our first solution is Monte-Carlo and outputs...

Fixed point theorems in spaces and -trees

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Kirk WA

2004-01-01

Full Text Available We show that if is a bounded open set in a complete space , and if is nonexpansive, then always has a fixed point if there exists such that for all . It is also shown that if is a geodesically bounded closed convex subset of a complete -tree with , and if is a continuous mapping for which for some and all , then has a fixed point. It is also noted that a geodesically bounded complete -tree has the fixed point property for continuous mappings. These latter results are used to obtain variants of the classical fixed edge theorem in graph theory.

Exploring Association between Morphology of Tree Planting and User Activities in Urban Public Space; An opportunity of Urban Public Space Revitalisation

Science.gov (United States)

Shen, Qi; Liu, Yan

2018-03-01

This paper discusses the association between the morphology of tree planting in urban riverside brown field and user activities. With the growth of popularity, the revitalisation of urban public space is also promising. This research used drone photography and mapping to systematically surveys sample sites. An original observation study of user activities proceed in four sample public spaces in Sheffield. The study results found there are huge popularity and duration difference of user activities between various tree planting morphologies and typologies. The public space with lawn and rounded by mature trees attracted most users with the most activity types; the neat and silent public space is the favourite choice of lunch and reading, meanwhile it got the longest activity duration; but the space with sparse morphology and small trees are more likely be forgotten and abandoned. This finding offered a great opportunity for urban public space revitalisation in post-industrial cities.

Steiner tree heuristic in the Euclidean d-space using bottleneck distances

DEFF Research Database (Denmark)

Lorenzen, Stephan Sloth; Winter, Pawel

2016-01-01

Some of the most efficient heuristics for the Euclidean Steiner minimal tree problem in the d-dimensional space, d ≥2, use Delaunay tessellations and minimum spanning trees to determine small subsets of geometrically close terminals. Their low-cost Steiner trees are determined and concatenated...... in a greedy fashion to obtain a low cost tree spanning all terminals. The weakness of this approach is that obtained solutions are topologically related to minimum spanning trees. To avoid this and to obtain even better solutions, bottleneck distances are utilized to determine good subsets of terminals...

Genetic bottlenecks in agroforestry systems: results of tree nursery surveys in East Africa

NARCIS (Netherlands)

Lengkeek, A.G.; Jaenicke, H.; Dawson, I.K.

2005-01-01

Seedlings sourced through tree nurseries are expected to form an important component of future tree cover on farms. As such, the genetic composition of nursery seedlings is expected to impact on the productivity and sustainability of agroforestry ecosystems. By surveying current practices of nursery

Genetic Inventory Task Final Report. Volume 2

Science.gov (United States)

Venkateswaran, Kasthuri; LaDuc, Myron T.; Vaishampayan, Parag

2012-01-01

Contaminant terrestrial microbiota could profoundly impact the scientific integrity of extraterrestrial life-detection experiments. It is therefore important to know what organisms persist on spacecraft surfaces so that their presence can be eliminated or discriminated from authentic extraterrestrial biosignatures. Although there is a growing understanding of the biodiversity associated with spacecraft and cleanroom surfaces, it remains challenging to assess the risk of these microbes confounding life-detection or sample-return experiments. A key challenge is to provide a comprehensive inventory of microbes present on spacecraft surfaces. To assess the phylogenetic breadth of microorganisms on spacecraft and associated surfaces, the Genetic Inventory team used three technologies: conventional cloning techniques, PhyloChip DNA microarrays, and 454 tag-encoded pyrosequencing, together with a methodology to systematically collect, process, and archive nucleic acids. These three analysis methods yielded considerably different results: Traditional approaches provided the least comprehensive assessment of microbial diversity, while PhyloChip and pyrosequencing illuminated more diverse microbial populations. The overall results stress the importance of selecting sample collection and processing approaches based on the desired target and required level of detection. The DNA archive generated in this study can be made available to future researchers as genetic-inventory-oriented technologies further mature.

Forecasting Shaharchay River Flow in Lake Urmia Basin using Genetic Programming and M5 Model Tree

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S. Samadianfard

2017-01-01

Full Text Available Introduction: Precise prediction of river flows is the key factor for proper planning and management of water resources. Thus, obtaining the reliable methods for predicting river flows has great importance in water resource engineering. In the recent years, applications of intelligent methods such as artificial neural networks, fuzzy systems and genetic programming in water science and engineering have been grown extensively. These mentioned methods are able to model nonlinear process of river flows without any need to geometric properties. A huge number of studies have been reported in the field of using intelligent methods in water resource engineering. For example, Noorani and Salehi (23 presented a model for predicting runoff in Lighvan basin using adaptive neuro-fuzzy network and compared the performance of it with neural network and fuzzy inference methods in east Azerbaijan, Iran. Nabizadeh et al. (21 used fuzzy inference system and adaptive neuro-fuzzy inference system in order to predict river flow in Lighvan river. Khalili et al. (13 proposed a BL-ARCH method for prediction of flows in Shaharchay River in Urmia. Khu et al. (16 used genetic programming for runoff prediction in Orgeval catchment in France. Firat and Gungor (11 evaluated the fuzzy-neural model for predicting Mendes river flow in Turkey. The goal of present study is comparing the performance of genetic programming and M5 model trees for prediction of Shaharchay river flow in the basin of Lake Urmia and obtaining a comprehensive insight of their abilities. Materials and Methods: Shaharchay river as a main source of providing drinking water of Urmia city and agricultural needs of surrounding lands and finally one of the main input sources of Lake Urmia is quite important in the region. For obtaining the predetermined goals of present study, average monthly flows of Shaharchay River in Band hydrometric station has been gathered from 1951 to 2011. Then, two third of mentioned

Genetic dissimilarity among jabuticaba trees native to southwestern Paraná, Brazil

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Moeses Andrigo Danner

2011-06-01

Full Text Available Knowledge on the genetic diversity within and between genotype groups is of great importance for breeding programs. The purpose of this study was to estimate the genetic dissimilarity among 36 native jabuticaba trees (Plinia cauliflora from five sites in the southwestern region of Paraná, Brazil. Sixteen fruit traits were analyzed, based on multivariate techniques (canonical variables, Tocher and UPGMA, using Mahalanobis' distance as dissimilarity measure. By the techniques of clustering and graphic dispersion, together with the comparison of means, the genetic diversity among native jabuticaba trees was efficiently identified, indicating a high potential of these genotypes for breeding programs. The traits of greatest importance for dissimilarity were percentage of pulp and of skin, which are easily measured. The clustering structure is related to the collection sites and for breeding programs, genotypes from different sites should be crossed to generate progenies to be tested. Genotypes 'CV5' and 'VT3' should be conserved in genebanks, due to its important agronomic traits.

Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

NARCIS (Netherlands)

DeWoody, J.; Viger, M.; Lakatos, F.; Tuba, K.; Taylor, G.; Smulders, M.J.M.

2013-01-01

Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common

High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae

Directory of Open Access Journals (Sweden)

Roberto Tarazi

2010-01-01

Full Text Available Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees.

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

Science.gov (United States)

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

2016-01-01

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

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

Energy Technology Data Exchange (ETDEWEB)

Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.; Shenoy, M.; DeSantis, T.; Wu, C.H.; Andersen, G.L.; Winston, J.; Sonnenburg, J.; Pasricha, P.J.; Spormann, A.

2010-12-01

Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.

Tree genetic engineering and applications to sustainable forestry and biomass production.

Science.gov (United States)

Harfouche, Antoine; Meilan, Richard; Altman, Arie

2011-01-01

Forest trees provide raw materials, help to maintain biodiversity and mitigate the effects of climate change. Certain tree species can also be used as feedstocks for bioenergy production. Achieving these goals may require the introduction or modified expression of genes to enhance biomass production in a sustainable and environmentally responsible manner. Tree genetic engineering has advanced to the point at which genes for desirable traits can now be introduced and expressed efficiently; examples include biotic and abiotic stress tolerance, improved wood properties, root formation and phytoremediation. Transgene confinement, including flowering control, may be needed to avoid ecological risks and satisfy regulatory requirements. This and stable expression are key issues that need to be resolved before transgenic trees can be used commercially. Copyright © 2010 Elsevier Ltd. All rights reserved.

Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.

Science.gov (United States)

Nye, Tom M W; Tang, Xiaoxian; Weyenberg, Grady; Yoshida, Ruriko

2017-12-01

Evolutionary relationships are represented by phylogenetic trees, and a phylogenetic analysis of gene sequences typically produces a collection of these trees, one for each gene in the analysis. Analysis of samples of trees is difficult due to the multi-dimensionality of the space of possible trees. In Euclidean spaces, principal component analysis is a popular method of reducing high-dimensional data to a low-dimensional representation that preserves much of the sample's structure. However, the space of all phylogenetic trees on a fixed set of species does not form a Euclidean vector space, and methods adapted to tree space are needed. Previous work introduced the notion of a principal geodesic in this space, analogous to the first principal component. Here we propose a geometric object for tree space similar to the [Formula: see text]th principal component in Euclidean space: the locus of the weighted Fréchet mean of [Formula: see text] vertex trees when the weights vary over the [Formula: see text]-simplex. We establish some basic properties of these objects, in particular showing that they have dimension [Formula: see text], and propose algorithms for projection onto these surfaces and for finding the principal locus associated with a sample of trees. Simulation studies demonstrate that these algorithms perform well, and analyses of two datasets, containing Apicomplexa and African coelacanth genomes respectively, reveal important structure from the second principal components.

The Tree Inclusion Problem: In Linear Space and Faster

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li

2011-01-01

Given two rooted, ordered, and labeled trees P and T the tree inclusion problem is to determine if P can be obtained from T by deleting nodes in T. This problem has recently been recognized as an important query primitive in XML databases. Kilpel äinen and Mannila [1995] presented the first....... This is particularly important in practical applications, such as XML databases, where the space is likely to be a bottleneck. © 2011 ACM....

Correlated genetic effects on reproduction define a domestication syndrome in a forest tree

Science.gov (United States)

Santos-del-Blanco, Luis; Alía, Ricardo; González-Martínez, Santiago C; Sampedro, Luis; Lario, Francisco; Climent, José

2015-01-01

Compared to natural selection, domestication implies a dramatic change in traits linked to fitness. A number of traits conferring fitness in the wild might be detrimental under domestication, and domesticated species typically differ from their ancestors in a set of traits known as the domestication syndrome. Specifically, trade-offs between growth and reproduction are well established across the tree of life. According to allocation theory, selection for growth rate is expected to indirectly alter life-history reproductive traits, diverting resources from reproduction to growth. Here we tested this hypothesis by examining the genetic change and correlated responses of reproductive traits as a result of selection for timber yield in the tree Pinus pinaster. Phenotypic selection was carried out in a natural population, and progenies from selected trees were compared with those of control trees in a common garden experiment. According to expectations, we detected a genetic change in important life-history traits due to selection. Specifically, threshold sizes for reproduction were much higher and reproductive investment relative to size significantly lower in the selected progenies just after a single artificial selection event. Our study helps to define the domestication syndrome in exploited forest trees and shows that changes affecting developmental pathways are relevant in domestication processes of long-lived plants. PMID:25926884

Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces

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York Thomas

2009-01-01

Full Text Available Abstract Background In phylogenetic inference one is interested in obtaining samples from the posterior distribution over the tree space on the basis of some observed DNA sequence data. One of the simplest sampling methods is the rejection sampler due to von Neumann. Here we introduce an auto-validating version of the rejection sampler, via interval analysis, to rigorously draw samples from posterior distributions over small phylogenetic tree spaces. Results The posterior samples from the auto-validating sampler are used to rigorously (i estimate posterior probabilities for different rooted topologies based on mitochondrial DNA from human, chimpanzee and gorilla, (ii conduct a non-parametric test of rate variation between protein-coding and tRNA-coding sites from three primates and (iii obtain a posterior estimate of the human-neanderthal divergence time. Conclusion This solves the open problem of rigorously drawing independent and identically distributed samples from the posterior distribution over rooted and unrooted small tree spaces (3 or 4 taxa based on any multiply-aligned sequence data.

Phylo-typing of clinical Escherichia coli isolates originating from bovine mastitis and canine pyometra and urinary tract infection by means of quadruplex PCR.

Science.gov (United States)

Müştak, Hamit Kaan; Günaydin, Elçin; Kaya, İnci Başak; Salar, Merve Özdal; Babacan, Orkun; Önat, Kaan; Ata, Zafer; Diker, Kadir Serdar

2015-01-01

Escherichia coli is one of the major causative agents of bovine mastitis worldwide, and is typically associated with acute, clinical mastitis. Besides this, E. coli strains which belong to the extra-intestinal pathogenic group are also the major cause of urinary tract infections and pyometra in dogs. In this study, it was aimed to investigate phylo-groups/subgroups in 155 E. coli isolates obtained from acute bovine mastitis, 43 from urinary tract infections of dogs and 20 from canine pyometra by a formerly described triplex PCR and recently described new quadruplex polymerase chain reaction (PCR) method. Group A1 (n = 118; 76%) and B1 (n = 71; 46%) were found to be the most prevalent groups by triplex and quadruplex PCR assays in mastitis isolates, respectively. Phylo-typing of 43 urinary tract isolates also revealed that most of the isolates belonged to A1 (n = 23; 54%) by triplex and B2 (n = 36; 84%) by quadruplex PCR assays. The isolates assigned as group A1 (n = 17; 85%) by triplex PCR could not be classified by quadruplex PCR in pyometra isolates. The results support the hypothesis that E. coli strains isolated from bovine mastitis cases are environmental. Also, groups C, E and F were identified as new phylo-groups for the first time in acute bovine mastitis cases. The comparison of triplex PCR with quadruplex PCR results revealed that most of the groups assigned in triplex PCR were altered by quadruplex PCR assay.

Modelling of electric tree progression due to space charge modified fields

International Nuclear Information System (INIS)

Seralathan, K E; Mahajan, A; Gupta, Nandini

2008-01-01

Tree initiation and growth require localized field enhancement that results in material erosion and formation of tree channels. Tree progression is linked to partial discharges within the tree tubules, characterized by recurrent periods of activity followed by quiescent states. Charge builds up across the non-conducting tree channels during the inactive regime, and discharge follows. In this work, the role of the space charge modified field during the non-discharging regime in deciding the site of subsequent discharges and thereby shaping tree structures is studied. A simple stochastic model was developed, in order to understand the respective effects of charges trapped on the walls of tree tubules, at channel tips, or in the volume of the dielectric. While some charge distributions are seen to arrest tree growth, others encourage axial growth towards the other electrode, and some aid in producing bushy trees clustered around the needle tip. The effect of carbon deposition within tree channels, making them effectively conducting, was also investigated. The insights gained from the simulations were successfully used to explain tree growth in the laboratory under high- and low-field conditions

A comparative analysis of genetic variation in rootstocks and scions of old olive trees - a window into the history of olive cultivation practices and past genetic variation.

Science.gov (United States)

Barazani, Oz; Westberg, Erik; Hanin, Nir; Dag, Arnon; Kerem, Zohar; Tugendhaft, Yizhar; Hmidat, Mohammed; Hijawi, Thameen; Kadereit, Joachim W

2014-05-28

Past clonal propagation of olive trees is intimately linked to grafting. However, evidence on grafting in ancient trees is scarce, and not much is known about the source of plant material used for rootstocks. Here, the Simple Sequence Repeat (SSR) marker technique was used to study genetic diversity of rootstocks and scions in ancient olive trees from the Levant and its implications for past cultivation of olives. Leaf samples were collected from tree canopies (scions) and shoots growing from the trunk base (suckers). A total of 310 trees were sampled in 32 groves and analyzed with 14 SSR markers. In 82.7% of the trees in which both scion and suckers could be genotyped, these were genetically different, and thus suckers were interpreted to represent the rootstock of grafted trees. Genetic diversity values were much higher among suckers than among scions, and 194 and 87 multi-locus genotypes (MLGs) were found in the two sample groups, respectively. Only five private alleles were found among scions, but 125 among suckers. A frequency analysis revealed a bimodal distribution of genetic distance among MLGs, indicating the presence of somatic mutations within clones. When assuming that MLGs differing by one mutation are identical, scion and sucker MLGs were grouped in 20 and 147 multi-locus lineages (MLLs). The majority of scions (90.0%) belonged to a single common MLL, whereas 50.5% of the suckers were single-sample MLLs. However, one MLL was specific to suckers and found in 63 (22.6%) of the samples. Our results provide strong evidence that the majority of olive trees in the study are grafted, that the large majority of scions belong to a single ancient cultivar containing somatic mutations, and that the widespread occurrence of one sucker genotype may imply rootstock selection. For the majority of grafted trees it seems likely that saplings were used as rootstocks; their genetic diversity probably is best explained as the result of a long history of sexual

Adaptive genetic potential of coniferous forest tree species under climate change: implications for sustainable forest management

Science.gov (United States)

Mihai, Georgeta; Birsan, Marius-Victor; Teodosiu, Maria; Dumitrescu, Alexandru; Daia, Mihai; Mirancea, Ionel; Ivanov, Paula; Alin, Alexandru

2017-04-01

Mountain ecosystems are extremely vulnerable to climate change. The real potential for adaptation depends upon the existence of a wide genetic diversity in trees populations, upon the adaptive genetic variation, respectively. Genetic diversity offers the guarantee that forest species can survive, adapt and evolve under the influence of changing environmental conditions. The aim of this study is to evaluate the genetic diversity and adaptive genetic potential of two local species - Norway spruce and European silver fir - in the context of regional climate change. Based on data from a long-term provenance experiments network and climate variables spanning over more than 50 years, we have investigated the impact of climatic factors on growth performance and adaptation of tree species. Our results indicate that climatic and geographic factors significantly affect forest site productivity. Mean annual temperature and annual precipitation amount were found to be statistically significant explanatory variables. Combining the additive genetic model with the analysis of nuclear markers we obtained different images of the genetic structure of tree populations. As genetic indicators we used: gene frequencies, genetic diversity, genetic differentiation, genetic variance, plasticity. Spatial genetic analyses have allowed identifying the genetic centers holding high genetic diversity which will be valuable sources of gene able to buffer the negative effects of future climate change. Correlations between the marginal populations and in the optimal vegetation, between the level of genetic diversity and ecosystem stability, will allow the assessment of future risks arising from current genetic structure. Therefore, the strategies for sustainable forest management have to rely on the adaptive genetic variation and local adaptation of the valuable genetic resources. This work was realized within the framework of the project GENCLIM (Evaluating the adaptive potential of the main

A comparative analysis of genetic variation in rootstocks and scions of old olive trees – a window into the history of olive cultivation practices and past genetic variation

Science.gov (United States)

2014-01-01

Background Past clonal propagation of olive trees is intimately linked to grafting. However, evidence on grafting in ancient trees is scarce, and not much is known about the source of plant material used for rootstocks. Here, the Simple Sequence Repeat (SSR) marker technique was used to study genetic diversity of rootstocks and scions in ancient olive trees from the Levant and its implications for past cultivation of olives. Leaf samples were collected from tree canopies (scions) and shoots growing from the trunk base (suckers). A total of 310 trees were sampled in 32 groves and analyzed with 14 SSR markers. Results In 82.7% of the trees in which both scion and suckers could be genotyped, these were genetically different, and thus suckers were interpreted to represent the rootstock of grafted trees. Genetic diversity values were much higher among suckers than among scions, and 194 and 87 multi-locus genotypes (MLGs) were found in the two sample groups, respectively. Only five private alleles were found among scions, but 125 among suckers. A frequency analysis revealed a bimodal distribution of genetic distance among MLGs, indicating the presence of somatic mutations within clones. When assuming that MLGs differing by one mutation are identical, scion and sucker MLGs were grouped in 20 and 147 multi-locus lineages (MLLs). The majority of scions (90.0%) belonged to a single common MLL, whereas 50.5% of the suckers were single-sample MLLs. However, one MLL was specific to suckers and found in 63 (22.6%) of the samples. Conclusions Our results provide strong evidence that the majority of olive trees in the study are grafted, that the large majority of scions belong to a single ancient cultivar containing somatic mutations, and that the widespread occurrence of one sucker genotype may imply rootstock selection. For the majority of grafted trees it seems likely that saplings were used as rootstocks; their genetic diversity probably is best explained as the result of a

The Optimization of In-Memory Space Partitioning Trees for Cache Utilization

Science.gov (United States)

Yeo, Myung Ho; Min, Young Soo; Bok, Kyoung Soo; Yoo, Jae Soo

In this paper, a novel cache conscious indexing technique based on space partitioning trees is proposed. Many researchers investigated efficient cache conscious indexing techniques which improve retrieval performance of in-memory database management system recently. However, most studies considered data partitioning and targeted fast information retrieval. Existing data partitioning-based index structures significantly degrade performance due to the redundant accesses of overlapped spaces. Specially, R-tree-based index structures suffer from the propagation of MBR (Minimum Bounding Rectangle) information by updating data frequently. In this paper, we propose an in-memory space partitioning index structure for optimal cache utilization. The proposed index structure is compared with the existing index structures in terms of update performance, insertion performance and cache-utilization rate in a variety of environments. The results demonstrate that the proposed index structure offers better performance than existing index structures.

Genetic Fuzzy Trees for Intelligent Control of Unmanned Combat Aerial Vehicles

Science.gov (United States)

Ernest, Nicholas D.

Fuzzy Logic Control is a powerful tool that has found great success in a variety of applications. This technique relies less on complex mathematics and more "expert knowledge" of a system to bring about high-performance, resilient, and efficient control through linguistic classification of inputs and outputs and if-then rules. Genetic Fuzzy Systems (GFSs) remove the need of this expert knowledge and instead rely on a Genetic Algorithm (GA) and have similarly found great success. However, the combination of these methods suffer severely from scalability; the number of rules required to control the system increases exponentially with the number of states the inputs and outputs can take. Therefor GFSs have thus far not been applicable to complex, artificial intelligence type problems. The novel Genetic Fuzzy Tree (GFT) method breaks down complex problems hierarchically, makes sub-decisions when possible, and thus greatly reduces the burden on the GA. This development significantly changes the field of possible applications for GFSs. Within this study, this is demonstrated through applying this technique to a difficult air combat problem. Looking forward to an autonomous Unmanned Combat Aerial Vehicle (UCAV) in the 2030 time-frame, it becomes apparent that the mission, flight, and ground controls will utilize the emerging paradigm of Intelligent Systems (IS); namely, the ability to learn, adapt, exhibit robustness in uncertain situations, make sense of the data collected in real-time and extrapolate when faced with scenarios significantly different from those used in training. LETHA (Learning Enhanced Tactical Handling Algorithm) was created to develop intelligent controllers for these advanced unmanned craft as the first GFT. A simulation space referred to as HADES (Hoplological Autonomous Defend and Engage Simulation) was created in which LETHA can train the UCAVs. Equipped with advanced sensors, a limited supply of Self-Defense Missiles (SDMs), and a recharging

Silviculture and the assessment of climate change genetic risk for southern Appalachian forest tree species

Science.gov (United States)

Kevin M. Potter; Barbara S. Crane

2012-01-01

Changing climate conditions and increasing insect and pathogen infestations will increase the likelihood that forest trees could experience population-level extirpation or species-level extinction during the next century. Gene conservation and silvicultural efforts to preserve forest tree genetic diversity present a particular challenge in species-rich regions such as...

Is there a positive relationship between naturalness and genetic diversity in forest tree communities?

OpenAIRE

Wehenkel, C.; Corral-Rivas, J. J.; Castellanos-Bocaz, H. A.; Pinedo-Alvarez, A.

2009-01-01

The concepts of genetic diversity and naturalness are well known as measures of conservation values and as descriptors of state or condition. A lack of research evaluating the relationship between genetic diversity and naturalness in biological communities, along with the possible implications in terms of evolutionary aspects and conservation management, make this subject particularly important as regards forest tree communities.We therefore examined the following hypothesis: the genetic dive...

Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species.

Science.gov (United States)

Lima, Jacqueline S; Ballesteros-Mejia, Liliana; Lima-Ribeiro, Matheus S; Collevatti, Rosane G

2017-11-01

The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long-lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions. © 2017 John Wiley & Sons Ltd.

Trade and Transfer of Tree Seed

DEFF Research Database (Denmark)

Schmidt, Lars Holger

2016-01-01

testing records. Genetic quality is documented as documents on origin or seed source. New types of tree planting by smallholders imply special problems in distribution and supply systems since production systems for tree seeds have large areas while many consumers have small space for planting....... A centralized forest seed supply contains large central units with good facilities for production and procurement but is far from seed users. Alternative decentralized systems with many small producers may have problems meeting high standards of seed quality and dealing with central regulations....

European genetic conservation strategies of forest trees in the context of currently running climate change

NARCIS (Netherlands)

Vries, de S.M.G.

2015-01-01

The diversity of forests, at the level of species and at the level of genetic diversity within species, is an important resource for Europe. Over the past several decades countries have made efforts to conserve the diversity of tree species and genetic diversity. However, there was no harmonised

Pollen, wind and fire: how to investigate genetic effects of disturbance-induced change in forest trees.

Science.gov (United States)

Bacles, Cecile F E

2014-01-01

Understanding the consequences of habitat disturbance on mating patterns although pollen and seed dispersal in forest trees has been a long-standing theme of forest and conservation genetics. Forest ecosystems face global environmental pressures from timber exploitation to genetic pollution and climate change, and it is therefore essential to comprehend how disturbances may alter the dispersal of genes and their establishment in tree populations in order to formulate relevant recommendations for sustainable resource management practices and realistic predictions of potential adaptation to climate change by means of range shift or expansion (Kremer et al. 2012). However, obtaining reliable evidence of disturbance-induced effects on gene dispersal processes from empirical evaluation of forest tree populations is difficult. Indeed, tree species share characteristics such as high longevity, long generation time and large reproductive population size, which may impede the experimenter's ability to assess parameters at the spatial and time scales at which any change may occur (Petit and Hampe 2006). It has been suggested that appropriate study designs should encompass comparison of populations before and after disturbance as well as account for demonstrated variation in conspecific density, that is, the spatial distribution of mates, and forest density, including all species and relating to alteration in landscape openness (Bacles & Jump 2011). However, more often than not, empirical studies aiming to assess the consequences of habitat disturbance on genetic processes in tree populations assume rather than quantify a change in tree densities in forests under disturbance and generally fail to account for population history, which may lead to inappropriate interpretation of a causal relationship between population genetic structure and habitat disturbance due to effects of unmonitored confounding variables (Gauzere et al. 2013). In this issue, Shohami and Nathan (2014

Assessment of diversity and genetic relationships of Neonectria ditissima: the causal agent of fruit tree canker.

Science.gov (United States)

Ghasemkhani, Marjan; Garkava-Gustavsson, Larisa; Liljeroth, Erland; Nybom, Hilde

2016-01-01

Neonectria ditissima is one of the most important fungal pathogens of apple trees, where it causes fruit tree canker. Information about the amount and partitioning of genetic variation of this fungus could be helpful for improving orchard management strategies and for breeding apple cultivars with high levels of genetically determined resistance. In this study single-spore Neonectria isolates originating from both the same and from different perithecia, apple cultivars and apple orchards in Sweden and Belgium, were evaluated for AFLP- and SSR-based genetic similarity and for mating system. Seven SSR loci produced a total of 31 alleles with an average of 4 alleles per locus, while 11 AFLP primer combinations produced an average of 35 fragments per primer combination and 71 % polymorphic fragments. An AFLP-based analysis of molecular variance (AMOVA) revealed that 89 % of the variation was found within orchards and 11 % between orchards. Genetic similarity among the studied isolates was illustrated with a principal coordinate analyseis (PCoA) and a dendrogram. AFLP-based Jaccard's similarity coefficients were the highest when single-ascospore isolates obtained from the same perithecium were compared, medium-high for isolates from different perithecia on the same tree, and lowest when isolates from different trees were compared. Based on the results of PCoA and AMOVA analysis, isolates from the same or geographically close orchards did not group together. Since AFLP profiles differed also when single-ascospore isolates from the same perithecium were compared, the mating system of N. ditissima is most likely heterothallic.

Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics

Directory of Open Access Journals (Sweden)

Alexander Safatli

2015-06-01

Full Text Available Summary. Pylogeny is a cross-platform library for the Python programming language that provides an object-oriented application programming interface for phylogenetic heuristic searches. Its primary function is to permit both heuristic search and analysis of the phylogenetic tree search space, as well as to enable the design of novel algorithms to search this space. To this end, the framework supports the structural manipulation of phylogenetic trees, in particular using rearrangement operators such as NNI, SPR, and TBR, the scoring of trees using parsimony and likelihood methods, the construction of a tree search space graph, and the programmatic execution of a few existing heuristic programs. The library supports a range of common phylogenetic file formats and can be used for both nucleotide and protein data. Furthermore, it is also capable of supporting GPU likelihood calculation on nucleotide character data through the BEAGLE library.Availability. Existing development and source code is available for contribution and for download by the public from GitHub (http://github.com/AlexSafatli/Pylogeny. A stable release of this framework is available for download through PyPi (Python Package Index at http://pypi.python.org/pypi/pylogeny.

Quantifying multi-dimensional functional trait spaces of trees: empirical versus theoretical approaches

Science.gov (United States)

Ogle, K.; Fell, M.; Barber, J. J.

2016-12-01

Empirical, field studies of plant functional traits have revealed important trade-offs among pairs or triplets of traits, such as the leaf (LES) and wood (WES) economics spectra. Trade-offs include correlations between leaf longevity (LL) vs specific leaf area (SLA), LL vs mass-specific leaf respiration rate (RmL), SLA vs RmL, and resistance to breakage vs wood density. Ordination analyses (e.g., PCA) show groupings of traits that tend to align with different life-history strategies or taxonomic groups. It is unclear, however, what underlies such trade-offs and emergent spectra. Do they arise from inherent physiological constraints on growth, or are they more reflective of environmental filtering? The relative importance of these mechanisms has implications for predicting biogeochemical cycling, which is influenced by trait distributions of the plant community. We address this question using an individual-based model of tree growth (ACGCA) to quantify the theoretical trait space of trees that emerges from physiological constraints. ACGCA's inputs include 32 physiological, anatomical, and allometric traits, many of which are related to the LES and WES. We fit ACGCA to 1.6 million USFS FIA observations of tree diameters and heights to obtain vectors of trait values that produce realistic growth, and we explored the structure of this trait space. No notable correlations emerged among the 496 trait pairs, but stepwise regressions revealed complicated multi-variate structure: e.g., relationships between pairs of traits (e.g., RmL and SLA) are governed by other traits (e.g., LL, radiation-use efficiency [RUE]). We also simulated growth under various canopy gap scenarios that impose varying degrees of environmental filtering to explore the multi-dimensional trait space (hypervolume) of trees that died vs survived. The centroid and volume of the hypervolumes differed among dead and live trees, especially under gap conditions leading to low mortality. Traits most predictive

Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change

OpenAIRE

Schueler, Silvio; Falk, Wolfgang; Koskela, Jarkko; Lefèvre, François; Bozzano, Michele; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C.

2014-01-01

A transnational network of genetic conservation units for forest trees was recently documented in Europe aiming at the conservation of evolutionary processes and the adaptive potential of natural or man-made tree populations. In this study, we quantified the vulnerability of individual conservation units and the whole network to climate change using climate favourability models and the estimated velocity of climate change. Compared to the overall climate niche of the analysed target species p...

Integrating environmental and genetic effects to predict responses of tree populations to climate.

Science.gov (United States)

Wang, Tongli; O'Neill, Gregory A; Aitken, Sally N

2010-01-01

Climate is a major environmental factor affecting the phenotype of trees and is also a critical agent of natural selection that has molded among-population genetic variation. Population response functions describe the environmental effect of planting site climates on the performance of a single population, whereas transfer functions describe among-population genetic variation molded by natural selection for climate. Although these approaches are widely used to predict the responses of trees to climate change, both have limitations. We present a novel approach that integrates both genetic and environmental effects into a single "universal response function" (URF) to better predict the influence of climate on phenotypes. Using a large lodgepole pine (Pinus contorta Dougl. ex Loud.) field transplant experiment composed of 140 populations planted on 62 sites to demonstrate the methodology, we show that the URF makes full use of data from provenance trials to: (1) improve predictions of climate change impacts on phenotypes; (2) reduce the size and cost of future provenance trials without compromising predictive power; (3) more fully exploit existing, less comprehensive provenance tests; (4) quantify and compare environmental and genetic effects of climate on population performance; and (5) predict the performance of any population growing in any climate. Finally, we discuss how the last attribute allows the URF to be used as a mechanistic model to predict population and species ranges for the future and to guide assisted migration of seed for reforestation, restoration, or afforestation and genetic conservation in a changing climate.

Building optimal regression tree by ant colony system-genetic algorithm: Application to modeling of melting points

Energy Technology Data Exchange (ETDEWEB)

Hemmateenejad, Bahram, E-mail: hemmatb@sums.ac.ir [Department of Chemistry, Shiraz University, Shiraz (Iran, Islamic Republic of); Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz (Iran, Islamic Republic of); Shamsipur, Mojtaba [Department of Chemistry, Razi University, Kermanshah (Iran, Islamic Republic of); Zare-Shahabadi, Vali [Young Researchers Club, Mahshahr Branch, Islamic Azad University, Mahshahr (Iran, Islamic Republic of); Akhond, Morteza [Department of Chemistry, Shiraz University, Shiraz (Iran, Islamic Republic of)

2011-10-17

Highlights: {yields} Ant colony systems help to build optimum classification and regression trees. {yields} Using of genetic algorithm operators in ant colony systems resulted in more appropriate models. {yields} Variable selection in each terminal node of the tree gives promising results. {yields} CART-ACS-GA could model the melting point of organic materials with prediction errors lower than previous models. - Abstract: The classification and regression trees (CART) possess the advantage of being able to handle large data sets and yield readily interpretable models. A conventional method of building a regression tree is recursive partitioning, which results in a good but not optimal tree. Ant colony system (ACS), which is a meta-heuristic algorithm and derived from the observation of real ants, can be used to overcome this problem. The purpose of this study was to explore the use of CART and its combination with ACS for modeling of melting points of a large variety of chemical compounds. Genetic algorithm (GA) operators (e.g., cross averring and mutation operators) were combined with ACS algorithm to select the best solution model. In addition, at each terminal node of the resulted tree, variable selection was done by ACS-GA algorithm to build an appropriate partial least squares (PLS) model. To test the ability of the resulted tree, a set of approximately 4173 structures and their melting points were used (3000 compounds as training set and 1173 as validation set). Further, an external test set containing of 277 drugs was used to validate the prediction ability of the tree. Comparison of the results obtained from both trees showed that the tree constructed by ACS-GA algorithm performs better than that produced by recursive partitioning procedure.

Genetic Augmentation of Syringyl Lignin in Low-lignin Aspen Trees, Final Report

Energy Technology Data Exchange (ETDEWEB)

Chung-Jui Tsai; Mark F. Davis; Vincent L. Chiang

2004-11-10

As a polysaccharide-encrusting component, lignin is critical to cell wall integrity and plant growth but also hinders recovery of cellulose fibers during the wood pulping process. To improve pulping efficiency, it is highly desirable to genetically modify lignin content and/or structure in pulpwood species to maximize pulp yields with minimal energy consumption and environmental impact. This project aimed to genetically augment the syringyl-to-guaiacyl lignin ratio in low-lignin transgenic aspen in order to produce trees with reduced lignin content, more reactive lignin structures and increased cellulose content. Transgenic aspen trees with reduced lignin content have already been achieved, prior to the start of this project, by antisense downregulation of a 4-coumarate:coenzyme A ligase gene (Hu et al., 1999 Nature Biotechnol 17: 808- 812). The primary objective of this study was to genetically augment syringyl lignin biosynthesis in these low-lignin trees in order to enhance lignin reactivity during chemical pulping. To accomplish this, both aspen and sweetgum genes encoding coniferaldehyde 5-hydroxylase (Osakabe et al., 1999 PNAS 96: 8955-8960) were targeted for over-expression in wildtype or low-lignin aspen under control of either a constitutive or a xylem-specific promoter. A second objective for this project was to develop reliable and cost-effective methods, such as pyrolysis Molecular Beam Mass Spectrometry and NMR, for rapid evaluation of cell wall chemical components of transgenic wood samples. With these high-throughput techniques, we observed increased syringyl-to-guaiacyl lignin ratios in the transgenic wood samples, regardless of the promoter used or gene origin. Our results confirmed that the coniferaldehyde 5-hydroxylase gene is key to syringyl lignin biosynthesis. The outcomes of this research should be readily applicable to other pulpwood species, and promise to bring direct economic and environmental benefits to the pulp and paper industry.

High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

Directory of Open Access Journals (Sweden)

Annika M E Noreen

Full Text Available Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter, 193 saplings (>1 yr, and 1,822 seedlings (<1 yr of the canopy tree Koompassia malaccensis (Fabaceae. We tested hypotheses relevant to the genetic consequences of habitat loss: (1 that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2 K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854, high allelic richness (R = 16.7-19.5, low inbreeding co-efficients (FIS = 0.013-0.076, and a large proportion (30.1% of rare alleles (i.e. frequency <1%. However, spatial genetic structure (SGS analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961, calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

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

Science.gov (United States)

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

2012-09-01

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

WITHIN-POPULATION GENETIC DIVERSITY OF CLIMBING PLANTS AND TREES IN A TEMPERATE FOREST IN CENTRAL CHILE

OpenAIRE

Torres-Díaz, Cristian; Ruiz, Eduardo; Salgado-Luarte, Cristian; Molina-Montenegro, Marco A; Gianoli, Ernesto

2013-01-01

The climbing habit is a key innovation in angiosperm evolution: climbing plant taxa have greater species richness than their non-climbing sister groups. It is considered that highly diversified clades should show increased among-population genetic differentiation. Less clear is the expected pattern regarding within-population genetic diversity in speciose lineages. We tested the hypothesis of greater within-population genetic diversity in climbing plants compared to trees in a temperate fores...

Genetic mapping in a full-sib family of apple

NARCIS (Netherlands)

Maliepaard, C.

2000-01-01

Genetic analysis in strictly outcrossing species is far more complicated than in species that can be selfed. When, in addition to that, a species has a long generation cycle, and when progenies from crosses require much space, as is the case for apple trees, then acquiring genetic knowledge

Utilizing forest tree genetic diversity for an adaptation of forest to climate change

Science.gov (United States)

Schueler, Silvio; Lackner, Magdalena; Chakraborty, Debojyoti

2017-04-01

Since climate conditions are considered to be major determinants of tree species' distribution ranges and drivers of local adaptation, anthropogenic climate change (CC) is expected to modify the distribution of tree species, tree species diversity and the forest ecosystems connected to these species. The expected speed of environmental change is significantly larger than the natural migration and adaptation capacity of trees and makes spontaneous adjustment of forest ecosystems improbable. Planting alternative tree species and utilizing the tree species' intrinsic adaptive capacity are considered to be the most promising adaptation strategy. Each year about 900 million seedlings of the major tree species are being planted in Central Europe. At present, the utilization of forest reproductive material is mainly restricted to nationally defined ecoregions (seed/provenance zones), but when seedlings planted today become adult, they might be maladapted, as the climate conditions within ecoregions changed significantly. In the cooperation project SUSTREE, we develop transnational delineation models for forest seed transfer and genetic conservation based on species distribution models and available intra-specific climate-response function. These models are being connected to national registers of forest reproductive material in order support nursery and forest managers by selecting the appropriate seedling material for future plantations. In the long-term, European and national policies as well as regional recommendations for provenances use need to adapted to consider the challenges of climate change.

Optimizing Conservation Strategies for a Threatened Tree Species: In Situ Conservation of White Ash (Fraxinus americana L. Genetic Diversity through Insecticide Treatment

Directory of Open Access Journals (Sweden)

Charles E. Flower

2018-04-01

Full Text Available Forest resources face numerous threats that require costly management. Hence, there is an increasing need for data-informed strategies to guide conservation practices. The introduction of the emerald ash borer to North America has caused rapid declines in ash populations (Fraxinus spp. L.. Natural resource managers are faced with a choice of either allowing ash trees to die, risking forest degradation and reduced functional resilience, or investing in conserving trees to preserve ecosystem structure and standing genetic diversity. The information needed to guide these decisions is not always readily available. Therefore, to address this concern, we used eight microsatellites to genotype 352 white ash trees (Fraxinus americana L. across 17 populations in the Allegheny National Forest; a subset of individuals sampled are part of an insecticide treatment regimen. Genetic diversity (number of alleles and He was equivalent in treated and untreated trees, with little evidence of differentiation or inbreeding, suggesting current insecticidal treatment is conserving local, neutral genetic diversity. Using simulations, we demonstrated that best practice is treating more populations rather than more trees in fewer populations. Furthermore, through genetic screening, conservation practitioners can select highly diverse and unique populations to maximize diversity and reduce expenditures (by up to 21%. These findings will help practitioners develop cost-effective strategies to conserve genetic diversity.

Genetically engineered trees for plantation forests: key considerations for environmental risk assessment.

Science.gov (United States)

Häggman, Hely; Raybould, Alan; Borem, Aluizio; Fox, Thomas; Handley, Levis; Hertzberg, Magnus; Lu, Meng-Zu; Macdonald, Philip; Oguchi, Taichi; Pasquali, Giancarlo; Pearson, Les; Peter, Gary; Quemada, Hector; Séguin, Armand; Tattersall, Kylie; Ulian, Eugênio; Walter, Christian; McLean, Morven

2013-09-01

Forests are vital to the world's ecological, social, cultural and economic well-being yet sustainable provision of goods and services from forests is increasingly challenged by pressures such as growing demand for wood and other forest products, land conversion and degradation, and climate change. Intensively managed, highly productive forestry incorporating the most advanced methods for tree breeding, including the application of genetic engineering (GE), has tremendous potential for producing more wood on less land. However, the deployment of GE trees in plantation forests is a controversial topic and concerns have been particularly expressed about potential harms to the environment. This paper, prepared by an international group of experts in silviculture, forest tree breeding, forest biotechnology and environmental risk assessment (ERA) that met in April 2012, examines how the ERA paradigm used for GE crop plants may be applied to GE trees for use in plantation forests. It emphasizes the importance of differentiating between ERA for confined field trials of GE trees, and ERA for unconfined or commercial-scale releases. In the case of the latter, particular attention is paid to characteristics of forest trees that distinguish them from shorter-lived plant species, the temporal and spatial scale of forests, and the biodiversity of the plantation forest as a receiving environment. © 2013 ILSI Research Foundation. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Tree rings provide a new class of phenotypes for genetic associations that foster insights into adaptation of conifers to climate change.

Science.gov (United States)

Housset, Johann M; Nadeau, Simon; Isabel, Nathalie; Depardieu, Claire; Duchesne, Isabelle; Lenz, Patrick; Girardin, Martin P

2018-04-01

Local adaptation in tree species has been documented through a long history of common garden experiments where functional traits (height, bud phenology) are used as proxies for fitness. However, the ability to identify genes or genomic regions related to adaptation to climate requires the evaluation of traits that precisely reflect how and when climate exerts selective constraints. We combine dendroecology with association genetics to establish a link between genotypes, phenotypes and interannual climatic fluctuations. We illustrate this approach by examining individual tree responses embedded in the annual rings of 233 Pinus strobus trees growing in a common garden experiment representing 38 populations from the majority of its range. We found that interannual variability in growth was affected by low temperatures during spring and autumn, and by summer heat and drought. Among-population variation in climatic sensitivity was significantly correlated with the mean annual temperature of the provenance, suggesting local adaptation. Genotype-phenotype associations using these new tree-ring phenotypes validated nine candidate genes identified in a previous genetic-environment association study. Combining dendroecology with association genetics allowed us to assess tree vulnerability to past climate at fine temporal scales and provides avenues for future genomic studies on functional adaptation in forest trees. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Genetic and environmental variation in rust frequency on mature mountain birch trees

Energy Technology Data Exchange (ETDEWEB)

Elamo, Pirjo; Saloniemi, Irma; Helander, M.L.; Neuvonen, Seppo [Turku Univ. (Finland). Dept. of Biology) and (Kevo Subarctic Research Inst., Turku (Finland)

2000-07-01

This study investigated genetic and environmental variation in the frequency of birch rust, the most important leaf disease of birch species, The same half-sib families of mature mountain birch trees were studied in two areas corresponding to their natural growing habitats over 3 yrs. The frequency of birch rust was examined both in the field and from detached leaves inoculated in the laboratory. The frequency of birch rust varied among the mountain birch families. However, the heritability of birch rust resistance was found to be fairly low, with the heritability of naturally occurring birch rust varying between 0.27 and 0.41. The frequency of birch rust varied highly between the two study areas and among study years. Nevertheless, the relative frequency of birch rust among tree individuals and tree families remained similar and as a result no notable genotype x environment interaction was observed. The field and in vitro results differed with respect to the ranking of birch families by birch rust resistance.

Phylogenetic trees in bioinformatics

Energy Technology Data Exchange (ETDEWEB)

Burr, Tom L [Los Alamos National Laboratory

2008-01-01

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

Tree growth and soil relations at the 1925 Wind River spacing test in coast Douglas-fir.

Science.gov (United States)

Richard E. Miller; Donald L. Reukema; Harry W. Anderson

2004-01-01

The 1925 Wind River spacing test is the earliest field trial seeking to determine the most appropriate spacing for planting Douglas-fir. Spacing treatments were not replicated, although individual spacings were subsampled by two to four tree-measurement plots. Previously, greater growth occurred at the wider spacings (10 and 12 ft) than at the closer spacings (4, 5, 6...

Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

Science.gov (United States)

Finger, Aline; Kaiser-Bunbury, Christopher N; Kettle, Chris J; Valentin, Terence; Ghazoul, Jaboury

2014-01-01

Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.

Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

Directory of Open Access Journals (Sweden)

Aline Finger

Full Text Available Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.

Two Trees: Migrating Fault Trees to Decision Trees for Real Time Fault Detection on International Space Station

Science.gov (United States)

Lee, Charles; Alena, Richard L.; Robinson, Peter

2004-01-01

We started from ISS fault trees example to migrate to decision trees, presented a method to convert fault trees to decision trees. The method shows that the visualizations of root cause of fault are easier and the tree manipulating becomes more programmatic via available decision tree programs. The visualization of decision trees for the diagnostic shows a format of straight forward and easy understands. For ISS real time fault diagnostic, the status of the systems could be shown by mining the signals through the trees and see where it stops at. The other advantage to use decision trees is that the trees can learn the fault patterns and predict the future fault from the historic data. The learning is not only on the static data sets but also can be online, through accumulating the real time data sets, the decision trees can gain and store faults patterns in the trees and recognize them when they come.

Genetic distances and phylogenetic trees of different Awassi sheep populations based on DNA sequencing.

Science.gov (United States)

Al-Atiyat, R M; Aljumaah, R S

2014-08-27

This study aimed to estimate evolutionary distances and to reconstruct phylogeny trees between different Awassi sheep populations. Thirty-two sheep individuals from three different geographical areas of Jordan and the Kingdom of Saudi Arabia (KSA) were randomly sampled. DNA was extracted from the tissue samples and sequenced using the T7 promoter universal primer. Different phylogenetic trees were reconstructed from 0.64-kb DNA sequences using the MEGA software with the best general time reverse distance model. Three methods of distance estimation were then used. The maximum composite likelihood test was considered for reconstructing maximum likelihood, neighbor-joining and UPGMA trees. The maximum likelihood tree indicated three major clusters separated by cytosine (C) and thymine (T). The greatest distance was shown between the South sheep and North sheep. On the other hand, the KSA sheep as an outgroup showed shorter evolutionary distance to the North sheep population than to the others. The neighbor-joining and UPGMA trees showed quite reliable clusters of evolutionary differentiation of Jordan sheep populations from the Saudi population. The overall results support geographical information and ecological types of the sheep populations studied. Summing up, the resulting phylogeny trees may contribute to the limited information about the genetic relatedness and phylogeny of Awassi sheep in nearby Arab countries.

The role of genetics and tree improvement in southern forest productivity

Science.gov (United States)

Ronald C. Schmidtling; T.L. Robison; S.E. McKeand; R.J. Rousseau; H.L. Allen; B. Goldfarb

2004-01-01

Because of space limitations, a thorough discussion of the rich history of tree improvement in the Southeastern United States cannot be totally accomplished in this forum. However, a synopsis of key program highlights and the people who forged and directed these programs is presented, together with a discussion of current and future work. This discussion covers...

Simulation of tree shade impacts on residential energy use for space conditioning in Sacramento

Science.gov (United States)

Simpson, J. R.; McPherson, E. G.

Tree shade reduces summer air conditioning demand and increases winter heating load by intercepting solar energy that would otherwise heat the shaded structure. We evaluate the magnitude of these effects here for 254 residential properties participating in a utility sponsored tree planting program in Sacramento, California. Tree and building characteristics and typical weather data are used to model hourly shading and energy used for space conditioning for each building for a period of one year. There were an average of 3.1 program trees per property which reduced annual and peak (8 h average from 1 to 9 p.m. Pacific Daylight Time) cooling energy use 153 kWh (7.1%) and 0.08 kW (2.3%) per tree, respectively. Annual heating load increased 0.85 GJ (0.80 MBtu, 1.9%) per tree. Changes in cooling load were smaller, but percentage changes larger, for newer buildings. Averaged over all homes, annual cooling savings of 15.25 per tree were reduced by a heating penalty of 5.25 per tree, for net savings of 10.00 per tree from shade. We estimate an annual cooling penalty of 2.80 per tree and heating savings of 6.80 per tree from reduced wind speed, for a net savings of 4.00 per tree, and total annual savings of 14.00 per tree (43.00 per property). Results are found to be consistent with previous simulations and the limited measurements available.

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

Science.gov (United States)

Tsai, Yi-Hsin E

2011-05-01

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

Risk of genetic maladaptation due to climate change in three major European tree species

Science.gov (United States)

Aline Frank; Glenn T. Howe; Christoph Sperisen; Peter Brang; Brad St. Clair; Dirk R. Schmatz; Caroline Heiri

2017-01-01

Tree populations usually show adaptations to their local environments as a result of natural selection. As climates change, populations can become locally maladapted and decline in fitness. Evaluating the expected degree of genetic maladaptation due to climate change will allow forest managers to assess forest vulnerability, and develop strategies to preserve forest...

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers

Science.gov (United States)

2010-01-01

The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with FST > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species. PMID:21637482

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers.

Science.gov (United States)

Enciso-Rodríguez, Felix; Martínez, Rodrigo; Lobo, Mario; Barrero, Luz Stella

2010-04-01

The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F(ST) > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII markers

Directory of Open Access Journals (Sweden)

Felix Enciso-Rodríguez

2010-01-01

Full Text Available The Lulo or naranjilla (Solanum quitoense Lam. and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt. are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32 and tree tomatoes (n = 30 through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII in other Solanaceae (Asterid species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested and tree tomatoes (26 out of 41 for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F ST > 0.90, which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

Pan-European strategy for genetic conservation of forest trees and establishment of a core network of dynamic conservation units

NARCIS (Netherlands)

Vries, de S.M.G.; Alan, Murat; Bozzano, Michele; Burianek, Vaclav

2015-01-01

The diversity of forests, at the level of species and at the level of genetic diversity within species, is an important resource for Europe. Over the past several decades European countries have made considerable efforts to conserve the genetic diversity of tree species. According to the EUFGIS

Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree.

Directory of Open Access Journals (Sweden)

Jennifer DeWoody

Full Text Available Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001 but negatively correlated with skeletonizer damage (P<0.01 in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast

Molecular basis of angiosperm tree architecture.

Science.gov (United States)

Hollender, Courtney A; Dardick, Chris

2015-04-01

The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science. No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.

Faster exact algorithms for computing Steiner trees in higher dimensional Euclidean spaces

DEFF Research Database (Denmark)

Fonseca, Rasmus; Brazil, Marcus; Winter, Pawel

The Euclidean Steiner tree problem asks for a network of minimum total length interconnecting a finite set of points in d-dimensional space. For d ≥ 3, only one practical algorithmic approach exists for this problem --- proposed by Smith in 1992. A number of refinements of Smith's algorithm have...

Tree spacing impacts the individual incidence of Moniliophthora roreri disease in cacao agroforests.

Science.gov (United States)

Ngo Bieng, Marie Ange; Alem, Laudine; Curtet, Chloé; Tixier, Philippe

2017-11-01

Using conventional pesticides in crop protection has raised serious environmental concerns and there is therefore a need for integrated pest management (IPM) methods. In this paper, we found that the spacing of trees can impact disease, which could result in a reduction in pesticide applications and may act as a potential IPM method. We studied Frosty Pod Rot (FPR) in 20 cacao agroforests in Costa Rica (Upala region). Using a generalized linear mixed model, we analyzed the impact of the neighborhood composition and distance from a studied cacao individual on its individual FPR incidence. We found that the number of cacao tree neighbors in a radius of 3.7 m and the number of fruit trees in a radius of 4.3 m had a significant negative influence on the incidence of FPR on individual cacao trees. Moreover, cacao tree neighbors had the most significant local influence compared to the neighborhood of other taller categories such as fruit or forest trees. The mechanisms involved are related to the barrier effect, due to the effectiveness of the cacao tree's architecture as an efficient barrier against FPR spore dispersal. This paper provides new insights into optimization of the spatial environment around each host as an original IPM method. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement.

Science.gov (United States)

Harfouche, Antoine; Meilan, Richard; Altman, Arie

2014-11-01

Abiotic stresses, such as drought, salinity and cold, are the major environmental stresses that adversely affect tree growth and, thus, forest productivity, and play a major role in determining the geographic distribution of tree species. Tree responses and tolerance to abiotic stress are complex biological processes that are best analyzed at a systems level using genetic, genomic, metabolomic and phenomic approaches. This will expedite the dissection of stress-sensing and signaling networks to further support efficient genetic improvement programs. Enormous genetic diversity for stress tolerance exists within some forest-tree species, and due to advances in sequencing technologies the molecular genetic basis for this diversity has been rapidly unfolding in recent years. In addition, the use of emerging phenotyping technologies extends the suite of traits that can be measured and will provide us with a better understanding of stress tolerance. The elucidation of abiotic stress-tolerance mechanisms will allow for effective pyramiding of multiple tolerances in a single tree through genetic engineering. Here we review recent progress in the dissection of the molecular basis of abiotic stress tolerance in forest trees, with special emphasis on Populus, Pinus, Picea, Eucalyptus and Quercus spp. We also outline practices that will enable the deployment of trees engineered for abiotic stress tolerance to land owners. Finally, recommendations for future work are discussed. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

IN SITU COMPARISON OF TREE-RING RESPONSES TO CLIMATE AND POPULATION GENETICS: THE NEED TO CONTROL FOR LOCAL CLIMATE AND SITE VARIABLES

Directory of Open Access Journals (Sweden)

Johann Mathias Housset

2016-10-01

Full Text Available Tree species responses to climate change will be greatly influenced by their evolutionary potential and their phenotypic plasticity. Investigating tree-rings responses to climate and population genetics at the regional scale is therefore crucial in assessing the tree behaviour to climate change. This study combined in situ dendroclimatology and population genetics over a latitudinal gradient and compared the variations between the two at the intra- and inter-population levels. This approach was applied on the northern marginal populations of Thuja occidentalis (eastern white-cedar in the Canadian boreal forest. We aimed first to assess the radial growth variability (response functional trait within populations across the gradient and to compare it with the genetic diversity (microsatellites. Second, we investigated the variability in the growth response to climate at the regional scale through the radial growth-climate relationships, and tested its correlation with environmental variables and population genetic structure. Model selection based on the Akaike Information Criteria revealed that the growth synchronicity between pairs of trees of a population covariates with both the genetic diversity of this population and the amount of precipitation (inverse correlation, although these variables only explained a small fraction of the observed variance. At the regional scale, variance partitioning and partial redundancy analysis indicate that the growth response to climate was greatly modulated by stand environmental variables, suggesting predominant plastic variations in growth-response to climate. Combining in situ dendroclimatology and population genetics is a promising way to investigate species’ response capacity to climate change in natural stands. We stress the need to control for local climate and site conditions effects on dendroclimatic response to climate to avoid misleading conclusions regarding the associations with genetic variables.

Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change.

Science.gov (United States)

Schueler, Silvio; Falk, Wolfgang; Koskela, Jarkko; Lefèvre, François; Bozzano, Michele; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C

2014-05-01

A transnational network of genetic conservation units for forest trees was recently documented in Europe aiming at the conservation of evolutionary processes and the adaptive potential of natural or man-made tree populations. In this study, we quantified the vulnerability of individual conservation units and the whole network to climate change using climate favourability models and the estimated velocity of climate change. Compared to the overall climate niche of the analysed target species populations at the warm and dry end of the species niche are underrepresented in the network. However, by 2100, target species in 33-65 % of conservation units, mostly located in southern Europe, will be at the limit or outside the species' current climatic niche as demonstrated by favourabilities below required model sensitivities of 95%. The highest average decrease in favourabilities throughout the network can be expected for coniferous trees although they are mainly occurring within units in mountainous landscapes for which we estimated lower velocities of change. Generally, the species-specific estimates of favourabilities showed only low correlations to the velocity of climate change in individual units, indicating that both vulnerability measures should be considered for climate risk analysis. The variation in favourabilities among target species within the same conservation units is expected to increase with climate change and will likely require a prioritization among co-occurring species. The present results suggest that there is a strong need to intensify monitoring efforts and to develop additional conservation measures for populations in the most vulnerable units. Also, our results call for continued transnational actions for genetic conservation of European forest trees, including the establishment of dynamic conservation populations outside the current species distribution ranges within European assisted migration schemes. © 2013 John Wiley & Sons Ltd.

Genetic and Genomic Analysis of the Tree Legume Pongamia pinnata as a Feedstock for Biofuels

Directory of Open Access Journals (Sweden)

Bandana Biswas

2013-11-01

Full Text Available The tree legume Pongamia { (L. Pierre [syn. (L. Panigrahi]} is emerging as an important biofuels feedstock. It produces about 30 kg per tree per year of seeds, containing up to 55% oil (w/v, of which approximately 50% is oleic acid (C. The capacity for biological N fixation places Pongamia in a more sustainable position than current nonlegume biofuel feedstocks. Also due to its drought and salinity tolerance, Pongamia can grow on marginal land not destined for production of food. As part of the effort to domesticate Pongamia our research group at The University of Queensland has started to develop specific genetic and genomic tools. Much of the preliminary work to date has focused on characterizing the genetic diversity of wild populations. This diversity is reflective of the outcrossing reproductive biology of Pongamia and necessitates the requirement to develop clonal propagation protocols. Both the chloroplast and mitochondrial genomes of Pongamia have been sequenced and annotated (152,968 and 425,718 bp, respectively, with similarities to previously characterized legume organelle genomes. Many nuclear genes associated with oil biosynthesis and nodulation in Pongamia have been characterized. The continued application of genetic and genomic tools will support the deployment of Pongamia as a sustainable biofuel feedstock.

Accelerating dynamic genetic conservation efforts: Use of FT-IR spectroscopy for the rapid identification of trees resistant to destructive pathogens

Science.gov (United States)

C. Villari; R.A. Sniezko; L.E. Rodriguez-Saona; P. Bonello

2017-01-01

A strong focus on tree germplasm that can resist threats such as non-native insects and pathogens, or a changing climate, is fundamental for successful genetic conservation efforts. However, the unavailability of tools for rapid screening of tree germplasm for resistance to critical pathogens and insect pests is becoming an increasingly serious bottleneck. Here we...

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Science.gov (United States)

Fouquier, Jennifer; Rideout, Jai Ram; Bolyen, Evan; Chase, John; Shiffer, Arron; McDonald, Daniel; Knight, Rob; Caporaso, J Gregory; Kelley, Scott T

2016-02-24

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non

Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

Energy Technology Data Exchange (ETDEWEB)

Sjolander, Kimmen [Univ. of California, Berkeley, CA (United States)

2014-12-08

The major advance during this last reporting period (8/15/12 to present) is our release of data on the PhyloFacts website: phylogenetic trees, multiple sequence alignments and other data for protein families are now available for download from http://phylogenomics.berkeley.edu/data/. This project as a whole aimed to develop high-throughput functional annotation systems that exploit information from protein 3D structure and evolution to provide highly precise inferences of various aspects of gene function, including molecular function, biological process, pathway association, Pfam domains, cellular localization and so on. We accomplished these aims by developing and testing different systems on a database of protein family trees: the PhyloFacts Phylogenomic Encyclopedia (at http://phylogenomics.berkeley.edu/phylofacts/ ).

Genetic differentiation for size at first reproduction through male versus female functions in the widespread Mediterranean tree Pinus pinaster.

Science.gov (United States)

Santos-del-Blanco, L; Climent, J; González-Martínez, S C; Pannell, J R

2012-11-01

The study of local adaptation in plant reproductive traits has received substantial attention in short-lived species, but studies conducted on forest trees are scarce. This lack of research on long-lived species represents an important gap in our knowledge, because inferences about selection on the reproduction and life history of short-lived species cannot necessarily be extrapolated to trees. This study considers whether the size for first reproduction is locally adapted across a broad geographical range of the Mediterranean conifer species Pinus pinaster. In particular, the study investigates whether this monoecious species varies genetically among populations in terms of whether individuals start to reproduce through their male function, their female function or both sexual functions simultaneously. Whether differences among populations could be attributed to local adaptation across a climatic gradient is then considered. Male and female reproduction and growth were measured during early stages of sexual maturity of a P. pinaster common garden comprising 23 populations sampled across the species range. Generalized linear mixed models were used to assess genetic variability of early reproductive life-history traits. Environmental correlations with reproductive life-history traits were tested after controlling for neutral genetic structure provided by 12 nuclear simple sequence repeat markers. Trees tended to reproduce first through their male function, at a size (height) that varied little among source populations. The transition to female reproduction was slower, showed higher levels of variability and was negatively correlated with vegetative growth traits. Several female reproductive traits were correlated with a gradient of growth conditions, even after accounting for neutral genetic structure, with populations from more unfavourable sites tending to commence female reproduction at a lower individual size. The study represents the first report of genetic

The production of homozygous tree material

Science.gov (United States)

Reinhard F. Stettler; George E. Howe

1966-01-01

Homozygous trees will never be the desired ultimate step in a forest tree improvement program. However, they will serve many purposes in forest genetics research: (1) in the detection of genetic markers; (2) in the isolation of traits under simple genetic control for the study of growth and differentiation phenomena; (3) as a tool as well as reference material in the...

Differential calculus on the space of Steiner minimal trees in Riemannian manifolds

International Nuclear Information System (INIS)

Ivanov, A O; Tuzhilin, A A

2001-01-01

It is proved that the length of a minimal spanning tree, the length of a Steiner minimal tree, and the Steiner ratio regarded as functions of finite subsets of a connected complete Riemannian manifold have directional derivatives in all directions. The derivatives of these functions are calculated and some properties of their critical points are found. In particular, a geometric criterion for a finite set to be critical for the Steiner ratio is found. This criterion imposes essential restrictions on the geometry of the sets for which the Steiner ratio attains its minimum, that is, the sets on which the Steiner ratio of the boundary set is equal to the Steiner ratio of the ambient space

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers

OpenAIRE

Enciso-Rodríguez, Felix; Martínez, Rodrigo; Lobo, Mario; Barrero, Luz Stella

2010-01-01

The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae...

Recursive algorithms for phylogenetic tree counting.

Science.gov (United States)

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

Science.gov (United States)

Ypma, Rolf J F; van Ballegooijen, W Marijn; Wallinga, Jacco

2013-11-01

Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology.

Discrete Approximations of Determinantal Point Processes on Continuous Spaces: Tree Representations and Tail Triviality

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Osada, Hirofumi; Osada, Shota

2018-01-01

We prove tail triviality of determinantal point processes μ on continuous spaces. Tail triviality has been proved for such processes only on discrete spaces, and hence we have generalized the result to continuous spaces. To do this, we construct tree representations, that is, discrete approximations of determinantal point processes enjoying a determinantal structure. There are many interesting examples of determinantal point processes on continuous spaces such as zero points of the hyperbolic Gaussian analytic function with Bergman kernel, and the thermodynamic limit of eigenvalues of Gaussian random matrices for Sine_2 , Airy_2 , Bessel_2 , and Ginibre point processes. Our main theorem proves all these point processes are tail trivial.

Neighbourhood density and genetic relatedness interact to determine fruit set and abortion rates in a continuous tropical tree population.

Science.gov (United States)

Jones, F A; Comita, L S

2008-12-07

Tropical trees may show positive density dependence in fruit set and maturation due to pollen limitation in low-density populations. However, pollen from closely related individuals in the local neighbourhood might reduce fruit set or increase fruit abortion in self-incompatible tree species. We investigated the role of neighbourhood density and genetic relatedness on individual fruit set and abortion in the neotropical tree Jacaranda copaia in a large forest plot in central Panama. Using nested neighbourhood models, we found a strong positive effect of increased conspecific density on fruit set and maturation. However, high neighbourhood genetic relatedness interacted with density to reduce total fruit set and increase the proportion of aborted fruit. Our results imply a fitness advantage for individuals growing in high densities as measured by fruit set, but realized fruit set is lowered by increased neighbourhood relatedness. We hypothesize that the mechanism involved is increased visitation by density-dependent invertebrate pollinators in high-density populations, which increases pollen quantity and carry-over and increases fruit set and maturation, coupled with self-incompatibility at early and late stages due to biparental inbreeding that lowers fruit set and increases fruit abortion. Implications for the reproductive ecology and conservation of tropical tree communities in continuous and fragmented habitats are discussed.

Effects of space flight factors on genetic diversity of Buchloe ...

African Journals Online (AJOL)

Jane

2011-10-05

Oct 5, 2011 ... results for wheat coleoptiles, lettuce hypocotyls, and garden-cress ... space radiation dose for plant seeds at linear energy transfer (LET) space was 4.79 ... information content (PIC), total genetic diversity of materials i and j.

All tree-level MHV form factors in N=4 SYM from twistor space

Energy Technology Data Exchange (ETDEWEB)

Koster, Laura [Institut für Mathematik, Institut für Physik und IRIS Adlershof,Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin (Germany); Mitev, Vladimir [Institut für Mathematik, Institut für Physik und IRIS Adlershof,Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin (Germany); PRISMA Cluster of Excellence, Institut für Physik, WA THEP,Johannes Gutenberg-Universität Mainz, Staudingerweg 7, 55128 Mainz (Germany); Staudacher, Matthias [Institut für Mathematik, Institut für Physik und IRIS Adlershof,Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin (Germany); Wilhelm, Matthias [Institut für Mathematik, Institut für Physik und IRIS Adlershof,Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin (Germany); Niels Bohr Institute, Copenhagen University,Blegdamsvej 17, 2100 Copenhagen (Denmark)

2016-06-28

We incorporate all gauge-invariant local composite operators into the twistor-space formulation of N=4 SYM theory, detailing and expanding on ideas we presented recently in http://arxiv.org/abs/1603.04471. The vertices for these operators contain infinitely many terms and we show how they can be constructed by taking suitable derivatives of a light-like Wilson loop in twistor space and shrinking it down to a point. In particular, these vertices directly yield the tree-level MHV super form factors of all composite operators in N=4 SYM theory.

Transforming phylogenetic networks: Moving beyond tree space

OpenAIRE

Huber, Katharina T.; Moulton, Vincent; Wu, Taoyang

2016-01-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transforme...

Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot

Science.gov (United States)

Bodare, Sofia; Tsuda, Yoshiaki; Ravikanth, Gudasalamani; Uma Shaanker, Ramanan; Lascoux, Martin

2013-01-01

The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species’ evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (FIS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies. PMID:24223264

Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot.

Science.gov (United States)

Bodare, Sofia; Tsuda, Yoshiaki; Ravikanth, Gudasalamani; Uma Shaanker, Ramanan; Lascoux, Martin

2013-09-01

The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (F IS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies.

Geodesic atlas-based labeling of anatomical trees

DEFF Research Database (Denmark)

Feragen, Aasa; Petersen, Jens; Owen, Megan

2015-01-01

We present a fast and robust atlas-based algorithm for labeling airway trees, using geodesic distances in a geometric tree-space. Possible branch label configurations for an unlabeled airway tree are evaluated using distances to a training set of labeled airway trees. In tree-space, airway tree t...... equally complete airway trees, and comparable in performance to that of experts in pulmonary medicine, emphasizing the suitability of the labeling algorithm for clinical use....

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

Science.gov (United States)

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays

Science.gov (United States)

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Zawada, David G.; Andersen, Gary L.

2013-01-01

Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes ‘white plague.’ PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (Orbicella annularis, formerly of the genus Montastraea [1]) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to Aurantimonas coralicida, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™ data presented here provide a broader characterization of the bacterial community changes that occur within Orbicella annularis during the shift from a healthy to diseased state.

Genetic algorithms for adaptive real-time control in space systems

Science.gov (United States)

Vanderzijp, J.; Choudry, A.

1988-01-01

Genetic Algorithms that are used for learning as one way to control the combinational explosion associated with the generation of new rules are discussed. The Genetic Algorithm approach tends to work best when it can be applied to a domain independent knowledge representation. Applications to real time control in space systems are discussed.

Aquaporins in the wild: natural genetic diversity and selective pressure in the PIP gene family in five Neotropical tree species

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Vendramin Giovanni G

2010-06-01

Full Text Available Abstract Background Tropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; they may therefore play a major adaptive role in these species. We describe genetic diversity in the PIP sub-family of the widespread gene family of Aquaporins in five Neotropical tree species covering four botanical families. Results PIP Aquaporin subfamily genes were isolated, and their DNA sequence polymorphisms characterised in natural populations. Sequence data were analysed with statistical tests of standard neutral equilibrium and demographic scenarios simulated to compare with the observed results. Chloroplast SSRs were also used to test demographic transitions. Most gene fragments are highly polymorphic and display signatures of balancing selection or bottlenecks; chloroplast SSR markers have significant statistics that do not conform to expectations for population bottlenecks. Although not incompatible with a purely demographic scenario, the combination of all tests tends to favour a selective interpretation of extant gene diversity. Conclusions Tropical tree PIP genes may generally undergo balancing selection, which may maintain high levels of genetic diversity at these loci. Genetic variation at PIP genes may represent a response to variable environmental conditions.

Physiology and Genetics of Tree-Phytophage Interactions

Science.gov (United States)

Frances Lieutier; William J. Mattson; Michael R. Wagner

1999-01-01

Interactions between trees and phytophagous organisms represent an important fundamental process in the evolution of forest ecosystems. Through evolutionary time, the special traits of trees have lead the herbivore populations to differentiate and evolve in order to cope with the variability in natural resistance mechanisms of their hosts. Conversely, damage by...

Toward a theory of statistical tree-shape analysis

DEFF Research Database (Denmark)

Feragen, Aasa; Lo, Pechin Chien Pau; de Bruijne, Marleen

2013-01-01

In order to develop statistical methods for shapes with a tree-structure, we construct a shape space framework for tree-shapes and study metrics on the shape space. This shape space has singularities, which correspond to topological transitions in the represented trees. We study two closely relat...

Water Tree Influence on Space Charge Distribution and on the Residual Electric Field in Polyethylene Insulation

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Cristina Stancu

2009-10-01

Full Text Available A computation method of the electricfield and ionic space charge density in planeinsulations with water trees (using a ComsolMultiphysics software and the thermal step currents(Im(t measured with Thermal Step Method ispresented. A parabolic spatial variation of volumecharge density, an exponential spatial variation ofthe electric permittivity ε and a linear dependency ofε and the temperature coefficient of permittivity αεwith the average water concentration in trees, areconsidered. For a water tree with a known length,different values of charge density are consideredand the electric field and the thermal step currentsIc(t are calculated. The currents Ic(t and Im(t arecompared and the volume of charge density andelectric field for which Ic(t is identical with Im(t arekept.

Mathematical foundations of event trees

International Nuclear Information System (INIS)

Papazoglou, Ioannis A.

1998-01-01

A mathematical foundation from first principles of event trees is presented. The main objective of this formulation is to offer a formal basis for developing automated computer assisted construction techniques for event trees. The mathematical theory of event trees is based on the correspondence between the paths of the tree and the elements of the outcome space of a joint event. The concept of a basic cylinder set is introduced to describe joint event outcomes conditional on specific outcomes of basic events or unconditional on the outcome of basic events. The concept of outcome space partition is used to describe the minimum amount of information intended to be preserved by the event tree representation. These concepts form the basis for an algorithm for systematic search for and generation of the most compact (reduced) form of an event tree consistent with the minimum amount of information the tree should preserve. This mathematical foundation allows for the development of techniques for automated generation of event trees corresponding to joint events which are formally described through other types of graphical models. Such a technique has been developed for complex systems described by functional blocks and it is reported elsewhere. On the quantification issue of event trees, a formal definition of a probability space corresponding to the event tree outcomes is provided. Finally, a short discussion is offered on the relationship of the presented mathematical theory with the more general use of event trees in reliability analysis of dynamic systems

tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

Science.gov (United States)

Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

2014-01-01

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

Species collapse via hybridization in Darwin's tree finches.

Science.gov (United States)

Kleindorfer, Sonia; O'Connor, Jody A; Dudaniec, Rachael Y; Myers, Steven A; Robertson, Jeremy; Sulloway, Frank J

2014-03-01

Species hybridization can lead to fitness costs, species collapse, and novel evolutionary trajectories in changing environments. Hybridization is predicted to be more common when environmental conditions change rapidly. Here, we test patterns of hybridization in three sympatric tree finch species (small tree finch Camarhynchus parvulus, medium tree finch Camarhynchus pauper, and large tree finch: Camarhynchus psittacula) that are currently recognized on Floreana Island, Galápagos Archipelago. Genetic analysis of microsatellite data from contemporary samples showed two genetic populations and one hybrid cluster in both 2005 and 2010; hybrid individuals were derived from genetic population 1 (small morph) and genetic population 2 (large morph). Females of the large and rare species were more likely to pair with males of the small common species. Finch populations differed in morphology in 1852-1906 compared with 2005/2010. An unsupervised clustering method showed (a) support for three morphological clusters in the historical tree finch sample (1852-1906), which is consistent with current species recognition; (b) support for two or three morphological clusters in 2005 with some (19%) hybridization; and (c) support for just two morphological clusters in 2010 with frequent (41%) hybridization. We discuss these findings in relation to species demarcations of Camarhynchus tree finches on Floreana Island.

Coalescent methods for estimating phylogenetic trees.

Science.gov (United States)

Liu, Liang; Yu, Lili; Kubatko, Laura; Pearl, Dennis K; Edwards, Scott V

2009-10-01

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

Maximum Gene-Support Tree

Directory of Open Access Journals (Sweden)

Yunfeng Shan

2008-01-01

Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

Comparing forest measurements from tree rings and a space-based index of vegetation activity in Siberia

International Nuclear Information System (INIS)

Bunn, Andrew G; Hughes, Malcolm K; Losleben, Mark; Kirdyanov, Alexander V; Shishov, Vladimir V; Vaganov, Eugene A; Berner, Logan T; Oltchev, Alexander

2013-01-01

Different methods have been developed for measuring carbon stocks and fluxes in the northern high latitudes, ranging from intensively measured small plots to space-based methods that use reflectance data to drive production efficiency models. The field of dendroecology has used samples of tree growth from radial increments to quantify long-term variability in ecosystem productivity, but these have very limited spatial domains. Since the cambium material in tree cores is itself a product of photosynthesis in the canopy, it would be ideal to link these two approaches. We examine the associations between the normalized differenced vegetation index (NDVI) and tree growth using 19 pairs of tree-ring widths (TRW) and maximum latewood density (MXD) across much of Siberia. We find consistent correlations between NDVI and both measures of tree growth and no systematic difference between MXD and TRW. At the regional level we note strong correspondence between the first principal component of tree growth and NDVI for MXD and TRW in a temperature-limited bioregion, indicating that canopy reflectance and cambial production are broadly linked. Using a network of 21 TRW chronologies from south of Lake Baikal, we find a similarly strong regional correspondence with NDVI in a markedly drier region. We show that tree growth is dominated by variation at decadal and multidecadal time periods, which the satellite record is incapable of recording given its relatively short record. (letter)

Microwave sensing of tree trunks

Science.gov (United States)

Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

2015-04-01

The main subject of this research is the observation of the inner part of living tree trunks using ground-penetrating radar (GPR). Trees are everyday part of human life and therefore it is important to pay attention to the tree conditions. The most obvious consequence of the poor tree condition is dead or injury caused by falling tree. The trunk internal structure is divided into three main parts: heartwood, sapwood and bark, which make this medium highly anisotropic and heterogeneous. Furthermore, the properties of the wood are not only specie-dependent but also depend on genetic and on environmental conditions. In urban areas the main problem for the stability of the trees relies in the apparition of decays provoked by fungi, insect or birds. This results in cavities or decreasing of the support capacity of the tree. GPR has proved itself to be a very powerful electromagnetic tool for non-destructive detection of buried objects. Since the beginning of the 20th century it has been used in several different areas (archaeology, landmine detection, civil engineering, ...). GPR uses the principle of the scattering of the electromagnetic waves that are radiated from a transmitting antenna. Then the waves propagate through the medium and are reflected from the object and then they are received by a receiving antenna. The velocity of the scattered signal is determined primarily by the permittivity of the material. The optimal functionality of the GPR was investigated using the numerical simulation tool gprMax2D. This tool is based on a Finite-Difference Time-Domain (FDTD) numerical model. Subsequently, the GPR functionality was tested using the laboratory model of a decayed tree trunk. Afterwards, the results and lessons learnt in the simplified tests will be used in the processing of the real data and will help to achieve deeper understanding of them. The laboratory model of the tree trunk was made by plastic or carton pipes and filled by sand. Space inside the model

The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus.

Science.gov (United States)

Valdazo-González, Begoña; Kim, Jan T; Soubeyrand, Samuel; Wadsworth, Jemma; Knowles, Nick J; Haydon, Daniel T; King, Donald P

2015-06-01

Full-genome sequences have been used to monitor the fine-scale dynamics of epidemics caused by RNA viruses. However, the ability of this approach to confidently reconstruct transmission trees is limited by the knowledge of the genetic diversity of viruses that exist within different epidemiological units. In order to address this question, this study investigated the variability of 45 foot-and-mouth disease virus (FMDV) genome sequences (from 33 animals) that were collected during 2007 from eight premises (10 different herds) in the United Kingdom. Bayesian and statistical parsimony analysis demonstrated that these sequences exhibited clustering which was consistent with a transmission scenario describing herd-to-herd spread of the virus. As an alternative to analysing all of the available samples in future epidemics, the impact of randomly selecting one sequence from each of these herds was used to assess cost-effective methods that might be used to infer transmission trees during FMD outbreaks. Using these approaches, 85% and 91% of the resulting topologies were either identical or differed by only one edge from a reference tree comprising all of the sequences generated within the outbreak. The sequence distances that accrued during sequential transmission events between epidemiological units was estimated to be 4.6 nucleotides, although the genetic variability between viruses recovered from chronic carrier animals was higher than between viruses from animals with acute-stage infection: an observation which poses challenges for the use of simple approaches to infer transmission trees. This study helps to develop strategies for sampling during FMD outbreaks, and provides data that will guide the development of further models to support control policies in the event of virus incursions into FMD free countries. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China.

Directory of Open Access Journals (Sweden)

He Li

Full Text Available The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces. Multilocus sequence typing was conducted for all isolates based on DNA sequences at fragments of four genes: the internal transcribed spacers of the nuclear ribosomal RNA gene cluster (539 bp, calmodulin (633 bp, glutamine synthetase (711 bp, and glyceraldehyde-3-phosphate dehydrogenase (190 bp, yielding 3.52%, 0.63%, 8.44%, and 7.89% of single nucleotide polymorphic sites and resulting in 15, 5, 12 and 11 alleles respectively at the four gene fragments in the total sample. The combined allelic information from all four loci identified 53 multilocus genotypes with the most frequent represented by 21 isolates distributed in eight tea-oil plantations in three provinces, consistent with long-distance clonal dispersal. However, despite evidence for clonal dispersal, statistically significant genetic differentiation among geographic populations was detected. In addition, while no evidence of recombination was found within any of the four gene fragments, signatures of recombination were found among the four gene fragments in most geographic populations, consistent with sexual mating of this species in nature. Our study provides the first insights into the population genetics and epidemiology of the important plant fungal pathogen C. fructicola.

Lack of genetic variation in tree ring delta13C suggests a uniform, stomatally-driven response to drought stress across Pinus radiata genotypes.

Science.gov (United States)

Rowell, Douglas M; Ades, Peter K; Tausz, Michael; Arndt, Stefan K; Adams, Mark A

2009-02-01

We assessed the variation in delta(13)C signatures of Pinus radiata D. Don stemwood taken from three genetic trials in southern Australia. We sought to determine the potential of using delta(13)C signatures as selection criteria for drought tolerance. Increment cores were taken from P. radiata and were used to determine the basal area increment and the delta(13)C signature of extracted cellulose. Both growth increment and cellulose delta(13)C were affected by water availability. Growth increment and delta(13)C were negatively correlated suggesting that growth was water-limited. While there was significant genetic variation in growth, there was no significant genetic variation in cellulose delta(13)C of tree rings. This suggests that different genotypes of P. radiata display significant differences in growth and yet respond similarly to drought stress. The delta(13)C response to drought stress was more due to changes in stomatal conductance than to the variation in photosynthetic capacity, and this may explain the lack of genetic variation in delta(13)C. The lack of genetic variation in cellulose delta(13)C of tree rings precludes its use as a selection criterion for drought tolerance among P. radiata genotypes.

Evaluation of the genetic diversity of Plum pox virus in a single plum tree.

Science.gov (United States)

Predajňa, Lukáš; Šubr, Zdeno; Candresse, Thierry; Glasa, Miroslav

2012-07-01

Genetic diversity of Plum pox virus (PPV) and its distribution within a single perennial woody host (plum, Prunus domestica) has been evaluated. A plum tree was triply infected by chip-budding with PPV-M, PPV-D and PPV-Rec isolates in 2003 and left to develop untreated under open field conditions. In September 2010 leaf and fruit samples were collected from different parts of the tree canopy. A 745-bp NIb-CP fragment of PPV genome, containing the hypervariable region encoding the CP N-terminal end was amplified by RT-PCR from each sample and directly sequenced to determine the dominant sequence. In parallel, the PCR products were cloned and a total of 105 individual clones were sequenced. Sequence analysis revealed that after 7 years of infection, only PPV-M was still detectable in the tree and that the two other isolates (PPV-Rec and PPV-D) had been displaced. Despite the fact that the analysis targeted a relatively short portion of the genome, a substantial amount of intra-isolate variability was observed for PPV-M. A total of 51 different haplotypes could be identified from the 105 individual sequences, two of which were largely dominant. However, no clear-cut structuration of the viral population by the tree architecture could be highlighted although the results obtained suggest the possibility of intra-leaf/fruit differentiation of the viral population. Comparison of the consensus sequence with the original source isolate showed no difference, suggesting within-plant stability of this original isolate under open field conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

Hardwood genetics and tree improvement - A Midwest USA perspective

Science.gov (United States)

C. H. Michler; R. Meilan; K. E. Woeste; P. M. Pijut; D. Jacobs; P. Aldrich; J. Glaubitz

2005-01-01

Fine hardwood trees in the Central Hardwoods region of the United States are an important resource for the furniture, cabinetry, flooring, modular home, and paneling manufacturing industries. Consumers find wood from these trees to be very desirable because of quality factors such as grain, strength and color. To enhance wood production, tree improvement programs can...

Assessing crown dynamics and inter-tree competition in southern pines

Science.gov (United States)

Timothy A. Martin; Angelica Garcia; Tania Quesada; Eric J. Jokela; Salvador Gezan

2015-01-01

Genetic improvement of southern pines has been underway for 50 years and during this time, deployment of germplasm has generally evolved from more genetically diverse to less genetically diverse. Information is needed on how deployment of individual genotypes in pure blocks will affect traits such as within-stand variation in individual tree traits, as well as tree-...

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

Directory of Open Access Journals (Sweden)

Nobushima Fuyuo

2006-10-01

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

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

Science.gov (United States)

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

2006-10-11

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

Gene pool conservation and tree improvement in Serbia

Directory of Open Access Journals (Sweden)

Isajev Vasilije

2009-01-01

Full Text Available This paper presents the concepts applied in the gene pool conservation and tree improvement in Serbia. Gene pool conservation of tree species in Serbia includes a series of activities aiming at the sustainability and protection of genetic and species variability. This implies the investigation of genetic resources and their identification through the research of the genetic structure and the breeding system of individual species. Paper also includes the study of intra- and inter-population variability in experiments - provenance tests, progeny tests, half- and full-sib lines, etc. The increased use of the genetic potential in tree improvement in Serbia should be intensified by the following activities: improvement of production of normal forest seed, application of the concept of new selections directed primarily to the improvement of only one character, because in that case the result would be certain, establishment and management of seed orchards as specialized plantations for long-term production of genetically good-quality forest seeds, and the shortening of the improvement process by introducing new techniques and methods (molecular markers, somaclonal variation, genetic engineering, protoplast fusion, micropropagation, etc..

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

Directory of Open Access Journals (Sweden)

Benjamin J Gosney

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

Design Optimization of Space Launch Vehicles Using a Genetic Algorithm

National Research Council Canada - National Science Library

Bayley, Douglas J

2007-01-01

.... A genetic algorithm (GA) was employed to optimize the design of the space launch vehicle. A cost model was incorporated into the optimization process with the goal of minimizing the overall vehicle cost...

FB-Tree: A B+-Tree for Flash-Based SSDs

DEFF Research Database (Denmark)

Jørgensen, Martin V.; Rasmussen, René B.; Saltenis, Simonas

2011-01-01

Due to their many advantages, flash-based SSDs (Solid-State Drives) have become a mainstream alternative to magnetic disks for database servers. Nevertheless, database systems, designed and optimized for magnetic disks, still do not fully exploit all the benefits of the new technology. We propose....... As a consequence, the FB-tree outperforms a regular B+-tree in all scenarios tested. For instance, the throughput of a random workload of 75% updates increases by a factor of three using only two times the space of the B+-tree....

Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests.

Science.gov (United States)

Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

2016-03-01

Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species.

Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests

Science.gov (United States)

Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

2016-01-01

Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species. PMID:26696137

Population genetic variation in the tree fern Alsophila spinulosa (Cyatheaceae): effects of reproductive strategy.

Science.gov (United States)

Wang, Ting; Su, Yingjuan; Li, Yuan

2012-01-01

Essentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation. Inter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG) in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations. Sexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

Population genetic variation in the tree fern Alsophila spinulosa (Cyatheaceae: effects of reproductive strategy.

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Ting Wang

Full Text Available BACKGROUND: Essentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation. METHODOLOGY/PRINCIPAL FINDINGS: Inter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations. CONCLUSIONS/SIGNIFICANCE: Sexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

Genetic signatures of variation in population size in a native fungal pathogen after the recent intensive plantation of its host tree

NARCIS (Netherlands)

Labbé, Frédéric; Fontaine, Michael Christophe; Robin, Cécile; Dutech, Cyril

2017-01-01

Historical fluctuations in forests’ distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that

Development of hybrid genetic-algorithm-based neural networks using regression trees for modeling air quality inside a public transportation bus.

Science.gov (United States)

Kadiyala, Akhil; Kaur, Devinder; Kumar, Ashok

2013-02-01

The present study developed a novel approach to modeling indoor air quality (IAQ) of a public transportation bus by the development of hybrid genetic-algorithm-based neural networks (also known as evolutionary neural networks) with input variables optimized from using the regression trees, referred as the GART approach. This study validated the applicability of the GART modeling approach in solving complex nonlinear systems by accurately predicting the monitored contaminants of carbon dioxide (CO2), carbon monoxide (CO), nitric oxide (NO), sulfur dioxide (SO2), 0.3-0.4 microm sized particle numbers, 0.4-0.5 microm sized particle numbers, particulate matter (PM) concentrations less than 1.0 microm (PM10), and PM concentrations less than 2.5 microm (PM2.5) inside a public transportation bus operating on 20% grade biodiesel in Toledo, OH. First, the important variables affecting each monitored in-bus contaminant were determined using regression trees. Second, the analysis of variance was used as a complimentary sensitivity analysis to the regression tree results to determine a subset of statistically significant variables affecting each monitored in-bus contaminant. Finally, the identified subsets of statistically significant variables were used as inputs to develop three artificial neural network (ANN) models. The models developed were regression tree-based back-propagation network (BPN-RT), regression tree-based radial basis function network (RBFN-RT), and GART models. Performance measures were used to validate the predictive capacity of the developed IAQ models. The results from this approach were compared with the results obtained from using a theoretical approach and a generalized practicable approach to modeling IAQ that included the consideration of additional independent variables when developing the aforementioned ANN models. The hybrid GART models were able to capture majority of the variance in the monitored in-bus contaminants. The genetic

Effects of nurse trees, spacing, and tree species on biomass production in mixed forest plantations

DEFF Research Database (Denmark)

Nord-Larsen, Thomas; Meilby, Henrik

2016-01-01

Growing concern about increasing concentrations of greenhouse gases in the atmosphere, and resulting global climate change, has spurred a growing demand for renewable energy. In this study, we hypothesized that a nurse tree crop may provide additional early yields of biomass for fuel, while...... was in most cases reduced due to competition. However, provided timely thinning of nurse trees, the qualitative development of the trees will allow for long-term timber production....

Spermatogenic and Phylo-molecular Characterizations of Isolated Fasciola Spp. From Cattle, North West Iran.

Science.gov (United States)

Rouhani, Soheila; Raeghi, Saber; Spotin, Adel

2017-01-01

Fascioliasis is economically important to the livestock industry that caused with Fasciola hepatica and Fasciola gigantica. The objective of this study was to identify these two species F. hepatica and F. gigantica by using nuclear and mitochondrial markers (ITS1, ND1 and CO1) and have been employed to analyze intraspecific phylogenetic relations of Fasciola spp. Approximately 150 Fasciola specimens were collected, then stained with haematoxylin-carmine dye and observed under an optical microscope to examine for the existence of sperm. The ITS1 marker was used to identify different Fasciola and phylogenetic analysis based on ND1 and CO1 sequence data were conducted by maximum likelihood algorithm. Fasciola samples were separated into 2 groups. Almost all specimens had many sperms in the seminal vesicle (spermic fluke) and one fluke did not contain any sperm in the seminal vesicle. The aspermic sample had F. gigantica RFLP pattern with ITS1 gene. Phylogenetic analysis based on NDI and COI sequence data were conducted by maximum likelihood showed a similar topology of the trees obtained particularly for F. hepatica and F. gigantica. This study demonstrated that aspermic Fasciola found in this region of Iran has same genetic structures through the spermic F. gigantica populations in accordance to phylogenetic tree.

Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot

OpenAIRE

Bodare, Sofia; Tsuda, Yoshiaki; Ravikanth, Gudasalamani; Uma Shaanker, Ramanan; Lascoux, Martin

2013-01-01

The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In ...

How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity.

Science.gov (United States)

Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

2014-11-01

Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and 'improved' trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity. © The Author 2014. Published by Oxford University Press. All rights reserved

Finiteness results for Abelian tree models

NARCIS (Netherlands)

Draisma, J.; Eggermont, R.H.

2015-01-01

Equivariant tree models are statistical models used in the reconstruction of phylogenetic trees from genetic data. Here equivariant refers to a symmetry group imposed on the root distribution and on the transition matrices in the model. We prove that if that symmetry group is Abelian, then the

Finiteness results for Abelian tree models

NARCIS (Netherlands)

Draisma, J.; Eggermont, R.H.

2012-01-01

Equivariant tree models are statistical models used in the reconstruction of phylogenetic trees from genetic data. Here equivariant refers to a symmetry group imposed on the root distribution and on the transition matrices in the model. We prove that if that symmetry group is Abelian, then the

Computing Refined Buneman Trees in Cubic Time

DEFF Research Database (Denmark)

Brodal, G.S.; Fagerberg, R.; Östlin, A.

2003-01-01

Reconstructing the evolutionary tree for a set of n species based on pairwise distances between the species is a fundamental problem in bioinformatics. Neighbor joining is a popular distance based tree reconstruction method. It always proposes fully resolved binary trees despite missing evidence...... in the underlying distance data. Distance based methods based on the theory of Buneman trees and refined Buneman trees avoid this problem by only proposing evolutionary trees whose edges satisfy a number of constraints. These trees might not be fully resolved but there is strong combinatorial evidence for each...... proposed edge. The currently best algorithm for computing the refined Buneman tree from a given distance measure has a running time of O(n 5) and a space consumption of O(n 4). In this paper, we present an algorithm with running time O(n 3) and space consumption O(n 2). The improved complexity of our...

Finiteness results for Abelian tree models

NARCIS (Netherlands)

Draisma, J.; Eggermont, R.H.

2015-01-01

Equivariant tree models are statistical models used in the reconstruction of phylogenetic trees from genetic data. Here equivariant§ refers to a symmetry group imposed on the root distribution and on the transition matrices in the model. We prove that if that symmetry group is Abelian, then the

A Benchmark of Lidar-Based Single Tree Detection Methods Using Heterogeneous Forest Data from the Alpine Space

Directory of Open Access Journals (Sweden)

Lothar Eysn

2015-05-01

Full Text Available In this study, eight airborne laser scanning (ALS-based single tree detection methods are benchmarked and investigated. The methods were applied to a unique dataset originating from different regions of the Alpine Space covering different study areas, forest types, and structures. This is the first benchmark ever performed for different forests within the Alps. The evaluation of the detection results was carried out in a reproducible way by automatically matching them to precise in situ forest inventory data using a restricted nearest neighbor detection approach. Quantitative statistical parameters such as percentages of correctly matched trees and omission and commission errors are presented. The proposed automated matching procedure presented herein shows an overall accuracy of 97%. Method based analysis, investigations per forest type, and an overall benchmark performance are presented. The best matching rate was obtained for single-layered coniferous forests. Dominated trees were challenging for all methods. The overall performance shows a matching rate of 47%, which is comparable to results of other benchmarks performed in the past. The study provides new insight regarding the potential and limits of tree detection with ALS and underlines some key aspects regarding the choice of method when performing single tree detection for the various forest types encountered in alpine regions.

TreeNetViz: revealing patterns of networks over tree structures.

Science.gov (United States)

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

Genetic variation of lodgepole pine, Pinus contorta var. latifolia, chemical and physical defenses that affect mountain pine beetle, Dendroctonus ponderosae, attack and tree mortality.

Science.gov (United States)

Ott, Daniel S; Yanchuk, Alvin D; Huber, Dezene P W; Wallin, Kimberly F

2011-09-01

Plant secondary chemistry is determined by both genetic and environmental factors, and while large intraspecific variation in secondary chemistry has been reported frequently, the levels of genetic variation of many secondary metabolites in forest trees in the context of potential resistance against pests have been rarely investigated. We examined the effect of tree genotype and environment/site on the variation in defensive secondary chemistry of lodgepole pine, Pinus contorta var. latifolia, against the fungus, Grosmannia clavigera (formerly known as Ophiostoma clavigerum), associated with the mountain pine beetle, Dendroctonus ponderosae. Terpenoids were analyzed in phloem samples from 887, 20-yr-old trees originating from 45 half-sibling families planted at two sites. Samples were collected both pre- and post-inoculation with G. clavigera. Significant variation in constitutive and induced terpenoid compounds was attributed to differences among families. The response to the challenge inoculation with G. clavigera was strong for some individual compounds, but primarily for monoterpenoids. Environment (site) also had a significant effect on the accumulation of some compounds, whereas for others, no significant environmental effect occurred. However, for a few compounds significant family x environment interactions were found. These results suggest that P. c. latifolia secondary chemistry is under strong genetic control, but the effects depend on the individual compounds and whether or not they are expressed constitutively or following induction.

Diversity and population structure of a dominant deciduous tree based on morphological and genetic data

Science.gov (United States)

Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

2015-01-01

Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon–Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. PMID:26311734

Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

Directory of Open Access Journals (Sweden)

Julianne M O'Reilly-Wapstra

Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

Is the extremely rare Iberian endemic plant species Castrilanthemum debeauxii (Compositae, Anthemideae) a 'living fossil'? Evidence from a multi-locus species tree reconstruction.

Science.gov (United States)

Tomasello, Salvatore; Álvarez, Inés; Vargas, Pablo; Oberprieler, Christoph

2015-01-01

The present study provides results of multi-species coalescent species tree analyses of DNA sequences sampled from multiple nuclear and plastid regions to infer the phylogenetic relationships among the members of the subtribe Leucanthemopsidinae (Compositae, Anthemideae), to which besides the annual Castrilanthemum debeauxii (Degen, Hervier & É.Rev.) Vogt & Oberp., one of the rarest flowering plant species of the Iberian Peninsula, two other unispecific genera (Hymenostemma, Prolongoa), and the polyploidy complex of the genus Leucanthemopsis belong. Based on sequence information from two single- to low-copy nuclear regions (C16, D35, characterised by Chapman et al. (2007)), the multi-copy region of the nrDNA internal transcribed spacer regions ITS1 and ITS2, and two intergenic spacer regions of the cpDNA gene trees were reconstructed using Bayesian inference methods. For the reconstruction of a multi-locus species tree we applied three different methods: (a) analysis of concatenated sequences using Bayesian inference (MrBayes), (b) a tree reconciliation approach by minimizing the number of deep coalescences (PhyloNet), and (c) a coalescent-based species-tree method in a Bayesian framework ((∗)BEAST). All three species tree reconstruction methods unequivocally support the close relationship of the subtribe with the hitherto unclassified genus Phalacrocarpum, the sister-group relationship of Castrilanthemum with the three remaining genera of the subtribe, and the further sister-group relationship of the clade of Hymenostemma+Prolongoa with a monophyletic genus Leucanthemopsis. Dating of the (∗)BEAST phylogeny supports the long-lasting (Early Miocene, 15-22Ma) taxonomical independence and the switch from the plesiomorphic perennial to the apomorphic annual life-form assumed for the Castrilanthemum lineage that may have occurred not earlier than in the Pliocene (3Ma) when the establishment of a Mediterranean climate with summer droughts triggered evolution towards

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome-Picea glauca system at an arctic treeline ecotone.

Science.gov (United States)

Eusemann, Pascal; Schnittler, Martin; Nilsson, R Henrik; Jumpponen, Ari; Dahl, Mathilde B; Würth, David G; Buras, Allan; Wilmking, Martin; Unterseher, Martin

2016-09-01

Plant-associated mycobiomes in extreme habitats are understudied and poorly understood. We analysed Illumina-generated ITS1 sequences from the needle mycobiome of white spruce (Picea glauca) at the northern treeline in Alaska (USA). Sequences were obtained from the same DNA that was used for tree genotyping. In the present study, fungal metabarcoding and tree microsatellite data were compared for the first time. In general, neighbouring trees shared more fungal taxa with each other than trees growing in further distance. Mycobiomes correlated strongly with phenological host traits and local habitat characteristics contrasting a dense forest stand with an open treeline site. Genetic similarity between trees did not influence fungal composition and no significant correlation existed between needle mycobiome and tree genotype. Our results suggest the pronounced influence of local habitat conditions and phenotypic tree traits on needle-inhabiting fungi. By contrast, the tree genetic identity cannot be benchmarked as a dominant driver for needle-inhabiting mycobiomes, at least not for white spruce in this extreme environment. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Genetic basis of aboveground productivity in two native Populus species and their hybrids.

Science.gov (United States)

Lojewski, Nathan R; Fischer, Dylan G; Bailey, Joseph K; Schweitzer, Jennifer A; Whitham, Thomas G; Hart, Stephen C

2009-09-01

Demonstration of genetic control over riparian tree productivity has major implications for responses of riparian systems to shifting environmental conditions and effects of genetics on ecosystems in general. We used field studies and common gardens, applying both molecular and quantitative techniques, to compare plot-level tree aboveground net primary productivity (ANPP(tree)) and individual tree growth rate constants in relation to plant genetic identity in two naturally occurring Populus tree species and their hybrids. In field comparisons of four cross types (Populus fremontii S. Wats., Populus angustifolia James, F(1) hybrids and backcross hybrids) across 11 natural stands, productivity was greatest for P. fremontii trees, followed by hybrids and lowest in P. angustifolia. A similar pattern was observed in four common gardens across a 290 m elevation and 100 km environmental gradient. Despite a doubling in productivity across the common gardens, the relative differences among the cross types remained constant. Using clonal replicates in a common garden, we found ANPP(tree) to be a heritable plant trait (i.e., broad-sense heritability), such that plant genetic factors explained between 38% and 82% of the variation in ANPP(tree). Furthermore, analysis of the genetic composition among individual tree genotypes using restriction fragment length polymorphism molecular markers showed that genetically similar trees also exhibited similar ANPP(tree). These findings indicate strong genetic contributions to natural variation in ANPP with important ecological implications.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

Science.gov (United States)

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

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

Science.gov (United States)

Goel, Namni; Dinges, David F.

2012-08-01

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

A hierarchical scheme for geodesic anatomical labeling of airway trees

DEFF Research Database (Denmark)

Feragen, Aasa; Petersen, Jens; Owen, Megan

2012-01-01

We present a fast and robust supervised algorithm for label- ing anatomical airway trees, based on geodesic distances in a geometric tree-space. Possible branch label configurations for a given unlabeled air- way tree are evaluated based on the distances to a training set of labeled airway trees....... In tree-space, the airway tree topology and geometry change continuously, giving a natural way to automatically handle anatomical differences and noise. The algorithm is made efficient using a hierarchical approach, in which labels are assigned from the top down. We only use features of the airway...

Morphology and genetics of Anadenanthera colubrina var. cebil (Fabaceae) tree from salta (Northwestern Argentina).

Science.gov (United States)

de Viana, Marta L; Giamminola, Eugenia; Russo, Roberta; Ciaccio, Mirella

2014-06-01

Anadenanthera colubrina var. cebil is an important tree species for its cultural, economic, and medicinal uses in South America. In order to characterize A. colubrina populations, we collected fruits from four different sites (San Bernardo, El Cebilar, Metán and El Gallinato) within the species distribution area in Salta Province, Northwestern Argentina. For this, a total of 75 fruits and seeds per site were collected and described using morphological (fruits size and weight; seed weight and number per fruit) and genetic descriptors (ribosomic DNA extraction and PCR; nucleotide alignment and phylogenetic analysis) with standard protocols. Our results showed that the San Bernardo population had the heaviest fruits and seeds (7.89 +/- 0.2g and 0.19 +/- 0.002, respectively), and the Cebilar population the lightest (6.25 +/- 0.18g and 0.15 +/- 0.002g, respectively). Fruits and seeds from Metán and El Gallinato showed similar and intermediate values. The proportion viable (39 to 55%) and aborted (43 to 57%) seeds was different, while the proportion of predated (1.7 to 4.2%) seeds was similar among populations. The genetic analysis showed variability of ITS sequences within the especies, and also when compared with the same Brazilian species. Both, morphologic and genetic descriptors showed a high level of similarity between San Bernardo and Metán, and between El Cebilar and El Gallinato populations. Further studies are needed to assess levels of phenotypic and genetic variability within and between populations of different plant species, since this information is crucial for biodiversity and germplasm long-term conservation.

Human action analysis with randomized trees

CERN Document Server

Yu, Gang; Liu, Zicheng

2014-01-01

This book will provide a comprehensive overview on human action analysis with randomized trees. It will cover both the supervised random trees and the unsupervised random trees. When there are sufficient amount of labeled data available, supervised random trees provides a fast method for space-time interest point matching. When labeled data is minimal as in the case of example-based action search, unsupervised random trees is used to leverage the unlabelled data. We describe how the randomized trees can be used for action classification, action detection, action search, and action prediction.

Taxon ordering in phylogenetic trees by means of evolutionary algorithms

Directory of Open Access Journals (Sweden)

Cerutti Francesco

2011-07-01

Full Text Available Abstract Background In in a typical "left-to-right" phylogenetic tree, the vertical order of taxa is meaningless, as only the branch path between them reflects their degree of similarity. To make unresolved trees more informative, here we propose an innovative Evolutionary Algorithm (EA method to search the best graphical representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa. Methods Starting from a West Nile virus phylogenetic tree, in a (1 + 1-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius next taxa. After having set the radius to the best performance, we evolved the trees with (λ + μ-EAs to study the influence of population on the algorithm. Results The (1 + 1-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (λ + μ-EAs performed as well as the (1 + 1, except the larger population (1000 + 1000. Conclusions The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close, and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe.

System Response Analysis and Model Order Reduction, Using Conventional Method, Bond Graph Technique and Genetic Programming

Directory of Open Access Journals (Sweden)

Lubna Moin

2009-04-01

Full Text Available This research paper basically explores and compares the different modeling and analysis techniques and than it also explores the model order reduction approach and significance. The traditional modeling and simulation techniques for dynamic systems are generally adequate for single-domain systems only, but the Bond Graph technique provides new strategies for reliable solutions of multi-domain system. They are also used for analyzing linear and non linear dynamic production system, artificial intelligence, image processing, robotics and industrial automation. This paper describes a unique technique of generating the Genetic design from the tree structured transfer function obtained from Bond Graph. This research work combines bond graphs for model representation with Genetic programming for exploring different ideas on design space tree structured transfer function result from replacing typical bond graph element with their impedance equivalent specifying impedance lows for Bond Graph multiport. This tree structured form thus obtained from Bond Graph is applied for generating the Genetic Tree. Application studies will identify key issues and importance for advancing this approach towards becoming on effective and efficient design tool for synthesizing design for Electrical system. In the first phase, the system is modeled using Bond Graph technique. Its system response and transfer function with conventional and Bond Graph method is analyzed and then a approach towards model order reduction is observed. The suggested algorithm and other known modern model order reduction techniques are applied to a 11th order high pass filter [1], with different approach. The model order reduction technique developed in this paper has least reduction errors and secondly the final model retains structural information. The system response and the stability analysis of the system transfer function taken by conventional and by Bond Graph method is compared and

Trees for future forests

DEFF Research Database (Denmark)

Lobo, Albin

Climate change creates new challenges in forest management. The increase in temperature may in the long run be beneficial for the forests in the northern latitudes, but the high rate at which climate change is predicted to proceed will make adaptation difficult because trees are long living sessile...... organisms. The aim of the present thesis is therefore to explore genetic resilience and phenotypic plasticity mechanisms that allows trees to adapt and evolve with changing climates. The thesis focus on the abiotic factors associated with climate change, especially raised temperatures and lack...... age of these tree species and the uncertainty around the pace and effect of climate, it remains an open question if the native populations can respond fast enough. Phenotypic plasticity through epigenetic regulation of spring phenology is found to be present in a tree species which might act...

Genome sequence and genetic diversity of European ash trees.

Science.gov (United States)

Sollars, Elizabeth S A; Harper, Andrea L; Kelly, Laura J; Sambles, Christine M; Ramirez-Gonzalez, Ricardo H; Swarbreck, David; Kaithakottil, Gemy; Cooper, Endymion D; Uauy, Cristobal; Havlickova, Lenka; Worswick, Gemma; Studholme, David J; Zohren, Jasmin; Salmon, Deborah L; Clavijo, Bernardo J; Li, Yi; He, Zhesi; Fellgett, Alison; McKinney, Lea Vig; Nielsen, Lene Rostgaard; Douglas, Gerry C; Kjær, Erik Dahl; Downie, J Allan; Boshier, David; Lee, Steve; Clark, Jo; Grant, Murray; Bancroft, Ian; Caccamo, Mario; Buggs, Richard J A

2017-01-12

Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we re-analyse association transcriptomic data, yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.

Representing Boolean Functions by Decision Trees

KAUST Repository

Chikalov, Igor

2011-01-01

A Boolean or discrete function can be represented by a decision tree. A compact form of decision tree named binary decision diagram or branching program is widely known in logic design [2, 40]. This representation is equivalent to other forms, and in some cases it is more compact than values table or even the formula [44]. Representing a function in the form of decision tree allows applying graph algorithms for various transformations [10]. Decision trees and branching programs are used for effective hardware [15] and software [5] implementation of functions. For the implementation to be effective, the function representation should have minimal time and space complexity. The average depth of decision tree characterizes the expected computing time, and the number of nodes in branching program characterizes the number of functional elements required for implementation. Often these two criteria are incompatible, i.e. there is no solution that is optimal on both time and space complexity. © Springer-Verlag Berlin Heidelberg 2011.

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

International Nuclear Information System (INIS)

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

2009-01-01

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

Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico.

Science.gov (United States)

Vázquez-Ovando, J A; Molina-Freaner, F; Nuñez-Farfán, J; Ovando-Medina, I; Salvador-Figueroa, M

2014-12-12

Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (FST = 0.123, P cocoa.

Optimization of Antennas using a Hybrid Genetic-Algorithm Space-Mapping Algorithm

DEFF Research Database (Denmark)

Pantoja, M.F.; Bretones, A.R.; Meincke, Peter

2006-01-01

A hybrid global-local optimization technique for the design of antennas is presented. It consists of the subsequent application of a Genetic Algorithm (GA) that employs coarse models in the simulations and a space mapping (SM) that refines the solution found in the previous stage. The technique...

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time.

Science.gov (United States)

Cai, Yunpeng; Sun, Yijun

2011-08-01

Taxonomy-independent analysis plays an essential role in microbial community analysis. Hierarchical clustering is one of the most widely employed approaches to finding operational taxonomic units, the basis for many downstream analyses. Most existing algorithms have quadratic space and computational complexities, and thus can be used only for small or medium-scale problems. We propose a new online learning-based algorithm that simultaneously addresses the space and computational issues of prior work. The basic idea is to partition a sequence space into a set of subspaces using a partition tree constructed using a pseudometric, then recursively refine a clustering structure in these subspaces. The technique relies on new methods for fast closest-pair searching and efficient dynamic insertion and deletion of tree nodes. To avoid exhaustive computation of pairwise distances between clusters, we represent each cluster of sequences as a probabilistic sequence, and define a set of operations to align these probabilistic sequences and compute genetic distances between them. We present analyses of space and computational complexity, and demonstrate the effectiveness of our new algorithm using a human gut microbiota data set with over one million sequences. The new algorithm exhibits a quasilinear time and space complexity comparable to greedy heuristic clustering algorithms, while achieving a similar accuracy to the standard hierarchical clustering algorithm.

Is All Urban Green Space the Same? A Comparison of the Health Benefits of Trees and Grass in New York City.

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Reid, Colleen E; Clougherty, Jane E; Shmool, Jessie L C; Kubzansky, Laura D

2017-11-18

Living near vegetation, often called "green space" or "greenness", has been associated with numerous health benefits. We hypothesized that the two key components of urban vegetation, trees and grass, may differentially affect health. We estimated the association between near-residence trees, grass, and total vegetation (from the 2010 High Resolution Land Cover dataset for New York City (NYC)) with self-reported health from a survey of NYC adults (n = 1281). We found higher reporting of "very good" or "excellent" health for respondents with the highest, compared to the lowest, quartiles of tree (RR = 1.23, 95% CI = 1.06-1.44) but not grass density (relative risk (RR) = 1.00, 95% CI = 0.86-1.17) within 1000 m buffers, adjusting for pertinent confounders. Significant positive associations between trees and self-reported health remained after adjustment for grass, whereas associations with grass remained non-significant. Adjustment for air pollutants increased beneficial associations between trees and self-reported health; adjustment for parks only partially attenuated these effects. Results were null or negative using a 300 m buffer. Findings imply that higher exposure to vegetation, particularly trees outside of parks, may be associated with better health. If replicated, this may suggest that urban street tree planting may improve population health.

Fractional Dynamics of Genetic Algorithms Using Hexagonal Space Tessellation

Directory of Open Access Journals (Sweden)

J. A. Tenreiro Machado

2013-01-01

Full Text Available The paper formulates a genetic algorithm that evolves two types of objects in a plane. The fitness function promotes a relationship between the objects that is optimal when some kind of interface between them occurs. Furthermore, the algorithm adopts an hexagonal tessellation of the two-dimensional space for promoting an efficient method of the neighbour modelling. The genetic algorithm produces special patterns with resemblances to those revealed in percolation phenomena or in the symbiosis found in lichens. Besides the analysis of the spacial layout, a modelling of the time evolution is performed by adopting a distance measure and the modelling in the Fourier domain in the perspective of fractional calculus. The results reveal a consistent, and easy to interpret, set of model parameters for distinct operating conditions.

Genetic structure and genetic diversity of Swietenia macrophylla in areas subjected to selective logging in Quintana Roo, Mexico

OpenAIRE

Alcalá, Raúl Ernesto; Cruz, Silvia De la; Gutiérrez-Granados, Gabriel

2015-01-01

The hypothesis that selective logging has a negative effect by altering the genetic parameters of tropical tree species was evaluated. The genetic diversity and genetic structure between adult trees (N = 47) and saplings (N = 50) of Swietenia macrophylla were contrasted within an area subjected to selective logging in the Mayan zone. Although differences in the number of alleles and in their frequencies were detected between both groups, the observed and expected heterozygosity and the coeffi...

OGDD (Olive Genetic Diversity Database): a microsatellite markers' genotypes database of worldwide olive trees for cultivar identification and virgin olive oil traceability.

Science.gov (United States)

Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Ben Marzoug, Riadh; Rebai, Ahmed

2016-01-01

Olive (Olea europaea), whose importance is mainly due to nutritional and health features, is one of the most economically significant oil-producing trees in the Mediterranean region. Unfortunately, the increasing market demand towards virgin olive oil could often result in its adulteration with less expensive oils, which is a serious problem for the public and quality control evaluators of virgin olive oil. Therefore, to avoid frauds, olive cultivar identification and virgin olive oil authentication have become a major issue for the producers and consumers of quality control in the olive chain. Presently, genetic traceability using SSR is the cost effective and powerful marker technique that can be employed to resolve such problems. However, to identify an unknown monovarietal virgin olive oil cultivar, a reference system has become necessary. Thus, an Olive Genetic Diversity Database (OGDD) (http://www.bioinfo-cbs.org/ogdd/) is presented in this work. It is a genetic, morphologic and chemical database of worldwide olive tree and oil having a double function. In fact, besides being a reference system generated for the identification of unkown olive or virgin olive oil cultivars based on their microsatellite allele size(s), it provides users additional morphological and chemical information for each identified cultivar. Currently, OGDD is designed to enable users to easily retrieve and visualize biologically important information (SSR markers, and olive tree and oil characteristics of about 200 cultivars worldwide) using a set of efficient query interfaces and analysis tools. It can be accessed through a web service from any modern programming language using a simple hypertext transfer protocol call. The web site is implemented in java, JavaScript, PHP, HTML and Apache with all major browsers supported. Database URL: http://www.bioinfo-cbs.org/ogdd/. © The Author(s) 2016. Published by Oxford University Press.

Dynamic Event Tree advancements and control logic improvements

International Nuclear Information System (INIS)

Alfonsi, Andrea; Rabiti, Cristian; Mandelli, Diego; Sen, Ramazan Sonat; Cogliati, Joshua Joseph

2015-01-01

-sampling of the input space characterized by epistemic uncertainties. The consequent Dynamic Event Tree performs the exploration of the aleatory space. In the RAVEN code, a more general approach has been developed, not limiting the exploration of the epistemic space through a Monte Carlo method but using all the forward sampling strategies RAVEN currently employs. The user can combine a Latin Hyper Cube, Grid, Stratified and Monte Carlo sampling in order to explore the epistemic space, without any limitation. From this pre-sampling, the Dynamic Event Tree sampler starts its aleatory space exploration. As reported by the authors, the Dynamic Event Tree is a good fit to develop a goal-oriented sampling strategy. The DET is used to drive a Limit Surface search. The methodology that has been developed by the authors last year, performs a Limit Surface search in the aleatory space only. This report documents how this approach has been extended in order to consider the epistemic space interacting with the Hybrid Dynamic Event Tree methodology.

Assessment of genetic diversity and variation of acer mono max seedlings after spaceflight

International Nuclear Information System (INIS)

Long, C.; Li, Y.; Zhang, Y.; Yang, M.

2015-01-01

Genetic diversity and variation of Acer Mono Maxim seedlings sampled from space-mutated (sm) populations were compared to seedlings from parallel control (ck) ones using molecular markers. RAMP analysis showed that the percentage of polymorphic band, Shannon diversity index and Nei gene diversity index of the space-mutated populations were higher than those of the control ones, which indicated that genetic variation increased after spaceflight in populations of Acer Mono Maxim. By using un-weighted pair group method with arithmetic mean (UPGMA) method, three space-mutated repeats (populations) were clustered together, and control groups clustered separately, which further indicated that there was difference between the space-mutated ones and the control ones, which may be caused by space mutation. Further analysis of genomic inconsistency between the root and leaf samples from the same tree showed that a total variation rate of 6.3% and 1.7% were obtained in ten space-mutated individuals by using RAMP and SSR markers, respectively, however, the variation rate was zero in control ones. It provided that space mutation may be caused the individual variation of Acer Mono Maxim. (author)

Strategic plans for the Hardwood Tree Improvement and Regeneration Center

Science.gov (United States)

Charles H. Michler; Keith E. Woeste

2002-01-01

The mission of the Hardwood Tree Improvement and Regeneration Center (HTIRC) at Purdue University is to advance the science of hardwood tree improvement and genomics in the central hardwood region of the United States by: developing and disseminating knowledge on improving the genetic quality of hardwood tree species; conserving fine hardwood germplasm; developing...

Constructing phylogenetic trees using interacting pathways.

Science.gov (United States)

Wan, Peng; Che, Dongsheng

2013-01-01

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships.

Los Angeles 1-Million tree canopy cover assessment

Science.gov (United States)

Gregory E. McPherson; James R. Simpson; Qingfu Xiao; Wu Chunxia

2008-01-01

The Million Trees LA initiative intends to chart a course for sustainable growth through planting and stewardship of trees. The purpose of this study was to measure Los Angeles's existing tree canopy cover (TCC), determine if space exists for 1 million additional trees, and estimate future benefits from the planting. High resolution QuickBird remote sensing data,...

Phylogenetic trees and Euclidean embeddings.

Science.gov (United States)

Layer, Mark; Rhodes, John A

2017-01-01

It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

Fruit self-thinning: a trait to consider for genetic improvement of apple tree.

Science.gov (United States)

Celton, Jean-Marc; Kelner, Jean-Jacques; Martinez, Sébastien; Bechti, Abdel; Khelifi Touhami, Amina; James, Marie José; Durel, Charles-Eric; Laurens, François; Costes, Evelyne

2014-01-01

In apple (Malus×domestica Borkh), as in many fruiting crops, fruit maintenance vs abscission is a major criteria for production profitability. Growers routinely make use of chemical thinning agents to control total fruit load. However, serious threats for the environment lead to the demand for new apple cultivars with self-thinning properties. In this project, we studied the genetic determinism of this trait using a F1 progeny derived from the cross between the hybrid INRA X3263, assumed to possess the self-thinning trait, and the cultivar 'Belrène'. Both counting and percentage variables were considered to capture the fruiting behaviour on different shoot types and over three consecutive years. Besides low to moderate but significant genetic effects, mixed models showed considerable effects of the year and the shoot type, as well as an interaction effect. Year effect resulted mainly from biennial fruiting. Eight Quantitative Trait Locus (QTL) were detected on several linkage groups (LG), either independent or specific of the year of observation or the shoot type. The QTL with highest LOD value was located on the top third of LG10. The screening of three QTL zones for candidate genes revealed a list of transcription factors and genes involved in fruit nutrition, xylem differentiation, plant responses to starvation and organ abscission that open new avenues for further molecular investigations. The detailed phenotyping performed revealed the dependency between the self-thinning trait and the fruiting status of the trees. Despite a moderate genetic control of the self-thinning trait, QTL and candidate genes were identified which will need further analyses involving other progenies and molecular investigations.

Genetic Diversity of Verticillium dahliae Isolates from Olive Trees in Algeria

Directory of Open Access Journals (Sweden)

M. Bellahcene

2005-12-01

Full Text Available Verticillium wilt of olive trees (Olea europaea L., a wilt caused by the soil-borne fungus Verticillium dahliae (Kleb, is one of the most serious diseases in Algerian olive groves. To assess the pathogenic and genetic diversity of olive-infecting V. dahliae populations in Algeria, orchards from the two main olive-producing regions (north-western Algeria and Kabylia were sampled and 27 V. dahliae isolates were recovered. For purposes of comparison, V. dahliae strains from France and Syria were added to the analysis. By means of PCR primers that specifically discriminate between defoliating (D and non-defoliating (ND V. dahliae pathotypes it was shown that all V. dahliae isolates belonged to the ND pathotype. The amount of genetic variation between the 43 isolates was assessed by random amplification of polymorphic DNA (RAPD. A total of 16 RAPD haplotypes were found on the basis of the presence or absence of 25 polymorphic DNA fragments. Genotypic diversity between the 27 Algerian isolates was low, with two RAPD haplotypes accounting for 70% of all isolates. Genotypic diversity was however greater between isolates from Kabylia than between isolates from north-western Algeria. Cluster analysis showed that most of the Algerian V. dahliae isolates grouped together with the French and Syrian isolates. On the basis of their ability to form heterokaryons with each other, a subset of 25 olive-pathogenic isolates was grouped into a single vegetative compatibility group (VCG. These results suggest that the olive-infecting V. dahliae populations in Algeria show limited diversity and that caution should be taken to prevent introduction of the D pathotype.

Genetic risks associated with radiation exposures during space flight

International Nuclear Information System (INIS)

Grahn, D.

1983-01-01

Although the genetic risks of space radiation do not pose a significant hazard to the general population, the risks may be very important to the individual astronaut. The present paper summarizes some experimental results on the induction of dominant lethal mutations and chromosomal damage in the first generation which may be used in the prediction of the genetic risks of radiation exposures of space crews. Young adult male mice were exposed to single, weekly and continuous doses of gamma rays, neutrons in single doses and weekly exposures and continuous doses of Pu-239 alpha particles. Evaluation of fetal survival rates in females mated to the exposed males shows the mutation rate in individuals exposed to gamma rays to decline as the exposure period is prolonged and the dose rate is reduced, while the response to neutrons is in the opposite direction. Cytological determinations show the rate of balanced chromosomal translocations to drop as gamma ray exposures change from one-time to continuous, however little or no dose rate effect is seen with neutron radiation and alpha particle exposure shows no regular dose-response. Based on the above results, it is predicted that the rate of dominant mutations and transmissible chromosome aberrations in astronauts on a 100-day mission will increase by 4.5 to 41.25 percent over the spontaneous rate. 35 references

Seeing the forest for the trees

DEFF Research Database (Denmark)

Ribbons, Relena Rose

Tree species influence soils above and belowground communities through leaf litter and root inputs. Soil microbial communities can directly influence tree growth and development through processes such as decomposition of leaves, and indirectly through chemical transformation of nutrients in soils...... as an influence of altered C:N ratios due to leaf litter inputs. This thesis aims to document some of the mechanisms by which trees influence soil microbial communities and nitrogen cycling processes like gross and net ammonification and nitrification. This thesis also aims to determine the role of site nitrogen...... status on modulating those tree species effects. The effects of tree species on ammonification and nitrification rates in forest floors and mineral soils were explored, and related to functional genetic markers for ammonia-oxidation by archaea and bacteria (amoA AOA and AOB), bacterial denitrification...

Genetic variation in growth, carbon isotope discrimination, and foliar N concentration in Picea mariana: analyses from a half-diallel mating design using field-grown trees

Science.gov (United States)

Kurt H. Johnsen; Lawrence B. Flanagan; Dudley A. Huber; John E. Major

1999-01-01

The authors performed genetic analyses of growth, carbon isotope discrimination (?13C), and foliar N concentration using a half-diallel subset of a 7 × 7 complete diallel planted on three sites ranging in water availability. Trees were 22 years old. Heritabilities; general and...

Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA

Directory of Open Access Journals (Sweden)

Nidia Gutiérrez-López

2016-04-01

Full Text Available Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations and genetic origin (based on a previous study. We identified six polymorphic sites, including five insertion/deletion (indels types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038. Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80 with 10 and 12 haplotypes, respectively. The common haplotype (H1 for both networks included cacao trees from all geographic locations (geographic approach and four genetic groups (genetic approach. This common haplotype (ancient derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (FST = 0 and SAMOVA (FST = 0.04393 results. One population (Mazatán showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding.

Optimal tree design for daylighting in residential buildings

Energy Technology Data Exchange (ETDEWEB)

Hongbing, Wang [College of Landscape Architecture, Beijing Forestry University, 35, East Qinghua Rd., Beijing (China); Shanghai Botanical Garden, 1111, Longwu Rd., Shanghai (China); Jun, Qin; Yonghong, Hu [Shanghai Botanical Garden, 1111, Longwu Rd., Shanghai (China); Li, Dong [College of Landscape Architecture, Beijing Forestry University, 35, East Qinghua Rd., Beijing (China)

2010-12-15

Urban reforestation is advocated as an efficient countermeasure to the intensification of urban heat islands. The greening and beautification of residential quarters is one of the main concerns of residents, while lighting and ventilation are two main energy-consuming building services. Hence, the tree layout in green space between buildings is important, and it is necessary to determine the relationships between trees and buildings. This study takes Shanghai as a case study to optimize tree design between residential buildings and meet good daylighting requirements. Models were made using software such as AutoCAD and SketchUp. The relationships between maximum tree height and building separation were determined. For the same building layout, there were different tree height limits according to crown shape; the order of decreasing height limits was cylindrical, conical, spherical, and inverted conical crowns. Three cases having different green space between building layouts were studied. Their maximum tree heights differed. Overall, our model helps us realize good daylighting of a building environment. The formula allows us to determine which trees to plant between buildings in that we can predict the effects of future tree growth on building daylighting. (author)

Part 2: Conserving and Planting Trees at Development Sites

Science.gov (United States)

Karen Cappiella; Tom Schueler; Tiffany Wright

2006-01-01

This manual presents specific ways to enable developers, engineers or landscape architects to incorporate more trees into a development site. The proposed approach focuses on protecting existing trees, planting trees in storm water treatment practices, and planting trees in other open spaces at the development site. This manual introduces conceptual designs for storm...

Improving disease resistance of butternut (Juglans cinerea), a threatened fine hardwood: a case for single-tree selection through genetic improvement and deployment.

Science.gov (United States)

Michler, Charles H; Pijut, Paula M; Jacobs, Douglass F; Meilan, Richard; Woeste, Keith E; Ostry, Michael E

2006-01-01

Approaches for the development of disease-resistant butternut (Juglans cinerea L.) are reviewed. Butternut is a threatened fine hardwood throughout its natural range in eastern North America because of the invasion of the exotic fungus, Sirococcus clavigignenti-juglandacearum Nair, Kostichka and Kuntz, which causes butternut canker. Early efforts were made to identify and collect putatively resistant germ plasm, identify vectors and to characterize the disease. More recently, molecular techniques have been employed to genetically characterize both the pathogen and the resistant germ plasm. Much of the host resistance may originate from hybridization with a close Asian relative, Japanese walnut (Juglans ailanthifolia Carr.), and from a few natural phenotypic variants. Further genetic characterization is needed before classical breeding or genetic modification can be used to produce canker-resistant trees.

Genetic and ecological outcomes of Inga vera subsp. affinis (Leguminosae) tree plantations in a fragmented tropical landscape.

Science.gov (United States)

Cruz Neto, Oswaldo; Aguiar, Antonio V; Twyford, Alex D; Neaves, Linda E; Pennington, R Toby; Lopes, Ariadna V

2014-01-01

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = -0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Energy Technology Data Exchange (ETDEWEB)

N. Price, Morgan; S. Dehal, Paramvir; P. Arkin, Adam

2009-07-31

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

A Polyphasic Approach for Phenotypic and Genetic Characterization of the Fastidious Aquatic Pathogen Francisella noatunensis subsp. orientalis

Directory of Open Access Journals (Sweden)

José G. Ramírez-Paredes

2017-12-01

Full Text Available Francisella noatunensis subsp. orientalis (Fno is the causative agent of piscine francisellosis, an emerging infectious disease in Asia and Latin America. In this study two outbreaks of francisellosis were diagnosed in the UK on the basis of histopathology, electron microscopy, PCR, bacterial isolation and fulfillment of Koch's postulates. Furthermore, a phenotypic fingerprint based on biochemical analyses, metabolic activity, chemotaxonomic composition, and antimicrobial assays was generated for the novel isolates, the Fno type strain Ehime-1 from Asia and other Fno from Latin America. The genetic relatedness between the novel Fno and other Francisellaceae species was investigated by sequencing and comparing the 16SrRNA gene, 8 housekeeping genes (individually and concatenated and the 16SrRNA-ITS-23SrRNA sequence. The phenotypic profiling indicated a high degree of similarity among the Fno strains as all were able to metabolize dextrin, N-acetyl-D glucosamine, D-fructose, α-D-glucose, D-mannose, methyl pyruvate, acetic acid, α-keto butyric acid, L-alaninamide, L-alanine, L-alanylglycine, L-asparagine, L-glutamic acid, L-proline, L-serine, L-threonine, inosine, uridine, glycerol, D L-α-glycerol phosphate, glucose-1-phosphate, and glucose-6-phosphate. The chemotaxonomic analyses indicated that 24:1 (20.3%, 18:1n-9 (16.9%, 24:0 (13.1% 14:0 (10.9%, 22:0 (7.8%, 16:0 (7.6%, and 18:0 (5.5% were the predominant structural fatty acids in Fno. The antimicrobial assays showed little variation between the isolates and high susceptibility to enrofloxacin, gentamicin, neomycin, streptomycin, amikacin, ciprofloxacin, gatifloxacin, nitrofurantoin, tobramycin, kanamycin, tetracycline, oxytetracycline, florfenicol, oxolinic acid, and streptomycin in all the Fno analyzed. In all the phylogenetic trees the Fno strains clustered together in independent branches confirming a high degree of homogeneity. Interestingly in five of the 11 trees i.e., mutS, putA, rpo

Genetic selection and improvement of hard wood tree species for fuelwood production on sodic soil with particular reference to Prosopis juliflora

Energy Technology Data Exchange (ETDEWEB)

Goel, V.L.; Behl, H.M. [National Botanical Research Inst., Lucknow (India). Dept. of Tree Biology

2001-07-01

This study is part of a research programme on selection and improvement of fast growing tree species suitable for wood fuel production on sodic wastelands (pH 8.6-10.5). Field trials of nine legumes (Acacia auriculiformis, A. nilotica, Albizia lebbeck, A. procera, Dalbergia sissoo, Leucaena leucocephala, Pongamia pinnata, Prosopis juliflora, Pithecellobium dulce) and three other tree species (Azadirachta indica, Eucalyptus tereticornis and Terminalai arjuna) were selected for this study. Prosopis juliflora was the most promising species in terms of its biomass productivity (68.7 t ha{sup -1}) and fuel value index (148.8) after 8-yr of growth. Acacia nilotica ranked second. Intra-specific variations were screened at provenance and individual tree level in order to improve fuelwood production potential of P. juliflora through selection and breeding. Successful populations (gene pools) and individuals (genotypes) were closed and conserved in clonal gardens to produce quality germplasm for plantations on sodic wastelands. Genetic testing, selection and multiplication of selected material are under progress. This will optimise gains in future afforestation programmes on sodic soils. (Author)

A Hybrid Genetic-Algorithm Space-Mapping Tool for the Optimization of Antennas

DEFF Research Database (Denmark)

Pantoja, Mario Fernández; Meincke, Peter; Bretones, Amelia Rubio

2007-01-01

A hybrid global-local optimization technique for the design of antennas is presented. It consists of the subsequent application of a genetic algorithm (GA) that employs coarse models in the simulations and a space mapping (SM) that refines the solution found in the previous stage. The technique...

Gene flow among established Puerto Rican populations of the exotic tree species, Albizia lebbeck.

Science.gov (United States)

Dunphy, B K; Hamrick, J L

2005-04-01

We estimate gene flow and patterns of genetic diversity in Albizia lebbeck, an invasive leguminous tree in the dry forest of southwestern Puerto Rico. Genetic diversity estimates calculated for 10 populations of 24 trees each indicated that these populations may have been formed from multiple introductions. The presence of unique genotypes in the northernmost populations suggests that novel genotypes are still immigrating into the area. This combination of individuals from disparate locations led to high estimates of genetic diversity (He = 0.266, P = 0.67). Indirect estimates of gene flow indicate that only 0.69 migrants per generation move between populations, suggesting that genetic diversity within populations should decrease due to genetic drift. Since migration-drift equilibrium was not found, however, this estimate needs to be viewed with caution. The regular production of pods in this outcrossing species (tm = 0.979) indicates that sufficient outcross pollen is received to insure successful reproduction. Direct estimates of gene flow indicate that between 44 and 100% of pollen received by trees in four small stands of trees (n < 11) was foreign. The role of gene flow in facilitating the spread of this invasive plant species is discussed.

Dynamic Event Tree advancements and control logic improvements

Energy Technology Data Exchange (ETDEWEB)

Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mandelli, Diego [Idaho National Lab. (INL), Idaho Falls, ID (United States); Sen, Ramazan Sonat [Idaho National Lab. (INL), Idaho Falls, ID (United States); Cogliati, Joshua Joseph [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-09-01

input space characterized by epistemic uncertainties. The consequent Dynamic Event Tree performs the exploration of the aleatory space. In the RAVEN code, a more general approach has been developed, not limiting the exploration of the epistemic space through a Monte Carlo method but using all the forward sampling strategies RAVEN currently employs. The user can combine a Latin Hyper Cube, Grid, Stratified and Monte Carlo sampling in order to explore the epistemic space, without any limitation. From this pre-sampling, the Dynamic Event Tree sampler starts its aleatory space exploration. As reported by the authors, the Dynamic Event Tree is a good fit to develop a goal-oriented sampling strategy. The DET is used to drive a Limit Surface search. The methodology that has been developed by the authors last year, performs a Limit Surface search in the aleatory space only. This report documents how this approach has been extended in order to consider the epistemic space interacting with the Hybrid Dynamic Event Tree methodology.

Age-related changes in tree growth and physiology

Science.gov (United States)

Andrew Groover

2017-01-01

Trees pass through specific developmental phases as they age, including juvenile to adult, and vegetative to reproductive phases. The timing of these transitions is regulated genetically but is also highly influenced by the environment. Tree species have evolved different strategies and life histories that affect how they age – for example some pioneer species are fast...

Genetic variation and recombination of RdRp and HSP 70h genes of Citrus tristeza virus isolates from orange trees showing symptoms of citrus sudden death disease

Directory of Open Access Journals (Sweden)

Pappas Georgios J

2008-01-01

Full Text Available Abstract Background Citrus sudden death (CSD, a disease that rapidly kills orange trees, is an emerging threat to the Brazilian citrus industry. Although the causal agent of CSD has not been definitively determined, based on the disease's distribution and symptomatology it is suspected that the agent may be a new strain of Citrus tristeza virus (CTV. CTV genetic variation was therefore assessed in two Brazilian orange trees displaying CSD symptoms and a third with more conventional CTV symptoms. Results A total of 286 RNA-dependent-RNA polymerase (RdRp and 284 heat shock protein 70 homolog (HSP70h gene fragments were determined for CTV variants infecting the three trees. It was discovered that, despite differences in symptomatology, the trees were all apparently coinfected with similar populations of divergent CTV variants. While mixed CTV infections are common, the genetic distance between the most divergent population members observed (24.1% for RdRp and 11.0% for HSP70h was far greater than that in previously described mixed infections. Recombinants of five distinct RdRp lineages and three distinct HSP70h lineages were easily detectable but respectively accounted for only 5.9 and 11.9% of the RdRp and HSP70h gene fragments analysed and there was no evidence of an association between particular recombinant mosaics and CSD. Also, comparisons of CTV population structures indicated that the two most similar CTV populations were those of one of the trees with CSD and the tree without CSD. Conclusion We suggest that if CTV is the causal agent of CSD, it is most likely a subtle feature of population structures within mixed infections and not merely the presence (or absence of a single CTV variant within these populations that triggers the disease.

Application of Genomic Technologies to the Breeding of Trees.

Science.gov (United States)

Badenes, Maria L; Fernández I Martí, Angel; Ríos, Gabino; Rubio-Cabetas, María J

2016-01-01

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the

Expressive Power of Tree and String Based Wrappers

OpenAIRE

Ikeda, Daisuke; Yamada, Yasuhiro; Hirokawa, Sachio

2003-01-01

There exist two types of wrappers: the string based wrapper such as the LR wrapper, and the tree based wrapper. A tree based wrapper designates extraction regions by nodes on the trees of semistructured documents. The tree based wrapper seems to be more powerful than the string based one. There exist, however, manyHTML documents on the Web such that a standard tree based wrapper fails to extract contents because they are structured by presentational tags, punctuation symbols, and white spaces...

Automatic Data Filter Customization Using a Genetic Algorithm

Science.gov (United States)

Mandrake, Lukas

2013-01-01

This work predicts whether a retrieval algorithm will usefully determine CO2 concentration from an input spectrum of GOSAT (Greenhouse Gases Observing Satellite). This was done to eliminate needless runtime on atmospheric soundings that would never yield useful results. A space of 50 dimensions was examined for predictive power on the final CO2 results. Retrieval algorithms are frequently expensive to run, and wasted effort defeats requirements and expends needless resources. This algorithm could be used to help predict and filter unneeded runs in any computationally expensive regime. Traditional methods such as the Fischer discriminant analysis and decision trees can attempt to predict whether a sounding will be properly processed. However, this work sought to detect a subsection of the dimensional space that can be simply filtered out to eliminate unwanted runs. LDAs (linear discriminant analyses) and other systems examine the entire data and judge a "best fit," giving equal weight to complex and problematic regions as well as simple, clear-cut regions. In this implementation, a genetic space of "left" and "right" thresholds outside of which all data are rejected was defined. These left/right pairs are created for each of the 50 input dimensions. A genetic algorithm then runs through countless potential filter settings using a JPL computer cluster, optimizing the tossed-out data s yield (proper vs. improper run removal) and number of points tossed. This solution is robust to an arbitrary decision boundary within the data and avoids the global optimization problem of whole-dataset fitting using LDA or decision trees. It filters out runs that would not have produced useful CO2 values to save needless computation. This would be an algorithmic preprocessing improvement to any computationally expensive system.

An efficient and extensible approach for compressing phylogenetic trees.

Science.gov (United States)

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community.

Genomics-assisted breeding in fruit trees

OpenAIRE

Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the pl...

Genetic consequences of selection cutting on sugar maple (Acer saccharum Marshall).

Science.gov (United States)

Graignic, Noémie; Tremblay, Francine; Bergeron, Yves

2016-07-01

Selection cutting is a treatment that emulates tree-by-tree replacement for forests with uneven-age structures. It creates small openings in large areas and often generates a more homogenous forest structure (fewer large leaving trees and defective trees) that differs from old-growth forest. In this study, we evaluated whether this type of harvesting has an impact on genetic diversity of sugar maple (Acer saccharum Marshall). Genetic diversity among seedlings, saplings, and mature trees was compared between selection cut and old-growth forest stands in Québec, Canada. We found higher observed heterozygosity and a lower inbreeding coefficient in mature trees than in younger regeneration cohorts of both forest types. We detected a recent bottleneck in all stands undergoing selection cutting. Other genetic indices of diversity (allelic richness, observed and expected heterozygosity, and rare alleles) were similar between forest types. We concluded that the effect of selection cutting on the genetic diversity of sugar maple was recent and no evidence of genetic erosion was detectable in Québec stands after one harvest. However, the cumulative effect of recurring applications of selection cutting in bottlenecked stands could lead to fixation of deleterious alleles, and this highlights the need for adopting better forest management practices.

Research progress on the space-flight mutation breeding of woodyplant

International Nuclear Information System (INIS)

Cui Binbin; Sun Yuhan; Li Yun

2013-01-01

The space-flight mutation breeding conception, characteristics, mutagenic effects, research progress at home and abroad in woody plant were reviewed in this paper. Compared with crops, although the research of the woody plants space-flight mutation breeding in China started later, but it has developed rapidly and has gotten certain achievement. Now the satellite and high-altitude balloon experiment were conducted with over 20 tree species such as Populus ussuriensis and 50 flower species such as Paeonia suffruticosa. The above work will has profound significance for space-flight breeding technology application on woody plants. In the end, this thesis analyzes the prospect in the future from four aspects such as using woody plants asexual reproduction characteristic, strengthening the space mutation mechanism study, enhancing new space mutation varieties screen and strengthening ornamental specific types selection. This thesis also thinks that the space mutation breeding is expected to become an effective way in woody plant genetic breeding. (authors)

The Effect of Tree Spacing and Size in Urban Areas: Strategies for Mitigating High Temperature in Urban Heat Islands

Science.gov (United States)

Berry, R.; Shandas, V.; Makido, Y.

2017-12-01

Many cities are unintentionally designed to be heat sinks, which absorb the sun's short-wave radiation and reemit as long-wave radiation. Long time reorganization of this `urban heat island' (UHI) phenomena has led researchers and city planners into developing strategies for reducing ambient temperatures through urban design. Specifically, greening areas have proven to reduce the temperature in UHI's, including strategies such as green streets, green facades, and green roofs have been implemented. Among the scientific community there is promoted study of how myriad greening strategies can reduce temperature, relatively limited work has focused on the distribution, density, and quantity of tree campaigns. This paper examines how the spacing and size of trees reduce temperatures differently. A major focus of the paper is to understand how to lower the temperature through tree planting, and provide recommendations to cities that are attempting to solve their own urban heat island issues. Because different cities have different room for planting greenery, we examined which strategies are more efficient given an area constraint. Areas that have less available room might not be able to plant a high density of trees. We compared the different experimental groups varying in density and size of trees against the control to see the effect the trees had. Through calibration with local weather stations, we used a micrometeorology program (ENVI-Met) to model and simulate the different experimental models and how they affect the temperature. The results suggest that some urban designs can reduce ambient temperatures by over 7 0C, and the inclusion of large form trees have the greatest contribution, by reducing temperatures over 15 0C. The results suggest that using specific strategies that combine placement of specific tree configurations with alternative distribution of urban development patterns can help to solve the current challenges of UHI's, and thereby support management

Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

Science.gov (United States)

Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

2012-09-01

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

MHV Vertices And Tree Amplitudes In Gauge Theory

International Nuclear Information System (INIS)

Cachazo, Freddy; Svrcek, Peter; Witten, Edward

2004-01-01

As an alternative to the usual Feynman graphs, tree amplitudes in Yang-Mills theory can be constructed from tree graphs in which the vertices are tree level MHV scattering amplitudes, continued off shell in a particular fashion. The formalism leads to new and relatively simple formulas for many amplitudes, and can be heuristically derived from twistor space. (author)

How effective are tree improvement programs in the 50 states?

Science.gov (United States)

Christopher D. Risbrudt; Stephen E. McDonald

1986-01-01

All 50 states were surveyed to determine the extent of their activities in producing genetically improved trees for timber production. Describes the funds expended, the species being improved, and the use of State and Private Forestry funds provided for genetic improvement. Projects future timber volumes attributable to genetic improvement, and estimates benefit cost...

Stratified B-trees and versioning dictionaries

OpenAIRE

Twigg, Andy; Byde, Andrew; Milos, Grzegorz; Moreton, Tim; Wilkes, John; Wilkie, Tom

2011-01-01

A classic versioned data structure in storage and computer science is the copy-on-write (CoW) B-tree -- it underlies many of today's file systems and databases, including WAFL, ZFS, Btrfs and more. Unfortunately, it doesn't inherit the B-tree's optimality properties; it has poor space utilization, cannot offer fast updates, and relies on random IO to scale. Yet, nothing better has been developed since. We describe the `stratified B-tree', which beats all known semi-external memory versioned B...

Million trees Los Angeles canopy cover and benefit assessment

Science.gov (United States)

E.G. McPherson; J.R. Simpson; Q. Xiao; C. Wu

2011-01-01

The Million Trees LA initiative intends to improve Los Angeles’s environment through planting and stewardship of 1 million trees. The purpose of this study was to measure Los Angeles’s existing tree canopy cover (TCC), determine if space exists for 1 million additional trees, and estimate future benefits from the planting. High-resolution QuickBird remote sensing data...

Improving and Conserving Sahelian Fruits Trees

DEFF Research Database (Denmark)

Ouedraogo, Moussa

Native Sahelian fruit trees are well known for their economic value and their nutritional importance for local populations. Their products are a source of income and a source of calories, vitamins, minerals and antioxidants, especially vital for children. Fruit trees are crucial for the people...... in West Africa Sahel during the food shortage period, lasting 6-8 months a year in this region. However, the availability of fruit trees is declining due to increased demographic pressure and climate variability (drought) that is occurring with increasing frequency and intensity. Besides compromising...... the availability of important resources for rural people, reduced abundance of target species can lead to loss of genetic variation within species, which again can reduce the capacity of trees and shrubs to adapt to environmental change and reduce the gain farmers can realize from selection. Parkia biglobosa...

Selective Tree-ring Models: A Novel Method for Reconstructing Streamflow Using Tree Rings

Science.gov (United States)

Foard, M. B.; Nelson, A. S.; Harley, G. L.

2017-12-01

Surface water is among the most instrumental and vulnerable resources in the Northwest United States (NW). Recent observations show that overall water quantity is declining in streams across the region, while extreme flooding events occur more frequently. Historical streamflow models inform probabilities of extreme flow events (flood or drought) by describing frequency and duration of past events. There are numerous examples of tree-rings being utilized to reconstruct streamflow in the NW. These models confirm that tree-rings are highly accurate at predicting streamflow, however there are many nuances that limit their applicability through time and space. For example, most models predict streamflow from hydrologically altered rivers (e.g. dammed, channelized) which may hinder our ability to predict natural prehistoric flow. They also have a tendency to over/under-predict extreme flow events. Moreover, they often neglect to capture the changing relationships between tree-growth and streamflow over time and space. To address these limitations, we utilized national tree-ring and streamflow archives to investigate the relationships between the growth of multiple coniferous species and free-flowing streams across the NW using novel species-and site-specific streamflow models - a term we coined"selective tree-ring models." Correlation function analysis and regression modeling were used to evaluate the strengths and directions of the flow-growth relationships. Species with significant relationships in the same direction were identified as strong candidates for selective models. Temporal and spatial patterns of these relationships were examined using running correlations and inverse distance weighting interpolation, respectively. Our early results indicate that (1) species adapted to extreme climates (e.g. hot-dry, cold-wet) exhibit the most consistent relationships across space, (2) these relationships weaken in locations with mild climatic variability, and (3) some

Conservation and restoration of forest trees impacted by non-native pathogens: the role of genetics and tree improvement

Science.gov (United States)

R.A. Sniezko; L.A. Winn

2017-01-01

North American native tree species in forest ecosystems, as well as managed forests and urban plantings, are being severely impacted by pathogens and insects. The impacts of these pathogens and insects often increase over time, and they are particularly acute for those species affected by non-native pathogens and insects. For restoration of affected tree species or for...

Papaya Tree Detection with UAV Images Using a GPU-Accelerated Scale-Space Filtering Method

Directory of Open Access Journals (Sweden)

Hao Jiang

2017-07-01

Full Text Available The use of unmanned aerial vehicles (UAV can allow individual tree detection for forest inventories in a cost-effective way. The scale-space filtering (SSF algorithm is commonly used and has the capability of detecting trees of different crown sizes. In this study, we made two improvements with regard to the existing method and implementations. First, we incorporated SSF with a Lab color transformation to reduce over-detection problems associated with the original luminance image. Second, we ported four of the most time-consuming processes to the graphics processing unit (GPU to improve computational efficiency. The proposed method was implemented using PyCUDA, which enabled access to NVIDIA’s compute unified device architecture (CUDA through high-level scripting of the Python language. Our experiments were conducted using two images captured by the DJI Phantom 3 Professional and a most recent NVIDIA GPU GTX1080. The resulting accuracy was high, with an F-measure larger than 0.94. The speedup achieved by our parallel implementation was 44.77 and 28.54 for the first and second test image, respectively. For each 4000 × 3000 image, the total runtime was less than 1 s, which was sufficient for real-time performance and interactive application.

Loss of Genetic Diversity of Jatropha curcas L. through Domestication: Implications for Its Genetic Improvement

DEFF Research Database (Denmark)

Sanou, Haby; Angel Angulo-Escalante, Miguel; Martinez-Herrera, Jorge

2015-01-01

Jatropha curcas L. has been promoted as a “miracle” tree in many parts of the world, but recent studies have indicated very low levels of genetic diversity in various landraces. In this study, the genetic diversity of landrace collections of J. curcas was compared with the genetic diversity...

Phase Transition and Critical Values of a Nearest-Neighbor System with Uncountable Local State Space on Cayley Trees

International Nuclear Information System (INIS)

Jahnel, Benedikt; Külske, Christof; Botirov, Golibjon I.

2014-01-01

We consider a ferromagnetic nearest-neighbor model on a Cayley tree of degree k ⩾ 2 with uncountable local state space [0,1] where the energy function depends on a parameter θ ∊[0, 1). We show that for 0 ⩽ θ ⩽ 5 3 k the model has a unique translation-invariant Gibbs measure. If 5 3 k < θ < 1 , there is a phase transition, in particular there are three translation-invariant Gibbs measures

The longevity of broadleaf deciduous trees in Northern Hemisphere temperate forests: insights from tree-ring series

Directory of Open Access Journals (Sweden)

Alfredo eDi Filippo

2015-05-01

Full Text Available Understanding the factors controlling the expression of longevity in trees is still an outstanding challenge for tree biologists and forest ecologists. We gathered tree-ring data and literature for broadleaf deciduous (BD temperate trees growing in closed-canopy old-growth forests in the Northern Hemisphere to explore the role of geographic patterns, climate variability, and growth rates on longevity. Our pan-continental analysis, covering 32 species from 12 genera, showed that 300-400 years can be considered a baseline threshold for maximum tree lifespan in many temperate deciduous forests. Maximum age varies greatly in relation to environmental features, even within the same species. Tree longevity is generally promoted by reduced growth rates across large genetic differences and environmental gradients. We argue that slower growth rates, and the associated smaller size, provide trees with an advantage against biotic and abiotic disturbance agents, supporting the idea that size, not age, is the main constraint to tree longevity. The oldest trees were living most of their life in subordinate canopy conditions and/or within primary forests in cool temperate environments and outside major storm tracks. Very old trees are thus characterized by slow growth and often live in forests with harsh site conditions and infrequent disturbance events that kill much of the trees. Temperature inversely controls the expression of longevity in mesophilous species (Fagus spp., but its role in Quercus spp. is more complex and warrants further research in disturbance ecology. Biological, ecological and historical drivers must be considered to understand the constraints imposed to longevity within different forest landscapes.

Leapfrogging of tree species provenances? Interaction of microclimate and genetics on upward shifts in tree species' range limits

Science.gov (United States)

Reinhardt, K.; Castanha, C.; Germino, M. J.; Kueppers, L. M.

2011-12-01

The elevation limit of tree growth (alpine treeline) is considered to be constrained by environmental (i.e., thermal) and genetic (i.e., inability to adapt to climatic conditions) limitations to growth. Warming conditions due to climate change are predicted to cause upward shifts in the elevation of alpine treelines, through relief of cold-induced physiological limitations on seedling recruitment beyond current treeline boundaries. To determine how genetics and climate may interact to affect seedling establishment, we transplanted recently germinated seedlings from high- and low-elevation provenances (HI and LO, respectively) of Pinus flexilis in common gardens arrayed along an elevation and canopy gradient from subalpine forest into the alpine zone at Niwot Ridge, CO. We compared differences in microclimate and seedling ecophysiology among sites and between provenances. During the first summer of growth, frequently cloudy skies resulted in similar solar radiation incidence and air and soil temperatures among sites, despite nearly a 500 m-span in elevation across all sites. Preliminary findings suggest that survival of seedlings was similar between the lowest and highest elevations, with greater survival of LO (60%) compared to HI (40%) seedlings at each of these sites. Photosynthesis, carbon balance (photosynthesis/respiration), and conductance increased more than 2X with elevation for both provenances, and were 35-77% greater in LO seedlings compared to HI seedlings. There were no differences in dark-adapted chlorophyll fluorescence (Fv/Fm) among sites or between provenances. However, in a common-garden study at low elevation, we observed no differences in carbon or water relations between two naturally-germinated mitochondrial haplotypes of P. flexilis (of narrow and wide-ranging distributions). We did observe water-related thresholds on seedling carbon balance and survival that occurred when soil volumetric water content dropped below 10% and seedling water

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

Science.gov (United States)

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

Fundamental geodesic deformations in spaces of treelike shapes

DEFF Research Database (Denmark)

Feragen, Aasa; Lauze, Francois Bernard; Nielsen, Mads

2010-01-01

This paper presents a new geometric framework for analysis of planar treelike shapes for applications such as shape matching, recognition and morphology, using the geometry of the space of treelike shapes. Mathematically, the shape space is given the structure of a stratified set which...... is a quotient of a normed vector space with a metric inherited from the vector space norm. We give examples of geodesic paths in tree-space corresponding to fundamental deformations of small trees, and discuss how these deformations are key building blocks for understanding deformations between larger trees....

An efficient and extensible approach for compressing phylogenetic trees

KAUST Repository

Matthews, Suzanne J

2011-01-01

Background: Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference.Results: On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings.Conclusions: TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. © 2011 Matthews and Williams; licensee BioMed Central Ltd.

Air pollution removal by trees in public green spaces in Strasbourg city, France

Science.gov (United States)

Wissal Selmi; Christiane Weber; Emmanuel Riviere; Nadege Blond; Lotfi Mehdi; David Nowak

2016-01-01

This study integrates i-Tree Eco model in order to estimate air pollution removal by urban trees in Strasbourg city, France. Applied for the first time in a French city, the model shows that public trees, i.e., trees managed by the city, removed about 88 t of pollutants during one year period (from July 2012 to June 2013): about 1 ton for CO; 14 tons for NO2...

Micropropagation of Pithecellobium dulce (Roxb.) Benth-a multipurpose leguminous tree and assessment of genetic fidelity of micropropagated plants using molecular markers.

Science.gov (United States)

Goyal, Pooja; Kachhwaha, Sumita; Kothari, S L

2012-04-01

An efficient and reproducible protocol has been developed for in vitro propagation of Pithecellobium dulce (Roxb.) Benth (a multipurpose leguminous tree) from field grown nodal segments (axillary bud). Shoot bud induction occurred from nodal explants of 15-years-old tree on Murashige and Skoog (MS) basal medium supplemented with 4.4 μM 6-benzyladenine (BA) and multiplication was achieved on MS medium supplemented with 4.4 μM BA + 0.73 μM phenylacetic acid (PAA) i.e. up to 7 shoot buds in the period of 5-6 weeks. Addition of adenine sulphate (AdS) to this medium further enhanced the number of shoot buds up to 10. Proliferating shoot cultures were established by repeatedly subculturing primary culture on fresh medium (MS + 4.4 μM BA + 0.73 μM PAA) after every 25 days. In vitro rooting was achieved on MS medium supplemented with 2.46 μM Indole-3-butyric acid (IBA) + 41.63 μM activated charcoal (AC). The micropropagated shoots with well developed roots were acclimatized in green house in pots containing sand, soil and manure (1:1:1). Genetic stability of micropropagated clones was evaluated using Random amplified polymorphic DNA (RAPD) and Inter simple sequence repeat (ISSR) markers. The amplification products were monomorphic in micropropagated plants and similar to those of mother plant. No polymorphism was detected revealing the genetic uniformity of micropropagated plants. This is the first report of an efficient protocol for regeneration of P. dulce through organogenesis, which can be used for further genetic transformation and pharmaceutical purposes.

Macroscopic Models of Clique Tree Growth for Bayesian Networks

Data.gov (United States)

National Aeronautics and Space Administration — In clique tree clustering, inference consists of propagation in a clique tree compiled from a Bayesian network. In this paper, we develop an analytical approach to...

AFLP marker analysis revealing genetic structure of the tree Parapiptadenia rigida (Benth. Brenan (Leguminosae-Mimosoideae in the southern Brazilian Tropical Rainforest

Directory of Open Access Journals (Sweden)

Laís Bérgamo de Souza

2013-01-01

Full Text Available Parapiptadenia rigida is a tropical early secondary succession tree characteristic of the Tropical Atlantic Rainforest. This species is of great ecological importance in the recovery of degraded areas. In this study we investigated the variability and population genetic structure of eight populations of P. rigida. Five AFLP primer combinations were used in a sample of 159 individuals representing these eight populations, rendering a total of 126 polymorphic fragments. The averages of percentage of polymorphic loci, gene diversity, and Shannon index were 60.45%, 0.217, and 0.322, respectively. A significant correlation between the population genetic variability and the population sizes was observed. The genetic variability within populations (72.20% was higher than between these (22.80%. No perfect correlation was observed between geographic and genetic distances, which might be explained by differences in deforestation intensities that occurred in these areas. A dendrogram constructed by the UPGMA method revealed the formation of two clusters, these also confirmed by Bayesian analysis for the number of K cluster. These results show that it is necessary to develop urgent management strategies for the conservation of certain populations of P. rigida, while other populations still preserve reasonably high levels of genetic variability.

Finding Minimum-Power Broadcast Trees for Wireless Networks

Science.gov (United States)

Arabshahi, Payman; Gray, Andrew; Das, Arindam; El-Sharkawi, Mohamed; Marks, Robert, II

2004-01-01

Some algorithms have been devised for use in a method of constructing tree graphs that represent connections among the nodes of a wireless communication network. These algorithms provide for determining the viability of any given candidate connection tree and for generating an initial set of viable trees that can be used in any of a variety of search algorithms (e.g., a genetic algorithm) to find a tree that enables the network to broadcast from a source node to all other nodes while consuming the minimum amount of total power. The method yields solutions better than those of a prior algorithm known as the broadcast incremental power algorithm, albeit at a slightly greater computational cost.

Breeding strategies for north central tree improvement programs

Science.gov (United States)

Ronald P. Overton; Hyun Kang

1985-01-01

The rationales and concepts of long-term tree breeding are discussed and compared with those for short-term breeding. A model breeding program is reviewed which maximizes short-term genetic gain for currently important traits and provides genetic resources that can be used effectively in future short-term breeding. The resources of the north-central region are examined...

Simulation of Canopy CO2/H2O Fluxes for a Rubber (Hevea Brasiliensis) Plantation in Central Cambodia: The Effect of the Regular Spacing of Planted Trees

Energy Technology Data Exchange (ETDEWEB)

Kumagai, Tomo' omi; Mudd, Ryan; Miyazawa, Yoshiyuki; Liu, Wen; Giambelluca, Thomas; Kobayashi, N.; Lim, Tiva Khan; Jomura, Mayuko; Matsumoto, Kazuho; Huang, Maoyi; Chen, Qi; Ziegler, Alan; Yin, Song

2013-09-10

We developed a soil-vegetation-atmosphere transfer (SVAT) model applicable to simulating CO2 and H2O fluxes from the canopies of rubber plantations, which are characterized by distinct canopy clumping produced by regular spacing of plantation trees. Rubber (Hevea brasiliensis Müll. Arg.) plantations, which are rapidly expanding into both climatically optimal and sub-optimal environments throughout mainland Southeast Asia, potentially change the partitioning of water, energy, and carbon at multiple scales, compared with traditional land covers it is replacing. Describing the biosphere-atmosphere exchange in rubber plantations via SVAT modeling is therefore essential to understanding the impacts on environmental processes. The regular spacing of plantation trees creates a peculiar canopy structure that is not well represented in most SVAT models, which generally assumes a non-uniform spacing of vegetation. Herein we develop a SVAT model applicable to rubber plantation and an evaluation method for its canopy structure, and examine how the peculiar canopy structure of rubber plantations affects canopy CO2 and H2O exchanges. Model results are compared with measurements collected at a field site in central Cambodia. Our findings suggest that it is crucial to account for intensive canopy clumping in order to reproduce observed rubber plantation fluxes. These results suggest a potentially optimal spacing of rubber trees to produce high productivity and water use efficiency.

Totally optimal decision trees for Boolean functions

KAUST Repository

Chikalov, Igor

2016-07-28

We study decision trees which are totally optimal relative to different sets of complexity parameters for Boolean functions. A totally optimal tree is an optimal tree relative to each parameter from the set simultaneously. We consider the parameters characterizing both time (in the worst- and average-case) and space complexity of decision trees, i.e., depth, total path length (average depth), and number of nodes. We have created tools based on extensions of dynamic programming to study totally optimal trees. These tools are applicable to both exact and approximate decision trees, and allow us to make multi-stage optimization of decision trees relative to different parameters and to count the number of optimal trees. Based on the experimental results we have formulated the following hypotheses (and subsequently proved): for almost all Boolean functions there exist totally optimal decision trees (i) relative to the depth and number of nodes, and (ii) relative to the depth and average depth.

Legalization of Tree Doctor System and the Role of KSPP

OpenAIRE

Byeongjin Cha

2017-01-01

In December of 2016, ‘The Forest Protection Act’ was amended partly in The National Assembly and the socalled ‘Tree Doctor Act’ was promulgated. Tree Doctor Act will be enforced from June 28, 2018. Under the new Act, none other than ‘Tree Hospital’ can do disease and pest management work for trees in public living space. The only exclusive qualification for tree hospital is a ‘Tree Doctor’, the government registered license which is newly established by the Act. To become a tree doctor, he/sh...

A review of pruning fruit trees

Science.gov (United States)

Zhang, L.; Koc, A. B.; Wang, X. N.; Jiang, Y. X.

2018-05-01

The focus of this review is to present the results of studies and articles about ways to prune fruit trees. Pruning should be done in late winter or early spring so that the infection risk can be significantly decreased. This review will also offer an overview of methods to prevent infections and speed up recovery on the trees. The following is an interpretation of why high-power ultrasonic assisted pruning in the fruits trees is needed and will elaborate on the efficiency, labor costs, and safety, as well as space, location, and some environmental issues.

Non-perturbative renormalization in coordinate space for Nf=2 maximally twisted mass fermions with tree-level Symanzik improved gauge action

International Nuclear Information System (INIS)

Cichy, Krzysztof; Adam Mickiewicz Univ., Poznan; Jansen, Karl; Korcyl, Piotr; Jagiellonian Univ., Krakow

2012-07-01

We present results of a lattice QCD application of a coordinate space renormalization scheme for the extraction of renormalization constants for flavour non-singlet bilinear quark operators. The method consists in the analysis of the small-distance behaviour of correlation functions in Euclidean space and has several theoretical and practical advantages, in particular: it is gauge invariant, easy to implement and has relatively low computational cost. The values of renormalization constants in the X-space scheme can be converted to the MS scheme via 4-loop continuum perturbative formulae. Our results for N f =2 maximally twisted mass fermions with tree-level Symanzik improved gauge action are compared to the ones from the RI-MOM scheme and show full agreement with this method. (orig.)

Visual exploration of parameter influence on phylogenetic trees.

Science.gov (United States)

Hess, Martin; Bremm, Sebastian; Weissgraeber, Stephanie; Hamacher, Kay; Goesele, Michael; Wiemeyer, Josef; von Landesberger, Tatiana

2014-01-01

Evolutionary relationships between organisms are frequently derived as phylogenetic trees inferred from multiple sequence alignments (MSAs). The MSA parameter space is exponentially large, so tens of thousands of potential trees can emerge for each dataset. A proposed visual-analytics approach can reveal the parameters' impact on the trees. Given input trees created with different parameter settings, it hierarchically clusters the trees according to their structural similarity. The most important clusters of similar trees are shown together with their parameters. This view offers interactive parameter exploration and automatic identification of relevant parameters. Biologists applied this approach to real data of 16S ribosomal RNA and protein sequences of ion channels. It revealed which parameters affected the tree structures. This led to a more reliable selection of the best trees.

Using trees to compute approximate solutions to ordinary differential equations exactly

Science.gov (United States)

Grossman, Robert

1991-01-01

Some recent work is reviewed which relates families of trees to symbolic algorithms for the exact computation of series which approximate solutions of ordinary differential equations. It turns out that the vector space whose basis is the set of finite, rooted trees carries a natural multiplication related to the composition of differential operators, making the space of trees an algebra. This algebraic structure can be exploited to yield a variety of algorithms for manipulating vector fields and the series and algebras they generate.

Population structure of Aphis spiraecola (Hemiptera: Aphididae) on pear trees in China identified using microsatellites.

Science.gov (United States)

Cao, Jinjun; Li, Jie; Niu, Jianqun; Liu, Xiaoxia; Zhang, Qingwen

2012-04-01

The spiraea aphid (Aphis spiraecola Patch) is a primary pest of fruit trees, particularly pear trees in China. Despite the economic importance of this pest, little is known about its genetic structure or its patterns of dispersal at local and regional scales; however, knowledge of these characteristics is important for establishing effective control strategies for this pest. The genetic variability of 431 individuals from 21 populations on pear trees in China was investigated using eight polymorphic microsatellite loci. The high polymorphism of these markers was evident from the expected heterozygosity value (He = 0.824) and the Polymorphism Information Content (PIC = 0.805), indicating that the spiraea aphid maintains a high level of genetic diversity. The analysis of molecular variance revealed a middle level of population differentiation (F(ST) = 0.1478) among A. spiraecola populations. This result is consistent with the results of the STRUCTURE analysis (K = 3), the unweighted pair-group method with arithmetic average tree and the Mantel test (r = 0.6392; P < 0.05). Our results indicate high levels of genetic exchange in the spiraea aphid, possibly facilitated by geography and climate. Our findings emphasize the importance of considering regional differences in studies of population structure, even when strong isolation-by-distance influences the genetic population structure of species.

Genomics-assisted breeding in fruit trees.

Science.gov (United States)

Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

Tools for valuing tree and park services

Science.gov (United States)

E.G. McPherson

2010-01-01

Arborists and urban foresters plan, design, construct, and manage trees and parks in cities throughout the world. These civic improvements create walkable, cool environments, save energy, reduce stormwater runoff, sequester carbon dioxide, and absorb air pollutants. The presence of trees and green spaces in cities is associated with increases in property values,...

Short-term load forecasting with increment regression tree

Energy Technology Data Exchange (ETDEWEB)

Yang, Jingfei; Stenzel, Juergen [Darmstadt University of Techonology, Darmstadt 64283 (Germany)

2006-06-15

This paper presents a new regression tree method for short-term load forecasting. Both increment and non-increment tree are built according to the historical data to provide the data space partition and input variable selection. Support vector machine is employed to the samples of regression tree nodes for further fine regression. Results of different tree nodes are integrated through weighted average method to obtain the comprehensive forecasting result. The effectiveness of the proposed method is demonstrated through its application to an actual system. (author)

Long-distance gene flow and adaptation of forest trees to rapid climate change

Science.gov (United States)

Kremer, Antoine; Ronce, Ophélie; Robledo-Arnuncio, Juan J; Guillaume, Frédéric; Bohrer, Gil; Nathan, Ran; Bridle, Jon R; Gomulkiewicz, Richard; Klein, Etienne K; Ritland, Kermit; Kuparinen, Anna; Gerber, Sophie; Schueler, Silvio

2012-01-01

Forest trees are the dominant species in many parts of the world and predicting how they might respond to climate change is a vital global concern. Trees are capable of long-distance gene flow, which can promote adaptive evolution in novel environments by increasing genetic variation for fitness. It is unclear, however, if this can compensate for maladaptive effects of gene flow and for the long-generation times of trees. We critically review data on the extent of long-distance gene flow and summarise theory that allows us to predict evolutionary responses of trees to climate change. Estimates of long-distance gene flow based both on direct observations and on genetic methods provide evidence that genes can move over spatial scales larger than habitat shifts predicted under climate change within one generation. Both theoretical and empirical data suggest that the positive effects of gene flow on adaptation may dominate in many instances. The balance of positive to negative consequences of gene flow may, however, differ for leading edge, core and rear sections of forest distributions. We propose future experimental and theoretical research that would better integrate dispersal biology with evolutionary quantitative genetics and improve predictions of tree responses to climate change. PMID:22372546

Molecular and genetic study of wheat rusts

African Journals Online (AJOL)

Nicholas Le Maitre

Phylogenetic trees were created for leaf and stem rust pathotypes. Field isolates of ... Key words: Prevalence, microsatellite, amplified fragment length polymorphisms (AFLP), phylogeny, Puccinia. INTRODUCTION. Puccinia triticina Eriks ..... Genetic distances and reconstruction phylogenetic trees from microsatellite DNA.

Genetic programming applied to RFI mitigation in radio astronomy

Science.gov (United States)

Staats, K.

2016-12-01

Genetic Programming is a type of machine learning that employs a stochastic search of a solutions space, genetic operators, a fitness function, and multiple generations of evolved programs to resolve a user-defined task, such as the classification of data. At the time of this research, the application of machine learning to radio astronomy was relatively new, with a limited number of publications on the subject. Genetic Programming had never been applied, and as such, was a novel approach to this challenging arena. Foundational to this body of research, the application Karoo GP was developed in the programming language Python following the fundamentals of tree-based Genetic Programming described in "A Field Guide to Genetic Programming" by Poli, et al. Karoo GP was tasked with the classification of data points as signal or radio frequency interference (RFI) generated by instruments and machinery which makes challenging astronomers' ability to discern the desired targets. The training data was derived from the output of an observation run of the KAT-7 radio telescope array built by the South African Square Kilometre Array (SKA-SA). Karoo GP, kNN, and SVM were comparatively employed, the outcome of which provided noteworthy correlations between input parameters, the complexity of the evolved hypotheses, and performance of raw data versus engineered features. This dissertation includes description of novel approaches to GP, such as upper and lower limits to the size of syntax trees, an auto-scaling multiclass classifier, and a Numpy array element manager. In addition to the research conducted at the SKA-SA, it is described how Karoo GP was applied to fine-tuning parameters of a weather prediction model at the South African Astronomical Observatory (SAAO), to glitch classification at the Laser Interferometer Gravitational-wave Observatory (LIGO), and to astro-particle physics at The Ohio State University.

Least Squares Methods for Equidistant Tree Reconstruction

OpenAIRE

Fahey, Conor; Hosten, Serkan; Krieger, Nathan; Timpe, Leslie

2008-01-01

UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves, also known as the Bergman complex of the graphical matroid for the complete graph $K_n$. We show that UPGMA performs an orthogonal projection of the data onto a maximal cell of the Bergman complex. We also show that the equidistant tree with the least (Eucl...

American chestnut: A test case for genetic engineering?

Science.gov (United States)

Leila Pinchot

2014-01-01

The thought of genetically engineered (GE) trees might conjure images of mutant trees with unnatural and invasive tendencies, but there is much more to the story. GE trees are a new reality that, like it or not, will probably be part of the future of forestry. The basic inclination of most Forest Guild stewards is to reject GE trees as violating our principle to...

Collaboration space division in collaborative product development based on a genetic algorithm

Science.gov (United States)

Qian, Xueming; Ma, Yanqiao; Feng, Huan

2018-02-01

The advance in the global environment, rapidly changing markets, and information technology has created a new stage for design. In such an environment, one strategy for success is the Collaborative Product Development (CPD). Organizing people effectively is the goal of Collaborative Product Development, and it solves the problem with certain foreseeability. The development group activities are influenced not only by the methods and decisions available, but also by correlation among personnel. Grouping the personnel according to their correlation intensity is defined as collaboration space division (CSD). Upon establishment of a correlation matrix (CM) of personnel and an analysis of the collaboration space, the genetic algorithm (GA) and minimum description length (MDL) principle may be used as tools in optimizing collaboration space. The MDL principle is used in setting up an object function, and the GA is used as a methodology. The algorithm encodes spatial information as a chromosome in binary. After repetitious crossover, mutation, selection and multiplication, a robust chromosome is found, which can be decoded into an optimal collaboration space. This new method can calculate the members in sub-spaces and individual groupings within the staff. Furthermore, the intersection of sub-spaces and public persons belonging to all sub-spaces can be determined simultaneously.

Drawing non-layered tidy trees in linear time

NARCIS (Netherlands)

A.J. van der Ploeg (Atze)

2013-01-01

htmlabstractThe well-known Reingold–Tilford algorithm produces tidy-layered drawings of trees: drawings where all nodes at the same depth are vertically aligned. However, when nodes have varying heights, layered drawing may use more vertical space than necessary. A non-layered drawing of a tree

Genetic diversity of Dyera polyphylla (Miq.) Steenis populations used in tropical peatland restoration in Indonesia

NARCIS (Netherlands)

Tata, Hesti Lestari; Muchugi, A.; Kariba, R.; Noordwijk, van M.

2018-01-01

Dyera polyphylla is a native tree species of peat swamp forests in Southeast Asia. Where it has been used in peatland restoration, the trees are of uncertain genetic origin. We analysed the genetic diversity of seven populations of D. polyphylla (9–20 individual trees per population) from both

The relationship between the number of loci and the statistical support for the topology of UPGMA trees obtained from genetic distance data.

Science.gov (United States)

Highton, R

1993-12-01

An analysis of the relationship between the number of loci utilized in an electrophoretic study of genetic relationships and the statistical support for the topology of UPGMA trees is reported for two published data sets. These are Highton and Larson (Syst. Zool.28:579-599, 1979), an analysis of the relationships of 28 species of plethodonine salamanders, and Hedges (Syst. Zool., 35:1-21, 1986), a similar study of 30 taxa of Holarctic hylid frogs. As the number of loci increases, the statistical support for the topology at each node in UPGMA trees was determined by both the bootstrap and jackknife methods. The results show that the bootstrap and jackknife probabilities supporting the topology at some nodes of UPGMA trees increase as the number of loci utilized in a study is increased, as expected for nodes that have groupings that reflect phylogenetic relationships. The pattern of increase varies and is especially rapid in the case of groups with no close relatives. At nodes that likely do not represent correct phylogenetic relationships, the bootstrap probabilities do not increase and often decline with the addition of more loci.

Phylogenetic search through partial tree mixing

Science.gov (United States)

2012-01-01

Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. Results When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda Conclusions The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution. PMID:23320449

Identification and characterization of twenty-seven short ...

Indian Academy of Sciences (India)

They have been successfully applied to resolve phylo- genetic relationships among various groups at different tax- onomic ranks (Nikaido et al. 2003; Chen et al. .... nizable flanking direct repeats (DRs) that are diagnostic of amplification via RNA intermediates during retrotransposi- tion (Weiner et al. 1986; Deininger 1989) ...

Expected genetic gain in teak (Tectona grandis L.f.) in Cordoba (Colombia)

International Nuclear Information System (INIS)

Espitia C, Miguel; Olman Murillo, G; Carlos Castillo, P

2011-01-01

The Cordoba department of Colombia programmed to establish 200000 ha of forest plantations by year 2025. Teak was priorized by its adaptation, wood quality and value in the asian markets. The objective of this research was to estimate the expected genetic gain, of phenotypically selected pluss trees in 5316 ha plantation in Cordoba, for diameter at breast height, commercial height, commercial volume and log quality traits. The selection based on the pheno typical evaluation of the tree candidate and its four best neighbors within a 20 m radius, qualifying, individually the first four segments of 2.5 m length. Selected trees were classified in list A as determined to be superior in both, volume and quality, according to the selection differential to all its four best neighbors. List B included those plus trees found superior only in commercial volume or in stem quality. Genetic gain was estimated by multiplying selection differential X average narrow sense heritability. We estimated a Selection Index that integrate commercial volume (60%) and stem quality (40%). From 46 selected trees, 18 were classified as plus A. In selecting and cloning the 18 best A plus trees, based on the Selection Index, we expected genetic gains of 5.52% (diameter); 17.50% (height); 41.71% (commercial volume) and 9,59% (stem quality). These results suggest an important genetic progress breeding teak in Cordoba, as long as they broaden the genetic base of the program and verify results with genetic testing in various potential production areas.

Searching Fragment Spaces with feature trees.

Science.gov (United States)

Lessel, Uta; Wellenzohn, Bernd; Lilienthal, Markus; Claussen, Holger

2009-02-01

Virtual combinatorial chemistry easily produces billions of compounds, for which conventional virtual screening cannot be performed even with the fastest methods available. An efficient solution for such a scenario is the generation of Fragment Spaces, which encode huge numbers of virtual compounds by their fragments/reagents and rules of how to combine them. Similarity-based searches can be performed in such spaces without ever fully enumerating all virtual products. Here we describe the generation of a huge Fragment Space encoding about 5 * 10(11) compounds based on established in-house synthesis protocols for combinatorial libraries, i.e., we encode practically evaluated combinatorial chemistry protocols in a machine readable form, rendering them accessible to in silico search methods. We show how such searches in this Fragment Space can be integrated as a first step in an overall workflow. It reduces the extremely huge number of virtual products by several orders of magnitude so that the resulting list of molecules becomes more manageable for further more elaborated and time-consuming analysis steps. Results of a case study are presented and discussed, which lead to some general conclusions for an efficient expansion of the chemical space to be screened in pharmaceutical companies.

Nodal distances for rooted phylogenetic trees.

Science.gov (United States)

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

2010-08-01

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

Canopy management, leaf fall and litter quality of dominant tree ...

African Journals Online (AJOL)

Small-scale farmers in the banana-coffee agro-zone of Central Uganda plant and maintain trees to provide a range of benefits. However, the impact of trees on soil fertility and crop yields is small. On many farms, trees exist in infinite numbers, compositions, with no proper spacing, sequencing and canopy management ...

Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants.

Science.gov (United States)

Rodríguez López, Carlos M; Wetten, Andrew C; Wilkinson, Michael J

2010-06-01

*Relatively little is known about the timing of genetic and epigenetic forms of somaclonal variation arising from callus growth. We surveyed for both types of change in cocoa (Theobroma cacao) plants regenerated from calli of various ages, and also between tissues from the source trees. *For genetic change, we used 15 single sequence repeat (SSR) markers from four source trees and from 233 regenerated plants. For epigenetic change, we used 386 methylation-sensitive amplified polymorphism (MSAP) markers on leaf and explant (staminode) DNA from two source trees and on leaf DNA from 114 regenerants. *Genetic variation within source trees was limited to one slippage mutation in one leaf. Regenerants were far more variable, with 35% exhibiting at least one mutation. Genetic variation initially accumulated with culture age but subsequently declined. MSAP (epigenetic) profiles diverged between leaf and staminode samples from source trees. Multivariate analysis revealed that leaves from regenerants occupied intermediate eigenspace between leaves and staminodes of source plants but became progressively more similar to source tree leaves with culture age. *Statistical analysis confirmed this rather counterintuitive finding that leaves of 'late regenerants' exhibited significantly less genetic and epigenetic divergence from source leaves than those exposed to short periods of callus growth.

Tree-average distances on certain phylogenetic networks have their weights uniquely determined.

Science.gov (United States)

Willson, Stephen J

2012-01-01

A phylogenetic network N has vertices corresponding to species and arcs corresponding to direct genetic inheritance from the species at the tail to the species at the head. Measurements of DNA are often made on species in the leaf set, and one seeks to infer properties of the network, possibly including the graph itself. In the case of phylogenetic trees, distances between extant species are frequently used to infer the phylogenetic trees by methods such as neighbor-joining. This paper proposes a tree-average distance for networks more general than trees. The notion requires a weight on each arc measuring the genetic change along the arc. For each displayed tree the distance between two leaves is the sum of the weights along the path joining them. At a hybrid vertex, each character is inherited from one of its parents. We will assume that for each hybrid there is a probability that the inheritance of a character is from a specified parent. Assume that the inheritance events at different hybrids are independent. Then for each displayed tree there will be a probability that the inheritance of a given character follows the tree; this probability may be interpreted as the probability of the tree. The tree-average distance between the leaves is defined to be the expected value of their distance in the displayed trees. For a class of rooted networks that includes rooted trees, it is shown that the weights and the probabilities at each hybrid vertex can be calculated given the network and the tree-average distances between the leaves. Hence these weights and probabilities are uniquely determined. The hypotheses on the networks include that hybrid vertices have indegree exactly 2 and that vertices that are not leaves have a tree-child.

Application of plant DNA markers in forensic botany: genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites.

Science.gov (United States)

Craft, Kathleen J; Owens, Jeffrey D; Ashley, Mary V

2007-01-05

As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.

Design optimization of space launch vehicles using a genetic algorithm

Science.gov (United States)

Bayley, Douglas James

The United States Air Force (USAF) continues to have a need for assured access to space. In addition to flexible and responsive spacelift, a reduction in the cost per launch of space launch vehicles is also desirable. For this purpose, an investigation of the design optimization of space launch vehicles has been conducted. Using a suite of custom codes, the performance aspects of an entire space launch vehicle were analyzed. A genetic algorithm (GA) was employed to optimize the design of the space launch vehicle. A cost model was incorporated into the optimization process with the goal of minimizing the overall vehicle cost. The other goals of the design optimization included obtaining the proper altitude and velocity to achieve a low-Earth orbit. Specific mission parameters that are particular to USAF space endeavors were specified at the start of the design optimization process. Solid propellant motors, liquid fueled rockets, and air-launched systems in various configurations provided the propulsion systems for two, three and four-stage launch vehicles. Mass properties models, an aerodynamics model, and a six-degree-of-freedom (6DOF) flight dynamics simulator were all used to model the system. The results show the feasibility of this method in designing launch vehicles that meet mission requirements. Comparisons to existing real world systems provide the validation for the physical system models. However, the ability to obtain a truly minimized cost was elusive. The cost model uses an industry standard approach, however, validation of this portion of the model was challenging due to the proprietary nature of cost figures and due to the dependence of many existing systems on surplus hardware.

Multiple-geographic-scale genetic structure of two mangrove tree species: the roles of mating system, hybridization, limited dispersal and extrinsic factors.

Directory of Open Access Journals (Sweden)

Gustavo M Mori

Full Text Available Mangrove plants comprise a unique group of organisms that grow within the intertidal zones of tropical and subtropical regions and whose distributions are influenced by both biotic and abiotic factors. To understand how these extrinsic and intrinsic processes influence a more fundamental level of the biological hierarchy of mangroves, we studied the genetic diversity of two Neotropical mangrove trees, Avicenniagerminans and A. schaueriana, using microsatellites markers. As reported for other sea-dispersed species, there was a strong differentiation between A. germinans and A. schaueriana populations sampled north and south of the northeastern extremity of South America, likely due to the influence of marine superficial currents. Moreover, we observed fine-scale genetic structures even when no obvious physical barriers were present, indicating pollen and propagule dispersal limitation, which could be explained by isolation-by-distance coupled with mating system differences. We report the first evidence of ongoing hybridization between Avicennia species and that these hybrids are fertile, although this interspecific crossing has not contributed to an increase in the genetic diversity the populations where A. germinans and A. schaueriana hybridize. These findings highlight the complex interplay between intrinsic and extrinsic factors that shape the distribution of the genetic diversity in these sea-dispersed colonizer species.

Smallholder tree farming systems for livelihood enhancement and carbon storage

DEFF Research Database (Denmark)

Roshetko, James Michael

Smallholder agroforestry (tree farming) systems are prominent components of ‘trees outside the forest’. The hypothesis of this thesis is that smallholder tree-farming systems are viable agricultural and natural resources management systems that contribute significantly to global environmental goals...... and local economic objectives. The thesis supports the hypothesis by reviewing global and Asian trends of deforestation, human population growth, and demand for forest and tree products. The potential of smallholders’ treebased systems to expand regional forest resources, produce forest products...... development of smallholder systems, how genetic diversity of smallholder systems supports adaptation to climate change, and the capacity of smallholder systems to simultaneously produce marketable timber and agricultural crops....

Coalgebraic structure of genetic inheritance.

Science.gov (United States)

Tian, Jianjun; Li, Bai-Lian

2004-09-01

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

Succinct partial sums and fenwick trees

DEFF Research Database (Denmark)

Bille, Philip; Christiansen, Anders Roy; Prezza, Nicola

2017-01-01

We consider the well-studied partial sums problem in succint space where one is to maintain an array of n k-bit integers subject to updates such that partial sums queries can be efficiently answered. We present two succint versions of the Fenwick Tree – which is known for its simplicity...... and practicality. Our results hold in the encoding model where one is allowed to reuse the space from the input data. Our main result is the first that only requires nk + o(n) bits of space while still supporting sum/update in O(logbn)/O(blogbn) time where 2 ≤ b ≤ log O(1)n. The second result shows how optimal...... time for sum/update can be achieved while only slightly increasing the space usage to nk + o(nk) bits. Beyond Fenwick Trees, the results are primarily based on bit-packing and sampling – making them very practical – and they also allow for simple optimal parallelization....

wANNOVAR: annotating genetic variants for personal genomes via the web.

Science.gov (United States)

Chang, Xiao; Wang, Kai

2012-07-01

High-throughput DNA sequencing platforms have become widely available. As a result, personal genomes are increasingly being sequenced in research and clinical settings. However, the resulting massive amounts of variants data pose significant challenges to the average biologists and clinicians without bioinformatics skills. We developed a web server called wANNOVAR to address the critical needs for functional annotation of genetic variants from personal genomes. The server provides simple and intuitive interface to help users determine the functional significance of variants. These include annotating single nucleotide variants and insertions/deletions for their effects on genes, reporting their conservation levels (such as PhyloP and GERP++ scores), calculating their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieving allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 5400 exomes), and implementing a 'variants reduction' protocol to identify a subset of potentially deleterious variants/genes. We illustrated how wANNOVAR can help draw biological insights from sequencing data, by analysing genetic variants generated on two Mendelian diseases. We conclude that wANNOVAR will help biologists and clinicians take advantage of the personal genome information to expedite scientific discoveries. The wANNOVAR server is available at http://wannovar.usc.edu, and will be continuously updated to reflect the latest annotation information.

Arquitectura de los árboles Tree architecture

Directory of Open Access Journals (Sweden)

Francis Hallé

2010-12-01

Full Text Available La forma de la copa nunca es aleatoria; cada árbol tiene su programa específico de desarrollo, controlado por genes, desde la germinación. La forma del árbol adulto puede ser modificada por factores ecológicos, pero siempre persisten las reglas de desarrollo; analizar estas reglas es el objetivo de la arquitectura. Llamaré «modelo arquitectural» al programa genético de crecimiento y desarrollo que aparece en un árbol joven. De los 22 modelos actualmente reconocidos, presentaré los cinco más comunes. Cuando el modelo tiene una expresión única, permaneciendo durante toda la vida, el árbol es «unitario»; estos árboles unitarios son arcaicos. El concepto de «reiteración» es clave para entender lo que es un árbol: este mecanismo transforma el árbol en una colonia; los «árboles reiterados» (AR crecen los unos encima de los otros, tal como parásitos. La reiteración da a luz un árbol entero, con tronco, ramas y raíces. Un AR todavía joven crece verticalmente; luego, con la plasticidad de la madera y la palanca, se inclina y se vuelve horizontal, lo que es eficaz para capturar la luz. Fue importante el descubrimiento, dentro de una misma copa, de variaciones genéticas de un AR al otro: en varias especies, el árbol es una colonia de genomas.Trees never have a random crown form; each tree has its specific developmental program, controlled by genes, since its germination. The form of the adult tree may be modified by ecological factors but developmental rules are ever lasting; analyzing these rules is the objective of architecture. The genetic program of growth and development of a young tree will be referred to as «architectural model». The five most common out of the 22 architectural models so far recognized will be presented. Whenever a model has a unique expression that persists during the whole life of a tree, the tree is called «unitary»; these unitary trees are ancient. The concept of «reiteration» is key to

Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests.

Science.gov (United States)

Ferretti, Luca; Ledda, Alice; Wiehe, Thomas; Achaz, Guillaume; Ramos-Onsins, Sebastian E

2017-09-01

We investigate the dependence of the site frequency spectrum on the topological structure of genealogical trees. We show that basic population genetic statistics, for instance, estimators of θ or neutrality tests such as Tajima's D , can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima's D and Fay and Wu's H depend in a direct way on a peculiar measure of tree balance, which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu's H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulas for these extreme values as a function of sample size and number of segregating sites. Copyright © 2017 by the Genetics Society of America.

Tree Inventory and Biometry Measurements, Tapajos National Forest, Para, Brazil, 2010

Data.gov (United States)

National Aeronautics and Space Administration — This dataset provides tree inventory, tree height, diameter at breast height (DBH), and estimated crown measurements from 30 plots located in the Tapajos National...

Growth following pruning of young loblolly pine trees: some early results

Science.gov (United States)

Ralph L. Amateis; Harold E. Burkhart

2006-01-01

In the spring of 2000, a designed experiment was established to study the effects of pruning on juvenile loblolly pine (Pinus taeda L.) tree growth and the subsequent formation of mature wood. Trees were planted at a 3 m x 3 m square spacing in plots of 6 rows with 6 trees per row, with the inner 16 trees constituting the measurement plot. Among the...

Modeling Trees with a Space Colonization Algorithm

OpenAIRE

Morell Higueras, Marc

2014-01-01

[CATALÀ] Aquest TFG tracta la implementació d'un algorisme de generació procedural que construeixi una estructura reminiscent a la d'un arbre de clima temperat, i també la implementació del pas de l'estructura a un model tridimensional, acompanyat de l'eina per a visualitzar el resultat i fer-ne l'exportació [ANGLÈS] This TFG consists of the implementation of a procedural generation algorithm that builds a structure reminiscent of that of a temperate climate tree, and also consists of the ...

Automated Generation of Attack Trees

DEFF Research Database (Denmark)

Vigo, Roberto; Nielson, Flemming; Nielson, Hanne Riis

2014-01-01

Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error-prone and impractica......Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error......-prone and impracticable for large systems. Nonetheless, the automated generation of attack trees has only been explored in connection to computer networks and levering rich models, whose analysis typically leads to an exponential blow-up of the state space. We propose a static analysis approach where attack trees...... are automatically inferred from a process algebraic specification in a syntax-directed fashion, encompassing a great many application domains and avoiding incurring systematically an exponential explosion. Moreover, we show how the standard propositional denotation of an attack tree can be used to phrase...

A review of tree root conflicts with sidewalks, curbs, and roads

Science.gov (United States)

T.B. Randrup; E.G. McPherson; L.R. Costello

2003-01-01

Literature relevant to tree root and urban infrastructure conflicts is reviewed. Although tree roots can conflict with many infrastructure elements, sidewalk and curb conflicts are the focus of this review. Construction protocols, urban soils, root growth, and causal factors (soil conditions, limited planting space, tree size, variation in root architecture, management...

Genetic diversity and domestication origin of tea plant Camellia taliensis (Theaceae) as revealed by microsatellite markers.

Science.gov (United States)

Zhao, Dong-Wei; Yang, Jun-Bo; Yang, Shi-Xiong; Kato, Kenji; Luo, Jian-Ping

2014-01-09

Tea is one of the most popular beverages in the world. Many species in the Thea section of the Camellia genus can be processed for drinking and have been domesticated. However, few investigations have focused on the genetic consequence of domestication and geographic origin of landraces on tea plants using credible wild and planted populations of a single species. Here, C. taliensis provides us with a unique opportunity to explore these issues. Fourteen nuclear microsatellite loci were employed to determine the genetic diversity and domestication origin of C. taliensis, which were represented by 587 individuals from 25 wild, planted and recently domesticated populations. C. taliensis showed a moderate high level of overall genetic diversity. The greater reduction of genetic diversity and stronger genetic drift were detected in the wild group than in the recently domesticated group, indicating the loss of genetic diversity of wild populations due to overexploitation and habitat fragmentation. Instead of the endangered wild trees, recently domesticated individuals were used to compare with the planted trees for detecting the genetic consequence of domestication. A little and non-significant reduction in genetic diversity was found during domestication. The long life cycle, selection for leaf traits and gene flow between populations will delay the emergence of bottleneck in planted trees. Both phylogenetic and assignment analyses suggested that planted trees may have been domesticated from the adjacent central forest of western Yunnan and dispersed artificially to distant places. This study contributes to the knowledge about levels and distribution of genetic diversity of C. taliensis and provides new insights into genetic consequence of domestication and geographic origin of planted trees of this species. As an endemic tea source plant, wild, planted and recently domesticated C. taliensis trees should all be protected for their unique genetic characteristics, which

Tree shrew (Tupaia belangeri as a novel laboratory disease animal model

Directory of Open Access Journals (Sweden)

Ji Xiao

2017-05-01

Full Text Available The tree shrew (Tupaia belangeri is a promising laboratory animal that possesses a closer genetic relationship to primates than to rodents. In addition, advantages such as small size, easy breeding, and rapid reproduction make the tree shrew an ideal subject for the study of human disease. Numerous tree shrew disease models have been generated in biological and medical studies in recent years. Here we summarize current tree shrew disease models, including models of infectious diseases, cancers, depressive disorders, drug addiction, myopia, metabolic diseases, and immune-related diseases. With the success of tree shrew transgenic technology, this species will be increasingly used in biological and medical studies in the future.

Assisted migration of forest populations for adapting trees to climate change

Science.gov (United States)

Cuauhtémoc Sáenz-Romero; Roberto A. Lindig-Cisneros; Dennis G. Joyce; Jean Beaulieu; J. Bradley St. Clair; Barry C. Jaquish

2016-01-01

We present evidence that climatic change is an ongoing process and that forest tree populations are genetically differentiated for quantitative traits because of adaptation to specific habitats. We discuss in detail indications that the shift of suitable climatic habitat for forest tree species and populations, as a result of rapid climatic change, is likely to cause...

Genome sequence and genetic diversity of European ash trees

DEFF Research Database (Denmark)

Sollars, Elizabeth S A; Harper, Andrea L; Kelly, Laura J

2017-01-01

-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re...

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

Science.gov (United States)

Kendall, Michelle; Colijn, Caroline

2016-10-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

Science.gov (United States)

Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

2016-12-01

The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

Growing quality of life: urban trees, birth weight, and crime

Science.gov (United States)

John Kirkland; Geoffrey Donovan

2011-01-01

City dwellers can find many reasons to value neighborhood trees. The urban greenery provides relief from the built environment that many find appealing. In fact, a previous study found that a tree in front of a home increased that home's sales price by more than $7,000. Two new studies explore the measurable effects that urban trees and green spaces have a human...

An understanding of the underlying genetic diversity within and ...

African Journals Online (AJOL)

AMuchugi

2016-08-03

AFLP). Four primer ... outcrossing and pollinated by small bees (e.g. Trigona) and other insects ... for assessing plants' genetic resources by improving our ..... populations of tropical trees and cultivated trees Meru oak (Vitex ...

Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea.

Science.gov (United States)

Miller, Allison; Schaal, Barbara

2005-09-06

Contemporary patterns of genetic variation in crops reflect historical processes associated with domestication, such as the geographic origin(s) of cultivated populations. Although significant progress has been made in identifying several global centers of domestication, few studies have addressed the issue of multiple origins of cultivated plant populations from different geographic regions within a domestication center. This study investigates the domestication history of jocote (Spondias purpurea), a Mesoamerican cultivated fruit tree. Sequences of the chloroplast spacer trnG-trnS were obtained for cultivated and wild S. purpurea trees, two sympatric taxa (Spondias mombin var. mombin and Spondias radlkoferi), and two outgroups (S. mombin var. globosa and Spondias testudinus). A phylogeographic approach was used and statistically significant associations of clades and geographical location were tested with a nested clade analysis. The sequences confirm that wild populations of S. purpurea are the likely progenitors of cultivated jocote trees. This study provides phylogeographic evidence of multiple domestications of this Mesoamerican cultivated fruit tree. Haplotypes detected in S. purpurea trees form two clusters, each of which includes alleles recovered in both cultivated and wild populations from distinct geographic regions. Cultivated S. purpurea populations have fewer unique trnG-trnS alleles than wild populations; however, five haplotypes were absent in the wild. The presence of unique alleles in cultivation may reflect contemporary extinction of the tropical dry forests of Mesoamerica. These data indicate that some agricultural habitats may be functioning as reservoirs of genetic variation in S. purpurea.

CosmoBon for studying wood formation under exotic gravitational environment for future space agriculture

Science.gov (United States)

Tomita-Yokotani, Kaori; Baba, Keiichi; Suzuki, Toshisada; Funada, Ryo; Nakamura, Teruko; Hashimoto, Hirofumi; Yamashita, Masamichi; Cosmobon, Jstwg

We are proposing to raise woody plants in space for several applications and plant science. Japanese flowering cherry tree is one of a candidate for these studies. Mechanism behind sensing gravity and controlling shape of tree has been studied quite extensively. Even molecular mechanism for the response of plant against gravity has been investigated quite intensively for various species, woody plants are left behind. Morphology of woody branch growth is different from that of stem growth in herbs. Morphology in tree is strongly dominated by the secondary xylem formation. Nobody knows the tree shape grown under the space environment. If whole tree could be brought up to space as research materials, it might provide important scientific knowledge. Furthermore, trees produce excess oxygen, wooden materials for living cabin, and provide biomass for cultivating mushroom and insect as for the space agriculture. Excellent tree shapes which would be deeply related to wood formation improve quality of life under stressful environment in outer space. The serious problem would be their size. Bonsai is one of the Japanese traditional arts. We can study secondly xylem formation, wood formation, under exotic gravitational environment using Bonsai. "CosmoBon" is the small tree Bonsai for our space experiment. It has been recognized that the reaction wood in CosmoBon is formed similar to natural trees. Our goal is to examine feasibility to grow various species of trees in space as bioresource for space agriculture.

Potential transgenic routes to increase tree biomass.

Science.gov (United States)

Dubouzet, Joseph G; Strabala, Timothy J; Wagner, Armin

2013-11-01

Biomass is a prime target for genetic engineering in forestry because increased biomass yield will benefit most downstream applications such as timber, fiber, pulp, paper, and bioenergy production. Transgenesis can increase biomass by improving resource acquisition and product utilization and by enhancing competitive ability for solar energy, water, and mineral nutrients. Transgenes that affect juvenility, winter dormancy, and flowering have been shown to influence biomass as well. Transgenic approaches have increased yield potential by mitigating the adverse effects of prevailing stress factors in the environment. Simultaneous introduction of multiple genes for resistance to various stress factors into trees may help forest trees cope with multiple or changing environments. We propose multi-trait engineering for tree crops, simultaneously deploying multiple independent genes to address a set of genetically uncorrelated traits that are important for crop improvement. This strategy increases the probability of unpredictable (synergistic or detrimental) interactions that may substantially affect the overall phenotype and its long-term performance. The very limited ability to predict the physiological processes that may be impacted by such a strategy requires vigilance and care during implementation. Hence, we recommend close monitoring of the resultant transgenic genotypes in multi-year, multi-location field trials. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Mating System and Effective Population Size of the Overexploited Neotropical Tree (Myroxylon peruiferum L.f.) and Their Impact on Seedling Production.

Science.gov (United States)

Silvestre, Ellida de Aguiar; Schwarcz, Kaiser Dias; Grando, Carolina; de Campos, Jaqueline Bueno; Sujii, Patricia Sanae; Tambarussi, Evandro Vagner; Macrini, Camila Menezes Trindade; Pinheiro, José Baldin; Brancalion, Pedro Henrique Santin; Zucchi, Maria Imaculada

2018-03-16

The reproductive system of a tree species has substantial impact on genetic diversity and structure within and among natural populations. Such information, should be considered when planning tree planting for forest restoration. Here, we describe the mating system and genetic diversity of an overexploited Neotropical tree, Myroxylon peruiferum L.f. (Fabaceae) sampled from a forest remnant (10 seed trees and 200 seeds) and assess whether the effective population size of nursery-grown seedlings (148 seedlings) is sufficient to prevent inbreeding depression in reintroduced populations. Genetic analyses were performed based on 8 microsatellite loci. M. peruiferum presented a mixed mating system with evidence of biparental inbreeding (t^m-t^s = 0.118). We found low levels of genetic diversity for M. peruiferum species (allelic richness: 1.40 to 4.82; expected heterozygosity: 0.29 to 0.52). Based on Ne(v) within progeny, we suggest a sample size of 47 seed trees to achieve an effective population size of 100. The effective population sizes for the nursery-grown seedlings were much smaller Ne = 27.54-34.86) than that recommended for short term Ne ≥ 100) population conservation. Therefore, to obtain a reasonable genetic representation of native tree species and prevent problems associated with inbreeding depression, seedling production for restoration purposes may require a much larger sampling effort than is currently used, a problem that is further complicated by species with a mixed mating system. This study emphasizes the need to integrate species reproductive biology into seedling production programs and connect conservation genetics with ecological restoration.

Phylogeography and genetic structure of a Tertiary relict tree species, Tapiscia sinensis (Tapisciaceae): implications for conservation.

Science.gov (United States)

Zhang, Jinju; Li, Zuozhou; Fritsch, Peter W; Tian, Hua; Yang, Aihong; Yao, Xiaohong

2015-10-01

The phylogeography of plant species in sub-tropical China remains largely unclear. This study used Tapiscia sinensis, an endemic and endangered tree species widely but disjunctly distributed in sub-tropical China, as a model to reveal the patterns of genetic diversity and phylogeographical history of Tertiary relict plant species in this region. The implications of the results are discussed in relation to its conservation management. Samples were taken from 24 populations covering the natural geographical distribution of T. sinensis. Genetic structure was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). Phylogenetic relationships among haplotypes were constructed with maximum parsimony and haplotype network methods. Historical population expansion events were tested with pairwise mismatch distribution analysis and neutrality tests. Species potential range was deduced by ecological niche modelling (ENM). A low level of genetic diversity was detected at the population level. A high level of genetic differentiation and a significant phylogeographical structure were revealed. The mean divergence time of the haplotypes was approx. 1·33 million years ago. Recent range expansion in this species is suggested by a star-like haplotype network and by the results from the mismatch distribution analysis and neutrality tests. Climatic oscillations during the Pleistocene have had pronounced effects on the extant distribution of Tapiscia relative to the Last Glacial Maximum (LGM). Spatial patterns of molecular variation and ENM suggest that T. sinensis may have retreated in south-western and central China and colonized eastern China prior to the LGM. Multiple montane refugia for T. sinense existing during the LGM are inferred in central and western China. The populations adjacent to or within these refugia of T. sinense should be given high priority in the development of conservation policies and management strategies for

Genetic Determinism of Sensitivity to Corynespora cassiicola Exudates in Rubber Tree (Hevea brasiliensis).

Science.gov (United States)

Tran, Dinh Minh; Clément-Demange, André; Déon, Marine; Garcia, Dominique; Le Guen, Vincent; Clément-Vidal, Anne; Soumahoro, Mouman; Masson, Aurélien; Label, Philippe; Le, Mau Tuy; Pujade-Renaud, Valérie

2016-01-01

An indirect phenotyping method was developed in order to estimate the susceptibility of rubber tree clonal varieties to Corynespora Leaf Fall (CLF) disease caused by the ascomycete Corynespora cassiicola. This method consists in quantifying the impact of fungal exudates on detached leaves by measuring the induced electrolyte leakage (EL%). The tested exudates were either crude culture filtrates from diverse C. cassiicola isolates or the purified cassiicolin (Cas1), a small secreted effector protein produced by the aggressive isolate CCP. The test was found to be quantitative, with the EL% response proportional to toxin concentration. For eight clones tested with two aggressive isolates, the EL% response to the filtrates positively correlated to the response induced by conidial inoculation. The toxicity test applied to 18 clones using 13 toxinic treatments evidenced an important variability among clones and treatments, with a significant additional clone x treatment interaction effect. A genetic linkage map was built using 306 microsatellite markers, from the F1 population of the PB260 x RRIM600 family. Phenotyping of the population for sensitivity to the purified Cas1 effector and to culture filtrates from seven C. cassiicola isolates revealed a polygenic determinism, with six QTL detected on five chromosomes and percentages of explained phenotypic variance varying from 11 to 17%. Two common QTL were identified for the CCP filtrate and the purified cassiicolin, suggesting that Cas1 may be the main effector of CCP filtrate toxicity. The CCP filtrate clearly contrasted with all other filtrates. The toxicity test based on Electrolyte Leakage Measurement offers the opportunity to assess the sensitivity of rubber genotypes to C. cassiicola exudates or purified effectors for genetic investigations and early selection, without risk of spreading the fungus in plantations. However, the power of this test for predicting field susceptibility of rubber clones to CLF will have

Non-perturbative renormalization in coordinate space for N{sub f}=2 maximally twisted mass fermions with tree-level Symanzik improved gauge action

Energy Technology Data Exchange (ETDEWEB)

Cichy, Krzysztof [DESY, Zeuthen (Germany). NIC; Adam Mickiewicz Univ., Poznan (Poland). Faculty of Physics; Jansen, Karl [DESY, Zeuthen (Germany). NIC; Korcyl, Piotr [DESY, Zeuthen (Germany). NIC; Jagiellonian Univ., Krakow (Poland). M. Smoluchowski Inst. of Physics

2012-07-15

We present results of a lattice QCD application of a coordinate space renormalization scheme for the extraction of renormalization constants for flavour non-singlet bilinear quark operators. The method consists in the analysis of the small-distance behaviour of correlation functions in Euclidean space and has several theoretical and practical advantages, in particular: it is gauge invariant, easy to implement and has relatively low computational cost. The values of renormalization constants in the X-space scheme can be converted to the MS scheme via 4-loop continuum perturbative formulae. Our results for N{sub f}=2 maximally twisted mass fermions with tree-level Symanzik improved gauge action are compared to the ones from the RI-MOM scheme and show full agreement with this method. (orig.)

Variability of the tree-rings structure of Gmelin’s larch at northern tree line (peninsula of Taymyr

Directory of Open Access Journals (Sweden)

V. V. Fakhrutdinova

2017-04-01

Full Text Available The study of tree-ring cell structure changes as the result of tree adaptation to varying environmental conditions becomes increasingly important to predict future vegetation shifts under projected climate changes. The estimate of intrapopulation annual variability of wood anatomy characteristics is particularly informative. It helps to divide the contribution of different ecological factors to total features dispersion. In this work, a comparative analysis of individual and climatic variability of tree ring structure characteristics of Gmelin’s larch Larix gmelinii (Rupr. growth within northernmost forest was carried out. The trees from forest-tundra boundary has greater radial growth intensity, forms the bigger conductive zone in rings with wider mean lumen area in comparison with trees from closed forest. This result can be explained by adaptive features and height ecological xylem plasticity of larch. The tree rings structure of larch from boundary with tundra is determined by largely current weather conditions. Is because these ones evince high adaptive plasticity on the level of xylem structure. The xylem reflects joint changes of climate factors and local ecological conditions. The trees from closed forest are characterized by larger individual variability. The local conditions in oldest forest (for example, bad hydrothermal soil conditions inhibit the radial growth and sensitivity to environmental factors. In this case, the trees on individual level are tended to save the normal functioning of water-transport system. The significant differences in ratio individual to climate variability of tree ring structure characteristics can be caused by the different in the level of ecological habitat heterogeneity or the different in the level genetic within-population heterogeneity.

Longest common extensions in trees

DEFF Research Database (Denmark)

Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

2016-01-01

to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

Longest Common Extensions in Trees

DEFF Research Database (Denmark)

Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

2015-01-01

to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites

Czech Academy of Sciences Publication Activity Database

Hampl, V.; Pavlíček, Adam; Flegr, J.

2001-01-01

Roč. 51, - (2001), s. 731-735 ISSN 1466-5026 R&D Projects: GA MŠk VS96142 Grant - others:GA UK(XC) 107/1998 Keywords : FreeTree software * fingerprinting * Trichomonas Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.004, year: 2001

Stable expression and phenotypic impact of attacin E transgene in orchard grown apple trees over a 12 year period.

Science.gov (United States)

Borejsza-Wysocka, Ewa; Norelli, John L; Aldwinckle, Herb S; Malnoy, Mickael

2010-06-03

Transgenic trees currently are being produced by Agrobacterium-mediated transformation and biolistics. The future use of transformed trees on a commercial basis depends upon thorough evaluation of the potential environmental and public health risk of the modified plants, transgene stability over a prolonged period of time and the effect of the gene on tree and fruit characteristics. We studied the stability of expression and the effect on resistance to the fire blight disease of the lytic protein gene, attacin E, in the apple cultivar 'Galaxy' grown in the field for 12 years. Using Southern and western blot analysis, we compared transgene copy number and observed stability of expression of this gene in the leaves and fruit in several transformed lines during a 12 year period. No silenced transgenic plant was detected. Also the expression of this gene resulted in an increase in resistance to fire blight throughout 12 years of orchard trial and did not affect fruit shape, size, acidity, firmness, weight or sugar level, tree morphology, leaf shape or flower morphology or color compared to the control. Overall, these results suggest that transgene expression in perennial species, such as fruit trees, remains stable in time and space, over extended periods and in different organs. This report shows that it is possible to improve a desirable trait in apple, such as the resistance to a pathogen, through genetic engineering, without adverse alteration of fruit characteristics and tree shape.

Genetic variation and geographical differentiation revealed using ...

Indian Academy of Sciences (India)

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

Nonlinearities, scale-dependence, and individualism of boreal forest trees to climate forcing

Science.gov (United States)

Wolken, J. M.; Mann, D. H.; Grant, T. A., III; Lloyd, A. H.; Hollingsworth, T. N.

2013-12-01

Our understanding of the climate-growth relationships of trees are complicated by the nonlinearity and variability of these responses through space and time. Furthermore, trees growing at the same site may exhibit opposing growth responses to climate, a phenomenon termed growth divergence. To date the majority of dendrochronological studies in Interior Alaska have involved white spruce growing at treeline, even though black spruce is the most abundant tree species. Although changing climate-growth relationships have been observed in black spruce, there is little known about the multivariate responses of individual trees to temperature and precipitation and whether or not black spruce exhibits growth divergences similar to those documented for white spruce. To evaluate the occurrence of growth divergences in black spruce, we collected cores from trees growing on a steep, north-facing toposequence having a gradient in environmental parameters. Our overall goal was to assess how the climate-growth relationships of black spruce change over space and time. Specifically, we evaluated how topography influences the climate-growth relationships of black spruce and if the growth responses to climate are homogeneous. At the site-level most trees responded negatively to temperature and positively to precipitation, while at the tree-level black spruce exhibited heterogenous growth responses to climate that varied in both space (i.e., between sites) and time (i.e., seasonally and annually). There was a dominant response-type at each site, but there was also considerable variability in the proportion of trees exhibiting each response-type combination. Even in a climatically extreme setting like Alaska's boreal forest, tree responses to climate variability are spatially and temporally complex, as well as highly nonlinear.

Automatic object recognition and change detection of urban trees

NARCIS (Netherlands)

Van der Sande, C.J.

2010-01-01

Monitoring of tree objects is relevant in many current policy issues and relate to the quality of the public space, municipal urban green management, management fees for green areas or Kyoto protocol reporting and all have one thing in common: the need for an up to date tree database. This study,

Somatic embryogenesis and cryostorage for conservation and restoration of threatened forest trees

Science.gov (United States)

S.A. Merkle; A.R. Tull; H.J. Gladfelter; P.M. Montello; J.E. Mitchell; C. Ahn; R.D. McNeill

2017-01-01

Threats to North American forest trees from exotic pests and pathogens or habitat loss, make it imperative that every available tool be employed for conservation and restoration of these at risk species. One such tool, in vitro propagation, could greatly enhance conservation of forest tree genetic material and selection and breeding of resistant or...

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill. (Sapindales: Simaroubaceae, an Important Pantropical Tree

Directory of Open Access Journals (Sweden)

Josphat K. Saina

2018-03-01

Full Text Available Ailanthus altissima (Mill. Swingle (Simaroubaceae is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA genes respectively and also 4 ribosomal RNA genes (rRNA with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.

Using tree diversity to compare phylogenetic heuristics.

Science.gov (United States)

Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

2009-04-29

Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

On the Shapley Value of Unrooted Phylogenetic Trees.

Science.gov (United States)

Wicke, Kristina; Fischer, Mareike

2018-01-17

The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split counts of a phylogenetic tree and the Shapley transformation matrix that allows for the calculation of the Shapley value from the edge lengths of a tree. We show that non-isomorphic trees may have permutation-equivalent Shapley transformation matrices and permutation-equivalent null spaces. This implies that estimating the split counts associated with a tree or the Shapley values of its leaves does not suffice to reconstruct the correct tree topology. We then turn to the use of the Shapley value as a prioritization criterion in biodiversity conservation and compare it to a greedy solution concept. Here, we show that for certain phylogenetic trees, the Shapley value may fail as a prioritization criterion, meaning that the diversity spanned by the top k species (ranked by their Shapley values) cannot approximate the total diversity of all n species.

Morphological and physiological characteristics of columnar apple trees

OpenAIRE

Gelvonauskis, Bronislovas; Brazaitytė, Aušra; Sasnauskas, Audrius; Duchovskis, Pavelas; Gelvonauskienė, Dalia

2006-01-01

There were investigated two columnar apple cultivars ‘Arbat’ and No. 24217 and apple cultivar ‘Aldas’ in an orchard at the Lithuanian Institute of Horticulture. The two latter cultivars were released at the Lithuanian Institute of Horticulture, ‘Arbat’ – in Russia. Cultivars and selections were budded on rootstocks P 60, M.26 and MM.106. In orchard apple trees were spaced at 1.0 x 3.5 m. Tree height, stem diameter, total length of one-year-old shoot, leaf area on a tree was measured and numbe...

A decision tree for the genetic diagnosis of deficiency of adenosine deaminase 2 (DADA2): a French reference centres experience.

Science.gov (United States)

Rama, Mélanie; Duflos, Claire; Melki, Isabelle; Bessis, Didier; Bonhomme, Axelle; Martin, Hélène; Doummar, Diane; Valence, Stéphanie; Rodriguez, Diana; Carme, Emilie; Genevieve, David; Heimdal, Ketil; Insalaco, Antonella; Franck, Nathalie; Queyrel-Moranne, Viviane; Tieulie, Nathalie; London, Jonathan; Uettwiller, Florence; Georgin-Lavialle, Sophie; Belot, Alexandre; Koné-Paut, Isabelle; Hentgen, Véronique; Boursier, Guilaine; Touitou, Isabelle; Sarrabay, Guillaume

2018-04-23

Deficiency of adenosine deaminase 2 (DADA2) is a recently described autoinflammatory disorder. Genetic analysis is required to confirm the diagnosis. We aimed to describe the identifying symptoms and genotypes of patients referred to our reference centres and to improve the indications for genetic testing. DNA from 66 patients with clinically suspected DADA2 were sequenced by Sanger or next-generation sequencing. Detailed epidemiological, clinical and biological features were collected by use of a questionnaire and were compared between patients with and without genetic confirmation of DADA2. We identified 13 patients (19.6%) carrying recessively inherited mutations in ADA2 that were predicted to be deleterious. Eight patients were compound heterozygous for mutations. Seven mutations were novel (4 missense variants, 2 predicted to affect mRNA splicing and 1 frameshift). The mean age of the 13 patients with genetic confirmation was 12.7 years at disease onset and 20.8 years at diagnosis. Phenotypic manifestations included fever (85%), vasculitis (85%) and neurological disorders (54%). Features best associated with a confirmatory genotype included fever with neurologic or cutaneous attacks (odds ratio [OR] 10.71, p = 0.003 and OR 10.9, p < 0.001), fever alone (OR 8.1, p = 0.01), and elevated C-reactive protein (CRP) level with neurologic involvement (OR 6.63, p = 0.017). Our proposed decision tree may help improve obtaining genetic confirmation of DADA2 in the context of autoinflammatory symptoms. Prerequisites for quick and low-cost Sanger analysis include one typical cutaneous or neurological sign, one marker of inflammation (fever or elevated CRP level), and recurrent or chronic attacks in adults.

The role of hybridization in facilitating tree invasion

Science.gov (United States)

Hybridization events can generate additional genetic diversity on which natural selection can act and at times enhance invasiveness of the species. Invasive tree species are a growing ecological concern worldwide, and some of these invasions involve hybridization events pre- or post-introduction. Th...

Performance of engineered soil and trees in a parking lot bioswale

Science.gov (United States)

Qingfu Xiao; Gregory McPherson

2011-01-01

A bioswale integrating an engineered soil and trees was installed in a parking lot to evaluate its ability to reduce storm runoff, pollutant loading, and support tree growth. The adjacent control and treatment sites each received runoff from eight parking spaces and were identical except that there was no bioswale for the control site. A tree was planted at both sites...

The contribution of woody plant materials on the several conditions in a space environment

Science.gov (United States)

Tomita-Yokotani, Kaori; Baba, Keiichi; Suzuki, Toshisada; Kimura, Shunta; Sato, Seigo; Katoh, Hiroshi; Abe, Yusuke; Katayama, Takeshi

Woody plant materials have several utilization elements in our habitation environment on earth. The studies of woody plants under a space-environment in the vegetable kingdom have a high contribution to the study of various and exotic environmental responses, too. Woody plants can produce an excess oxygen, woody materials for the living cabin, and provide a biomass by cultivating crops and other species of creatures. Tree material would become to be a tool in closed bio-ecosystems such as an environment in a space. We named the trees used as material for the experiment related to space environments “CosmoBon”, small tree bonsai. Japanese cherry tree, “Sakura”, is famous and lovely tree in Japan. One species of “Sakura”, “Mamezakura, Prunus incisa”, is not only lovely tree species, but also suitable tree for the model tree of our purpose. The species of Prunus incisa is originally grown in volcano environment. That species of Sakura is originally grown on Mt. Fuji aria, oligotrophic place. We will try to build the best utilization usage of woody plant under the space environment by “Mamezakura” as a model tree. Here, we will show the importance of uniformity of materials when we will use the tree materials in a space environment. We will also discuss that tree has a high possibility of utilization under the space environments by using our several results related to this research.

Impact of Whole Body Irradiation on the Intestinal Microbiome- Considerations for Space Flight

Science.gov (United States)

Karouia, Fathi; Santos, Orlando; Valdivia-Silva, Julio E.; Jones, Jeffrey; Greenberger, Joel S.; Epperly, Michael W.

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. Spaceflight-related changes have been reported in the musculo-skeletal, cardiovascular, neurovestibular, endocrine, and immune systems to just name a few. However, to date, radiation exposure is one of the main limiting factors for long duration space exploration missions and especially a mission to Mars. Over the past few years through advances in technology, the characterization of the microbiome has revealed a large and complex community of microorganisms living in symbiosis with the human host. However, heterogeneity of the intestinal microbial spectrum in humans has been associated with a variety of diseases and susceptibility to infectious and toxic agents. Limited information is known about the influence of space environment in general and radiation in particular on the microbiome. Furthermore, multiple spaceflight and simulated microgravity experiments have shown changes in phenotypic microbial characteristics such as microbial growth, morphology, metabolism, genetic transfer, antibiotic and stress susceptibility, and an increase in virulence factors. We now report a study of the bacterial composition of the intestine in C57BL/6NTAC mice and the types of microbes entering the body at two time points after the LD 50/30 dose of total body irradiation using microarray-based assay, G3 PhyloChip 16S rRNA, and bioinformatics methods. Bacteria and archaea taxon richness was determined at the genus level and ranged from 2 to 107 and 0 to 3 respectively. As expected, pre-exposure blood samples exhibited less bacterial and archaeal genus richness compared to all other samples. However, the study shows a significant shift in the mouse gut microbial speciation in several bacterial families, with increases in the Turicibacteraceae and Enterobacteriaceae and decreases in the Lachnospiraceae and Ruminococcaceae families. The findings most relevant to occupational

MARRT: Medial Axis biased rapidly-exploring random trees

KAUST Repository

Denny, Jory

2014-05-01

© 2014 IEEE. Motion planning is a difficult and widely studied problem in robotics. Current research aims not only to find feasible paths, but to ensure paths have certain properties, e.g., shortest or safest paths. This is difficult for current state-of-the-art sampling-based techniques as they typically focus on simply finding any path. Despite this difficulty, sampling-based techniques have shown great success in planning for a wide range of applications. Among such planners, Rapidly-Exploring Random Trees (RRTs) search the planning space by biasing exploration toward unexplored regions. This paper introduces a novel RRT variant, Medial Axis RRT (MARRT), which biases tree exploration to the medial axis of free space by pushing all configurations from expansion steps towards the medial axis. We prove that this biasing increases the tree\\'s clearance from obstacles. Improving obstacle clearance is useful where path safety is important, e.g., path planning for robots performing tasks in close proximity to the elderly. Finally, we experimentally analyze MARRT, emphasizing its ability to effectively map difficult passages while increasing obstacle clearance, and compare it to contemporary RRT techniques.

Genetic structure of populations and differentiation in forest trees

Science.gov (United States)

Raymond P. Guries; F. Thomas Ledig

1981-01-01

Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

Design of data structures for mergeable trees

DEFF Research Database (Denmark)

Georgiadis, Loukas; Tarjan, Robert Endre; Werneck, Renato Fonseca F.

2006-01-01

merge operation can change many arcs. In spite of this, we develop a data structure that supports merges and all other standard tree operations in O(log2 n) amortized time on an n-node forest. For the special case that occurs in the motivating application, in which arbitrary arc deletions...... are not allowed, we give a data structure with an O(log n) amortized time bound per operation, which is asymptotically optimal. The analysis of both algorithms is not straightforward and requires ideas not previously used in the study of dynamic trees. We explore the design space of algorithms for the problem......Motivated by an application in computational topology, we consider a novel variant of the problem of efficiently maintaining dynamic rooted trees. This variant allows an operation that merges two tree paths. In contrast to the standard problem, in which only one tree arc at a time changes, a single...

Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

Science.gov (United States)

van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

2012-01-01

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

Genetic Regulation of Vascular Development: Building the Zebrafish Vascular Tree

NARCIS (Netherlands)

R.L.J.M. Herpers (Robert)

2010-01-01

textabstractThe extensive networks of blood and lymphatic vessels within the vertebrate body are essential for the transport and delivery of fluids, gases, macromolecules and cells, and play important roles in facilitating immune responses. The development of the vascular tree requires a highly

Genetic and environmental control of seasonal carbohydrate dynamics in trees of diverse Pinus sylvestris populations.

Science.gov (United States)

Oleksyn, J.; Zytkowiak, R.; Karolewski, P.; Reich, P. B.; Tjoelker, M. G.

2000-06-01

We explored environmental and genetic factors affecting seasonal dynamics of starch and soluble nonstructural carbohydrates in needle and twig cohorts and roots of Scots pine (Pinus sylvestris L.) trees of six populations originating between 49 degrees and 60 degrees N, and grown under common garden conditions in western Poland. Trees of each population were sampled once or twice per month over a 3-year period from age 15 to 17 years. Based on similarity in starch concentration patterns in needles, two distinct groups of populations were identified; one comprised northern populations from Sweden and Russia (59-60 degrees N), and another comprised central European populations from Latvia, Poland, Germany and France (49-56 degrees N). Needle starch concentrations of northern populations started to decline in late spring and reached minimum values earlier than those of central populations. For all populations, starch accumulation in spring started when minimum air temperature permanently exceeded 0 degrees C. Starch accumulation peaked before bud break and was highest in 1-year-old needles, averaging 9-13% of dry mass. Soluble carbohydrate concentrations were lowest in spring and summer and highest in autumn and winter. There were no differences among populations in seasonal pattern of soluble carbohydrate concentrations. Averaged across all populations, needle soluble carbohydrate concentrations increased from about 4% of needle dry mass in developing current-year needles, to about 9% in 1- and 2-year-old needles. Root carbohydrate concentration exhibited a bimodal pattern with peaks in spring and autumn. Northern populations had higher concentrations of fine-root starch in spring and autumn than central populations. Late-summer carbohydrate accumulation in roots started only after depletion of starch in needles and woody shoots. We conclude that Scots pine carbohydrate dynamics depend partially on inherited properties that are probably related to phenology of root

DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae).

Science.gov (United States)

Dang, Ning-Xin; Sun, Feng-Hui; Lv, Yun-Yun; Zhao, Bo-Han; Wang, Ji-Chao; Murphy, Robert W; Wang, Wen-Zhi; Li, Jia-Tang

2016-07-01

The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.

Somatic Embryogenesis Induction and Plant Regeneration in Strawberry Tree (Arbutus unedo L.).

Science.gov (United States)

Martins, João F; Correia, Sandra I; Canhoto, Jorge M

2016-01-01

Somatic embryogenesis is a powerful tool both for cloning and studies of genetic transformation and embryo development. Most protocols for somatic embryogenesis induction start from zygotic embryos or embryonic-derived tissues which do not allow the propagation of elite trees. In the present study, a reliable protocol for somatic embryogenesis induction from adult trees of strawberry tree is described. Leaves from in vitro proliferating shoots were used to induce somatic embryo formation on a medium containing an auxin and a cytokinin. Somatic embryos germinated in a plant growth regulator-free medium.

A note on the relevance of human population genetic variation and molecular epidemiology to assessing radiation health risk for space travellers

International Nuclear Information System (INIS)

Brackley, M.E.; Curry, J.; Glickman, B.W.

1999-01-01

We discuss the relevance to space medicine of studies concerning human genetic variation and consequent variable disease susceptibility or sensitivity between individuals. The size of astronaut and cosmonaut populations is both presently and cumulatively small, and despite the launch of the International Space Station, unlikely to increase by orders of magnitude within the foreseeable future. In addition, astronauts-cosmonauts constitute unrepresentative samples of their national populations. While the context of exposure for the astronaut-cosmonaut group is one unlikely to be replicated elsewhere than in space, aspects of specific exposures may be simulated by events such as occupational radiation exposure or radiation therapy. Hence, population-based studies of genetic susceptibility or sensitivity to disease, especially where it is precipitated by events that may simulate consequences of the space environment, likely will prove of value in assessing long-term health risks

Strategic conservation of orchard germplasm based on indigenous knowledge and genetic diversity: a case study of sour orange populations in China.

Science.gov (United States)

Ming, Feng; Liu, Qi-Kun; Shi, Jin-Lei; Wang, Wei; Lu, Bao-Rong

2009-01-01

To effectively conserve sour orange (Citrus aurantium L.) germplasm on two islands at the estuary of the Yangtze River in China, we estimated genetic variation and relationships of the known parental trees and their proposed descendents (young trees) using the fingerprints of random amplified polymorphic DNA (RAPD). Results based on RAPD analyses showed considerable genetic diversity in the parental populations (H(e)=0.202). The overall populations including the parental and young trees showed slightly higher genetic diversity (H(e)=0.298) than the parents, with about 10% variation between populations. An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands, although the young trees showed a clear association with parental trees. This indicates a significant contribution of parental trees in establishing the sour orange populations on the two islands. According to farmers' knowledge, conservation of only one or two parental trees would be sufficient because they believed that the whole populations were generated from a single mother tree. However, this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands.

Using decision tree induction systems for modeling space-time behavior

NARCIS (Netherlands)

Arentze, T.A.; Hofman, F.; Mourik, van H.; Timmermans, H.J.P.; Wets, G.

2000-01-01

Discrete choice models are commonly used to predict individuals' activity and travel choices either separately or simultaneously in activity scheduling models. This paper investigates the possibilities of decision tree induction systems as an alternative approach. The ability of decision frees to

Numerical evaluation of Feynman loop integrals by reduction to tree graphs

International Nuclear Information System (INIS)

Kleinschmidt, T.

2007-12-01

We present a method for the numerical evaluation of loop integrals, based on the Feynman Tree Theorem. This states that loop graphs can be expressed as a sum of tree graphs with additional external on-shell particles. The original loop integral is replaced by a phase space integration over the additional particles. In cross section calculations and for event generation, this phase space can be sampled simultaneously with the phase space of the original external particles. Since very sophisticated matrix element generators for tree graph amplitudes exist and phase space integrations are generically well understood, this method is suited for a future implementation in a fully automated Monte Carlo event generator. A scheme for renormalization and regularization is presented. We show the construction of subtraction graphs which cancel ultraviolet divergences and present a method to cancel internal on-shell singularities. Real emission graphs can be naturally included in the phase space integral of the additional on-shell particles to cancel infrared divergences. As a proof of concept, we apply this method to NLO Bhabha scattering in QED. Cross sections are calculated and are in agreement with results from conventional methods. We also construct a Monte Carlo event generator and present results. (orig.)

Numerical evaluation of Feynman loop integrals by reduction to tree graphs

Energy Technology Data Exchange (ETDEWEB)

Kleinschmidt, T.

2007-12-15

We present a method for the numerical evaluation of loop integrals, based on the Feynman Tree Theorem. This states that loop graphs can be expressed as a sum of tree graphs with additional external on-shell particles. The original loop integral is replaced by a phase space integration over the additional particles. In cross section calculations and for event generation, this phase space can be sampled simultaneously with the phase space of the original external particles. Since very sophisticated matrix element generators for tree graph amplitudes exist and phase space integrations are generically well understood, this method is suited for a future implementation in a fully automated Monte Carlo event generator. A scheme for renormalization and regularization is presented. We show the construction of subtraction graphs which cancel ultraviolet divergences and present a method to cancel internal on-shell singularities. Real emission graphs can be naturally included in the phase space integral of the additional on-shell particles to cancel infrared divergences. As a proof of concept, we apply this method to NLO Bhabha scattering in QED. Cross sections are calculated and are in agreement with results from conventional methods. We also construct a Monte Carlo event generator and present results. (orig.)

Edge effects enhance selfing and seed harvesting efforts in the insect-pollinated Neotropical tree Copaifera langsdorffii (Fabaceae).

Science.gov (United States)

Tarazi, R; Sebbenn, A M; Kageyama, P Y; Vencovsky, R

2013-06-01

Edge effects may affect the mating system of tropical tree species and reduce the genetic diversity and variance effective size of collected seeds at the boundaries of forest fragments because of a reduction in the density of reproductive trees, neighbour size and changes in the behaviour of pollinators. Here, edge effects on the genetic diversity, mating system and pollen pool of the insect-pollinated Neotropical tree Copaifera langsdorffii were investigated using eight microsatellite loci. Open-pollinated seeds were collected from 17 seed trees within continuous savannah woodland (SW) and were compared with seeds from 11 seed trees at the edge of the savannah remnant. Seeds collected from the SW had significantly higher heterozygosity levels (Ho=0.780; He=0.831) than seeds from the edge (Ho=0.702; He=0.800). The multilocus outcrossing rate was significantly higher in the SW (tm=0.859) than in the edge (tm=0.759). Pollen pool differentiation was significant, however, it did not differ between the SW (=0.105) and the edge (=0.135). The variance effective size within the progenies was significantly higher in the SW (Ne=2.65) than at the edge (Ne=2.30). The number of seed trees to retain the reference variance effective size of 500 was 189 at the SW and 217 at the edge. Therefore, it is preferable that seed harvesting for conservation and environmental restoration strategies be conducted in the SW, where genetic diversity and variance effective size within progenies are higher.

Random trees between two walls: exact partition function

International Nuclear Information System (INIS)

Bouttier, J; Di Francesco, P; Guitter, E

2003-01-01

We derive the exact partition function for a discrete model of random trees embedded in a one-dimensional space. These trees have vertices labelled by integers representing their position in the target space, with the solid-on-solid constraint that adjacent vertices have labels differing by ±1. A non-trivial partition function is obtained whenever the target space is bounded by walls. We concentrate on the two cases where the target space is (i) the half-line bounded by a wall at the origin or (ii) a segment bounded by two walls at a finite distance. The general solution has a soliton-like structure involving elliptic functions. We derive the corresponding continuum scaling limit which takes the remarkable form of the Weierstrass p function with constrained periods. These results are used to analyse the probability for an evolving population spreading in one dimension to attain the boundary of a given domain with the geometry of the target (i) or (ii). They also translate, via suitable bijections, into generating functions for bounded planar graphs

Linear genetic programming

CERN Document Server

Brameier, Markus

2007-01-01

Presents a variant of Genetic Programming that evolves imperative computer programs as linear sequences of instructions, in contrast to the more traditional functional expressions or syntax trees. This book serves as a reference for researchers, but also contains sufficient introduction for students and those who are new to the field

Spatial and population genetic structure of microsatellites in white pine

Science.gov (United States)

Paula E. Marquardt; Bryan K. Epperson

2004-01-01

We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

Categorizing ideas about trees: a tree of trees.

Science.gov (United States)

Fisler, Marie; Lecointre, Guillaume

2013-01-01

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a "tree of trees." Then, we categorize schools of tree-representations. Classical schools like "cladists" and "pheneticists" are recovered but others are not: "gradists" are separated into two blocks, one of them being called here "grade theoreticians." We propose new interesting categories like the "buffonian school," the "metaphoricians," and those using "strictly genealogical classifications." We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.

Search for major genes with progeny test data to accelerate the development of genetically superior loblolly pine

Energy Technology Data Exchange (ETDEWEB)

NCSU

2003-12-30

This research project is to develop a novel approach that fully utilized the current breeding materials and genetic test information available from the NCSU-Industry Cooperative Tree Improvement Program to identify major genes that are segregating for growth and disease resistance in loblolly pine. If major genes can be identified in the existing breeding population, they can be utilized directly in the conventional loblolly pine breeding program. With the putative genotypes of parents identified, tree breeders can make effective decisions on management of breeding populations and operational deployment of genetically superior trees. Forest productivity will be significantly enhanced if genetically superior genotypes with major genes for economically important traits could be deployed in an operational plantation program. The overall objective of the project is to develop genetic model and analytical methods for major gene detection with progeny test data and accelerate the development of genetically superior loblolly pine. Specifically, there are three main tasks: (1) Develop genetic models for major gene detection and implement statistical methods and develop computer software for screening progeny test data; (2) Confirm major gene segregation with molecular markers; and (3) Develop strategies for using major genes for tree breeding.

Tracking a genetic signal of extinction-recolonization events in a neotropical tree species: Vouacapoua americana Aublet in French Guiana.

Science.gov (United States)

Dutech, Cyril; Maggia, Laurent; Tardy, Christophe; Joly, Hélène I; Jarne, Philippe

2003-12-01

Drier periods from the late Pleistocene and early Holocene have been hypothesized to have caused the disappearance of various rainforest species over large geographical areas in South America and restricted the extant populations to mesic sites. Subsequent improvement in climatic conditions has been associated with recolonization. Changes in population size associated with these extinction-recolonization events should have affected genetic diversity within species. However, these historical hypotheses and their genetic consequences have rarely been tested in South America. Here, we examine the diversity of the chloroplast and nuclear genomes in a Neotropical rainforest tree species, Vouacapoua americana (Leguminosae, Caesalpinioideae) in French Guiana. The chloroplast diversity was analyzed using a polymerase chain reaction-restriction fragment length polymorphism method (six pairs of primers) in 29 populations distributed over most of French Guiana, and a subset of 17 populations was also analyzed at nine polymorphic microsatellite loci. To determine whether this species has experienced extinction-recolonization, we sampled populations in areas supposedly not or only slightly affected by climatic changes, where the populations would not have experienced frequent extinction, and in areas that appear to have been recently recolonized. In the putatively recolonized areas, we found patches of several thousands of hectares homogeneous for chloroplast variation that can be interpreted as the effect of recolonization processes from several geographical origins. In addition, we observed that, for both chloroplast and nuclear genomes, the populations in newly recolonized areas exhibited a significantly smaller allelic richness than others. Controlling for geographic distance, we also detected a significant correlation between chloroplast and nuclear population differentiation. This result indicates a cytonuclear disequilibrium that can be interpreted as a historical signal

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

Science.gov (United States)

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

2010-01-01

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

Building Phylogenetic Trees from DNA Sequence Data: Investigating Polar Bear and Giant Panda Ancestry.

Science.gov (United States)

Maier, Caroline Alexandra

2001-01-01

Presents an activity in which students seek answers to questions about evolutionary relationships by using genetic databases and bioinformatics software. Students build genetic distance matrices and phylogenetic trees based on molecular sequence data using web-based resources. Provides a flowchart of steps involved in accessing, retrieving, and…

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.

Science.gov (United States)

Lee, Tae-Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H

2014-02-26

Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

Radiation densitometry in tree-ring analysis: a review and procedure manual

Energy Technology Data Exchange (ETDEWEB)

Parker, M.L.; Taylor, F.G.; Doyle, T.W.; Foster, B.E.; Cooper, C.; West, D.C.

1985-01-01

An x-ray densitometry of wood facility is being established by the Environmental Sciences Division, Oak Ridge Natioanl Laboratory (ORNL). The objective is to apply tree-ring data to determine whether or not there is a fertilizer effect on tree growth from increased atmospheric carbon dioxide since the beginning of the industrial era. Intra-ring width and density data, including ring-mass will be detemined from tree-ring samples collected from sites located throughout the United States and Canada. This report is designed as a guide to assist ORNL scientists in building the x-ray densitometry system. The history and development of x-ray densitometry in tree-ring research is examined and x-ray densitometry is compared with other techniques. Relative wood and tree characteristics are described as are environmental and genetic factors affecting tree growth responses. Methods in x-ray densitometry are examined in detail and the techniques used at four operating laboratories are described. Some ways that dendrochronology has been applied in dating, in wood quality, and environmental studies are presented, and a number of tree-ring studies in Canada are described. An annotated bibliography of radiation densitometry in tree-ring analysis and related subjects is included.

Radiation densitometry in tree-ring analysis: a review and procedure manual

International Nuclear Information System (INIS)

Parker, M.L.; Taylor, F.G.; Doyle, T.W.; Foster, B.E.; Cooper, C.; West, D.C.

1985-01-01

An x-ray densitometry of wood facility is being established by the Environmental Sciences Division, Oak Ridge Natioanl Laboratory (ORNL). The objective is to apply tree-ring data to determine whether or not there is a fertilizer effect on tree growth from increased atmospheric carbon dioxide since the beginning of the industrial era. Intra-ring width and density data, including ring-mass will be detemined from tree-ring samples collected from sites located throughout the United States and Canada. This report is designed as a guide to assist ORNL scientists in building the x-ray densitometry system. The history and development of x-ray densitometry in tree-ring research is examined and x-ray densitometry is compared with other techniques. Relative wood and tree characteristics are described as are environmental and genetic factors affecting tree growth responses. Methods in x-ray densitometry are examined in detail and the techniques used at four operating laboratories are described. Some ways that dendrochronology has been applied in dating, in wood quality, and environmental studies are presented, and a number of tree-ring studies in Canada are described. An annotated bibliography of radiation densitometry in tree-ring analysis and related subjects is included

Structure theorems for game trees.

Science.gov (United States)

Govindan, Srihari; Wilson, Robert

2002-06-25

Kohlberg and Mertens [Kohlberg, E. & Mertens, J. (1986) Econometrica 54, 1003-1039] proved that the graph of the Nash equilibrium correspondence is homeomorphic to its domain when the domain is the space of payoffs in normal-form games. A counterexample disproves the analog for the equilibrium outcome correspondence over the space of payoffs in extensive-form games, but we prove an analog when the space of behavior strategies is perturbed so that every path in the game tree has nonzero probability. Without such perturbations, the graph is the closure of the union of a finite collection of its subsets, each diffeomorphic to a corresponding path-connected open subset of the space of payoffs. As an application, we construct an algorithm for computing equilibria of an extensive-form game with a perturbed strategy space, and thus approximate equilibria of the unperturbed game.

Mapping Urban Tree Canopy Cover Using Fused Airborne LIDAR and Satellite Imagery Data

Science.gov (United States)

Parmehr, Ebadat G.; Amati, Marco; Fraser, Clive S.

2016-06-01

Urban green spaces, particularly urban trees, play a key role in enhancing the liveability of cities. The availability of accurate and up-to-date maps of tree canopy cover is important for sustainable development of urban green spaces. LiDAR point clouds are widely used for the mapping of buildings and trees, and several LiDAR point cloud classification techniques have been proposed for automatic mapping. However, the effectiveness of point cloud classification techniques for automated tree extraction from LiDAR data can be impacted to the point of failure by the complexity of tree canopy shapes in urban areas. Multispectral imagery, which provides complementary information to LiDAR data, can improve point cloud classification quality. This paper proposes a reliable method for the extraction of tree canopy cover from fused LiDAR point cloud and multispectral satellite imagery data. The proposed method initially associates each LiDAR point with spectral information from the co-registered satellite imagery data. It calculates the normalised difference vegetation index (NDVI) value for each LiDAR point and corrects tree points which have been misclassified as buildings. Then, region growing of tree points, taking the NDVI value into account, is applied. Finally, the LiDAR points classified as tree points are utilised to generate a canopy cover map. The performance of the proposed tree canopy cover mapping method is experimentally evaluated on a data set of airborne LiDAR and WorldView 2 imagery covering a suburb in Melbourne, Australia.

SLE as a Mating of Trees in Euclidean Geometry

Science.gov (United States)

Holden, Nina; Sun, Xin

2018-05-01

The mating of trees approach to Schramm-Loewner evolution (SLE) in the random geometry of Liouville quantum gravity (LQG) has been recently developed by Duplantier et al. (Liouville quantum gravity as a mating of trees, 2014. arXiv:1409.7055). In this paper we consider the mating of trees approach to SLE in Euclidean geometry. Let {η} be a whole-plane space-filling SLE with parameter {κ > 4} , parameterized by Lebesgue measure. The main observable in the mating of trees approach is the contour function, a two-dimensional continuous process describing the evolution of the Minkowski content of the left and right frontier of {η} . We prove regularity properties of the contour function and show that (as in the LQG case) it encodes all the information about the curve {η} . We also prove that the uniform spanning tree on {Z^2} converges to SLE8 in the natural topology associated with the mating of trees approach.

Performance Evaluation of Tree Object Matching

DEFF Research Database (Denmark)

Somchaipeng, Kerawit; Sporring, Jon; Kreiborg, Sven

2005-01-01

Multi-Scale Singularity Trees (MSSTs) represents the deep structure of images in scale-space and provide both the connections between image features at different scales and their strengths. In this report we present and evaluate an algorithm that exploits the MSSTs for image matching. Two versions...

[Graft hybridization and the specificity of heredity in fruit trees].

Science.gov (United States)

Liu, Yong-Sheng; Li, Bao-Yin; Li, Gui-Rong; Zhou, Xiu-Mei

2004-09-01

Emphatically discusses the relationship between graft hybridization and the specificity of heredity in fruit trees on the basis of introducing the recent achievements in plant graft hybridization. We propose that genetic materials in rootstock being translocated and integrated into the genome of the germ cells and embryonic cells in scion are the main reasons why the majority of the hybrid seedlings have wild properties and the heredity of fruit trees violate Mendel's laws of heredity. The potential of graft hybridization in fruit breeding are also discussed.

Provenance research: investigation of genetic diversity associated with geography

Science.gov (United States)

Robert Z. Callaham

1963-01-01

Provenance in forestry refers to the population of trees growing at n particular place of origin. Provenance research defines the genetic and environmental components of phenotypic variation associated with geographic source. Information on provenance is important in assuring sources of seed to give well-adapted, productive trees and in directing breeding of...

Object-oriented fault tree evaluation program for quantitative analyses

Science.gov (United States)

Patterson-Hine, F. A.; Koen, B. V.

1988-01-01

Object-oriented programming can be combined with fault free techniques to give a significantly improved environment for evaluating the safety and reliability of large complex systems for space missions. Deep knowledge about system components and interactions, available from reliability studies and other sources, can be described using objects that make up a knowledge base. This knowledge base can be interrogated throughout the design process, during system testing, and during operation, and can be easily modified to reflect design changes in order to maintain a consistent information source. An object-oriented environment for reliability assessment has been developed on a Texas Instrument (TI) Explorer LISP workstation. The program, which directly evaluates system fault trees, utilizes the object-oriented extension to LISP called Flavors that is available on the Explorer. The object representation of a fault tree facilitates the storage and retrieval of information associated with each event in the tree, including tree structural information and intermediate results obtained during the tree reduction process. Reliability data associated with each basic event are stored in the fault tree objects. The object-oriented environment on the Explorer also includes a graphical tree editor which was modified to display and edit the fault trees.

Impact of tree planting configuration on canopy interception and soil hydrological properties: Implications for flood mitigation in silvopastoral systems

Science.gov (United States)

Lunka, Peter; Patil, Sopan

2015-04-01

Compaction of upper soil layers by intensive sheep grazing has been connected with increased local flood risk in silvopastoral systems. A 12 week field study was conducted at the Henfaes Research Station near Bangor, Wales to compare two silvopastoral configurations, trees planted in fenced off clumps and trees planted evenly spaced, in terms of canopy throughfall, soil water infiltration and soil bulk density. The study's aim was to characterize the potential of these tree planting configurations to reduce local flood risk. The study site (Henfaes) was established in 1992 on 14 ha of agricultural land and is part of the Silvopastoral National Network Experiment sites that have been set up across the UK to examine the potential of silvopasture and agroforestry on UK farms. Automated throughfall gauges were installed in each silvopastoral treatment along with a similarly designed control gauge located in the grazed control pasture. Soil water infiltration and bulk density were measured 20 times in a stratified random design for each treatment and the control. Soil infiltration capacity in the clumped configuration was significantly higher than in the even spaced configuration and control pasture. The clumped configuration had mean infiltration capacity 504% greater than the control pasture and 454% greater than the even spaced configuration. Canopy interception was higher in the clumped trees than in the evenly spaced trees. Average canopy interception was 34% in the clumped treatment and 28% in the evenly spaced treatment. Soil bulk density was lower in the clumped configuration than in the control pasture and evenly spaced configuration. Results suggest that in silvopastoral systems the clumped tree configuration is more likely to reduce local flood risk than the evenly spaced tree configuration due to enhanced infiltration and increased canopy interception.

Comparison between Decision Tree and Genetic Programming to distinguish healthy from stroke postural sway patterns.

Science.gov (United States)

Marrega, Luiz H G; Silva, Simone M; Manffra, Elisangela F; Nievola, Julio C

2015-01-01

Maintaining balance is a motor task of crucial importance for humans to perform their daily activities safely and independently. Studies in the field of Artificial Intelligence have considered different classification methods in order to distinguish healthy subjects from patients with certain motor disorders based on their postural strategies during the balance control. The main purpose of this paper is to compare the performance between Decision Tree (DT) and Genetic Programming (GP) - both classification methods of easy interpretation by health professionals - to distinguish postural sway patterns produced by healthy and stroke individuals based on 16 widely used posturographic variables. For this purpose, we used a posturographic dataset of time-series of center-of-pressure displacements derived from 19 stroke patients and 19 healthy matched subjects in three quiet standing tasks of balance control. Then, DT and GP models were trained and tested under two different experiments where accuracy, sensitivity and specificity were adopted as performance metrics. The DT method has performed statistically significant (P < 0.05) better in both cases, showing for example an accuracy of 72.8% against 69.2% from GP in the second experiment of this paper.

Genetic Diversity of Colletotrichum spp. an Endophytic Fungi in a Medicinal Plant, Brazilian Pepper Tree

Science.gov (United States)

Lima, J. S.; Figueiredo, J. G.; Gomes, R. G.; Stringari, D.; Goulin, E. H.; Adamoski, D.; Kava-Cordeiro, V.; Galli-Terasawa, L. V.; Glienke, C.

2012-01-01

In this study, we reported thirty-nine endophytic fungi identified as Colletotrichum spp. associated with Brazilian pepper tree or aroeira (Schinus terebinthifolius Raddi. Anacardiaceae) in Paraná state, Brazil. These endophytes were identified by morphological and molecular methods, using PCR taxon-specific with CaInt/ITS4, CgInt/ITS4, and Col1/ITS4 primers, which amplify specific bands in C. acutatum, C. gloeosporioides lato sensu, and Colletotrichum boninensis, respectively, and by DNA sequence analysis of the nrDNA internal transcribed spacer region (ITS1, 5.8S, ITS2). We also assayed the presence of dsRNA particles in Colletotrichum spp. isolates. Combining both morphological characters and molecular data, we identified the species C. gloeosporioides, C. boninense, and C. simmondsii. However, we found a high genetic variability intraspecific in C. gloeosporioides which suggests the existence of several other species. Bands of double-stranded RNA (dsRNA) were detected in three of thirty-nine isolates. Identity of these bands was confirmed by RNAse, DNAse, and S1 nuclease treatments for the isolates LGMF633, LGMF726, and LGMF729. This is the first study reporting these particles of dsRNA in C. gloeosporioides. PMID:23724319

Genetic comparisons of Egyptian date palm cultivars (Phoenix ...

African Journals Online (AJOL)

Random amplified polymorphic DNA technique was used to compare genetic material from four females date palm and four unknown male trees of Egyptian date palm. The genetic similarity between the four females date palm (Zaghloul, Amhat, Samany and Siwi) ranged from 87.5 to 98.9%. The banding profiles obtained ...

Australian toon planted in Hawaii: tree quality, growth, and stocking

Science.gov (United States)

Herbert L. Wick; Robert E. Nelson; Libert K. Landgraf

1971-01-01

Tree quality and rates of growth and survival were higher in 5- to 8-year-old Australian toon (Toona australis) plantations on sites with deep soils, good drainage, and as or broken pahoehoe rock than in plantations on sites with poor drainage or unbroken pahoehoe rock. Stocking averaged 236 trees per acre. Spacing in initial plants should be about 6...

Divergence and genetic variability among superior rubber tree genotypes Divergência e variabilidade genética de genótipos superiores de seringueira

Directory of Open Access Journals (Sweden)

Lígia Regina Lima Gouvêa

2010-02-01

Full Text Available The objective of this work was to estimate the genetic variability and divergence among 22 superior rubber tree (Hevea sp. genotypes of the IAC 400 series. Univariate and multivariate analyses were performed using eight quantitative traits (descriptors, including yield. In the univariate analyses, the estimated parameters were: genetic and environmental variances; genetic and environmental coefficients of variation; and the variation index. The Mahalanobis generalized distance, the Tocher agglomerative method and canonical variables were used for the multivariate analyses. In the univariate analyses, variability was verified among the genotypes for all the variables evaluated. The Tocher method grouped the genotypes into 11 clusters of dissimilarity. The first four canonical variables explained 87.93% of the cumulative variation. The highest genetic variability was found in rubber yield-related traits, which contributed the most to the genetic divergence. The most divergent pairs of genotypes are suggested for crossbreeding. The genotypes evaluated are suitable for breeding and may be used to continue the IAC rubber tree breeding program.O objetivo deste trabalho foi estimar a divergência e a variabilidade genética entre 22 genótipos superiores de seringueira (Hevea sp. da série IAC 400. Análises univariadas e multivariadas foram realizadas com oito caracteres quantitativos (descritores, incluindo produtividade. Na análise univariada, os parâmetros estimados foram: variâncias genética e ambiental, coeficientes de variação genética e ambiental, e índice de variação. A distância generalizada de Mahalanobis, o método aglomerativo de Tocher e variáveis canônicas foram utilizados nas análises multivariadas. Nas análises univariadas, verificou-se variabilidade entre os genótipos para todas as variáveis avaliadas. O método de Tocher agrupou os genótipos em 11 grupos de dissimilaridade. As quatro primeiras variáveis can

Tree cover and species composition effects on academic performance of primary school students.

Science.gov (United States)

Sivarajah, Sivajanani; Smith, Sandy M; Thomas, Sean C

2018-01-01

Human exposure to green space and vegetation is widely recognized to result in physical and mental health benefits; however, to date, the specific effects of tree cover, diversity, and species composition on student academic performance have not been investigated. We compiled standardized performance scores in Grades 3 and 6 for the collective student body in 387 schools across the Toronto District School Board (TDSB), and examined variation in relation to tree cover, tree diversity, and tree species composition based on comprehensive inventories of trees on school properties combined with aerial-photo-based assessments of tree cover. Analyses accounted for variation due to socioeconomic factors using the learning opportunity index (LOI), a regional composite index of external challenges to learning that incorporates income and other factors, such as students with English as a second language. As expected, LOI had the greatest influence on student academic performance; however, the proportion of tree cover, as distinct from other types of "green space" such as grass, was found to be a significant positive predictor of student performance, accounting for 13% of the variance explained in a statistical model predicting mean student performance assessments. The effects of tree cover and species composition were most pronounced in schools that showed the highest level of external challenges, suggesting the importance of urban forestry investments in these schools.

Genetic diversity and population structure of 20 North European cattle breeds

DEFF Research Database (Denmark)

kantanen, J; Olsaker, Ingrid; Holm, Lars-Erik

2000-01-01

Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic......, allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random...... drift-based genetic distance estimates. The breeds were classified on the basis of the tree topology into four major breed groups, defined as Northern indigenous breeds, Southern breeds, Ayrshire and Friesian breeds, and Jersey. Grouping of Nordic breeds was supported by documented breed history...

Does initial spacing influence crown and hydraulic architecture of Eucalyptus marginata?

Science.gov (United States)

Grigg, A H; Macfarlane, C; Evangelista, C; Eamus, D; Adams, M A

2008-05-01

Long-term declines in rainfall in south-western Australia have resulted in increased interest in the hydraulic characteristics of jarrah (Eucalyptus marginata Donn ex Smith) forest established in the region's drinking water catchments on rehabilitated bauxite mining sites. We hypothesized that in jarrah forest established on rehabilitated mine sites: (1) leaf area index (L) is independent of initial tree spacing; and (2) more densely planted trees have less leaf area for the same leaf mass, or the same sapwood area, and have denser sapwood. Initial stand densities ranged from about 600 to 9000 stems ha(-1), and trees were 18 years old at the time of sampling. Leaf area index was unaffected by initial stand density, except in the most sparsely stocked stands where L was 1.2 compared with 2.0-2.5 in stands at other spacings. The ratio of leaf area to sapwood area (A(l):A(s)) was unaffected by tree spacing or tree size and was 0.2 at 1.3 m height and 0.25 at the crown base. There were small increases in sapwood density and decreases in leaf specific area with increased spacing. Tree diameter or basal area was a better predictor of leaf area than sapwood area. At the stand scale, basal area was a good predictor of L (r(2) = 0.98, n = 15) except in the densest stands. We conclude that the hydraulic attributes of this forest type are largely independent of initial tree spacing, thus simplifying parameterization of stand and catchment water balance models.

The Hardwood Tree Improvement and Regeneration Center: its strategic plans for sustaining the hardwood resource

Science.gov (United States)

Charles H. Michler; Michael J. Bosela; Paula M. Pijut; Keith E. Woeste

2003-01-01

A regional center for hardwood tree improvement, genomics, and regeneration research, development and technology transfer will focus on black walnut, black cherry, northern red oak and, in the future, on other fine hardwoods as the effort is expanded. The Hardwood Tree Improvement and Regeneration Center (HTIRC) will use molecular genetics and genomics along with...

Forest adaptation to global climate change through silvicultural treatments and genetic improvement

International Nuclear Information System (INIS)

Farnum, P.

1991-01-01

The research being conducted by one forest products company into silviculture and plant genetics as a response to future problems caused by the greenhouse effect is reviewed. The company's research priorities have been adjusted to be technologically prepared for greenhouse-effect warming, including the effects of fire, shorter planting seasons, insect problems, and drought-related mortality. The review focuses on research into improving drought-related mortality by developing drought-resistant trees and then growing such trees by making use of biotechnological techniques such as somatic embryogenesis. In silvicultural research, emphasis is placed on quantifying how thinning can mitigate the effects of drought by stand density control. In genetics and physiology research, the applicability of greenhouse studies of drought resistance to stands of older trees was tested. This research led to an examination of the role of root systems and identification of possible characteristics to screen for in genetic tests. 2 refs

Multiple hypothesis tracking based extraction of airway trees from CT data

DEFF Research Database (Denmark)

Raghavendra, Selvan; Petersen, Jens; de Bruijne, Marleen

Segmentation of airway trees from CT scans of lungs has important clinical applications, in relation to the diagnosis of chronic obstructive pulmonary disease (COPD). Here we present a method based on multiple hypothesis tracking (MHT) and template matching, originally devised for vessel...... segmentation, to extract airway trees. Idealized tubular templates are constructed and ranked using scores assigned based on the image data. Several such regularly spaced hypotheses are used in constructing a hypothesis tree, which is then traversed to obtain improved segmentation results....

Genetic variability of South African fiscal shrikes ( Lanius collaris ...

African Journals Online (AJOL)

Rogers' (1972) mean genetic distance (D) was 0.094, and Nei's (1978) mean unbiased genetic distance was 0.019. A phenogram (unweighted pair group method) and a phylogenetic tree (distance Wagner network), both based on Rogers' (1972) distance, showed some degree of geographical subgrouping. The high ...

Management intensity and genetics affect loblolly pine seedling performance

Science.gov (United States)

Scott D. Roberts; Randall J. Rousseau; B. Landis Herrin

2012-01-01

Capturing potential genetic gains from tree improvement programs requires selection of the appropriate genetic stock and application of appropriate silvicultural management techniques. Limited information is available on how specific loblolly pine varietal genotypes perform under differing growing environments and management approaches. This study was established in...

In silico prediction of toxicity of phenols to Tetrahymena pyriformis by using genetic algorithm and decision tree-based modeling approach.

Science.gov (United States)

Abbasitabar, Fatemeh; Zare-Shahabadi, Vahid

2017-04-01

Risk assessment of chemicals is an important issue in environmental protection; however, there is a huge lack of experimental data for a large number of end-points. The experimental determination of toxicity of chemicals involves high costs and time-consuming process. In silico tools such as quantitative structure-toxicity relationship (QSTR) models, which are constructed on the basis of computational molecular descriptors, can predict missing data for toxic end-points for existing or even not yet synthesized chemicals. Phenol derivatives are known to be aquatic pollutants. With this background, we aimed to develop an accurate and reliable QSTR model for the prediction of toxicity of 206 phenols to Tetrahymena pyriformis. A multiple linear regression (MLR)-based QSTR was obtained using a powerful descriptor selection tool named Memorized_ACO algorithm. Statistical parameters of the model were 0.72 and 0.68 for R training 2 and R test 2 , respectively. To develop a high-quality QSTR model, classification and regression tree (CART) was employed. Two approaches were considered: (1) phenols were classified into different modes of action using CART and (2) the phenols in the training set were partitioned to several subsets by a tree in such a manner that in each subset, a high-quality MLR could be developed. For the first approach, the statistical parameters of the resultant QSTR model were improved to 0.83 and 0.75 for R training 2 and R test 2 , respectively. Genetic algorithm was employed in the second approach to obtain an optimal tree, and it was shown that the final QSTR model provided excellent prediction accuracy for the training and test sets (R training 2 and R test 2 were 0.91 and 0.93, respectively). The mean absolute error for the test set was computed as 0.1615. Copyright © 2016 Elsevier Ltd. All rights reserved.

On the salty side of life: molecular, physiological and anatomical adaptation and acclimation of trees to extreme habitats.

Science.gov (United States)

Polle, Andrea; Chen, Shaoliang

2015-09-01

Saline and sodic soils that cannot be used for agriculture occur worldwide. Cultivating stress-tolerant trees to obtain biomass from salinized areas has been suggested. Various tree species of economic importance for fruit, fibre and timber production exhibit high salinity tolerance. Little is known about the mechanisms enabling tree crops to cope with high salinity for extended periods. Here, the molecular, physiological and anatomical adjustments underlying salt tolerance in glycophytic and halophytic model tree species, such as Populus euphratica in terrestrial habitats, and mangrove species along coastlines are reviewed. Key mechanisms that have been identified as mediating salt tolerance are discussed at scales from the genetic to the morphological level, including leaf succulence and structural adjustments of wood anatomy. The genetic and transcriptomic bases for physiological salt acclimation are salt sensing and signalling networks that activate target genes; the target genes keep reactive oxygen species under control, maintain the ion balance and restore water status. Evolutionary adaptation includes gene duplication in these pathways. Strategies for and limitations to tree improvement, particularly transgenic approaches for increasing salt tolerance by transforming trees with single and multiple candidate genes, are discussed. © 2014 John Wiley & Sons Ltd.

Escaping Depressions in LRTS Based on Incremental Refinement of Encoded Quad-Trees

Directory of Open Access Journals (Sweden)

Yue Hu

2017-01-01

Full Text Available In the context of robot navigation, game AI, and so on, real-time search is extensively used to undertake motion planning. Though it satisfies the requirement of quick response to users’ commands and environmental changes, learning real-time search (LRTS suffers from the heuristic depressions where agents behave irrationally. There have introduced several effective solutions, such as state abstractions. This paper combines LRTS and encoded quad-tree abstraction which represent the search space in multiresolutions. When exploring the environments, agents are enabled to locally repair the quad-tree models and incrementally refine the spatial cognition. By virtue of the idea of state aggregation and heuristic generalization, our EQ LRTS (encoded quad-tree based LRTS possesses the ability of quickly escaping from heuristic depressions with less state revisitations. Experiments and analysis show that (a our encoding principle for quad-trees is a much more memory-efficient method than other data structures expressing quad-trees, (b EQ LRTS differs a lot in several characteristics from classical PR LRTS which represent the space and refine the paths hierarchically, and (c EQ LRTS substantially reduces the planning amount and curtails heuristic updates compared with LRTS on uniform cells.

Dynamic conservation of forest genetic resources in 33 European countries

NARCIS (Netherlands)

Lefevre, F.; Koskela, J.; Hubert, J.; Kraigher, H.; Longauer, R.; Olrik, D.C.; Vries, de S.M.G.

2013-01-01

Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across

Trees and networks before and after Darwin

Directory of Open Access Journals (Sweden)

Ragan Mark A

2009-11-01

Full Text Available Abstract It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859. Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate description of order in nature, and by about 1780 it had been largely abandoned without a satisfactory alternative having been agreed upon. In 1750 Donati described aquatic and terrestrial organisms as forming a network, and a few years later Buffon depicted a network of genealogical relationships among breeds of dogs. In 1764 Bonnet asked whether the Chain might actually branch at certain points, and in 1766 Pallas proposed that the gradations among organisms resemble a tree with a compound trunk, perhaps not unlike the tree of animal life later depicted by Eichwald. Other trees were presented by Augier in 1801 and by Lamarck in 1809 and 1815, the latter two assuming a transmutation of species over time. Elaborate networks of affinities among plants and among animals were depicted in the late Eighteenth and very early Nineteenth centuries. In the two decades immediately prior to 1837, so-called affinities and/or analogies among organisms were represented by diverse geometric figures. Series of plant and animal fossils in successive geological strata were represented as trees in a popular textbook from 1840, while in 1858 Bronn presented a system of animals, as evidenced by the fossil record, in a form of a tree. Darwin's 1859 tree and its subsequent elaborations by Haeckel came to be accepted in many but not all areas of biological sciences, while network diagrams were used in others. Beginning in the early 1960s trees were inferred from protein and nucleic acid sequences, but networks were re-introduced in the mid-1990s to represent lateral genetic transfer, increasingly regarded as a fundamental mode of evolution at least for

Domestication of the neotropical tree Chrysophyllum cainito from a geographically limited yet genetically diverse gene pool in Panama.

Science.gov (United States)

Petersen, Jennifer J; Parker, Ingrid M; Potter, Daniel

2014-03-01

Species in the early stages of domestication, in which wild and cultivated forms co-occur, provide important opportunities to develop and test hypotheses about the origins of crop species. Chrysophyllum cainito (Sapotaceae), the star apple or caimito, is a semidomesticated tree widely cultivated for its edible fruits; it is known to be native to the neotropics, but its precise geographic origins have not been firmly established. Here, we report results of microsatellite marker analyses supporting the hypothesis that the center of domestication for caimito was the Isthmus of Panama, a region in which few crop species are believed to have originated, despite its importance as a crossroads for the dispersal of domesticated plants between North and South America. Our data suggest that caimito was domesticated in a geographically restricted area while incorporating a diverse gene pool. These results refute the generally accepted Antillean origin of caimito, as well as alternative hypotheses that the species was domesticated independently in the two areas or over a broad geographic range including both. Human-mediated dispersal from Panama to the north and east was accompanied by strong reductions in both genotypic and phenotypic diversity. Within Panama, cultivated and wild trees show little neutral genetic divergence, in contrast to striking phenotypic differentiation in fruit and seed traits. In addition to providing a rare example of data that support the hypothesis of a narrow geographic origin on the Isthmus of Panama for a now widespread cultivated plant species, this study is one of the first investigations of the origins of an edible species of the large pantropical family Sapotaceae.

Constructing multi-labelled decision trees for junction design using the predicted probabilities

NARCIS (Netherlands)

Bezembinder, Erwin M.; Wismans, Luc J. J.; Van Berkum, Eric C.

2017-01-01

In this paper, we evaluate the use of traditional decision tree algorithms CRT, CHAID and QUEST to determine a decision tree which can be used to predict a set of (Pareto optimal) junction design alternatives (e.g. signal or roundabout) for a given traffic demand pattern and available space. This is

Farmers' contributions to the conservation of tree diversity in the Groundnut Basin, Senegal

Institute of Scientific and Technical Information of China (English)

Antoine Sambou; Bienvenu Sambou; Anders R(ae)bild

2017-01-01

Tree diversity in West Africa is threatened by intensified land uses and salinization,and farmers' role in conservation of tree species is unclear.We hypothesized that farmers contribute to conservation of tree diversity through protection of trees in their agroforestry landscapes and compared the diversity and structure of the tree vegetation across landscape classes.Inventories were carried out in three villages in the Groundnut Basin in Senegal,assessing tree diversity,density and crown cover.Tree diversity as assessed by species accumulation curves was high in forests,but cultivated landscapes had comparable or almost comparable diversity,especially in the cases where the forest was planted or was affected by charcoal production.However,the occurrence of exotic species was higher in cultivated parts of the landscape,and although many species were in common,ordination plots indicated that forests and cultivated landscapes to some degree had different species composition.Salinity had a strong influence on vegetation,not only in the tans (salt marshes) but also across the other landscape classes.In conclusion,agroforestry landscapes in the three villages harbor considerable tree diversity,but insufficient to fully conserve the tree species.We argue that informing and including farmers in tree management in the region will contribute to overall conservation of tree genetic resources.

Bayesian state space models for dynamic genetic network construction across multiple tissues.

Science.gov (United States)

Liang, Yulan; Kelemen, Arpad

2016-08-01

Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models. The unevenly spaced short time courses with unseen time points are treated as hidden state variables. Hierarchical Bayesian approaches with various prior and hyper-prior models with Monte Carlo Markov Chain and Gibbs sampling algorithms are used to estimate the model parameters and the hidden state variables. We apply the proposed Hierarchical Bayesian state space models to multiple tissues (liver, skeletal muscle, and kidney) Affymetrix time course data sets following corticosteroid (CS) drug administration. Both simulation and real data analysis results show that the genomic changes over time and gene-gene interaction in response to CS treatment can be well captured by the proposed models. The proposed dynamic Hierarchical Bayesian state space modeling approaches could be expanded and applied to other large scale genomic data, such as next generation sequence (NGS) combined with real time and time varying electronic health record (EHR) for more comprehensive and robust systematic and network based analysis in order to transform big biomedical data into predictions and diagnostics for precision medicine and personalized healthcare with better decision making and patient outcomes.

PMA-PhyloChip DNA Microarray to Elucidate Viable Microbial Community Structure

Science.gov (United States)

Venkateswaran, Kasthuri J.; Stam, Christina N.; Andersen, Gary L.; DeSantis, Todd

2011-01-01

in the dark. Thereafter, the sample is exposed to visible light for five minutes, so that the DNA from dead cells will be cross-linked. Following this PMA treatment step, the sample is concentrated by centrifugation and washed (to remove excessive PMA) before DNA is extracted. The 16S rRNA gene fragments will be amplified by PCR to screen the total microbial community using PhyloChip DNA microarray analysis. This approach will detect only the viable microbial community since the PMA intercalated DNA from dead cells would be unavailable for PCR amplification. The total detection time including PCR reaction for low biomass samples will be a few hours. Numerous markets may use this technology. The food industry uses spore detection to validate new alternative food processing technologies, sterility, and quality. Pharmaceutical and medical equipment companies also detect spores as a marker for sterility. This system can be used for validating sterilization processes, water treatment systems, and in various public health and homeland security applications.

Study of quantitative genetics of gum arabic production complicated by variability in ploidy level of Acacia senegal (L.) Willd

DEFF Research Database (Denmark)

Diallo, Adja Madjiguene; Nielsen, Lene Rostgaard; Hansen, Jon Kehlet

2015-01-01

Gum arabic is an important international commodity produced by trees of Acacia senegal across Sahelian Africa, but documented results of breeding activities are limited. The objective of this study was to provide reliable estimates of quantitative genetic parameters in order to shed light on the ...... stress the importance of testing ploidy levels of selected material and use of genetic markers to qualify the assumptions in the quantitative genetic analysis....... that progenies consisted of both diploid and polyploid trees, and growth, gum yield, and gum quality varied substantially among ploidy level, populations, and progenies. Analysis of molecular variance and estimates of outcrossing rate supported that trees within open-pollinated families of diploids were half...... sibs, while the open-pollinated families of polyploids showed low variation within families. The difference in sibling relationship observed between ploidy levels complicated estimation of genetic parameters. However, based on the diploid trees, we conclude that heritability in gum arabic production...

Meta-analysis of susceptibility of woody plants to loss of genetic diversity through habitat fragmentation.

Science.gov (United States)

Vranckx, Guy; Jacquemyn, Hans; Muys, Bart; Honnay, Olivier

2012-04-01

Shrubs and trees are assumed less likely to lose genetic variation in response to habitat fragmentation because they have certain life-history characteristics such as long lifespans and extensive pollen flow. To test this assumption, we conducted a meta-analysis with data on 97 woody plant species derived from 98 studies of habitat fragmentation. We measured the weighted response of four different measures of population-level genetic diversity to habitat fragmentation with Hedge's d and Spearman rank correlation. We tested whether the genetic response to habitat fragmentation was mediated by life-history traits (longevity, pollination mode, and seed dispersal vector) and study characteristics (genetic marker and plant material used). For both tests of effect size habitat fragmentation was associated with a substantial decrease in expected heterozygosity, number of alleles, and percentage of polymorphic loci, whereas the population inbreeding coefficient was not associated with these measures. The largest proportion of variation among effect sizes was explained by pollination mechanism and by the age of the tissue (progeny or adult) that was genotyped. Our primary finding was that wind-pollinated trees and shrubs appeared to be as likely to lose genetic variation as insect-pollinated species, indicating that severe habitat fragmentation may lead to pollen limitation and limited gene flow. In comparison with results of previous meta-analyses on mainly herbaceous species, we found trees and shrubs were as likely to have negative genetic responses to habitat fragmentation as herbaceous species. We also found that the genetic variation in offspring was generally less than that of adult trees, which is evidence of a genetic extinction debt and probably reflects the genetic diversity of the historical, less-fragmented landscape. ©2011 Society for Conservation Biology.

Microclimate and development of 'Conilon' coffee intercropped with rubber trees

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Fábio Luiz Partelli

2014-11-01

Full Text Available The objective of this work was to evaluate the influence of intercropping 'Conilon' coffee (Coffea canephora with rubber trees on coffee tree microclimate, nutrition, growth, and yield. Rubber trees were planted in two double rows 33 m apart, with 4x2.3 m spacing between plants. Treatments consisted of the distances from the coffee plants to the rubber trees: 3, 6, 9, 12, and 15 m. Measurements of atmospheric variables (temperature, irradiance, and relative humidity, leaf nutrient concentration, internode length of plagiotropic and orthotropic branches, individual leaf area, chlorophyll content, and yield were performed. Intercropping promotes changes in the microclimatic conditions of coffee plants close to rubber trees, with reduction of temperature and irradiance level and increase in air relative humidity. The proximity of the coffee tree to the rubber trees promotes the elongation of the plagiotropic and orthotropic branches and increases the individual leaf area; however, it does not affect leaf concentrations of N, K, Mg, Fe, Zn, and B in 'Conilon' coffee and does not have a negative impact on yield.

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space.

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Luis Zea

Full Text Available Bacteria behave differently in space, as indicated by reports of reduced lag phase, higher final cell counts, enhanced biofilm formation, increased virulence, and reduced susceptibility to antibiotics. These phenomena are theorized, at least in part, to result from reduced mass transport in the local extracellular environment, where movement of molecules consumed and excreted by the cell is limited to diffusion in the absence of gravity-dependent convection. However, to date neither empirical nor computational approaches have been able to provide sufficient evidence to confirm this explanation. Molecular genetic analysis findings, conducted as part of a recent spaceflight investigation, support the proposed model. This investigation indicated an overexpression of genes associated with starvation, the search for alternative energy sources, increased metabolism, enhanced acetate production, and other systematic responses to acidity-all of which can be associated with reduced extracellular mass transport.

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space

Science.gov (United States)

Prasad, Nripesh; Levy, Shawn E.; Stodieck, Louis; Jones, Angela; Shrestha, Shristi; Klaus, David

2016-01-01

Bacteria behave differently in space, as indicated by reports of reduced lag phase, higher final cell counts, enhanced biofilm formation, increased virulence, and reduced susceptibility to antibiotics. These phenomena are theorized, at least in part, to result from reduced mass transport in the local extracellular environment, where movement of molecules consumed and excreted by the cell is limited to diffusion in the absence of gravity-dependent convection. However, to date neither empirical nor computational approaches have been able to provide sufficient evidence to confirm this explanation. Molecular genetic analysis findings, conducted as part of a recent spaceflight investigation, support the proposed model. This investigation indicated an overexpression of genes associated with starvation, the search for alternative energy sources, increased metabolism, enhanced acetate production, and other systematic responses to acidity—all of which can be associated with reduced extracellular mass transport. PMID:27806055

Tree compression with top trees

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

2013-01-01

We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

Tree compression with top trees

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

2015-01-01

We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

Estimation of Total Tree Height from Renewable Resources Evaluation Data

Science.gov (United States)

Charles E. Thomas

1981-01-01

Many ecological, biological, and genetic studies use the measurement of total tree height. Until recently, the Southern Forest Experiment Station's inventory procedures through Renewable Resources Evaluation (RRE) have not included total height measurements. This note provides equations to estimate total height based on other RRE measurements.

Automated Tree Crown Delineation and Biomass Estimation from Airborne LiDAR data: A Comparison of Statistical and Machine Learning Methods

Science.gov (United States)

Gleason, C. J.; Im, J.

2011-12-01

Airborne LiDAR remote sensing has been used effectively in assessing forest biomass because of its canopy penetrating effects and its ability to accurately describe the canopy surface. Current research in assessing biomass using airborne LiDAR focuses on either the individual tree as a base unit of study or statistical representations of a small aggregation of trees (i.e., plot level), and both methods usually rely on regression against field data to model the relationship between the LiDAR-derived data (e.g., volume) and biomass. This study estimates biomass for mixed forests and coniferous plantations (Picea Abies) within Heiberg Memorial Forest, Tully, NY, at both the plot and individual tree level. Plots are regularly spaced with a radius of 13m, and field data include diameter at breast height (dbh), tree height, and tree species. Field data collection and LiDAR data acquisition were seasonally coincident and both obtained in August of 2010. Resulting point cloud density was >5pts/m2. LiDAR data were processed to provide a canopy height surface, and a combination of watershed segmentation, active contouring, and genetic algorithm optimization was applied to delineate individual trees from the surface. This updated delineation method was shown to be more accurate than traditional watershed segmentation. Once trees had been delineated, four biomass estimation models were applied and compared: support vector regression (SVR), linear mixed effects regression (LME), random forest (RF), and Cubist regression. Candidate variables to be used in modeling were derived from the LiDAR surface, and include metrics of height, width, and volume per delineated tree footprint. Previously published allometric equations provided field estimates of biomass to inform the regressions and calculate their accuracy via leave-one-out cross validation. This study found that for forests such as found in the study area, aggregation of individual trees to form a plot-based estimate of

Genome sequence of the olive tree, Olea europaea.

Science.gov (United States)

Cruz, Fernando; Julca, Irene; Gómez-Garrido, Jèssica; Loska, Damian; Marcet-Houben, Marina; Cano, Emilio; Galán, Beatriz; Frias, Leonor; Ribeca, Paolo; Derdak, Sophia; Gut, Marta; Sánchez-Fernández, Manuel; García, Jose Luis; Gut, Ivo G; Vargas, Pablo; Alioto, Tyler S; Gabaldón, Toni

2016-06-27

The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

Tree-ring C-H-O isotope variability and sampling

International Nuclear Information System (INIS)

Leavitt, Steven W.

2010-01-01

In light of the proliferation of tree-ring isotope studies, the magnitude and cause of variability of tree-ring δ 13 C, δ 18 O and δ 2 H within individual trees (circumferential) and among trees at a site is examined in reference to field and laboratory sampling requirements and strategies. Within this framework, this paper provides a state-of-knowledge summary of the influence of 'juvenile' isotope effects, ageing effects, and genetic effects, as well as the interchangeability of species, choice of ring segment to analyze (whole ring, earlywood or latewood), and the option of sample pooling. The range of isotopic composition of the same ring among trees at a site is ca. 1-3 per mille for δ 13 C, 1-4 per mille δ 18 O, and 5-30 per mille for δ 2 H, whereas the circumferential variability within a tree is lower. A standard prescription for sampling and analysis does not exist because of differences in field environmental circumstances and mixed findings represented in relevant published literature. Decisions in this regard will usually be tightly constrained by goals of the study and project resources. Sampling 4-6 trees at a site while avoiding juvenile effects in rings near the pith seems to be the most commonly used methodology, and although there are some reasoned arguments for analyzing only latewood and developing separate isotope records from each tree, the existence of some contradictory findings together with efforts to reduce cost and effort have prompted alternate strategies (e.g., most years pooled with occasional analysis of rings in the sequence separately for each tree) that have produced useful results in many studies.

EEG feature selection method based on decision tree.

Science.gov (United States)

Duan, Lijuan; Ge, Hui; Ma, Wei; Miao, Jun

2015-01-01

This paper aims to solve automated feature selection problem in brain computer interface (BCI). In order to automate feature selection process, we proposed a novel EEG feature selection method based on decision tree (DT). During the electroencephalogram (EEG) signal processing, a feature extraction method based on principle component analysis (PCA) was used, and the selection process based on decision tree was performed by searching the feature space and automatically selecting optimal features. Considering that EEG signals are a series of non-linear signals, a generalized linear classifier named support vector machine (SVM) was chosen. In order to test the validity of the proposed method, we applied the EEG feature selection method based on decision tree to BCI Competition II datasets Ia, and the experiment showed encouraging results.

Fungal and Oomycete Diseases of Tropical Tree Fruit Crops.

Science.gov (United States)

Drenth, André; Guest, David I

2016-08-04

The tropics produce a range of fruit from tree crops that cannot be grown in colder climates. Bananas, mangos, several nuts, spices, coffee, and cacao are widely traded and much sought after around the world. However, the sustainable production of these tropical tree fruit crops faces significant challenges. Among these, losses due to pests and diseases play a large part in reducing yields, quality, and profitability. Using bananas and cacao as key examples, we outline some of the reasons fungal and oomycete diseases cause such significant losses to tropical tree crops. Cultivation of monocultures derived from limited genetic diversity, environmental conditions conducive for disease development, high levels of disease incidence and severity, a lack of disease resistance in planting materials, shortages of labor, and inadequate infrastructure and investment pose significant challenges, especially for smallholder producers. The expansion of travel and trade has given rise to emerging infectious plant diseases that add further insecurity and pressure. We conclude that holistic actions are needed on multiple fronts to address the growing problem of disease in tropical fruit tree crops.

Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

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Lígia Regina Lima Gouvêa

2010-01-01

Full Text Available Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC, Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (H T' = 0.58 and high gene differentiation (Gst' = 0.61 were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability.

A novel approach to internal crown characterization for coniferous tree species classification

Science.gov (United States)

Harikumar, A.; Bovolo, F.; Bruzzone, L.

2016-10-01

The knowledge about individual trees in forest is highly beneficial in forest management. High density small foot- print multi-return airborne Light Detection and Ranging (LiDAR) data can provide a very accurate information about the structural properties of individual trees in forests. Every tree species has a unique set of crown structural characteristics that can be used for tree species classification. In this paper, we use both the internal and external crown structural information of a conifer tree crown, derived from a high density small foot-print multi-return LiDAR data acquisition for species classification. Considering the fact that branches are the major building blocks of a conifer tree crown, we obtain the internal crown structural information using a branch level analysis. The structure of each conifer branch is represented using clusters in the LiDAR point cloud. We propose the joint use of the k-means clustering and geometric shape fitting, on the LiDAR data projected onto a novel 3-dimensional space, to identify branch clusters. After mapping the identified clusters back to the original space, six internal geometric features are estimated using a branch-level analysis. The external crown characteristics are modeled by using six least correlated features based on cone fitting and convex hull. Species classification is performed using a sparse Support Vector Machines (sparse SVM) classifier.

Inventory of Green Spaces and Woody Plants in the Urban Landscape in Ariogala

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Lina Straigytė

2012-12-01

Full Text Available Background and Purpose: Regulation of urban greenery design, management and protection was approved in 2008 in Lithuania after the Green Space Law was passed, allowing protection of public green spaces and woody plants. Protection of these resources first requires an inventory, and we have created a digital database that will help in management of urban green spaces. Material and Methods: An inventory of green spaces and woody plants was conducted in the public urban territory of Ariogala, using GIS technology. A digital cartographic database was created using ArcGis 9.1 software. Results and Conclusion: Most of the woody plants in the survey area are deciduous trees, and the survey results highlighted the major green space management problems. Often, planted trees grow under power lines, and their crowns touch the power cables. Near blocks of flats, trees are often in the wrong place-planted too close to buildings, trees shade windows and their roots heave pavers and penetrate building foundations. According to the inventory, street trees sustain the most damage, most commonly showing injuries on their trunks and roots. Leaves of Aesculus hipocastanum L. show massive damage from Cameraria ohridella Deschka & Dimić, and Tilia cordata Mill. are damaged by Cercospora microsora Sacc. T. cordata is a favourite city tree, but is susceptible to infestation and when damaged appears unsightly, ending its vegetation period very early. The inventory of green spaces also showed that there are sufficient public parks.

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

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Wolf Yuri I

2009-09-01

Full Text Available Abstract Background The elucidation of the dominant role of horizontal gene transfer (HGT in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL concept and intense debates on this subject. Concept Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns and processes of evolution. We posit that replication of the genetic material is the singular fundamental biological process and that replication with an error rate below a certain threshold both enables and necessitates evolution by drift and selection. Starting from this proposition, we outline a general concept of evolution that consists of three major precepts. 1. The primary agency of evolution consists of Fundamental Units of Evolution (FUEs, that is, units of genetic material that possess a substantial degree of evolutionary independence. The FUEs include both bona fide selfish elements such as viruses, viroids, transposons, and plasmids, which encode some of the information required for their own replication, and regular genes that possess quasi-independence owing to their distinct selective value that provides for their transfer between ensembles of FUEs (genomes and preferential replication along with the rest of the recipient genome. 2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language. Recombination within a FUE is common between very closely related sequences where homologous recombination is feasible but becomes negligible for longer evolutionary distances. In contrast, shuffling of FUEs occurs at all evolutionary distances. Thus, a tree is a natural representation of the evolution of an individual FUE on the macro scale, but not of an ensemble of FUEs such as a genome. 3. The history of life is properly represented by the "forest" of evolutionary trees for individual FUEs (Forest of Life, or

Cercosporiose progression in the agroforestry consortium coffee-rubber trees

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Humberto Godoy Androcioli

2015-12-01

Full Text Available Cercospora coffeicola is one of the primary diseases that affect coffee plants. Studies indicate that shaded coffee plants reduce the incidence of this disease and that the management of trees and coffee plants arrangement influence in the dissemination of cercospora. The objective of this study was to evaluate the incidence and severity of C. coffeicola at different distances from double rows of rubber trees (Hevea brasiliensis muell. arg. at two different sunlight exposures (north and south. This study was conducted in Londrina, Parana, between 2008 and 2010, with adult plants of the IAPAR 59 cultivar (Coffea arabica L. grown at a spacing of 2.5 m x 1.0 m. The distances between the double rows of rubber trees were 13, 16 and 22 m, compared to plants grown under full sun. The disease incidence was assessed monthly by using a non-destructive method. This analysis was conducted on coffee leaves from the third and fourth pairs of two plagiotropic branches, on eight plants per plot, with five replications. These data were used to calculate the area under the curve for the incidence of the brown eye spot. The highest disease incidence occurred in the coffee plants grown under full sun, whereas lowest disease occurred on plants located at up to two meters away from double rows of rubber trees. The incidence of Cercospora leaf spot increased with the distance from the double rows of rubber trees. The results demonstrate that the mapping of cercospora incidence in shaded coffee plants is essential to determinate the best spacing and plants arrangement.

Cryopreservation of eucalyptus genetic resources

Science.gov (United States)

The long-term preservation of forest genetic resources is a vital part of preserving our forest crops for future generations. Unfortunately there are few genebanks dedicated to forest trees and very few methods aside from field plantings of germplasm collections of elite clonal individuals. The use ...

Generalising tree traversals and tree transformations to DAGs

DEFF Research Database (Denmark)

Bahr, Patrick; Axelsson, Emil

2017-01-01

We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead. The resul......We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead...... as the complementing theory with a number of examples....

Climate-related genetic variation in a threatened tree species, Pinus albicaulis

Science.gov (United States)

Marcus V. Warwell; Ruth G. Shaw

2017-01-01

PREMISE OF THE STUDY: With ongoing climate change, understanding of intraspecific adaptive variation is critical for conservation and restoration of plant species. Such information is especially scarce for threatened and endangered tree species, such as Pinus albicaulis Engelm. Therefore, our principal aims were to assess adaptive variation and characterize its...

Investigation on electrical tree propagation in polyethylene based on etching method

Directory of Open Access Journals (Sweden)

Zexiang Shi

2017-11-01

Full Text Available To investigate the characteristic of electrical tree propagation in semi-crystalline polymers, the low-density polyethylene (LDPE samples containing electrical trees are cut into slices by using ultramicrotome. Then the slice samples are etched by potassium permanganate etchant. Finally, the crystalline structure and the electrical tree propagation path in samples are observed by polarized light microscopy (PLM. According to the observation, the LDPE spherocrystal structure model is established on the basis of crystallization kinetics and morphology of polymers. And the electrical tree growth process in LDPE is discussed based on the free volume breakdown theory, the molecular chain relaxation theory, the electromechanical force theory, the thermal expansion effect and the space charge shielding effect.

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli

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Lapointe François-Joseph

2011-07-01

Full Text Available Abstract Background We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL approaches. Results We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study, and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements. Conclusions Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc., forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to

Estimating the actual subject-specific genetic correlations in behavior genetics.

Science.gov (United States)

Molenaar, Peter C M

2012-10-01

Generalization of the standard behavior longitudinal genetic factor model for the analysis of interindividual phenotypic variation to a genetic state space model for the analysis of intraindividual variation enables the possibility to estimate subject-specific heritabilities.