Applications and Benefits for Big Data Sets Using Tree Distances and The T-SNE Algorithm

DTIC Science & Technology

2016-03-01

BENEFITS FOR BIG DATA SETS USING TREE DISTANCES AND THE T-SNE ALGORITHM by Suyoung Lee March 2016 Thesis Advisor: Samuel E. Buttrey...REPORT TYPE AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE APPLICATIONS AND BENEFITS FOR BIG DATA SETS USING TREE DISTANCES AND THE T-SNE...this work we use tree distance computed using Buttrey’s treeClust package in R, as discussed by Buttrey and Whitaker in 2015, to process mixed data

BAOBAB: a Java editor for large phylogenetic trees.

PubMed

Dutheil, J; Galtier, N

2002-06-01

BAOBAB is a Java user interface dedicated to viewing and editing large phylogenetic trees. Original features include: (i) a colour-mediated overview of magnified subtrees; (ii) copy/cut/paste of (sub)trees within or between windows; (iii) compressing/ uncompressing subtrees; and (iv) managing sequence files together with tree files. http://www.univ-montp2.fr/~genetix/.

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance

PubMed Central

2013-01-01

Background Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. Results We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem. We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. Conclusions Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets. PMID:24180377

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

PubMed

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.

MASTtreedist: visualization of tree space based on maximum agreement subtree.

PubMed

Huang, Hong; Li, Yongji

2013-01-01

Phylogenetic tree construction process might produce many candidate trees as the "best estimates." As the number of constructed phylogenetic trees grows, the need to efficiently compare their topological or physical structures arises. One of the tree comparison's software tools, the Mesquite's Tree Set Viz module, allows the rapid and efficient visualization of the tree comparison distances using multidimensional scaling (MDS). Tree-distance measures, such as Robinson-Foulds (RF), for the topological distance among different trees have been implemented in Tree Set Viz. New and sophisticated measures such as Maximum Agreement Subtree (MAST) can be continuously built upon Tree Set Viz. MAST can detect the common substructures among trees and provide more precise information on the similarity of the trees, but it is NP-hard and difficult to implement. In this article, we present a practical tree-distance metric: MASTtreedist, a MAST-based comparison metric in Mesquite's Tree Set Viz module. In this metric, the efficient optimizations for the maximum weight clique problem are applied. The results suggest that the proposed method can efficiently compute the MAST distances among trees, and such tree topological differences can be translated as a scatter of points in two-dimensional (2D) space. We also provide statistical evaluation of provided measures with respect to RF-using experimental data sets. This new comparison module provides a new tree-tree pairwise comparison metric based on the differences of the number of MAST leaves among constructed phylogenetic trees. Such a new phylogenetic tree comparison metric improves the visualization of taxa differences by discriminating small divergences of subtree structures for phylogenetic tree reconstruction.

Edit distance for marked point processes revisited: An implementation by binary integer programming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirata, Yoshito; Aihara, Kazuyuki

2015-12-15

We implement the edit distance for marked point processes [Suzuki et al., Int. J. Bifurcation Chaos 20, 3699–3708 (2010)] as a binary integer program. Compared with the previous implementation using minimum cost perfect matching, the proposed implementation has two advantages: first, by using the proposed implementation, we can apply a wide variety of software and hardware, even spin glasses and coherent ising machines, to calculate the edit distance for marked point processes; second, the proposed implementation runs faster than the previous implementation when the difference between the numbers of events in two time windows for a marked point process ismore » large.« less

Dependency Tree Annotation Software

DTIC Science & Technology

2015-11-01

formats, and it provides numerous options for customizing how dependency trees are displayed. Built entirely in Java , it can run on a wide range of...tree can be saved as an image, .mxe (a mxGraph editing file), a .conll file, and several other file formats. DTE uses the open source Java version

Editing Distance Education Materials. Knowledge Series.

ERIC Educational Resources Information Center

Swales, Christine

Distance education (DE) materials take a learner-centered approach rather than the traditionally content-centered approach of textbooks. This fact has several implications for the editing of DE materials. The role of the editor within the DE organization will depend on the organization's size and structure. The basic features of the DE program or…

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes.

PubMed

Shao, Mingfu; Lin, Yu; Moret, Bernard M E

2015-05-01

Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under the DCJ model can be computed in linear time for genomes without duplicate genes, while the problem becomes NP-hard in the presence of duplicate genes. In this article, we propose an integer linear programming (ILP) formulation to compute the DCJ distance between two genomes with duplicate genes. We also provide an efficient preprocessing approach to simplify the ILP formulation while preserving optimality. Comparison on simulated genomes demonstrates that our method outperforms MSOAR in computing the edit distance, especially when the genomes contain long duplicated segments. We also apply our method to assign orthologous gene pairs among human, mouse, and rat genomes, where once again our method outperforms MSOAR.

Using P-Stat, BMDP and SPSS for a cross-products factor analysis.

PubMed

Tanner, B A; Leiman, J M

1983-06-01

The major disadvantage of the Q factor analysis with Euclidean distances described by Tanner and Koning [Comput. Progr. Biomed. 12 (1980) 201-202] is the considerable editing required. An alternative procedure with commercially distributed software, and with cross-products in place of Euclidean distances is described. This procedure does not require any editing.

Distance of response to host tree models by female apple maggot flies,Rhagoletis pomonella (Walsh) (Diptera: Tephritidae): Interaction of visual and olfactory stimuli.

PubMed

Green, T A; Prokopy, R J; Hosmer, D W

1994-09-01

Mature female apple maggot flies,Rhagoletis pomonella (Walsh), were released individually onto a single potted, fruitless hawthorne tree in the center of an open field. The tree was surrounded by four 1-m(2) plywood host tree models painted green or white, with or without synthetic host fruit odor (butyl hexanoate), and placed at one of several distances from the release tree. Each fly was permitted to forage freely on the release tree for up to 1 hr, or until it left the tree. Flies left the tree significantly sooner when green models with host fruit were present at 0.5, 1.5, or 2.5 m distance from the release tree than when these models were placed at a greater distance (4.5 m) from the release tree or when no models were present. Flies responded detectably to 1-m(2) models without odor up to a maximum distance of 1.5 m. These results suggest that female apple maggot flies did not detect green 1-m(2) models with odor 4.5 m away or models without odor 2.5 m or more away. Flies responded to white models with and without odor to a much lesser extent, both in terms of response distance and flight to and alightment upon models. Increasing model size to 2 m(2) increased the distance to 2.5 m at which flies responded to green models without odor. Decreasing model size to 0.5 m(2) reduced fly responsiveness to green or white models. The presence of host fruit odor alone, without the visual stimulus of a green model, did not influence residence time on the release tree.

Per tree estimates with n-tree distance sampling: an application to increment core data

Treesearch

Thomas B. Lynch; Robert F. Wittwer

2002-01-01

Per tree estimates using the n trees nearest a point can be obtained by using a ratio of per unit area estimates from n-tree distance sampling. This ratio was used to estimate average age by d.b.h. classes for cottonwood trees (Populus deltoides Bartr. ex Marsh.) on the Cimarron National Grassland. Increment...

Towards a hybrid energy efficient multi-tree-based optimized routing protocol for wireless networks.

PubMed

Mitton, Nathalie; Razafindralambo, Tahiry; Simplot-Ryl, David; Stojmenovic, Ivan

2012-12-13

This paper considers the problem of designing power efficient routing with guaranteed delivery for sensor networks with unknown geographic locations. We propose HECTOR, a hybrid energy efficient tree-based optimized routing protocol, based on two sets of virtual coordinates. One set is based on rooted tree coordinates, and the other is based on hop distances toward several landmarks. In HECTOR, the node currently holding the packet forwards it to its neighbor that optimizes ratio of power cost over distance progress with landmark coordinates, among nodes that reduce landmark coordinates and do not increase distance in tree coordinates. If such a node does not exist, then forwarding is made to the neighbor that reduces tree-based distance only and optimizes power cost over tree distance progress ratio. We theoretically prove the packet delivery and propose an extension based on the use of multiple trees. Our simulations show the superiority of our algorithm over existing alternatives while guaranteeing delivery, and only up to 30% additional power compared to centralized shortest weighted path algorithm.

Towards a Hybrid Energy Efficient Multi-Tree-Based Optimized Routing Protocol for Wireless Networks

PubMed Central

Mitton, Nathalie; Razafindralambo, Tahiry; Simplot-Ryl, David; Stojmenovic, Ivan

2012-01-01

This paper considers the problem of designing power efficient routing with guaranteed delivery for sensor networks with unknown geographic locations. We propose HECTOR, a hybrid energy efficient tree-based optimized routing protocol, based on two sets of virtual coordinates. One set is based on rooted tree coordinates, and the other is based on hop distances toward several landmarks. In HECTOR, the node currently holding the packet forwards it to its neighbor that optimizes ratio of power cost over distance progress with landmark coordinates, among nodes that reduce landmark coordinates and do not increase distance in tree coordinates. If such a node does not exist, then forwarding is made to the neighbor that reduces tree-based distance only and optimizes power cost over tree distance progress ratio. We theoretically prove the packet delivery and propose an extension based on the use of multiple trees. Our simulations show the superiority of our algorithm over existing alternatives while guaranteeing delivery, and only up to 30% additional power compared to centralized shortest weighted path algorithm. PMID:23443398

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

PubMed

McTavish, Emily Jane; Hinchliff, Cody E; Allman, James F; Brown, Joseph W; Cranston, Karen A; Holder, Mark T; Rees, Jonathan A; Smith, Stephen A

2015-09-01

Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git's version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the 'phylesystem-api', which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements. Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api. The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem. A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator. Code for that tool is available from https://github.com/OpenTreeOfLife/opentree. mtholder@gmail.com. © The Author 2015. Published by Oxford University Press.

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

PubMed

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.

Spatial Characteristics of Tree Diameter Distributions in a Temperate Old-Growth Forest

PubMed Central

Zhao, Xiuhai; von Gadow, Klaus

2013-01-01

This contribution identifies spatial characteristics of tree diameter in a temperate forest in north-eastern China, based on a fully censused observational study area covering 500×600 m. Mark correlation analysis with three null hypothesis models was used to determine departure from expectations at different neighborhood distances. Tree positions are clumped at all investigated scales in all 37 studied species, while the diameters of most species are spatially negatively correlated, especially at short distances. Interestingly, all three cases showing short-distance attraction of dbh marks are associated with light-demanding shrub species. The short-distance attraction of dbh marks indicates spatially aggregated cohorts of stems of similar size. The percentage of species showing significant dbh suppression peaked at a 4 m distance under the heterogeneous Poisson model. At scales exceeding the peak distance, the percentage of species showing significant dbh suppression decreases sharply with increasing distances. The evidence from this large observational study shows that some of the variation of the spatial characteristics of tree diameters is related variations of topography and soil chemistry. However, an obvious interpretation of this result is still lacking. Thus, removing competitors surrounding the target trees is an effective way to avoid neighboring competition effects reducing the growth of valuable target trees in forest management practice. PMID:23527066

Spatial characteristics of tree diameter distributions in a temperate old-growth forest.

PubMed

Zhang, Chunyu; Wei, Yanbo; Zhao, Xiuhai; von Gadow, Klaus

2013-01-01

This contribution identifies spatial characteristics of tree diameter in a temperate forest in north-eastern China, based on a fully censused observational study area covering 500×600 m. Mark correlation analysis with three null hypothesis models was used to determine departure from expectations at different neighborhood distances. Tree positions are clumped at all investigated scales in all 37 studied species, while the diameters of most species are spatially negatively correlated, especially at short distances. Interestingly, all three cases showing short-distance attraction of dbh marks are associated with light-demanding shrub species. The short-distance attraction of dbh marks indicates spatially aggregated cohorts of stems of similar size. The percentage of species showing significant dbh suppression peaked at a 4 m distance under the heterogeneous Poisson model. At scales exceeding the peak distance, the percentage of species showing significant dbh suppression decreases sharply with increasing distances. The evidence from this large observational study shows that some of the variation of the spatial characteristics of tree diameters is related variations of topography and soil chemistry. However, an obvious interpretation of this result is still lacking. Thus, removing competitors surrounding the target trees is an effective way to avoid neighboring competition effects reducing the growth of valuable target trees in forest management practice.

Foundations of Distance Education. Third Edition. Routledge Studies in Distance Education.

ERIC Educational Resources Information Center

Keegan, Desmond

This text gives an overview of distance education for students, administrators, and practitioners in distance education. Chapter 1 discusses the study of distance education. Chapter 2 analyzes forms of nonconventional education (open, nontraditional) that may have similarities to distance education but are not to be identified with it. Chapter 3…

Taï chimpanzees anticipate revisiting high-valued fruit trees from further distances.

PubMed

Ban, Simone D; Boesch, Christophe; Janmaat, Karline R L

2014-11-01

The use of spatio-temporal memory has been argued to increase food-finding efficiency in rainforest primates. However, the exact content of this memory is poorly known to date. This study investigated what specific information from previous feeding visits chimpanzees (Pan troglodytes verus), in Taï National Park, Côte d'Ivoire, take into account when they revisit the same feeding trees. By following five adult females for many consecutive days, we tested from what distance the females directed their travels towards previously visited feeding trees and how previous feeding experiences and fruit tree properties influenced this distance. To exclude the influence of sensory cues, the females' approach distance was measured from their last significant change in travel direction until the moment they entered the tree's maximum detection field. We found that chimpanzees travelled longer distances to trees at which they had previously made food grunts and had rejected fewer fruits compared to other trees. In addition, the results suggest that the chimpanzees were able to anticipate the amount of fruit that they would find in the trees. Overall, our findings are consistent with the hypothesis that chimpanzees act upon a retrieved memory of their last feeding experiences long before they revisit feeding trees, which would indicate a daily use of long-term prospective memory. Further, the results are consistent with the possibility that positive emotional experiences help to trigger prospective memory retrieval in forest areas that are further away and have fewer cues associated with revisited feeding trees.

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.

PubMed

Sayyari, Erfan; Mirarab, Siavash

2016-11-11

Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves. We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times.

Using traveling salesman problem algorithms for evolutionary tree construction.

PubMed

Korostensky, C; Gonnet, G H

2000-07-01

The construction of evolutionary trees is one of the major problems in computational biology, mainly due to its complexity. We present a new tree construction method that constructs a tree with minimum score for a given set of sequences, where the score is the amount of evolution measured in PAM distances. To do this, the problem of tree construction is reduced to the Traveling Salesman Problem (TSP). The input for the TSP algorithm are the pairwise distances of the sequences and the output is a circular tour through the optimal, unknown tree plus the minimum score of the tree. The circular order and the score can be used to construct the topology of the optimal tree. Our method can be used for any scoring function that correlates to the amount of changes along the branches of an evolutionary tree, for instance it could also be used for parsimony scores, but it cannot be used for least squares fit of distances. A TSP solution reduces the space of all possible trees to 2n. Using this order, we can guarantee that we reconstruct a correct evolutionary tree if the absolute value of the error for each distance measurement is smaller than f2.gif" BORDER="0">, where f3.gif" BORDER="0">is the length of the shortest edge in the tree. For data sets with large errors, a dynamic programming approach is used to reconstruct the tree. Finally simulations and experiments with real data are shown.

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

Extremal values on Zagreb indices of trees with given distance k-domination number.

PubMed

Pei, Lidan; Pan, Xiangfeng

2018-01-01

Let [Formula: see text] be a graph. A set [Formula: see text] is a distance k -dominating set of G if for every vertex [Formula: see text], [Formula: see text] for some vertex [Formula: see text], where k is a positive integer. The distance k -domination number [Formula: see text] of G is the minimum cardinality among all distance k -dominating sets of G . The first Zagreb index of G is defined as [Formula: see text] and the second Zagreb index of G is [Formula: see text]. In this paper, we obtain the upper bounds for the Zagreb indices of n -vertex trees with given distance k -domination number and characterize the extremal trees, which generalize the results of Borovićanin and Furtula (Appl. Math. Comput. 276:208-218, 2016). What is worth mentioning, for an n -vertex tree T , is that a sharp upper bound on the distance k -domination number [Formula: see text] is determined.

AceTree: a major update and case study in the long term maintenance of open-source scientific software.

PubMed

Katzman, Braden; Tang, Doris; Santella, Anthony; Bao, Zhirong

2018-04-04

AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software. Large scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration. By responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.

The Kirchhoff Index of Quasi-Tree Graphs

NASA Astrophysics Data System (ADS)

Xu, Kexiang; Liu, Hongshuang; Das, Kinkar Ch.

2015-03-01

Resistance distance was introduced by Klein and Randić as a generalisation of the classical distance. The Kirchhoff index Kf(G) of a graph G is the sum of resistance distances between all unordered pairs of vertices. In this article we characterise the extremal graphs with the maximal Kirchhoff index among all non-trivial quasi-tree graphs of order n. Moreover, we obtain a lower bound on the Kirchhoff index for all non-trivial quasi-tree graphs of order n.

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing.

PubMed

Zhang, Rui; Deng, Patricia; Jacobson, Dionna; Li, Jin Billy

2017-02-01

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3'UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3'UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions.

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

PubMed Central

Jacobson, Dionna

2017-01-01

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3’UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3’UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions. PMID:28166241

Occurrence of plastid RNA editing in all major lineages of land plants

PubMed Central

Freyer, Regina; Kiefer-Meyer, Marie-Christine; Kössel, Hans

1997-01-01

RNA editing changes posttranscriptionally single nucleotides in chloroplast-encoded transcripts. Although much work has been done on mechanistic and functional aspects of plastid editing, little is known about evolutionary aspects of this RNA processing step. To gain a better understanding of the evolution of RNA editing in plastids, we have investigated the editing patterns in ndhB and rbcL transcripts from various species comprising all major groups of land plants. Our results indicate that RNA editing occurs in plastids of bryophytes, fern allies, true ferns, gymnosperms, and angiosperms. Both editing frequencies and editing patterns show a remarkable degree of interspecies variation. Furthermore, we have found that neither plastid editing frequencies nor the editing pattern of a specific transcript correlate with the phylogenetic tree of the plant kingdom. The poor evolutionary conservation of editing sites among closely related species as well as the occurrence of single species-specific editing sites suggest that the differences in the editing patterns and editing frequencies are probably due both to independent loss and to gain of editing sites. In addition, our results indicate that RNA editing is a relatively ancient process that probably predates the evolution of land plants. This supposition is in good agreement with the phylogenetic data obtained for plant mitochondrial RNA editing, thus providing additional evidence for common evolutionary roots of the two plant organellar editing systems. PMID:9177209

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

PubMed

Chaudhary, Ruchi; Fernández-Baca, David; Burleigh, John Gordon

2015-02-01

MulRF is a platform-independent software package for phylogenetic analysis using multi-copy gene trees. It seeks the species tree that minimizes the Robinson-Foulds (RF) distance to the input trees using a generalization of the RF distance to multi-labeled trees. The underlying generic tree distance measure and fast running time make MulRF useful for inferring phylogenies from large collections of gene trees, in which multiple evolutionary processes as well as phylogenetic error may contribute to gene tree discord. MulRF implements several features for customizing the species tree search and assessing the results, and it provides a user-friendly graphical user interface (GUI) with tree visualization. The species tree search is implemented in C++ and the GUI in Java Swing. MulRF's executable as well as sample datasets and manual are available at http://genome.cs.iastate.edu/CBL/MulRF/, and the source code is available at https://github.com/ruchiherself/MulRFRepo. ruchic@ufl.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Audiences and Providers of Distance Education

ERIC Educational Resources Information Center

Nazarinia Roy, R. Roudi; Schumm, Walter R.

2011-01-01

As noted by Moore (2007, xxiii), the fifth section of the second edition of the "Handbook of Distance Education" focused on "some of the main consumers and suppliers of distance education programs," including elementary and secondary education, community colleges, universities, the corporate sector, continuing professional…

[Prediction of regional soil quality based on mutual information theory integrated with decision tree algorithm].

PubMed

Lin, Fen-Fang; Wang, Ke; Yang, Ning; Yan, Shi-Guang; Zheng, Xin-Yu

2012-02-01

In this paper, some main factors such as soil type, land use pattern, lithology type, topography, road, and industry type that affect soil quality were used to precisely obtain the spatial distribution characteristics of regional soil quality, mutual information theory was adopted to select the main environmental factors, and decision tree algorithm See 5.0 was applied to predict the grade of regional soil quality. The main factors affecting regional soil quality were soil type, land use, lithology type, distance to town, distance to water area, altitude, distance to road, and distance to industrial land. The prediction accuracy of the decision tree model with the variables selected by mutual information was obviously higher than that of the model with all variables, and, for the former model, whether of decision tree or of decision rule, its prediction accuracy was all higher than 80%. Based on the continuous and categorical data, the method of mutual information theory integrated with decision tree could not only reduce the number of input parameters for decision tree algorithm, but also predict and assess regional soil quality effectively.

High-resolution tree canopy mapping for New York City using LIDAR and object-based image analysis

NASA Astrophysics Data System (ADS)

MacFaden, Sean W.; O'Neil-Dunne, Jarlath P. M.; Royar, Anna R.; Lu, Jacqueline W. T.; Rundle, Andrew G.

2012-01-01

Urban tree canopy is widely believed to have myriad environmental, social, and human-health benefits, but a lack of precise canopy estimates has hindered quantification of these benefits in many municipalities. This problem was addressed for New York City using object-based image analysis (OBIA) to develop a comprehensive land-cover map, including tree canopy to the scale of individual trees. Mapping was performed using a rule-based expert system that relied primarily on high-resolution LIDAR, specifically its capacity for evaluating the height and texture of aboveground features. Multispectral imagery was also used, but shadowing and varying temporal conditions limited its utility. Contextual analysis was a key part of classification, distinguishing trees according to their physical and spectral properties as well as their relationships to adjacent, nonvegetated features. The automated product was extensively reviewed and edited via manual interpretation, and overall per-pixel accuracy of the final map was 96%. Although manual editing had only a marginal effect on accuracy despite requiring a majority of project effort, it maximized aesthetic quality and ensured the capture of small, isolated trees. Converting high-resolution LIDAR and imagery into usable information is a nontrivial exercise, requiring significant processing time and labor, but an expert system-based combination of OBIA and manual review was an effective method for fine-scale canopy mapping in a complex urban environment.

[Phylogenetic analysis of CO I gene of Oncomelania snails from project of afforestation for schistosomiasis control in marshland endemic regions].

PubMed

Xu, Yu-Mei; Zhang, Shi-Qing; Zhu, Chuan-Gang

2012-04-01

To investigate the genetic difference of cytochrome oxidase I (CO I ) of Oncomelania snails from the project of afforestation for schistosomiasis control in marshland regions, so as to explore the effects of different ecological environments. The snails were collected from 3 different areas, Anqing, Tongling, Wuwei, i.e. the upstream, midstream and downstream regions along the Yangtz River in Anhui Province. Genomic DNA was extracted from the snails, and CO I gene fragments were amplified by PCR, then purified and sequenced. The sequences were edited by using Blast. The CO I genes of O. h. minima and Biomphalaria glabrata were used as the reference of exogenous gene. The genetic distances of the various regions were calculated by the Kimura method and phylogenetic trees were constructed with UPGMA and the NJ method of MEGA (3.1) software. The amplified CO I gene of the snail was a fragment about 700 bp including 2 primers in length. There were little genetic diversity among the different areas, the identities were higher than or equal to 98%. The genetic distances indicated that the distance between the projects of afforestation and woodland in Anqing was 0.003, while Tongling was 0.019, Wuwei was 0.007. The distances among the three projects of afforestation were 0.003-0.012. The two phylogenetic trees were constructed by the methods of UPGMA and NJ respectively, which took on very similar topo-structure in which isolates of Biomphalaria glabrata located in one clade and all the others in the other one. In the other one clade, O. H. minima located in one clade. There was little genetic diversity among Anqing, Tongling, Wuwei clusters. The afforestations of Anqing and Wuwei clustered into one group, while the woodlands of Anqing and Wuwei appeared as another group. There is a little genetic diversity of the snail cytochrome oxidase I (CO I ) in different ecological environments among the upstream, midstream and downstream regions along the Yangtz River in Anhui Province.

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees.

PubMed

Zhang, Huangkai; Gao, Shenghan; Lercher, Martin J; Hu, Songnian; Chen, Wei-Hua

2012-07-01

EvolView is a web application for visualizing, annotating and managing phylogenetic trees. First, EvolView is a phylogenetic tree viewer and customization tool; it visualizes trees in various formats, customizes them through built-in functions that can link information from external datasets, and exports the customized results to publication-ready figures. Second, EvolView is a tree and dataset management tool: users can easily organize related trees into distinct projects, add new datasets to trees and edit and manage existing trees and datasets. To make EvolView easy to use, it is equipped with an intuitive user interface. With a free account, users can save data and manipulations on the EvolView server. EvolView is freely available at: http://www.evolgenius.info/evolview.html.

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

PubMed Central

Zhang, Huangkai; Gao, Shenghan; Lercher, Martin J.; Hu, Songnian; Chen, Wei-Hua

2012-01-01

EvolView is a web application for visualizing, annotating and managing phylogenetic trees. First, EvolView is a phylogenetic tree viewer and customization tool; it visualizes trees in various formats, customizes them through built-in functions that can link information from external datasets, and exports the customized results to publication-ready figures. Second, EvolView is a tree and dataset management tool: users can easily organize related trees into distinct projects, add new datasets to trees and edit and manage existing trees and datasets. To make EvolView easy to use, it is equipped with an intuitive user interface. With a free account, users can save data and manipulations on the EvolView server. EvolView is freely available at: http://www.evolgenius.info/evolview.html. PMID:22695796

Minimum triplet covers of binary phylogenetic X-trees.

PubMed

Huber, K T; Moulton, V; Steel, M

2017-12-01

Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed from the distances between the leaves (when the edges are given any strictly positive lengths). Moreover, a linear number of these pairwise distance values suffices to determine both the tree and its edge lengths. A natural set of pairs of leaves is provided by any 'triplet cover' of the tree (based on the fact that each non-leaf vertex is the median vertex of three leaves). In this paper we describe a number of new results concerning triplet covers of minimum size. In particular, we characterize such covers in terms of an associated graph being a 2-tree. Also, we show that minimum triplet covers are 'shellable' and thereby provide a set of pairs for which the inter-leaf distance values will uniquely determine the underlying tree and its associated branch lengths.

Field efficiency and bias of snag inventory methods

Treesearch

Robert S. Kenning; Mark J. Ducey; John C. Brissette; Jeffery H. Gove

2005-01-01

Snags and cavity trees are important components of forests, but can be difficult to inventory precisely and are not always included in inventories because of limited resources. We tested the application of N-tree distance sampling as a time-saving snag sampling method and compared N-tree distance sampling to fixed-area sampling and modified horizontal line sampling in...

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

PubMed

Puigbò, Pere; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."

Seeing the Forest for the Trees: Prevalence of Low Scores on the Wechsler Intelligence Scale for Children, Fourth Edition (WISC-IV)

ERIC Educational Resources Information Center

Brooks, Brian L.

2010-01-01

Low scores across a battery of tests are common in healthy people and vary by demographic characteristics. The purpose of the present article was to present the base rates of low scores for the Wechsler Intelligence Scale for Children, fourth edition (WISC-IV; D. Wechsler, 2003). Participants included 2,200 children and adolescents between 6 and…

Distance Education and Training Council Constitution and Bylaws. 2012 Edition

ERIC Educational Resources Information Center

Distance Education and Training Council, 2012

2012-01-01

The mission of the Distance Education and Training Council (hereinafter referred to as the Council or DETC) is to promote, by means of standard-setting, evaluation, and consultation processes, the development and maintenance of high educational and ethical standards in education and training programs delivered through distance learning. The…

New methods, algorithms, and software for rapid mapping of tree positions in coordinate forest plots

Treesearch

A. Dan Wilson

2000-01-01

The theories and methodologies for two new tree mapping methods, the Sequential-target method and the Plot-origin radial method, are described. The methods accommodate the use of any conventional distance measuring device and compass to collect horizontal distance and azimuth data between source or reference positions (origins) and target trees. Conversion equations...

Testing Accuracy of Long-Range Ultrasonic Sensors for Olive Tree Canopy Measurements

PubMed Central

Gamarra-Diezma, Juan Luis; Miranda-Fuentes, Antonio; Llorens, Jordi; Cuenca, Andrés; Blanco-Roldán, Gregorio L.; Rodríguez-Lizana, Antonio

2015-01-01

Ultrasonic sensors are often used to adjust spray volume by allowing the calculation of the crown volume of tree crops. The special conditions of the olive tree require the use of long-range sensors, which are less accurate and faster than the most commonly used sensors. The main objectives of the study were to determine the suitability of the sensor in terms of sound cone determination, angle errors, crosstalk errors and field measurements. Different laboratory tests were performed to check the suitability of a commercial long-range ultrasonic sensor, as were the experimental determination of the sound cone diameter at several distances for several target materials, the determination of the influence of the angle of incidence of the sound wave on the target and distance on the accuracy of measurements for several materials and the determination of the importance of the errors due to interference between sensors for different sensor spacings and distances for two different materials. Furthermore, sensor accuracy was tested under real field conditions. The results show that the studied sensor is appropriate for olive trees because the sound cone is narrower for an olive tree than for the other studied materials, the olive tree canopy does not have a large influence on the sensor accuracy with respect to distance and angle, the interference errors are insignificant for high sensor spacings and the sensor's field distance measurements were deemed sufficiently accurate. PMID:25635414

The effect of different distance measures in detecting outliers using clustering-based algorithm for circular regression model

NASA Astrophysics Data System (ADS)

Di, Nur Faraidah Muhammad; Satari, Siti Zanariah

2017-05-01

Outlier detection in linear data sets has been done vigorously but only a small amount of work has been done for outlier detection in circular data. In this study, we proposed multiple outliers detection in circular regression models based on the clustering algorithm. Clustering technique basically utilizes distance measure to define distance between various data points. Here, we introduce the similarity distance based on Euclidean distance for circular model and obtain a cluster tree using the single linkage clustering algorithm. Then, a stopping rule for the cluster tree based on the mean direction and circular standard deviation of the tree height is proposed. We classify the cluster group that exceeds the stopping rule as potential outlier. Our aim is to demonstrate the effectiveness of proposed algorithms with the similarity distances in detecting the outliers. It is found that the proposed methods are performed well and applicable for circular regression model.

Spray deposition from ground-based applications of carbaryl to protect individual trees from bark beetle attack.

PubMed

Fettig, Christopher J; Munson, A Steven; McKelvey, Stephen R; Bush, Parshall B; Borys, Robert R

2008-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) are recognized as the most important tree mortality agent in western coniferous forests. A common method of protecting trees from bark beetle attack is to saturate the tree bole with carbaryl (1-naphthyl methylcarbamate) using a hydraulic sprayer. In this study, we evaluate the amount of carbaryl drift (ground deposition) occurring at four distances from the tree bole (7.6, 15.2, 22.9, and 38.1 m) during conventional spray applications for protecting individual lodgepole pine (Pinus contorta Dougl. ex Loud.) from mountain pine beetle (Dendroctonus ponderosae Hopkins) attack and Engelmann spruce (Picea engelmannii Parry ex Engelm.) from spruce beetle (D. rufipennis [Kirby]) attack. Mean deposition (carbaryl + alpha-naphthol) did not differ significantly among treatments (nozzle orifices) at any distance from the tree bole. Values ranged from 0.04 +/- 0.02 mg carbaryl m(-2) at 38.1 m to 13.30 +/- 2.54 mg carbaryl m(-2) at 7.6 m. Overall, distance from the tree bole significantly affected the amount of deposition. Deposition was greatest 7.6 m from the tree bole and quickly declined as distance from the tree bole increased. Approximately 97% of total spray deposition occurred within 15.2 m of the tree bole. Application efficiency (i.e., percentage of insecticide applied that is retained on trees) ranged from 80.9 to 87.2%. Based on review of the literature, this amount of drift poses little threat to adjacent aquatic environments. No-spray buffers of 7.6 m should be sufficient to protect freshwater fish, amphibians, crustaceans, bivalves, and most aquatic insects. Buffers >22.9 m appear sufficient to protect the most sensitive aquatic insects (Plecoptera).

GENOME-WIDE COMPARATIVE ANALYSIS OF PHYLOGENETIC TREES: THE PROKARYOTIC FOREST OF LIFE

PubMed Central

Puigbò, Pere; Wolf, Yuri I.; Koonin, Eugene V.

2013-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the applications methods used to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a ‘species tree’. PMID:22399455

Natural migration rates of trees: Global terrestrial carbon cycle implications. Book chapter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solomon, A.M.

The paper discusses the forest-ecological processes which constrain the rate of response by forests to rapid future environmental change. It establishes a minimum response time by natural tree populations which invade alien landscapes and reach the status of a mature, closed canopy forest when maximum carbon storage is realized. It considers rare long-distance and frequent short-distance seed transport, seedling and tree establishment, sequential tree and stand maturation, and spread between newly established colonies.

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

PubMed

Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

2014-10-01

One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Distance-Based Phylogenetic Methods Around a Polytomy.

PubMed

Davidson, Ruth; Sullivant, Seth

2014-01-01

Distance-based phylogenetic algorithms attempt to solve the NP-hard least-squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean space properly containing the space of all tree metrics as a polyhedral fan. Outputs of distance-based tree reconstruction algorithms such as UPGMA and neighbor-joining are points in the maximal cones in the fan. Tree metrics with polytomies lie at the intersections of maximal cones. A phylogenetic algorithm divides the space of all dissimilarity maps into regions based upon which combinatorial tree is reconstructed by the algorithm. Comparison of phylogenetic methods can be done by comparing the geometry of these regions. We use polyhedral geometry to compare the local nature of the subdivisions induced by least-squares phylogeny, UPGMA, and neighbor-joining when the true tree has a single polytomy with exactly four neighbors. Our results suggest that in some circumstances, UPGMA and neighbor-joining poorly match least-squares phylogeny.

Probability of Damage to Sidewalks and Curbs by Street Trees in the Tropics

Treesearch

John K. Francis; Bernard R. Parresol; Juana Marin de Patino

1996-01-01

For 75 trees each of 12 species growing along streets in San Juan, Puerto Rico and Merida, Mexico, diameter at breast height and distance to sidewalk or curb was measured and damage (cracking or raising) was evaluated. Logistic analysis was used to construct a model to predict probability of damage to sidewalk or curb. Distance to the pavement, diameter of the tree,...

Approximate string matching algorithms for limited-vocabulary OCR output correction

NASA Astrophysics Data System (ADS)

Lasko, Thomas A.; Hauser, Susan E.

2000-12-01

Five methods for matching words mistranslated by optical character recognition to their most likely match in a reference dictionary were tested on data from the archives of the National Library of Medicine. The methods, including an adaptation of the cross correlation algorithm, the generic edit distance algorithm, the edit distance algorithm with a probabilistic substitution matrix, Bayesian analysis, and Bayesian analysis on an actively thinned reference dictionary were implemented and their accuracy rates compared. Of the five, the Bayesian algorithm produced the most correct matches (87%), and had the advantage of producing scores that have a useful and practical interpretation.

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

PubMed Central

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

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

PubMed

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

2012-04-01

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. © 2012 Blackwell Publishing Ltd/CNRS.

Integrating information about location and value of resources by white-faced saki monkeys (Pithecia pithecia).

PubMed

Cunningham, Elena; Janson, Charles

2007-07-01

Most studies of spatial memory in primates focus on species that inhabit large home ranges and have dispersed, patchy resources. Researchers assume that primates use memory to minimize distances traveled between resources. We investigated the use of spatial memory in a group of six white-faced sakis (Pithecia pithecia) on 12.8-ha Round Island, Guri Lake, Venezuela during a period of fruit abundance. The sakis' movements were analyzed with logistic regressions, a predictive computer model and a computer model that simulates movements. We considered all the resources available to the sakis and compared observed distances to predicted distances from a computer model for foragers who know nothing about the location of resources. Surprisingly, the observed distances were four times greater than the predicted distances, suggesting that the sakis passed by a majority of the available fruit trees without feeding. The odds of visiting a food tree, however, were significantly increased if the tree had been visited in the previous 3 days and had more than 100 fruit. The sakis' preferred resources were highly productive fruit trees, Capparis trees, and trees with water holes. They traveled efficiently to these sites. The sakis choice of feeding sites indicate that they combined knowledge acquired by repeatedly traveling through their home range with 'what' and 'where' information gained from individual visits to resources. Although the sakis' foraging choices increased the distance they traveled overall, choosing more valued sites allowed the group to minimize intra-group feeding competition, maintain intergroup dominance over important resources, and monitor the state of resources throughout their home range. The sakis' foraging decisions appear to have used spatial memory, elements of episodic-like memory and social and nutritional considerations.

ColorTree: a batch customization tool for phylogenic trees

PubMed Central

Chen, Wei-Hua; Lercher, Martin J

2009-01-01

Background Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. Findings In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. Conclusion ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files. PMID:19646243

ColorTree: a batch customization tool for phylogenic trees.

PubMed

Chen, Wei-Hua; Lercher, Martin J

2009-07-31

Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.

Answer Markup Algorithms for Southeast Asian Languages.

ERIC Educational Resources Information Center

Henry, George M.

1991-01-01

Typical markup methods for providing feedback to foreign language learners are not applicable to languages not written in a strictly linear fashion. A modification of Hart's edit markup software is described, along with a second variation based on a simple edit distance algorithm adapted to a general Southeast Asian font system. (10 references)…

Species divergence and phylogenetic variation of ecophysiological traits in lianas and trees.

PubMed

Rios, Rodrigo S; Salgado-Luarte, Cristian; Gianoli, Ernesto

2014-01-01

The climbing habit is an evolutionary key innovation in plants because it is associated with enhanced clade diversification. We tested whether patterns of species divergence and variation of three ecophysiological traits that are fundamental for plant adaptation to light environments (maximum photosynthetic rate [A(max)], dark respiration rate [R(d)], and specific leaf area [SLA]) are consistent with this key innovation. Using data reported from four tropical forests and three temperate forests, we compared phylogenetic distance among species as well as the evolutionary rate, phylogenetic distance and phylogenetic signal of those traits in lianas and trees. Estimates of evolutionary rates showed that R(d) evolved faster in lianas, while SLA evolved faster in trees. The mean phylogenetic distance was 1.2 times greater among liana species than among tree species. Likewise, estimates of phylogenetic distance indicated that lianas were less related than by chance alone (phylogenetic evenness across 63 species), and trees were more related than expected by chance (phylogenetic clustering across 71 species). Lianas showed evenness for R(d), while trees showed phylogenetic clustering for this trait. In contrast, for SLA, lianas exhibited phylogenetic clustering and trees showed phylogenetic evenness. Lianas and trees showed patterns of ecophysiological trait variation among species that were independent of phylogenetic relatedness. We found support for the expected pattern of greater species divergence in lianas, but did not find consistent patterns regarding ecophysiological trait evolution and divergence. R(d) followed the species-level pattern, i.e., greater divergence/evolution in lianas compared to trees, while the opposite occurred for SLA and no pattern was detected for A(max). R(d) may have driven lianas' divergence across forest environments, and might contribute to diversification in climber clades.

Species Divergence and Phylogenetic Variation of Ecophysiological Traits in Lianas and Trees

PubMed Central

Rios, Rodrigo S.; Salgado-Luarte, Cristian; Gianoli, Ernesto

2014-01-01

The climbing habit is an evolutionary key innovation in plants because it is associated with enhanced clade diversification. We tested whether patterns of species divergence and variation of three ecophysiological traits that are fundamental for plant adaptation to light environments (maximum photosynthetic rate [Amax], dark respiration rate [Rd], and specific leaf area [SLA]) are consistent with this key innovation. Using data reported from four tropical forests and three temperate forests, we compared phylogenetic distance among species as well as the evolutionary rate, phylogenetic distance and phylogenetic signal of those traits in lianas and trees. Estimates of evolutionary rates showed that Rd evolved faster in lianas, while SLA evolved faster in trees. The mean phylogenetic distance was 1.2 times greater among liana species than among tree species. Likewise, estimates of phylogenetic distance indicated that lianas were less related than by chance alone (phylogenetic evenness across 63 species), and trees were more related than expected by chance (phylogenetic clustering across 71 species). Lianas showed evenness for Rd, while trees showed phylogenetic clustering for this trait. In contrast, for SLA, lianas exhibited phylogenetic clustering and trees showed phylogenetic evenness. Lianas and trees showed patterns of ecophysiological trait variation among species that were independent of phylogenetic relatedness. We found support for the expected pattern of greater species divergence in lianas, but did not find consistent patterns regarding ecophysiological trait evolution and divergence. Rd followed the species-level pattern, i.e., greater divergence/evolution in lianas compared to trees, while the opposite occurred for SLA and no pattern was detected for Amax. Rd may have driven lianas' divergence across forest environments, and might contribute to diversification in climber clades. PMID:24914958

Software Reviews.

ERIC Educational Resources Information Center

Classroom Computer Learning, 1990

1990-01-01

Reviewed are three computer software packages including "Martin Luther King, Jr.: Instant Replay of History,""Weeds to Trees," and "The New Print Shop, School Edition." Discussed are hardware requirements, costs, grade levels, availability, emphasis, strengths, and weaknesses. (CW)

RNA editing in bryophytes and a molecular phylogeny of land plants.

PubMed Central

Malek, O; Lättig, K; Hiesel, R; Brennicke, A; Knoop, V

1996-01-01

RNA editing has been observed to date in all groups of vascular plants, but not in bryophytes. Its occurrence was therefore assumed to correlate with the evolution of tracheophytes. To gain more insight into both the phylogeny of early land plants and the evolution of mitochondrial RNA editing we have investigated a number of vascular and non-vascular plant species. Contrary to the belief that editing is absent from bryophytes, here we report mitochondrial RNA editing in cox3 mRNA of the liverwort Pellia epiphylla, the mosses Tetraphis pellucida and Ceratodon purpureus and the hornwort Anthroceros crispulus. RNA editing in plants consequently predates the evolution of tracheophytes. Editing is also found in the eusporangiate ferns Ophioglossum petiolatum and Angiopteris palmiformis, the whisk fern Tmesipteris elongata and the gnetopsid Ephedra gerardiana, but was not detected in Gnetum gnemon.cox3 mRNA of the lycopsid Isoetes lacustris shows the highest frequency of RNA editing ever observed in a plant, with 39% of all cytidine residues converted to uridines. The frequency of RNA editing correlates with the genomic GC content rather than with the phylogenetic position of a species. Phylogenetic trees derived from the slowly evolving mitochondrial sequences find external support from the assessments of classical systematics. Images PMID:8635473

An Isometric Mapping Based Co-Location Decision Tree Algorithm

NASA Astrophysics Data System (ADS)

Zhou, G.; Wei, J.; Zhou, X.; Zhang, R.; Huang, W.; Sha, H.; Chen, J.

2018-05-01

Decision tree (DT) induction has been widely used in different pattern classification. However, most traditional DTs have the disadvantage that they consider only non-spatial attributes (ie, spectral information) as a result of classifying pixels, which can result in objects being misclassified. Therefore, some researchers have proposed a co-location decision tree (Cl-DT) method, which combines co-location and decision tree to solve the above the above-mentioned traditional decision tree problems. Cl-DT overcomes the shortcomings of the existing DT algorithms, which create a node for each value of a given attribute, which has a higher accuracy than the existing decision tree approach. However, for non-linearly distributed data instances, the euclidean distance between instances does not reflect the true positional relationship between them. In order to overcome these shortcomings, this paper proposes an isometric mapping method based on Cl-DT (called, (Isomap-based Cl-DT), which is a method that combines heterogeneous and Cl-DT together. Because isometric mapping methods use geodetic distances instead of Euclidean distances between non-linearly distributed instances, the true distance between instances can be reflected. The experimental results and several comparative analyzes show that: (1) The extraction method of exposed carbonate rocks is of high accuracy. (2) The proposed method has many advantages, because the total number of nodes, the number of leaf nodes and the number of nodes are greatly reduced compared to Cl-DT. Therefore, the Isomap -based Cl-DT algorithm can construct a more accurate and faster decision tree.

Woody climbers show greater population genetic differentiation than trees: Insights into the link between ecological traits and diversification.

PubMed

Gianoli, Ernesto; Torres-Díaz, Cristian; Ruiz, Eduardo; Salgado-Luarte, Cristian; Molina-Montenegro, Marco A; Saldaña, Alfredo; Ríos, Rodrigo S

2016-12-01

The climbing habit is a key innovation in plants: climbing taxa have higher species richness than nonclimbing sister groups. We evaluated the hypothesis that climbing plant species show greater among-population genetic differentiation than nonclimber species. We compared the among-population genetic distance in woody climbers (eight species, 30 populations) and trees (seven species, 29 populations) coexisting in nine communities in a temperate rainforest. We also compared within-population genetic diversity in co-occurring woody climbers and trees in two communities. Mean genetic distance between populations of climbers was twice that of trees. Isolation by distance (increase in genetic distance with geographic distance) was greater for climbers. Climbers and trees showed similar within-population genetic diversity. Our longevity estimate suggested that climbers had shorter generation times, while other biological features often associated with diversification (dispersal and pollination syndromes, mating system, size, and metabolic rate) did not show significant differences between groups. We hypothesize that the greater population differentiation in climbers could result from greater evolutionary responses to local selection acting on initially higher within-population genetic diversity, which could be driven by neutral processes associated with shorter generation times. Increased population genetic differentiation could be incorporated as another line of evidence when testing for key innovations. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Five-year radial growth of red oaks in mixed bottomland hardwood stands

Treesearch

Luben D. Dimov; Jim L. Chambers; Brian Roy Lockhart

2008-01-01

We studied the relationships among 5-year radial (diameter and basal area) growth of red oak (genus Quercus, subgenus Erythrobalanus) crop trees and predictor variables representing individual tree vigor, distance-dependant competition measures, and distance-independent competition measures. The red oaks we examined are...

Mason’s equation application for prediction of voltage of oil shale treeing breakdown

NASA Astrophysics Data System (ADS)

Martemyanov, S. M.

2017-05-01

The application of the formula, which is used to calculate the maximum field at the tip of the pin-plane electrode system was proposed to describe the process of electrical treeing and treeing breakdown in an oil shale. An analytical expression for the calculation of the treeing breakdown voltage in the oil shale, as a function of the inter-electrode distance, was taken. A high accuracy of the correspondence of the model to the experimental data in the range of inter-electrode distances from 0.03 to 0.5 m was taken.

Efficient algorithms for fast integration on large data sets from multiple sources.

PubMed

Mi, Tian; Rajasekaran, Sanguthevar; Aseltine, Robert

2012-06-28

Recent large scale deployments of health information technology have created opportunities for the integration of patient medical records with disparate public health, human service, and educational databases to provide comprehensive information related to health and development. Data integration techniques, which identify records belonging to the same individual that reside in multiple data sets, are essential to these efforts. Several algorithms have been proposed in the literatures that are adept in integrating records from two different datasets. Our algorithms are aimed at integrating multiple (in particular more than two) datasets efficiently. Hierarchical clustering based solutions are used to integrate multiple (in particular more than two) datasets. Edit distance is used as the basic distance calculation, while distance calculation of common input errors is also studied. Several techniques have been applied to improve the algorithms in terms of both time and space: 1) Partial Construction of the Dendrogram (PCD) that ignores the level above the threshold; 2) Ignoring the Dendrogram Structure (IDS); 3) Faster Computation of the Edit Distance (FCED) that predicts the distance with the threshold by upper bounds on edit distance; and 4) A pre-processing blocking phase that limits dynamic computation within each block. We have experimentally validated our algorithms on large simulated as well as real data. Accuracy and completeness are defined stringently to show the performance of our algorithms. In addition, we employ a four-category analysis. Comparison with FEBRL shows the robustness of our approach. In the experiments we conducted, the accuracy we observed exceeded 90% for the simulated data in most cases. 97.7% and 98.1% accuracy were achieved for the constant and proportional threshold, respectively, in a real dataset of 1,083,878 records.

Effects of competitor spacing in a new class of individual-tree indices of competition: semidistance-independent indices computed for Bitterlich versus fixed-area plots

Treesearch

Albert R. Stage; Thomas Ledermann

2008-01-01

We illustrate effects of competitor spacing for a new class of individual-tree indices of competition that we call semi-distance-independent. This new class is similar to the class of distance-independent indices except that the index is computed independently at each subsampling plot surrounding a subject tree for which growth is to be modelled. We derive the effects...

Performance analysis of a dual-tree algorithm for computing spatial distance histograms

PubMed Central

Chen, Shaoping; Tu, Yi-Cheng; Xia, Yuni

2011-01-01

Many scientific and engineering fields produce large volume of spatiotemporal data. The storage, retrieval, and analysis of such data impose great challenges to database systems design. Analysis of scientific spatiotemporal data often involves computing functions of all point-to-point interactions. One such analytics, the Spatial Distance Histogram (SDH), is of vital importance to scientific discovery. Recently, algorithms for efficient SDH processing in large-scale scientific databases have been proposed. These algorithms adopt a recursive tree-traversing strategy to process point-to-point distances in the visited tree nodes in batches, thus require less time when compared to the brute-force approach where all pairwise distances have to be computed. Despite the promising experimental results, the complexity of such algorithms has not been thoroughly studied. In this paper, we present an analysis of such algorithms based on a geometric modeling approach. The main technique is to transform the analysis of point counts into a problem of quantifying the area of regions where pairwise distances can be processed in batches by the algorithm. From the analysis, we conclude that the number of pairwise distances that are left to be processed decreases exponentially with more levels of the tree visited. This leads to the proof of a time complexity lower than the quadratic time needed for a brute-force algorithm and builds the foundation for a constant-time approximate algorithm. Our model is also general in that it works for a wide range of point spatial distributions, histogram types, and space-partitioning options in building the tree. PMID:21804753

Occasional Papers in Distance Education: Number 12, Charles Sturt University.

ERIC Educational Resources Information Center

Donnan, Peter, Ed.

The five papers in this edition address issues of general interest in distance education. In the first paper, "Study Methods and Study Notes: Interim Report," Stephen Relf and Terry Geddes report on a study designed to identify patterns of use and trends in the ways in which distance students use their study notes. In the second paper,…

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.

PubMed

Junier, Thomas; Zdobnov, Evgeny M

2010-07-01

We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes. C source code, Python bindings and executables for various platforms are available from http://cegg.unige.ch/newick_utils. The distribution includes a manual and example data. The package is distributed under the BSD License. thomas.junier@unige.ch

Soil-borne pathogens restrict the recruitment of a subtropical tree: a distance-dependent effect.

PubMed

Xu, Meng; Wang, Yongfan; Liu, Yu; Zhang, Zhiming; Yu, Shixiao

2015-03-01

The Janzen-Connell hypothesis suggests that density- and/or distance-dependent juvenile mortality driven by host-specific natural enemies can explain high species diversity in tropical forests. However, such density and distance effects may not occur simultaneously and may not be driven by the same mechanism. Also, reports of attempts to identify and quantify the differences between these processes in tropical forests are scarce. In a primary subtropical forest in China, we (1) experimentally examined the relative influence of the distance to parent trees vs. conspecific seedling density on mortality patterns in Engelhardia fenzelii, (2) tested the role of soil-borne pathogens in driving density- or distance-dependent processes that cause seedling mortality, and (3) inspected the susceptibilities of different tree species to soil biota of E. fenzelii and the effects of soil biota from different tree species on E. fenzelii. The results from these field experiments showed that distance- rather than density-dependent processes driven by soil pathogens strongly affect the seedling survival of this species in its first year. We also observed increased survival of a fungicide treatment for E. fenzelii seedlings in the parent soil but not for the seedlings of the other three species in the E. fenzelii parent soil, or for E. fenzelii seedlings in the parent soil of three other species. This study illustrates how the distance-dependent pattern of seedling recruitment for this species is driven by soil pathogens, a mechanism that likely restricts the dominance of this abundant species.

Private genome analysis through homomorphic encryption

PubMed Central

2015-01-01

Background The rapid development of genome sequencing technology allows researchers to access large genome datasets. However, outsourcing the data processing o the cloud poses high risks for personal privacy. The aim of this paper is to give a practical solution for this problem using homomorphic encryption. In our approach, all the computations can be performed in an untrusted cloud without requiring the decryption key or any interaction with the data owner, which preserves the privacy of genome data. Methods We present evaluation algorithms for secure computation of the minor allele frequencies and χ2 statistic in a genome-wide association studies setting. We also describe how to privately compute the Hamming distance and approximate Edit distance between encrypted DNA sequences. Finally, we compare performance details of using two practical homomorphic encryption schemes - the BGV scheme by Gentry, Halevi and Smart and the YASHE scheme by Bos, Lauter, Loftus and Naehrig. Results The approach with the YASHE scheme analyzes data from 400 people within about 2 seconds and picks a variant associated with disease from 311 spots. For another task, using the BGV scheme, it took about 65 seconds to securely compute the approximate Edit distance for DNA sequences of size 5K and figure out the differences between them. Conclusions The performance numbers for BGV are better than YASHE when homomorphically evaluating deep circuits (like the Hamming distance algorithm or approximate Edit distance algorithm). On the other hand, it is more efficient to use the YASHE scheme for a low-degree computation, such as minor allele frequencies or χ2 test statistic in a case-control study. PMID:26733152

T-RMSD: a web server for automated fine-grained protein structural classification.

PubMed

Magis, Cedrik; Di Tommaso, Paolo; Notredame, Cedric

2013-07-01

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd.

T-RMSD: a web server for automated fine-grained protein structural classification

PubMed Central

Magis, Cedrik; Di Tommaso, Paolo; Notredame, Cedric

2013-01-01

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd. PMID:23716642

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions.

PubMed

Bogdanowicz, Damian; Giaro, Krzysztof

2017-05-01

Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance. In this article, we define a new metric for rooted trees-the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events.

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers.

PubMed

Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters' approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.

Spatial patterns of a tropical tree species growing under an eucalyptus plantation in South-East Brazil.

PubMed

Higuchi, P; Silva, A C; Louzada, J N C; Machado, E L M

2010-05-01

The objectives of this study were to evaluate the influence of propagules source and the implication of tree size class on the spatial pattern of Xylopia brasiliensis Spreng. individuals growing under the canopy of an experimental plantation of eucalyptus. To this end, all individuals of Xylopia brasiliensis with diameter at soil height (dsh) > 1 cm were mapped in the understory of a 3.16 ha Eucalyptus spp. and Corymbia spp. plantation, located in the municipality of Lavras, SE Brazil. The largest nearby mature tree of X. brasiliensis was considered as the propagules source. Linear regressions were used to assess the influence of the distance of propagules source on the population parameters (density, basal area and height). The spatial pattern of trees was assessed through the Ripley K function. The overall pattern showed that the propagules source distance had strong influence over spatial distribution of trees, mainly the small ones, indicating that the closer the distance from the propagules source, the higher the tree density and the lower the mean tree height. The population showed different spatial distribution patterns according to the spatial scale and diameter class considered. While small trees tended to be aggregated up to around 80 m, the largest individuals were randomly distributed in the area. A plausible explanation for observed patterns might be limited seed rain and intra-population competition.

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak.

PubMed

Pec, Gregory J; Karst, Justine; Taylor, D Lee; Cigan, Paul W; Erbilgin, Nadir; Cooke, Janice E K; Simard, Suzanne W; Cahill, James F

2017-01-01

Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Root density of cherry trees grafted on prunus mahaleb in a semi-arid region

NASA Astrophysics Data System (ADS)

Paltineanu, Cristian; Septar, Leinar; Gavat, Corina; Chitu, Emil; Oprita, Alexandru; Moale, Cristina; Lamureanu, Gheorghe; Vrinceanu, Andrei

2016-07-01

Root density was investigated using the trench method in a cherry (Prunus avium grafted on Prunus mahaleb) orchard with clean cultivation in inter-rows and in-row. Trenches of 1 m width and 1.2 m depth were dug up between neighbouring trees. The objectives of the paper were to clarify the spatial distribution of root density of cherry trees under the soil and climate conditions of the region to expand knowledge of optimum planting distance and orchard management for a broad area of chernozems. Some soil physical properties were significantly worsened in inter-rows versus in-row, mainly due to soil compaction, and there were higher root density values in in-row versus inter-rows. Root density decreased more intensely with soil depth than with distance from trees. The pattern of root density suggests that the cherry tree density and fruit yield could be increased. However, other factors concerning orchard management and fruit yield should also be considered. The results obtained have a potential impact to improve irrigation and fertilizer application by various methods, considering the soil depth and distance from trees to wet soil, in accordance with root development.

[Mahalanobis distance based hyperspectral characteristic discrimination of leaves of different desert tree species].

PubMed

Lin, Hai-jun; Zhang, Hui-fang; Gao, Ya-qi; Li, Xia; Yang, Fan; Zhou, Yan-fei

2014-12-01

The hyperspectral reflectance of Populus euphratica, Tamarix hispida, Haloxylon ammodendron and Calligonum mongolicum in the lower reaches of Tarim River and Turpan Desert Botanical Garden was measured by using the HR-768 field-portable spectroradiometer. The method of continuum removal, first derivative reflectance and second derivative reflectance were used to deal with the original spectral data of four tree species. The method of Mahalanobis Distance was used to select the bands with significant differences in the original spectral data and transform spectral data to identify the different tree species. The progressive discrimination analyses were used to test the selective bands used to identify different tree species. The results showed that The Mahalanobis Distance method was an effective method in feature band extraction. The bands for identifying different tree species were most near-infrared bands. The recognition accuracy of four methods was 85%, 93.8%, 92.4% and 95.5% respectively. Spectrum transform could improve the recognition accuracy. The recognition accuracy of different research objects and different spectrum transform methods were different. The research provided evidence for desert tree species classification, monitoring biodiversity and the analysis of area in desert by using large scale remote sensing method.

Teach beyond Your Reach: An Instructor's Guide to Developing and Running Successful Distance Learning Classes, Workshops, Training Sessions, and More. Second Edition

ERIC Educational Resources Information Center

Neidorf, Robin

2012-01-01

Distance education is enabling individuals to earn college and graduate degrees, professional certificates, and a wide range of skills and credentials. In addition to the expanding role of distance learning in higher education, all types of organizations now offer web-based training courses to employees, clients, and other associates. In this…

Evolutionary history and distance dependence control survival of dipterocarp seedlings.

PubMed

Bagchi, Robert; Press, Malcolm C; Scholes, Julie D

2010-01-01

One important hypothesis to explain tree-species coexistence in tropical forests suggests that increased attack by natural enemies near conspecific trees gives locally rare species a competitive advantage. Host ranges of natural enemies generally encompass several closely related plant taxa suggesting that seedlings should also do poorly around adults of closely related species. We investigated the effects of adult Parashorea malaanonan on seedling survival in a Bornean rain forest. Survival of P. malaanonan seedlings was highest at intermediate distances from parent trees while heterospecific seedlings were unaffected by distance. Leaf herbivores did not drive this relationship. Survival of seedlings was lowest for P. malaanonan, and increased with phylogenetic dissimilarity from this species, suggesting that survival of close relatives of common species is reduced. This study suggests that distance dependence contributes to species coexistence and highlights the need for further investigation into the role of shared plant enemies in community dynamics.

Phylogenomics with paralogs

PubMed Central

Hellmuth, Marc; Wieseke, Nicolas; Lechner, Marcus; Lenhof, Hans-Peter; Middendorf, Martin; Stadler, Peter F.

2015-01-01

Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer. PMID:25646426

Thematic and spatial resolutions affect model-based predictions of tree species distribution.

PubMed

Liang, Yu; He, Hong S; Fraser, Jacob S; Wu, ZhiWei

2013-01-01

Subjective decisions of thematic and spatial resolutions in characterizing environmental heterogeneity may affect the characterizations of spatial pattern and the simulation of occurrence and rate of ecological processes, and in turn, model-based tree species distribution. Thus, this study quantified the importance of thematic and spatial resolutions, and their interaction in predictions of tree species distribution (quantified by species abundance). We investigated how model-predicted species abundances changed and whether tree species with different ecological traits (e.g., seed dispersal distance, competitive capacity) had different responses to varying thematic and spatial resolutions. We used the LANDIS forest landscape model to predict tree species distribution at the landscape scale and designed a series of scenarios with different thematic (different numbers of land types) and spatial resolutions combinations, and then statistically examined the differences of species abundance among these scenarios. Results showed that both thematic and spatial resolutions affected model-based predictions of species distribution, but thematic resolution had a greater effect. Species ecological traits affected the predictions. For species with moderate dispersal distance and relatively abundant seed sources, predicted abundance increased as thematic resolution increased. However, for species with long seeding distance or high shade tolerance, thematic resolution had an inverse effect on predicted abundance. When seed sources and dispersal distance were not limiting, the predicted species abundance increased with spatial resolution and vice versa. Results from this study may provide insights into the choice of thematic and spatial resolutions for model-based predictions of tree species distribution.

Thematic and Spatial Resolutions Affect Model-Based Predictions of Tree Species Distribution

PubMed Central

Liang, Yu; He, Hong S.; Fraser, Jacob S.; Wu, ZhiWei

2013-01-01

Subjective decisions of thematic and spatial resolutions in characterizing environmental heterogeneity may affect the characterizations of spatial pattern and the simulation of occurrence and rate of ecological processes, and in turn, model-based tree species distribution. Thus, this study quantified the importance of thematic and spatial resolutions, and their interaction in predictions of tree species distribution (quantified by species abundance). We investigated how model-predicted species abundances changed and whether tree species with different ecological traits (e.g., seed dispersal distance, competitive capacity) had different responses to varying thematic and spatial resolutions. We used the LANDIS forest landscape model to predict tree species distribution at the landscape scale and designed a series of scenarios with different thematic (different numbers of land types) and spatial resolutions combinations, and then statistically examined the differences of species abundance among these scenarios. Results showed that both thematic and spatial resolutions affected model-based predictions of species distribution, but thematic resolution had a greater effect. Species ecological traits affected the predictions. For species with moderate dispersal distance and relatively abundant seed sources, predicted abundance increased as thematic resolution increased. However, for species with long seeding distance or high shade tolerance, thematic resolution had an inverse effect on predicted abundance. When seed sources and dispersal distance were not limiting, the predicted species abundance increased with spatial resolution and vice versa. Results from this study may provide insights into the choice of thematic and spatial resolutions for model-based predictions of tree species distribution. PMID:23861828

An Instructional Media Selection Guide for Distance Learning. Fourth Edition

ERIC Educational Resources Information Center

Holden, Jolly T.; Westfall, Philip J.-L.

2007-01-01

Increasingly, educators and trainers are challenged within their respective organizations to provide for the efficient distribution of instructional content using instructional media. The appropriate selection of instructional media to support distance learning is not intuitive and does not occur as a matter of personal preference. On the…

Size of Douglas-fir trees in relation to distance from a mixed red alder - Douglas-fir stand

Treesearch

R.E. Miller; D.L. Reukema; T.A. Max

1993-01-01

Variation in diameter, height, and stem volume of 57-year-old Douglas-fir(Pseudotsuga menziesii var. menziesii (Mirb.) Franco) was related to distance of these trees from a 27 m wide strip in the same Douglas-fir plantation that had been interplanted with red alder (Alnus rubra Bong.). Within the...

Spread of dwarfmistletoe into Jeffrey pine plantation..

Treesearch

Robert F. Scarpf; J.R. Parmeter

1967-01-01

A study at the Institute of Forest Genetics, Placerville. Calif . showed that dwarfmistletoe could spread from infected overstory ponderosa pine into planted Jeffrey pine--a maximum distance of about 145 feet. About one-third of the trees within this distance were infected after 22 years. The level of infection in the trees remained low. however and the parasite had...

How Mobile App Design Impacts User Responses to Mixed Self-Tracking Outcomes: Randomized Online Experiment to Explore the Role of Spatial Distance for Hedonic Editing

PubMed Central

Lorenz, Jana

2018-01-01

Background Goal setting is among the most common behavioral change techniques employed in contemporary self-tracking apps. For these techniques to be effective, it is relevant to understand how the visual presentation of goal-related outcomes employed in the app design affects users’ responses to their self-tracking outcomes. Objective This study examined whether a spatially close (vs distant) presentation of mixed positive and negative self-tracking outcomes from multiple domains (ie, activity, diet) on a digital device’s screen can provide users the opportunity to hedonically edit their self-tracking outcome profile (ie, to view their mixed self-tracking outcomes in the most positive light). Further, this study examined how the opportunity to hedonically edit one’s self-tracking outcome profile relates to users’ future health behavior intentions. Methods To assess users’ responses to a spatially close (vs distant) presentation of a mixed-gain (vs mixed-loss) self-tracking outcome profile, a randomized 2×2 between-subjects online experiment with a final sample of 397 participants (mean age 27.4, SD 7.2 years; 71.5%, 284/397 female) was conducted in Germany. The experiment started with a cover story about a fictitious self-tracking app. Thereafter, participants saw one of four manipulated self-tracking outcome profiles. Variables of interest measured were health behavior intentions, compensatory health beliefs, health motivation, and recall of the outcome profile. We analyzed data using chi-square tests (SPSS version 23) and moderated mediation analyses with the PROCESS macro 2.16.1. Results Spatial distance facilitated hedonic editing, which was indicated by systematic memory biases in users’ recall of positive and negative self-tracking outcomes. In the case of a mixed-gain outcome profile, a spatially close (vs distant) presentation tended to increase the underestimation of the negative outcome (P=.06). In the case of a mixed-loss outcome profile, a spatially distant (vs close) presentation facilitated the exact recognition of the positive outcome (P=.04). When the presentation of self-tracking outcomes provided the opportunity for hedonic editing, users with a low (vs high) health motivation produced compensatory health beliefs, which led to lower health behavior intentions (index of moderated mediation=0.0352, 95% CI 0.0011-0.0923). Conclusions When spatial distance between the presentations of mixed self-tracking outcomes provided the opportunity to hedonically edit one’s self-tracking outcome profile, users recalled their self-tracking outcomes in a more positive light. Especially for users with lower health motivation, the opportunity to hedonically edit one’s mixed self-tracking outcome profile led to reduced health behavior intentions. To prevent the occurrence of hedonic editing in users’ responses to visually presented self-tracking outcome profiles, further research is necessary to determine the ideal distance that should be employed in the app design for the presentation of mixed self-tracking outcomes on a digital device’s screen. PMID:29643051

The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell

PubMed Central

Junier, Thomas; Zdobnov, Evgeny M.

2010-01-01

Summary: We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes. Availability: C source code, Python bindings and executables for various platforms are available from http://cegg.unige.ch/newick_utils. The distribution includes a manual and example data. The package is distributed under the BSD License. Contact: thomas.junier@unige.ch PMID:20472542

Removal of Competition Bias from Forest Genetics Experiments

Treesearch

D. T. Cooper; Robert B. Ferguson

1977-01-01

Estimates of genetic gains and of juvenile-mature correlations in small-plot breeding experiments may be inflated because trees that grow rapidly early continue to be the largest trees, and trees that begin slowly usually stay small. A procedure which takes missing trees, relative sizes and distances between competing trees, and the intensity of competition into...

Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests.

PubMed

Wills, Christopher; Harms, Kyle E; Wiegand, Thorsten; Punchi-Manage, Ruwan; Gilbert, Gregory S; Erickson, David; Kress, W John; Hubbell, Stephen P; Gunatilleke, C V Savitri; Gunatilleke, I A U Nimal

2016-01-01

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species' gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees' lifetimes.

Trees as huge flowers and flowers as oversized floral guides: the role of floral color change and retention of old flowers in Tibouchina pulchra

PubMed Central

Brito, Vinícius L. G.; Weynans, Kevin; Sazima, Marlies; Lunau, Klaus

2015-01-01

Floral color changes and retention of old flowers are frequently combined phenomena restricted to the floral guide or single flowers in few-flowered inflorescences. They are thought to increase the attractiveness over long distances and to direct nearby pollinators toward the rewarding flowers. In Tibouchina pulchra, a massively flowering tree, the whole flower changes its color during anthesis. On the first day, the flowers are white and on the next 3 days, they change to pink. This creates a new large-scale color pattern in which the white pre-changed flowers contrast against the pink post-changed ones over the entire tree. We describe the spectral characteristics of floral colors of T. pulchra and test bumblebees’ response to this color pattern when viewed at different angles (simulating long and short distances). The results indicated the role of different color components in bumblebee attraction and the possible scenario in which this flower color pattern has evolved. We tested bumblebees’ preference for simulated trees with 75% pink and 25% white flowers resembling the color patterns of T. pulchra, and trees with green leaves and pink flowers (control) in long-distance approach. We also compared an artificial setting with three pink flowers and one white flower (T. pulchra model) against four pink flowers with white floral guides (control) in short-distance approach. Bumblebees spontaneously preferred the simulated T. pulchra patterns in both approaches despite similar reward. Moreover, in short distances, pollinator visits to peripheral, non-rewarding flowers occurred only half as frequently in the simulated T. pulchra when compared to the control. Thefore, this exceptional floral color change and the retention of old flowers in T. pulchra favors the attraction of pollinators over long distances in a deception process while it honestly directs them toward the rewarding flowers at short distances possibly exploring their innate color preferences. PMID:26052335

An iterative method for airway segmentation using multiscale leakage detection

NASA Astrophysics Data System (ADS)

Nadeem, Syed Ahmed; Jin, Dakai; Hoffman, Eric A.; Saha, Punam K.

2017-02-01

There are growing applications of quantitative computed tomography for assessment of pulmonary diseases by characterizing lung parenchyma as well as the bronchial tree. Many large multi-center studies incorporating lung imaging as a study component are interested in phenotypes relating airway branching patterns, wall-thickness, and other morphological measures. To our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. Even when there are failures in a small fraction of segmentation results, the airway tree masks must be manually reviewed for all results which is laborious considering that several thousands of image data sets are evaluated in large studies. In this paper, we present a CT-based novel airway tree segmentation algorithm using iterative multi-scale leakage detection, freezing, and active seed detection. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity based connectivity and a new leakage detection algorithm to iteratively grow an airway tree starting from an initial seed inside the trachea. It begins with a conservative threshold and then, iteratively shifts toward generous values. The method was applied on chest CT scans of ten non-smoking subjects at total lung capacity and ten at functional residual capacity. Airway segmentation results were compared to an expert's manually edited segmentations. Branch level accuracy of the new segmentation method was examined along five standardized segmental airway paths (RB1, RB4, RB10, LB1, LB10) and two generations beyond these branches. The method successfully detected all branches up to two generations beyond these segmental bronchi with no visual leakages.

Growth process and model simulation of three different classes of Schima superba in a natural subtropical forest in China

NASA Astrophysics Data System (ADS)

Wei, Hui; Deng, Xiangwen; Ouyang, Shuai; Chen, Lijun; Chu, Yonghe

2017-01-01

Schima superba is an important fire-resistant, high-quality timber species in southern China. Growth in height, diameter at breast height (DBH), and volume of the three different classes (overtopped, average and dominant) of S. superba were examined in a natural subtropical forest. Four growth models (Richards, edited Weibull, Logistic and Gompertz) were selected to fit the growth of the three different classes of trees. The results showed that there was a fluctuation phenomenon in height and DBH current annual growth process of all three classes. Multiple intersections were found between current annual increment (CAI) and mean annual increment (MAI) curves of both height and DBH, but there was no intersection between volume CAI and MAI curves. All selected models could be used to fit the growth of the three classes of S. superba, with determinant coefficients above 0.9637. However, the edited Weibull model performed best with the highest R2 and the lowest root of mean square error (RMSE). S. superba is a fast-growing tree with a higher growth rate during youth. The height and DBH CAIs of overtopped, average and dominant trees reached growth peaks at ages 5-10, 10-15 and 15-20 years, respectively. According to model simulation, the volume CAIs of overtopped, average and dominant trees reached growth peaks at ages 17, 55 and 76 years, respectively. The biological rotation ages of the overtopped, average and dominant trees of S. superba were 29, 85 and 128 years, respectively.

Supertrees Based on the Subtree Prune-and-Regraft Distance

PubMed Central

Whidden, Christopher; Zeh, Norbert; Beiko, Robert G.

2014-01-01

Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Many supertree approaches use optimality criteria that do not reflect underlying processes, have known biases, and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and > 50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of benchmark datasets simulated under plausible rates of LGT, we show that SPR supertrees are more similar to correct species histories than supertrees based on parsimony or Robinson–Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera. A Small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT. [Lateral gene transfer; matrix representation with parsimony; phylogenomics; prokaryotic phylogeny; Robinson–Foulds; subtree prune-and-regraft; supertrees.] PMID:24695589

Effect of larval growth conditions on adult body mass and long-distance flight endurance in a wood-boring beetle: Do smaller beetles fly better?

PubMed

Brown, Stav; Soroker, Victoria; Ribak, Gal

2017-04-01

The tropical fig borer, Batocera rufomaculata De Geer, is a large beetle that is a pest on a number of fruit trees, including fig and mango. Adults feed on the leaves and twigs and females lay their eggs under the bark of the tree. The larvae bore into the tree trunk, causing substantial damage that may lead to the collapse and death of the host tree. We studied how larval development under inferior feeding conditions (experienced during development in dying trees) affects flight endurance in the adult insect. We grew larvae either in their natural host or on sawdust enriched with stale fig tree twigs. Flight endurance of the adults was measured using a custom-built flight-mill. Beetles emerging from the natural host were significantly larger but flew shorter distances than beetles reared on less favourable substrates. There was no difference in the allometric slope of wing area with body mass between the beetles groups; however flight muscle mass scaled with total body mass with an exponent significantly lower than 1.0. Hence, smaller beetles had proportionally larger flight muscles. These findings suggest that beetles that developed smaller as a result from poor nutritional conditions in deteriorating hosts, are better equipped to fly longer distances in search of a new host tree. Copyright © 2017 Elsevier Ltd. All rights reserved.

Indo-European languages tree by Levenshtein distance

NASA Astrophysics Data System (ADS)

Serva, M.; Petroni, F.

2008-03-01

The evolution of languages closely resembles the evolution of haploid organisms. This similarity has been recently exploited (Gray R. D. and Atkinson Q. D., Nature, 426 (2003) 435; Gray R. D. and Jordan F. M., Nature, 405 (2000) 1052) to construct language trees. The key point is the definition of a distance among all pairs of languages which is the analogous of a genetic distance. Many methods have been proposed to define these distances; one of these, used by glottochronology, computes the distance from the percentage of shared "cognates". Cognates are words inferred to have a common historical origin, and subjective judgment plays a relevant role in the identification process. Here we push closer the analogy with evolutionary biology and we introduce a genetic distance among language pairs by considering a renormalized Levenshtein distance among words with same meaning and averaging on all words contained in a Swadesh list (Swadesh M., Proc. Am. Philos. Soc., 96 (1952) 452). The subjectivity of process is consistently reduced and the reproducibility is highly facilitated. We test our method against the Indo-European group considering fifty different languages and the two hundred words of the Swadesh list for any of them. We find out a tree which closely resembles the one published in Gray and Atkinson (2003), with some significant differences.

3D reconstruction of a tree stem using video images and pulse distances

Treesearch

N. E. Clark

2002-01-01

This paper demonstrates how a 3D tree stem model can be reconstructed using video imagery combined with laser pulse distance measurements. Perspective projection is used to place the data collected with the portable video laser-rangefinding device into a real world coordinate system. This hybrid methodology uses a relatively small number of range measurements (compared...

A combined NLP-differential evolution algorithm approach for the optimization of looped water distribution systems

NASA Astrophysics Data System (ADS)

Zheng, Feifei; Simpson, Angus R.; Zecchin, Aaron C.

2011-08-01

This paper proposes a novel optimization approach for the least cost design of looped water distribution systems (WDSs). Three distinct steps are involved in the proposed optimization approach. In the first step, the shortest-distance tree within the looped network is identified using the Dijkstra graph theory algorithm, for which an extension is proposed to find the shortest-distance tree for multisource WDSs. In the second step, a nonlinear programming (NLP) solver is employed to optimize the pipe diameters for the shortest-distance tree (chords of the shortest-distance tree are allocated the minimum allowable pipe sizes). Finally, in the third step, the original looped water network is optimized using a differential evolution (DE) algorithm seeded with diameters in the proximity of the continuous pipe sizes obtained in step two. As such, the proposed optimization approach combines the traditional deterministic optimization technique of NLP with the emerging evolutionary algorithm DE via the proposed network decomposition. The proposed methodology has been tested on four looped WDSs with the number of decision variables ranging from 21 to 454. Results obtained show the proposed approach is able to find optimal solutions with significantly less computational effort than other optimization techniques.

Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests

PubMed Central

Wills, Christopher; Harms, Kyle E.; Wiegand, Thorsten; Punchi-Manage, Ruwan; Gilbert, Gregory S.; Erickson, David; Kress, W. John; Hubbell, Stephen P.; Gunatilleke, C. V. Savitri; Gunatilleke, I. A. U. Nimal

2016-01-01

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species’ gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees’ lifetimes. PMID:27305092

Disturbance and density-dependent processes (competition and facilitation) influence the fine-scale genetic structure of a tree species' population.

PubMed

Fajardo, Alex; Torres-Díaz, Cristian; Till-Bottraud, Irène

2016-01-01

Disturbances, dispersal and biotic interactions are three major drivers of the spatial distribution of genotypes within populations, the last of which has been less studied than the other two. This study aimed to determine the role of competition and facilitation in the degree of conspecific genetic relatedness of nearby individuals of tree populations. It was expected that competition among conspecifics will lead to low relatedness, while facilitation will lead to high relatedness (selection for high relatedness within clusters). The stand structure and spatial genetic structure (SGS) of trees were examined within old-growth and second-growth forests (including multi-stemmed trees at the edge of forests) of Nothofagus pumilio following large-scale fires in Patagonia, Chile. Genetic spatial autocorrelations were computed on a spatially explicit sampling of the forests using five microsatellite loci. As biotic plant interactions occur among immediate neighbours, mean nearest neighbour distance (MNND) among trees was computed as a threshold for distinguishing the effects of disturbances and biotic interactions. All forests exhibited a significant SGS for distances greater than the MNND. The old-growth forest genetic and stand structure indicated gap recolonization from nearby trees (significantly related trees at distances between 4 and 10 m). At distances smaller than the MNND, trees of the second-growth interior forest showed significantly lower relatedness, suggesting a fading of the recolonization structure by competition, whereas the second-growth edge forest showed a positive and highly significant relatedness among trees (higher among stems of a cluster than among stems of different clusters), resulting from facilitation. Biotic interactions are shown to influence the genetic composition of a tree population. However, facilitation can only persist if individuals are related. Thus, the genetic composition in turn influences what type of biotic interactions will take place among immediate neighbours in post-disturbance forests. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Spatial and spatiotemporal pattern analysis of coconut lethal yellowing in Mozambique.

PubMed

Bonnot, F; de Franqueville, H; Lourenço, E

2010-04-01

Coconut lethal yellowing (LY) is caused by a phytoplasma and is a major threat for coconut production throughout its growing area. Incidence of LY was monitored visually on every coconut tree in six fields in Mozambique for 34 months. Disease progress curves were plotted and average monthly disease incidence was estimated. Spatial patterns of disease incidence were analyzed at six assessment times. Aggregation was tested by the coefficient of spatial autocorrelation of the beta-binomial distribution of diseased trees in quadrats. The binary power law was used as an assessment of overdispersion across the six fields. Spatial autocorrelation between symptomatic trees was measured by the BB join count statistic based on the number of pairs of diseased trees separated by a specific distance and orientation, and tested using permutation methods. Aggregation of symptomatic trees was detected in every field in both cumulative and new cases. Spatiotemporal patterns were analyzed with two methods. The proximity of symptomatic trees at two assessment times was investigated using the spatiotemporal BB join count statistic based on the number of pairs of trees separated by a specific distance and orientation and exhibiting the first symptoms of LY at the two times. The semivariogram of times of appearance of LY was calculated to characterize how the lag between times of appearance of LY was related to the distance between symptomatic trees. Both statistics were tested using permutation methods. A tendency for new cases to appear in the proximity of previously diseased trees and a spatially structured pattern of times of appearance of LY within clusters of diseased trees were detected, suggesting secondary spread of the disease.

Course Development. A Manual for Editors of Distance-Teaching Materials.

ERIC Educational Resources Information Center

Jenkins, Janet

This manual is intended to train distance education staff in how to develop and edit teaching materials. Addressed in the individual units of the guide are the following topics: appointing writers, preparing to write, developing a course outline, selecting the structure of a unit, presenting the subject matter, developing student activities,…

The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.

PubMed

Soria-Carrasco, Víctor; Talavera, Gerard; Igea, Javier; Castresana, Jose

2007-11-01

We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length variation. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree. http://molevol.ibmb.csic.es/Ktreedist.html

Stratigraphic correlation of well logs using relational tree

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang, J.H.; Tsay, F.; Lai, P.F.

A heuristic waveform correlation scheme of well logs is based on a relational tree matching. Waveforms (well logs) are represented in a data structure known as a relational tree. A relational tree provides a complete description of the contextural relationships, as defined by peaks and valleys of the waveforms. The correlational scheme consists of a distance-measuring process using all possible peak attributes. First, a distance function is defined for any two nodes in terms of peak attributes. To find the best match for a given node of a given waveform, the authors measure the distance between the given node andmore » each node from a predefined subset of the second waveform. The closest one is considered to be the matched node. The process is repeated for every node in the waveform. This quantitative correlation method has been implemented and tested with well logs from the Black Warrior basin, north Alabama. Results showed that the procedure has the capability of handling the thickening and thinning strata, as well as missing intervals.« less

Population Structure of the Primary Malaria Vector in South America, Anopheles darlingi, Using Isozyme, Random Amplified Polymorphic DNA, Internal Transcribed Spacer 2, and Morphologic Markers

DTIC Science & Technology

1999-01-01

distances and identities and Roger?’ genetic distances were clustered by the unweighted pair group method using arithmetic average ( UPGMA ) to produce...Seattle, WA) using the NEIGHBOR program with the UPGMA option and a phenogram was produced with DRAWGRAM, also in PHYLIP 3.X RAPDBOOT5’ was used to...generate 100 pseudoreplicate distance matrices, which were collapsed to form 100 trees with UPGMA . The bootstrap consensus tree was derived from the 100

Pollen dispersion of some forest trees

Treesearch

Jonathan W. Wright

1952-01-01

The distance the pollen of forest trees travels is of practical and theoretical importance not only in tree breeding, but also in silviculture. For example, one way to produce elite or hybrid tree seed where vegetative propagation is impractical is by the establishment of "seed orchards" or natural-crossing plots. The success of such orchards will depend...

The Importance of Tree Size and Fecundity for Wind Dispersal of Big-Leaf Mahogany

PubMed Central

Norghauer, Julian M.; Nock, Charles A.; Grogan, James

2011-01-01

Seed dispersal by wind is a critical yet poorly understood process in tropical forest trees. How tree size and fecundity affect this process at the population level remains largely unknown because of insufficient replication across adults. We measured seed dispersal by the endangered neotropical timber species big-leaf mahogany (Swietenia macrophylla King, Meliaceae) in the Brazilian Amazon at 25 relatively isolated trees using multiple 1-m wide belt transects extended 100 m downwind. Tree diameter and fecundity correlated positively with increased seed shadow extent; but in combination large, high fecundity trees contributed disproportionately to longer-distance dispersal events (>60 m). Among three empirical models fitted to seed density vs. distance in one dimension, the Student-t (2Dt) generally fit best (compared to the negative exponential and inverse power). When seedfall downwind was modelled in two dimensions using a normalised sample, it peaked furthest downwind (c. 25 m) for large, high-fecundity trees; with the inverse Gaussian and Weibull functions providing comparable fits that were slightly better than the lognormal. Although most seeds fell within 30 m of parent trees, relatively few juveniles were found within this distance, resulting in juvenile-to-seed ratios peaking at c. 35–45 m. Using the 2Dt model fits to predict seed densities downwind, coupled with known fecundity data for 2000–2009, we evaluated potential Swietenia regeneration near adults (≤30 m dispersal) and beyond 30 m. Mean seed arrival into canopy gaps >30 m downwind was more than 3× greater for large, high fecundity trees than small, high-fecundity trees. Tree seed production did not necessarily scale up proportionately with diameter, and was not consistent across years, and this resulting intraspecific variation can have important consequences for local patterns of dispersal in forests. Our results have important implications for management and conservation of big-leaf mahogany populations, and may apply to other threatened wind-dispersed Meliaceae trees. PMID:21408184

The applicability of ordinary least squares to consistently short distances between taxa in phylogenetic tree construction and the normal distribution test consequences.

PubMed

Roux, C Z

2009-05-01

Short phylogenetic distances between taxa occur, for example, in studies on ribosomal RNA-genes with slow substitution rates. For consistently short distances, it is proved that in the completely singular limit of the covariance matrix ordinary least squares (OLS) estimates are minimum variance or best linear unbiased (BLU) estimates of phylogenetic tree branch lengths. Although OLS estimates are in this situation equal to generalized least squares (GLS) estimates, the GLS chi-square likelihood ratio test will be inapplicable as it is associated with zero degrees of freedom. Consequently, an OLS normal distribution test or an analogous bootstrap approach will provide optimal branch length tests of significance for consistently short phylogenetic distances. As the asymptotic covariances between branch lengths will be equal to zero, it follows that the product rule can be used in tree evaluation to calculate an approximate simultaneous confidence probability that all interior branches are positive.

Distribution of fine roots of ponderosa pine and Douglas-fir in a central Idaho forest

Treesearch

Gabriel Dumm; Lauren Fins; Russell T. Graham; Theresa B. Jain

2008-01-01

This study describes soil horizon depth and fine root distribution in cores collected at two distances from the boles of Douglas-fir and ponderosa pine trees at a study site in a central Idaho forest. Concentration and content of fine roots extracted from soil cores were compared among species, soil horizons, tree size, and distance from bole. Approximately 80% of...

Plastid genome sequence of an ornamental and editable fruit tree of Rosaceae, Prunus mume.

PubMed

Wang, Shuo; Gao, Cheng-Wen; Gao, Li-Zhi

2016-11-01

Here we assembled and analyzed the complete chloroplast genome of Prunus mume, a popular ornamental and editable fruit tree of Rosaceae. The cp genome exhibited a circular DNA molecule of 157 712 bp with a typical quadripartite structure consisted of two inverted repeat regions (IRa and IRb) of 26 394 bp separated by large (LSC) and small (SSC) single-copy regions of 85 861 and 19 063 bp, respectively. It encoded 112 unique genes, 19 of which were duplicated in the IR regions, giving a total of 131 genes. Eighteen of these genes harbored one or two introns. GC content was 38.9%, and coding regions accounted for 51.3% of the genome. Phylogenetic analysis showed that P. mume clustered with P. persica and P. kansuensis in the genus Punus. This newly determined chloroplast genome will enhance modern breeding programs for the purpose of genetic improvement of this valuable plant.

Whatever Happened to the Silent Scientific Revolution?--Research, Theory and Practice in Distance Education.

ERIC Educational Resources Information Center

Morgan, Alistair

The point of departure for this article is the title of a book edited by David Fetterman, "Qualitative Approaches to Educational Evaluation--The Silent Scientific Revolution." This article addresses the question of how the shift to a qualitative, phenomenological approach has impinged on research and evaluation in distance education.…

Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest.

PubMed

Stone, Bram W G; Jackson, Colin R

2016-05-01

The phyllosphere presents a unique system of discrete and easily replicable surfaces colonized primarily by bacteria. However, the biogeography of bacteria in the phyllosphere is little understood, especially at small to intermediate scales. Bacterial communities on the leaves of 91 southern magnolia (Magnolia grandiflora) trees 1-452 m apart in a small forest plot were analyzed and fragments of the 16S ribosomal RNA (rRNA) gene sequenced using the Illumina platform. Assemblages were dominated by members of the Alphaproteobacteria, Bacteroidetes, and Acidobacteria. Patterns in community composition were measured by both relative abundance (theta) and presence-absence (Jaccard) dissimilarity metrics. Distance-based Moran's eigenvector map analyses of the distance-decay relationship found a significant, positive relationship between each dissimilarity metric and significant eigenfunctions derived from geographic distance between trees, indicating trees that were closer together had more similar bacterial phyllosphere communities. Indirect gradient analyses revealed that several environmental parameters (canopy cover, tree elevation, and the slope and aspect of the ground beneath trees) were significantly related to multivariate ordination scores based on relative bacterial sequence abundances; however, these relationships were not significant when looking at the incidence of bacterial taxa. This suggests that bacterial growth and abundance in the phyllosphere is shaped by different assembly mechanisms than bacterial presence or absence. More broadly, this study demonstrates that the distance-decay relationship applies to phyllosphere communities at local scales, and that environmental parameters as well as neutral forces may both influence spatial patterns in the phyllosphere.

Competition and facilitation in industrial barrens: variation in performance of mountain birch seedlings with distance from nurse plants.

PubMed

Eränen, Janne K; Kozlov, Mikhail V

2007-04-01

In stressful environments inter-plant facilitation is an important phenomenon co-occurring with competition. However, most experiments in natural ecosystems have only contrasted "sheltered" and "exposed" microsites, thus missing possible non-linearity of effects and not giving any information about the scale at which these interactions operate. In the current experiment we studied the net effect of nurse trees on mountain birch seedlings at various planting distances. Seedlings were planted in two highly stressful subarctic industrial barren sites around the nickel-copper smelter in Monchegorsk, NW Russia, at five distances (from 10 to 100 cm) from mature birch trees that were circa 100 cm in height. The survival and growth of seedlings were monitored for six years and the results were analyzed in respect to several environmental characteristics. Despite the fact that interaction strengths varied between years and between two study sites, both survival and growth of seedlings indicated optimum performance at middle distances and decreasing performance closer to and further from the nurse tree. We suggest that adverse effects on seedling performance at short distances are explained by competition and/or accumulation of pollutants under nurse plants, whereas at long distances these adverse effects appear due to lack of shelter, as shown by higher wind stress and lower soil water content.

Persistence of long-distance, insect-mediated pollen movement for a tropical canopy tree species in remnant forest patches in an urban landscape.

PubMed

Noreen, A M E; Niissalo, M A; Lum, S K Y; Webb, E L

2016-12-01

As deforestation and urbanization continue at rapid rates in tropical regions, urban forest patches are essential repositories of biodiversity. However, almost nothing is known about gene flow of forest-dependent tree species in urban landscapes. In this study, we investigated gene flow in the insect-pollinated, wind-dispersed tropical tree Koompassia malaccensis in and among three remnant forest patches in the urbanized landscape of Singapore. We genotyped the vast majority of adults (N=179) and a large number of recruits (N=2103) with 8 highly polymorphic microsatellite markers. Spatial genetic structure of the recruit and adult cohorts was significant, showing routine gene dispersal distances of ~100-400 m. Parentage analysis showed that 97% of recruits were within 100 m of their mother tree, and a high frequency of relatively short-distance pollen dispersal (median ~143-187 m). Despite routine seed and pollen dispersal distances of within a few hundred meters, interpatch gene flow occurred between all patches and was dominated by pollen movement: parentage analysis showed 76 pollen versus 2 seed interpatch dispersal events, and the seedling neighborhood model estimated ~1-6% seed immigration and ~21-46% pollen immigration rates, depending on patch. In addition, the smallest patch (containing five adult K. malaccensis trees) was entirely surrounded by >2.5 km of 'impervious' substrate, yet had the highest proportional pollen and seed immigration estimates of any patch. Hence, contrary to our hypothesis, insect-mediated gene flow persisted across an urban landscape, and several of our results also parallel key findings from insect-pollinated canopy trees sampled in mixed agricultural-forest landscapes.

Metric Sex Determination of the Human Coxal Bone on a Virtual Sample using Decision Trees.

PubMed

Savall, Frédéric; Faruch-Bilfeld, Marie; Dedouit, Fabrice; Sans, Nicolas; Rousseau, Hervé; Rougé, Daniel; Telmon, Norbert

2015-11-01

Decision trees provide an alternative to multivariate discriminant analysis, which is still the most commonly used in anthropometric studies. Our study analyzed the metric characterization of a recent virtual sample of 113 coxal bones using decision trees for sex determination. From 17 osteometric type I landmarks, a dataset was built with five classic distances traditionally reported in the literature and six new distances selected using the two-step ratio method. A ten-fold cross-validation was performed, and a decision tree was established on two subsamples (training and test sets). The decision tree established on the training set included three nodes and its application to the test set correctly classified 92% of individuals. This percentage was similar to the data of the literature. The usefulness of decision trees has been demonstrated in numerous fields. They have been already used in sex determination, body mass prediction, and ancestry estimation. This study shows another use of decision trees enabling simple and accurate sex determination. © 2015 American Academy of Forensic Sciences.

The history of mercury pollution near the Spolana chlor-alkali plant (Neratovice, Czech Republic) as recorded by Scots pine tree rings and other bioindicators

USGS Publications Warehouse

Navrátil, Tomáš; Šimeček, Martin; Shanley, James B.; Rohovec, Jan; Hojdová, Maria; Houška, Jakub

2017-01-01

We assessed > 100 years of mercury (Hg) pollution recorded in the tree rings of Scots Pine near a Czech chlor-alkali plant operating since 1941. Hg concentrations in tree rings increased with the launching of plant operations and decreased when Hg emissions decreased in 1975 due to an upgrade in production technology. Similar to traditional bioindicators of pollution such as pine needles, bark and forest floor humus, Hg concentrations in Scots Pine boles decreased with distance from the plant. Mean Hg in pine bole in the 1940s ranged from 32.5 μg/kg Hg at a distance of 0.5 km from the plant to 5.4 μg/kg at a distance of > 4.7 km, where tree ring Hg was the same as at a reference site, and other bioindicators also suggest that the effect of the plant was no longer discernible. Tree ring Hg concentrations decreased by 8–29 μg/kg since the 1940s at all study sites including the reference site. The lack of exact correspondence between changes at the plant and tree ring Hg indicated some smearing of the signal due to lateral translocation of Hg from sapwood to heartwood. Bole Hg concentrations reflected local and regional atmospheric Hg concentrations, and not Hg wet deposition.

Object-oriented fault tree evaluation program for quantitative analyses

NASA Technical Reports Server (NTRS)

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.

Forestry. Teacher Edition.

ERIC Educational Resources Information Center

Oklahoma State Dept. of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

This curriculum is designed to provide training in skills used by technicians and foresters throughout the world who plant, care for, and harvest trees. It contains 16 units. Each instructional unit includes some or all of the basic components of a unit of instruction: performance objectives, suggested activities, handouts, information sheets,…

An improved tree height measurement technique tested on mature southern pines

Treesearch

Don C. Bragg

2008-01-01

Virtually all techniques for tree height determination follow one of two principles: similar triangles or the tangent method. Most people apply the latter approach, which uses the tangents of the angles to the top and bottom and a true horizontal distance to the subject tree. However, few adjust this method for ground slope, tree lean, crown shape, and crown...

Development of Longleaf Pine Seedlings Under Parent Trees

Treesearch

William D. Boyer

1963-01-01

In southwest Alabama, unburned seedlings under overstories ranging up to 90 square feet of basal area per acre survived as well as those with no tree competition. After 7 years, milacre stocking averaged 99 percent and survival 72 percent. Growth, but not survival, improved with distance from parent trees. Seedlings under tree crowns had less brown spot than those in...

Educational Issues in Utah: Governance, Legislation, Technology, and Finance. 1994-95 Conditions of Education in Utah Yearbook.

ERIC Educational Resources Information Center

Galvin, Patrick F., Ed.; Johnson, Bob L., Jr., Ed.

This document is the third edition of "Conditions of Education in Utah," covering the 1994-95 academic year. The first three chapters analyze issues relative to distance education and the Internet. Chapters 1 and 2 examine the pros and cons of distance education, and chapter 3 describes the construction, maintenance, and staffing costs…

Observaciones geomagnéticas de la Isla Livingston, Antártida 2000, 2001 y campaña 2001-2002 %t Livingston Island geomagnetic observations, Antarctica 2000, 2001, and 2001-2002 survey

NASA Astrophysics Data System (ADS)

Gaya-Piqué, L.; Torta, J. M.; Curto, J. J.; Sanclement, E.; Marsal, S.; Solé, J. G.; Altadill, D.; Ugalde, A.; de Santis, A.; Apostolov, E. M.; Alberca, L. F.; Garcí A.

This CD-ROM presents the Livingston Island Geomagnetic Observatory Bulletin, edited by Observatori de l'Ebre, containing the data obtained during the years 2000, 2001 and the first two months of the year 2002. For the first time this Bulletin is edited in digital format, being it the continuation of the paper-edited series as Misceláneas 41, 42 and 43 (ISSN 0211-4534). The structure of the CD-ROM consists of one file with the Bulletin contents in PDF and of a tree of directories and subdirectories with the data corresponding to the different years and months of the Bulletin. These data files and their names were built according to the IAGA-2000 data exchange format.

Talking Trees

ERIC Educational Resources Information Center

Tolman, Marvin

2005-01-01

Students love outdoor activities and will love them even more when they build confidence in their tree identification and measurement skills. Through these activities, students will learn to identify the major characteristics of trees and discover how the pace--a nonstandard measuring unit--can be used to estimate not only distances but also the…

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

PubMed

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.

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions

PubMed Central

Giaro, Krzysztof

2017-01-01

Abstract Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson–Foulds distance. In this article, we define a new metric for rooted trees—the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events. PMID:28177699

Spatial pattern of long-distance symplasmic transport and communication in trees

PubMed Central

Sokołowska, Katarzyna; Brysz, Alicja Maria; Zagórska-Marek, Beata

2013-01-01

Symplasmic short- and long-distance communication may be regulated at different levels of plant body organization. It depends on cell-to-cell transport modulated by plasmodesmata conductivity and frequency but above all on morphogenetic fields that integrate a plant at the supracellular level. Their control of physiological and developmental processes is especially important in trees, where the continuum consists of 3-dimensional systems of: 1) stem cells in cambium, and 2) living parenchyma cells in the secondary conductive tissues. We found that long-distance symplasmic transport in trees is spatially regulated. Uneven distribution of fluorescent tracer in cambial cells along the branches examined illustrates an unknown intrinsic phenomenon that can possibly be important for plant organism integration. Here we illustrate the spatial dynamics of symplasmic transport in cambium, test and exclude the role of callose in its regulation, and discuss the mechanism that could possibly be responsible for the maintenance of this spatial pattern. PMID:23989002

Conspecific Plant-Soil Feedbacks of Temperate Tree Species in the Southern Appalachians, USA

PubMed Central

Reinhart, Kurt O.; Johnson, Daniel; Clay, Keith

2012-01-01

Many tree species have seedling recruitment patterns suggesting that they are affected by non-competitive distance-dependent sources of mortality. We conducted an experiment, with landscape-level replication, to identify cases of negative distance-dependent effects and whether variation in these effects corresponded with tree recruitment patterns in the southern Appalachian Mountains region. Specifically, soil was collected from 14 sites and used as inocula in a 62 day growth chamber experiment determining whether tree seedling growth was less when interacting with soil from conspecific (like) than heterospecific (other) tree species. Tests were performed on six tree species. Three of the tree species had been previously described as having greater recruitment around conspecifics (i.e. facilitator species group) compared to the other half (i.e. inhibitor species group). We were then able to determine whether variation in negative distance-dependent effects corresponded with recruitment patterns in the field. Across the six species, none were negatively affected by soil inocula from conspecific relative to heterospecific sources. Most species (four of six) were unaffected by soil source. Two species (Prunus serotina and Tsuga canadensis) had enhanced growth in pots inoculated with soil from conspecific trees vs. heterospecifics. Species varied in their susceptibility to soil pathogens, but trends across all species revealed that species classified as inhibitors were not more negatively affected by conspecific than heterospecific soil inocula or more susceptible to pathogenic effects than facilitators. Although plant-soil biota interactions may be important for individual species and sites, it may be difficult to scale these interactions over space or levels of ecological organization. Generalizing the importance of plant-soil feedbacks or other factors across regional scales may be especially problematic for hyperdiverse temperate forests where interactions may be spatially variable. PMID:22808231

Conspecific plant-soil feedbacks of temperate tree species in the southern Appalachians, USA.

PubMed

Reinhart, Kurt O; Johnson, Daniel; Clay, Keith

2012-01-01

Many tree species have seedling recruitment patterns suggesting that they are affected by non-competitive distance-dependent sources of mortality. We conducted an experiment, with landscape-level replication, to identify cases of negative distance-dependent effects and whether variation in these effects corresponded with tree recruitment patterns in the southern Appalachian Mountains region. Specifically, soil was collected from 14 sites and used as inocula in a 62 day growth chamber experiment determining whether tree seedling growth was less when interacting with soil from conspecific (like) than heterospecific (other) tree species. Tests were performed on six tree species. Three of the tree species had been previously described as having greater recruitment around conspecifics (i.e. facilitator species group) compared to the other half (i.e. inhibitor species group). We were then able to determine whether variation in negative distance-dependent effects corresponded with recruitment patterns in the field. Across the six species, none were negatively affected by soil inocula from conspecific relative to heterospecific sources. Most species (four of six) were unaffected by soil source. Two species (Prunus serotina and Tsuga canadensis) had enhanced growth in pots inoculated with soil from conspecific trees vs. heterospecifics. Species varied in their susceptibility to soil pathogens, but trends across all species revealed that species classified as inhibitors were not more negatively affected by conspecific than heterospecific soil inocula or more susceptible to pathogenic effects than facilitators. Although plant-soil biota interactions may be important for individual species and sites, it may be difficult to scale these interactions over space or levels of ecological organization. Generalizing the importance of plant-soil feedbacks or other factors across regional scales may be especially problematic for hyperdiverse temperate forests where interactions may be spatially variable.

Forest chimpanzees (Pan troglodytes verus) remember the location of numerous fruit trees.

PubMed

Normand, Emmanuelle; Ban, Simone Dagui; Boesch, Christophe

2009-11-01

It is assumed that spatial memory contributes crucially to animal cognition since animals' habitats entail a large number of dispersed and unpredictable food sources. Spatial memory has been investigated under controlled conditions, with different species showing and different conditions leading to varying performance levels. However, the number of food sources investigated is very low compared to what exists under natural conditions, where food resources are so abundant that it is difficult to precisely identify what is available. By using a detailed botanical map containing over 12,499 trees known to be used by the Taï chimpanzees, we created virtual maps of all productive fruit trees to simulate potential strategies used by wild chimpanzees to reach resources without spatial memory. First, we simulated different assumptions concerning the chimpanzees' preference for a particular tree species, and, second, we varied the detection field to control for the possible use of smell to detect fruiting trees. For all these assumptions, we compared simulated distance travelled, frequencies of trees visited, and revisit rates with what we actually observed in wild chimpanzees. Our results show that chimpanzees visit rare tree species more frequently, travel shorter distances to reach them, and revisit the same trees more often than if they had no spatial memory. In addition, we demonstrate that chimpanzees travel longer distances to reach resources where they will eat for longer periods of time, and revisit resources more frequently where they ate for a long period of time during their first visit. Therefore, this study shows that forest chimpanzees possess a precise spatial memory which allows them to remember the location of numerous resources and use this information to select the most attractive resources.

Mycorrhizal networks and distance from mature trees alter patterns of competition and facilitation in dry Douglas-fir forests.

PubMed

Teste, François P; Simard, Suzanne W

2008-11-01

The distribution of dry Douglas-fir forests in western North America is expected to shift northward with climate change and disappear from the grassland interface in the southern interior of British Columbia. This shift may be accentuated by clearcutting, a common harvesting practice that aims to reduce the competitive effects of residual mature trees on new regeneration, but in so doing, ignores their facilitative effects. In this study, we investigated the net effects of competition from and facilitation by mature trees retained on harvested sites on seedling establishment in the dry interface Douglas-fir forests. We demonstrate that access to a mycorrhizal network (MN) and proximity to trees have important influences on seedling performance. On six sites, we established trenched plots around 24 mature Pseudotsuga menziesii var. glauca (Douglas-fir) trees, then planted Douglas-fir seedlings into four mesh treatments that served to restrict MN access (i.e., planted into mesh bags with 0.5-, 35-, or 250-microm pores, or without mesh) or into impermeable bags (grown in isolation) at four distances (0.5, 1.0, 2.5, or 5.0 m). Seedling survival tended to be greater and water stress lower where seedlings had full access to the MN. Seedling height, shoot biomass, needle biomass, and nutrient uptake peaked at 2.5-5.0 m from mature trees. Seedlings 0.5 m from mature trees had lower CO2 assimilation rates and wood delta(13)C compared to seedlings 5.0 m away. Competition for soil resources was highest near mature trees but facilitation was relatively greater at further distances, resulting in a zone of net benefit for seedlings. These results show that intraspecific tree-seedling interactions are both competitive and facilitative in dry Douglas-fir forests, and that they are spatially dependent. After disturbance, maintaining residual mature trees may be important for their beneficial regeneration zones.

Comparison of Insertional RNA Editing in Myxomycetes

PubMed Central

Chen, Cai; Frankhouser, David; Bundschuh, Ralf

2012-01-01

RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails. PMID:22383871

Life on Guam: Schoolyard Surveys. 1977 Edition.

ERIC Educational Resources Information Center

Flores, Magdalena T.

As part of an updated series of activity oriented educational materials dealing with aspects of the Guam environment, this publication focuses on the common plants and animals found in schoolyards on Guam. Like a field guide, this publication contains descriptions, ecological information, and some historical notes about the common trees, shrubs,…

Disease Vector Ecology Profile: Somalia. Fourth Edition

DTIC Science & Technology

1993-09-15

excrement, decaying plant material and other debris). Eggs hatch in 1-3 weeks. Larval stage 4-6 weeks. Often associated with termite mounds . Biting...lengths of up to 14 feet. It occurs primarily in the forest and open bush country of northern Somalia, where it is found in tree stumps, termite mounds

Journal of Special Operations Medicine, Volume 4, Edition 4, Fall 2004

DTIC Science & Technology

2004-01-01

Zaichik D, Caspi G, Kotler D, Freund HR. Evacuation priorities in mass casualty terror-related events: Implications for contingency plan- ning. Annals of...John Prados Vietnam Above The Tree Tops: A Forward Air Controller Reports John F Flanagan Vietnam in American Literature Philip H Melling Vietnam

Litter Prevention & Recycling. Ohio Science Workbook: 1987 Edition

ERIC Educational Resources Information Center

Elfner, Lynn Edward, Ed.

Every active family and business produces solid waste, some of which are the nonhazardous discards of society. Taken as individual substances, our newspapers, food leftovers, containers and wrappings, grass clippings and tree limbs seem harmless enough. But huge volumes of these materials are generated daily. It has been projected that many…

Clustering Genes of Common Evolutionary History

PubMed Central

Gori, Kevin; Suchan, Tomasz; Alvarez, Nadir; Goldman, Nick; Dessimoz, Christophe

2016-01-01

Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent—due to events such as incomplete lineage sorting or horizontal gene transfer—it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such “process-agnostic” approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward’s method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta. We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl). PMID:26893301

Long range lateral root activity by neo-tropical savanna trees.

Treesearch

Leonel da S. L. Sternberg; Sandra Bucci; Augusto Franco; Guillermo Goldstein; William A. Hoffman; Frederick C. Meinzer; Marcelo Z. Moreira; Fabian Scholz

2004-01-01

The extent of water uptake by lateral roots of savanna trees in the Brazilian highlands was measured by irrigating two 2 by 2 m plots with deuterium-enriched water and assaying for the abundance of deuterium in stem water from trees inside and at several distances from the irrigation plots. Stem water of trees inside the irrigation plots was highly enriched compared to...

A method for locating potential tree-planting sites in urban areas: a case study of Los Angeles, USA

Treesearch

Chunxia Wua; Qingfu Xiaoa; Gregory E. McPherson

2008-01-01

A GIS-based method for locating potential tree-planting sites based on land cover data is introduced. Criteria were developed to identify locations that are spatially available for potential tree planting based on land cover, sufficient distance from impervious surfaces, a minimum amount of pervious surface, and no crown overlap with other trees. In an ArcGIS...

Downstream impacts of a Central Amazonian hydroelectric dam on tree growth and mortality in floodplain forests

NASA Astrophysics Data System (ADS)

Resende, A. F. D.; Silva, T. S. F.; Silva, J. D. S.; Piedade, M. T. F.; Streher, A. S.; Ferreira-Ferreira, J.; Schongart, J.

2017-12-01

The flood pulse of large Amazonian Rivers is characterized by predictable high- and low-water periods during the annual cycle, and is the main driving force in the floodplains regulating decomposition, nutrient cycles, productivity, life cycles and growth rhythms of floodplains' biota. Over at least 20 millions of years, tree species in these ecosystems developed complex adaptative mechanisms to tolerate flooding, such as the tree species Macrolobium acaciifolium (Fabaceae) and Eschweilera tenuifolia (Lecythidaceae) occupying the lower topographic positions in the floodplain forests along the oligothrophic black-water rivers. Tree growth occurs mainly during terrestrial phase, while during the aquatic phase the anoxic conditions result into a cambial dormancy and formation of annual tree rings. The hydroelectric dam Balbina which was installed in the Uatumã River (central Amazonia) during the 1980s altered significantly the flood pulse regime resulting into higher minimum and lower maximum annual water levels. The suppression of the terrestrial phase caused large-scale mortality of flood-adapted trees growing on the lower topographic positions, as evidenced by radiocarbon dating and cross-dating techniques (dendrochronology). In this study we estimated the extension of dead forests using high resolution ALOS/PALSAR radar images, for their detection along a fluvial distance of more than 280 km downstream of the power plant. Further we analyzed tree growth of 60 living individuals of E. tenuifolia by tree-ring analyses comparing the post- and pre-dam periods. We evaluated the impacts of the altered hydrological regime on tree growth considering ontogenetic effects and the fluvial distance of the trees to the dam. Since the Balbina power plant started operating the associated igapó forests lost about 11% of its cover. We found a significant reduction of tree growth of E. tenuifolia during the post-dam period as a consequence of the increasing aquatic phase duration. This impact was stronger for younger trees (<200 yr) and for those growing closer to the hydroelectric dam (<100 km distance). Considering the planning of construction of several dozen dams in the Amazon there is an urgent need to consider these downstream impacts in all discussions of hydroelectric power plants implementation and operation.

Microarray-based Resequencing of Multiple Bacillus anthracis Isolates

DTIC Science & Technology

2004-12-17

generated an Unweighted Pair Group Method Arithmetic Mean ( UPGMA ) tree (see methods [56]; Figure 3). The strains group together in a manner broadly similar...was created using DNADIST, plotted as a UPGMA tree using NEIGHBOR and the tree plotted using DRAWGRAM [56]. The B1 strain A0465 was used as an...distance matrix was created using DNADIST, plotted as a UPGMA tree using NEIGHBOR and the tree plotted using DRAWGRAM [57]. Additional data files The

Effects of male fecundity, interindividual distance and anisotropic pollen dispersal on mating success in a Scots pine (Pinus sylvestris) seed orchard

PubMed Central

Torimaru, T; Wennström, U; Lindgren, D; Wang, X-R

2012-01-01

Quantifying the effect of pollen dispersal and flowering traits on mating success is essential for understanding evolutionary responses to changing environments and establishing strategies for forest tree breeding. This study examined, quantitatively, the effects of male fecundity, interindividual distance and anisotropic pollen dispersal on the mating success of Scots pine (Pinus sylvestris), utilizing a well-mapped Scots pine seed orchard. Paternity analysis of 1021 seeds sampled from 87 trees representing 28 clones showed that 53% of the seeds had at least one potential pollen parent within the orchard. Pronounced variation in paternal contribution was observed among clones. Variations in pollen production explained up to 78% of the variation in mating success, which was 11.2 times greater for clones producing the largest amount of pollen than for clones producing the least pollen. Mating success also varied with intertree distance and direction, which explained up to 28% of the variance. Fertilization between neighboring trees 2.3 m apart was 2.4 times more frequent than between trees 4.6 m apart, and up to 12.4 times higher for trees downwind of the presumed prevailing wind direction than for upwind trees. The effective number of pollen donors recorded in the seed orchard (12.2) was smaller than the theoretical expectation (19.7). Based on the empirical observations, a mating model that best describes the gene dispersal pattern in clonal seed orchards was constructed. PMID:21897440

Identifying species of moths (Lepidoptera) from Baihua Mountain, Beijing, China, using DNA barcodes

PubMed Central

Liu, Xiao F; Yang, Cong H; Han, Hui L; Ward, Robert D; Zhang, Ai-bing

2014-01-01

DNA barcoding has become a promising means for the identification of organisms of all life-history stages. Currently, distance-based and tree-based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups. Alternatively, DNA barcoding can deploy a “character-based” method, whereby species are identified through the discrete nucleotide substitutions. Our research focuses on the delimitation of moth species using DNA-barcoding methods. We analyzed 393 Lepidopteran specimens belonging to 80 morphologically recognized species with a standard cytochrome c oxidase subunit I (COI) sequencing approach, and deployed tree-based, distance-based, and diagnostic character-based methods to identify the taxa. The tree-based method divided the 393 specimens into 79 taxa (species), and the distance-based method divided them into 84 taxa (species). Although the diagnostic character-based method found only 39 so-identifiable species in the 80 species, with a reduction in sample size the accuracy rate substantially improved. For example, in the Arctiidae subset, all 12 species had diagnostics characteristics. Compared with traditional morphological method, molecular taxonomy performed well. All three methods enable the rapid delimitation of species, although they have different characteristics and different strengths. The tree-based and distance-based methods can be used for accurate species identification and biodiversity studies in large data sets, while the character-based method performs well in small data sets and can also be used as the foundation of species-specific biochips. PMID:25360280

Individual-tree probability of survival model for the Northeastern United States

Treesearch

Richard M. Teck; Donald E. Hilt

1990-01-01

Describes a distance-independent individual-free probability of survival model for the Northeastern United States. Survival is predicted using a sixparameter logistic function with species-specific coefficients. Coefficients are presented for 28 species groups. The model accounts for variability in annual survival due to species, tree size, site quality, and the tree...

Key algorithms used in GR02: A computer simulation model for predicting tree and stand growth

Treesearch

Garrett A. Hughes; Paul E. Sendak; Paul E. Sendak

1985-01-01

GR02 is an individual tree, distance-independent simulation model for predicting tree and stand growth over time. It performs five major functions during each run: (1) updates diameter at breast height, (2) updates total height, (3) estimates mortality, (4) determines regeneration, and (5) updates crown class.

A New Tool for Managing Students' Self-Evaluations in Traditional and Distance Education Courses.

ERIC Educational Resources Information Center

Contreras-Castillo, Juan; Block, Arthur Edwards

This paper describes a Web-based question-answering system called E-teacher that can be used in both traditional and distance learning courses to review academic contents. E-teacher is a self-editing template-based system that consists of a set of PHP scripts that generate the HTML code dynamically, or "on the fly." The entire E-teacher…

Observaciones geomagnéticas de la Isla Livingston, Antártida 2003 y campaña 2003-2004 %t Livingston Island geomagnetic observations, Antarctica 2003 and 2003-2004 survey

NASA Astrophysics Data System (ADS)

Marsal, S.; Torta, J. M.; Gaya-Piqué, L.; Curto, J. J.; Sanclement, E.; Solé, J. G.; Altadill, D.; Ugalde, A.; de Santis, A.; Apostolov, E. M.; Alberca, L. F.; García, A.

This CD-ROM presents the Livingston Island Geomagnetic Observatory Bulletin, edited by Observatori de l'Ebre, containing the data obtained during the years 2003 including the 2003-2004 Austral summer survey. edited in digital format, The structure of the CD-ROM consists of one file with the Bulletin contents in PDF and of a tree of directories and subdirectories with the data corresponding to the different years and months of the Bulletin. These data files and their names were built according to the IAGA-2002 data exchange format.

Mirroring co-evolving trees in the light of their topologies.

PubMed

Hajirasouliha, Iman; Schönhuth, Alexander; de Juan, David; Valencia, Alfonso; Sahinalp, S Cenk

2012-05-01

Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain families through maximizing the similarity between trimmed versions of their phylogenetic trees. Since maximization of any natural similarity score is computationally difficult, many approaches employ heuristics to evaluate the distance matrices corresponding to the tree topologies in question. In this article, we devise an efficient deterministic algorithm which directly maximizes the similarity between two leaf labeled trees with edge lengths, obtaining a score-optimal alignment of the two trees in question. Our algorithm is significantly faster than those methods based on distance matrix comparison: 1 min on a single processor versus 730 h on a supercomputer. Furthermore, we outperform the current state-of-the-art exhaustive search approach in terms of precision, while incurring acceptable losses in recall. A C implementation of the method demonstrated in this article is available at http://compbio.cs.sfu.ca/mirrort.htm

Spatial Distribution of Oak Mistletoe as It Relates to Habits of Oak Woodland Frugivores

PubMed Central

Wilson, Ethan A.; Sullivan, Patrick J.; Dickinson, Janis L.

2014-01-01

This study addresses the underlying spatial distribution of oak mistletoe, Phoradendron villosum, a hemi-parasitic plant that provides a continuous supply of berries for frugivorous birds overwintering the oak savanna habitat of California's outer coast range. As the winter community of birds consuming oak mistletoe varies from group-living territorial species to birds that roam in flocks, we asked if mistletoe volume was spatially autocorrelated at the scale of persistent territories or whether the patterns predicted by long-term territory use by western bluebirds are overcome by seed dispersal by more mobile bird species. The abundance of mistletoe was mapped on trees within a 700 ha study site in Carmel Valley, California. Spatial autocorrelation of mistletoe volume was analyzed using the variogram method and spatial distribution of oak mistletoe trees was analyzed using Ripley's K and O-ring statistics. On a separate set of 45 trees, mistletoe volume was highly correlated with the volume of female, fruit-bearing plants, indicating that overall mistletoe volume is a good predictor of fruit availability. Variogram analysis showed that mistletoe volume was spatially autocorrelated up to approximately 250 m, a distance consistent with persistent territoriality of western bluebirds and philopatry of sons, which often breed next door to their parents and are more likely to remain home when their parents have abundant mistletoe. Using Ripley's K and O-ring analyses, we showed that mistletoe trees were aggregated for distances up to 558 m, but for distances between 558 to 724 m the O-ring analysis deviated from Ripley's K in showing repulsion rather than aggregation. While trees with mistletoe were aggregated at larger distances, mistletoe was spatially correlated at a smaller distance, consistent with what is expected based on persistent group territoriality of western bluebirds in winter and the extreme philopatry of their sons. PMID:25389971

Genome-editing technologies and their potential application in horticultural crop breeding

PubMed Central

Xiong, Jin-Song; Ding, Jing; Li, Yi

2015-01-01

Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed. PMID:26504570

Classroom Ideas-Winter 1983. Focus on Geology: Rocks, Sand and Crystals. Primary Edition.

ERIC Educational Resources Information Center

Kern County Superintendent of Schools, Bakersfield, Ca. Div. of Instructional Services.

One of a series of activity guides, this publication offers a variety of learning activities and resource materials for primary grade students. The activities and resources include: science activities (especially dealing with soil and rocks); word puzzles and other puzzles; arts and crafts activities (including Christmas tree ornaments);…

Study of the effectiveness of several tree canopy types on roadside green belt in influencing the distribution of NO2 gas emitted from transportation

NASA Astrophysics Data System (ADS)

Desyana, R. D.; Sulistyantara, B.; Nasrullah, N.; Fatimah, I. S.

2017-03-01

Transportation is one significant factor which contributes to urban air pollution. One of the pollutants emitted from transportation which affect human’s health is NO2. Plants, especially trees, have high potential in reducing air pollutants from transportation through diffusion, absorbtion, adsorption and deposition. Purpose of this study was to analyze the effectiveness of several tree canopy types on roadside green belt in influencing distribution of NO2 gas emitted from transportation. The study conducted in three plots of tree canopy in Jagorawi Highway: Bungur (Lagerstroemia speciosa), Gmelina (Gmelina arborea) and Tanjung (Mimusops elengi). The tree canopy ability in absorbing pollutant is derived by comparing air quality on vegetated area with ambience air quality at control area (open field). Air sampling was conducted to measure NO2 concentration at elevation 1.5m, 5m and 10m at distance 0m, 10m and 30m, using Air Sampler Impinger. Concentration of NO2 was analyzed with Griess-Saltzman method. From this research, the result of ANOVA showed that tree plot (vegetated area) affected significantly to NO2 concentration. However the effect of distance from road and elevation was not significant. Among the plots, the highest NO2 concentration was found on Control plot (area without tree canopy), while the lowest NO2 concentration was found in Tanjung plot. Tanjung plot with round shape and high density canopy performed better in reducing NO2 than Bungur plot with round shape and medium density canopy, regardless the sampling elevation and distance. Gmelina plot performed the best in reducing horizontal distribution of NO2 concentration at elevation 1.5 and 5m, but the result at elevation 10m was not significant.

From Curves to Trees: A Tree-like Shapes Distance Using the Elastic Shape Analysis Framework.

PubMed

Mottini, A; Descombes, X; Besse, F

2015-04-01

Trees are a special type of graph that can be found in various disciplines. In the field of biomedical imaging, trees have been widely studied as they can be used to describe structures such as neurons, blood vessels and lung airways. It has been shown that the morphological characteristics of these structures can provide information on their function aiding the characterization of pathological states. Therefore, it is important to develop methods that analyze their shape and quantify differences between their structures. In this paper, we present a method for the comparison of tree-like shapes that takes into account both topological and geometrical information. This method, which is based on the Elastic Shape Analysis Framework, also computes the mean shape of a population of trees. As a first application, we have considered the comparison of axon morphology. The performance of our method has been evaluated on two sets of images. For the first set of images, we considered four different populations of neurons from different animals and brain sections from the NeuroMorpho.org open database. The second set was composed of a database of 3D confocal microscopy images of three populations of axonal trees (normal and two types of mutations) of the same type of neurons. We have calculated the inter and intra class distances between the populations and embedded the distance in a classification scheme. We have compared the performance of our method against three other state of the art algorithms, and results showed that the proposed method better distinguishes between the populations. Furthermore, we present the mean shape of each population. These shapes present a more complete picture of the morphological characteristics of each population, compared to the average value of certain predefined features.

Sanio's laws revisited. Size-dependent changes in the xylem architecture of trees.

PubMed

Mencuccini, Maurizio; Hölttä, Teemu; Petit, Giai; Magnani, Federico

2007-11-01

Early observations led Sanio [Wissen. Bot., 8, (1872) 401] to state that xylem conduit diameters and lengths in a coniferous tree increase from the apex down to a height below which they begin to decrease towards the tree base. Sanio's law of vertical tapering has been repeatedly tested with contradictory results and the debate over the scaling of conduit diameters with distance from the apex has not been settled. The debate has recently acquired new vigour, as an accurate knowledge of the vertical changes in wood anatomy has been shown to be crucial to scaling metabolic properties to plant and ecosystem levels. Contrary to Sanio's hypothesis, a well known model (MST, metabolic scaling theory) assumes that xylem conduits monotonically increase in diameter with distance from the apex following a power law. This has been proposed to explain the three-fourth power scaling between size and metabolism seen across plants. Here, we (i) summarized available data on conduit tapering in trees and (ii) propose a new numerical model that could explain the observed patterns. Data from 101 datasets grouped into 48 independent profiles supported the notions that phylogenetic group (angiosperms versus gymnosperms) and tree size strongly affected the vertical tapering of conduit diameter. For both angiosperms and gymnosperms, within-tree tapering also varied with distance from the apex. The model (based on the concept that optimal conduit tapering occurs when the difference between photosynthetic gains and wall construction costs is maximal) successfully predicted all three major empirical patterns. Our results are consistent with Sanio's law only for large trees and reject the MST assumptions that vertical tapering in conduit diameter is universal and independent of rank number.

Stand-structural effects on Heterobasidion abietinum-related mortality following drought events in Abies pinsapo.

PubMed

Linares, Juan Carlos; Camarero, Jesús Julio; Bowker, Matthew A; Ochoa, Victoria; Carreira, José Antonio

2010-12-01

Climate change may affect tree-pathogen interactions. This possibility has important implications for drought-prone forests, where stand dynamics and disease pathogenicity are especially sensitive to climatic stress. In addition, stand structural attributes including density-dependent tree-to-tree competition may modulate the stands' resistance to drought events and pathogen outbreaks. To assess the effects of stand structure on root-rot-related mortality after severe droughts, we focused on Heterobasidion abietinum mortality in relict Spanish stands of Abies pinsapo, a drought-sensitive fir. We compared stand attributes and tree spatial patterns in three plots with H. abietinum root-rot disease and three plots without root-rot. Point-pattern analyses were used to investigate the scale and extent of mortality patterns and to test hypotheses related to the spread of the disease. Dendrochronology was used to date the year of death and to assess the association between droughts and growth decline. We applied a structural equation modelling approach to test if tree mortality occurs more rapidly than predicted by a simple distance model when trees are subjected to high tree-to-tree competition and following drought events. Contrary to expectations of drought mortality, the effect of precipitation on the year of death was strong and negative, indicating that a period of high precipitation induced an earlier tree death. Competition intensity, related to the size and density of neighbour trees, also induced an earlier tree death. The effect of distance to the disease focus was negligible except in combination with intensive competition. Our results indicate that infected trees have decreased ability to withstand drought stress, and demonstrate that tree-to-tree competition and fungal infection act as predisposing factors of forest decline and mortality.

Dynamics of water transport and storage in conifers studied with deuterium and heat tracing techniques.

Treesearch

F.C. Meinzer; J.R. Brooks; J.-C. Domec; B.L. Gartner; J.M. Warren; D.R. Woodruff; K. Bible; D.C. Shaw

2006-01-01

The volume and complexity of their vascular systems make the dynamics of tong-distance water transport in large trees difficult to study. We used heat and deuterated water (D20) as tracers to characterize whole-tree water transport and storage properties in individual trees belonging to the coniferous species Pseudotsuga menziesii...

Modeling the effectiveness of tree planting to mitigate habitat loss in blue oak woodlands

Treesearch

Richard B. Standiford; Douglas McCreary; William Frost

2002-01-01

Many local conservation policies have attempted to mitigate the loss of oak woodland habitat resulting from conversion to urban or intensive agricultural land uses through tree planting. This paper models the development of blue oak (Quercus douglasii) stand structure attributes over 50 years after planting. The model uses a single tree, distance...

Rapid Assessment of Tree Debris Following Urban Forest Ice Storms

Treesearch

Richard J. Hauer; Angela J. Hauer; Dudley R. Hartel; Jill R. Johnson

2011-01-01

This paper presents a rapid assessment method to estimate urban tree debris following an ice storm. Data were collected from 60 communities to quantify tree debris volumes, mostly from public rights-of-way, following ice storms based on community infrastructure, weather parameters, and urban forest structure. Ice thickness, area of a community, and street distance are...

[Identification of pyrrosiae folium and its adulterants based on psbA-trnH sequence].

PubMed

Zhang, Ya-Qin; Shi, Yue; Song, Ming; Lin, Yun-Han; Ma, Xiao-Xi; Sun, Wei; Xiang, Li; Liu, Xi

2014-06-01

In this study, the psbA-trnH sequence as DNA barcode was used to evaluate the accuracy and stability for identification pteridophyte medicinal material Pyrrosiae Foliumas from adulterants. Genomic DNA from 106 samples were extracted successfully. The Kimura 2-Parameter (K2P) distances and ML tree were calculated using software MEGA 6.0. The intra-specific genetic distances of 3 original plants were lower than inter-specific genetic distances of adulterants. The ML tree indicated that Pyrrosiae Folium can be distinguished from its adulterants obviously. Therefore, the psbA-trnH sequence as a barcode of the pteridophyte, can accurately and stably distinguish Pyrrosiae Folium from its adulterants.

Mistletoe Infection in an Oak Forest Is Influenced by Competition and Host Size

PubMed Central

Matula, Radim; Svátek, Martin; Pálková, Marcela; Volařík, Daniel; Vrška, Tomáš

2015-01-01

Host size and distance from an infected plant have been previously found to affect mistletoe occurrence in woody vegetation but the effect of host plant competition on mistletoe infection has not been empirically tested. For an individual tree, increasing competition from neighbouring trees decreases its resource availability, and resource availability is also known to affect the establishment of mistletoes on host trees. Therefore, competition is likely to affect mistletoe infection but evidence for such a mechanism is lacking. Based on this, we hypothesised that the probability of occurrence as well as the abundance of mistletoes on a tree would increase not only with increasing host size and decreasing distance from an infected tree but also with decreasing competition by neighbouring trees. Our hypothesis was tested using generalized linear models (GLMs) with data on Loranthus europaeus Jacq., one of the two most common mistletoes in Europe, on 1015 potential host stems collected in a large fully mapped plot in the Czech Republic. Because many trees were multi-stemmed, we ran the analyses for both individual stems and whole trees. We found that the probability of mistletoe occurrence on individual stems was affected mostly by stem size, whereas competition had the most important effects on the probability of mistletoe occurrence on whole trees as well as on mistletoe abundance. Therefore, we confirmed our hypothesis that competition among trees has a negative effect on mistletoe occurrence. PMID:25992920

A Recursive Partitioning Method for the Prediction of Preference Rankings Based Upon Kemeny Distances.

PubMed

D'Ambrosio, Antonio; Heiser, Willem J

2016-09-01

Preference rankings usually depend on the characteristics of both the individuals judging a set of objects and the objects being judged. This topic has been handled in the literature with log-linear representations of the generalized Bradley-Terry model and, recently, with distance-based tree models for rankings. A limitation of these approaches is that they only work with full rankings or with a pre-specified pattern governing the presence of ties, and/or they are based on quite strict distributional assumptions. To overcome these limitations, we propose a new prediction tree method for ranking data that is totally distribution-free. It combines Kemeny's axiomatic approach to define a unique distance between rankings with the CART approach to find a stable prediction tree. Furthermore, our method is not limited by any particular design of the pattern of ties. The method is evaluated in an extensive full-factorial Monte Carlo study with a new simulation design.

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

PubMed Central

2010-01-01

Background Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. Results We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. Conclusions GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events. PMID:20534164

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

PubMed

Thomas, Paul D

2010-06-09

Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events.

Spatial effects of aboveground biomass on soil ecological parameters and trace gas fluxes in a savannah ecosystem of Mount Kilimanjaro

NASA Astrophysics Data System (ADS)

Becker, Joscha; Gütlein, Adrian; Sierra Cornejo, Natalia; Kiese, Ralf; Hertel, Dietrich; Kuzyakov, Yakov

2015-04-01

The savannah biome is a hotspot for biodiversity and wildlife conservation in Africa and recently got in the focus of research on carbon sequestration. Savannah ecosystems are under strong pressure from climate and land-use change, especially around populous areas like the Mt. Kilimanjaro region. Savannah vegetation in this area consists of grassland with isolated trees and is therefore characterized by high spatial variation of canopy cover, aboveground biomass and root structure. Canopy structure is known to affect microclimate, throughfall and evapotranspiration and thereby controls soil moisture conditions. Consequently, the canopy structure is a major regulator for soil ecological parameters and soil-atmospheric trace gas exchange (CO2, N2O, CH4) in water limited environments. The spatial distribution of these parameters and the connection between above and belowground processes are important to understand and predict ecosystem changes and estimate its vulnerability. Our objective was to determine trends and changes of soil parameters and relate their spatial variability to the vegetation structure. We chose three trees from each of the two most dominant species (Acacia nilotica and Balanites aegyptiaca) in our research area. For each tree, we selected transects with nine sampling points of the same relative distances to the stem. Distances were calculated in relation to the crown radius. At these each sampling point a soil core was taken and separated in 0-10 cm and 10-30 cm depth. We measured soil carbon (C) and nitrogen (N) storage, microbial biomass carbon C and N, soil respiration as well as root biomass and -density, soil temperature and soil water content. Each tree was characterized by crown spread, leaf area index and basal area. Preliminary results show that C and N stocks decreased about 50% with depth independently of distance to the tree. Soil water content under the tree crown increased with depth while it decreased under grass cover. Microbial Biomass C and N in the upper 10 cm decreased with distance (C: r²=0.22, p<0.001; N: r²=0.3, p<0.001) as well as total soil respiration. This decrease was affected by tree size but independent from tree species. We conclude that savannah ecosystems exhibit a large spatial variability of soil parameters within the upper horizons which is strongly depend on the structure of aboveground biomass.

Fire reinforces structure of pondcypress (Taxodium distichum var. imbricarium) domes in a wetland landscape

USGS Publications Warehouse

Watts, Adam C.; Kobziar, Leda N.; Snyder, James R.

2012-01-01

Fire periodically affects wetland forests, particularly in landscapes with extensive fire-prone uplands. Rare occurrence and difficulty of access have limited efforts to understand impacts of wildfires fires in wetlands. Following a 2009 wildfire, we measured tree mortality and structural changes in wetland forest patches. Centers of these circular landscape features experienced lower fire severity, although no continuous patch-size or edge effect was evident. Initial survival of the dominant tree, pondcypress (Taxodium distichum var. imbricarium), was high (>99%), but within one year of the fire approximately 23% of trees died. Delayed mortality was correlated with fire severity, but unrelated to other hypothesized factors such as patch size or edge distance. Tree diameter and soil elevation were important predictors of mortality, with smaller trees and those in areas with lower elevation more likely to die following severe fire. Depressional cypress forests typically exhibit increasing tree size towards their interiors, and differential mortality patterns were related to edge distance. These patterns result in the exaggeration of a dome-shaped profile. Our observations quantify roles of fire and hydrology in determining cypress mortality in these swamps, and imply the existence of feedbacks that maintain the characteristic shape of cypress domes.

Polyhedral geometry of phylogenetic rogue taxa.

PubMed

Cueto, María Angélica; Matsen, Frederick A

2011-06-01

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.

Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

PubMed

Santos, Bráulio A; Arroyo-Rodríguez, Víctor; Moreno, Claudia E; Tabarelli, Marcelo

2010-09-08

Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment of tree assemblages reduce the phylogenetic diversity of the remaining tree assemblages. We detected a significant loss of tree phylogenetic diversity in forest edges, but not in core areas of small (<80 ha) forest fragments. This was attributed to a reduction of 11% in the average phylogenetic distance between any two randomly chosen individuals from forest edges; an increase of 17% in the average phylogenetic distance to closest non-conspecific relative for each individual in forest edges; and to the potential manifestation of late edge effects in the core areas of small forest remnants. We found no evidence supporting fragmentation-induced phylogenetic clustering or evenness. This could be explained by the low phylogenetic conservatism of key life-history traits corresponding to vulnerable species. Edge effects must be reduced to effectively protect tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

PubMed

Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

Multiphase Interface Tracking with Fast Semi-Lagrangian Contouring.

PubMed

Li, Xiaosheng; He, Xiaowei; Liu, Xuehui; Zhang, Jian J; Liu, Baoquan; Wu, Enhua

2016-08-01

We propose a semi-Lagrangian method for multiphase interface tracking. In contrast to previous methods, our method maintains an explicit polygonal mesh, which is reconstructed from an unsigned distance function and an indicator function, to track the interface of arbitrary number of phases. The surface mesh is reconstructed at each step using an efficient multiphase polygonization procedure with precomputed stencils while the distance and indicator function are updated with an accurate semi-Lagrangian path tracing from the meshes of the last step. Furthermore, we provide an adaptive data structure, multiphase distance tree, to accelerate the updating of both the distance function and the indicator function. In addition, the adaptive structure also enables us to contour the distance tree accurately with simple bisection techniques. The major advantage of our method is that it can easily handle topological changes without ambiguities and preserve both the sharp features and the volume well. We will evaluate its efficiency, accuracy and robustness in the results part with several examples.

Scaling of xylem and phloem transport capacity and resource usage with tree size

PubMed Central

Hölttä, Teemu; Kurppa, Miika; Nikinmaa, Eero

2013-01-01

Xylem and phloem need to maintain steady transport rates of water and carbohydrates to match the exchange rates of these compounds at the leaves. A major proportion of the carbon and nitrogen assimilated by a tree is allocated to the construction and maintenance of the xylem and phloem long distance transport tissues. This proportion can be expected to increase with increasing tree size due to the growing transport distances between the assimilating tissues, i.e., leaves and fine roots, at the expense of their growth. We formulated whole tree level scaling relations to estimate how xylem and phloem volume, nitrogen content and hydraulic conductance scale with tree size, and how these properties are distributed along a tree height. Xylem and phloem thicknesses and nitrogen contents were measured within varying positions in four tree species from Southern Finland. Phloem volume, nitrogen amount and hydraulic conductance were found to be concentrated toward the branch and stem apices, in contrast to the xylem where these properties were more concentrated toward the tree base. All of the species under study demonstrated very similar trends. Total nitrogen amount allocated to xylem and phloem was predicted to be comparable to the nitrogen amount allocated to the leaves in small and medium size trees, and to increase significantly above the nitrogen content of the leaves in larger trees. Total volume, hydraulic conductance and nitrogen content of the xylem were predicted to increase faster than that of the phloem with increasing tree height in small trees (<~10 m in height). In larger trees, xylem sapwood turnover to heartwood, if present, would maintain phloem conductance at the same level with xylem conductance with further increases in tree height. Further simulations with a previously published xylem-phloem transport model demonstrated that the Münch pressure flow hypothesis could explain phloem transport with increasing tree height even for the tallest trees. PMID:24367373

Dynamic Ising model: reconstruction of evolutionary trees

NASA Astrophysics Data System (ADS)

de Oliveira, P. M. C.

2013-09-01

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. ‘Species’ here is a general denomination for biological species, spoken languages or any other entity which evolves through heredity. From the N currently alive species within a clade, distances are measured through pairwise comparisons made by geneticists, linguists, etc. The larger is such a distance that, for a pair of species, the older is their last common ancestor. The aim is to reconstruct the previously unknown bifurcations, i.e. the whole clade, from knowledge of the N(N - 1)/2 quoted distances, which are taken for granted. A mechanical method is presented and its applicability is discussed.

Molecular phylogenetic trees - On the validity of the Goodman-Moore augmentation algorithm

NASA Technical Reports Server (NTRS)

Holmquist, R.

1979-01-01

A response is made to the reply of Nei and Tateno (1979) to the letter of Holmquist (1978) supporting the validity of the augmentation algorithm of Moore (1977) in reconstructions of nucleotide substitutions by means of the maximum parsimony principle. It is argued that the overestimation of the augmented numbers of nucleotide substitutions (augmented distances) found by Tateno and Nei (1978) is due to an unrepresentative data sample and that it is only necessary that evolution be stochastically uniform in different regions of the phylogenetic network for the augmentation method to be useful. The importance of the average value of the true distance over all links is explained, and the relative variances of the true and augmented distances are calculated to be almost identical. The effects of topological changes in the phylogenetic tree on the augmented distance and the question of the correctness of ancestral sequences inferred by the method of parsimony are also clarified.

Soil pH and extractable sulfate-sulfur distribution as influenced by tree species and distance from the stem. [Acer rubrum; Quercus coccinea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolfe, M.H.; Kelly, J.M.; Wolt, J.D.

Stemflow influence on the distribution of soil (NaH/sub 2/PO/sub 4/ extractable) SO/sub 4/-S and pH was evaluated as a function of tree size class and distance from the stem for red maple (Acer rubrum L.) and scarlet oak (Quercus coccinea Muenchh.) at two locations in Tennessee which have received different historical inputs of S from atmospheric sources. Soil profiles around the base of each study tree were sampled by horizon at 25, 50, 100, and 200 cm from the stem along four transects radiating from the stem at 90/sup 0/ angles. Distance from the stem influenced soil pH of Amore » horizons at 25 cm from the stem of red maple and scarlet oak at both sites. Species had an effect on Bt2 and Bt3 soil SO/sub 4/-S concentrations. The Bt2 (0.49 cmol kg/sup -1/) and Bt3 (0.67 cmol kg/sup -1/) horizons beneath scarlet oaks had greater SO/sub 4/-S concentrations than corresponding horizons beneath red maple (0.29 and 0.43 cmol kg/sup -1/, respectively). The results of this study indicate that increased sampling intensity combined with tracer studies will be need to clearly determine the effect of stemflow, tree species, and tree size on subtlety-manifested soil properties such as pH and SO/sub 4/-S as well as other elements of interest.« less

Bottom flange reinforcement in NU I-girders.

DOT National Transportation Integrated Search

2010-08-01

"The 1996 edition of AASHTO Standard Specifications for Highway Bridges stated that nominal confinement reinforcement be placed to enclose prestressing steel in the bottom flange of bridge girders from girder ends to at least a distance eq changed th...

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

PubMed Central

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-01-01

Background The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. Results We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. Conclusion By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development. PMID:16740163

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.

PubMed

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-06-01

The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development.

Individual-tree diameter growth model for managed, even-aged, upland oak stands

Treesearch

Donald E. Hilt

1983-01-01

A distance-independent, individual-tree diameter growth model was developed for managed, even-aged, upland oak stands. The 5-year basal-area growth of individual trees is first modeled as a function of dbh squared for given stands. Parameters from these models are then modeled as a function of mean stand diameter, percent stocking of the stand, and site index. A...

Extracting whole short rotation trees with a skidder and a front-end loader

Treesearch

R. Spinelli; B.R. Hartsough

2001-01-01

We time-studied a Caterpillar 950F front-end loader and a Caterpillar 528 grapple skidder used to extract bunched whole trees to a landing in a short rotation Eucalyptus plantation. The loader was 40-60% more productive than the grapple skidder, depending on extraction distance. Alternatively, the single loader could both extract trees and handle the landing duties,...

Tree-oriented interactive processing with an application to theorem-proving, appendix E

NASA Technical Reports Server (NTRS)

Hammerslag, David; Kamin, Samuel N.; Campbell, Roy H.

1985-01-01

The concept of unstructured structure editing and ted, an editor for unstructured trees, is described. Ted is used to manipulate hierarchies of information in an unrestricted manner. The tool was implemented and applied to the problem of organizing formal proofs. As a proof management tool, it maintains the validity of a proof and its constituent lemmas independently from the methods used to validate the proof. It includes an adaptable interface which may be used to invoke theorem provers and other aids to proof construction. Using ted, a user may construct, maintain, and verify formal proofs using a variety of theorem provers, proof checkers, and formatters.

Phylogenetic turnover along local environmental gradients in tropical forest communities.

PubMed

Baldeck, C A; Kembel, S W; Harms, K E; Yavitt, J B; John, R; Turner, B L; Madawala, S; Gunatilleke, N; Gunatilleke, S; Bunyavejchewin, S; Kiratiprayoon, S; Yaacob, A; Supardi, M N N; Valencia, R; Navarrete, H; Davies, S J; Chuyong, G B; Kenfack, D; Thomas, D W; Dalling, J W

2016-10-01

While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3 % and 0.4-8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved.

Towards a formal genealogical classification of the Lezgian languages (North Caucasus): testing various phylogenetic methods on lexical data.

PubMed

Kassian, Alexei

2015-01-01

A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ), Neighbor joining (NJ), Unweighted pair group method with arithmetic mean (UPGMA), Bayesian Markov chain Monte Carlo (MCMC), Unweighted maximum parsimony (UMP). Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances). Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists), the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA) have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP) have yielded less likely topologies.

Towards a Formal Genealogical Classification of the Lezgian Languages (North Caucasus): Testing Various Phylogenetic Methods on Lexical Data

PubMed Central

Kassian, Alexei

2015-01-01

A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ), Neighbor joining (NJ), Unweighted pair group method with arithmetic mean (UPGMA), Bayesian Markov chain Monte Carlo (MCMC), Unweighted maximum parsimony (UMP). Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances). Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists), the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA) have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP) have yielded less likely topologies. PMID:25719456

Democratization in a passive dendritic tree: an analytical investigation.

PubMed

Timofeeva, Y; Cox, S J; Coombes, S; Josić, K

2008-10-01

One way to achieve amplification of distal synaptic inputs on a dendritic tree is to scale the amplitude and/or duration of the synaptic conductance with its distance from the soma. This is an example of what is often referred to as "dendritic democracy". Although well studied experimentally, to date this phenomenon has not been thoroughly explored from a mathematical perspective. In this paper we adopt a passive model of a dendritic tree with distributed excitatory synaptic conductances and analyze a number of key measures of democracy. In particular, via moment methods we derive laws for the transport, from synapse to soma, of strength, characteristic time, and dispersion. These laws lead immediately to synaptic scalings that overcome attenuation with distance. We follow this with a Neumann approximation of Green's representation that readily produces the synaptic scaling that democratizes the peak somatic voltage response. Results are obtained for both idealized geometries and for the more realistic geometry of a rat CA1 pyramidal cell. For each measure of democratization we produce and contrast the synaptic scaling associated with treating the synapse as either a conductance change or a current injection. We find that our respective scalings agree up to a critical distance from the soma and we reveal how this critical distance decreases with decreasing branch radius.

Application of the Classification Tree Model in Predicting Learner Dropout Behaviour in Open and Distance Learning

ERIC Educational Resources Information Center

Yasmin, Dr.

2013-01-01

This paper demonstrates the meaningful application of learning analytics for determining dropout predictors in the context of open and distance learning in a large developing country. The study was conducted at the Directorate of Distance Education at the University of North Bengal, West Bengal, India. This study employed a quantitative research…

Phylogenetic trees and Euclidean embeddings.

PubMed

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.

Distribution of Mercury Concentrations in Tree Rings and Surface Soils Adjacent to a Phosphate Fertilizer Plant in Southern Korea.

PubMed

Jung, Raae; Ahn, Young Sang

2017-08-01

This study aimed to determine mercury concentrations in tree rings and surface soils at distances of 4, 26 and 40 km from a fertilizer plant located in Yeosu City, Korea. Mercury concentrations in all tree rings were low prior to the establishment of the plant in 1977 and became elevated thereafter. The highest average mercury concentration in the tree rings was 11.96 ng g -1 at the Yeosu site located nearest to the plant, with the lowest average mercury concentration of 4.45 ng g -1 at the Suncheon site furthest away from the plant. In addition, the highest mercury content in the surface soil was 108.51 ng cm -3 at the Yeosu site, whereas the lowest mercury content in the surface soil was 31.47 ng cm -3 at the Suncheon site. The mercury levels decreased gradually with increasing distance from the plant.

Journal of Air Transportation, Volume 12, No. 2 (ATRS Special Edition)

NASA Technical Reports Server (NTRS)

Bowen, Brent D. (Editor); Kabashkin, Igor (Editor); Fink, Mary (Editor)

2007-01-01

Topics covered include: Competition and Change in the Long-Haul Markets from Europe; Insights into the Maintenance, Repair, and Overhaul Configurations of European Airlines; Validation of Fault Tree Analysis in Aviation Safety Management; An Investigation into Airline Service Quality Performance between U.S. Legacy Carriers and Their EU Competitors and Partners; and Climate Impact of Aircraft Technology and Design Changes.

A program to compute the soft Robinson-Foulds distance between phylogenetic networks.

PubMed

Lu, Bingxin; Zhang, Louxin; Leong, Hon Wai

2017-03-14

Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks. Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.

Reduced density due to logging and its consequences on mating system and pollen flow in the African mahogany Entandrophragma cylindricum.

PubMed

Lourmas, M; Kjellberg, F; Dessard, H; Joly, H I; Chevallier, M-H

2007-08-01

In tropical forests, selective logging removes large trees that are often the main contributors to pollination. We studied pollination patterns of the African mahogany, Entandrophragma cylindricum (Sapelli). We investigated two plots in Cameroon corresponding to three tree densities: unlogged forest (Ndama 2002), a mildly logged forest 1 year after logging (Ndama 2003) and a severely logged forest 30 years after logging (Dimako). We used four microsatellite markers to perform paternity analysis. Selfing remained below 2% in all treatments. Pollen flow was mainly long distance but with some proximity effects. Average observed within-plot pollination distances were 338, 266 and 385 m, and pollination by trees outside the plots was 70% (Ndama 2002), 74% (Ndama 2003) and 66% (Dimako). Despite sampling a limited number of seeds from a limited number of mother trees, we obtained seeds sired by 35.6-38.3% of the potential within-plot pollen donors. While trees 20 cm in diameter contributed to pollination, results in Dimako suggest that individual larger trees contribute more to pollination than small ones. This effect was not detected in the other treatments. The results suggest extensive pollen flow in Sapelli. Hence, in Sapelli, the main limiting factor for regeneration after logging may be a reduction in the number of trees capable of producing seeds rather genetic effects due to limits to pollen dispersal.

Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition.

PubMed

Penny, D; Hasegawa, M; Waddell, P J; Hendy, M D

1999-03-01

We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.

Seed rain under native and non-native tree species in the Cabo Rojo National Wildlife Refuge, Puerto Rico.

PubMed

Arias Garcia, Andrea; Chinea, J Danilo

2014-09-01

Seed dispersal is a fundamental process in plant ecology and is of critical importance for the restoration of tropical communities. The lands of the Cabo Rojo National Wildlife Refuge (CRNWR), formerly under agriculture, were abandoned in the 1970s and colonized mainly by non-native tree species of degraded pastures. Here we described the seed rain under the most common native and non-native trees in the refuge in an attempt to determine if focal tree geographic origin (native versus non-native) influences seed dispersal. For this, seed rain was sampled for one year under the canopies of four native and four non-native tree species common in this refuge using 40 seed traps. No significant differences were found for the abundance of seeds, or their diversity, dispersing under native versus non-native focal tree species, nor under the different tree species. A significantly different seed species composition was observed reaching native versus non-native focal species. However, this last result could be more easily explained as a function of distance of the closest adults of the two most abundantly dispersed plant species to the seed traps than as a function of the geographic origin of the focal species. We suggest to continue the practice of planting native tree species, not only as a way to restore the community to a condition similar to the original one, but also to reduce the distances needed for effective dispersal.

Gene flow of common ash (Fraxinus excelsior L.) in a fragmented landscape.

PubMed

Semizer-Cuming, Devrim; Kjær, Erik Dahl; Finkeldey, Reiner

2017-01-01

Gene flow dynamics of common ash (Fraxinus excelsior L.) is affected by several human activities in Central Europe, including habitat fragmentation, agroforestry expansion, controlled and uncontrolled transfer of reproductive material, and a recently introduced emerging infectious disease, ash dieback, caused by Hymenoscyphus fraxineus. Habitat fragmentation may alter genetic connectivity and effective population size, leading to loss of genetic diversity and increased inbreeding in ash populations. Gene flow from cultivated trees in landscapes close to their native counterparts may also influence the adaptability of future generations. The devastating effects of ash dieback have already been observed in both natural and managed populations in continental Europe. However, potential long-term effects of genetic bottlenecks depend on gene flow across fragmented landscapes. For this reason, we studied the genetic connectivity of ash trees in an isolated forest patch of a fragmented landscape in Rösenbeck, Germany. We applied two approaches to parentage analysis to estimate gene flow patterns at the study site. We specifically investigated the presence of background pollination at the landscape level and the degree of genetic isolation between native and cultivated trees. Local meteorological data was utilized to understand the effect of wind on the pollen and seed dispersal patterns. Gender information of the adult trees was considered for calculating the dispersal distances. We found that the majority of the studied seeds (55-64%) and seedlings (75-98%) in the forest patch were fathered and mothered by the trees within the same patch. However, we determined a considerable amount of pollen flow (26-45%) from outside of the study site, representing background pollination at the landscape level. Limited pollen flow was observed from neighbouring cultivated trees (2%). Both pollen and seeds were dispersed in all directions in accordance with the local wind directions. Whereas there was no positive correlation between pollen dispersal distance and wind speed, the correlation between seed dispersal distance and wind speed was significant (0.71, p < 0.001), indicating that strong wind favours long-distance dispersal of ash seeds. Finally, we discussed the implications of establishing gene conservation stands and the use of enrichment planting in the face of ash dieback.

Gene flow of common ash (Fraxinus excelsior L.) in a fragmented landscape

PubMed Central

Kjær, Erik Dahl; Finkeldey, Reiner

2017-01-01

Gene flow dynamics of common ash (Fraxinus excelsior L.) is affected by several human activities in Central Europe, including habitat fragmentation, agroforestry expansion, controlled and uncontrolled transfer of reproductive material, and a recently introduced emerging infectious disease, ash dieback, caused by Hymenoscyphus fraxineus. Habitat fragmentation may alter genetic connectivity and effective population size, leading to loss of genetic diversity and increased inbreeding in ash populations. Gene flow from cultivated trees in landscapes close to their native counterparts may also influence the adaptability of future generations. The devastating effects of ash dieback have already been observed in both natural and managed populations in continental Europe. However, potential long-term effects of genetic bottlenecks depend on gene flow across fragmented landscapes. For this reason, we studied the genetic connectivity of ash trees in an isolated forest patch of a fragmented landscape in Rösenbeck, Germany. We applied two approaches to parentage analysis to estimate gene flow patterns at the study site. We specifically investigated the presence of background pollination at the landscape level and the degree of genetic isolation between native and cultivated trees. Local meteorological data was utilized to understand the effect of wind on the pollen and seed dispersal patterns. Gender information of the adult trees was considered for calculating the dispersal distances. We found that the majority of the studied seeds (55–64%) and seedlings (75–98%) in the forest patch were fathered and mothered by the trees within the same patch. However, we determined a considerable amount of pollen flow (26–45%) from outside of the study site, representing background pollination at the landscape level. Limited pollen flow was observed from neighbouring cultivated trees (2%). Both pollen and seeds were dispersed in all directions in accordance with the local wind directions. Whereas there was no positive correlation between pollen dispersal distance and wind speed, the correlation between seed dispersal distance and wind speed was significant (0.71, p < 0.001), indicating that strong wind favours long-distance dispersal of ash seeds. Finally, we discussed the implications of establishing gene conservation stands and the use of enrichment planting in the face of ash dieback. PMID:29053740

Productivity and cost of the ponsse 15-series, cust-to-length harvesting systems in southern pine plantations

Treesearch

Robert A. Tufts

1997-01-01

Machine productivity data were collected for a Ponsse HS-15 harvester and S-15 forwarder from study sites in central Alabama during a second thinning. Tree size, in terms of diameter at breast height and volume, and the number of pieces processed per tree, were the variables with the greatest impact on harvester productivity. The distance fiom the machine to the tree...

Comparison of a Skidder and Front-End Loader for Primary Transport of Short-Rotation Trees

Treesearch

Raffaele Spinelli; Bruce R. Hartsough

1999-01-01

We time-studied a Cat 950F and a Cat 528 grapple skidder as extraction devices for moving bunched whole trees to a landing in a short rotation eucalyptus plantation. The front-end loader was 40 to 60% more productive than the grapple skidder, depending on extraction distance. Alternatively, the single loader could both extract trees and handle the landing duties such...

Semiautomated landscape feature extraction and modeling

NASA Astrophysics Data System (ADS)

Wasilewski, Anthony A.; Faust, Nickolas L.; Ribarsky, William

2001-08-01

We have developed a semi-automated procedure for generating correctly located 3D tree objects form overhead imagery. Cross-platform software partitions arbitrarily large, geocorrected and geolocated imagery into management sub- images. The user manually selected tree areas from one or more of these sub-images. Tree group blobs are then narrowed to lines using a special thinning algorithm which retains the topology of the blobs, and also stores the thickness of the parent blob. Maxima along these thinned tree grous are found, and used as individual tree locations within the tree group. Magnitudes of the local maxima are used to scale the radii of the tree objects. Grossly overlapping trees are culled based on a comparison of tree-tree distance to combined radii. Tree color is randomly selected based on the distribution of sample tree pixels, and height is estimated form tree radius. The final tree objects are then inserted into a terrain database which can be navigated by VGIS, a high-resolution global terrain visualization system developed at Georgia Tech.

A possible biochemical missing link among archaebacteria

NASA Technical Reports Server (NTRS)

Achenbach-Richter, Laurie; Woese, Carl R.; Stetter, Karl O.

1987-01-01

The characteristics of the newly discovered strain of archaebacteria, VC-16, the only archaebacterium known to reduce sulfate, suggest that VC-16 might represent a transitional form between an anaerobic thermophilic sulfur-based type of metabolism and methanogenesis. It is shown here, using a matrix of evolutionary distances derived from an alignment of various archaebacterial 16S rRNAs and the phylogenetic tree derived from these evolutionary distances, that the lineage represented by strain VC-16 arises from the archaebacterial tree precisely where such an interpretation would predict that it would, between the Methanococcus lineage and that of Thermococcus.

Historical Human Footprint on Modern Tree Species Composition in the Purus-Madeira Interfluve, Central Amazonia

PubMed Central

Levis, Carolina; de Souza, Priscila Figueira; Schietti, Juliana; Emilio, Thaise; Pinto, José Luiz Purri da Veiga; Clement, Charles R.; Costa, Flavia R. C.

2012-01-01

Background Native Amazonian populations managed forest resources in numerous ways, often creating oligarchic forests dominated by useful trees. The scale and spatial distribution of forest modification beyond pre-Columbian settlements is still unknown, although recent studies propose that human impact away from rivers was minimal. We tested the hypothesis that past human management of the useful tree community decreases with distance from rivers. Methodology/Principal Findings In six sites, we inventoried trees and palms with DBH≥10 cm and collected soil for charcoal analysis; we also mapped archaeological evidence around the sites. To quantify forest manipulation, we measured the relative abundance, richness and basal area of useful trees and palms. We found a strong negative exponential relationship between forest manipulation and distance to large rivers. Plots located from 10 to 20 km from a main river had 20–40% useful arboreal species, plots between 20 and 40 km had 12–23%, plots more than 40 km had less than 15%. Soil charcoal abundance was high in the two sites closest to secondary rivers, suggesting past agricultural practices. The shortest distance between archaeological evidence and plots was found in sites near rivers. Conclusions/Significance These results strongly suggest that past forest manipulation was not limited to the pre-Columbian settlements along major rivers, but extended over interfluvial areas considered to be primary forest today. The sustainable use of Amazonian forests will be most effective if it considers the degree of past landscape domestication, as human-modified landscapes concentrate useful plants for human sustainable use and management today. PMID:23185264

Spatial variability in oviposition damage by periodical cicadas in a fragmented landscape.

PubMed

Cook, William M; Holt, Robert D; Yao, Jin

2001-03-01

Effects of the periodical cicada (Magicicada spp.) on forest dynamics are poorly documented. A 1998 emergence of M. cassini in eastern Kansas led to colonization of a fragmented experimental landscape undergoing secondary succession. We hypothesized that per-tree rates of oviposition damage by cicadas would reflect: (1) distance from the source of the emergence, (2) patch size, and (3) local tree density. Ovipositing females displayed clear preferences for host species and damage incidence showed predictable spatial patterns. Two species (smooth sumac, Rhus glabra, and eastern red cedar, Juniperus virginiana) were rarely attacked, whereas others (rough-leaved dogwood, Cornus drummondii; slippery elm, Ulmus rubra; box elder, Acer negundo, and honey locust, Gleditsia triacanthos) were strongly attacked. The dominant early successional tree, dogwood, received on average the most attacks. As predicted, attacks per stem declined strongly with distance from the emergence source, and with local stem density (a "dilution" effect). Contrary to expectations, there were more attacks per stem on larger patches. Because ovipositing cicadas cut damaging slits in host tree branches, potentially affecting tree growth rate, competitive ability, and capacity to reproduce, cicada damage could potentially influence spatial variation in secondary succession.

A Metric on Phylogenetic Tree Shapes

PubMed Central

Plazzotta, G.

2018-01-01

Abstract The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees’ branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. PMID:28472435

A Path Loss Model for Non-Line-of-Sight Ultraviolet Multiple Scattering Channels

DTIC Science & Technology

2010-01-01

scattering is self -governed, and the distances and angles for different scattering events are conditioned on previous quantities. Therefore, the arrival...solid angle of the receiver determined by the receiver area and distance rn. Note that no integration over rn is needed because it is a function of...www.eurasip.org). This year edition will take place in Barcelona, capital city of Catalonia (Spain), and will be jointly organized by the Centre Tecnològic de

Dynamic Shortest Path Algorithms for Hypergraphs

DTIC Science & Technology

2014-01-01

the concept of relationship tree to indicate the parent –child relationship along shortest hy- perpaths. The concept can be easily explained in the...four possible relationship trees to indicate the parent –child relationship in these shortest hyperpaths. We will show in Section III that the choice of...distance of a vertex to the source on the shortest hyperpath, the parent of in the chosen relationship tree associated with the shortest hyperpaths, This

Europe Today: A Reproducible Atlas. 1996 Revised Edition.

ERIC Educational Resources Information Center

World Eagle, Inc., Wellesley, MA.

This book contains blank outline maps of the European continent and tables and graphics depicting various aspects of Europe. Sections of the book include: (1) "Same Scale Maps, Silhouettes, Distances, Area"; (2) "Population"; (3) "Demographics, Ethnic, Religion, Health"; (4) "Economic, GDP, Import, Export,…

Oak tree-rings record spatial-temporal pollution trends from different sources in Terni (Central Italy).

PubMed

Perone, A; Cocozza, C; Cherubini, P; Bachmann, O; Guillong, M; Lasserre, B; Marchetti, M; Tognetti, R

2018-02-01

Monitoring atmospheric pollution in industrial areas near urban center is essential to infer past levels of contamination and to evaluate the impact for environmental health and safety. The main aim of this study was to understand if the chemical composition of tree-ring wood can be used for monitoring spatial-temporal variability of pollutants in Terni, Central Italy, one of the most polluted towns in Italy. Tree cores were taken from 32 downy oaks (Quercus pubescens) located at different distances from several pollutant sources, including a large steel factory. Trace element (Cr, Co, Cu, Pb, Hg, Mo, Ni, Tl, W, U, V, and Zn) index in tree-ring wood was determined using high-resolution laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). We hypothesized that the presence of contaminants detected in tree-rings reflected industrial activities over time. The accumulation of contaminants in tree-rings was affected by anthropogenic activities in the period 1958-2009, though signals varied in intensity with the distance of trees from the industrial plant. A stronger limitation of tree growth was observed in the proximity of the industrial plant in comparison with other pollutant sources. Levels of Cr, Ni, Mo, V, U and W increased in tree-ring profiles of trees close to the steel factory, especially during the 80's and 90's, in correspondence to a peak of pollution in this period, as recorded by air quality monitoring stations. Uranium contents in our tree-rings were difficult to explain, while the higher contents of Cu, Hg, Pb, and Tl could be related to the contaminants released from an incinerator located close to the industrial plant. The accumulation of contaminants in tree-rings reflected the historical variation of environmental pollution in the considered urban context. Copyright © 2017 Elsevier Ltd. All rights reserved.

Efficient and Scalable Graph Similarity Joins in MapReduce

PubMed Central

Chen, Yifan; Zhang, Weiming; Tang, Jiuyang

2014-01-01

Along with the emergence of massive graph-modeled data, it is of great importance to investigate graph similarity joins due to their wide applications for multiple purposes, including data cleaning, and near duplicate detection. This paper considers graph similarity joins with edit distance constraints, which return pairs of graphs such that their edit distances are no larger than a given threshold. Leveraging the MapReduce programming model, we propose MGSJoin, a scalable algorithm following the filtering-verification framework for efficient graph similarity joins. It relies on counting overlapping graph signatures for filtering out nonpromising candidates. With the potential issue of too many key-value pairs in the filtering phase, spectral Bloom filters are introduced to reduce the number of key-value pairs. Furthermore, we integrate the multiway join strategy to boost the verification, where a MapReduce-based method is proposed for GED calculation. The superior efficiency and scalability of the proposed algorithms are demonstrated by extensive experimental results. PMID:25121135

Efficient and scalable graph similarity joins in MapReduce.

PubMed

Chen, Yifan; Zhao, Xiang; Xiao, Chuan; Zhang, Weiming; Tang, Jiuyang

2014-01-01

Along with the emergence of massive graph-modeled data, it is of great importance to investigate graph similarity joins due to their wide applications for multiple purposes, including data cleaning, and near duplicate detection. This paper considers graph similarity joins with edit distance constraints, which return pairs of graphs such that their edit distances are no larger than a given threshold. Leveraging the MapReduce programming model, we propose MGSJoin, a scalable algorithm following the filtering-verification framework for efficient graph similarity joins. It relies on counting overlapping graph signatures for filtering out nonpromising candidates. With the potential issue of too many key-value pairs in the filtering phase, spectral Bloom filters are introduced to reduce the number of key-value pairs. Furthermore, we integrate the multiway join strategy to boost the verification, where a MapReduce-based method is proposed for GED calculation. The superior efficiency and scalability of the proposed algorithms are demonstrated by extensive experimental results.

Cognitive Maps of a Naturalistic Setting.

ERIC Educational Resources Information Center

Cohen, Robert; And Others

1978-01-01

Distance estimates of locations in a camp setting were obtained from 9- and 10-year-olds and adults. Each subject estimated distance on two tasks: magnitude estimation and reconstruction. Data were analyzed for the effects of certain environmental features such as buildings, trees, and hills. (JMB)

Leucaena: promising forage and tree crop for the tropics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1984-01-01

A report mainly on L. leucocephala with similar chapters to those found in the first edition, and additional chapters on: experiences with Leucaena - illustrating the growth and use of L. leucocephala throughout the tropics and subtropics; and other Leucaena species - giving very brief descriptions of L. diversifolia, L. esulenta, L. macrophylla, L. pulverulenta, L. shannoni, L. retusa, L. lanceolata, L. collinsii and L. trichodes. 34 references.

TREE Simulation Facilities, Second Edition, Revision 2

DTIC Science & Technology

1979-01-01

included radiation effects on propellants , ordnance, electronics and chemicals, vehicle shielding, neutron radiography , dosimetry, and health physics...Special Capabilities 2.11.10.1 Radiography Facility 2.11.10.2 Flexo-Rabbit System Support Capabilities 2.11.11.1 Staff 2.11.11.2 Electronics...5,400-MW pulsing operation (experimental dosimetry values for a typical core loading of 94 fuel elements). 2-156 2-46 ACPR radiography facility

A Two-Tiered-Testing Decision Tree for Assays in the USEPA-EDSP Screening Battery: Using 15 years of Experience to Improve Screening and Testing for Endocrine Active Chemicals##

EPA Science Inventory

This product is a brief description of the oral presentation given by Dr LE Gray Jr at the meeting for the T4 workshop report-Lessons learned, challenges, ansd opportunities: The U.S. Endocrine Disruptor Scrrening Program published in the journal ALTEX, edited by the Swiss Societ...

Application of agglomerative clustering for analyzing phylogenetically on bacterium of saliva

NASA Astrophysics Data System (ADS)

Bustamam, A.; Fitria, I.; Umam, K.

2017-07-01

Analyzing population of Streptococcus bacteria is important since these species can cause dental caries, periodontal, halitosis (bad breath) and more problems. This paper will discuss the phylogenetically relation between the bacterium Streptococcus in saliva using a phylogenetic tree of agglomerative clustering methods. Starting with the bacterium Streptococcus DNA sequence obtained from the GenBank, then performed characteristic extraction of DNA sequences. The characteristic extraction result is matrix form, then performed normalization using min-max normalization and calculate genetic distance using Manhattan distance. Agglomerative clustering technique consisting of single linkage, complete linkage and average linkage. In this agglomerative algorithm number of group is started with the number of individual species. The most similar species is grouped until the similarity decreases and then formed a single group. Results of grouping is a phylogenetic tree and branches that join an established level of distance, that the smaller the distance the more the similarity of the larger species implementation is using R, an open source program.

Molecular phylogeny of the hominoid primates as indicated by two-dimensional protein electrophoresis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldman, D.; Giri, P.R.; O'Brien, J.O.

1987-05-01

A molecular phylogeny for the hominoid primates was constructed by using genetic distances from a survey of 383 radiolabeled fibroblast polypeptides resolved by two-dimensional electrophoresis (2DE). An internally consistent matrix of Nei genetic distances was generated on the basis of variants in electrophoretic position. The derived phylogenetic tree indicated a branching sequence, from oldest to most recent, of cercopithecoids (Macaca fascicularis), gibbon-siamang, orangutan, gorilla, and human-chimpanzee. A cladistic analysis of 240 electrophoretic characters that varied between ape species produced an identical tree. Genetic distance measures obtained by 2DE are largely consistent with those generated by other molecular procedures. In addition,more » the 2DE data set appears to resolve the human-chimpanzee-gorilla trichotomy in favor of a more recent association of chimpanzees and humans.« less

Ash content of loblolly pine wood as related to specific gravity, growth rate, and distance from pith

Treesearch

Charles W. McMillin

1968-01-01

In earlywood of Pinus taeda L. grown in central Louisiana, ash content generally decreased with increasing distance from the pith and icnreased with increases in rate of tree growth (as measured in rings per inch). Latewood ash content was unrelated to the gross wood factors of distance, from the pith, specific gravity, and growth rate. The ash...

Pollen dispersal of tropical trees (Dinizia excelsa: Fabaceae) by native insects and African honeybees in pristine and fragmented Amazonian rainforest.

PubMed

Dick, Christopher W; Etchelecu, Gabriela; Austerlitz, Frédéric

2003-03-01

Tropical rainforest trees typically occur in low population densities and rely on animals for cross-pollination. It is of conservation interest therefore to understand how rainforest fragmentation may alter the pollination and breeding structure of remnant trees. Previous studies of the Amazonian tree Dinizia excelsa (Fabaceae) found African honeybees (Apis mellifera scutellata) as the predominant pollinators of trees in highly disturbed habitats, transporting pollen up to 3.2 km between pasture trees. Here, using microsatellite genotypes of seed arrays, we compare outcrossing rates and pollen dispersal distances of (i) remnant D. excelsa in three large ranches, and (ii) a population in undisturbed forest in which African honeybees were absent. Self-fertilization was more frequent in the disturbed habitats (14%, n = 277 seeds from 12 mothers) than in undisturbed forest (10%, n = 295 seeds from 13 mothers). Pollen dispersal was extensive in all three ranches compared to undisturbed forest, however. Using a twogener analysis, we estimated a mean pollen dispersal distance of 1509 m in Colosso ranch, assuming an exponential dispersal function, and 212 m in undisturbed forest. The low effective density of D. excelsa in undisturbed forest (approximately 0.1 trees/ha) indicates that large areas of rainforest must be preserved to maintain minimum viable populations. Our results also suggest, however, that in highly disturbed habitats Apis mellifera may expand genetic neighbourhood areas, thereby linking fragmented and continuous forest populations.

Progression of ash canopy thinning and dieback outward from the initial infestation of emerald ash borer (Coleoptera: Buprestidae) in southeastern Michigan.

PubMed

Smitley, David; Davis, Terrance; Rebek, Eric

2008-10-01

Our objective was to characterize the rate at which ash (Fraxinus spp.) trees decline in areas adjacent to the leading edge of visible ash canopy thinning due to emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae). Trees in southeastern Michigan were surveyed from 2003 to 2006 for canopy thinning and dieback by comparing survey trees with a set of 11 standard photographs. Freeways stemming from Detroit in all directions were used as survey transects. Between 750 and 1,100 trees were surveyed each year. A rapid method of sampling populations of emerald ash borer was developed by counting emerald ash borer emergence holes with binoculars and then felling trees to validate binocular counts. Approximately 25% of the trees surveyed for canopy thinning in 2005 and 2006 also were sampled for emerald ash borer emergence holes using binoculars. Regression analysis indicates that 41-53% of the variation in ash canopy thinning can be explained by the number of emerald ash borer emergence holes per tree. Emerald ash borer emergence holes were found at every site where ash canopy thinning averaged > 40%. In 2003, ash canopy thinning averaged 40% at a distance of 19.3 km from the epicenter of the emerald ash borer infestation in Canton. By 2006, the point at which ash trees averaged 40% canopy thinning had increased to a distance of 51.2 km away from Canton. Therefore, the point at which ash trees averaged 40% canopy thinning, a state of decline clearly visible to the average person, moved outward at a rate of 10.6 km/yr during this period.

A Fast Exact k-Nearest Neighbors Algorithm for High Dimensional Search Using k-Means Clustering and Triangle Inequality.

PubMed

Wang, Xueyi

2012-02-08

The k-nearest neighbors (k-NN) algorithm is a widely used machine learning method that finds nearest neighbors of a test object in a feature space. We present a new exact k-NN algorithm called kMkNN (k-Means for k-Nearest Neighbors) that uses the k-means clustering and the triangle inequality to accelerate the searching for nearest neighbors in a high dimensional space. The kMkNN algorithm has two stages. In the buildup stage, instead of using complex tree structures such as metric trees, kd-trees, or ball-tree, kMkNN uses a simple k-means clustering method to preprocess the training dataset. In the searching stage, given a query object, kMkNN finds nearest training objects starting from the nearest cluster to the query object and uses the triangle inequality to reduce the distance calculations. Experiments show that the performance of kMkNN is surprisingly good compared to the traditional k-NN algorithm and tree-based k-NN algorithms such as kd-trees and ball-trees. On a collection of 20 datasets with up to 10(6) records and 10(4) dimensions, kMkNN shows a 2-to 80-fold reduction of distance calculations and a 2- to 60-fold speedup over the traditional k-NN algorithm for 16 datasets. Furthermore, kMkNN performs significant better than a kd-tree based k-NN algorithm for all datasets and performs better than a ball-tree based k-NN algorithm for most datasets. The results show that kMkNN is effective for searching nearest neighbors in high dimensional spaces.

Fine-Scale Genetic Structure of Monilinia fructicola During Brown Rot Epidemics Within Individual Peach Tree Canopies.

PubMed

Everhart, S E; Scherm, H

2015-04-01

The purpose of this study was to determine the fine-scale genetic structure of populations of the brown rot pathogen Monilinia fructicola within individual peach tree canopies to better understand within-tree plant pathogen diversity and to complement previous work on spatiotemporal development of brown rot disease at the canopy level. Across 3 years in a total of six trees, we monitored disease development, collected isolates from every M. fructicola symptom during the course of the season, and created high-resolution three-dimensional maps of all symptom and isolate locations within individual canopies using an electromagnetic digitizer. Each canopy population (65 to 173 isolates per tree) was characterized using a set of 13 microsatellite markers and analyzed for evidence of spatial genetic autocorrelation among isolates during the epidemic phase of the disease. Results showed high genetic diversity (average uh=0.529) and high genotypic diversity (average D=0.928) within canopies. The percentage of unique multilocus genotypes within trees was greater for blossom blight isolates (78.2%) than for fruit rot isolates (51.3%), indicating a greater contribution of clonal reproduction during the preharvest epidemic. For fruit rot isolates, between 54.2 and 81.7% of isolates were contained in one to four dominant clonal genotypes per tree having at least 10 members. All six fruit rot populations showed positive and significant spatial genetic autocorrelation for distance classes between 0.37 and 1.48 m. Despite high levels of within-tree pathogen diversity, the contribution of locally available inoculum combined with short-distance dispersal is likely the main factor generating clonal population foci and associated spatial genetic clustering within trees.

Africa Today: A Reproducible Atlas. 1996 Revised Edition. World Eagle's Today Series.

ERIC Educational Resources Information Center

Independent Broadcasting Associates, Inc., Littleton, MA.

This book contains blank outline maps of the continent or region, tables, and graphics depicting various aspects of Africa. Sections of the book include: (1) "Same Scale Maps, Silhouettes, Distances, Area"; (2) "Population"; (3) "Demographics, Education, Ethnic, Religion, Health"; (4) "Climate, Land,…

2. Photocopy of Photograph, c. 1980. VIEW LOOKING WEST ALONG ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. Photocopy of Photograph, c. 1980. VIEW LOOKING WEST ALONG THE SAN FRANCISCO CANAL. NOTE THE COTTONWOOD TREE IN THE DISTANCE. THESE TREES ORIGINALLY LINED THE CANAL TO PREVENT EVAPORATION. WHEN IT WAS DISCOVERED THAT THE TREES' ROOTS SOAKED UP MORE WATER THAN THEIR SHADE PROTECTED, THEY WERE CUT DOWN. Photographer: Mark Durben, June 1986 Source: Salt River Project Archives - San Francisco Canal, Between Fortieth & Weir & Thirty-sixth Street & Roeser Road, Phoenix, Maricopa County, AZ

[Identification of common medicinal snakes in medicated liquor of Guangdong by COI barcode sequence].

PubMed

Liao, Jing; Chao, Zhi; Zhang, Liang

2013-11-01

To identify the common snakes in medicated liquor of Guangdong using COI barcode sequence,and to test the feasibility. The COI barcode sequences of collected medicinal snakes were amplified and sequenced. The sequences combined with the data from GenBank were analyzed for divergence and building a neighbor-joining(NJ) tree with MEGA 5.0. The genetic distance and NJ tree demonstrated that there were 241 variable sites in these species, and the average (A + T) content of 56.2% was higher than the average (G + C) content of 43.7%. The maximum interspecific genetic distance was 0.2568, and the minimum was 0. 1519. In the NJ tree,each species formed a monophyletic clade with bootstrap supports of 100%. DNA barcoding identification method based on the COI sequence is accurate and can be applied to identify the common medicinal snakes.

Individual tree-diameter growth model for the Northeastern United States

Treesearch

Richard M. Teck; Donald E. Hilt

1991-01-01

Describes a distance-independent individual-tree diameter growth model for the Northeastern United States. Diameter growth is predicted in two steps using a two parameter, sigmoidal growth function modified by a one parameter exponential decay function with species-specific coefficients. Coefficients are presented for 28 species groups. The model accounts for...

Geographical ecology of dry forest tree communities in the West Indies

Treesearch

Janet Franklin; Riley Andrade; Mark L. Daniels; Patrick Fairbairn; Maria C. Fandino; Thomas W. Gillespie; Grizelle González; Otto Gonzalez; Daniel Imbert; Valerie Kapos; Daniel L. Kelly; Humfredo Marcano-Vega; Elvia J. Meléndez-Ackerman; Kurt P. McLaren; Morag A. McDonald; Julie Ripplinger; Julissa Rojas-Sandoval; Michael S. Ross; Jorge Ruiz; David W. Steadman; Edmund V. J. Tanner; Inge Terrill; Michel Vennetier

2018-01-01

Aim: Seasonally dry tropical forest (SDTF) of the Caribbean Islands (primarily West Indies) is floristically distinct from Neotropical SDTF in Central and South America. We evaluate whether tree species composition was associated with climatic gradients or geographical distance. Turnover (dissimilarity) in species composition of different islands or among more distant...

An Individual-Tree Growth and Yield Prediction System for Uneven-Aged Shortleaf Pine Stands

Treesearch

Michael M. Huebschmann; Lawrence R. Gering; Thomas B. Lynch; Onesphore Bitoki; Paul A. Murphy

2000-01-01

A system of equations modeling the growth and development of uneven-aged shortleaf pine (Pinus echinata Mill.) stands is described. The prediction system consists of two main components: (1) a distance-independent, individual-tree simulator containing equations that forecast ingrowth, basal-area growth, probability of survival, total and...

DYNAMICS OF WATER TRANSPORT AND STORAGE IN CONIFERS STUDIED WITH DEUTERIUM AND HEAT TRACING TECHNIQUES

EPA Science Inventory

The volume and complexity of their vascular systems make the dynamics of long-distance water transport difficult to study. We used heat and deuterated water (D2O) as tracers to characterize whole-tree water transport and storage properties in individual trees belonging to the co...

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

ERIC Educational Resources Information Center

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…

Don't Move Firewood

Treesearch

Northeastern Area, S& PF USDA Forest Service

2006-01-01

Our forests are threatened by nonnative insects that can kill large numbers of trees. Three recently introduced insects, emerald ash borer, Asian longhorned beetle, and Sirex woodwasp are wood-infesting species that can be transported long distances in firewood. Once transported into new areas, these insects can become established and kill local trees. We must STOP THE...

A review of past research on dendrometers

Treesearch

Neil Clark; Randolph H. Wynne; Daniel L. Schmoldt

2000-01-01

The purpose of a dendrometer is to measure tree diameter. Contact and noncontact dendrometers accomplish this task by collecting different metrics, including girth or distance between tangent points on a tree stem. Many dendrometers have been developed in the last quarter century and many have been retired. This article summarizes instrument developments and...

Chapter 6: Characteristics of Marbled Murrelet Nest Trees and Nesting Stands

Treesearch

Thomas E. Hamer; S. Kim Nelson

1995-01-01

We summarize the characteristics of 61 tree nests and nesting stands of the Marbled Murrelet ( Brachyramphus marmoratus ) located from 1974 to 1993 in Alaska, British Columbia, Washington, Oregon, and California. Evidence of breeding 30-60 km inland was common in California, Oregon, and Washington. Nesting greater distances from the coast may have...

YBYRÁ facilitates comparison of large phylogenetic trees.

PubMed

Machado, Denis Jacob

2015-07-01

The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

Black bear (Ursus americanus Pallas) feeding damage across timber harvest edges in northern California coast redwood (Sequoia sempervirens[D. Don] Endl.) forests, USA

USGS Publications Warehouse

Russell, W.H.; Carnell, K.; McBride, J.R.

2001-01-01

Feeding damage to trees by black bears (Ursus americanus Pallas) was recorded in proximity to timber harvest edges in harvested and old-growth stands of coast redwood (Sequoia sempervirens [D. Don] Endl.) in northern California, USA. Bears exhibited distinct preference in their feeding patterns related to stand structure and composition and to distance from the timber-harvest edge. Most damage was recorded within regenerating stands. Regression analysis indicated that density of damaged trees was negatively correlated with distance from timber harvest edges within old-growth stands. A significant negative correlation was also found between the density of trees damaged by bears and habitat diversity (H') as measured by the Shannon diversity index. In addition, bears exhibited preference for pole-size trees (dbh = 10-50 cm) over all other size classes, and coast redwood over other species. In general, damage by bears appeared to act as a natural thinning agent in even-aged stands. No damage was recorded in old-growth stands except in close proximity to the timber-harvest edge where subcanopy recruitment was high.

A Metric on Phylogenetic Tree Shapes.

PubMed

Colijn, C; Plazzotta, G

2018-01-01

The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees' branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

A novel dendrochronological approach reveals drivers of carbon sequestration in tree species of riparian forests across spatiotemporal scales.

PubMed

Rieger, Isaak; Kowarik, Ingo; Cherubini, Paolo; Cierjacks, Arne

2017-01-01

Aboveground carbon (C) sequestration in trees is important in global C dynamics, but reliable techniques for its modeling in highly productive and heterogeneous ecosystems are limited. We applied an extended dendrochronological approach to disentangle the functioning of drivers from the atmosphere (temperature, precipitation), the lithosphere (sedimentation rate), the hydrosphere (groundwater table, river water level fluctuation), the biosphere (tree characteristics), and the anthroposphere (dike construction). Carbon sequestration in aboveground biomass of riparian Quercus robur L. and Fraxinus excelsior L. was modeled (1) over time using boosted regression tree analysis (BRT) on cross-datable trees characterized by equal annual growth ring patterns and (2) across space using a subsequent classification and regression tree analysis (CART) on cross-datable and not cross-datable trees. While C sequestration of cross-datable Q. robur responded to precipitation and temperature, cross-datable F. excelsior also responded to a low Danube river water level. However, CART revealed that C sequestration over time is governed by tree height and parameters that vary over space (magnitude of fluctuation in the groundwater table, vertical distance to mean river water level, and longitudinal distance to upstream end of the study area). Thus, a uniform response to climatic drivers of aboveground C sequestration in Q. robur was only detectable in trees of an intermediate height class and in taller trees (>21.8m) on sites where the groundwater table fluctuated little (≤0.9m). The detection of climatic drivers and the river water level in F. excelsior depended on sites at lower altitudes above the mean river water level (≤2.7m) and along a less dynamic downstream section of the study area. Our approach indicates unexploited opportunities of understanding the interplay of different environmental drivers in aboveground C sequestration. Results may support species-specific and locally adapted forest management plans to increase carbon dioxide sequestration from the atmosphere in trees. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of Acacia trees on soil nutrient levels in arid lands

NASA Astrophysics Data System (ADS)

De Boever, Maarten; Gabriels, Donald; Ouessar, Mohamed; Cornelis, Wim

2014-05-01

The potential of scattered trees as keystone structures in restoring degraded environments is gaining importance. Scattered trees have strong influence on their abiotic environment, mainly causing changes in microclimate, water budget and soil properties. They often function as 'nursing trees', facilitating the recruitment of other plants. Acacia raddiana is such a keystone species which persists on the edge of the Sahara desert. The study was conducted in a forest-steppe ecosystem in central Tunisia where several reforestation campaigns with Acacia took place. To indentify the impact of those trees on soil nutrients, changes in nutrient levels under scattered trees of three age stages were examined for the upper soil layer (0-10 cm) at five microsites with increasing distance from the trunk. In addition, changes in soil nutrient levels with depth underneath and outside the canopy were determined for the 0-30 cm soil layer. Higher concentrations of organic matter (OM) were found along the gradient from underneath to outside the canopy for large trees compared to medium and small trees, especially at microsites close to the trunk. Levels of soluble K, electrical conductivity (EC), available P, OM, total C and N decreased whereas pH and levels of soluble Mg increased with increasing distance from tree. Levels of soluble Ca and Na remained unchanged along the gradient. At the microsite closest to the trunk a significant decrease in levels of soluble K, EC, OM, available P, total C and N, while a significant increase in pH was found with increasing depth. The concentration of other nutrients remained unchanged or declined not differently underneath compared to outside the canopy with increasing depth. Differences in nutrient levels were largely driven by greater inputs of organic matter under trees. Hence, Acacia trees can affect the productivity and reproduction of understory species with the latter in term an important source of organic matter. This positive feedback mechanism is of crucial importance for soil nutrient conservation and the restoration of degraded arid environments.

Pronounced Seasonal Changes in the Movement Ecology of a Highly Gregarious Central-Place Forager, the African Straw-Coloured Fruit Bat (Eidolon helvum)

PubMed Central

Fahr, Jakob; Abedi-Lartey, Michael; Esch, Thomas; Machwitz, Miriam; Suu-Ire, Richard; Wikelski, Martin; Dechmann, Dina K. N.

2015-01-01

Background Straw-coloured fruit bats (Eidolon helvum) migrate over vast distances across the African continent, probably following seasonal bursts of resource availability. This causes enormous fluctuations in population size, which in turn may influence the bats’ impact on local ecosystems. We studied the movement ecology of this central-place forager with state-of-the-art GPS/acceleration loggers and concurrently monitored the seasonal fluctuation of the colony in Accra, Ghana. Habitat use on the landscape scale was assessed with remote sensing data as well as ground-truthing of foraging areas. Principal Findings During the wet season population low (~ 4000 individuals), bats foraged locally (3.5–36.7 km) in urban areas with low tree cover. Major food sources during this period were fruits of introduced trees. Foraging distances almost tripled (24.1–87.9 km) during the dry season population peak (~ 150,000 individuals), but this was not compensated for by reduced resting periods. Dry season foraging areas were random with regard to urban footprint and tree cover, and food consisted almost exclusively of nectar and pollen of native trees. Conclusions and Significance Our study suggests that straw-coloured fruit bats disperse seeds in the range of hundreds of meters up to dozens of kilometres, and pollinate trees for up to 88 km. Straw-coloured fruit bats forage over much larger distances compared to most other Old World fruit bats, thus providing vital ecosystem services across extensive landscapes. We recommend increased efforts aimed at maintaining E. helvum populations throughout Africa since their keystone role in various ecosystems is likely to increase due to the escalating loss of other seed dispersers as well as continued urbanization and habitat fragmentation. PMID:26465139

On the Accuracy of Language Trees

PubMed Central

Pompei, Simone; Loreto, Vittorio; Tria, Francesca

2011-01-01

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical, phonological, syntactic) features or characters for many different languages: a set of parallel corpora whose compilation represents a paramount achievement in linguistics. From this perspective the reconstruction of language trees is an example of inverse problems: starting from present, incomplete and often noisy, information, one aims at inferring the most likely past evolutionary history. A fundamental issue in inverse problems is the evaluation of the inference made. A standard way of dealing with this question is to generate data with artificial models in order to have full access to the evolutionary process one is going to infer. This procedure presents an intrinsic limitation: when dealing with real data sets, one typically does not know which model of evolution is the most suitable for them. A possible way out is to compare algorithmic inference with expert classifications. This is the point of view we take here by conducting a thorough survey of the accuracy of reconstruction methods as compared with the Ethnologue expert classifications. We focus in particular on state-of-the-art distance-based methods for phylogeny reconstruction using worldwide linguistic databases. In order to assess the accuracy of the inferred trees we introduce and characterize two generalizations of standard definitions of distances between trees. Based on these scores we quantify the relative performances of the distance-based algorithms considered. Further we quantify how the completeness and the coverage of the available databases affect the accuracy of the reconstruction. Finally we draw some conclusions about where the accuracy of the reconstructions in historical linguistics stands and about the leading directions to improve it. PMID:21674034

Pronounced Seasonal Changes in the Movement Ecology of a Highly Gregarious Central-Place Forager, the African Straw-Coloured Fruit Bat (Eidolon helvum).

PubMed

Fahr, Jakob; Abedi-Lartey, Michael; Esch, Thomas; Machwitz, Miriam; Suu-Ire, Richard; Wikelski, Martin; Dechmann, Dina K N

2015-01-01

Straw-coloured fruit bats (Eidolon helvum) migrate over vast distances across the African continent, probably following seasonal bursts of resource availability. This causes enormous fluctuations in population size, which in turn may influence the bats' impact on local ecosystems. We studied the movement ecology of this central-place forager with state-of-the-art GPS/acceleration loggers and concurrently monitored the seasonal fluctuation of the colony in Accra, Ghana. Habitat use on the landscape scale was assessed with remote sensing data as well as ground-truthing of foraging areas. During the wet season population low (~ 4000 individuals), bats foraged locally (3.5-36.7 km) in urban areas with low tree cover. Major food sources during this period were fruits of introduced trees. Foraging distances almost tripled (24.1-87.9 km) during the dry season population peak (~ 150,000 individuals), but this was not compensated for by reduced resting periods. Dry season foraging areas were random with regard to urban footprint and tree cover, and food consisted almost exclusively of nectar and pollen of native trees. Our study suggests that straw-coloured fruit bats disperse seeds in the range of hundreds of meters up to dozens of kilometres, and pollinate trees for up to 88 km. Straw-coloured fruit bats forage over much larger distances compared to most other Old World fruit bats, thus providing vital ecosystem services across extensive landscapes. We recommend increased efforts aimed at maintaining E. helvum populations throughout Africa since their keystone role in various ecosystems is likely to increase due to the escalating loss of other seed dispersers as well as continued urbanization and habitat fragmentation.

Runout distance and dynamic pressure of pyroclastic density currents: Evidence from 18 May 1980 blast surge of Mount St. Helens

NASA Astrophysics Data System (ADS)

Gardner, J. E.; Andrews, B. J.

2016-12-01

Pyroclastic density currents (flows and surges) are one of the most deadly hazards associated with volcanic eruptions. Understanding what controls how far such currents will travel, and how their dynamic pressure evolves, could help mitigate their hazards. The distance a ground hugging, pyroclastic density current travels is partly limited by when it reverses buoyancy and lifts off into the atmosphere. The 1980 blast surge of Mount St. Helens offers an example of a current seen to lift off. Before lofting, it had traveled up to 20 km and leveled more than 600 km3 of thick forest (the blowdown zone). The outer edge of the devastated area - where burned trees that were left standing (the singe zone) - is where the surge is thought to have lifted off. We recently examined deposits in the outer parts of the blowdown and in the singe zone at 32 sites. The important finding is that the laterally moving surge travelled into the singe zone, and hence the change in tree damage does not mark the run out distance of the ground hugging surge. Eyewitness accounts and impacts on trees and vehicles reveal that the surge consisted of a fast, dilute "overcurrent" and a slower "undercurrent", where most of the mass (and heat) was retained. Reasonable estimates for flow density and velocity show that dynamic pressure of the surge (i.e., its ability to topple trees) peaked near the base of the overcurrent. We propose that when the overcurrent began to lift off, the height of peak dynamic pressure rose above the trees and stopped toppling them. The slower undercurrent continued forward, burning trees but it lacked the dynamic pressure needed to topple them. Grain-size variations argue that it slowed from 30 m/s when it entered the singe zone to 3 m/s at the far end. Buoyancy reversal and liftoff are thus not preserved in the deposits where the surge lofted upwards.

Indexing and retrieving point and region objects

NASA Astrophysics Data System (ADS)

Ibrahim, Azzam T.; Fotouhi, Farshad A.

1996-03-01

R-tree and its variants are examples of spatial data structures for paged-secondary memory. To process a query, these structures require multiple path traversals. In this paper, we present a new image access method, SB+-tree which requires a single path traversal to process a query. Also, SB+-tree will allow commercial databases an access method for spatial objects without a major change, since most commercial databases already support B+-tree as an access method for text data. The SB+-tree can be used for zero and non-zero size data objects. Non-zero size objects are approximated by their minimum bounding rectangles (MBRs). The number of SB+-trees generated is dependent upon the number of dimensions of the approximation of the object. The structure supports efficient spatial operations such as regions-overlap, distance and direction. In this paper, we experimentally and analytically demonstrate the superiority of SB+-tree over R-tree.

Habitat selection models for Pacific sand lance (Ammodytes hexapterus) in Prince William Sound, Alaska

USGS Publications Warehouse

Ostrand, William D.; Gotthardt, Tracey A.; Howlin, Shay; Robards, Martin D.

2005-01-01

We modeled habitat selection by Pacific sand lance (Ammodytes hexapterus) by examining their distribution in relation to water depth, distance to shore, bottom slope, bottom type, distance from sand bottom, and shoreline type. Through both logistic regression and classification tree models, we compared the characteristics of 29 known sand lance locations to 58 randomly selected sites. The best models indicated a strong selection of shallow water by sand lance, with weaker association between sand lance distribution and beach shorelines, sand bottoms, distance to shore, bottom slope, and distance to the nearest sand bottom. We applied an information-theoretic approach to the interpretation of the logistic regression analysis and determined importance values of 0.99, 0.54, 0.52, 0.44, 0.39, and 0.25 for depth, beach shorelines, sand bottom, distance to shore, gradual bottom slope, and distance to the nearest sand bottom, respectively. The classification tree model indicated that sand lance selected shallow-water habitats and remained near sand bottoms when located in habitats with depths between 40 and 60 m. All sand lance locations were at depths <60 m and 93% occurred at depths <40 m. Probable reasons for the modeled relationships between the distribution of sand lance and the independent variables are discussed.

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis

PubMed Central

2011-01-01

Background CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions. Results Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices. Conclusions Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously. PMID:21388552

Intellectual Property in Higher Education: A Legal Compendium. Second Edition.

ERIC Educational Resources Information Center

Byman, Abigail, Ed.; Geller, Randolph, Ed.

This compendium focuses on intellectual property law, which includes copyrights, patents, and trademarks as well as applications of intellectual property in distance learning software, the Internet, and research data. It includes formal journal articles, policies, and outlines from the National Association of College and University Attorneys. Ten…

Teaching Measurement to Children: Grades K-6. Revised Edition.

ERIC Educational Resources Information Center

Borelli, Michael L.; Morelli, Sandra Z.

Objectives are listed describing the progression which students follow in learning to measure. These objectives follow a sequence that corresponds closely with the intellectual sequence found in students' learning. Grade-level recommendation charts follow the objectives. Topics dealt with are length, distance, area, volume, capacity, mass, and…

Ammonium nitrate, urea, and biuret fertilizers increase volume growth of 57-year-old douglas-fir trees within a gradient of nitrogen deficiency. Forest Service research paper

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, R.E.; Reukema, D.L.; Hazard, J.W.

1996-03-01

In a nitrogen-deficient plantation in southwest Washington, the authors (1) compared effects of 224 kg N/ha as ammonium nitrate, urea, and biuret on volume growth of dominant and codominant Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco); (2) determined how 8-year response of these trees to fertilization was related to their distance from a strip of the plantation interplanted with nitrogen-fixing red alder (alnus rubra Bong.); and (3) observed effects of biuret on understory vegetation. On both sides of the strip centerline, the authors grouped subject trees into 30 plots of 4 trees each, based on slope position and distance frommore » alder. The authors randomly assigned three fertilizers and a control within each plot. They analyzed separately data from east and west of the mixed stand certerline. Initial volume differed greatly among the 120 trees on each side, so they used covariance analysis to adjust observed treatment means. Adjusted mean volume growth was increased (p equal to or less than 0.10) by 22 to 28 percent on the east side and by 11 to 14 percent on the west side, with no significant difference in response to the three fertilizers.« less

Beyond Flory theory: Distribution functions for interacting lattice trees

NASA Astrophysics Data System (ADS)

Rosa, Angelo; Everaers, Ralf

2017-01-01

While Flory theories [J. Isaacson and T. C. Lubensky, J. Physique Lett. 41, 469 (1980), 10.1051/jphyslet:019800041019046900; M. Daoud and J. F. Joanny, J. Physique 42, 1359 (1981), 10.1051/jphys:0198100420100135900; A. M. Gutin et al., Macromolecules 26, 1293 (1993), 10.1021/ma00058a016] provide an extremely useful framework for understanding the behavior of interacting, randomly branching polymers, the approach is inherently limited. Here we use a combination of scaling arguments and computer simulations to go beyond a Gaussian description. We analyze distribution functions for a wide variety of quantities characterizing the tree connectivities and conformations for the four different statistical ensembles, which we have studied numerically in [A. Rosa and R. Everaers, J. Phys. A: Math. Theor. 49, 345001 (2016), 10.1088/1751-8113/49/34/345001 and J. Chem. Phys. 145, 164906 (2016), 10.1063/1.4965827]: (a) ideal randomly branching polymers, (b) 2 d and 3 d melts of interacting randomly branching polymers, (c) 3 d self-avoiding trees with annealed connectivity, and (d) 3 d self-avoiding trees with quenched ideal connectivity. In particular, we investigate the distributions (i) pN(n ) of the weight, n , of branches cut from trees of mass N by severing randomly chosen bonds; (ii) pN(l ) of the contour distances, l , between monomers; (iii) pN(r ⃗) of spatial distances, r ⃗, between monomers, and (iv) pN(r ⃗|l ) of the end-to-end distance of paths of length l . Data for different tree sizes superimpose, when expressed as functions of suitably rescaled observables x ⃗=r ⃗/√{ } or x =l / . In particular, we observe a generalized Kramers relation for the branch weight distributions (i) and find that all the other distributions (ii-iv) are of Redner-des Cloizeaux type, q (x ⃗) =C |x| θexp(-(K|x |) t) . We propose a coherent framework, including generalized Fisher-Pincus relations, relating most of the RdC exponents to each other and to the contact and Flory exponents for interacting trees.

Species-richness of the Anopheles annulipes Complex (Diptera: Culicidae) Revealed by Tree and Model-Based Allozyme Clustering Analyses

DTIC Science & Technology

2007-01-01

including tree- based methods such as the unweighted pair group method of analysis ( UPGMA ) and Neighbour-joining (NJ) (Saitou & Nei, 1987). By...based Bayesian approach and the tree-based UPGMA and NJ cluster- ing methods. The results obtained suggest that far more species occur in the An...unlikely that groups that differ by more than these levels are conspecific. Genetic distances were clustered using the UPGMA and NJ algorithms in MEGA

Visualizing phylogenetic tree landscapes.

PubMed

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees. We demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.

Image retrieval by information fusion based on scalable vocabulary tree and robust Hausdorff distance

NASA Astrophysics Data System (ADS)

Che, Chang; Yu, Xiaoyang; Sun, Xiaoming; Yu, Boyang

2017-12-01

In recent years, Scalable Vocabulary Tree (SVT) has been shown to be effective in image retrieval. However, for general images where the foreground is the object to be recognized while the background is cluttered, the performance of the current SVT framework is restricted. In this paper, a new image retrieval framework that incorporates a robust distance metric and information fusion is proposed, which improves the retrieval performance relative to the baseline SVT approach. First, the visual words that represent the background are diminished by using a robust Hausdorff distance between different images. Second, image matching results based on three image signature representations are fused, which enhances the retrieval precision. We conducted intensive experiments on small-scale to large-scale image datasets: Corel-9, Corel-48, and PKU-198, where the proposed Hausdorff metric and information fusion outperforms the state-of-the-art methods by about 13, 15, and 15%, respectively.

[Molecular identification of Hibiscus syriacus and its adulterants using ITS2 barcode].

PubMed

Liu, Yi-Mei; Jin, Li-Na; Xiong, Yong-Xin; Wu, Lan; Chen, Ke-Li

2014-03-01

To identify Hibiscus syriacus and its adulterants using DNA barcoding technique. Nine samples of five species were PCR amplified and sequenced, and twelve samples were downloaded from the GenBank. The intra-specific and interspecific K2P distances were calculated, and neighbor-joining( NJ) tree was constructed by MEGA 5.0. The results showed the intra-specific genetic distances of Hibiscus syriacus were ranged from 0.009 to 0.056, which were far lower than inter-specific genetic distances between Hibiscus syriacus and its adulterants (0.236 - 0.301). Variable sites within Hibiscus syriacus ranged from 2 to 9 which were far less than the adulterants (45 - 52); Different samples of Hibiscus syriacus were gathered together and could be distinguished from its adulterants by NJ tree. ITS2 can discriminate Hibiscus syriacus from its adulterants correctly. The ITS2 region is an efficient barcode for authentication of Hibiscus syriacus and its adulterants.

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

PubMed

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-phylogenetic methods for larger effect sizes. The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees. ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree .

Tree mortality in response to typhoon-induced floods and mudslides is determined by tree species, size, and position in a riparian Formosan gum forest in subtropical Taiwan

PubMed Central

Tzeng, Hsy-Yu; Wang, Wei; Tseng, Yen-Hsueh; Chiu, Ching-An; Kuo, Chu-Chia

2018-01-01

Global warming-induced extreme climatic changes have increased the frequency of severe typhoons bringing heavy rains; this has considerably affected the stability of the forest ecosystems. Since the Taiwan 921 earthquake occurred in 21 September 1999, the mountain geology of the Island of Taiwan has become unstable and typhoon-induced floods and mudslides have changed the topography and geomorphology of the area; this has further affected the stability and functions of the riparian ecosystem. In this study, the vegetation of the unique Aowanda Formosan gum forest in Central Taiwan was monitored for 3 years after the occurrence of floods and mudslides during 2009–2011. Tree growth and survival, effects of floods and mudslides, and factors influencing tree survival were investigated. We hypothesized that (1) the effects of floods on the survival are significantly different for each tree species; (2) tree diameter at breast height (DBH) affects tree survival–i.e., the larger the DBH, the higher the survival rate; and (3) the relative position of trees affects tree survival after disturbances by floods and mudslides–the farther trees are from the river, the higher is their survival rate. Our results showed that after floods and mudslides, the lifespans of the major tree species varied significantly. Liquidambar formosana displayed the highest flood tolerance, and the trunks of Lagerstoemia subcostata began rooting after disturbances. Multiple regression analysis indicated that factors such as species, DBH, distance from sampled tree to the above boundary of sample plot (far from the riverbank), and distance from the upstream of the river affected the lifespans of trees; the three factors affected each tree species to different degrees. Furthermore, we showed that insect infestation had a critical role in determining tree survival rate. Our 3-year monitoring investigation revealed that severe typhoon-induced floods and mudslides disturbed the riparian vegetation in the Formosan gum forest, replacing the original vegetation and beginning secondary succession. Moreover, flooding provided new habitats for various plants to establish their progeny. By using our results, lifecycles of trees (including death) can be understood in detail, facilitating riparian vegetation engineering in forests severely disturbed by typhoon-induced floods and mudslides. PMID:29304149

Tree mortality in response to typhoon-induced floods and mudslides is determined by tree species, size, and position in a riparian Formosan gum forest in subtropical Taiwan.

PubMed

Tzeng, Hsy-Yu; Wang, Wei; Tseng, Yen-Hsueh; Chiu, Ching-An; Kuo, Chu-Chia; Tsai, Shang-Te

2018-01-01

Global warming-induced extreme climatic changes have increased the frequency of severe typhoons bringing heavy rains; this has considerably affected the stability of the forest ecosystems. Since the Taiwan 921 earthquake occurred in 21 September 1999, the mountain geology of the Island of Taiwan has become unstable and typhoon-induced floods and mudslides have changed the topography and geomorphology of the area; this has further affected the stability and functions of the riparian ecosystem. In this study, the vegetation of the unique Aowanda Formosan gum forest in Central Taiwan was monitored for 3 years after the occurrence of floods and mudslides during 2009-2011. Tree growth and survival, effects of floods and mudslides, and factors influencing tree survival were investigated. We hypothesized that (1) the effects of floods on the survival are significantly different for each tree species; (2) tree diameter at breast height (DBH) affects tree survival-i.e., the larger the DBH, the higher the survival rate; and (3) the relative position of trees affects tree survival after disturbances by floods and mudslides-the farther trees are from the river, the higher is their survival rate. Our results showed that after floods and mudslides, the lifespans of the major tree species varied significantly. Liquidambar formosana displayed the highest flood tolerance, and the trunks of Lagerstoemia subcostata began rooting after disturbances. Multiple regression analysis indicated that factors such as species, DBH, distance from sampled tree to the above boundary of sample plot (far from the riverbank), and distance from the upstream of the river affected the lifespans of trees; the three factors affected each tree species to different degrees. Furthermore, we showed that insect infestation had a critical role in determining tree survival rate. Our 3-year monitoring investigation revealed that severe typhoon-induced floods and mudslides disturbed the riparian vegetation in the Formosan gum forest, replacing the original vegetation and beginning secondary succession. Moreover, flooding provided new habitats for various plants to establish their progeny. By using our results, lifecycles of trees (including death) can be understood in detail, facilitating riparian vegetation engineering in forests severely disturbed by typhoon-induced floods and mudslides.

23. TERMINUS, NORTH BRANCH PRAIRIE CITY DITCH. DITCH COMES FROM ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

23. TERMINUS, NORTH BRANCH PRAIRIE CITY DITCH. DITCH COMES FROM ISOLATED GROUP OF TREES IN MIDDLE DISTANCE, AND ENDS AT CENTER RIGHT. WATER THEN PROCEEDED DOWN SWALE, INTO TREES AT LEFT. VIEW TO NORTH. - Natomas Ditch System, Rhoades' Branch Ditch, Approximately 7 miles between Nesmith Court and White Rock Road, Folsom, Sacramento County, CA

BEHAVE: fire behavior prediction and fuel modeling system - BURN subsystem, Part 2

Treesearch

Patricia L. Andrews; Carolyn H. Chase

1989-01-01

This is the third publication describing the BEHAVE system of computer programs for predicting behavior of wildland fires. This publication adds the following predictive capabilities: distance firebrands are lofted ahead of a wind-driven surface fire, probabilities of firebrands igniting spot fires, scorch height of trees, and percentage of tree mortality. The system...

Discovering Decision Knowledge from Web Log Portfolio for Managing Classroom Processes by Applying Decision Tree and Data Cube Technology.

ERIC Educational Resources Information Center

Chen, Gwo-Dong; Liu, Chen-Chung; Ou, Kuo-Liang; Liu, Baw-Jhiune

2000-01-01

Discusses the use of Web logs to record student behavior that can assist teachers in assessing performance and making curriculum decisions for distance learning students who are using Web-based learning systems. Adopts decision tree and data cube information processing methodologies for developing more effective pedagogical strategies. (LRW)

An Individual-Tree Growth and Yield Prediction System for Even-Aged Natural Shortleaf Pine Forests

Treesearch

Thomas B. Lynch; Kenneth L. Hitch; Michael M. Huebschmann; Paul A. Murphy

1999-01-01

The development of a system of equations that model the growth and development of even-aged natural shortleaf (Pinus echinata Mill.) pine forests is described. The growth prediction system is a distance-independent individual-tree simulator containing equations that predict basal-area growth, survival, total and merchantable heights, and total and...

Quantitative Trait Inheritance in a Forty-Year-Old Longleaf Pine Partial Diallel Test

Treesearch

Michael Stine; Jim Roberds; C. Dana Nelson; David P. Gwaze; Todd Shupe; Les Groom

2002-01-01

A longleaf pine (Pinus palustris Mill.) 13 parent partial diallel field experiment was established at two locations on the Harrison Experimental Forest in 1960. Parent trees were randomly selected from a natural population growing on the Harrison Experimental Forest, near Gulfport, Miss. Distance between trees chosen as parents ranged from 13 to 357...

SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations

PubMed Central

2013-01-01

Background Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling, which may critically compromise analyses. Some approaches have been proposed to integrate non-molecular phylogenetic information into incomplete molecular phylogenies. An expanded tree approach consists of adding missing species to random locations within their clade. The information contained in the topology of the resulting expanded trees can be captured by the pairwise phylogenetic distance between species and stored in a matrix for further statistical analysis. Thus, the random expansion and processing of multiple phylogenetic trees can be used to estimate the phylogenetic uncertainty through a simulation procedure. Because of the computational burden required, unless this procedure is efficiently implemented, the analyses are of limited applicability. Results In this paper, we present efficient algorithms and implementations for randomly expanding and processing phylogenetic trees so that simulations involved in comparative phylogenetic analysis with uncertainty can be conducted in a reasonable time. We propose algorithms for both randomly expanding trees and calculating distance matrices. We made available the source code, which was written in the C++ language. The code may be used as a standalone program or as a shared object in the R system. The software can also be used as a web service through the link: http://purl.oclc.org/NET/sunplin/. Conclusion We compare our implementations to similar solutions and show that significant performance gains can be obtained. Our results open up the possibility of accounting for phylogenetic uncertainty in evolutionary and ecological analyses of large datasets. PMID:24229408

SUNPLIN: simulation with uncertainty for phylogenetic investigations.

PubMed

Martins, Wellington S; Carmo, Welton C; Longo, Humberto J; Rosa, Thierson C; Rangel, Thiago F

2013-11-15

Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling, which may critically compromise analyses. Some approaches have been proposed to integrate non-molecular phylogenetic information into incomplete molecular phylogenies. An expanded tree approach consists of adding missing species to random locations within their clade. The information contained in the topology of the resulting expanded trees can be captured by the pairwise phylogenetic distance between species and stored in a matrix for further statistical analysis. Thus, the random expansion and processing of multiple phylogenetic trees can be used to estimate the phylogenetic uncertainty through a simulation procedure. Because of the computational burden required, unless this procedure is efficiently implemented, the analyses are of limited applicability. In this paper, we present efficient algorithms and implementations for randomly expanding and processing phylogenetic trees so that simulations involved in comparative phylogenetic analysis with uncertainty can be conducted in a reasonable time. We propose algorithms for both randomly expanding trees and calculating distance matrices. We made available the source code, which was written in the C++ language. The code may be used as a standalone program or as a shared object in the R system. The software can also be used as a web service through the link: http://purl.oclc.org/NET/sunplin/. We compare our implementations to similar solutions and show that significant performance gains can be obtained. Our results open up the possibility of accounting for phylogenetic uncertainty in evolutionary and ecological analyses of large datasets.

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

PubMed

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

2013-11-01

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

Spatial Arrangement of Branches in Relation to Slope and Neighbourhood Competition

PubMed Central

SUMIDA, AKIHIRO; TERAZAWA, IKUE; TOGASHI, ASAKO; KOMIYAMA, AKIRA

2002-01-01

To gain a better understanding of the effects of spatial structure on patterns of neighbourhood competition among hardwood trees, the three‐dimensional extension of primary branches was surveyed for ten community‐grown Castanea crenata (Fagaceae) trees with respect to the positioning of neighbouring branches and the slope of the forest floor. There were significantly more branches extending towards the lower side of the slope than towards the upper side, but structural properties such as branch length and vertical angle were not affected by slope. When horizontal extension of a branch towards its neighbour was compared for a C. crenata branch and a neighbouring heterospecific, the former was significantly narrower than the latter when the inter‐branch distance (horizontal distance between the base positions of two neighbouring branches) was short (< approx. 5 m). Castanea crenata branches tended to extend in a direction avoiding neighbouring branches of heterospecifics when the inter‐branch distance was short. Furthermore, for an inter‐branch distance <3 m, the horizontal extension of a C. crenata branch was less when it was neighbouring a heterospecific branch than when neighbouring a conspecific branch. These results suggest that horizontal extension of C. crenata branches is more prone to spatial invasion by nearby neighbouring branches of heterospecifics, and that the invasion can be lessened when C. crenata trees are spatially aggregated. The reason why such an arrangement occurs is discussed in relation to the later leaf‐flush of C. crenata compared with that of other species in the forest. PMID:12096742

Land management practices associated with house loss in wildfires.

PubMed

Gibbons, Philip; van Bommel, Linda; Gill, A Malcolm; Cary, Geoffrey J; Driscoll, Don A; Bradstock, Ross A; Knight, Emma; Moritz, Max A; Stephens, Scott L; Lindenmayer, David B

2012-01-01

Losses to life and property from unplanned fires (wildfires) are forecast to increase because of population growth in peri-urban areas and climate change. In response, there have been moves to increase fuel reduction--clearing, prescribed burning, biomass removal and grazing--to afford greater protection to peri-urban communities in fire-prone regions. But how effective are these measures? Severe wildfires in southern Australia in 2009 presented a rare opportunity to address this question empirically. We predicted that modifying several fuels could theoretically reduce house loss by 76%-97%, which would translate to considerably fewer wildfire-related deaths. However, maximum levels of fuel reduction are unlikely to be feasible at every house for logistical and environmental reasons. Significant fuel variables in a logistic regression model we selected to predict house loss were (in order of decreasing effect): (1) the cover of trees and shrubs within 40 m of houses, (2) whether trees and shrubs within 40 m of houses was predominantly remnant or planted, (3) the upwind distance from houses to groups of trees or shrubs, (4) the upwind distance from houses to public forested land (irrespective of whether it was managed for nature conservation or logging), (5) the upwind distance from houses to prescribed burning within 5 years, and (6) the number of buildings or structures within 40 m of houses. All fuel treatments were more effective if undertaken closer to houses. For example, 15% fewer houses were destroyed if prescribed burning occurred at the observed minimum distance from houses (0.5 km) rather than the observed mean distance from houses (8.5 km). Our results imply that a shift in emphasis away from broad-scale fuel-reduction to intensive fuel treatments close to property will more effectively mitigate impacts from wildfires on peri-urban communities.

Passive phloem loading and long-distance transport in a synthetic tree-on-a-chip.

PubMed

Comtet, Jean; Jensen, Kaare H; Turgeon, Robert; Stroock, Abraham D; Hosoi, A E

2017-03-20

Vascular plants rely on differences in osmotic pressure to export sugars from regions of synthesis (mature leaves) to sugar sinks (roots, fruits). In this process, known as Münch pressure flow, the loading of sugars from photosynthetic cells to the export conduit (the phloem) is crucial, as it sets the pressure head necessary to power long-distance transport. Whereas most herbaceous plants use active mechanisms to increase phloem sugar concentration above that of the photosynthetic cells, in most tree species, for which transport distances are largest, loading seems, counterintuitively, to occur by means of passive symplastic diffusion from the mesophyll to the phloem. Here, we use a synthetic microfluidic model of a passive loader to explore the non-linear dynamics that arise during export and determine the ability of passive loading to drive long-distance transport. We first demonstrate that in our device, the phloem concentration is set by the balance between the resistances to diffusive loading from the source and convective export through the phloem. Convection-limited export corresponds to classical models of Münch transport, where the phloem concentration is close to that of the source; in contrast, diffusion-limited export leads to small phloem concentrations and weak scaling of flow rates with hydraulic resistance. We then show that the effective regime of convection-limited export is predominant in plants with large transport resistances and low xylem pressures. Moreover, hydrostatic pressures developed in our synthetic passive loader can reach botanically relevant values as high as 10 bars. We conclude that passive loading is sufficient to drive long-distance transport in large plants, and that trees are well suited to take full advantage of passive phloem loading strategies.

Land Management Practices Associated with House Loss in Wildfires

PubMed Central

Gibbons, Philip; van Bommel, Linda; Gill, A. Malcolm; Cary, Geoffrey J.; Driscoll, Don A.; Bradstock, Ross A.; Knight, Emma; Moritz, Max A.; Stephens, Scott L.; Lindenmayer, David B.

2012-01-01

Losses to life and property from unplanned fires (wildfires) are forecast to increase because of population growth in peri-urban areas and climate change. In response, there have been moves to increase fuel reduction—clearing, prescribed burning, biomass removal and grazing—to afford greater protection to peri-urban communities in fire-prone regions. But how effective are these measures? Severe wildfires in southern Australia in 2009 presented a rare opportunity to address this question empirically. We predicted that modifying several fuels could theoretically reduce house loss by 76%–97%, which would translate to considerably fewer wildfire-related deaths. However, maximum levels of fuel reduction are unlikely to be feasible at every house for logistical and environmental reasons. Significant fuel variables in a logistic regression model we selected to predict house loss were (in order of decreasing effect): (1) the cover of trees and shrubs within 40 m of houses, (2) whether trees and shrubs within 40 m of houses was predominantly remnant or planted, (3) the upwind distance from houses to groups of trees or shrubs, (4) the upwind distance from houses to public forested land (irrespective of whether it was managed for nature conservation or logging), (5) the upwind distance from houses to prescribed burning within 5 years, and (6) the number of buildings or structures within 40 m of houses. All fuel treatments were more effective if undertaken closer to houses. For example, 15% fewer houses were destroyed if prescribed burning occurred at the observed minimum distance from houses (0.5 km) rather than the observed mean distance from houses (8.5 km). Our results imply that a shift in emphasis away from broad-scale fuel-reduction to intensive fuel treatments close to property will more effectively mitigate impacts from wildfires on peri-urban communities. PMID:22279530

Impact assessment of a high-speed railway line on species distribution: application to the European tree frog (Hyla arborea) in Franche-Comté.

PubMed

Clauzel, Céline; Girardet, Xavier; Foltête, Jean-Christophe

2013-09-30

The aim of the present work is to assess the potential long-distance effect of a high-speed railway line on the distribution of the European tree frog (Hyla arborea) in eastern France by combining graph-based analysis and species distribution models. This combination is a way to integrate patch-level connectivity metrics on different scales into a predictive model. The approach used is put in place before the construction of the infrastructure and allows areas potentially affected by isolation to be mapped. Through a diachronic analysis, comparing species distribution before and after the construction of the infrastructure, we identify changes in the probability of species presence and we determine the maximum distance of impact. The results show that the potential impact decreases with distance from the high-speed railway line and the largest disturbances occur within the first 500 m. Between 500 m and 3500 m, the infrastructure generates a moderate decrease in the probability of presence with maximum values close to -40%. Beyond 3500 m the average disturbance is less than -10%. The spatial extent of the impact is greater than the dispersal distance of the tree frog, confirming the assumption of the long-distance effect of the infrastructure. This predictive modelling approach appears to be a useful tool for environmental impact assessment and strategic environmental assessment. The results of the species distribution assessment may provide guidance for field surveys and support for conservation decisions by identifying the areas most affected. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fractal spectral triples on Kellendonk's C∗-algebra of a substitution tiling

NASA Astrophysics Data System (ADS)

Mampusti, Michael; Whittaker, Michael F.

2017-02-01

We introduce a new class of noncommutative spectral triples on Kellendonk's C∗-algebra associated with a nonperiodic substitution tiling. These spectral triples are constructed from fractal trees on tilings, which define a geodesic distance between any two tiles in the tiling. Since fractals typically have infinite Euclidean length, the geodesic distance is defined using Perron-Frobenius theory, and is self-similar with scaling factor given by the Perron-Frobenius eigenvalue. We show that each spectral triple is θ-summable, and respects the hierarchy of the substitution system. To elucidate our results, we construct a fractal tree on the Penrose tiling, and explicitly show how it gives rise to a collection of spectral triples.

Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce

PubMed Central

Nacke, Heiko; Goldmann, Kezia; Schöning, Ingo; Pfeiffer, Birgit; Kaiser, Kristin; Castillo-Villamizar, Genis A.; Schrumpf, Marion; Buscot, François; Daniel, Rolf; Wubet, Tesfaye

2016-01-01

The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species (Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0–10, 10–20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0–10 vs. 10–20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees. PMID:28066384

Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce.

PubMed

Nacke, Heiko; Goldmann, Kezia; Schöning, Ingo; Pfeiffer, Birgit; Kaiser, Kristin; Castillo-Villamizar, Genis A; Schrumpf, Marion; Buscot, François; Daniel, Rolf; Wubet, Tesfaye

2016-01-01

The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species ( Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0-10, 10-20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora ) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0-10 vs. 10-20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees.

Interception loss, throughfall and stemflow in a maritime pine stand. I. Variability of throughfall and stemflow beneath the pine canopy

NASA Astrophysics Data System (ADS)

Loustau, D.; Berbigier, P.; Granier, A.; Moussa, F. El Hadj

1992-10-01

Patterns of spatial variability of throughfall and stemflow were determined in a maritime pine ( Pinus pinaster Ait.) stand for two consecutive years. Data were obtained from 52 fixed rain gauges and 12 stemflow measuring devices located in a 50m × 50m plot at the centre of an 18-year-old stand. The pine trees had been sown in rows 4m apart and had reached an average height of 12.6m. The spatial distribution of stems had a negligible effect on the throughfall partitioning beneath the canopy. Variograms of throughfall computed for a sample of storms did not reveal any spatial autocorrelation of throughfall for the sampling design used. Differences in throughfall, in relation to the distance from the rows, were not consistently significant. In addition, the distance from the tree stem did not influence the amount of throughfall. The confidence interval on the amount of throughfall per storm was between 3 and 8%. The stemflow was highly variable between trees. The effect of individual trees on stemflow was significant but the amount of stemflow per tree was not related to tree size (i.e. height, trunk diameter, etc.). The cumulative sampling errors on stemflow and throughfall for a single storm created a confidence interval of between ±7 and ±51% on interception. This resulted mainly from the low interception rate and sampling error on throughfall.

Clustering Tree-structured Data on Manifold

PubMed Central

Lu, Na; Miao, Hongyu

2016-01-01

Tree-structured data usually contain both topological and geometrical information, and are necessarily considered on manifold instead of Euclidean space for appropriate data parameterization and analysis. In this study, we propose a novel tree-structured data parameterization, called Topology-Attribute matrix (T-A matrix), so the data clustering task can be conducted on matrix manifold. We incorporate the structure constraints embedded in data into the non-negative matrix factorization method to determine meta-trees from the T-A matrix, and the signature vector of each single tree can then be extracted by meta-tree decomposition. The meta-tree space turns out to be a cone space, in which we explore the distance metric and implement the clustering algorithm based on the concepts like Fréchet mean. Finally, the T-A matrix based clustering (TAMBAC) framework is evaluated and compared using both simulated data and real retinal images to illus trate its efficiency and accuracy. PMID:26660696

Resolving Partial Name Mentions Using String Metrics

DTIC Science & Technology

2007-12-01

Ladin) Pair 5: ( Franz Liszt , Franz Listz) These examples typically require one or two string edits to revert from the source to the target name...0.9556 Franz Listz Franz Liszt 2 0.1818 9 franz listz|fran z lisz 0.8182 0.9697 0.9818 The Levenshtein distance metric gives some indication of

Exploring the Airways for Adult Education. Section 310, Final Report.

ERIC Educational Resources Information Center

Morris, Betty

Intended to enable an individual to converse with satellite antenna dealers and to select a dealer and acquire an antenna to suit his/her needs at the lowest cost, this edited version of a final project report provides detailed guidelines for purchasing of communications satellites distance education delivery systems and specific technical…

Developing a hybrid dictionary-based bio-entity recognition technique.

PubMed

Song, Min; Yu, Hwanjo; Han, Wook-Shin

2015-01-01

Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall.

Developing a hybrid dictionary-based bio-entity recognition technique

PubMed Central

2015-01-01

Background Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. Methods This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. Results The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. Conclusions The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall. PMID:26043907

PCG: A prototype incremental compilation facility for the SAGA environment, appendix F

NASA Technical Reports Server (NTRS)

Kimball, Joseph John

1985-01-01

A programming environment supports the activity of developing and maintaining software. New environments provide language-oriented tools such as syntax-directed editors, whose usefulness is enhanced because they embody language-specific knowledge. When syntactic and semantic analysis occur early in the cycle of program production, that is, during editing, the use of a standard compiler is inefficient, for it must re-analyze the program before generating code. Likewise, it is inefficient to recompile an entire file, when the editor can determine that only portions of it need updating. The pcg, or Pascal code generation, facility described here generates code directly from the syntax trees produced by the SAGA syntax directed Pascal editor. By preserving the intermediate code used in the previous compilation, it can limit recompilation to the routines actually modified by editing.

Logging methods and peeling of Aspen

Treesearch

T. Schantz-Hansen

1948-01-01

The logging of forest products is influenced by many factors, including the size of the trees, density of the stand, the soundness of the trees, size of the area logged, topography and soil, weather conditions, the degree of utilization, the skill of the logger and the equipment used, the distance from market, etc. Each of these factors influences not only the method...

Migration of tree species in New England based on elevational and regional analyses

Treesearch

Dale S. Solomon; William B. Leak

1994-01-01

With field measurements of migration patterns, we used two complementary approaches to examine tree-species movement after a documented increase in temperatures. The advancing-front theory was used to examine age trends over distance and elevation for both a mountain site in New Hampshire and a regional comparison across the State of Maine. Well-defined stationary...

Post-fire tree establishment patterns at the alpine treeline ecotone: Mount Rainier National Park, Washington, USA

Treesearch

Kirk M. Stueve; Dawna L. Cerney; Regina M. Rochefort; Laurie L. Kurth

2009-01-01

Questions: Does tree establishment: (1) occur at a treeline depressed by fire, (2) cause the forest line to ascend upslope, and/or (3) alter landscape heterogeneity? (4) What abiotic and biotic local site conditions are most important in structuring establishment patterns? (5) Does the abiotic setting become more important with increasing upslope distance from the...

How disturbance, competition, and dispersal interact to prevent tree range boundaries from keeping pace with climate change

Treesearch

Yu Liang; Matthew J. Duveneck; Eric J. Gustafson; Josep M. Serra-Diaz; Jonathan R. Thompson

2018-01-01

Climate change is expected to cause geographic shifts in tree species' ranges, but such shifts may not keep pace with climate changes because seed dispersal distances are often limited and competition-induced changes in community composition can be relatively slow. Disturbances may speed changes in community composition, but the interactions among climate change,...

Effects of photographic distance on tree crown atributes calculated using urbancrowns image analysis software

Treesearch

Mason F. Patterson; P. Eric Wiseman; Matthew F. Winn; Sang-mook Lee; Philip A. Araman

2011-01-01

UrbanCrowns is a software program developed by the USDA Forest Service that computes crown attributes using a side-view digital photograph and a few basic field measurements. From an operational standpoint, it is not known how well the software performs under varying photographic conditions for trees of diverse size, which could impact measurement reproducibility and...

Spatial prediction of landslides using a hybrid machine learning approach based on Random Subspace and Classification and Regression Trees

NASA Astrophysics Data System (ADS)

Pham, Binh Thai; Prakash, Indra; Tien Bui, Dieu

2018-02-01

A hybrid machine learning approach of Random Subspace (RSS) and Classification And Regression Trees (CART) is proposed to develop a model named RSSCART for spatial prediction of landslides. This model is a combination of the RSS method which is known as an efficient ensemble technique and the CART which is a state of the art classifier. The Luc Yen district of Yen Bai province, a prominent landslide prone area of Viet Nam, was selected for the model development. Performance of the RSSCART model was evaluated through the Receiver Operating Characteristic (ROC) curve, statistical analysis methods, and the Chi Square test. Results were compared with other benchmark landslide models namely Support Vector Machines (SVM), single CART, Naïve Bayes Trees (NBT), and Logistic Regression (LR). In the development of model, ten important landslide affecting factors related with geomorphology, geology and geo-environment were considered namely slope angles, elevation, slope aspect, curvature, lithology, distance to faults, distance to rivers, distance to roads, and rainfall. Performance of the RSSCART model (AUC = 0.841) is the best compared with other popular landslide models namely SVM (0.835), single CART (0.822), NBT (0.821), and LR (0.723). These results indicate that performance of the RSSCART is a promising method for spatial landslide prediction.

Genetic structure, mating system, and long-distance gene flow in heart of palm (Euterpe edulis Mart.).

PubMed

Gaiotto, F A; Grattapaglia, D; Vencovsky, R

2003-01-01

We report a detailed analysis of the population genetic structure, mating system, and gene flow of heart of palm (Euterpe edulis Mart.-Arecaceae) in central Brazil. This palm is considered a keystone species because it supplies fruits for birds and rodents all year and is intensively harvested for culinary purposes. Two populations of this palm tree were examined, using 18 microsatellite loci. The species displays a predominantly outcrossed mating system (tm = 0.94), with a probability of full sibship greater than 70% within open-pollinated families. The following estimates of interpopulation genetic variation were calculated and found significant: FIT = 0.17, FIS = 0.12, FST = 0.06, and RST = 0.07. This low but significant level of interpopulation genetic variation indicates high levels of gene flow. Two adult trees were identified as likely seed parents (P > 99.9%) of juveniles located at a distance of 22 km. Gene flow over such distances has not been reported before for tropical tree species. The establishment and management of in situ genetic reserves or ex situ conservation and breeding populations for E. edulis should contemplate the collection of several hundreds open-pollinated maternal families from relatively few distant populations to maximize the genetic sampling of a larger number of pollen parents.

Mega-fire Recovery in Dry Conifer Forests of the Interior West

NASA Astrophysics Data System (ADS)

Malone, S. L.; Fornwalt, P.; Chambers, M. E.; Battaglia, M.

2015-12-01

Wildfire is a complex landscape process with great uncertainty in whether trends in size and severity are shifting trajectories for ecosystem recovery that are outside of the historical range of variability. Considering that wildfire size and severity is likely to increase into the future with a drier climate, it is important that we understand wildfire effects and ecosystem recovery. To evaluate how ecosystems recover from wildfire we measured spatial patterns in regeneration and mapped tree refugia within mega-fire perimeters (Hayman, Jasper, Bobcat, and Grizzly Gulch) in ponderosa pine (Pinus ponderosa) dominated forest. On average, high severity fire effects accounted for > 15% of burned area and increased with fire size. Areas with high severity fire effects contained 1 - 15% tree refugia cover, compared to 37 - 70% observed in low severity areas . Large high severity patches with low coverage of tree refugia, were more frequent in larger fires and regeneration distances required to initiate forest recovery far exceeded 1.5 canopy height or 200 m, distances where the vast majority of regeneration is likely to arise. Using a recovery model driven by distance, we estimate recovery times between 300 to > 1000 years for these mega-fires. In Western dry conifer forests, large patches of stand replacing fire are likely to lead to uneven aged forest and very long recovery times.

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

PubMed

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae)1

PubMed Central

Narayan, Lakshmi; Dodd, Richard S.; O’Hara, Kevin L.

2015-01-01

Premise of the study: Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, null alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens). Methods: Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees. Results: Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average. Discussion: The methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well. PMID:25798341

A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae).

PubMed

Narayan, Lakshmi; Dodd, Richard S; O'Hara, Kevin L

2015-03-01

Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, null alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens). Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees. Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average. The methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well.

Node Redeployment Algorithm Based on Stratified Connected Tree for Underwater Sensor Networks

PubMed Central

Liu, Jun; Jiang, Peng; Wu, Feng; Yu, Shanen; Song, Chunyue

2016-01-01

During the underwater sensor networks (UWSNs) operation, node drift with water environment causes network topology changes. Periodic node location examination and adjustment are needed to maintain good network monitoring quality as long as possible. In this paper, a node redeployment algorithm based on stratified connected tree for UWSNs is proposed. At every network adjustment moment, self-examination and adjustment on node locations are performed firstly. If a node is outside the monitored space, it returns to the last location recorded in its memory along straight line. Later, the network topology is stratified into a connected tree that takes the sink node as the root node by broadcasting ready information level by level, which can improve the network connectivity rate. Finally, with synthetically considering network coverage and connectivity rates, and node movement distance, the sink node performs centralized optimization on locations of leaf nodes in the stratified connected tree. Simulation results show that the proposed redeployment algorithm can not only keep the number of nodes in the monitored space as much as possible and maintain good network coverage and connectivity rates during network operation, but also reduce node movement distance during node redeployment and prolong the network lifetime. PMID:28029124

Rumor Processes in Random Environment on and on Galton-Watson Trees

NASA Astrophysics Data System (ADS)

Bertacchi, Daniela; Zucca, Fabio

2013-11-01

The aim of this paper is to study rumor processes in random environment. In a rumor process a signal starts from the stations of a fixed vertex (the root) and travels on a graph from vertex to vertex. We consider two rumor processes. In the firework process each station, when reached by the signal, transmits it up to a random distance. In the reverse firework process, on the other hand, stations do not send any signal but they “listen” for it up to a random distance. The first random environment that we consider is the deterministic 1-dimensional tree with a random number of stations on each vertex; in this case the root is the origin of . We give conditions for the survival/extinction on almost every realization of the sequence of stations. Later on, we study the processes on Galton-Watson trees with random number of stations on each vertex. We show that if the probability of survival is positive, then there is survival on almost every realization of the infinite tree such that there is at least one station at the root. We characterize the survival of the process in some cases and we give sufficient conditions for survival/extinction.

DNA Fingerprinting Validates Seed Dispersal Curves from Observational Studies in the Neotropical Legume Parkia

PubMed Central

Heymann, Eckhard W.; Lüttmann, Kathrin; Michalczyk, Inga M.; Saboya, Pedro Pablo Pinedo; Ziegenhagen, Birgit; Bialozyt, Ronald

2012-01-01

Background Determining the distances over which seeds are dispersed is a crucial component for examining spatial patterns of seed dispersal and their consequences for plant reproductive success and population structure. However, following the fate of individual seeds after removal from the source tree till deposition at a distant place is generally extremely difficult. Here we provide a comparison of observationally and genetically determined seed dispersal distances and dispersal curves in a Neotropical animal-plant system. Methodology/Principal Findings In a field study on the dispersal of seeds of three Parkia (Fabaceae) species by two Neotropical primate species, Saguinus fuscicollis and Saguinus mystax, in Peruvian Amazonia, we observationally determined dispersal distances. These dispersal distances were then validated through DNA fingerprinting, by matching DNA from the maternally derived seed coat to DNA from potential source trees. We found that dispersal distances are strongly right-skewed, and that distributions obtained through observational and genetic methods and fitted distributions do not differ significantly from each other. Conclusions/Significance Our study showed that seed dispersal distances can be reliably estimated through observational methods when a strict criterion for inclusion of seeds is observed. Furthermore, dispersal distances produced by the two primate species indicated that these primates fulfil one of the criteria for efficient seed dispersers. Finally, our study demonstrated that DNA extraction methods so far employed for temperate plant species can be successfully used for hard-seeded tropical plants. PMID:22514748

The clonal root system of balsam poplar in upland sites of Quebec and Alberta.

PubMed

Adonsou, Kokouvi E; DesRochers, Annie; Tremblay, Francine; Thomas, Barb R; Isabel, Nathalie

2016-10-01

Balsam poplar seeds are short-lived and require moist seedbeds soon after they are released to germinate. In addition to sexual reproduction, balsam poplar stands can regenerate clonally by root suckering. The origin of stands will in turn affect their genetic structure and root system architecture, which are poorly understood for upland forest stands. Three stands were hydraulically excavated in Quebec (moist) and Alberta (dry) to determine the origin of trees and to characterize root systems with respect to presence of parental roots and root grafts connections. Clones were identified using single-nucleotide polymorphism (SNPs), and all stems, roots and root grafts were aged using dendrochronology techniques. All 82 excavated trees were of sucker origin, and four of the six stands contained a single clone. Parental root connections were found between 22% and 25% of excavated trees, and 53% and 48% of trees were linked with a root graft between the same or different clones, in Alberta and Quebec, respectively. Mean distance between trees connected by parental root was significantly lower than the distance between unconnected trees (0.47 ± 0.25 m vs. 3.14 ± 0.15 m and 1.55 ± 0.27 m vs. 4.25 ± 0.13 m) in Alberta and in Quebec, respectively. The excavations also revealed many dead stumps with live roots, maintained through root connections with live trees. This research highlights that balsam poplar growing in upland stands is a clonal species that can maintain relatively high genotypic diversity, with frequent root connections between trees at maturity. Maintaining an extensive root system through root connections increases the chances of a clone surviving when the above ground tree is dead and may also enhance the resilience of balsam poplar stands after disturbance.

Segmentation editing improves efficiency while reducing inter-expert variation and maintaining accuracy for normal brain tissues in the presence of space-occupying lesions

PubMed Central

Deeley, MA; Chen, A; Datteri, R; Noble, J; Cmelak, A; Donnelly, EF; Malcolm, A; Moretti, L; Jaboin, J; Niermann, K; Yang, Eddy S; Yu, David S; Dawant, BM

2013-01-01

Image segmentation has become a vital and often rate limiting step in modern radiotherapy treatment planning. In recent years the pace and scope of algorithm development, and even introduction into the clinic, have far exceeded evaluative studies. In this work we build upon our previous evaluation of a registration driven segmentation algorithm in the context of 8 expert raters and 20 patients who underwent radiotherapy for large space-occupying tumors in the brain. In this work we tested four hypotheses concerning the impact of manual segmentation editing in a randomized single-blinded study. We tested these hypotheses on the normal structures of the brainstem, optic chiasm, eyes and optic nerves using the Dice similarity coefficient, volume, and signed Euclidean distance error to evaluate the impact of editing on inter-rater variance and accuracy. Accuracy analyses relied on two simulated ground truth estimation methods: STAPLE and a novel implementation of probability maps. The experts were presented with automatic, their own, and their peers’ segmentations from our previous study to edit. We found, independent of source, editing reduced inter-rater variance while maintaining or improving accuracy and improving efficiency with at least 60% reduction in contouring time. In areas where raters performed poorly contouring from scratch, editing of the automatic segmentations reduced the prevalence of total anatomical miss from approximately 16% to 8% of the total slices contained within the ground truth estimations. These findings suggest that contour editing could be useful for consensus building such as in developing delineation standards, and that both automated methods and even perhaps less sophisticated atlases could improve efficiency, inter-rater variance, and accuracy. PMID:23685866

Assessing Greater Sage-Grouse Selection of Brood-Rearing Habitat Using Remotely-Sensed Imagery: Can Readily Available High-Resolution Imagery Be Used to Identify Brood-Rearing Habitat Across a Broad Landscape?

PubMed

Westover, Matthew; Baxter, Jared; Baxter, Rick; Day, Casey; Jensen, Ryan; Petersen, Steve; Larsen, Randy

2016-01-01

Greater sage-grouse populations have decreased steadily since European settlement in western North America. Reduced availability of brood-rearing habitat has been identified as a limiting factor for many populations. We used radio-telemetry to acquire locations of sage-grouse broods from 1998 to 2012 in Strawberry Valley, Utah. Using these locations and remotely-sensed NAIP (National Agricultural Imagery Program) imagery, we 1) determined which characteristics of brood-rearing habitat could be used in widely available, high resolution imagery 2) assessed the spatial extent at which sage-grouse selected brood-rearing habitat, and 3) created a predictive habitat model to identify areas of preferred brood-rearing habitat. We used AIC model selection to evaluate support for a list of variables derived from remotely-sensed imagery. We examined the relationship of these explanatory variables at three spatial extents (45, 200, and 795 meter radii). Our top model included 10 variables (percent shrub, percent grass, percent tree, percent paved road, percent riparian, meters of sage/tree edge, meters of riparian/tree edge, distance to tree, distance to transmission lines, and distance to permanent structures). Variables from each spatial extent were represented in our top model with the majority being associated with the larger (795 meter) spatial extent. When applied to our study area, our top model predicted 75% of naïve brood locations suggesting reasonable success using this method and widely available NAIP imagery. We encourage application of our methodology to other sage-grouse populations and species of conservation concern.

Accumulation of sulfur and heavy metals in soil and tree leaves sampled from the surroundings of Tuncbilek Thermal Power Plant.

PubMed

Cicek, A; Koparal, A S

2004-11-01

In this study, the quantities of sulfur and heavy metals, resulting from the Tuncbilek Thermal Power Plant (TPP) in Turkey, have been assessed in tree leaves and soil samples within a 10 km radius of the plant. Leaves of Salix alba L., Populus tremula L., Robinia pseudoacacia L., Quercus infectoria L., Pinus nigra Arn. ssp. pallasiana (Lamb) Holmboe. trees have been used with the aim of determining how far the gas and particles emitted from the TPP are carried, and for assessment of environmental impact. The results obtained from locations chosen at various distances to the TPP, indicate that the contaminating agents are very dense and effective; particularly in the prevailing wind direction and within 10 km of the plant. They gradually lose their density and effect beyond this distance. The sulfur and heavy metal analyses made in soils taken from these locations indicate a similarity with the data obtained from the leaves.

MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL

PubMed Central

Hua, Guan-Jie; Hung, Che-Lun; Lin, Chun-Yuan; Wu, Fu-Che; Chan, Yu-Wei; Tang, Chuan Yi

2017-01-01

A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the computational performance issue. Although several new methods with high-performance hardware and frameworks have been proposed, the issue still exists. In this work, a novel parallel Unweighted Pair Group Method with Arithmetic Mean approach on multiple Graphics Processing Units is proposed to construct a phylogenetic tree from extremely large set of sequences. The experimental results present that the proposed approach on a DGX-1 server with 8 NVIDIA P100 graphic cards achieves approximately 3-fold to 7-fold speedup over the implementation of Unweighted Pair Group Method with Arithmetic Mean on a modern CPU and a single GPU, respectively. PMID:29051701

MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL.

PubMed

Hua, Guan-Jie; Hung, Che-Lun; Lin, Chun-Yuan; Wu, Fu-Che; Chan, Yu-Wei; Tang, Chuan Yi

2017-01-01

A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the computational performance issue. Although several new methods with high-performance hardware and frameworks have been proposed, the issue still exists. In this work, a novel parallel Unweighted Pair Group Method with Arithmetic Mean approach on multiple Graphics Processing Units is proposed to construct a phylogenetic tree from extremely large set of sequences. The experimental results present that the proposed approach on a DGX-1 server with 8 NVIDIA P100 graphic cards achieves approximately 3-fold to 7-fold speedup over the implementation of Unweighted Pair Group Method with Arithmetic Mean on a modern CPU and a single GPU, respectively.

Comparative Issues and Methods in Organizational Diagnosis. Report II. The Decision Tree Approach.

DTIC Science & Technology

organizational diagnosis . The advantages and disadvantages of the decision-tree approach generally, and in this study specifically, are examined. A pre-test, using a civilian sample of 174 work groups with Survey of Organizations data, was conducted to assess various decision-tree classification criteria, in terms of their similarity to the distance function used by Bowers and Hausser (1977). The results suggested the use of a large developmental sample, which should result in more distinctly defined boundary lines between classification profiles. Also, the decision matrix

Nodal distances for rooted phylogenetic trees.

PubMed

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).

Investigating distribution patterns of airborne magnetic grains trapped in tree barks in Milan, Italy: insights for pollution mitigation strategies

NASA Astrophysics Data System (ADS)

Vezzola, Laura C.; Muttoni, Giovanni; Merlini, Marco; Rotiroti, Nicola; Pagliardini, Luca; Hirt, Ann M.; Pelfini, Manuela

2017-08-01

High levels of air particulate matter (PM) have been positively correlated with respiratory diseases. In this study, we performed a biomonitoring investigation using samples of bark obtained from trees in a selected study area in the city of Milan (northern Italy). Here, we analyse the magnetic and mineralogical properties of the outer and inner barks of 147 trees, finding that magnetite is the prevalent magnetic mineral. The relative concentration of magnetite is estimated in the samples using saturation isothermal remanent magnetization (SIRM) and hysteresis parameters. We also make a first-order estimate of absolute magnetite concentration from the SIRM. The spatial distribution of the measured magnetic parameters is evaluated as a function of the distance to the main sources of magnetic PM in the study area, for example, roads and tram stops. These results are compared with data from a substantially pollution-free control site in the Central Italian Alps. Magnetic susceptibility, SIRM and magnetite concentration are found to be the highest in the outer tree barks for samples that are closest to roads and especially tram stops. In contrast, the inner bark samples are weakly magnetic and are not correlated to the distance from magnetite PM sources. The results illustrate that trees play an important role acting as a sink for airborne PM in urban areas.

The challenges of editorship: a reflection on editing the Jung-Neumann correspondence.

PubMed

Liebscher, Martin

2016-04-01

The complete correspondence between C.G. Jung and Erich Neumann was published in 2015. This article attempts to provide insight into the practical task, as well as the theoretical background, of the editing process. The advantages and possibilities of an unabridged edition with an extensive historical contextualization are demonstrated, and compared to the approach of the editors of the Jung Letters and their selection therein of Jung's letters to Neumann. The practical points under consideration include the establishment of the letter corpus, the ascertainment of dates and the chronological arrangement of the letter exchange, as well as the deciphering of handwritten letters. Theoretical aspects under discussion involve the question of the merits of a critical contextualisation and the position of the editor vis-à-vis the research object. The example of the selecting and editing of Jung's letters to Neumann by Aniela Jaffé and Gerhard Adler reveals how drastically the close ties of those editors with Jung, Neumann, and members of the Zurich analytical circles compromised their editorial work at times. The advantage for an editor being able to work from an historical distance is appreciated. © 2016, The Society of Analytical Psychology.

Long-distance dispersal helps germinating mahogany seedlings escape defoliation by a specialist caterpillar

Treesearch

Julian M. Norghauer; James Grogan; Jay R. Malcolm; Jeanine M. Felfili

2010-01-01

Herbivores and pathogens with acute host specificity may promote high tree diversity in tropical forests by causing distance- and density-dependent mortality of seedlings, but evidence is scarce. Although Lepidoptera larvae are the most abundant and host-specific guild of herbivores in these forests, their impact upon seedling distributions remains largely unknown. A...

Topological leakage detection and freeze-and-grow propagation for improved CT-based airway segmentation

NASA Astrophysics Data System (ADS)

Nadeem, Syed Ahmed; Hoffman, Eric A.; Sieren, Jered P.; Saha, Punam K.

2018-03-01

Numerous large multi-center studies are incorporating the use of computed tomography (CT)-based characterization of the lung parenchyma and bronchial tree to understand chronic obstructive pulmonary disease status and progression. To the best of our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. A failure in even a fraction of segmentation results necessitates manual revision of all segmentation masks which is laborious considering the thousands of image data sets evaluated in large studies. In this paper, we present a novel CT-based airway tree segmentation algorithm using topological leakage detection and freeze-and-grow propagation. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity-based connectivity and a freeze-and-grow propagation algorithm to iteratively grow the airway tree starting from an initial seed inside the trachea. It begins with a conservative parameter and then, gradually shifts toward more generous parameter values. The method was applied on chest CT scans of fifteen subjects at total lung capacity. Airway segmentation results were qualitatively assessed and performed comparably to established airway segmentation method with no major visual leakages.

Pulse sequence programming in a dynamic visual environment: SequenceTree.

PubMed

Magland, Jeremy F; Li, Cheng; Langham, Michael C; Wehrli, Felix W

2016-01-01

To describe SequenceTree, an open source, integrated software environment for implementing MRI pulse sequences and, ideally, exporting them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for programmers and nonprogrammers alike. The integrated user interface was programmed using the Qt4/C++ toolkit. As parameters and code are modified, the pulse sequence diagram is automatically updated within the user interface. Several aspects of pulse programming are handled automatically, allowing users to focus on higher-level aspects of sequence design. Sequences can be simulated using a built-in Bloch equation solver and then exported for use on a Siemens MRI scanner. Ideally, other types of scanners will be supported in the future. SequenceTree has been used for 8 years in our laboratory and elsewhere and has contributed to more than 50 peer-reviewed publications in areas such as cardiovascular imaging, solid state and nonproton NMR, MR elastography, and high-resolution structural imaging. SequenceTree is an innovative, open source, visual pulse sequence environment for MRI combining simplicity with flexibility and is ideal both for advanced users and users with limited programming experience. © 2015 Wiley Periodicals, Inc.

FTUC: A Flooding Tree Uneven Clustering Protocol for a Wireless Sensor Network.

PubMed

He, Wei; Pillement, Sebastien; Xu, Du

2017-11-23

Clustering is an efficient approach in a wireless sensor network (WSN) to reduce the energy consumption of nodes and to extend the lifetime of the network. Unfortunately, this approach requires that all cluster heads (CHs) transmit their data to the base station (BS), which gives rise to the long distance communications problem, and in multi-hop routing, the CHs near the BS have to forward data from other nodes that lead those CHs to die prematurely, creating the hot zones problem. Unequal clustering has been proposed to solve these problems. Most of the current algorithms elect CH only by considering their competition radius, leading to unevenly distributed cluster heads. Furthermore, global distances values are needed when calculating the competition radius, which is a tedious task in large networks. To face these problems, we propose a flooding tree uneven clustering protocol (FTUC) suited for large networks. Based on the construction of a tree type sub-network to calculate the minimum and maximum distances values of the network, we then apply the unequal cluster theory. We also introduce referenced position circles to evenly elect cluster heads. Therefore, cluster heads are elected depending on the node's residual energy and their distance to a referenced circle. FTUC builds the best inter-cluster communications route by evaluating a cluster head cost function to find the best next hop to the BS. The simulation results show that the FTUC algorithm decreases the energy consumption of the nodes and balances the global energy consumption effectively, thus extending the lifetime of the network.

Cost of skid roads for arch logging in West Virginia

Treesearch

George R., Jr. Trimble; Carl R. Barr

1960-01-01

In the mountain hardwood country of the northern Appalachians, tree-length skidding with tractor and arch has proved to be economical logging. One essential part of this type of logging is that tree-length logs are winched to the skid roads: tractor and arch do not run around through the woods. Winching distance is commonly 200 to 300 feet; and occasionally an extra...

Grow--a computer subroutine that projects the growth of trees in the Lake States' forests.

Treesearch

Gary J. Brand

1981-01-01

A computer subroutine, Grow, has been written in 1977 Standard FORTRAN to implement a distance-independent, individual tree growth model for Lake States' forests. Grow is a small and easy-to-use version of the growth model. All the user has to do is write a calling program to read initial conditions, call Grow, and summarize the results.

Using a stochastic model and cross-scale analysis to evaluate controls on historical low-severity fire regimes

Treesearch

Maureen C. Kennedy; Donald McKenzie

2010-01-01

Fire-scarred trees provide a deep temporal record of historical fire activity, but identifying the mechanisms therein that controlled landscape fire patterns is not straightforward. We use a spatially correlated metric for fire co-occurrence between pairs of trees (the Sørensen distance variogram), with output from a neutral model for fire history, to infer the...

Creating animal models, why not use the Chinese tree shrew (Tupaia belangeri chinensis)?

PubMed

Yao, Yong-Gang

2017-05-18

The Chinese tree shrew ( Tupaia belangeri chinensis ), a squirrel-like and rat-sized mammal, has a wide distribution in Southeast Asia, South and Southwest China and has many unique characteristics that make it suitable for use as an experimental animal. There have been many studies using the tree shrew ( Tupaia belangeri ) aimed at increasing our understanding of fundamental biological mechanisms and for the modeling of human diseases and therapeutic responses. The recent release of a publicly available annotated genome sequence of the Chinese tree shrew and its genome database (www.treeshrewdb.org) has offered a solid base from which it is possible to elucidate the basic biological properties and create animal models using this species. The extensive characterization of key factors and signaling pathways in the immune and nervous systems has shown that tree shrews possess both conserved and unique features relative to primates. Hitherto, the tree shrew has been successfully used to create animal models for myopia, depression, breast cancer, alcohol-induced or non-alcoholic fatty liver diseases, herpes simplex virus type 1 (HSV-1) and hepatitis C virus (HCV) infections, to name a few. The recent successful genetic manipulation of the tree shrew has opened a new avenue for the wider usage of this animal in biomedical research. In this opinion paper, I attempt to summarize the recent research advances that have used the Chinese tree shrew, with a focus on the new knowledge obtained by using the biological properties identified using the tree shrew genome, a proposal for the genome-based approach for creating animal models, and the genetic manipulation of the tree shrew. With more studies using this species and the application of cutting-edge gene editing techniques, the tree shrew will continue to be under the spot light as a viable animal model for investigating the basis of many different human diseases.

Contamination of apple orchard soils and fruit trees with copper-based fungicides: sampling aspects.

PubMed

Wang, Quanying; Liu, Jingshuang; Liu, Qiang

2015-01-01

Accumulations of copper in orchard soils and fruit trees due to the application of Cu-based fungicides have become research hotspots. However, information about the sampling strategies, which can affect the accuracy of the following research results, is lacking. This study aimed to determine some sampling considerations when Cu accumulations in the soils and fruit trees of apple orchards are studied. The study was conducted in three apple orchards from different sites. Each orchard included two different histories of Cu-based fungicides usage, varying from 3 to 28 years. Soil samples were collected from different locations varying with the distances from tree trunk to the canopy drip line. Fruits and leaves from the middle heights of tree canopy at two locations (outer canopy and inner canopy) were collected. The variation in total soil Cu concentrations between orchards was much greater than the variation within orchards. Total soil Cu concentrations had a tendency to increase with the increasing history of Cu-based fungicides usage. Moreover, total soil Cu concentrations had the lowest values at the canopy drip line, while the highest values were found at the half distances between the trunk and the canopy drip line. Additionally, Cu concentrations of leaves and fruits from the outer parts of the canopy were significantly higher than from the inner parts. Depending on the findings of this study, not only the between-orchard variation but also the within-orchard variation should be taken into consideration when conducting future soil and tree samplings in apple orchards.

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9.

PubMed

Paquet, Dominik; Kwart, Dylan; Chen, Antonia; Sproul, Andrew; Jacob, Samson; Teo, Shaun; Olsen, Kimberly Moore; Gregg, Andrew; Noggle, Scott; Tessier-Lavigne, Marc

2016-05-05

The bacterial CRISPR/Cas9 system allows sequence-specific gene editing in many organisms and holds promise as a tool to generate models of human diseases, for example, in human pluripotent stem cells. CRISPR/Cas9 introduces targeted double-stranded breaks (DSBs) with high efficiency, which are typically repaired by non-homologous end-joining (NHEJ) resulting in nonspecific insertions, deletions or other mutations (indels). DSBs may also be repaired by homology-directed repair (HDR) using a DNA repair template, such as an introduced single-stranded oligo DNA nucleotide (ssODN), allowing knock-in of specific mutations. Although CRISPR/Cas9 is used extensively to engineer gene knockouts through NHEJ, editing by HDR remains inefficient and can be corrupted by additional indels, preventing its widespread use for modelling genetic disorders through introducing disease-associated mutations. Furthermore, targeted mutational knock-in at single alleles to model diseases caused by heterozygous mutations has not been reported. Here we describe a CRISPR/Cas9-based genome-editing framework that allows selective introduction of mono- and bi-allelic sequence changes with high efficiency and accuracy. We show that HDR accuracy is increased dramatically by incorporating silent CRISPR/Cas-blocking mutations along with pathogenic mutations, and establish a method termed 'CORRECT' for scarless genome editing. By characterizing and exploiting a stereotyped inverse relationship between a mutation's incorporation rate and its distance to the DSB, we achieve predictable control of zygosity. Homozygous introduction requires a guide RNA targeting close to the intended mutation, whereas heterozygous introduction can be accomplished by distance-dependent suboptimal mutation incorporation or by use of mixed repair templates. Using this approach, we generated human induced pluripotent stem cells with heterozygous and homozygous dominant early onset Alzheimer's disease-causing mutations in amyloid precursor protein (APP(Swe)) and presenilin 1 (PSEN1(M146V)) and derived cortical neurons, which displayed genotype-dependent disease-associated phenotypes. Our findings enable efficient introduction of specific sequence changes with CRISPR/Cas9, facilitating study of human disease.

OAEditor--A Framework for Editing Adaptive Learning Objects

ERIC Educational Resources Information Center

Pereira, Joao Carlos Rodrigues; Cabral, Lucidio dos Anjos Formiga; Oiveira, Ronei dos Santos; Bezerra, Lucimar Leandro; de Melo, Nisston Moraes Tavares

2012-01-01

Distance Learning supported by the WEB is a reality which is growing fast and, like any technological or empirical innovation, it reveals positive and negative aspects. An important aspect is in relation to the monitoring of the activities done by the students since an accurate online assessment of the knowledge acquired is an open and, therefore,…

Selected Track and Field Articles. Sports Articles Reprint Series. First Edition.

ERIC Educational Resources Information Center

Harkins, Dorothy, Ed.

This is a collection of articles from the 1962-70 DGWS Track and Field Guides and from National Institute Proceedings on the subject of girl's track and field activity. Included among the selections are articles on teaching outlines for track and field; distance running for girls and women; athletic injuries; hurdling for girls and women; adaption…

Wiki or Word? Evaluating Tools for Collaborative Writing and Editing

ERIC Educational Resources Information Center

Dishaw, Mark; Eierman, Michael A.; Iversen, Jakob H.; Philip, George C.

2011-01-01

Businesses and other organizations are relying increasingly on virtual teams to perform a range of business activities. A key challenge in utilizing virtual teams is to support collaboration among team members who are separated by distance and/or time. In this paper we use a research model based on a combination of the Technology Acceptance Model…

Data Processing Procedures and Methodology for Estimating Trip Distances for the 1995 American Travel Survey (ATS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hwang, H.-L.; Rollow, J.

2000-05-01

The 1995 American Travel Survey (ATS) collected information from approximately 80,000 U.S. households about their long distance travel (one-way trips of 100 miles or more) during the year of 1995. It is the most comprehensive survey of where, why, and how U.S. residents travel since 1977. ATS is a joint effort by the U.S. Department of Transportation (DOT) Bureau of Transportation Statistics (BTS) and the U.S. Department of Commerce Bureau of Census (Census); BTS provided the funding and supervision of the project, and Census selected the samples, conducted interviews, and processed the data. This report documents the technical support formore » the ATS provided by the Center for Transportation Analysis (CTA) in Oak Ridge National Laboratory (ORNL), which included the estimation of trip distances as well as data quality editing and checking of variables required for the distance calculations.« less

Randomized Approaches for Nearest Neighbor Search in Metric Space When Computing the Pairwise Distance Is Extremely Expensive

NASA Astrophysics Data System (ADS)

Wang, Lusheng; Yang, Yong; Lin, Guohui

Finding the closest object for a query in a database is a classical problem in computer science. For some modern biological applications, computing the similarity between two objects might be very time consuming. For example, it takes a long time to compute the edit distance between two whole chromosomes and the alignment cost of two 3D protein structures. In this paper, we study the nearest neighbor search problem in metric space, where the pair-wise distance between two objects in the database is known and we want to minimize the number of distances computed on-line between the query and objects in the database in order to find the closest object. We have designed two randomized approaches for indexing metric space databases, where objects are purely described by their distances with each other. Analysis and experiments show that our approaches only need to compute O(logn) objects in order to find the closest object, where n is the total number of objects in the database.

A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra.

PubMed

Moseley, Hunter N B; Riaz, Nadeem; Aramini, James M; Szyperski, Thomas; Montelione, Gaetano T

2004-10-01

We present an algorithm and program called Pattern Picker that performs editing of raw peak lists derived from multidimensional NMR experiments with characteristic peak patterns. Pattern Picker detects groups of correlated peaks within peak lists from reduced dimensionality triple resonance (RD-TR) NMR spectra, with high fidelity and high yield. With typical quality RD-TR NMR data sets, Pattern Picker performs almost as well as human analysis, and is very robust in discriminating real peak sets from noise and other artifacts in unedited peak lists. The program uses a depth-first search algorithm with short-circuiting to efficiently explore a search tree representing every possible combination of peaks forming a group. The Pattern Picker program is particularly valuable for creating an automated peak picking/editing process. The Pattern Picker algorithm can be applied to a broad range of experiments with distinct peak patterns including RD, G-matrix Fourier transformation (GFT) NMR spectra, and experiments to measure scalar and residual dipolar coupling, thus promoting the use of experiments that are typically harder for a human to analyze. Since the complexity of peak patterns becomes a benefit rather than a drawback, Pattern Picker opens new opportunities in NMR experiment design.

[Effects of crop tree release on stand growth and stand structure of Cunninghamia lanceolata plantation].

PubMed

Wu, Jian-qiang; Wang, Yi-xiang; Yang, Yi; Zhu, Ting-ting; Zhu, Xu-dan

2015-02-01

Crop trees were selected in a 26-year-old even-aged Cunninghamia lanceolata plantation in Lin' an, and compared in plots that were released and unreleased to examine growth and structure responses for 3 years after thinning. Crop tree release significantly increased the mean increments of diameter and volume of individual tree by 1.30 and 1.25 times relative to trees in control stands, respectively. The increments of diameter and volume of crop trees were significantly higher than those of general trees in thinning plots, crop trees and general trees in control plots, which suggested that the responses from different tree types to crop tree release treatment were different. Crop tree release increased the average distances of crop trees to the nearest neighboring trees, reducing competition among crop trees by about 68.2%. 3-year stand volume increment for thinning stands had no significant difference with that of control stands although the number of trees was only 81.5% of the control. Crop trees in thinned plots with diameters over than 14 cm reached 18.0% over 3 years, compared with 12.0% for trees without thinning, suggesting that crop tree release benefited the larger individual trees. The pattern of tree locations in thinning plots tended to be random, complying with the rule that tree distribution pattern changes with growth. Crop tree release in C. lanceolata plantation not only promoted the stand growth, but also optimized the stand structure, benefiting crop trees sustained rapid growth and larger diameter trees production.

Facilitation or Competition? Tree Effects on Grass Biomass across a Precipitation Gradient

PubMed Central

Moustakas, Aristides; Kunin, William E.; Cameron, Tom C.; Sankaran, Mahesh

2013-01-01

Savanna ecosystems are dominated by two distinct plant life forms, grasses and trees, but the interactions between them are poorly understood. Here, we quantified the effects of isolated savanna trees on grass biomass as a function of distance from the base of the tree and tree height, across a precipitation gradient in the Kruger National Park, South Africa. Our results suggest that mean annual precipitation (MAP) mediates the nature of tree-grass interactions in these ecosystems, with the impact of trees on grass biomass shifting qualitatively between 550 and 737 mm MAP. Tree effects on grass biomass were facilitative in drier sites (MAP≤550 mm), with higher grass biomass observed beneath tree canopies than outside. In contrast, at the wettest site (MAP = 737 mm), grass biomass did not differ significantly beneath and outside tree canopies. Within this overall precipitation-driven pattern, tree height had positive effect on sub-canopy grass biomass at some sites, but these effects were weak and not consistent across the rainfall gradient. For a more synthetic understanding of tree-grass interactions in savannas, future studies should focus on isolating the different mechanisms by which trees influence grass biomass, both positively and negatively, and elucidate how their relative strengths change over broad environmental gradients. PMID:23451137

Inventory implications of using sampling variances in estimation of growth model coefficients

Treesearch

Albert R. Stage; William R. Wykoff

2000-01-01

Variables based on stand densities or stocking have sampling errors that depend on the relation of tree size to plot size and on the spatial structure of the population, ignoring the sampling errors of such variables, which include most measures of competition used in both distance-dependent and distance-independent growth models, can bias the predictions obtained from...

Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

PubMed

Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang

2015-08-03

The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

Comparison of different methods for estimating snowcover in forested, mountainous basins using LANDSAT (ERTS) images. [Washington and Santiam River, Oregon

NASA Technical Reports Server (NTRS)

Meier, M. J.; Evans, W. E.

1975-01-01

Snow-covered areas on LANDSAT (ERTS) images of the Santiam River basin, Oregon, and other basins in Washington were measured using several operators and methods. Seven methods were used: (1) Snowline tracing followed by measurement with planimeter, (2) mean snowline altitudes determined from many locations, (3) estimates in 2.5 x 2.5 km boxes of snow-covered area with reference to snow-free images, (4) single radiance-threshold level for entire basin, (5) radiance-threshold setting locally edited by reference to altitude contours and other images, (6) two-band color-sensitive extraction locally edited as in (5), and (7) digital (spectral) pattern recognition techniques. The seven methods are compared in regard to speed of measurement, precision, the ability to recognize snow in deep shadow or in trees, relative cost, and whether useful supplemental data are produced.

LinkEHR-Ed: a multi-reference model archetype editor based on formal semantics.

PubMed

Maldonado, José A; Moner, David; Boscá, Diego; Fernández-Breis, Jesualdo T; Angulo, Carlos; Robles, Montserrat

2009-08-01

To develop a powerful archetype editing framework capable of handling multiple reference models and oriented towards the semantic description and standardization of legacy data. The main prerequisite for implementing tools providing enhanced support for archetypes is the clear specification of archetype semantics. We propose a formalization of the definition section of archetypes based on types over tree-structured data. It covers the specialization of archetypes, the relationship between reference models and archetypes and conformance of data instances to archetypes. LinkEHR-Ed, a visual archetype editor based on the former formalization with advanced processing capabilities that supports multiple reference models, the editing and semantic validation of archetypes, the specification of mappings to data sources, and the automatic generation of data transformation scripts, is developed. LinkEHR-Ed is a useful tool for building, processing and validating archetypes based on any reference model.

Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions.

PubMed

Sundaram, Mekala; Willoughby, Janna R; Lichti, Nathanael I; Steele, Michael A; Swihart, Robert K

2015-01-01

The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27-73%), and combined effects of seed traits and phylogeny of hardwood trees (5-55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 "global" axes of traits that were phylogenetically autocorrelated at the family and genus level and a third "local" axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30-76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.

Scalable parallel distance field construction for large-scale applications

DOE PAGES

Yu, Hongfeng; Xie, Jinrong; Ma, Kwan -Liu; ...

2015-10-01

Computing distance fields is fundamental to many scientific and engineering applications. Distance fields can be used to direct analysis and reduce data. In this paper, we present a highly scalable method for computing 3D distance fields on massively parallel distributed-memory machines. Anew distributed spatial data structure, named parallel distance tree, is introduced to manage the level sets of data and facilitate surface tracking overtime, resulting in significantly reduced computation and communication costs for calculating the distance to the surface of interest from any spatial locations. Our method supports several data types and distance metrics from real-world applications. We demonstrate itsmore » efficiency and scalability on state-of-the-art supercomputers using both large-scale volume datasets and surface models. We also demonstrate in-situ distance field computation on dynamic turbulent flame surfaces for a petascale combustion simulation. In conclusion, our work greatly extends the usability of distance fields for demanding applications.« less

Scalable Parallel Distance Field Construction for Large-Scale Applications.

PubMed

Yu, Hongfeng; Xie, Jinrong; Ma, Kwan-Liu; Kolla, Hemanth; Chen, Jacqueline H

2015-10-01

Computing distance fields is fundamental to many scientific and engineering applications. Distance fields can be used to direct analysis and reduce data. In this paper, we present a highly scalable method for computing 3D distance fields on massively parallel distributed-memory machines. A new distributed spatial data structure, named parallel distance tree, is introduced to manage the level sets of data and facilitate surface tracking over time, resulting in significantly reduced computation and communication costs for calculating the distance to the surface of interest from any spatial locations. Our method supports several data types and distance metrics from real-world applications. We demonstrate its efficiency and scalability on state-of-the-art supercomputers using both large-scale volume datasets and surface models. We also demonstrate in-situ distance field computation on dynamic turbulent flame surfaces for a petascale combustion simulation. Our work greatly extends the usability of distance fields for demanding applications.

Recognizing human actions by learning and matching shape-motion prototype trees.

PubMed

Jiang, Zhuolin; Lin, Zhe; Davis, Larry S

2012-03-01

A shape-motion prototype-based approach is introduced for action recognition. The approach represents an action as a sequence of prototypes for efficient and flexible action matching in long video sequences. During training, an action prototype tree is learned in a joint shape and motion space via hierarchical K-means clustering and each training sequence is represented as a labeled prototype sequence; then a look-up table of prototype-to-prototype distances is generated. During testing, based on a joint probability model of the actor location and action prototype, the actor is tracked while a frame-to-prototype correspondence is established by maximizing the joint probability, which is efficiently performed by searching the learned prototype tree; then actions are recognized using dynamic prototype sequence matching. Distance measures used for sequence matching are rapidly obtained by look-up table indexing, which is an order of magnitude faster than brute-force computation of frame-to-frame distances. Our approach enables robust action matching in challenging situations (such as moving cameras, dynamic backgrounds) and allows automatic alignment of action sequences. Experimental results demonstrate that our approach achieves recognition rates of 92.86 percent on a large gesture data set (with dynamic backgrounds), 100 percent on the Weizmann action data set, 95.77 percent on the KTH action data set, 88 percent on the UCF sports data set, and 87.27 percent on the CMU action data set.

Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes.

PubMed

Xie, Lei; Wang, Ying Wei; Guan, Shan Yue; Xie, Li Jing; Long, Xin; Sun, Cheng Ye

2014-10-01

Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes (matK, rbcL, and ITS) were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment (PWG) distance, and Tree-Building were tested for discrimination power. The primer universality of all the three markers was high. Except in the case of ITS for Hemerocallis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method. DNA barcoding technique provides us a fast tool for clinical identification of poisonous plants in China. We suggest matK, rbcL, ITS used in combination as DNA barcodes for authentication of poisonous plants. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Assessing atmospheric particulate matter distribution based on Saturation Isothermal Remanent Magnetization of herbaceous and tree leaves in a tropical urban environment.

PubMed

Barima, Yao Sadaiou Sabas; Angaman, Djédoux Maxime; N'gouran, Kobenan Pierre; Koffi, N'guessan Achille; Kardel, Fatemeh; De Cannière, Charles; Samson, Roeland

2014-02-01

Particulate matter (PM) emissions, and the associated human health risks, are likely to continue increasing in urban environments of developing countries like Abidjan (Ivory Cost). This study evaluated the potential of leaves of several herbaceous and tree species as bioindicators of urban particulate matter pollution, and its variation over different land use classes, in a tropical area. Four species well distributed (presence frequencies >90%) over all land use classes, easy to harvest and whose leaves are wide enough to be easily scanned were selected, i.e.: Amaranthus spinosus (Amaranthaceae), Eleusine indica (Poaceae), Panicum maximum (Poaceae) and Ficus benjamina (Moraceae). Leaf sampling of these species was carried out at 3 distances from the road and at 3 height levels. Traffic density was also noted and finally biomagnetic parameters of these leaves were determined. Results showed that Saturation Isothermal Remanent Magnetization (SIRM) of leaves was at least 4 times higher (27.5×10(-6)A) in the vicinity of main roads and industrial areas than in parks and residential areas. The main potential sources of PM pollution were motor vehicles and industries. The slightly hairy leaves of the herbaceous plant A. spinosus and the waxy leaves of the tree F. benjamina showed the highest SIRM (25×10(-6)A). Leaf SIRM increased with distance to road (R(2)>0.40) and declined with sampling height (R(2)=0.17). The distance between 0 and 5m from the road seemed to be the most vulnerable in terms of PM pollution. This study has showed that leaf SIRM of herbaceous and tree species can be used to assess PM exposure in tropical urban environments. © 2013.

Patterns of woody plant invasion in an Argentinean coastal grassland

NASA Astrophysics Data System (ADS)

Alberio, Constanza; Comparatore, Viviana

2014-01-01

Coastal dune grasslands are fragile ecosystems that have historically been subjected to various types of uses and human activities. In Buenos Aires Province (Argentina), these areas are frequently afforested for urban and touristic development. The introduction and subsequent spread of exotic tree species is one of the main threats to conservation of natural grasslands as invasive trees strongly transform their structure and composition. The aim of this study was to identify patterns of woody plant invasion comparing plant communities and environmental variables between invaded and non-invaded areas surrounding the coastal village of Mar Azul, Argentina. Coastal grasslands in this area are being invaded by Populus alba (white poplar) and Acacia longifolia (coast wattle). The height of the saplings and the richness of the accompanying vegetation were evaluated in relation to the distance from the edge of the mature tree patches. Also, the cover, richness and diversity of all species in the invaded and non-invaded areas were measured, as well as soil pH, temperature and particle size. Negative correlations were found between the height of the saplings and distance to mature tree patches in all areas. The richness of the accompanying vegetation was negatively and positively correlated with the distance from the poplar and acacia area, respectively. The most abundant native species was Cortaderia selloana. Less cover, richness and diversity of native plant species and greater soil particle size were found in invaded areas, where the proportion of bare soil was higher. Also, a higher proportion of leaf litter in the invaded areas was registered. The results emphasize the invasive capacity of P. alba and A. longifolia advancing on the native communities and reducing their richness. Knowledge of the impact of invasive woody plants in coastal grasslands is important to design active management strategies for conservation purposes.

Long-distance seed and pollen dispersal inferred from spatial genetic structure in the very low-density rainforest tree, Baillonella toxisperma Pierre, in Central Africa.

PubMed

Ndiade-Bourobou, D; Hardy, O J; Favreau, B; Moussavou, H; Nzengue, E; Mignot, A; Bouvet, J-M

2010-11-01

We analysed the spatial distribution of genetic diversity to infer gene flow for Baillonella toxisperma Pierre (Moabi), a threatened entomophilous pollinated and animal-dispersed Central African tree, with typically low density (5-7 adults trees/km(2)). Fifteen nuclear and three universal chloroplast microsatellites markers were used to type 247 individuals localized in three contiguous areas with differing past logging intensity. These three areas were within a natural forest block of approximately 2886 km(2) in Gabon. Expected heterozygosity and chloroplast diversity were He(nuc) = 0.570 and H(cp) = 0.761, respectively. F(IS) was only significant in one area (F(IS) = 0.076, P < 0.01) and could be attributed to selfing. For nuclear loci, Bayesian clustering did not detect discrete gene pools within and between the three areas and global differentiation (F(STnuc) = 0.007, P > 0.05) was not significant, suggesting that they are one population. At the level of the whole forest, both nuclear and chloroplast markers revealed a weak correlation between genetic relatedness and spatial distance between individuals: Sp(nuc) = 0.003 and Sp(cp) = 0.015, respectively. The extent of gene flow (σ) was partitioned into global gene flow (σ(g)) from 6.6 to 9.9 km, seed dispersal (σ(s)) from 4.0 to 6.3 km and pollen dispersal (σ(p)) from 9.8 to 10.8 km. These uncommonly high dispersal distances indicate that low-density canopy trees in African rainforests could be connected by extensive gene flow, although, given the current threats facing many seed disperser species in Central Africa, this may no longer be the case. © 2010 Blackwell Publishing Ltd.

Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae

NASA Technical Reports Server (NTRS)

Springer, E.; Sachs, M. S.; Woese, C. R.; Boone, D. R.

1995-01-01

Representatives of the family Methanosarcinaceae were analyzed phylogenetically by comparing partial sequences of their methyl-coenzyme M reductase (mcrI) genes. A 490-bp fragment from the A subunit of the gene was selected, amplified by the PCR, cloned, and sequenced for each of 25 strains belonging to the Methanosarcinaceae. The sequences obtained were aligned with the corresponding portions of five previously published sequences, and all of the sequences were compared to determine phylogenetic distances by Fitch distance matrix methods. We prepared analogous trees based on 16S rRNA sequences; these trees corresponded closely to the mcrI trees, although the mcrI sequences of pairs of organisms had 3.01 +/- 0.541 times more changes than the respective pairs of 16S rRNA sequences, suggesting that the mcrI fragment evolved about three times more rapidly than the 16S rRNA gene. The qualitative similarity of the mcrI and 16S rRNA trees suggests that transfer of genetic information between dissimilar organisms has not significantly affected these sequences, although we found inconsistencies between some mcrI distances that we measured and and previously published DNA reassociation data. It is unlikely that multiple mcrI isogenes were present in the organisms that we examined, because we found no major discrepancies in multiple determinations of mcrI sequences from the same organism. Our primers for the PCR also match analogous sites in the previously published mcrII sequences, but all of the sequences that we obtained from members of the Methanosarcinaceae were more closely related to mcrI sequences than to mcrII sequences, suggesting that members of the Methanosarcinaceae do not have distinct mcrII genes.

Maximum likelihood clustering with dependent feature trees

NASA Technical Reports Server (NTRS)

Chittineni, C. B. (Principal Investigator)

1981-01-01

The decomposition of mixture density of the data into its normal component densities is considered. The densities are approximated with first order dependent feature trees using criteria of mutual information and distance measures. Expressions are presented for the criteria when the densities are Gaussian. By defining different typs of nodes in a general dependent feature tree, maximum likelihood equations are developed for the estimation of parameters using fixed point iterations. The field structure of the data is also taken into account in developing maximum likelihood equations. Experimental results from the processing of remotely sensed multispectral scanner imagery data are included.

Linking growth and yield and process models to estimate impact of environmental changes on growth of loblolly pine

Treesearch

V. Clark Baldwin; Harold E. Burkhart; James A. Westfall; Kelly D. Peterson

2001-01-01

PTAEDA2 is a distance-dependent, individual tree model that simulates the growth and yield of a plantation of loblolly pine (Pinus taeda L.)on an annual basis. The MAESTRO model utilizes an array of trees in a stand to calculate and integrate the effects of biological and physical variables on the photosynthesis and respiration processes of a target...

Productivity and cost of manual felling and cable skidding in central Appalachian hardwood forests

Treesearch

Jingxin Wang; Charlie Long; Joe McNeel; John Baumgras; John Baumgras

2004-01-01

A field production study was conducted for a manual harvesting system using a chainsaw and cable skidder in a central Appalachian hardwood forest site. A partial cut was performed on a 50-acre tract with an average slope of 25 percent. Felling time pre tree was most affected by diameter at breast height and the distance between harvested trees while skidding cycle time...

Mapping growing stock volume and forest live biomass: a case study of the Polissya region of Ukraine

NASA Astrophysics Data System (ADS)

Bilous, Andrii; Myroniuk, Viktor; Holiaka, Dmytrii; Bilous, Svitlana; See, Linda; Schepaschenko, Dmitry

2017-10-01

Forest inventory and biomass mapping are important tasks that require inputs from multiple data sources. In this paper we implement two methods for the Ukrainian region of Polissya: random forest (RF) for tree species prediction and k-nearest neighbors (k-NN) for growing stock volume and biomass mapping. We examined the suitability of the five-band RapidEye satellite image to predict the distribution of six tree species. The accuracy of RF is quite high: ~99% for forest/non-forest mask and 89% for tree species prediction. Our results demonstrate that inclusion of elevation as a predictor variable in the RF model improved the performance of tree species classification. We evaluated different distance metrics for the k-NN method, including Euclidean or Mahalanobis distance, most similar neighbor (MSN), gradient nearest neighbor, and independent component analysis. The MSN with the four nearest neighbors (k = 4) is the most precise (according to the root-mean-square deviation) for predicting forest attributes across the study area. The k-NN method allowed us to estimate growing stock volume with an accuracy of 3 m3 ha-1 and for live biomass of about 2 t ha-1 over the study area.

Disentangling environmental and spatial effects on phylogenetic structure of angiosperm tree communities in China.

PubMed

Qian, Hong; Chen, Shengbin; Zhang, Jin-Long

2017-07-17

Niche-based and neutrality-based theories are two major classes of theories explaining the assembly mechanisms of local communities. Both theories have been frequently used to explain species diversity and composition in local communities but their relative importance remains unclear. Here, we analyzed 57 assemblages of angiosperm trees in 0.1-ha forest plots across China to examine the effects of environmental heterogeneity (relevant to niche-based processes) and spatial contingency (relevant to neutrality-based processes) on phylogenetic structure of angiosperm tree assemblages distributed across a wide range of environment and space. Phylogenetic structure was quantified with six phylogenetic metrics (i.e., phylogenetic diversity, mean pairwise distance, mean nearest taxon distance, and the standardized effect sizes of these three metrics), which emphasize on different depths of evolutionary histories and account for different degrees of species richness effects. Our results showed that the variation in phylogenetic metrics explained independently by environmental variables was on average much greater than that explained independently by spatial structure, and the vast majority of the variation in phylogenetic metrics was explained by spatially structured environmental variables. We conclude that niche-based processes have played a more important role than neutrality-based processes in driving phylogenetic structure of angiosperm tree species in forest communities in China.

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

PubMed

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.

Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl.

PubMed

Cloutier, D; Kanashiro, M; Ciampi, A Y; Schoen, D J

2007-02-01

Selective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect-pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre- and post-harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre- vs. post-harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre- and post-harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short-term genetic impact of selective logging on this population of C. guianensis.

Pasture succession in the Neotropics: extending the nucleation hypothesis into a matrix discontinuity hypothesis.

PubMed

Peterson, Chris J; Dosch, Jerald J; Carson, Walter P

2014-08-01

The nucleation hypothesis appears to explain widespread patterns of succession in tropical pastures, specifically the tendency for isolated trees to promote woody species recruitment. Still, the nucleation hypothesis has usually been tested explicitly for only short durations and in some cases isolated trees fail to promote woody recruitment. Moreover, at times, nucleation occurs in other key habitat patches. Thus, we propose an extension, the matrix discontinuity hypothesis: woody colonization will occur in focal patches that function to mitigate the herbaceous vegetation effects, thus providing safe sites or regeneration niches. We tested predictions of the classical nucleation hypothesis, the matrix discontinuity hypothesis, and a distance from forest edge hypothesis, in five abandoned pastures in Costa Rica, across the first 11 years of succession. Our findings confirmed the matrix discontinuity hypothesis: specifically, rotting logs and steep slopes significantly enhanced woody colonization. Surprisingly, isolated trees did not consistently significantly enhance recruitment; only larger trees did so. Finally, woody recruitment consistently decreased with distance from forest. Our results as well as results from others suggest that the nucleation hypothesis needs to be broadened beyond its historical focus on isolated trees or patches; the matrix discontinuity hypothesis focuses attention on a suite of key patch types or microsites that promote woody species recruitment. We argue that any habitat discontinuities that ameliorate the inhibition by dense graminoid layers will be foci for recruitment. Such patches could easily be manipulated to speed the transition of pastures to closed canopy forests.

Colonization of weakened trees by mass-attacking bark beetles: no penalty for pioneers, scattered initial distributions and final regular patterns

PubMed Central

Gabriel, Edith; Louis, Marceau; Deneubourg, Jean-Louis; Grégoire, Jean-Claude

2018-01-01

Bark beetles use aggregation pheromones to promote group foraging, thus increasing the chances of an individual to find a host and, when relevant, to overwhelm the defences of healthy trees. When a male beetle finds a suitable host, it releases pheromones that attract potential mates as well as other ‘spying’ males, which result in aggregations on the new host. To date, most studies have been concerned with the use of aggregation pheromones by bark beetles to overcome the defences of living, well-protected trees. How insects behave when facing undefended or poorly defended hosts remains largely unknown. The spatio-temporal pattern of resource colonization by the European eight-toothed spruce bark beetle, Ips typographus, was quantified when weakly defended hosts (fallen trees) were attacked. In many of the replicates, colonization began with the insects rapidly scattering over the available surface and then randomly filling the gaps until a regular distribution was established, which resulted in a constant decrease in nearest-neighbour distances to a minimum below which attacks were not initiated. The scattered distribution of the first attacks suggested that the trees were only weakly defended. A minimal theoretical distance of 2.5 cm to the earlier settlers (corresponding to a density of 3.13 attacks dm−2) was calculated, but the attack density always remained lower, between 0.4 and 1.2 holes dm−2, according to our observations. PMID:29410791

A study of hierarchical structure on South China industrial electricity-consumption correlation

NASA Astrophysics Data System (ADS)

Yao, Can-Zhong; Lin, Ji-Nan; Liu, Xiao-Feng

2016-02-01

Based on industrial electricity-consumption data of five southern provinces of China from 2005 to 2013, we study the industrial correlation mechanism with MST (minimal spanning tree) and HT (hierarchical tree) models. First, we comparatively analyze the industrial electricity-consumption correlation structure in pre-crisis and after-crisis period using MST model and Bootstrap technique of statistical reliability test of links. Results exhibit that all industrial electricity-consumption trees of five southern provinces of China in pre-crisis and after-crisis time are in formation of chain, and the "center-periphery structure" of those chain-like trees is consistent with industrial specialization in classical industrial chain theory. Additionally, the industrial structure of some provinces is reorganized and transferred in pre-crisis and after-crisis time. Further, the comparative analysis with hierarchical tree and Bootstrap technique demonstrates that as for both observations of GD and overall NF, the industrial electricity-consumption correlation is non-significant clustered in pre-crisis period, whereas it turns significant clustered in after-crisis time. Therefore we propose that in perspective of electricity-consumption, their industrial structures are directed to optimized organization and global correlation. Finally, the analysis of distance of HTs verifies that industrial reorganization and development may strengthen market integration, coordination and correlation of industrial production. Except GZ, other four provinces have a shorter distance of industrial electricity-consumption correlation in after-crisis period, revealing a better performance of regional specialization and integration.

The Development of PIPA: An Integrated and Automated Pipeline for Genome-Wide Protein Function Annotation

DTIC Science & Technology

2008-01-25

limitations and plans for improvement Perhaps, one of PIPA’s main limitations is that all of its currently integrated resources to predict protein function...are planning on expending PIPA’s function prediction capabilities by incorporating comparative analysis approaches, e.g., phy- logenetic tree analysis...tools and services. Nucleic Acids Res 2005/12/31 edition. 2006, 34(Database issue):D247-51. 6. Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S

Polynomial Supertree Methods Revisited

PubMed Central

Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian

2011-01-01

Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study comparing the performance of MRP and the polynomial supertree methods MinCut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, PhySIC_IST, and super distance matrix. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the tradeoff between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches. Based on our results, we make some general suggestions for supertree methods yet to come. PMID:22229028

The spectrum of genomic signatures: from dinucleotides to chaos game representation.

PubMed

Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

2005-02-14

In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

Application of the Near Miss Strategy and Edit Distance to Handle Dirty Data

NASA Astrophysics Data System (ADS)

Varol, Cihan; Bayrak, Coskun; Wagner, Rick; Goff, Dana

In today’s information age, processing customer information in a standardized and accurate manner is known to be a difficult task. Data collection methods vary from source to source by format, volume, and media type. Therefore, it is advantageous to deploy customized data hygiene techniques to standardize the data for meaningfulness and usefulness based on the organization.

Application of the Near Miss Strategy and Edit Distance to Handle Dirty Data

NASA Astrophysics Data System (ADS)

Varol, Cihan; Bayrak, Coskun; Wagner, Rick; Goff, Dana

In today's information age, processing customer information in a standardized and accurate manner is known to be a difficult task. Data collection methods vary from source to source by format, volume, and media type. Therefore, it is advantageous to deploy customized data hygiene techniques to standardize the data for meaningfulness and usefulness based on the organization.

Using Edit Distance to Analyse Errors in a Natural Language to Logic Translation Corpus

ERIC Educational Resources Information Center

Barker-Plummer, Dave; Dale, Robert; Cox, Richard; Romanczuk, Alex

2012-01-01

We have assembled a large corpus of student submissions to an automatic grading system, where the subject matter involves the translation of natural language sentences into propositional logic. Of the 2.3 million translation instances in the corpus, 286,000 (approximately 12%) are categorized as being in error. We want to understand the nature of…

SlideSort: all pairs similarity search for short reads

PubMed Central

Shimizu, Kana; Tsuda, Koji

2011-01-01

Motivation: Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses. Results: In this study, we designed and implemented an exact algorithm SlideSort that finds all similar pairs from a string pool in terms of edit distance. Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to existing methods based on single k-mers, our method is more effective in reducing the number of edit distance calculations. In comparison to backtracking methods such as BWA, our method is much faster in finding remote matches, scaling easily to tens of millions of sequences. Our software has an additional function of single link clustering, which is useful in summarizing short reads for further processing. Availability: Executable binary files and C++ libraries are available at http://www.cbrc.jp/~shimizu/slidesort/ for Linux and Windows. Contact: slidesort@m.aist.go.jp; shimizu-kana@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21148542

Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.

PubMed

Yang, Jiaoyun; Wang, Haipeng; Ding, Huitong; An, Ning; Alterovitz, Gil

2017-01-19

Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately labeled data, etc. As crowdsourcing-based synthetic biology databases face similar data quality issues, we propose to visualize biobricks to tackle them. However, existing dimensionality reduction methods could not be directly applied on biobricks datasets. Hereby, we use normalized edit distance to enhance dimensionality reduction methods, including Isomap and Laplacian Eigenmaps. By extracting biobricks from synthetic biology database Registry of Standard Biological Parts, six combinations of various types of biobricks are tested. The visualization graphs illustrate discriminated biobricks and inappropriately labeled biobricks. Clustering algorithm K-means is adopted to quantify the reduction results. The average clustering accuracy for Isomap and Laplacian Eigenmaps are 0.857 and 0.844, respectively. Besides, Laplacian Eigenmaps is 5 times faster than Isomap, and its visualization graph is more concentrated to discriminate biobricks. By combining normalized edit distance with Isomap and Laplacian Eigenmaps, synthetic biology biobircks are successfully visualized in two dimensional space. Various types of biobricks could be discriminated and inappropriately labeled biobricks could be determined, which could help to assess crowdsourcing-based synthetic biology databases' quality, and make biobricks selection.

The sine method as a more accurate height predictor for hardwoods

Treesearch

Don C. Bragg

2007-01-01

Most hypsometers apply a mathematical technique that utilizes the tangent of angles and a horizontal distance to deliver the exact height of a tree under idealized circumstances. Unfortunately, these conditions are rarely met for hardwoods in the field. A “new” predictor based on sine and slope distance and discussed here does not require the same assumptions for...

Distance and phenology influence pollen gene flow, male reproductive success, and female mate choice in a northern red oak (Quercus rubra L.) seed orchard

USDA-ARS?s Scientific Manuscript database

Northern red oak is a high-value hardwood used for lumber, furniture and veneer. Intensively managed northern red oak orchards require genetic gain for trait improvement. Data from conifer seed orchards and natural and managed stands of hardwood trees have shed light on the distance over which polle...

Spread of dwarf mistletoe from discrete seed sources into young stands of ponderosa and Jeffrey pines

Treesearch

J. R. Parmeter Jr.

1972-01-01

The maximum distance of spread of dwarf mistletoes from isolated overstory pines into surrounding reproduction averages 120 feet. The rate of infection in young trees declined as distance from the seed source increased and was generally greatest in the direction of prevailing winds. This pattern of infection was similar to the previously reported pattern of seed...

Tree-level contributions to the rare decays B+→π+νν¯, B+→K+νν¯, and B+→K*νν¯ in the Standard Model

NASA Astrophysics Data System (ADS)

Kamenik, Jernej F.; Smith, Christopher

2009-10-01

The tree-level contributions to the rare decays B+ →π+ ννbar, B+ →K+ ννbar, and B+ →K*+ ννbar are analyzed and compared to those occurring in K+ →π+ ννbar, D+ →π+ ννbar, and Ds+ →π+ ννbar. It is shown that these purely long-distance contributions, arising from the exchange of a charged lepton, can be significant in B+ decays for an intermediate τ, potentially blurring the distinction between the modes used to extract B+ →τ+ντ and those used to probe the genuine short-distance b → dννbar and b → sννbar FCNC transitions. Numerically, the tree-level contributions are found to account for 98%, 12% and 14% of the total B+ →π+ ννbar, B+ →K+ ννbar, and B+ →K*+ ννbar rates, respectively.

Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

PubMed Central

Guidugli, M C; Nazareno, A G; Feres, J M; Contel, E P B; Mestriner, M A; Alzate-Marin, A L

2016-01-01

Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm−ts=−0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population. PMID:26732014

Inference of Transmission Network Structure from HIV Phylogenetic Trees

DOE PAGES

Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan; ...

2017-01-13

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic.more » Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.« less

Agroforestry management in vineyards: effects on soil microbial communities

NASA Astrophysics Data System (ADS)

Montagne, Virginie; Nowak, Virginie; Guilland, Charles; Gontier, Laure; Dufourcq, Thierry; Guenser, Josépha; Grimaldi, Juliette; Bourgade, Emilie; Ranjard, Lionel

2017-04-01

Some vineyard practices (tillage, chemical weeding or pest management) are generally known to impact the environment with particular negative effects on the diversity and the abundance of soil microorganisms, and cause water and soil pollutions. In an agro-ecological context, innovative cropping systems have been developed to improve ecosystem services. Among them, agroforestry offers strategies of sustainable land management practices. It consists in intercropping trees with annual/perennial/fodder crop on the same plot but it is weakly referenced with grapevine. The present study assesses the effects of intercropped and neighbouring trees on the soil of three agroforestry vineyards, in south-western France regions. More precisely soils of the different plots were sampled and the impact of the distance to the tree or to the neighbouring trees (forest) on soil microbial community has been considered. Indigenous soil microbial communities were characterized by a metagenomic approach that consisted in extracting the molecular microbial biomass, then in calculating the soil fungi/bacteria ratio - obtained by qPCR - and then in characterizing the soil microbial diversity - through Illumina sequencing of 16S and 18S regions. Our results showed a significant difference between the soil of agroforestry vineyards and the soil sampled in the neighbouring forest in terms of microbial abundance and diversity. However, only structure and composition of bacterial community seem to be influenced by the implanted trees in the vine plots. In addition, the comparison of microbial co-occurrence networks between vine and forest plots as well as inside vine plots according to distance to the tree allow revealing a more sensitive impact of agroforestry practices. Altogether, the results we obtained build up the first references for concerning the soil of agroforestry vineyards which will be interpreted in terms of soil quality, functioning and sustainability.

Inference of Transmission Network Structure from HIV Phylogenetic Trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic.more » Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.« less

Response of a boreal forest to canopy opening: assessing vertical and lateral tree growth with multi-temporal lidar data.

PubMed

Vepakomma, Udayalakshmi; St-Onge, Benoit; Kneeshaw, Daniel

2011-01-01

Fine-scale height-growth response of boreal trees to canopy openings is difficult to measure from the ground, and there are important limitations in using stereophotogrammetry in defining gaps and determining individual crowns and height. However, precise knowledge on height growth response to different openings is critical for refining partial harvesting techniques. In this study, we question whether conifers and hardwoods respond equally in terms of sapling growth or lateral growth to openings. We also ask to what distance gaps affect tree growth into the forest. We use multi-temporal lidar to characterize tree/sapling height and lateral growth responses over five years to canopy openings and high resolution images to identify conifers and hardwoods. Species-class-wise height-growth patterns of trees/saplings in various neighborhood contexts were determined across a 6-km matrix of Canadian boreal mixed deciduous coniferous forests. We then use statistical techniques to probe how these growth responses vary by spatial location with respect to the gap edge. Results confirm that both mechanisms of gap closure contribute to the closing of canopies at a rate of 1.2% per annum. Evidence also shows that both hardwood and conifer gap edge trees have a similar lateral growth (average of 22 cm/yr) and similar rates of height growth irrespective of their location and initial height. Height growth of all saplings, however, was strongly dependent on their position within the gap and the size of the gap. Results suggest that hardwood and softwood saplings in gaps have greatest growth rates at distances of 0.5-2 m and 1.5-4 m from the gap edge and in openings smaller than 800 m2 and 250 m2, respectively. Gap effects on the height growth of trees in the intact forest were evident up to 30 m and 20 m from gap edges for hardwood and softwood overstory trees, respectively. Our results thus suggest that foresters should consider silvicultural techniques that create many small openings in mixed coniferous deciduous boreal forests to maximize the growth response of both residual and regenerating trees.

libFLASM: a software library for fixed-length approximate string matching.

PubMed

Ayad, Lorraine A K; Pissis, Solon P P; Retha, Ahmad

2016-11-10

Approximate string matching is the problem of finding all factors of a given text that are at a distance at most k from a given pattern. Fixed-length approximate string matching is the problem of finding all factors of a text of length n that are at a distance at most k from any factor of length ℓ of a pattern of length m. There exist bit-vector techniques to solve the fixed-length approximate string matching problem in time [Formula: see text] and space [Formula: see text] under the edit and Hamming distance models, where w is the size of the computer word; as such these techniques are independent of the distance threshold k or the alphabet size. Fixed-length approximate string matching is a generalisation of approximate string matching and, hence, has numerous direct applications in computational molecular biology and elsewhere. We present and make available libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching under both the edit and the Hamming distance models. Moreover we describe how fixed-length approximate string matching is applied to solve real problems by incorporating libFLASM into established applications for multiple circular sequence alignment as well as single and structured motif extraction. Specifically, we describe how it can be used to improve the accuracy of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies; and we also describe how it is used to efficiently find motifs in molecular sequences representing regulatory or functional regions. The comparison of the performance of the library to other algorithms show how it is competitive, especially with increasing distance thresholds. Fixed-length approximate string matching is a generalisation of the classic approximate string matching problem. We present libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching. The extensive experimental results presented here suggest that other applications could benefit from using libFLASM, and thus further maintenance and development of libFLASM is desirable.

Phylogenetic tree construction based on 2D graphical representation

NASA Astrophysics Data System (ADS)

Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

2006-04-01

A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

Computerization of guidelines: a knowledge specification method to convert text to detailed decision tree for electronic implementation.

PubMed

Aguirre-Junco, Angel-Ricardo; Colombet, Isabelle; Zunino, Sylvain; Jaulent, Marie-Christine; Leneveut, Laurence; Chatellier, Gilles

2004-01-01

The initial step for the computerization of guidelines is the knowledge specification from the prose text of guidelines. We describe a method of knowledge specification based on a structured and systematic analysis of text allowing detailed specification of a decision tree. We use decision tables to validate the decision algorithm and decision trees to specify and represent this algorithm, along with elementary messages of recommendation. Edition tools are also necessary to facilitate the process of validation and workflow between expert physicians who will validate the specified knowledge and computer scientist who will encode the specified knowledge in a guide-line model. Applied to eleven different guidelines issued by an official agency, the method allows a quick and valid computerization and integration in a larger decision support system called EsPeR (Personalized Estimate of Risks). The quality of the text guidelines is however still to be developed further. The method used for computerization could help to define a framework usable at the initial step of guideline development in order to produce guidelines ready for electronic implementation.

Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia

PubMed Central

Walsh, Neville G.; Cantrill, David J.; Holmes, Gareth D.; Murphy, Daniel J.

2017-01-01

In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, x¯ = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5–99.5%) and of species was low (25.6–44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1–44.6% and 25.6–31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of “correct” (97.6%) and a low percentage of “incorrect” (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are encountered in the application of genetic and morphological data to species delimitations, with taxonomic signal limited by extensive infra-specific variation and shared polymorphisms among species in both data types. PMID:29084279

Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia.

PubMed

Birch, Joanne L; Walsh, Neville G; Cantrill, David J; Holmes, Gareth D; Murphy, Daniel J

2017-01-01

In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5-99.5%) and of species was low (25.6-44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1-44.6% and 25.6-31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of "correct" (97.6%) and a low percentage of "incorrect" (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are encountered in the application of genetic and morphological data to species delimitations, with taxonomic signal limited by extensive infra-specific variation and shared polymorphisms among species in both data types.

Stay tuned: active amplification tunes tree cricket ears to track temperature-dependent song frequency.

PubMed

Mhatre, Natasha; Pollack, Gerald; Mason, Andrew

2016-04-01

Tree cricket males produce tonal songs, used for mate attraction and male-male interactions. Active mechanics tunes hearing to conspecific song frequency. However, tree cricket song frequency increases with temperature, presenting a problem for tuned listeners. We show that the actively amplified frequency increases with temperature, thus shifting mechanical and neuronal auditory tuning to maintain a match with conspecific song frequency. Active auditory processes are known from several taxa, but their adaptive function has rarely been demonstrated. We show that tree crickets harness active processes to ensure that auditory tuning remains matched to conspecific song frequency, despite changing environmental conditions and signal characteristics. Adaptive tuning allows tree crickets to selectively detect potential mates or rivals over large distances and is likely to bestow a strong selective advantage by reducing mate-finding effort and facilitating intermale interactions. © 2016 The Author(s).

Rooting the archaebacterial tree: the pivotal role of Thermococcus celer in archaebacterial evolution

NASA Technical Reports Server (NTRS)

Achenbach-Richter, L.; Gupta, R.; Zillig, W.; Woese, C. R.

1988-01-01

The sequence of the 16S ribosomal RNA gene from the archaebacterium Thermococcus celer shows the organism to be related to the methanogenic archaebacteria rather than to its phenotypic counterparts, the extremely thermophilic archaebacteria. This conclusion turns on the position of the root of the archaebacterial phylogenetic tree, however. The problems encountered in rooting this tree are analyzed in detail. Under conditions that suppress evolutionary noise both the parsimony and evolutionary distance methods yield a root location (using a number of eubacterial or eukaryotic outgroup sequences) that is consistent with that determined by an "internal rooting" method, based upon an (approximate) determination of relative evolutionary rates.

From statistics of regular tree-like graphs to distribution function and gyration radius of branched polymers

NASA Astrophysics Data System (ADS)

Grosberg, Alexander Y.; Nechaev, Sergei K.

2015-08-01

We consider flexible branched polymer, with quenched branch structure, and show that its conformational entropy as a function of its gyration radius R, at large R, obeys, in the scaling sense, Δ S˜ {R}2/({a}2L), with a bond length (or Kuhn segment) and L defined as an average spanning distance. We show that this estimate is valid up to at most the logarithmic correction for any tree. We do so by explicitly computing the largest eigenvalues of Kramers matrices for both regular and ‘sparse’ three-branched trees, uncovering on the way their peculiar mathematical properties.

Using stochastic gradient boosting to infer stopover habitat selection and distribution of Hooded Cranes Grus monacha during spring migration in Lindian, Northeast China.

PubMed

Cai, Tianlong; Huettmann, Falk; Guo, Yumin

2014-01-01

The Hooded Crane (Grus monacha) is a globally vulnerable species, and habitat loss is the primary cause of its decline. To date, little is known regarding the specific habitat needs, and stopover habitat selection in particular, of the Hooded Crane. In this study we used stochastic gradient boosting (TreeNet) to develop three specific habitat selection models for roosting, daytime resting, and feeding site selection. In addition, we used a geographic information system (GIS) combined with TreeNet to develop a species distribution model. We also generated a digital map of the relative occurrence index (ROI) of this species at daytime resting sites in the study area. Our study indicated that the water depth, distance to village, coverage of deciduous leaves, open water area, and density of plants were the major predictors of roosting site selection. For daytime resting site selection, the distance to wetland, distance to farmland, and distance to road were the primary predictors. For feeding site selection, the distance to road, quantity of food, plant coverage, distance to village, plant density, distance to wetland, and distance to river were contributing factors, and the distance to road and quantity of food were the most important predictors. The predictive map showed that there were two consistent multi-year daytime resting sites in our study area. Our field work in 2013 using systematic ground-truthing confirmed that this prediction was accurate. Based on this study, we suggest that Lindian plays an important role for migratory birds and that cultivation practices should be adjusted locally. Furthermore, public education programs to promote the concept of the harmonious coexistence of humans and cranes can help successfully protect this species in the long term and eventually lead to its delisting by the IUCN.

Using Stochastic Gradient Boosting to Infer Stopover Habitat Selection and Distribution of Hooded Cranes Grus monacha during Spring Migration in Lindian, Northeast China

PubMed Central

Cai, Tianlong; Huettmann, Falk; Guo, Yumin

2014-01-01

The Hooded Crane (Grus monacha) is a globally vulnerable species, and habitat loss is the primary cause of its decline. To date, little is known regarding the specific habitat needs, and stopover habitat selection in particular, of the Hooded Crane. In this study we used stochastic gradient boosting (TreeNet) to develop three specific habitat selection models for roosting, daytime resting, and feeding site selection. In addition, we used a geographic information system (GIS) combined with TreeNet to develop a species distribution model. We also generated a digital map of the relative occurrence index (ROI) of this species at daytime resting sites in the study area. Our study indicated that the water depth, distance to village, coverage of deciduous leaves, open water area, and density of plants were the major predictors of roosting site selection. For daytime resting site selection, the distance to wetland, distance to farmland, and distance to road were the primary predictors. For feeding site selection, the distance to road, quantity of food, plant coverage, distance to village, plant density, distance to wetland, and distance to river were contributing factors, and the distance to road and quantity of food were the most important predictors. The predictive map showed that there were two consistent multi-year daytime resting sites in our study area. Our field work in 2013 using systematic ground-truthing confirmed that this prediction was accurate. Based on this study, we suggest that Lindian plays an important role for migratory birds and that cultivation practices should be adjusted locally. Furthermore, public education programs to promote the concept of the harmonious coexistence of humans and cranes can help successfully protect this species in the long term and eventually lead to its delisting by the IUCN. PMID:24587118

Protein space: a natural method for realizing the nature of protein universe.

PubMed

Yu, Chenglong; Deng, Mo; Cheng, Shiu-Yuen; Yau, Shek-Chung; He, Rong L; Yau, Stephen S-T

2013-02-07

Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe. Copyright © 2012 Elsevier Ltd. All rights reserved.

Reconstructing the spatial pattern of trees from routine stand examination measurements

USGS Publications Warehouse

Hanus, M.L.; Hann, D.W.; Marshall, D.D.

1998-01-01

Reconstruction of the spatial pattern of trees is important for the accurate visual display of unmapped stands. The proposed process for generating the spatial pattern is a nonsimple sequential inhibition process, with the inhibition zone proportionate to the scaled maximum crown width of an open-grown tree of the same species and same diameter at breast height as the subject tree. The results of this coordinate generation procedure are compared with mapped stem data from nine natural stands of Douglas-fir at two ages by the use of a transformed Ripley's K(d) function. The results of this comparison indicate that the proposed method, based on complete tree lists, successfully replicated the spatial patterns of the trees in all nine stands at both ages and over the range of distances examined. On the basis of these findings and the procedure's ability to model effects through time, the nonsimple sequential inhibition process has been chosen to generate tree coordinates in the VIZ4ST computer program for displaying forest stand structure in naturally regenerated young Douglas-fir stands. For. Sci.

Using tree diversity to compare phylogenetic heuristics.

PubMed

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.

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.

PubMed

Mai, Uyen; Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

PubMed Central

Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods. PMID:28800608

Efficient visualization of urban spaces

NASA Astrophysics Data System (ADS)

Stamps, A. E.

2012-10-01

This chapter presents a new method for calculating efficiency and applies that method to the issues of selecting simulation media and evaluating the contextual fit of new buildings in urban spaces. The new method is called "meta-analysis". A meta-analytic review of 967 environments indicated that static color simulations are the most efficient media for visualizing urban spaces. For contextual fit, four original experiments are reported on how strongly five factors influence visual appeal of a street: architectural style, trees, height of a new building relative to the heights of existing buildings, setting back a third story, and distance. A meta-analysis of these four experiments and previous findings, covering 461 environments, indicated that architectural style, trees, and height had effects strong enough to warrant implementation, but the effects of setting back third stories and distance were too small to warrant implementation.

Movement of Xylosandrus germanus (Coleoptera: Curculionidae) in Ornamental Nurseries and Surrounding Habitats.

PubMed

Reding, Michael E; Ranger, Christopher M; Sampson, Blair J; Werle, Christopher T; Oliver, Jason B; Schultz, Peter B

2015-08-01

Some exotic ambrosia beetles are damaging pests in ornamental nurseries. Xylosandrus germanus (Blandford) is the most problematic ambrosia beetle in Ohio nurseries. Movement of X. germanus in nurseries has not been characterized, and knowledge is lacking on whether infestations originate from within nurseries or surrounding habitats. Flight activity of X. germanus was monitored in nurseries and adjacent wooded areas to determine the source of beetles infesting nurseries, and characterize their movement within nurseries. Ethanol-baited bottle traps were positioned within wooded areas adjacent to commercial nurseries and within nurseries at various distances from the nursery woodlot interface. Flight activity of overwintered X. germanus occurred in wooded areas adjacent to nurseries before occurrence within nurseries. There was a direct relationship between degree-days and the distance from woodlots when X. germanus were first found in traps in spring, with earlier captures closest to wooded areas and latest ones furthest away into the nursery. X. germanus appeared to move into nurseries from adjacent wooded areas, with numbers trapped within nurseries decreasing with distance away from wooded areas. Trees in the interior of nurseries would appear to be subjected to less attack pressure than trees near the nursery border. Intercepting beetles as they move into nurseries might be an effective strategy to reduce attack pressure on valuable trees. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

E-Learning for the Environment: The Universidade Aberta (Portuguese Open Distance University) Experience in the Environmental Sciences Post-Graduate Courses

ERIC Educational Resources Information Center

Bacelar-Nicolau, P.; Caeiro, S.; Martinho, A. P.; Azeiteiro, U. M.; Amador, F.

2009-01-01

Purpose: In recent decades, there has been an increase of public awareness about environmental problems. A simultaneous effort to increase educational course offerings in this area has been made. The purpose of this paper is to evaluate the first edition of the blended learning MSc in Environmental Citizenship and Participation that is offered by…

Analyzing Process Data from Game/Scenario-Based Tasks: An Edit Distance Approach

ERIC Educational Resources Information Center

Hao, Jiangang; Shu, Zhan; von Davier, Alina

2015-01-01

Students' activities in game/scenario-based tasks (G/SBTs) can be characterized by a sequence of time-stamped actions of different types with different attributes. For a subset of G/SBTs in which only the order of the actions is of great interest, the process data can be well characterized as a string of characters (i.e., action string) if we…

Proceedings of the International Conference on Educational Data Mining (EDM) (8th, Madrid, Spain, June 26-29, 2015)

ERIC Educational Resources Information Center

Santos, Olga Cristina, Ed.; Boticario, Jesus Gonzalez, Ed.; Romero, Cristobal, Ed.; Pechenizkiy, Mykola, Ed.; Merceron, Agathe, Ed.; Mitros, Piotr, Ed.; Luna, Jose Maria, Ed.; Mihaescu, Cristian, Ed.; Moreno, Pablo, Ed.; Hershkovitz, Arnon, Ed.; Ventura, Sebastian, Ed.; Desmarais, Michel, Ed.

2015-01-01

The 8th International Conference on Educational Data Mining (EDM 2015) is held under auspices of the International Educational Data Mining Society at UNED, the National University for Distance Education in Spain. The conference held in Madrid, Spain, July 26-29, 2015, follows the seven previous editions (London 2014, Memphis 2013, Chania 2012,…

A Review of the Literature on the Open Education Faculty in Turkey 1982-2007. A Revised and Expanded the Fifth Edition

ERIC Educational Resources Information Center

Demiray, Ugur, Ed.; Inceeli, Ayse, Ed.; Candemir, Ozden, Ed.

2008-01-01

Communication technologies have a manipulative power an effect on the field of education in general. These technologies have been increasingly used in education and training for many years to meet different needs. Distance education has proven particularly useful for training people into remote locations who can not attend to the classes at…

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology.

PubMed

Poon, Art F Y

2015-09-01

The shapes of phylogenetic trees relating virus populations are determined by the adaptation of viruses within each host, and by the transmission of viruses among hosts. Phylodynamic inference attempts to reverse this flow of information, estimating parameters of these processes from the shape of a virus phylogeny reconstructed from a sample of genetic sequences from the epidemic. A key challenge to phylodynamic inference is quantifying the similarity between two trees in an efficient and comprehensive way. In this study, I demonstrate that a new distance measure, based on a subset tree kernel function from computational linguistics, confers a significant improvement over previous measures of tree shape for classifying trees generated under different epidemiological scenarios. Next, I incorporate this kernel-based distance measure into an approximate Bayesian computation (ABC) framework for phylodynamic inference. ABC bypasses the need for an analytical solution of model likelihood, as it only requires the ability to simulate data from the model. I validate this "kernel-ABC" method for phylodynamic inference by estimating parameters from data simulated under a simple epidemiological model. Results indicate that kernel-ABC attained greater accuracy for parameters associated with virus transmission than leading software on the same data sets. Finally, I apply the kernel-ABC framework to study a recent outbreak of a recombinant HIV subtype in China. Kernel-ABC provides a versatile framework for phylodynamic inference because it can fit a broader range of models than methods that rely on the computation of exact likelihoods. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

[Response of the ant community to attributes of fragments and vegetation in a northeastern Atlantic Rain Forest area, Brazil].

PubMed

Gomes, Juliana P; Iannuzzi, Luciana; Leal, Inara R

2010-01-01

The objective of this study was to determine the effects of forest fragmentation on ant richness in a landscape of Atlantic Forest in Northeast Brazil. More specifically, the ant richness was related to the attributes of fragments (area and distance from the fragment central point to the edge), landscape (forest cover surrounding the fragments), and tree community (plant density, richness, and percentage of shade tolerant species). The surveys were carried out in 19 fragments located in Alagoas State from October 2007 to March 2008. Samples were collected through a 300 m transect established in the center of each fragment, where 30 1-m² leaf litter samples were collected at 10 m intervals. A total of 146 ant species was collected, which belonged to 42 genera, 24 tribes and nine subfamilies. The attributes of fragments and landscape did not influence ant richness. On the other hand, tree density explained ca. 23% of ant richness. In relation to functional groups, both density and richness of trees explained the richness of general myrmicines (the whole model explained ca. 42% of the variation in this group) and percentage of shade tolerant trees explained the richness of specialist predator ants (30% for the whole model). These results indicate that ant fauna is more influenced by vegetation integrity than by fragment size, distance to edge or forest cover surrounding fragments.

Detection of dead standing Eucalyptus camaldulensis without tree delineation for managing biodiversity in native Australian forest

NASA Astrophysics Data System (ADS)

Miltiadou, Milto; Campbell, Neil D. F.; Gonzalez Aracil, Susana; Brown, Tony; Grant, Michael G.

2018-05-01

In Australia, many birds and arboreal animals use hollows for shelters, but studies predict shortage of hollows in near future. Aged dead trees are more likely to contain hollows and therefore automated detection of them plays a substantial role in preserving biodiversity and consequently maintaining a resilient ecosystem. For this purpose full-waveform LiDAR data were acquired from a native Eucalypt forest in Southern Australia. The structure of the forest significantly varies in terms of tree density, age and height. Additionally, Eucalyptus camaldulensis have multiple trunk splits making tree delineation very challenging. For that reason, this paper investigates automated detection of dead standing Eucalyptus camaldulensis without tree delineation. It also presents the new feature of the open source software DASOS, which extracts features for 3D object detection in voxelised FW LiDAR. A random forest classifier, a weighted-distance KNN algorithm and a seed growth algorithm are used to create a 2D probabilistic field and to then predict potential positions of dead trees. It is shown that tree health assessment is possible without tree delineation but since it is a new research directions there are many improvements to be made.

Dynamics of market correlations: taxonomy and portfolio analysis.

PubMed

Onnela, J-P; Chakraborti, A; Kaski, K; Kertész, J; Kanto, A

2003-11-01

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the "asset tree" has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for "business as usual" and "crash" periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity.

PubMed

Hou, Gang; Chen, Wei-Tao; Lu, Huo-Sheng; Cheng, Fei; Xie, Song-Guang

2018-01-01

DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.31%, 8.71% and 14.52%, respectively. A neighbour-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding gap analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95.2%), with the minimum interspecific distance to the nearest neighbour larger than the maximum intraspecific distance. A group of three Thunnus species (T. albacares, T. obesus and T. tonggol), a pair of Gerres species (G. oyena and G. japonicus), a pair of Istiblennius species (I. edentulous and I. lineatus) and a pair of Uranoscopus species (U. oligolepis and U. kaianus) were observed with low interspecific distances and overlaps between intra- and interspecific genetic distances. Three species (Apogon ellioti, Naucrates ductor and Psenopsis anomala) showed deep intraspecific divergences and generated two lineages each, suggesting the possibility of cryptic species. Our results demonstrated that DNA barcodes are highly reliable for delineating species of Perciformes in the SCS. The DNA barcode library established in this study will shed light on further research on the diversity of Perciformes in the SCS. © 2017 John Wiley & Sons Ltd.

Contemporary pollen and seed dispersal in natural populations of Bertholletia excelsa (Bonpl.).

PubMed

Baldoni, A B; Wadt, L H O; Campos, T; Silva, V S; Azevedo, V C R; Mata, L R; Botin, A A; Mendes, N O; Tardin, F D; Tonini, H; Hoogerheide, E S S; Sebbenn, A M

2017-09-21

Due to the nutritional content and commercial value of its seeds, Bertholletia excelsa is one of the most important species exploited in the Amazon region. The species is hermaphroditic, insect pollinated, and its seeds are dispersed by barochory and animals. Because the fruit set is dependent on natural pollinator activity, gene flow plays a key role in fruit production. However, to date, there have been no studies on pollen and seed flow in natural populations of B. excelsa. Herein, we used microsatellite loci and parentage analysis to investigate the spatial genetic structure (SGS), realized pollen and seed dispersal, and effective pollen dispersal for two B. excelsa populations in the Brazilian Amazon forest. Two plots were established in natural forests from which adults, juveniles, and seeds were sampled. Realized and effective pollen flow was greater than realized seed flow. The distance of realized pollen dispersal ranged from 36 to 2060 m, and the distance of realized seed dispersal ranged from 30 to 1742 m. Both pollen and seeds showed a dispersal pattern of isolation by distance, indicating a high frequency of mating among near-neighbor trees and seed dispersal near to mother trees. Both populations present SGS up to 175 m, which can be explained by isolation by distance pollen and seed dispersal patterns. Our results suggested that fragmentation of these forest populations may result in a significant decrease in gene flow, due to the isolation by distance pollen and seed dispersal patterns.

Expansion of forest stands into tundra in the Noatak National Preserve, northwest Alaska

USGS Publications Warehouse

Suarez, F.; Binkley, Dan; Kaye, Margot W.; Stottlemyer, R.

1999-01-01

Temperatures across the northern regions of North America have been increasing for 150 years, and forests have responded to this increase. In the Noatak National Preserve in Alaska, white spruce (Picea glauca [Moench] Voss) forests reach their northern limit, occurring primarily on well-drained sites and as gallery forests along streams. Rolling plateaus of tundra separate the white spruce forests into disjunct stands. We examined patterns of tree age, tree growth, and tree encroachment into tundra ecosystems in six stands along the Agashashok River. Warming over the past 150 years appears to have increased tree growth and resulted in forest expansion into adjacent tundra ecosystems. The forest/tundra ecotone shifted by about 80 to 100 m into the tundra in the past 200 years, as evidenced by declining maximum tree age with distance towards the tundra. The decadal-scale pattern of tree establishment at the farthest extent of trees into the tundra (the tundra-forest ecotone) correlated with the detrended growth index for trees within the forests; climate conditions that led to higher tree growth appeared to foster tree establishment in the tundra. This recent forest expansion has occurred across topographic boundaries, from well-drained soils on slopes onto poorly drained, flatter areas of tundra. Further expansion of the forests may be limited by more severe wind exposure and poor drainage that make the majority of tundra less suitable for trees.

[Molecular identification of medicinal plant genus Uncaria in Guizhou].

PubMed

Gang, Tao; Liu, Tao; Zhu, Ying; Liu, Zuo-Yi

2008-06-01

To analyze rDNA ITS regions of the Medicinal Plant Genus Uncaria in Guizhou and construct their phylogenetic tree in order to supply molecular evidence of taxonomy and identification of these Medicinal Plants in genetic level. The ITS gene fragments of the 4 Medicinal Plants were PCR amplified and sequenced. The rDNA ITS regions were analyzed by means of the software of ClustalX, BioEdit and PAUP* 4.0 beta 10. The entire sequences of rDNA ITS1, ITS2, and 5.8S rDNA were obtained, The Maximum-parsimony tree of four ITS regions together with those of similar sequences from GenBank were found, as Mitrayna rubrostipulata (AJ492621 ) and Mitragyna rubrostipulata (AJ605988) were designated as outgroup. The 4 medicinal plants are the 4 species in the genus Uncaria, and are mostly similar to the Uncaria rhynhcophylla.

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

PubMed Central

Huang, Ya-Yi; Matzke, Antonius J. M.; Matzke, Marjori

2013-01-01

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available. PMID:24023703

Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera).

PubMed

Huang, Ya-Yi; Matzke, Antonius J M; Matzke, Marjori

2013-01-01

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.

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

PubMed

Gil, Manuel

2014-01-01

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

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

PubMed Central

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error. PMID:25279263

Paleoecological insights on fixed tree island development in the Florida Everglades: I. environmental controls: Chapter 4

USGS Publications Warehouse

Willard, Debra A.; Murray, James B.; Holmes, Charles W.; Korvela, Michael S.; Mason, Daniel; Orem, William H.; Towles, D. Timothy; Sklar, Fred H.; van der Valk, A.

2002-01-01

Palynological and geochemical analyses of sediment cores collected on two tree islands in the Florida Everglades indicate long-term hydrologic and chemical differences between tree islands and surrounding marshes and sloughs. Gumbo Limbo and Nuthouse tree islands are elongate, teardrop-shaped islands in Water Conservation Area 3B. Prior to tree island formation at both sites, pollen records indicate that sites on modern tree island heads were covered with sawgrass marshes with abundant weedy annuals. Such vegetation is characteristic of moderate water depths and hydroperiods with frequent droughts or disturbances. Contemporaneously deposited sediments on tree island tails indicate progressively deeper water conditions with increasing distance from the head; wetlands surrounding tree islands were covered by sloughs with deep water and long hydroperiods. Tree island formation occurred at about 1200 BC on Gumbo Limbo Island, with mature tree island vegetation established by about 800 AD. On Nuthouse Island, tree island formation occurred around 300 AD, shifting to mature tree island vegetation around 1400 AD. Thus, tree island formation began on these islands between 3.2 Ka and 1.7 Ka. Maturation of tree islands took between 1,000 and 2,000 years, and vegetation on these tree islands has been relatively stable for the last 600–1,200 years. Phosphorus levelson tree island heads have been extremely high (approximately six times greaterthan baseline levels in marshes) throughout the history of the sites, and phosphorus content in tree island tails began increasing when tree island formation occurred. Elevated phosphorus content may reflect the long-termpresence of wading birds at these sites and provide a proxy for reconstructing the historic distribution of wading bird populations.

Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae).

PubMed

Mishra, Priyanka; Kumar, Amit; Rodrigues, Vereena; Shukla, Ashutosh K; Sundaresan, Velusamy

2016-01-01

The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista . This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated s equences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

PubMed Central

Matsen IV, Frederick A.; Evans, Steven N.

2013-01-01

Principal components analysis (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples taken from a given environment. They have led to many insights regarding the structure of microbial communities. We have developed two new complementary methods that leverage how this microbial community data sits on a phylogenetic tree. Edge principal components analysis enables the detection of important differences between samples that contain closely related taxa. Each principal component axis is a collection of signed weights on the edges of the phylogenetic tree, and these weights are easily visualized by a suitable thickening and coloring of the edges. Squash clustering outputs a (rooted) clustering tree in which each internal node corresponds to an appropriate “average” of the original samples at the leaves below the node. Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA, the most widely used hierarchical clustering method in this context. We present these methods and illustrate their use with data from the human microbiome. PMID:23505415

Performance trends in individual medley events during FINA World Master Championships from 1986 to 2014.

PubMed

Nikolaidis, Pantelis T; Knechtle, Beat

2018-05-01

Performance trends during the last decades in elite individual medley swimmers are known, but not for age groups swimmers. Therefore, the aim of the present study was to examine participation and performance trends in age groups swimmers competing in FINA World Masters Championships (1986-2014) in individual 200-m and 400-m medley. We included all swimmers (6424 women, 7588 men) for each distance and age groups (25-29 to 95-99 years) in the analysis to avoid a selection bias by limiting to a fixed sample (e.g. the ten fastest). Changes in participation and changes in sex difference across editions were analyzed using linear regression models. Changes in performance across editions were analyzed using a mixed-effects regression model with finisher as random variable to consider finishers who completed several races. Sex, distance and calendar year were included as fixed variables. We also considered interaction effects between sex and distance. The men-to-women ratio was compared using a paired t-test. In 200 m, the participation of women increased from 35-39 to 75-79 years and of men from 35-39 to 85-89 years (P<0.05). In 400 m, the participation of women increased from 50-54 to 75-79 years and of men from 60-64 to 85-89 years (P<0.05). From 25-29 to 90-94 years, women and men improved performance in both editions (P<0.05). Men were faster than women from 25-29 to 80-84 years (P<0.05), but not in 85-90 and 90-94 years. Sex and distance showed a significant interaction from 25-29 to 85-89 years (P<0.05), but not in 90-94 years. Women reduced the gap to men in 40-44 and 45-49 years in 200 m, and 40-44 years in 400 m (P<0.05). In summary, the participation increased in older age groups (>35 years), women and men from 25-29 to 90-94 years improved, and men were faster than women from 25-29 to 80-84 years, but not from 85-89 to 90-94 years. These data suggest that master swimmers will continue to increase participation and improve performance in individual medley. The findings of the present study might help coaches and fitness trainers of medley swimmers to tailor their training programs considering the age of their swimmers.

Distance Estimation to Flashes in a Simulated Night Vision Environment

DTIC Science & Technology

2007-12-01

indirect perception, which has influenced theorists since, is Hermann von Helmholtz’s theory of unconscious conclusions or unconscious inference [6...Goldstein et al. (Eds.), Blackwell handbook of perception (pp. 53-91). Malden, MA: Blackwell Publishers. [6] Helmholtz, H. von (1867/1925). Treatise on...physiological optics (from 3rd German edition, Vol. III). New York: Dover Publications. [7] Helmholtz, H. von (1878/1968). The facts of perception. In

[Therapy through film].

PubMed

Nicli, Pierrette

2012-01-01

For psychiatric patients, playing the role of their life, producing a film, editing it and presenting it to the public with the support of a group made up of patients and caregivers is a real form of self-distancing, a type of therapy. The video group from the Saint Ouen day hospital has been carrying out this creative and therapeutic work for several years. Screenings and exchanges between care centres are regularly organised.

Problem Solving: The "Wright" Math. The Centennial of Flight Special Edition. An Educator Guide with Activities in Mathematics, Science, and Technology. NASA CONNECT[TM].

ERIC Educational Resources Information Center

National Aeronautics and Space Administration, Hampton, VA. Langley Research Center.

NASA CONNECT is an annual series of integrated mathematics, science, and technology instructional distance learning programs for students in grades 6-8. This program is designed for students to learn about the evolution of flight. The program has three components--television broadcast, Web activity, and lesson guide--which are designed as an…

Synthesis of Nonlinear Guidance Laws for Missiles with Uncertain Dynamics

DTIC Science & Technology

2007-11-01

and Astronautics, Progress in Astronautics and Aeronautics, Volume 199, 2002. 2. Gurfil , M. Jodorkovsky and M. Guelman, Neoclassical Guidance for...658-666, July-August 2002. 19. P. Gurfil , “Robust Guidance for Electro-Optical Missiles,” IEEE Transactions on Aerospace and Electronic Systems, Vol...edition, Upper Saddle River, NJ: Prentice-Hall, 2002. 23. P. Gurfil , ”Zero-Miss Distance Guidance Law Based on Line-of-Sight Rate Measuremenbt Only

Species are not most abundant in the centre of their geographic range or climatic niche.

PubMed

Dallas, Tad; Decker, Robin R; Hastings, Alan

2017-12-01

The pervasive idea that species should be most abundant in the centre of their geographic range or centre of their climatic niche is a key assumption in many existing ecological hypotheses and has been declared a general macroecological rule. However, empirical support for decreasing population abundance with increasing distance from geographic range or climatic niche centre (distance-abundance relationships) remains fairly weak. We examine over 1400 bird, mammal, fish and tree species to provide a thorough test of distance-abundance relationships, and their associations with species traits and phylogenetic relationships. We failed to detect consistent distance-abundance relationships, and found no association between distance-abundance slope and species traits or phylogenetic relatedness. Together, our analyses suggest that distance-abundance relationships may be rare, difficult to detect, or are an oversimplification of the complex biogeographical forces that determine species spatial abundance patterns. © 2017 John Wiley & Sons Ltd/CNRS.

Large old trees influence patterns of delta13C and delta15N in forests.

PubMed

Weber, Pascale; Bol, Roland; Dixon, Liz; Bardgett, Richard D

2008-06-01

Large old trees are the dominant primary producers of native pine forest, but their influence on spatial patterns of soil properties and potential feedback to tree regeneration in their neighbourhood is poorly understood. We measured stable isotopes of carbon (delta(13)C) and nitrogen (delta(15)N) in soil and litter taken from three zones of influence (inner, middle and outer zone) around the trunk of freestanding old Scots pine (Pinus sylvestris L.) trees, to determine the trees' influence on below-ground properties. We also measured delta(15)N and delta(13)C in wood cores extracted from the old trees and from regenerating trees growing within their three zones of influence. We found a significant and positive gradient in soil delta(15)N from the inner zone, nearest to the tree centre, to the outer zone beyond the tree crown. This was probably caused by the higher input of (15)N-depleted litter below the tree crown. In contrast, the soil delta(13)C did not change along the gradient of tree influence. Distance-related trends, although weak, were visible in the wood delta(15)N and delta(13)C of regenerating trees. Moreover, the wood delta(15)N of small trees showed a weak negative relationship with soil N content in the relevant zone of influence. Our results indicate that large old trees control below-ground conditions in their immediate surroundings, and that stable isotopes might act as markers for the spatial and temporal extent of these below-ground effects. John Wiley & Sons, Ltd

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruan, D; Shao, W; Low, D

Purpose: To evaluate and test the hypothesis that plan quality may be systematically affected by treatment delivery techniques and target-tocritical structure geometric relationship in radiotherapy for brain tumor. Methods: Thirty-four consecutive brain tumor patients treated between 2011–2014 were analyzed. Among this cohort, 10 were planned with 3DCRT, 11 with RadipArc, and 13 with helical IMRT on TomoTherapy. The selected dosimetric endpoints (i.e., PTV V100, maximum brainstem/chiasm/ optic nerve doses) were considered as a vector in a highdimensional space. A Pareto analysis was performed to identify the subset of Pareto-efficient plans.The geometric relationships, specifically the overlapping volume and centroid-of-mass distance betweenmore » each critical structure to the PTV were extracted as potential geometric features. The classification-tree analyses were repeated using these geometric features with and without the treatment modality as an additional categorical predictor. In both scenarios, the dominant features to prognosticate the Pareto membership were identified and the tree structures to provide optimal inference were recorded. The classification performance was further analyzed to determine the role of treatment modality in affecting plan quality. Results: Seven Pareto-efficient plans were identified based on dosimetric endpoints (3 from 3DCRT, 3 from RapicArc, 1 from Tomo), which implies that the evaluated treatment modality may have a minor influence on plan quality. Classification trees with/without the treatment modality as a predictor both achieved accuracy of 88.2%: with 100% sensitivity and 87.1% specificity for the former, and 66.7% sensitivity and 96.0% specificity for the latter. The coincidence of accuracy from both analyses further indicates no-to-weak dependence of plan quality on treatment modality. Both analyses have identified the brainstem to PTV distance as the primary predictive feature for Pareto-efficiency. Conclusion: Pareto evaluation and classification-tree analyses have indicated that plan quality depends strongly on geometry for brain tumor, specifically PTV-tobrain-stem-distance but minimally on treatment modality.« less

Reconstructing (super)trees from data sets with missing distances: not all is lost.

PubMed

Kettleborough, George; Dicks, Jo; Roberts, Ian N; Huber, Katharina T

2015-06-01

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, presents significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for data sets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial data sets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for data sets of all sizes, including large data sets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological data sets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso's ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial data sets. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Trace Element Concentrations in Tree Leaves and Lichen Collected Along a Metal Pollution Gradient Near Olkusz (Southern Poland).

PubMed

Zakrzewska, Marta; Klimek, Beata

2018-02-01

The aim of the study was to assess the metal pollution in the vicinity of the Bukowno smelter near Olkusz in southern Poland. Birch and oak leaves, pine needles and a lichen Hypogymnia physodes, overgrowing pine bark were collected at stands at different distances from the smelter and analysed for cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn) content. Concentrations of metals in the lichen were usually higher than in the tree leaves/needles and decreased with distance from the smelter, apart from the Cu content. The strongest correlation was noticed between Cd and Pb concentrations, which indicates a common pollution source (the smelter). Our results show that birch leaves can be potentially useful as a bioindicator of Zn air pollution since this species was shown to accumulate high amounts of zinc, related to environmental pollution with that metal, in their leaves.

Analysis of linkage effects among industry sectors in China's stock market before and after the financial crisis

NASA Astrophysics Data System (ADS)

Yang, Rui; Li, Xiangyang; Zhang, Tong

2014-10-01

This paper uses two physics-derived techniques, the minimum spanning tree and the hierarchical tree, to investigate the networks formed by CITIC (China International Trust and Investment Corporation) industry indices in three periods from 2006 to 2013. The study demonstrates that obvious industry clustering effects exist in the networks, and Durable Consumer Goods, Industrial Products, Information Technology, Frequently Consumption and Financial Industry are the core nodes in the networks. We also use the rolling window technique to investigate the dynamic evolution of the networks' stability, by calculating the mean correlations and mean distances, as well as the variance of correlations and the distances of these indices. China's stock market is still immature and subject to administrative interventions. Therefore, through this analysis, regulators can focus on monitoring the core nodes to ensure the overall stability of the entire market, while investors can enhance their portfolio allocations or investment decision-making.

Local habitat and landscape influence predation of bird nests on afforested Mediterranean cropland

NASA Astrophysics Data System (ADS)

Sánchez-Oliver, J. S.; Rey Benayas, J. M.; Carrascal, L. M.

2014-07-01

Afforestation programs such as the one promoted by the EU Common Agrarian Policy have contributed to spread tree plantations on former cropland. Nevertheless these afforestations may cause severe damage to open habitat species, especially birds of high conservation value. We investigated predation of artificial bird nests at young tree plantations and at the open farmland habitat adjacent to the tree plantations in central Spain. Predation rates were very high at both tree plantations (95.6%) and open farmland habitat (94.2%) after two and three week exposure. Plantation edge/area ratio and development of the tree canopy decreased predation rates and plantation area and magpie (Pica pica) abundance increased predation rates within tree plantations, which were also affected by land use types around plantations. The area of nearby tree plantations (positive effect), distance to the tree plantation edge (negative effect), and habitat type (mainly attributable to the location of nests in vineyards) explained predation rates at open farmland habitat. We conclude that predation rates on artificial nests were particularly high and rapid at or nearby large plantations, with high numbers of magpies and low tree development, and located in homogenous landscapes dominated by herbaceous crops and pastures with no remnants of semi-natural woody vegetation. Landscape planning should not favour tree plantations as the ones studied here in Mediterranean agricultural areas that are highly valuable for ground-nesting bird species.

Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

PubMed

Bae, Juhee; Watson, Benjamin

2014-12-01

In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

Object based technique for delineating and mapping 15 tree species using VHR WorldView-2 imagery

NASA Astrophysics Data System (ADS)

Mustafa, Yaseen T.; Habeeb, Hindav N.

2014-10-01

Monitoring and analyzing forests and trees are required task to manage and establish a good plan for the forest sustainability. To achieve such a task, information and data collection of the trees are requested. The fastest way and relatively low cost technique is by using satellite remote sensing. In this study, we proposed an approach to identify and map 15 tree species in the Mangish sub-district, Kurdistan Region-Iraq. Image-objects (IOs) were used as the tree species mapping unit. This is achieved using the shadow index, normalized difference vegetation index and texture measurements. Four classification methods (Maximum Likelihood, Mahalanobis Distance, Neural Network, and Spectral Angel Mapper) were used to classify IOs using selected IO features derived from WorldView-2 imagery. Results showed that overall accuracy was increased 5-8% using the Neural Network method compared with other methods with a Kappa coefficient of 69%. This technique gives reasonable results of various tree species classifications by means of applying the Neural Network method with IOs techniques on WorldView-2 imagery.

Dynamics of market correlations: Taxonomy and portfolio analysis

NASA Astrophysics Data System (ADS)

Onnela, J.-P.; Chakraborti, A.; Kaski, K.; Kertész, J.; Kanto, A.

2003-11-01

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the “asset tree” has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for “business as usual” and “crash” periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

Mercury levels in lichens from different host trees around a chlor-alkali plant in New Brunswick, Canada.

PubMed

Sensen, Marion; Richardson, David H S

2002-07-03

Mercury concentrations were determined in the epiphytic lichen Hypogymnia physodes along five transects starting from a chlor-alkali plant located at Dalhousie, New Brunswick, a landfill site and a nearby electricity generating station. Lichen samples were collected from white birch (Betula papyrifera) and spruce (Picea sp.) or balsam fir (Abies balsamea). Average lichen background mercury values were 0.088+/-0.005 microg/g from white birch and 0.148+/-0.046 microg/g from spruce trees, with a detection limit of 0.05 microg/g. The chlor-alkali plant and a power plant were identified, respectively, as a major source and a minor source of elevated mercury levels in lichens. At 125 m north-west of the New Brunswick Power plant, 0.28 microg/g Hg were found in Hypogymnia physodes from spruce trees, while at 250 m west (downwind) of the chlor-alkali plant, 3.66 microg/g of mercury were determined. High values, 0.98 microg/g in lichens from spruce trees and 0.79 microg/g in lichen samples from white birch were also measured at 125 m south of the chlor-alkali plant and decreased exponentially with distance. The sphere of influence of the chlor-alkali plant with respect to mercury deposition was estimated to extend 2.4-3.4 km from the plant. The mercury concentrations in Hypogymnia physodes collected from white birch were significantly lower than the concentrations in the same lichen from spruce trees in areas with elevated levels of mercury, but not in areas with low mercury levels. The magnitude of this difference dropped with distance from the source.

A Structured Light Sensor System for Tree Inventory

NASA Technical Reports Server (NTRS)

Chien, Chiun-Hong; Zemek, Michael C.

2000-01-01

Tree Inventory is referred to measurement and estimation of marketable wood volume in a piece of land or forest for purposes such as investment or for loan applications. Exist techniques rely on trained surveyor conducting measurements manually using simple optical or mechanical devices, and hence are time consuming subjective and error prone. The advance of computer vision techniques makes it possible to conduct automatic measurements that are more efficient, objective and reliable. This paper describes 3D measurements of tree diameters using a uniquely designed ensemble of two line laser emitters rigidly mounted on a video camera. The proposed laser camera system relies on a fixed distance between two parallel laser planes and projections of laser lines to calculate tree diameters. Performance of the laser camera system is further enhanced by fusion of information induced from structured lighting and that contained in video images. Comparison will be made between the laser camera sensor system and a stereo vision system previously developed for measurements of tree diameters.

Environmental and hormonal control of cambial stem cell dynamics.

PubMed

Bhalerao, Rishikesh P; Fischer, Urs

2017-01-01

Perennial trees have the amazing ability to adjust their growth rate to both adverse and favorable seasonally reoccurring environmental conditions over hundreds of years. In trunks and stems, the basis for the tuning of seasonal growth rate is the regulation of cambial stem cell activity. Cambial stem cell quiescence and dormancy protect the tree from potential physiological and genomic damage caused by adverse growing conditions and may permit a long lifespan. Cambial dormancy and longevity are both aspects of a tree's life for which the study of cambial stem cell behavior in the annual model plant Arabidopsis is inadequate. Recent functional analyses of hormone perception and catabolism mutants in Populus indicate that shoot-derived long-range signals, as well as local cues, steer cambial activity. Auxin is central to the regulation of cambial activity and probably also maintenance. Emerging genome editing and phenotyping technologies will enable the identification of down-stream targets of hormonal action and facilitate the genetic dissection of complex traits of cambial biology. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Ecological Implications of a Flower Size/Number Trade-Off in Tropical Forest Trees

PubMed Central

Kettle, Chris J.; Maycock, Colin R.; Ghazoul, Jaboury; Hollingsworth, Pete M.; Khoo, Eyen; Sukri, Rahayu Sukmaria Haji; Burslem, David F. R. P.

2011-01-01

Background In angiosperms, flower size commonly scales negatively with number. The ecological consequences of this trade-off for tropical trees remain poorly resolved, despite their potential importance for tropical forest conservation. We investigated the flower size number trade-off and its implications for fecundity in a sample of tree species from the Dipterocarpaceae on Borneo. Methodology/Principal Findings We combined experimental exclusion of pollinators in 11 species, with direct and indirect estimates of contemporary pollen dispersal in two study species and published estimates of pollen dispersal in a further three species to explore the relationship between flower size, pollinator size and mean pollen dispersal distance. Maximum flower production was two orders of magnitude greater in small-flowered than large-flowered species of Dipterocarpaceae. In contrast, fruit production was unrelated to flower size and did not differ significantly among species. Small-flowered species had both smaller-sized pollinators and lower mean pollination success than large-flowered species. Average pollen dispersal distances were lower and frequency of mating between related individuals was higher in a smaller-flowered species than a larger-flowered confamilial. Our synthesis of pollen dispersal estimates across five species of dipterocarp suggests that pollen dispersal scales positively with flower size. Conclusions and Their Significance Trade-offs embedded in the relationship between flower size and pollination success contribute to a reduction in the variance of fecundity among species. It is therefore plausible that these processes could delay competitive exclusion and contribute to maintenance of species coexistence in this ecologically and economically important family of tropical trees. These results have practical implications for tree species conservation and restoration. Seed collection from small-flowered species may be especially vulnerable to cryptic genetic erosion. Our findings also highlight the potential for differential vulnerability of tropical tree species to the deleterious consequences of forest fragmentation. PMID:21408110

Liftoff of the 18 May 1980 surge of Mount St. Helens (USA) and the deposits left behind

NASA Astrophysics Data System (ADS)

Gardner, James E.; Andrews, Benjamin J.; Dennen, Robert

2017-01-01

The distance that ground-hugging pyroclastic density currents travel is limited partly by when they reverse buoyancy and liftoff into the atmosphere. It is not clear, however, what deposits are left behind by lofting flows. One current that was seen to liftoff was the surge erupted from Mount St. Helens on the morning of 18 May 1980. Before lofting, it had leveled a large area of thick forest (the blowdown zone). The outer edge of the devastated area—where trees were scorched but left standing (the scorched zone)—is where the surge is thought to have lifted off. Deposits in the outer parts of the blowdown and in the scorched zone were examined at 32 sites. The important finding is that the laterally moving surge traveled through the scorched zone, and hence, the change in tree damage does not mark the runout distance of the surge. Buoyancy reversal and liftoff are thus not preserved in the deposits where the surge lofted upwards. We propose, based on interpretation of eyewitness accounts and the impacts of the surge on trees and vehicles, that the surge consisted of a faster, dilute "overcurrent" and a slower "undercurrent," where most of the mass (and heat) was retained. Reasonable estimates for flow density and velocity show that dynamic pressure of the surge (i.e., its ability to topple trees) peaked near the base of the overcurrent. We propose that where the overcurrent began to liftoff, the height of peak dynamic pressure rose above the trees and stopped toppling them. The slower undercurrent continued forward, however, scorching trees, but lacked the dynamic pressure needed to topple them. Grain-size variations argue that it slowed from ˜30 m s-1 when it entered the scorched zone to ˜3 m s-1 at the far end.

Efficient algorithms for dilated mappings of binary trees

NASA Technical Reports Server (NTRS)

Iqbal, M. Ashraf

1990-01-01

The problem is addressed to find a 1-1 mapping of the vertices of a binary tree onto those of a target binary tree such that the son of a node on the first binary tree is mapped onto a descendent of the image of that node in the second binary tree. There are two natural measures of the cost of this mapping, namely the dilation cost, i.e., the maximum distance in the target binary tree between the images of vertices that are adjacent in the original tree. The other measure, expansion cost, is defined as the number of extra nodes/edges to be added to the target binary tree in order to ensure a 1-1 mapping. An efficient algorithm to find a mapping of one binary tree onto another is described. It is shown that it is possible to minimize one cost of mapping at the expense of the other. This problem arises when designing pipelined arithmetic logic units (ALU) for special purpose computers. The pipeline is composed of ALU chips connected in the form of a binary tree. The operands to the pipeline can be supplied to the leaf nodes of the binary tree which then process and pass the results up to their parents. The final result is available at the root. As each new application may require a distinct nesting of operations, it is useful to be able to find a good mapping of a new binary tree over existing ALU tree. Another problem arises if every distinct required binary tree is known beforehand. Here it is useful to hardwire the pipeline in the form of a minimal supertree that contains all required binary trees.

GIS-based groundwater potential mapping using boosted regression tree, classification and regression tree, and random forest machine learning models in Iran.

PubMed

Naghibi, Seyed Amir; Pourghasemi, Hamid Reza; Dixon, Barnali

2016-01-01

Groundwater is considered one of the most valuable fresh water resources. The main objective of this study was to produce groundwater spring potential maps in the Koohrang Watershed, Chaharmahal-e-Bakhtiari Province, Iran, using three machine learning models: boosted regression tree (BRT), classification and regression tree (CART), and random forest (RF). Thirteen hydrological-geological-physiographical (HGP) factors that influence locations of springs were considered in this research. These factors include slope degree, slope aspect, altitude, topographic wetness index (TWI), slope length (LS), plan curvature, profile curvature, distance to rivers, distance to faults, lithology, land use, drainage density, and fault density. Subsequently, groundwater spring potential was modeled and mapped using CART, RF, and BRT algorithms. The predicted results from the three models were validated using the receiver operating characteristics curve (ROC). From 864 springs identified, 605 (≈70 %) locations were used for the spring potential mapping, while the remaining 259 (≈30 %) springs were used for the model validation. The area under the curve (AUC) for the BRT model was calculated as 0.8103 and for CART and RF the AUC were 0.7870 and 0.7119, respectively. Therefore, it was concluded that the BRT model produced the best prediction results while predicting locations of springs followed by CART and RF models, respectively. Geospatially integrated BRT, CART, and RF methods proved to be useful in generating the spring potential map (SPM) with reasonable accuracy.

Discovery of long-distance gamete dispersal in a lichen-forming ascomycete.

PubMed

Ronnås, Cecilia; Werth, Silke; Ovaskainen, Otso; Várkonyi, Gergely; Scheidegger, Christoph; Snäll, Tord

2017-10-01

Accurate estimates of gamete and offspring dispersal range are required for the understanding and prediction of spatial population dynamics and species persistence. Little is known about gamete dispersal in fungi, especially in lichen-forming ascomycetes. Here, we estimate the dispersal functions of clonal propagules, gametes and ascospores of the epiphytic lichen Lobaria pulmonaria. We use hierarchical Bayesian parentage analysis, which integrates genetic and ecological information from multiannual colonization and dispersal source data collected in a large, old-growth forest landscape. The effective dispersal range of gametes is several hundred metres to kilometres from potential paternal individuals. By contrast, clonal propagules disperse only tens of metres, and ascospores disperse over several thousand metres. Our study reveals the dispersal distances of individual reproductive units; clonal propagules, gametes and ascospores, which is of great importance for a thorough understanding of the spatial dynamics of ascomycetes. Sexual reproduction occurs between distant individuals. However, whereas gametes and ascospores disperse over long distances, the overall rate of colonization of trees is low. Hence, establishment is the limiting factor for the colonization of new host trees by the lichen in old-growth landscapes. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers

PubMed Central

Montenegro, M; Llambí, S; Castro, G; Barlocco, N; Vadell, A; Landi, V; Delgado, JV; Martínez, A

2015-01-01

In this study, we genetically characterized the Uruguayan pig breed Pampa Rocha. Genetic variability was assessed by analyzing a panel of 25 microsatellite markers from a sample of 39 individuals. Pampa Rocha pigs showed high genetic variability with observed and expected heterozygosities of 0.583 and 0.603, respectively. The mean number of alleles was 5.72. Twenty-four markers were polymorphic, with 95.8% of them in Hardy Weinberg equilibrium. The level of endogamy was low (FIS = 0.0475). A factorial analysis of correspondence was used to assess the genetic differences between Pampa Rocha and other pig breeds; genetic distances were calculated, and a tree was designed to reflect the distance matrix. Individuals were also allocated into clusters. This analysis showed that the Pampa Rocha breed was separated from the other breeds along the first and second axes. The neighbour-joining tree generated by the genetic distances DA showed clustering of Pampa Rocha with the Meishan breed. The allocation of individuals to clusters showed a clear separation of Pampa Rocha pigs. These results provide insights into the genetic variability of Pampa Rocha pigs and indicate that this breed is a well-defined genetic entity. PMID:25983624

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

PubMed

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.

A Computational Model for Path Loss in Wireless Sensor Networks in Orchard Environments

PubMed Central

Anastassiu, Hristos T.; Vougioukas, Stavros; Fronimos, Theodoros; Regen, Christian; Petrou, Loukas; Zude, Manuela; Käthner, Jana

2014-01-01

A computational model for radio wave propagation through tree orchards is presented. Trees are modeled as collections of branches, geometrically approximated by cylinders, whose dimensions are determined on the basis of measurements in a cherry orchard. Tree canopies are modeled as dielectric spheres of appropriate size. A single row of trees was modeled by creating copies of a representative tree model positioned on top of a rectangular, lossy dielectric slab that simulated the ground. The complete scattering model, including soil and trees, enhanced by periodicity conditions corresponding to the array, was characterized via a commercial computational software tool for simulating the wave propagation by means of the Finite Element Method. The attenuation of the simulated signal was compared to measurements taken in the cherry orchard, using two ZigBee receiver-transmitter modules. Near the top of the tree canopies (at 3 m), the predicted attenuation was close to the measured one—just slightly underestimated. However, at 1.5 m the solver underestimated the measured attenuation significantly, especially when leaves were present and, as distances grew longer. This suggests that the effects of scattering from neighboring tree rows need to be incorporated into the model. However, complex geometries result in ill conditioned linear systems that affect the solver's convergence. PMID:24625738

Unequal Probability Marking Approach to Enhance Security of Traceback Scheme in Tree-Based WSNs.

PubMed

Huang, Changqin; Ma, Ming; Liu, Xiao; Liu, Anfeng; Zuo, Zhengbang

2017-06-17

Fog (from core to edge) computing is a newly emerging computing platform, which utilizes a large number of network devices at the edge of a network to provide ubiquitous computing, thus having great development potential. However, the issue of security poses an important challenge for fog computing. In particular, the Internet of Things (IoT) that constitutes the fog computing platform is crucial for preserving the security of a huge number of wireless sensors, which are vulnerable to attack. In this paper, a new unequal probability marking approach is proposed to enhance the security performance of logging and migration traceback (LM) schemes in tree-based wireless sensor networks (WSNs). The main contribution of this paper is to overcome the deficiency of the LM scheme that has a higher network lifetime and large storage space. In the unequal probability marking logging and migration (UPLM) scheme of this paper, different marking probabilities are adopted for different nodes according to their distances to the sink. A large marking probability is assigned to nodes in remote areas (areas at a long distance from the sink), while a small marking probability is applied to nodes in nearby area (areas at a short distance from the sink). This reduces the consumption of storage and energy in addition to enhancing the security performance, lifetime, and storage capacity. Marking information will be migrated to nodes at a longer distance from the sink for increasing the amount of stored marking information, thus enhancing the security performance in the process of migration. The experimental simulation shows that for general tree-based WSNs, the UPLM scheme proposed in this paper can store 1.12-1.28 times the amount of stored marking information that the equal probability marking approach achieves, and has 1.15-1.26 times the storage utilization efficiency compared with other schemes.

Unequal Probability Marking Approach to Enhance Security of Traceback Scheme in Tree-Based WSNs

PubMed Central

Huang, Changqin; Ma, Ming; Liu, Xiao; Liu, Anfeng; Zuo, Zhengbang

2017-01-01

Fog (from core to edge) computing is a newly emerging computing platform, which utilizes a large number of network devices at the edge of a network to provide ubiquitous computing, thus having great development potential. However, the issue of security poses an important challenge for fog computing. In particular, the Internet of Things (IoT) that constitutes the fog computing platform is crucial for preserving the security of a huge number of wireless sensors, which are vulnerable to attack. In this paper, a new unequal probability marking approach is proposed to enhance the security performance of logging and migration traceback (LM) schemes in tree-based wireless sensor networks (WSNs). The main contribution of this paper is to overcome the deficiency of the LM scheme that has a higher network lifetime and large storage space. In the unequal probability marking logging and migration (UPLM) scheme of this paper, different marking probabilities are adopted for different nodes according to their distances to the sink. A large marking probability is assigned to nodes in remote areas (areas at a long distance from the sink), while a small marking probability is applied to nodes in nearby area (areas at a short distance from the sink). This reduces the consumption of storage and energy in addition to enhancing the security performance, lifetime, and storage capacity. Marking information will be migrated to nodes at a longer distance from the sink for increasing the amount of stored marking information, thus enhancing the security performance in the process of migration. The experimental simulation shows that for general tree-based WSNs, the UPLM scheme proposed in this paper can store 1.12–1.28 times the amount of stored marking information that the equal probability marking approach achieves, and has 1.15–1.26 times the storage utilization efficiency compared with other schemes. PMID:28629135

Seeing the Forest Through the Trees: The Distribution and Properties of Dense Molecular Gas in the Milky Way Galaxy

NASA Astrophysics Data System (ADS)

Ellsworth-Bowers, Timothy P.

The Milky Way Galaxy serves as a vast laboratory for studying the dynamics and evolution of the dense interstellar medium and the processes of and surrounding massive star formation. From our vantage point within the Galactic plane, however, it has been extremely difficult to construct a coherent picture of Galactic structure; we cannot see the forest for the trees. The principal difficulties in studying the structure of the Galactic disk have been obscuration by the ubiquitous dust and molecular gas and confusion between objects along a line of sight. Recent technological advances have led to large-scale blind surveys of the Galactic plane at (sub-)millimeter wavelengths, where Galactic dust is generally optically thin, and have opened a new avenue for studying the forest. The Bolocam Galactic Plane Survey (BGPS) observed over 190 deg 2 of the Galactic plane in dust continuum emission near lambda = 1.1 mm, producing a catalog of over 8,000 dense molecular cloud structures across a wide swath of the Galactic disk. Deriving the spatial distribution and physical properties of these objects requires knowledge of distance, a component lacking in the data themselves. This thesis presents a generalized Bayesian probabilistic distance estimation method for dense molecular cloud structures, and demonstrates it with the BGPS data set. Distance probability density functions (DPDFs) are computed from kinematic distance likelihoods (which may be double- peaked for objects in the inner Galaxy) and an expandable suite of prior information to produce a comprehensive tally of our knowledge (and ignorance) of the distances to dense molecular cloud structures. As part of the DPDF formalism, this thesis derives several prior DPDFs for resolving the kinematic distance ambiguity in the inner Galaxy. From the collection of posterior DPDFs, a set of objects with well-constrained distance estimates is produced for deriving Galactic structure and the physical properties of dense molecular cloud structures. This distance catalog of 1,802 objects across the Galactic plane represents the first large-scale analysis of clump-scale objects in a variety of Galactic environments. The Galactocentric positions of these objects begin to trace out the spiral structure of the Milky Way, and suggest that dense molecular gas settles nearer the Galactic midplane than tracers of less-dense gas such as CO. Physical properties computed from the DPDFs reveal that BGPS objects trace a continuum of scales within giant molecular clouds, and extend the scaling relationships known as Larson's Laws to lower-mass substructures. The results presented here represent the first step on the road to seeing the molecular content of the Milky Way as a forest rather than individual nearby trees.

Alignment-free genome tree inference by learning group-specific distance metrics.

PubMed

Patil, Kaustubh R; McHardy, Alice C

2013-01-01

Understanding the evolutionary relationships between organisms is vital for their in-depth study. Gene-based methods are often used to infer such relationships, which are not without drawbacks. One can now attempt to use genome-scale information, because of the ever increasing number of genomes available. This opportunity also presents a challenge in terms of computational efficiency. Two fundamentally different methods are often employed for sequence comparisons, namely alignment-based and alignment-free methods. Alignment-free methods rely on the genome signature concept and provide a computationally efficient way that is also applicable to nonhomologous sequences. The genome signature contains evolutionary signal as it is more similar for closely related organisms than for distantly related ones. We used genome-scale sequence information to infer taxonomic distances between organisms without additional information such as gene annotations. We propose a method to improve genome tree inference by learning specific distance metrics over the genome signature for groups of organisms with similar phylogenetic, genomic, or ecological properties. Specifically, our method learns a Mahalanobis metric for a set of genomes and a reference taxonomy to guide the learning process. By applying this method to more than a thousand prokaryotic genomes, we showed that, indeed, better distance metrics could be learned for most of the 18 groups of organisms tested here. Once a group-specific metric is available, it can be used to estimate the taxonomic distances for other sequenced organisms from the group. This study also presents a large scale comparison between 10 methods--9 alignment-free and 1 alignment-based.

First-in-human Phase 1 CRISPR Gene Editing Cancer Trials: Are We Ready?

PubMed

Baylis, Francoise; McLeod, Marcus

2017-01-01

A prospective first-in-human Phase 1 CRISPR gene editing trial in the United States for patients with melanoma, synovial sarcoma, and multiple myeloma offers hope that gene editing tools may usefully treat human disease. An overarching ethical challenge with first-in-human Phase 1 clinical trials, however, is knowing when it is ethically acceptable to initiate such trials on the basis of safety and efficacy data obtained from pre-clinical studies. If the pre-clinical studies that inform trial design are themselves poorly designed - as a result of which the quality of pre-clinical evidence is deficient - then the ethical requirement of scientific validity for clinical research may not be satisfied. In turn, this could mean that the Phase 1 clinical trial will be unsafe and that trial participants will be exposed to risk for no potential benefit. To assist sponsors, researchers, clinical investigators and reviewers in deciding when it is ethically acceptable to initiate first-in-human Phase 1 CRISPR gene editing clinical trials, structured processes have been developed to assess and minimize translational distance between pre-clinical and clinical research. These processes draw attention to various features of internal validity, construct validity, and external validity. As well, the credibility of supporting evidence is to be critically assessed with particular attention to optimism bias, financial conflicts of interest and publication bias. We critically examine the pre-clinical evidence used to justify the first-inhuman Phase 1 CRISPR gene editing cancer trial in the United States using these tools. We conclude that the proposed trial cannot satisfy the ethical requirement of scientific validity because the supporting pre-clinical evidence used to inform trial design is deficient. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Slower phloem transport in gymnosperm trees can be attributed to higher sieve element resistance.

PubMed

Liesche, Johannes; Windt, Carel; Bohr, Tomas; Schulz, Alexander; Jensen, Kaare H

2015-04-01

In trees, carbohydrates produced in photosynthesizing leaves are transported to roots and other sink organs over distances of up to 100 m inside a specialized transport tissue, the phloem. Angiosperm and gymnosperm trees have a fundamentally different phloem anatomy with respect to cell size, shape and connectivity. Whether these differences have an effect on the physiology of carbohydrate transport, however, is not clear. A meta-analysis of the experimental data on phloem transport speed in trees yielded average speeds of 56 cm h(-1) for angiosperm trees and 22 cm h(-1) for gymnosperm trees. Similar values resulted from theoretical modeling using a simple transport resistance model. Analysis of the model parameters clearly identified sieve element (SE) anatomy as the main factor for the significantly slower carbohydrate transport speed inside the phloem in gymnosperm compared with angiosperm trees. In order to investigate the influence of SE anatomy on the hydraulic resistance, anatomical data on SEs and sieve pores were collected by transmission electron microscopy analysis and from the literature for 18 tree species. Calculations showed that the hydraulic resistance is significantly higher in the gymnosperm than in angiosperm trees. The higher resistance is only partially offset by the considerably longer SEs of gymnosperms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Competitive code-based fast palmprint identification using a set of cover trees

NASA Astrophysics Data System (ADS)

Yue, Feng; Zuo, Wangmeng; Zhang, David; Wang, Kuanquan

2009-06-01

A palmprint identification system recognizes a query palmprint image by searching for its nearest neighbor from among all the templates in a database. When applied on a large-scale identification system, it is often necessary to speed up the nearest-neighbor searching process. We use competitive code, which has very fast feature extraction and matching speed, for palmprint identification. To speed up the identification process, we extend the cover tree method and propose to use a set of cover trees to facilitate the fast and accurate nearest-neighbor searching. We can use the cover tree method because, as we show, the angular distance used in competitive code can be decomposed into a set of metrics. Using the Hong Kong PolyU palmprint database (version 2) and a large-scale palmprint database, our experimental results show that the proposed method searches for nearest neighbors faster than brute force searching.

The inverse Wiener polarity index problem for chemical trees.

PubMed

Du, Zhibin; Ali, Akbar

2018-01-01

The Wiener polarity number (which, nowadays, known as the Wiener polarity index and usually denoted by Wp) was devised by the chemist Harold Wiener, for predicting the boiling points of alkanes. The index Wp of chemical trees (chemical graphs representing alkanes) is defined as the number of unordered pairs of vertices (carbon atoms) at distance 3. The inverse problems based on some well-known topological indices have already been addressed in the literature. The solution of such inverse problems may be helpful in speeding up the discovery of lead compounds having the desired properties. This paper is devoted to solving a stronger version of the inverse problem based on Wiener polarity index for chemical trees. More precisely, it is proved that for every integer t ∈ {n - 3, n - 2,…,3n - 16, 3n - 15}, n ≥ 6, there exists an n-vertex chemical tree T such that Wp(T) = t.

Description of an establishment event by the invasive Asian longhorned beetle (Anoplophora glabripennis) in a suburban landscape in the northeastern United States

PubMed Central

Pepper, Eugene; Davis, Kevin; Trotter, Robert Talbot

2017-01-01

The establishment of non-native species is commonly described as occurring in three phases: arrival, establishment, and dispersal. Both arrival and dispersal by the Asian longhorned beetle (Anoplophora glabripennis Motschulsky), a xylophagous Cerambycid native to China and the Korean peninsula, has been documented for multiple locations in both North America and Europe, however the transitional phase, establishment, is not well understood for this species due to the need to rapidly remove populations to prevent dispersal and assist eradication, and the evident variation in the behavior of populations. Here we describe the dynamics of an establishment event for the Asian longhorned beetle in a small, isolated population within the regulated quarantine zone near Worcester, Massachusetts, USA. These data were collected during an opportunity afforded by logistical limits on the Cooperative Asian Longhorned Beetle Eradication Program administered by state, federal, and local government partners. Seventy-one infested red maple (Acer rubrum) trees and 456 interspersed un-infested trees were surveyed in an isolated, recently established population within a ~0.29 ha stand in a suburban wetland conservation area in which nearly 90% of the trees were host species, and nearly 80% were Acer rubrum. Tree-ring analyses show that within this establishing population, Asian longhorned beetles initially infested one or two A. rubrum, before moving through the stand to infest additional A. rubrum based not on distance or direction, but on tree size, with infestation biased towards trees with larger trunk diameters. Survey data from the larger landscape suggest this population may have generated long-distance dispersers (~1400 m), and that these dispersal events occurred before the originally infested host trees were fully exploited by the beetle. The distribution and intensity of damage documented in this population suggest dispersal here may have been spatially more rapid and diffuse than in other documented infestations. Dispersal at these larger spatial scales also implies that when beetles move beyond the closed canopy of the stand, the direction of dispersal may be linked to prevailing winds. PMID:28727772

Spatial and temporal analyses of citrus sudden death as a tool to generate hypotheses concerning its etiology.

PubMed

Bassanezi, Renato B; Bergamin Filho, Armando; Amorim, Lilian; Gimenes-Fernandes, Nelson; Gottwald, Tim R; Bové, Joseph M

2003-04-01

ABSTRACT Citrus sudden death (CSD), a new disease of unknown etiology that affects sweet orange grafted on Rangpur lime, was visually monitored for 14 months in 41 groves in Brazil. Ordinary runs analysis of CSD-symptomatic trees indicated a departure from randomness of symptomatic trees status among immediately adjacent trees mainly within rows. The binomial index of dispersion (D) and the intraclass correlation (k) for various quadrat sizes suggested aggregation of CSD-symptomatic trees for almost all plots within the quadrat sizes tested. Estimated parameters of the binary form of Taylor's power law provided an overall measure of aggregation of CSD-symptomatic trees for all quadrat sizes tested. Aggregation in each plot was dependent on disease incidence. Spatial autocorrelation analysis of proximity patterns suggested that aggregation often existed among quadrats of various sizes up to three lag distances; however, significant lag positions discontinuous from main proximity patterns were rare, indicating a lack of spatial association among discrete foci. Some asymmetry was also detected for some spatial autocorrelation proximity patterns, indicating that within-row versus across-row distributions are not necessarily equivalent. These results were interpreted to mean that the cause of the disease was most likely biotic and its dissemination was common within a local area of influence that extended to approximately six trees in all directions, including adjacent trees. Where asymmetry was indicated, this area of influence was somewhat elliptical. Longer-distance patterns were not detected within the confines of the plot sizes tested. Annual rates of CSD progress based on the Gompertz model ranged from 0.37 to 2.02. Numerous similarities were found between the spatial patterns of CSD and Citrus tristeza virus (CTV) described in the literature, both in the presence of the aphid vector, Toxoptera citricida. CSD differs from CTV in that symptoms occur in sweet orange grafted on Rangpur lime. Based on the symptoms of CSD and on its spatial and temporal patterns, our hypothesis is that CSD may be caused by a similar but undescribed pathogen such as a virus and probably vectored by insects such as aphids by similar spatial processes to those affecting CTV.

SPACE PROPULSION SYSTEM PHASED-MISSION PROBABILITY ANALYSIS USING CONVENTIONAL PRA METHODS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtis Smith; James Knudsen

As part of a series of papers on the topic of advance probabilistic methods, a benchmark phased-mission problem has been suggested. This problem consists of modeling a space mission using an ion propulsion system, where the mission consists of seven mission phases. The mission requires that the propulsion operate for several phases, where the configuration changes as a function of phase. The ion propulsion system itself consists of five thruster assemblies and a single propellant supply, where each thruster assembly has one propulsion power unit and two ion engines. In this paper, we evaluate the probability of mission failure usingmore » the conventional methodology of event tree/fault tree analysis. The event tree and fault trees are developed and analyzed using Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE). While the benchmark problem is nominally a "dynamic" problem, in our analysis the mission phases are modeled in a single event tree to show the progression from one phase to the next. The propulsion system is modeled in fault trees to account for the operation; or in this case, the failure of the system. Specifically, the propulsion system is decomposed into each of the five thruster assemblies and fed into the appropriate N-out-of-M gate to evaluate mission failure. A separate fault tree for the propulsion system is developed to account for the different success criteria of each mission phase. Common-cause failure modeling is treated using traditional (i.e., parametrically) methods. As part of this paper, we discuss the overall results in addition to the positive and negative aspects of modeling dynamic situations with non-dynamic modeling techniques. One insight from the use of this conventional method for analyzing the benchmark problem is that it requires significant manual manipulation to the fault trees and how they are linked into the event tree. The conventional method also requires editing the resultant cut sets to obtain the correct results. While conventional methods may be used to evaluate a dynamic system like that in the benchmark, the level of effort required may preclude its use on real-world problems.« less

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes.

PubMed

Seberg, Ole; Petersen, Gitte; Davis, Jerrold I; Pires, J Chris; Stevenson, Dennis W; Chase, Mark W; Fay, Michael F; Devey, Dion S; Jørgensen, Tina; Sytsma, Kenneth J; Pillon, Yohan

2012-05-01

The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial. Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated. The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent. Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.

12. OVERVIEW FROM FORMER RESIDENTIAL AREA NORTH OF SAR2, SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. OVERVIEW FROM FORMER RESIDENTIAL AREA NORTH OF SAR-2, SHOWING TRAIL UP TO FOREBAY, RETAINING WALL, PEPPER TREES, AND SAR-2 IN DISTANCE. VIEW TO SOUTH-SOUTHEAST. - Santa Ana River Hydroelectric System, Redlands, San Bernardino County, CA

Bayes Forest: a data-intensive generator of morphological tree clones

PubMed Central

Järvenpää, Marko; Åkerblom, Markku; Raumonen, Pasi; Kaasalainen, Mikko

2017-01-01

Abstract Detailed and realistic tree form generators have numerous applications in ecology and forestry. For example, the varying morphology of trees contributes differently to formation of landscapes, natural habitats of species, and eco-physiological characteristics of the biosphere. Here, we present an algorithm for generating morphological tree “clones” based on the detailed reconstruction of the laser scanning data, statistical measure of similarity, and a plant growth model with simple stochastic rules. The algorithm is designed to produce tree forms, i.e., morphological clones, similar (and not identical) in respect to tree-level structure, but varying in fine-scale structural detail. Although we opted for certain choices in our algorithm, individual parts may vary depending on the application, making it a general adaptable pipeline. Namely, we showed that a specific multipurpose procedural stochastic growth model can be algorithmically adjusted to produce the morphological clones replicated from the target experimentally measured tree. For this, we developed a statistical measure of similarity (structural distance) between any given pair of trees, which allows for the comprehensive comparing of the tree morphologies by means of empirical distributions describing the geometrical and topological features of a tree. Finally, we developed a programmable interface to manipulate data required by the algorithm. Our algorithm can be used in a variety of applications for exploration of the morphological potential of the growth models (both theoretical and experimental), arising in all sectors of plant science research. PMID:29020742

The space of ultrametric phylogenetic trees.

PubMed

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.

Spatial variability of biotic and abiotic tree establishment constraints across a treeline ecotone in the Alaska range.

PubMed

Stueve, Kirk M; Isaacs, Rachel E; Tyrrell, Lucy E; Densmore, Roseann V

2011-02-01

Throughout interior Alaska (U.S.A.), a gradual warming trend in mean monthly temperatures occurred over the last few decades (approximatlely 2-4 degrees C). The accompanying increases in woody vegetation at many alpine treeline (hereafter treeline) locations provided an opportunity to examine how biotic and abiotic local site conditions interact to control tree establishment patterns during warming. We devised a landscape ecological approach to investigate these relationships at an undisturbed treeline in the Alaska Range. We identified treeline changes between 1953 (aerial photography) and 2005 (satellite imagery) in a geographic information system (GIS) and linked them with corresponding local site conditions derived from digital terrain data, ancillary climate data, and distance to 1953 trees. Logistic regressions enabled us to rank the importance of local site conditions in controlling tree establishment. We discovered a spatial transition in the importance of tree establishment controls. The biotic variable (proximity to 1953 trees) was the most important tree establishment predictor below the upper tree limit, providing evidence of response lags with the abiotic setting and suggesting that tree establishment is rarely in equilibrium with the physical environment or responding directly to warming. Elevation and winter sun exposure were important predictors of tree establishment at the upper tree limit, but proximity to trees persisted as an important tertiary predictor, indicating that tree establishment may achieve equilibrium with the physical environment. However, even here, influences from the biotic variable may obscure unequivocal correlations with the abiotic setting (including temperature). Future treeline expansion will likely be patchy and challenging to predict without considering the spatial variability of influences from biotic and abiotic local site conditions.

Spatial variability of biotic and abiotic tree establishment constraints across a treeline ecotone in the Alaska Range

USGS Publications Warehouse

Stueve, K.M.; Isaacs, R.E.; Tyrrell, L.E.; Densmore, R.V.

2011-01-01

Throughout interior Alaska (USA), a gradual warming trend in mean monthly temperatures occurred over the last few decades (;2-48C). The accompanying increases in woody vegetation at many alpine treeline (hereafter treeline) locations provided an opportunity to examine how biotic and abiotic local site conditions interact to control tree establishment patterns during warming. We devised a landscape ecological approach to investigate these relationships at an undisturbed treeline in the Alaska Range. We identified treeline changes between 1953 (aerial photography) and 2005 (satellite imagery) in a geographic information system (GIS) and linked them with corresponding local site conditions derived from digital terrain data, ancillary climate data, and distance to 1953 trees. Logistic regressions enabled us to rank the importance of local site conditions in controlling tree establishment. We discovered a spatial transition in the importance of tree establishment controls. The biotic variable (proximity to 1953 trees) was the most important tree establishment predictor below the upper tree limit, providing evidence of response lags with the abiotic setting and suggesting that tree establishment is rarely in equilibrium with the physical environment or responding directly to warming. Elevation and winter sun exposure were important predictors of tree establishment at the upper tree limit, but proximity to trees persisted as an important tertiary predictor, indicating that tree establishment may achieve equilibrium with the physical environment. However, even here, influences from the biotic variable may obscure unequivocal correlations with the abiotic setting (including temperature). Future treeline expansion will likely be patchy and challenging to predict without considering the spatial variability of influences from biotic and abiotic local site conditions. ?? 2011 by the Ecological Society of America.

Glide performance and aerodynamics of non-equilibrium glides in northern flying squirrels (Glaucomys sabrinus)

PubMed Central

Bahlman, Joseph W.; Swartz, Sharon M.; Riskin, Daniel K.; Breuer, Kenneth S.

2013-01-01

Gliding is an efficient form of travel found in every major group of terrestrial vertebrates. Gliding is often modelled in equilibrium, where aerodynamic forces exactly balance body weight resulting in constant velocity. Although the equilibrium model is relevant for long-distance gliding, such as soaring by birds, it may not be realistic for shorter distances between trees. To understand the aerodynamics of inter-tree gliding, we used direct observation and mathematical modelling. We used videography (60–125 fps) to track and reconstruct the three-dimensional trajectories of northern flying squirrels (Glaucomys sabrinus) in nature. From their trajectories, we calculated velocities, aerodynamic forces and force coefficients. We determined that flying squirrels do not glide at equilibrium, and instead demonstrate continuously changing velocities, forces and force coefficients, and generate more lift than needed to balance body weight. We compared observed glide performance with mathematical simulations that use constant force coefficients, a characteristic of equilibrium glides. Simulations with varying force coefficients, such as those of live squirrels, demonstrated better whole-glide performance compared with the theoretical equilibrium state. Using results from both the observed glides and the simulation, we describe the mechanics and execution of inter-tree glides, and then discuss how gliding behaviour may relate to the evolution of flapping flight. PMID:23256188

[Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

PubMed

Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

2013-07-04

Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

Application of Decision Tree on Collision Avoidance System Design and Verification for Quadcopter

NASA Astrophysics Data System (ADS)

Chen, C.-W.; Hsieh, P.-H.; Lai, W.-H.

2017-08-01

The purpose of the research is to build a collision avoidance system with decision tree algorithm used for quadcopters. While the ultrasonic range finder judges the distance is in collision avoidance interval, the access will be replaced from operator to the system to control the altitude of the UAV. According to the former experiences on operating quadcopters, we can obtain the appropriate pitch angle. The UAS implement the following three motions to avoid collisions. Case1: initial slow avoidance stage, Case2: slow avoidance stage and Case3: Rapid avoidance stage. Then the training data of collision avoidance test will be transmitted to the ground station via wireless transmission module to further analysis. The entire decision tree algorithm of collision avoidance system, transmission data, and ground station have been verified in some flight tests. In the flight test, the quadcopter can implement avoidance motion in real-time and move away from obstacles steadily. In the avoidance area, the authority of the collision avoidance system is higher than the operator and implements the avoidance process. The quadcopter can successfully fly away from the obstacles in 1.92 meter per second and the minimum distance between the quadcopter and the obstacle is 1.05 meters.

Glide performance and aerodynamics of non-equilibrium glides in northern flying squirrels (Glaucomys sabrinus).

PubMed

Bahlman, Joseph W; Swartz, Sharon M; Riskin, Daniel K; Breuer, Kenneth S

2013-03-06

Gliding is an efficient form of travel found in every major group of terrestrial vertebrates. Gliding is often modelled in equilibrium, where aerodynamic forces exactly balance body weight resulting in constant velocity. Although the equilibrium model is relevant for long-distance gliding, such as soaring by birds, it may not be realistic for shorter distances between trees. To understand the aerodynamics of inter-tree gliding, we used direct observation and mathematical modelling. We used videography (60-125 fps) to track and reconstruct the three-dimensional trajectories of northern flying squirrels (Glaucomys sabrinus) in nature. From their trajectories, we calculated velocities, aerodynamic forces and force coefficients. We determined that flying squirrels do not glide at equilibrium, and instead demonstrate continuously changing velocities, forces and force coefficients, and generate more lift than needed to balance body weight. We compared observed glide performance with mathematical simulations that use constant force coefficients, a characteristic of equilibrium glides. Simulations with varying force coefficients, such as those of live squirrels, demonstrated better whole-glide performance compared with the theoretical equilibrium state. Using results from both the observed glides and the simulation, we describe the mechanics and execution of inter-tree glides, and then discuss how gliding behaviour may relate to the evolution of flapping flight.

VizieR Online Data Catalog: DIA OGLE2 candidate variable stars catalog (Wozniak+, 2002)

NASA Astrophysics Data System (ADS)

Wozniak, P. R.; Udalski, A.; Szymanski, M.; Kubiak, M.; Pietrzynski, G.; Soszinski, I.; Zebrun, K.

2005-07-01

We present the first edition of a catalog of variable stars from OGLE-II Galactic bulge data covering 3 years: 1997-1999. Typically 200-300 I band data points are available in 49 fields between -11 and +11 degrees in galactic longitude, totaling roughly 11 square degrees in sky coverage. Photometry was obtained using the Difference Image Analysis (DIA) software and tied to the OGLE data base with the DoPhot package. The present version of the catalog comprises 221801 light curves. In this preliminary work the level of contamination by spurious detections is still about 10%. Parts of the catalog have only crude calibration, insufficient for distance determinations. The next, fully calibrated, edition will include the data collected in year 2000. The data is accessible via ftp, at ftp://bulge.princeton.edu/ogle/ogle2/bulgediavariables (1 data file).

2. Context view showing FrankJensen Summer Home in foreground and ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. Context view showing Frank-Jensen Summer Home in foreground and new home under construction in background. Lake Wenatchee is visible in distance through the trees. - Frank-Jensen Summer Home, 17423 North Lake Shore Drive, Telma, Chelan County, WA

Evaluation That Goes the Distance.

ERIC Educational Resources Information Center

Bernthal, Paul R.

1995-01-01

A modification of Donald Kirkpatrick's model suggests use of a training-impact tree to identify variables that could establish links between training and organizational values. Steps include identifying organizational values and practices; identifying skills, knowledge, and attitudes; defining scope and purpose of evaluation; gathering data; and…

The role of red alder in riparian forest structure along headwater streams in southeastern Alaska

USGS Publications Warehouse

Orlikowska, E.H.; Deal, R.L.; Hennon, P.E.; Wipfli, M.S.

2004-01-01

We assessed the influence of red alder on tree species composition, stand density, tree size distribution, tree mortality, and potential for producing large conifers, in 38-42 yr old riparian forests along 13 headwater streams in the Maybeso and Harris watersheds on Prince of Wales Island, Alaska. Red alder ranged from 0 to 53% of the total live basal area of the stands. Tree density, basal area of live and dead trees, and mean diameter of live conifers were not significantly related to the percent of alder as a proportion of total stand live basal area within these riparian forests. The mean diameter of the 100 largest conifers per hectare (the largest trees) was similar among different sites and appeared unrelated to the amount of alder in the stands. The mean diameter of dead conifers increased slightly with increasing proportion of red alder. Most dead trees were small and died standing. Red alder was much more concentrated immediately along stream margins (within 0-1 m distance from the stream bank vs. > 1 m). The presence of red alder did not inhibit the production of large-diameter conifers, and both alder and conifers provided small woody debris for fishless headwater streams in southeastern Alaska. Red alder is an important structural component of young-growth riparian stands.

Maximum parsimony, substitution model, and probability phylogenetic trees.

PubMed

Weng, J F; Thomas, D A; Mareels, I

2011-01-01

The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.

DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

PubMed

Kelly, Steven; Maini, Philip K

2013-01-01

The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

Optimal Path Planning Program for Autonomous Speed Sprayer in Orchard Using Order-Picking Algorithm

NASA Astrophysics Data System (ADS)

Park, T. S.; Park, S. J.; Hwang, K. Y.; Cho, S. I.

This study was conducted to develop a software program which computes optimal path for autonomous navigation in orchard, especially for speed sprayer. Possibilities of autonomous navigation in orchard were shown by other researches which have minimized distance error between planned path and performed path. But, research of planning an optimal path for speed sprayer in orchard is hardly founded. In this study, a digital map and a database for orchard which contains GPS coordinate information (coordinates of trees and boundary of orchard) and entity information (heights and widths of trees, radius of main stem of trees, disease of trees) was designed. An orderpicking algorithm which has been used for management of warehouse was used to calculate optimum path based on the digital map. Database for digital map was created by using Microsoft Access and graphic interface for database was made by using Microsoft Visual C++ 6.0. It was possible to search and display information about boundary of an orchard, locations of trees, daily plan for scattering chemicals and plan optimal path on different orchard based on digital map, on each circumstance (starting speed sprayer in different location, scattering chemicals for only selected trees).

iNJclust: Iterative Neighbor-Joining Tree Clustering Framework for Inferring Population Structure.

PubMed

Limpiti, Tulaya; Amornbunchornvej, Chainarong; Intarapanich, Apichart; Assawamakin, Anunchai; Tongsima, Sissades

2014-01-01

Understanding genetic differences among populations is one of the most important issues in population genetics. Genetic variations, e.g., single nucleotide polymorphisms, are used to characterize commonality and difference of individuals from various populations. This paper presents an efficient graph-based clustering framework which operates iteratively on the Neighbor-Joining (NJ) tree called the iNJclust algorithm. The framework uses well-known genetic measurements, namely the allele-sharing distance, the neighbor-joining tree, and the fixation index. The behavior of the fixation index is utilized in the algorithm's stopping criterion. The algorithm provides an estimated number of populations, individual assignments, and relationships between populations as outputs. The clustering result is reported in the form of a binary tree, whose terminal nodes represent the final inferred populations and the tree structure preserves the genetic relationships among them. The clustering performance and the robustness of the proposed algorithm are tested extensively using simulated and real data sets from bovine, sheep, and human populations. The result indicates that the number of populations within each data set is reasonably estimated, the individual assignment is robust, and the structure of the inferred population tree corresponds to the intrinsic relationships among populations within the data.

Use of tree-ring chemistry to document historical ground-water contamination events

USGS Publications Warehouse

Vroblesky, Don A.; Yanosky, Thomas M.

1990-01-01

The annual growth rings of tulip trees (Liriodendron tulipifera L.) appear to preserve a chemical record of ground-water contamination at a landfill in Maryland. Zones of elevated iron and chlorine concentrations in growth rings from trees immediately downgradient from the landfill are closely correlated temporally with activities in the landfill expected to generate iron and chloride contamination in the ground water. Successively later iron peaks in trees increasingly distant from the landfill along the general direction of ground-water flow imply movement of iron-contaminated ground water away from the landfill. The historical velocity of iron movement (2 to 9 m/yr) and chloride movement (at least 40 m/yr) in ground water at the site was estimated from element-concentration trends of trees at successive distances from the landfill. The tree-ring-derived chloride-transport velocity approximates the known ground-water velocity (30 to 80 m/yr). A minimum horizontal hydraulic conductivity (0.01 to .02 cm/s) calculated from chloride velocity agrees well with values derived from aquifer tests (about 0.07 cm/s) and from ground-water modeling results (0.009 to 0.04 cm/s).

A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin.

PubMed

Degen, Bernd; Blanc-Jolivet, Céline; Stierand, Katrin; Gillet, Elizabeth

2017-03-01

During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as "country of origin". In this paper, we present a new nearest neighbour approach to individual assignment or classification within a given but potentially imperfect grouping of reference samples. This method, which is based on the genetic distance between individuals, functions better in many cases than commonly used methods. We demonstrate the operation of our assignment method using two data sets. One set is simulated for a large number of trees distributed in a 120km by 120km landscape with individual genotypes at 150 SNPs, and the other set comprises experimental data of 1221 individuals of the African tropical tree species Entandrophragma cylindricum (Sapelli) genotyped at 61 SNPs. Judging by the level of correct self-assignment, our approach outperformed the commonly used frequency and Bayesian approaches by 15% for the simulated data set and by 5-7% for the Sapelli data set. Our new approach is less sensitive to overlapping sources of genetic differentiation, such as genetic differences among closely-related species, phylogeographic lineages and isolation by distance, and thus operates better even for suboptimal grouping of individuals. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Landscape genomic insights into the historic migration of mountain hemlock in response to Holocene climate change.

PubMed

Johnson, Jeremy S; Gaddis, Keith D; Cairns, David M; Konganti, Kranti; Krutovsky, Konstantin V

2017-03-01

Untangling alternative historic dispersal pathways in long-lived tree species is critical to better understand how temperate tree species may respond to climatic change. However, disentangling these alternative pathways is often difficult. Emerging genomic technologies and landscape genetics techniques improve our ability to assess these pathways in natural systems. We address the question to what degree have microrefugial patches and long-distance dispersal been responsible for the colonization of mountain hemlock ( Tsuga mertensiana ) on the Alaskan Kenai Peninsula. We used double-digest restriction-associated DNA sequencing (ddRADseq) to identify genetic variants across eight mountain hemlock sample sites on the Kenai Peninsula, Alaska. We assessed genetic diversity and linkage disequilibrium using landscape and population genetics approaches. Alternative historic dispersal pathways were assessed using discriminant analysis of principle components and electrical circuit theory. A combination of decreasing diversity, high gene flow, and landscape connectivity indicates that mountain hemlock colonization on the Kenai Peninsula is the result of long-distance dispersal. We found that contemporary climate best explained gene flow patterns and that isolation by resistance was a better model explaining genetic variation than isolation by distance. Our findings support the conclusion that mountain hemlock colonization is the result of several long-distance dispersal events following Pleistocene glaciation. The high dispersal capability suggests that mountain hemlock may be able to respond to future climate change and expand its range as new habitat opens along its northern distribution. © 2017 Botanical Society of America.

Tree shoot bending generates hydraulic pressure pulses: a new long-distance signal?

PubMed Central

Lopez, Rosana; Badel, Eric

2014-01-01

When tree stems are mechanically stimulated, a rapid long-distance signal is induced that slows down primary growth. An investigation was carried out to determine whether the signal might be borne by a mechanically induced pressure pulse in the xylem. Coupling xylem flow meters and pressure sensors with a mechanical testing device, the hydraulic effects of mechanical deformation of tree stem and branches were measured. Organs of several tree species were studied, including gymnosperms and angiosperms with different wood densities and anatomies. Bending had a negligible effect on xylem conductivity, even when deformations were sustained or were larger than would be encountered in nature. It was found that bending caused transient variation in the hydraulic pressure within the xylem of branch segments. This local transient increase in pressure in the xylem was rapidly propagated along the vascular system in planta to the upper and lower regions of the stem. It was shown that this hydraulic pulse originates from the apoplast. Water that was mobilized in the hydraulic pulses came from the saturated porous material of the conduits and their walls, suggesting that the poroelastic behaviour of xylem might be a key factor. Although likely to be a generic mechanical response, quantitative differences in the hydraulic pulse were found in different species, possibly related to differences in xylem anatomy. Importantly the hydraulic pulse was proportional to the strained volume, similar to known thigmomorphogenetic responses. It is hypothesized that the hydraulic pulse may be the signal that rapidly transmits mechanobiological information to leaves, roots, and apices. PMID:24558073

Tree shoot bending generates hydraulic pressure pulses: a new long-distance signal?

PubMed

Lopez, Rosana; Badel, Eric; Peraudeau, Sebastien; Leblanc-Fournier, Nathalie; Beaujard, François; Julien, Jean-Louis; Cochard, Hervé; Moulia, Bruno

2014-05-01

When tree stems are mechanically stimulated, a rapid long-distance signal is induced that slows down primary growth. An investigation was carried out to determine whether the signal might be borne by a mechanically induced pressure pulse in the xylem. Coupling xylem flow meters and pressure sensors with a mechanical testing device, the hydraulic effects of mechanical deformation of tree stem and branches were measured. Organs of several tree species were studied, including gymnosperms and angiosperms with different wood densities and anatomies. Bending had a negligible effect on xylem conductivity, even when deformations were sustained or were larger than would be encountered in nature. It was found that bending caused transient variation in the hydraulic pressure within the xylem of branch segments. This local transient increase in pressure in the xylem was rapidly propagated along the vascular system in planta to the upper and lower regions of the stem. It was shown that this hydraulic pulse originates from the apoplast. Water that was mobilized in the hydraulic pulses came from the saturated porous material of the conduits and their walls, suggesting that the poroelastic behaviour of xylem might be a key factor. Although likely to be a generic mechanical response, quantitative differences in the hydraulic pulse were found in different species, possibly related to differences in xylem anatomy. Importantly the hydraulic pulse was proportional to the strained volume, similar to known thigmomorphogenetic responses. It is hypothesized that the hydraulic pulse may be the signal that rapidly transmits mechanobiological information to leaves, roots, and apices.

The weight of the past: land-use legacies and recolonization of pine plantations by oak trees.

PubMed

Navarro-González, Irene; Pérez-Luque, Antonio J; Bonet, Francisco J; Zamora, Regino

2013-09-01

Most of the world's plantations were established on previously disturbed sites with an intensive land-use history. Our general hypothesis was that native forest regeneration within forest plantations depends largely on in situ biological legacies as a source of propagules. To test this hypothesis, we analyzed native oak regeneration in 168 pine plantation plots in southern Spain in relation to land use in 1956, oak patch proximity, and pine tree density. Historical land-use patterns were determined from aerial photography from 1956, and these were compared with inventory data from 2004-2005 and additional orthophoto images. Our results indicate that oak forest regeneration in pine plantations depends largely on land-use legacies, although nearby, well-conserved areas can provide propagules for colonization from outside the plantation, and pine tree density also affected oak recruit density. More intense land uses in the past meant fewer biological legacies and, therefore, lower likelihood of regenerating native forest. That is, oak recruit density was lower when land use in 1956 was croplands (0.004 +/- 0.002 recruits/m2 [mean +/- SE]) or pasture (0.081 +/- 0.054 recruits/m2) instead of shrubland (0.098 +/- 0.031 recruits/m2) or oak formations (0.314 +/- 0.080 recruits/m2). Our study shows that land use in the past was more important than propagule source distance or pine tree density in explaining levels of native forest regeneration in plantations. Thus, strategies for restoring native oak forests in pine plantations may benefit from considering land-use legacies as well as distance to propagule sources and pine density.

Living on the edge: Fig tree phenology at the northern range limit of monoecious Ficus in China

NASA Astrophysics Data System (ADS)

Zhang, Lu-Shui; Compton, Stephen G.; Xiao, Hui; Lu, Qian; Chen, Yan

2014-05-01

Fig trees (Ficus) are a species-rich group of mainly tropical and subtropical plants that are of ecological importance because of the large numbers of vertebrates that utilise their figs for food. Factors limiting their distributions to warmer regions are still poorly understood, but are likely to include factors linked to their specialised pollination biology, because each Ficus species is dependent on one or a small number of host-specific fig wasps (Agaonidae) for pollination. Adult fig wasps are short-lived, but some species are capable of dispersing extremely long distances to pollinate their hosts. Close to its northern range limit we investigated the phenology of Ficus virens, the monoecious fig tree that reaches furthest north in China. Relatively few trees produced any figs, and very few retained figs throughout the winter. Despite this, new crops produced in spring were pollinated, with seasonally migrant pollinators from plants growing further south the most likely pollen vectors. An inability to initiate new crops at low temperatures may limit the distribution of monoecious fig trees to warmer areas.

Associating seasonal range characteristics with survival of female white-tailed deer

USGS Publications Warehouse

Klaver, R.W.; Jenks, J.A.; Deperno, C.S.; Griffin, S.L.

2008-01-01

Delineating populations is critical for understanding population dynamics and managing habitats. Our objective was to delineate subpopulations of migratory female white-tailed deer (Odocoileus virginianus) in the central Black Hills, South Dakota and Wyoming, USA, on summer and winter ranges. We used fuzzy classification to assign radiocollared deer to subpopulations based on spatial location, characterized subpopulations by trapping sites, and explored relationships among survival of subpopulations and habitat variables. In winter, Kaplan-Meier estimates for subpopulations indicated 2 groups: high (S = 0.991 ?? 0.005 [x- ?? SE]) and low (S = 0.968 ?? 0.007) weekly survivorship. Survivorship increased with basal area per hectare of trees, average diameter at breast height of trees, percent cover of slash, and total point-center quarter distance of trees. Cover of grass and forbs were less for the high survivorship than the lower survivorship group. In summer, deer were spaced apart with mixed associations among subpopulations. Habitat manipulations that promote or maintain large trees (i.e., basal area = 14.8 m2/ha and average dbh of trees = 8.3 cm) would seem to improve adult survival of deer in winter.

What controls stemflow? A LiDAR-based investigation of individual tree canopy structure, neighborhood conditions, and meteorological factors

NASA Astrophysics Data System (ADS)

Yankine, S. A.; Van Stan, J. T., II; Mesta, D. C.; Côté, J. F.; Hildebrandt, A.; Friesen, J.; Maldonado, G.

2017-12-01

Stemflow is a pointed hydrologic flux at the base of tree stems that has been linked to a host of biogeochemical processes in vegetated landscapes. Much work has been done to examine controls over stemflow water yield, finding three major factors: individual tree canopy structure, meteorological variables, and neighborhood conditions. However, the authors are unaware of any study to directly quantify all factors using a combination of terrestrial LiDAR and micrometeorological monitoring methods. This study directly quantifies individual Pinus palustris tree canopy characteristics (trunk volume and angle, branch volume and angle from 1st-to-3rd order, bark roughness, and height), 10-m radius neighborhood properties (number of trees, mean diameter and height, mean distance from study tree, and canopy overlap), and above-canopy storm conditions (magnitude, intensity, mean/max wind speed, and vapor pressure deficit) directly at the site. Stemflow production was 1% of rainfall, ranging from 0.3-59 L per storm from individual trees. Preliminary findings from storms (5-176 mm in magnitude) indicate that all individual tree characteristics, besides bark roughness, have little influence on stemflow generation. Bark roughness altered stemflow generation by affecting trunk water storage (0.1-0.7 mm) and wet trunk evaporation rates (0.005-0.03 mm/h). The strongest influence over stemflow generation from individual trees was the interaction between neighborhood characteristics and meteorological conditions (primarily rainfall amount and, secondarily, rainfall intensity).

Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses

PubMed Central

Steinbrück, Lars; McHardy, Alice Carolyn

2012-01-01

Distinguishing mutations that determine an organism's phenotype from (near-) neutral ‘hitchhikers’ is a fundamental challenge in genome research, and is relevant for numerous medical and biotechnological applications. For human influenza viruses, recognizing changes in the antigenic phenotype and a strains' capability to evade pre-existing host immunity is important for the production of efficient vaccines. We have developed a method for inferring ‘antigenic trees’ for the major viral surface protein hemagglutinin. In the antigenic tree, antigenic weights are assigned to all tree branches, which allows us to resolve the antigenic impact of the associated amino acid changes. Our technique predicted antigenic distances with comparable accuracy to antigenic cartography. Additionally, it identified both known and novel sites, and amino acid changes with antigenic impact in the evolution of influenza A (H3N2) viruses from 1968 to 2003. The technique can also be applied for inference of ‘phenotype trees’ and genotype–phenotype relationships from other types of pairwise phenotype distances. PMID:22532796

Multiple alignment analysis on phylogenetic tree of the spread of SARS epidemic using distance method

NASA Astrophysics Data System (ADS)

Amiroch, S.; Pradana, M. S.; Irawan, M. I.; Mukhlash, I.

2017-09-01

Multiple Alignment (MA) is a particularly important tool for studying the viral genome and determine the evolutionary process of the specific virus. Application of MA in the case of the spread of the Severe acute respiratory syndrome (SARS) epidemic is an interesting thing because this virus epidemic a few years ago spread so quickly that medical attention in many countries. Although there has been a lot of software to process multiple sequences, but the use of pairwise alignment to process MA is very important to consider. In previous research, the alignment between the sequences to process MA algorithm, Super Pairwise Alignment, but in this study used a dynamic programming algorithm Needleman wunchs simulated in Matlab. From the analysis of MA obtained and stable region and unstable which indicates the position where the mutation occurs, the system network topology that produced the phylogenetic tree of the SARS epidemic distance method, and system area networks mutation.

Systemic risk and causality dynamics of the world international shipping market

NASA Astrophysics Data System (ADS)

Zhang, Xin; Podobnik, Boris; Kenett, Dror Y.; Eugene Stanley, H.

2014-12-01

Various studies have reported that many economic systems have been exhibiting an increase in the correlation between different market sectors, a factor that exacerbates the level of systemic risk. We measure this systemic risk of three major world shipping markets, (i) the new ship market, (ii) the second-hand ship market, and (iii) the freight market, as well as the shipping stock market. Based on correlation networks during three time periods, that prior to the financial crisis, during the crisis, and after the crisis, minimal spanning trees (MSTs) and hierarchical trees (HTs) both exhibit complex dynamics, i.e., different market sectors tend to be more closely linked during financial crisis. Brownian distance correlation and Granger causality test both can be used to explore the directional interconnectedness of market sectors, while Brownian distance correlation captures more dependent relationships, which are not observed in the Granger causality test. These two measures can also identify and quantify market regression periods, implying that they contain predictive power for the current crisis.

Genetic analysis of eight population groups living in Taiwan using a 13 X-chromosomal STR loci multiplex system.

PubMed

Hwa, Hsiao-Lin; Lee, James Chun-I; Chang, Yih-Yuan; Yin, Hsiang-Yi; Chen, Ya-Hui; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

2011-01-01

A 13 X-chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, and DXS7423) was tested on 1,037 DNA samples from eight population groups currently living in Taiwan. Different distributions of the allelic frequencies in different populations were presented. DXS8377 and DXS101 were the two most polymorphic loci in these eight populations, whereas DXS7423 was the least informative marker in most of the populations studied. The genetic distances between the populations and the constructed phylogenetic tree revealed a long genetic distance between Asian and Caucasian populations as well as isolation of the Tao population. The phylogenetic tree grouped populations into clusters compatible with their ethnogeographic relationships. This 13 X-chromosomal short tandem repeat multiplex system offers a considerable number of polymorphic patterns in different populations. This system can be useful in forensic identification casework and ethnogeographic research.

Microwave sensing of tree trunks

NASA Astrophysics Data System (ADS)

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 was divided into three sections to separate parts with different moisture (heartwood and sapwood) or empty space (decays). For easier manipulation with the antenna we developed a special ruler for measuring the distance along the scans. Instead of the surveying wheel we read the distance with a camera, which was fixed on the antenna and focused on the ruler with a binary pattern. Hence, during whole measurement and the data processing we were able to identify an accurate position on the tree in view of the scan. Some preliminary measurements on the trees were also conducted. They were performed using a GSSI 900 MHz antenna. Several tree species (beech, horse-chestnut, birch, ...) in Louvain-la-Neuve and Brussels, Belgium, have been investigated to see the internal structure of the tree decays. The measurements were carried out mainly by circumferential measurement around the trunk and also by vertical measurement along the trunk for approximate detection of the cavity. The comparison between the numerical simulations, simplified tree trunk model and real data from trees is presented. This research is funded by the Fonds de la Recherche Scientifique (FNRS, Belgium) and benefits from networking activities carried out within the EU COST Action TU1208 "Civil Engineering Applications of Ground Penetrating Radar".

Discriminating tests of information and topological indices. Animals and trees.

PubMed

Konstantinova, Elena V; Vidyuk, Maxim V

2003-01-01

In this paper we consider 13 information and topological indices based on the distance in a molecular graph with respect to their discrimination power. The numerical results of discriminating tests on 3490528 trees up to 21 vertices are given. The indices of the highest sensitivity are listed on the set of 1528775 alkane trees. The discrimination powers of indices are also examined on the classes of 849285 hexagonal, 298382 square, and 295365 triangular simply connected animals. The first class of animals corresponds to the structural formulas of planar benzenoid hydrocarbons. The values of all indices were calculated for all classes of animals as well as for the united set of 1443032 animals. The inspection of the data indicates the great sensitivity of four information indices and one topological index.

Extensive long-distance pollen dispersal in a fragmented landscape maintains genetic diversity in white spruce.

PubMed

O'Connell, Lisa M; Mosseler, Alex; Rajora, Om P

2007-01-01

Conifers are among the most genetically diverse plants but show the lowest levels of genetic differentiation, even among geographically distant populations. High gene flow among populations may be one of the most important factors in maintaining these genetic patterns. Here, we provide empirical evidence for extensive pollen-mediated gene dispersal between natural stands of a widespread northern temperate/boreal conifer, Picea glauca. We used 6 polymorphic allozyme loci to quantify the proportion of seeds sired by pollen originating from different sources in a landscape fragmented by agriculture in North Central Ontario, Canada. In 7 stands, a small proportion of seeds were sired by self-pollen or neighboring trees but 87.1% (+/-1.7% standard error [SE]) of seeds were sired by pollen from at least 250 to 3000 m away. In 4 single isolated trees, self-fertilization rates were low and more than 96% (+/-1.3% SE) of seeds were sired by immigrant pollen. The average minimum pollen dispersal distance in outcrossed matings was 619 m. These results provide strong evidence that extensive long-distance pollen dispersal plays a primary role in maintaining low genetic differentiation among natural populations of P. glauca and helps maintain genetic diversity and minimize inbreeding in small stands in a fragmented landscape.

Influence of Tree-Scale Environmental Variability on Tree-Ring Reconstructions of Temperature at Sonora Pass, CA

NASA Astrophysics Data System (ADS)

Ma, L.; Stine, A.

2016-12-01

Tree-ring width from treeline environments tend to covary with local interannual temperature variabilities. However, other environmental factors such as moisture and light availability may further modulate tree growth in cold climates. We investigate the influence of various environmental factors on a tree-ring record from a research plot near Sonora Pass, CA (38.32N, 119.64W; elev. 3130 m). This treeline ecotone is dominated by whitebark pine (Pinus albicaulis) growing as individuals and as stands, and at the transition between tree form and krummholtz. We surveyed all trees in the 160m x 90m site, mapping and coring all trees with a diameter at breast height greater than 10 cm. We use survey data to test for an influence of inter-tree competition on growth. We also test for modulation of growth by variation in distance from surface water, aspect and slope, and soil types. Initial result shows a relationship between tree ring width and local May-July temperature (R = 0.33, p < 0.01), suggesting summer temperature as a large-scale control on growth. Incorporating the tree-level metadata, we test for the effect of spatial variability on mean growth rate and on reconstructed temperatures. Trees that have larger or closer neighboring trees experience greater competition, and we hypothesize that competition will be inversely related to average growth rate. Further, we test the sensitivity of ring-width interannual variability to other non-temperature environmental drivers such as moisture availability, light competition, and spatial relations in the microenvironment. We hypothesize that trees that have ready access to light and water will likely produce ring records more closely correlated with the temperature record, and thus will produce a temperature reconstruction with a higher signal-to-noise ratio; whereas trees that experience more microenvironment limitations or competition will produce ring records resembling temperature and additional environmental factors or will contain more noise.

Remnant Pachira quinata pasture trees have greater opportunities to self and suffer reduced reproductive success due to inbreeding depression.

PubMed

Rymer, P D; Sandiford, M; Harris, S A; Billingham, M R; Boshier, D H

2015-08-01

Habitat fragmentation is extensive throughout the world, converting natural ecosystems into fragments of varying size, density and connectivity. The potential value of remnant trees in agricultural landscapes as seed sources and in connecting fragments has formed a fertile area of debate. This study contrasted the mating patterns of bat-pollinated Pachira quinata trees in a continuous forest to those in pasture through microsatellite-based paternity analysis of progeny. The breeding system was determined by analysis of pollen tube growth and seed production from controlled pollinations. Fitness of selfed and outcrossed seed was compared by germination and seedling growth. There was more inbreeding within pasture trees (outcrossing=0.828±0.015) compared with forest trees (0.926±0.005). Pasture trees had fewer sires contributing to mating events, but pollen dispersal distances were greater than those in the forest. Paternity analysis showed variation in outcrossing rates among pasture trees with high proportions of external and self pollen sources detected. A leaky self-incompatibility system was found, with self pollen having reduced germination on stigmas and slower growth rate through the style. Controlled pollinations also showed a varied ability to self among trees, which was reflected in the selfing rates among pasture trees shown by the paternity analysis (0-80% selfing). Self pollination resulted in lower seed set, germination and seedling growth compared with outcrossing. While remnant trees in agricultural landscapes are involved in broader mating patterns, they show increased but varied levels of inbreeding, which result in reduced fitness.

Association between split selection instability and predictive error in survival trees.

PubMed

Radespiel-Tröger, M; Gefeller, O; Rabenstein, T; Hothorn, T

2006-01-01

To evaluate split selection instability in six survival tree algorithms and its relationship with predictive error by means of a bootstrap study. We study the following algorithms: logrank statistic with multivariate p-value adjustment without pruning (LR), Kaplan-Meier distance of survival curves (KM), martingale residuals (MR), Poisson regression for censored data (PR), within-node impurity (WI), and exponential log-likelihood loss (XL). With the exception of LR, initial trees are pruned by using split-complexity, and final trees are selected by means of cross-validation. We employ a real dataset from a clinical study of patients with gallbladder stones. The predictive error is evaluated using the integrated Brier score for censored data. The relationship between split selection instability and predictive error is evaluated by means of box-percentile plots, covariate and cutpoint selection entropy, and cutpoint selection coefficients of variation, respectively, in the root node. We found a positive association between covariate selection instability and predictive error in the root node. LR yields the lowest predictive error, while KM and MR yield the highest predictive error. The predictive error of survival trees is related to split selection instability. Based on the low predictive error of LR, we recommend the use of this algorithm for the construction of survival trees. Unpruned survival trees with multivariate p-value adjustment can perform equally well compared to pruned trees. The analysis of split selection instability can be used to communicate the results of tree-based analyses to clinicians and to support the application of survival trees.

Automatic tree parameter extraction by a Mobile LiDAR System in an urban context.

PubMed

Herrero-Huerta, Mónica; Lindenbergh, Roderik; Rodríguez-Gonzálvez, Pablo

2018-01-01

In an urban context, tree data are used in city planning, in locating hazardous trees and in environmental monitoring. This study focuses on developing an innovative methodology to automatically estimate the most relevant individual structural parameters of urban trees sampled by a Mobile LiDAR System at city level. These parameters include the Diameter at Breast Height (DBH), which was estimated by circle fitting of the points belonging to different height bins using RANSAC. In the case of non-circular trees, DBH is calculated by the maximum distance between extreme points. Tree sizes were extracted through a connectivity analysis. Crown Base Height, defined as the length until the bottom of the live crown, was calculated by voxelization techniques. For estimating Canopy Volume, procedures of mesh generation and α-shape methods were implemented. Also, tree location coordinates were obtained by means of Principal Component Analysis. The workflow has been validated on 29 trees of different species sampling a stretch of road 750 m long in Delft (The Netherlands) and tested on a larger dataset containing 58 individual trees. The validation was done against field measurements. DBH parameter had a correlation R2 value of 0.92 for the height bin of 20 cm which provided the best results. Moreover, the influence of the number of points used for DBH estimation, considering different height bins, was investigated. The assessment of the other inventory parameters yield correlation coefficients higher than 0.91. The quality of the results confirms the feasibility of the proposed methodology, providing scalability to a comprehensive analysis of urban trees.

Remnant Pachira quinata pasture trees have greater opportunities to self and suffer reduced reproductive success due to inbreeding depression

PubMed Central

Rymer, P D; Sandiford, M; Harris, S A; Billingham, M R; Boshier, D H

2015-01-01

Habitat fragmentation is extensive throughout the world, converting natural ecosystems into fragments of varying size, density and connectivity. The potential value of remnant trees in agricultural landscapes as seed sources and in connecting fragments has formed a fertile area of debate. This study contrasted the mating patterns of bat-pollinated Pachira quinata trees in a continuous forest to those in pasture through microsatellite-based paternity analysis of progeny. The breeding system was determined by analysis of pollen tube growth and seed production from controlled pollinations. Fitness of selfed and outcrossed seed was compared by germination and seedling growth. There was more inbreeding within pasture trees (outcrossing=0.828±0.015) compared with forest trees (0.926±0.005). Pasture trees had fewer sires contributing to mating events, but pollen dispersal distances were greater than those in the forest. Paternity analysis showed variation in outcrossing rates among pasture trees with high proportions of external and self pollen sources detected. A leaky self-incompatibility system was found, with self pollen having reduced germination on stigmas and slower growth rate through the style. Controlled pollinations also showed a varied ability to self among trees, which was reflected in the selfing rates among pasture trees shown by the paternity analysis (0–80% selfing). Self pollination resulted in lower seed set, germination and seedling growth compared with outcrossing. While remnant trees in agricultural landscapes are involved in broader mating patterns, they show increased but varied levels of inbreeding, which result in reduced fitness. PMID:23963342

Automatic tree parameter extraction by a Mobile LiDAR System in an urban context

PubMed Central

Lindenbergh, Roderik; Rodríguez-Gonzálvez, Pablo

2018-01-01

In an urban context, tree data are used in city planning, in locating hazardous trees and in environmental monitoring. This study focuses on developing an innovative methodology to automatically estimate the most relevant individual structural parameters of urban trees sampled by a Mobile LiDAR System at city level. These parameters include the Diameter at Breast Height (DBH), which was estimated by circle fitting of the points belonging to different height bins using RANSAC. In the case of non-circular trees, DBH is calculated by the maximum distance between extreme points. Tree sizes were extracted through a connectivity analysis. Crown Base Height, defined as the length until the bottom of the live crown, was calculated by voxelization techniques. For estimating Canopy Volume, procedures of mesh generation and α-shape methods were implemented. Also, tree location coordinates were obtained by means of Principal Component Analysis. The workflow has been validated on 29 trees of different species sampling a stretch of road 750 m long in Delft (The Netherlands) and tested on a larger dataset containing 58 individual trees. The validation was done against field measurements. DBH parameter had a correlation R2 value of 0.92 for the height bin of 20 cm which provided the best results. Moreover, the influence of the number of points used for DBH estimation, considering different height bins, was investigated. The assessment of the other inventory parameters yield correlation coefficients higher than 0.91. The quality of the results confirms the feasibility of the proposed methodology, providing scalability to a comprehensive analysis of urban trees. PMID:29689076

Indirect effects of ecosystem engineering combine with consumer behaviour to determine the spatial distribution of herbivory.

PubMed

Griffen, Blaine D; Riley, Megan E; Cannizzo, Zachary J; Feller, Ilka C

2017-10-01

Ecosystem engineers alter environments by creating, modifying or destroying habitats. The indirect impacts of ecosystem engineering on trophic interactions should depend on the combination of the spatial distribution of engineered structures and the foraging behaviour of consumers that use these structures as refuges. In this study, we assessed the indirect effects of ecosystem engineering by a wood-boring beetle in a neotropical mangrove forest system. We identified herbivory patterns in a dwarf mangrove forest on the archipelago of Twin Cays, Belize. Past wood-boring activity impacted more than one-third of trees through the creation of tree holes that are now used, presumably as predation or thermal refuge, by the herbivorous mangrove tree crab Aratus pisonii. The presence of these refuges had a significant impact on plant-animal interactions; herbivory was more than fivefold higher on trees influenced by tree holes relative to those that were completely isolated from these refuges. Additionally, herbivory decreased exponentially with increasing distance from tree holes. We use individual-based simulation modelling to demonstrate that the creation of these herbivory patterns depends on a combination of the use of engineered tree holes for refuge by tree crabs, and the use of two behaviour patterns in this species-site fidelity to a "home tree," and more frequent foraging near their home tree. We demonstrate that understanding the spatial distribution of herbivory in this system depends on combining both the use of ecosystem engineering structures with individual behavioural patterns of herbivores. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Nearest neighbor imputation using spatial–temporal correlations in wireless sensor networks

PubMed Central

Li, YuanYuan; Parker, Lynne E.

2016-01-01

Missing data is common in Wireless Sensor Networks (WSNs), especially with multi-hop communications. There are many reasons for this phenomenon, such as unstable wireless communications, synchronization issues, and unreliable sensors. Unfortunately, missing data creates a number of problems for WSNs. First, since most sensor nodes in the network are battery-powered, it is too expensive to have the nodes retransmit missing data across the network. Data re-transmission may also cause time delays when detecting abnormal changes in an environment. Furthermore, localized reasoning techniques on sensor nodes (such as machine learning algorithms to classify states of the environment) are generally not robust enough to handle missing data. Since sensor data collected by a WSN is generally correlated in time and space, we illustrate how replacing missing sensor values with spatially and temporally correlated sensor values can significantly improve the network’s performance. However, our studies show that it is important to determine which nodes are spatially and temporally correlated with each other. Simple techniques based on Euclidean distance are not sufficient for complex environmental deployments. Thus, we have developed a novel Nearest Neighbor (NN) imputation method that estimates missing data in WSNs by learning spatial and temporal correlations between sensor nodes. To improve the search time, we utilize a kd-tree data structure, which is a non-parametric, data-driven binary search tree. Instead of using traditional mean and variance of each dimension for kd-tree construction, and Euclidean distance for kd-tree search, we use weighted variances and weighted Euclidean distances based on measured percentages of missing data. We have evaluated this approach through experiments on sensor data from a volcano dataset collected by a network of Crossbow motes, as well as experiments using sensor data from a highway traffic monitoring application. Our experimental results show that our proposed 𝒦-NN imputation method has a competitive accuracy with state-of-the-art Expectation–Maximization (EM) techniques, while using much simpler computational techniques, thus making it suitable for use in resource-constrained WSNs. PMID:28435414

Rainfall induced landslide susceptibility mapping using weight-of-evidence, linear and quadratic discriminant and logistic model tree method

NASA Astrophysics Data System (ADS)

Hong, H.; Zhu, A. X.

2017-12-01

Climate change is a common phenomenon and it is very serious all over the world. The intensification of rainfall extremes with climate change is of key importance to society and then it may induce a large impact through landslides. This paper presents GIS-based new ensemble data mining techniques that weight-of-evidence, logistic model tree, linear and quadratic discriminant for landslide spatial modelling. This research was applied in Anfu County, which is a landslide-prone area in Jiangxi Province, China. According to a literature review and research the study area, we select the landslide influencing factor and their maps were digitized in a GIS environment. These landslide influencing factors are the altitude, plan curvature, profile curvature, slope degree, slope aspect, topographic wetness index (TWI), Stream Power Index (SPI), Topographic Wetness Index (SPI), distance to faults, distance to rivers, distance to roads, soil, lithology, normalized difference vegetation index and land use. According to historical information of individual landslide events, interpretation of the aerial photographs, and field surveys supported by the government of Jiangxi Meteorological Bureau of China, 367 landslides were identified in the study area. The landslide locations were divided into two subsets, namely, training and validating (70/30), based on a random selection scheme. In this research, Pearson's correlation was used for the evaluation of the relationship between the landslides and influencing factors. In the next step, three data mining techniques combined with the weight-of-evidence, logistic model tree, linear and quadratic discriminant, were used for the landslide spatial modelling and its zonation. Finally, the landslide susceptibility maps produced by the mentioned models were evaluated by the ROC curve. The results showed that the area under the curve (AUC) of all of the models was > 0.80. At the same time, the highest AUC value was for the linear and quadratic discriminant model (0.864), followed by logistic model tree (0.832), and weight-of-evidence (0.819). In general, the landslide maps can be applied for land use planning and management in the Anfu area.

A combined field and numerical approach to understanding dilute pyroclastic density current dynamics and hazard potential: Auckland Volcanic Field, New Zealand

NASA Astrophysics Data System (ADS)

Brand, Brittany D.; Gravley, Darren M.; Clarke, Amanda B.; Lindsay, Jan M.; Bloomberg, Simon H.; Agustin-Flores, Javier; Németh, Károly

2014-04-01

The most dangerous and deadly hazards associated with phreatomagmatic eruptions in the Auckland Volcanic Field (AVF; Auckland, New Zealand) are those related to volcanic base surges - dilute, ground-hugging, particle laden currents with dynamic pressures capable of severe to complete structural damage. We use the well-exposed base surge deposits of the Maungataketake tuff ring (Manukau coast, Auckland), to reconstruct flow dynamics and destructive potential of base surges produced during the eruption. The initial base surge(s) snapped trees up to 0.5 m in diameter near their base as far as 0.7-0.9 km from the vent. Beyond this distance the trees were encapsulated and buried by the surge in growth position. Using the tree diameter and yield strength of the wood we calculate that dynamic pressures (Pdyn) in excess of 12-35 kPa are necessary to cause the observed damage. Next we develop a quantitative model for flow of and sedimentation from a radially-spreading, dilute pyroclastic density currents (PDCs) to determine the damage potential of the base surges produced during the early phases of the eruption and explore the implications of this potential on future eruptions in the region. We find that initial conditions with velocities on the order of 65 m s- 1, bulk density of 38 kg m- 3 and initial, near-vent current thicknesses of 60 m reproduce the field-based Pdyn estimates and runout distances. A sensitivity analysis revealed that lower initial bulk densities result in shorter run-out distances, more rapid deceleration of the current and lower dynamic pressures. Initial velocity does not have a strong influence on run-out distance, although higher initial velocity and slope slightly decrease runout distance due to higher rates of atmospheric entrainment. Using this model we determine that for base surges with runout distances of up to 4 km, complete destruction can be expected within 0.5 km from the vent, moderate destruction can be expected up to 2 km, but much less damage is expected up to the final runout distance of 4 km. For larger eruptions (base surge runout distance 4-6 km), Pdyn of > 35 kPa can be expected up to 2.5 km from source, ensuring complete destruction within this area. Moderate damage to reinforced structures and damage to weaker structures can be expected up to 6 km from source. In both cases hot ash may still cause damage due to igniting flammable materials in the distal-most regions of a base surge. This work illustrates our ability to combine field observations and numerical models to explore the depositional mechanisms, macroscale current dynamics, and potential impact of dilute PDCs. Thus, this approach may serve as a tool to understand the damage potential and extent of previous and potential future eruptions in the AVF.

Ecological Importance of Large-Diameter Trees in a Temperate Mixed-Conifer Forest

PubMed Central

Lutz, James A.; Larson, Andrew J.; Swanson, Mark E.; Freund, James A.

2012-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. Although both scaling theory and competition theory make predictions about the relative composition and spatial patterns of large-diameter trees compared to smaller diameter trees, these predictions are rarely tested. We established a 25.6 ha permanent plot within which we tagged and mapped all trees ≥1 cm dbh, all snags ≥10 cm dbh, and all shrub patches ≥2 m2. We sampled downed woody debris, litter, and duff with line intercept transects. Aboveground live biomass of the 23 woody species was 507.9 Mg/ha, of which 503.8 Mg/ha was trees (SD = 114.3 Mg/ha) and 4.1 Mg/ha was shrubs. Aboveground live and dead biomass was 652.0 Mg/ha. Large-diameter trees comprised 1.4% of individuals but 49.4% of biomass, with biomass dominated by Abies concolor and Pinus lambertiana (93.0% of tree biomass). The large-diameter component dominated the biomass of snags (59.5%) and contributed significantly to that of woody debris (36.6%). Traditional scaling theory was not a good model for either the relationship between tree radii and tree abundance or tree biomass. Spatial patterning of large-diameter trees of the three most abundant species differed from that of small-diameter conspecifics. For A. concolor and P. lambertiana, as well as all trees pooled, large-diameter and small-diameter trees were spatially segregated through inter-tree distances <10 m. Competition alone was insufficient to explain the spatial patterns of large-diameter trees and spatial relationships between large-diameter and small-diameter trees. Long-term observations may reveal regulation of forest biomass and spatial structure by fire, wind, pathogens, and insects in Sierra Nevada mixed-conifer forests. Sustaining ecosystem functions such as carbon storage or provision of specialist species habitat will likely require different management strategies when the functions are performed primarily by a few large trees as opposed to many smaller trees. PMID:22567132

Parallel beta/alpha-barrels of alpha-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of beta-amylase: evolutionary distance is a reflection of unrelated sequences.

PubMed

Janecek, S

1994-10-17

The structures of functionally related beta/alpha-barrel starch hydrolases, alpha-amylase, beta-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase, are discussed, their mutual sequence similarities being emphasized. Since these enzymes (except for beta-amylase) along with the predicted set of more than ten beta/alpha-barrels from the alpha-amylase enzyme superfamily fulfil the criteria characteristic of the products of divergent evolution, their unrooted distance tree is presented.

Proximity to Parks in the Durham, NC EnviroAtlas Community Area

EPA Science Inventory

People use parks to socialize, exercise, recreate, and enjoy nature. Having a park within walking distance creates opportunities for individuals to experience the benefits of trees and other green space on health and well-being. These maps are part of the US Environmental Protect...

Case-based explanation of non-case-based learning methods.

PubMed Central

Caruana, R.; Kangarloo, H.; Dionisio, J. D.; Sinha, U.; Johnson, D.

1999-01-01

We show how to generate case-based explanations for non-case-based learning methods such as artificial neural nets or decision trees. The method uses the trained model (e.g., the neural net or the decision tree) as a distance metric to determine which cases in the training set are most similar to the case that needs to be explained. This approach is well suited to medical domains, where it is important to understand predictions made by complex machine learning models, and where training and clinical practice makes users adept at case interpretation. PMID:10566351

Migrating foreign body in the tracheobronchial tree: an unusual case of firework penetrating neck injury.

PubMed

Khan, M Sarwar; Kirkland, P M; Kumar, R

2002-02-01

Firework injuries can manifest themselves in many different ways; usually as an explosive or burn injury. This case describes an unusual presentation of a firework penetrating injury resulting in a sharp coiled metal foreign body travelling through a small entry wound in the neck and subsequently lodging itself in the tracheobronchial tree. A foreign body such as this can potentially travel a considerable distance through the soft tissues and end up in an unsuspecting distant site. There must, therefore, be a high index of suspicion with the appropriate radiological investigations for appropriate management of such cases.

Numerical taxonomy on data: Experimental results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cohen, J.; Farach, M.

1997-12-01

The numerical taxonomy problems associated with most of the optimization criteria described above are NP - hard [3, 5, 1, 4]. In, the first positive result for numerical taxonomy was presented. They showed that if e is the distance to the closest tree metric under the L{sub {infinity}} norm. i.e., e = min{sub T} [L{sub {infinity}} (T-D)], then it is possible to construct a tree T such that L{sub {infinity}} (T-D) {le} 3e, that is, they gave a 3-approximation algorithm for this problem. We will refer to this algorithm as the Single Pivot (SP) heuristic.