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PubMed1999

The rooting of the universal tree of life is not reliable.

Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria-Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.

Adenosine Triphosphatases↗

PubMed2006

Tree-girdling to separate root and heterotrophic respiration in two Eucalyptus stands in Brazil.

The release of carbon as CO2 from belowground processes accounts for about 70% of total ecosystem respiration. Insights about factors controlling soil CO2 efflux are constrained by the challenge of apportioning sources of CO2 between autotrophic tree roots (and mycorrhizal fungi) and heterotrophic microorganisms. In some temperate conifer forests, the reduction in soil CO2 efflux after girdling (phloem removal) has been used to separate these sources. Girdling stops the flow of carbohydrates to the belowground portion of the ecosystem, which should slow respiration by roots and mycorrhizae while heterotrophic respiration should remain constant or be enhanced by the decomposition of newly dead roots. Therefore, the reduction in CO2 efflux after girdling should be a conservative estimate of the belowground flux of C from trees. We tested this approach in two tropical Eucalyptus plantations. Tree canopies remained intact for more than 3 months after girdling, showing no reduction in light interception. The reduction in soil CO2 efflux averaged 16-24% for the 3-month period after girdling. The reduction in CO2 efflux was similar for plots with one half of the trees girdled and those with all of the trees girdled. Girdling did not reduce live fine root biomass for at least 5 months after treatment, indicating that large reserves of carbohydrates in the root systems of Eucalyptus trees maintained the roots and root respiration. Our results suggest that the girdling approach is unlikely to provide useful insights into the contribution of tree roots and heterotrophs to soil CO2 efflux in this type of forest ecosystem.

Brazil↗

PubMed2007

Relation between branching patterns and perfusion in stochastic generated coronary arterial trees.

Biological variation in branching patterns is likely to affect perfusion of tissue. To assess the fundamental consequences of branching characteristics, 50 stochastic asymmetrical coronary trees and one non-stochastic symmetrical branching tree were generated. In the stochastic trees, area growth, A, at branching points was varied: A = random; 1.00; 1.10; 1.13 and 1.15 and symmetry, S, was varied: S = random; 1.00; 0.70; 0.58; 0.50 and 0.48. With random S and A values, a large variation in flow and volume was found, linearly related to the number of vessels in the trees. Large A values resulted in high number of vessels and high flow and volume values, indicating vessels connected in parallel. Lowering symmetry values increased the number of vessels, however, without changing flow, indicating a dominant connection of vessels in series. Both large A and small S values gave more realistic gradual pressure drops compared to the symmetrical non-stochastic branching tree. This study showed large variations in tree realizations, which may reflect real biological variations in tree anatomies. Furthermore, perfusion of tissue clearly depends on the branching rules applied.

Arteries↗

PubMed1987

Small artery occlusion: a theoretical approach to the definition of coronary architecture and resistance by a branching tree model.

The aim of this study was to evaluate the theoretical possibility of assessing the architecture of the coronary small artery circulation in vivo by the analysis of the increments in the total resistance of the vascular system caused by the progressive occlusion of the terminal vessels as would be possible in animal experiments by microsphere embolization. Different distributions of the resistance values of all the vessels have been obtained in branching tree models by means of only two parameters: (a) the resistance ratio between daughter and parent vessels at each branching site (KO); and (b) the resistance ratio between the two daughter vessels at each branching site (KV). Simulation of branching tree occlusion has been performed under two main conditions of resistance distribution: (1) symmetric resistance distribution, characterized by equal KO values at each branching site of the same level and by KV = 1, that is, equal resistance values for the vessel of the same level; and (2) asymmetric resistance distribution in dichotomous branching trees, wherein all the vessels may have different values of resistance; the variability in these values has however been restricted on the basis of physiological considerations. The analysis of the function of the total resistance vs the number of occluded vessels, obtained by a simulated progressive occlusion of the terminal vessels in these two systems, gives the following results: (1) in a symmetric branching tree, discontinuities are present in the occlusion function which permit identification of both the architecture and the resistance value of each single vessel of any unknown vascular tree; and (2) in the asymmetric model, the function does not allow a direct definition of the branching architecture and the values of resistance of each vessel; however, also in this case, any branching tree can be analyzed by means of a nonlinear optimization procedure which produces an equivalent symmetric branching tree. We conclude that, theoretically, the analysis of the occlusion function represents a valuable indirect approach to the quantitative study of the coronary microcirculation as well as of other vascular districts under steady flow conditions.

Animals↗

PubMed1996

Size-mediated foliar response to ozone in black cherry trees.

Local ozone concentration and visible foliar injury were measured over the 1994 growing season on open-grown black cherry (Prunus serotina Ehrh.) trees of varying size (age) within forest stands and adjacent openings at a site in north-central Pennsylvania. Relationships were determined between visible ozone injury and ozone exposure, as well as calculated between injury and ozone uptake expressed as the product of stomatal conductance and ozone concentration. In addition, simultaneous measurements of visible symptoms and leaf gas exchange were also conducted to determine the correlation between visible and physiological injury and ozone exposure. By September, the amount of leaf area affected by visible foliar ozone injury was greatest for seedlings (46%), followed by canopy trees (20%) and saplings (15%). A large amount of variability in foliar ozone symptom expression was observed among trees within a size class. Sum40 and Sum60 (ozone concentration > 40 and > 60 nl liter(-1)) cumulative exposure statistics were the most meaningful indices for interpretation of foliar injury response. Seedlings were apparently more sensitive to ozone injury than larger trees because their higher rates of stomatal conductance resulted in higher rates of ozone uptake. Seedlings also had higher rates of early leaf abscission than larger trees with an average of nearly 30% of the leaves on a shoot abscised by 1 September compared to approximately 5% for larger trees. However, per unit ozone uptake into the leaf, larger trees exhibited larger amounts of foliar injury. The amount of visible foliar injury was negatively correlated (r(2) = 0.82) with net photosynthetic rates, but was not related to stomatal conductance. Net photosynthesis and stomatal conductance thus became uncoupled at high levels of visible foliar injury.

Journal Article↗

PubMed1992

Phylogenetic inference based on matrix representation of trees.

Rooted phylogenetic trees can be represented as matrices in which the rows correspond to termini, and columns correspond to internal nodes (elements of the n-tree). Parsimony analysis of such a matrix will fully recover the topology of the original tree. The maximum size of the represented matrix depends only on the number of termini in the tree; for a tree derived from molecular sequences, the represented matrix may be orders of magnitude smaller than the original data matrix. Representations of multiple trees (which may or may not have identical termini) can readily be combined into a single matrix; columns of discrete-character-state data can be added and, if desired, weighted differentially. Parsimony analysis of the resulting composite matrix yields a hybrid supertree which typically provides greater resolution than conventional consensus trees. Use of this method is illustrated with examples involving multiple tRNA genes in organelles and multiple protein-coding genes in eukaryotes.

Animals↗

PubMed2005

Representation in stochastic search for phylogenetic tree reconstruction.

Phylogenetic tree reconstruction is a process in which the ancestral relationships among a group of organisms are inferred from their DNA sequences. For all but trivial sized data sets, finding the optimal tree is computationally intractable. Many heuristic algorithms exist, but the branch-swapping algorithm used in the software package PAUP* is the most popular. This method performs a stochastic search over the space of trees, using a branch-swapping operation to construct neighboring trees in the search space. This study introduces a new stochastic search algorithm that operates over an alternative representation of trees, namely as permutations of taxa giving the order in which they are processed during stepwise addition. Experiments on several data sets suggest that this algorithm for generating an initial tree, when followed by branch-swapping, can produce better trees for a given total amount of time.

Algorithms↗

PubMed2005

Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

The identification of the whole set of protein interactions taking place in an organism is one of the main tasks in genomics, proteomics and systems biology. One of the computational techniques used by many investigators for studying and predicting protein interactions is the comparison of evolutionary histories (phylogenetic trees), under the hypothesis that interacting proteins would be subject to a similar evolutionary pressure resulting in a similar topology of the corresponding trees. Here, we present a new approach to predict protein interactions from phylogenetic trees, which incorporates information on the overall evolutionary histories of the species (i.e. the canonical "tree of life") in order to correct by the expected background similarity due to the underlying speciation events. We test the new approach in the largest set of annotated interacting proteins for Escherichia coli. This assessment of co-evolution in the context of the tree of life leads to a highly significant improvement (P(N) by sign test approximately 10E-6) in predicting interaction partners with respect to the previous technique, which does not incorporate information on the overall speciation tree. For half of the proteins we found a real interactor among the 6.4% top scores, compared with the 16.5% by the previous method. We applied the new method to the whole E.coli proteome and propose functions for some hypothetical proteins based on their predicted interactors. The new approach allows us also to detect non-canonical evolutionary events, in particular horizontal gene transfers. We also show that taking into account these non-canonical evolutionary events when assessing the similarity between evolutionary trees improves the performance of the method predicting interactions.

Algorithms↗

PubMed2005

Sap flow, gas exchange, and hydraulic conductance of young apricot trees growing under a shading net and different water supplies.

The experiment was carried out in a research field near Murcia, Spain, over a 3-week period between September 26 and October 16, 2000. Sixteen trees were used in the experiment, eight of which were placed under a rectangular shading net, while the other eight were maintained in the open air. Trees were irrigated once per day and, after October 5th, water was witheld from eight trees (four shaded and four unprotected for 5 days). The leaf stomatal conductance and the photosynthesis rates were higher in the shaded trees than in the exposed plants, probably because the leaf water potential was lower in the unshaded plants. This higher leaf conductance partially compensated for the effect of low radiation on transpiration, and the reduction of daily sap flow registered in shaded trees was only around 10-20%. The net also affected trunk diameter changes, with the shaded trees showing lower values of maximum daily shrinkage. Soil water deficit and high radiation had a similar effect on plant water parameters, lowering leaf water potential, leaf stomatal conductance, and the photosynthesis rate. The effects of both conditions were accumulative and so the exposed water-stressed plants showed the lowest values of total hydraulic resistance and water use efficiency, while the shaded well-irrigated trees registered the highest values for both parameters. For this reason, we think that net shading could be extended to apricot culture in many areas in which irrigation water is scarce and insolation is high.

Agriculture↗

PubMed1991

Propagation of action potentials along complex axonal trees. Model and implementation.

Axonal trees are typically morphologically and physiologically complicated structures. Because of this complexity, axonal trees show a large repertoire of behavior: from transmission lines with delay, to frequency filtering devices in both temporal and spatial domains. Detailed theoretical exploration of the electrical behavior of realistically complex axonal trees is notably lacking, mainly because of the absence of a simple modeling tool. AXONTREE is an attempt to provide such a simulator. It is written in C for the SUN workstation and implements both a detailed compartmental modeling of Hodgkin and Huxley-like kinetics, and a more abstract, event-driven, modeling approach. The computing module of AXONTREE is introduced together with its input/output features. These features allow graphical construction of arbitrary trees directly on the computer screen, and superimposition of the results on the simulated structure. Several numerical improvements that increase the computational efficiency by a factor of 5-10 are presented; most notable is a novel method of dynamic lumping of the modeled tree into simpler representations ("equivalent cables"). AXONTREE's performance is examined using a reconstructed terminal of an axon from a Y cell in cat visual cortex. It is demonstrated that realistically complicated axonal trees can be handled efficiently. The application of AXONTREE for the study of propagation delays along axonal trees is presented in the companion paper (Manor et al., 1991).

Action Potentials↗

PubMed2001

Properties of phylogenetic trees generated by Yule-type speciation models.

We investigate some discrete structural properties of evolutionary trees generated under simple null models of speciation, such as the Yule model. These models have been used as priors in Bayesian approaches to phylogenetic analysis, and also to test hypotheses concerning the speciation process. In this paper we describe new results for three properties of trees generated under such models. Firstly, for a rooted tree generated by the Yule model we describe the probability distribution on the depth (number of edges from the root) of the most recent common ancestor of a random subset of k species. Next we show that, for trees generated under the Yule model, the approximate position of the root can be estimated from the associated unrooted tree, even for trees with a large number of leaves. Finally, we analyse a biologically motivated extension of the Yule model and describe its distribution on tree shapes when speciation occurs in rapid bursts.

Animals↗

PubMed2003

The effect of long-term atmospheric CO2 enrichment on the intrinsic water-use efficiency of sour orange trees.

Every two months of 1992, as well as on three occasions in 1994-1995, we obtained leaf samples together with samples of surrounding air from eight well-watered and fertilized sour orange (Citrus aurantium L.) trees that were growing out-of-doors at Phoenix, Arizona, USA. These trees had been planted in the ground as small seedlings in July of 1987 and enclosed in pairs by four clear-plastic-wall open-top chambers of which two have been continuously maintained since November of that year at a CO2 concentration of 400 micromol mol(-1) and two have been maintained at 700 micromol mol(-1). In September 2000, we also extracted north-south and east-west oriented wood cores that passed through the center of each tree's trunk at a height of 45 cm above the ground. Stable-carbon isotope ratios (13C/12C) derived from these leaf, wood and air samples were used to evaluate each tree's intrinsic water-use efficiency (iWUE). The grand-average result was an 80% increase in this important plant parameter in response to the 300 micromol mol(-1) increase in atmospheric CO2 concentration employed in the study. This increase in sour orange tree iWUE is identical to the long-term CO2-induced increase in the trees' production of wood and fruit biomass, which suggests there could be little to no change in total water-use per unit land area for this species as the air's CO2 content continues to rise. It is also identical to the increase in the mean iWUE reported for 23 groups of naturally occurring trees scattered across western North America that was caused by the historical rise in the air's CO2 content that occurred between 1800 and 1985.

Atmosphere↗

PubMed2000

Role of climate, crown position, tree age and altitude in calculated ozone flux into needles of Picea abies and Pinus cembra: a synthesis.

Ozone (O(3)) flux into Norway spruce (Picea abies) and cembran pine (Pinus cembra) needles was estimated under ambient conditions at six rural sites between 580 and 1950 m a.s.l. We also assessed age-related differences in O(3) flux by examining changes in leaf conductance across the life span of Norway spruce. At the leaf level O(3) flux into the needles was effectively controlled by stomatal conductance and, hence by factors such as temperature, irradiance and humidity, which control stomatal conductance. Seasonal variations in O(3) flux were mainly attributed to the course of the prevailing temperature. During the growing season, however, data have emphasised leaf-air vapour pressure difference as the environmental factor most likely to control stomatal conductance and O(3) flux into the needles. In the sun crown stomatal conductance averaged over the growing season decreased with increasing tree age from 42.0+/-3.5 mmol O(3) m(-2) s(-1) in 17-year-old trees to 7.1+/-1.0 mmol O(3) m(-2) s(-1) in 216-year-old trees, indicating that O(3) concentration in the substomatal cavities is higher in young than in old trees. Independent from tree age stomatal conductance and O(3) flux were approximately 50% lower in shade needles as compared to sun-exposed needles. Stomatal conductance was also greater in the current flush (24+/-5.6 mmol O(3) m(-2) s(-1)) and in 1-year old needles (16+/-4 mmol O(3) m(-2) s(-1)) than in older needle age classes (12+/-1 mmol O(3) m(-2) s(-1), averaged across the four older needle age classes). In trees similar in age (60-65 years old) average O(3) flux into sun needles increased from 0.55+/-0.36 nmol m(-2) s(-1) at the valley floor to 0.9 nmol m(-2) s(-1) in 1950 m a.s.l. Cumulative O(3) uptake during the vegetation period increased from 11.4+/-1.7 mol m(-2) in the valley to 14 mol m(-2) at the alpine timberline. Although stomatal conductance provides the principal limiting factor for O(3) flux, additional field research is necessary in order to improve our understanding concerning the quantitative 'physiological threshold dose' which internally can be active and can have adverse effects of O(3) on forest trees.

Journal Article↗

PubMed1997

A general method for tree-comparison based on subtree similarity and its use in a taxonomic database.

A number of metrics for comparing the branching structure of trees have been used as important tools in the quantitative analysis of evolutionary trees. Less attention has been paid to developing a general comparison methodology for different leaf-labeled N-trees such as classification trees and various types of dendrograms. In this paper a method for measuring overall similarity based on subtree similarity is proposed. Association coefficients can be used to measure the similarity between each pair of subtrees in two trees, and an algorithm called the 'webbing matrix method' is outlined in order to calculate the overall similarity in this method. In addition, the use of this method for tree searching and tree comparison in a taxonomic database is introduced.

Animals↗

PubMed2000

Mutations in the p53 tumor suppressor gene in tree shrew hepatocellular carcinoma associated with hepatitis B virus infection and intake of aflatoxin B1.

Infection with hepadnaviruses and exposure to aflatoxin B1 (AFB1) are considered to be major risk factors in the development of hepatocellular carcinoma (HCC) in humans. A high rate of p53 mutations at codon 249 has been reported in these tumors. The tree shrew (Tupaia belangeri chinensis) is a useful animal model for the development of HCC after human hepatitis B virus (HBV) infection or AFB1 treatment. Therefore, it was of particular interest to determine whether the p53 gene in tree shrew HCCs associated with HBV infection and/or with exposure to AFB1 is affected in the same manner as in human HCCs. We determined the tree shrew p53 wild-type nucleotide sequences by RT-PCR and automatic DNA-sequencing. Tree shrew wild-type p53 sequence showed 91.7 and 93.4% homologies with human p53 nucleotide and amino acids sequences, respectively, while it showed 77.2 and 73.7% homologies in mice. One HCC and normal liver tissue from AFB1 treated and one HCC from AFB1- and HBV-treated tree shrew showed no change in p53 sequences, while three HCCs from AFB1- and HBV-treated tree shrews showed point mutations in p53 sequences. One HCC showed point mutations at codon 275, which is on the DNA-binding domain of p53 gene, which might be a cause of gain-of-function during the development of HCC. As a result, our finding indicates that tree shrews exposed to AFB1 and/or HBV had neither codon 249 mutations nor significant levels of other mutations in the p53 gene, as is the case with humans.

Aflatoxin B1↗

PubMedDate not supplied

Vascular tree object segmentation by deskeletonization of valley courses.

In this paper, we propose a valley-course-based image segmentation technique for tree-like object delineation, as an alternative to the traditional centerline-based methods. This technique consists of valley-course extraction, skeleton pruning and deskeletonization. Valley courses, constructed from valley points that are obtained by star-pattern scanning over an image, offer a natural manner of identifying tree skeletons. Unattached segments are removed using morphological operations. A structured tree is then constructed from the skeletons by using a tree pruning/spanning algorithm. A fleshy tree-like object is obtained by a deskeletonization procedure, which consists of extracting tree boundary in vicinity of the skeletons in the original image. The tree boundary is determined by identifying paired edge points at a valley point. A derivative-free edge identification approach is proposed, which defines an edge point at a side-slope by a relative intensity drop with respect to the local background. An empirical formula using a logarithmic function of local intensity contrast offers desirable characteristics of adaptability and stability. The adaptability of edge points to the local background is attributed to the compression behavior of logarithmic function. Furthermore, stability to noise is resulted because derivative operations are not used. The segmentation technique was validated using coronary angiographic images.

Algorithms↗

PubMed2002

A survival model for unthinned loblolly pine plantations that incorporates non-planted tree competition, site quality, and incidence of fusiform rust.

Future biomass yields are functionally related to the number of trees surviving at a given age. A stand level survival model was developed that incorporates competition of non-planted trees, site quality, and the incidence of fusiform rust (Cronartium quercuum [Berk.] Miyabe ex Shirai f. sp. fusiforme). The model consists of a system of two equations, one of which represents the number of surviving trees infected by fusiform rust while the other represents the number of trees not infected by fusiform rust. Data from unthinned loblolly pine (Pinus taeda L.) plantations in East Texas were used to fit and evaluate the survival model and illustrate its use. The model successfully predicted that the number of surviving loblolly pine trees decreased as the number of non-planted trees increased. The model also successfully predicted the transition of loblolly pine trees from an uninfected to an infected status by fusiform rust.

Basidiomycota↗

PubMed2002

Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes.

Two different methods of using paralogous genes for phylogenetic inference have been proposed: reconciled trees (or gene tree parsimony) and uninode coding. Gene tree parsimony suffers from 10 serious problems, including differential weighting of nucleotide and gap characters, undersampling which can be misinterpreted as synapomorphy, all of the characters not being allowed to interact, and conflict between gene trees being given equal weight, regardless of branch support. These problems are largely avoided by using uninode coding. The uninode coding method is elaborated to address multiple gene duplications within a single gene tree family and handle problems caused by lack of gene tree resolution. An example of vertebrate phylogeny inferred from nine genes is reanalyzed using uninode coding. We suggest that uninode coding be used instead of gene tree parsimony for phylogenetic inference from paralogous genes.

Animals↗