The hydraulic system of trees: theoretical framework and numerical simulation

Empirical studies pose the problem of the physiological integration of the tree organism, which is also important on the scale of ecosystems. Recently, spatially distributed models emerged, which approach this problem by reflecting the close linkage between physiological processes and the structures of trees and tree stands. In the case of water flow, the tree organism can be regarded as hydraulic system and the branched tree architecture as hydraulic network. Previous models of the hydraulic system either did not take into account the network structure, or they had shortcomings regarding the translation of the underlying physiological assumptions by the discrete computation method. We have developed a theoretical framework which takes the form of a numerical simulation model of tree water flow. A discrete initial boundary value problem (IBVP) combines the phenomena of Darcy flow, water storage and conductivity losses in the hydraulic network. The software HYDRA computes the solution of the IBVP. The theoretical derivation and model tests corroborate the consistent translation of the physiological assumptions by the computational method. Simulation studies enabled us to formulate hypotheses on the following points: (1) differences in the hydraulic segmentation between Picea abies and Thuja occidentalis, (2) responses of the hydraulic system to rapid transpiration changes and to a scenario of drought stress, and (3) how these responses depend on architectural quantities of the trees. The simulation studies demonstrated our possibilities of deriving theoretically well-founded hypotheses about the functioning of the hydraulic system and its relation to system structure. The numerical simulation model is designed as a tool for structure-function studies, which is able to treat tree architecture as independent variable. The model supports the integration of data on tree level, and it can be used for computer experiments which quantify the dynamics of the hydraulic system according to the concepts of system theory. Copyright 1999 Academic Press.     

CHLOROPLAST DNA EVOLUTION AND PHYLOGENETIC RELATIONSHIPS IN CLARKIA SECT. PERIPETASMA (ONAGRACEAE)

Restriction-site analysis of chloroplast DNA in Clarkia sect. Peripetasma (Onagraceae) was done to test previously proposed phylogenetic models. One hundred nineteen restriction-site mutations were identified among the nine species using 29 restriction enzymes, and these were used to construct rooted most parsimonious trees (Wagner and Dollo). A chloroplast DNA evolutionary clock could not be statistically rejected. Branch points of this tree were statistically tested by Felsenstein's bootstrap method. This tree 1) provided an unambiguous and detailed genealogical history for the section, 2) verified a previous partial phylogenetic model for the section based on gene duplications and differential silencing, 3) provided details of the phylogenetic model not inferred or expected based on morphology and reproductive isolation, and 4) indicated that morphology evolves at markedly different rates within and between lineages in the section.     

Comprehensive decision tree models in bioinformatics

Purpose

Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible.

Methods

This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree.

Results

The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree.

Conclusions

The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly redundant attributes that are very common in bioinformatics.     

What Can Causal Networks Tell Us about Metabolic Pathways?

Graphical models describe the linear correlation structure of data and have been used to establish causal relationships among phenotypes in genetic mapping populations. Data are typically collected at a single point in time. Biological processes on the other hand are often non-linear and display time varying dynamics. The extent to which graphical models can recapitulate the architecture of an underlying biological processes is not well understood. We consider metabolic networks with known stoichiometry to address the fundamental question: “What can causal networks tell us about metabolic pathways?”. Using data from an Arabidopsis BaySha population and simulated data from dynamic models of pathway motifs, we assess our ability to reconstruct metabolic pathways using graphical models. Our results highlight the necessity of non-genetic residual biological variation for reliable inference. Recovery of the ordering within a pathway is possible, but should not be expected. Causal inference is sensitive to subtle patterns in the correlation structure that may be driven by a variety of factors, which may not emphasize the substrate-product relationship. We illustrate the effects of metabolic pathway architecture, epistasis and stochastic variation on correlation structure and graphical model-derived networks. We conclude that graphical models should be interpreted cautiously, especially if the implied causal relationships are to be used in the design of intervention strategies.     

Genetic determinism of the vegetative and reproductive traits in an F1 olive tree progeny

The agronomic performance of fruit trees is significantly influenced by tree internal organization. Introducing architectural traits in breeding programs could thus lead to select new varieties with a regular bearing and lower input demand in order to reduce training and environmental costs. However, an interaction between tree ontogeny and genetic factors is expected. In this study, we investigated the genetic determinism of architectural traits in the olive tree, accounting for tree development over 5 years until first flowering occurrence. We studied an F1 progeny issued from a cross between two contrasted genotypes, ‘Olivière’ and ‘Arbequina’. Tree architecture was decomposed in quantitative traits, related to (1) growth and branching, (2) first flowering and fruiting. Models, including the year of growth, branching order and genotype effects, were built with variance function and covariance structure when necessary. After a model selection, broad sense heritabilities were calculated. During the first 3 years, both the mean values of vegetative traits and genetic factor significance depended on the shoot within-tree position. Dependencies between consecutive years were revealed for traits related to whole tree form. Whole tree form variables showed medium to high broad sense heritability values, whereas reproductive traits were highly heritable. This study demonstrates the existence of ontogenic trends in the olive tree, which result in traits heritable only at the tree periphery. A phenotyping strategy adapted to its architectural characteristics and a list of relevant traits, such as maximal internode length, is proposed. Transgressive effects suggest that genetic progress could be performed in future selection programs.     

Didelotia idae in the Gola Forest,sierra leone

Economic Botany - The place ofDidelotia idae Oldeman, de Wit & Leonard in the Gola Forest is discussed with regard to forest structure, exploitation and species distributions. At present,...     

CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Colless's coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability-generating models for bifurcating tree shapes. The Equal-Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.     

A joint individual‐based model coupling growth and mortality reveals that tree vigor is a key component of tropical forest dynamics

Tree vigor is often used as a covariate when tree mortality is predicted from tree growth in tropical forest dynamic models, but it is rarely explicitly accounted for in a coherent modeling framework. We quantify tree vigor at the individual tree level, based on the difference between expected and observed growth. The available methods to join nonlinear tree growth and mortality processes are not commonly used by forest ecologists so that we develop an inference methodology based on an MCMC approach, allowing us to sample the parameters of the growth and mortality model according to their posterior distribution using the joint model likelihood. We apply our framework to a set of data on the 20‐year dynamics of a forest in Paracou, French Guiana, taking advantage of functional trait‐based growth and mortality models already developed independently. Our results showed that growth and mortality are intimately linked and that the vigor estimator is an essential predictor of mortality, highlighting that trees growing more than expected have a far lower probability of dying. Our joint model methodology is sufficiently generic to be used to join two longitudinal and punctual linked processes and thus may be applied to a wide range of growth and mortality models. In the context of global changes, such joint models are urgently needed in tropical forests to analyze, and then predict, the effects of the ongoing changes on the tree dynamics in hyperdiverse tropical forests.     

Community structure of arboreal caterpillars within and among four tree species of the eastern deciduous forest

Abstract.  1. A seasonally replicated experimental design was used to address the question of how differences within and among host tree species affect arboreal caterpillar communities.
2. Seasonal variation influenced caterpillar community composition most significantly, and the similarity among caterpillar assemblages did not necessarily follow the pattern of phylogenetic relatedness among host trees.
3. Species richness and abundance of caterpillars were higher on oaks and maples than on American beech. Diversity partitioning models revealed that β diversity was only occasionally greater or less than expected by chance alone.
4. When β diversity was significant, values tended to be greater than expected by chance among replicate trees within each species and lower than expected by chance among the four tree species.
5. Differences among trees appeared important for determining patterns of species presence/absence for rare species and influencing patterns of species dominance within caterpillar assemblages. Differences among tree species had a significant effect on overall lepidopteran community composition and mean species diversity (i.e. α diversity).
6. Because β diversity of caterpillars among host trees was lower than expected by chance, host specificity within the Lepidoptera may be less prevalent than thought previously.     

木荷树干夜间水分补充的季节动态及其与树形特征和叶片生物量的关系

利用热消散探针(TDP)法对位于中国科学院华南植物园的木荷(Schima superba)人工纯林的15株样树进行了树干液流监测, 并结合光合有效辐射(PAR)和土壤含水量的测定, 探讨了不同季节的夜间水分补充量与树形特征和叶片生物量的关系。结果表明: 1)夜间液流活动时间与PAR同步, 但其结束时间不受PAR影响; 春、夏季夜间液流明显比秋冬季活跃。2)春、夏、秋季的夜间水分补充量与样树的胸径、冠幅、边材面积、叶片生物量呈极显著线性关系, 与树高仅在春季呈显著线性关系。3)春、夏季的夜间水分补充量主要受样树冠幅影响, 成正相关; 秋季主要受胸径影响, 成正相关; 冬季仅受树高影响。该试验说明木荷夜间水分补充与树形特征、叶片生物量关系密切, 但起主要作用的树形特征和具体关系具有季节差别。     

Spatial associations of tree species in a subtropical evergreen broad-leaved forest

Aims The spatial segregation hypothesis and the low-frequency hypothesis are two important proposed mechanisms that delay or prevent competitive exclusion in ecosystems. Because tree species interact with their neighbors, the importance of these potential processes can be investigated by analyzing the spatial structures of tree species.Methods The distribution of the adults of 27 common tree species in a fully mapped 5-ha subtropical forest plot in Baishanzu, eastern China, was analyzed to investigate the community-level intra- and interspecific spatial association patterns. We first tested for the overall spatial pattern in the 5- to 40-m neighborhoods and classified first-order bivariate associations with a diametric scheme based on Ripley's K and nearest-neighbor statistic (G -function). Then heterogeneous Poisson null models were used to distinguish second-order interactions from overall spatial associations (including first-order effects). Finally, we analyzed correlations between the existence of species interactions and some attributes of the species involved.Important findings Partial overlap and segregation increased with scale, whereas mixing decreased. Nearly 70% of the species pairs occurred less than expected at random, and only 3.4% of the species pairs were well mixed; 11.0% of all species pairs showed significant small-scale interactions, which was a greater frequency than expected by chance if species are abundant or prefer the same habitat, but less frequent than expected if species are highly aggregated. This suggests that both spatial segregation and low frequency of species facilitate species coexistence by reducing the opportunity that trees of two species encounter each other. The study also revealed that positive interactions were more prevalent than negative interactions in the forest, which indicates that positive interactions may have important effects on forest species assemblies.     

Modeling process and material alternatives in life cycle assessments

Background, Aims and Scope  Although LCA is frequently used in product comparison, many practitioners are interested in identifying and assessing improvements within a life cycle. Thus, the goals of this work are to provide guidelines for scenario formulation for process and material alternatives within a life cycle inventory and to evaluate the usefulness of decision tree and matrix computational structures in the assessment of material and process alternatives. We assume that if the analysis goal is to guide the selection among alternatives towards reduced life cycle environmental impacts, then the analysis should estimate the inventory results in a manner that: (1) reveals the optimal set of processes with respect to minimization of each impact of interest, and (2) minimizes and organizes computational and data collection needs. Methods  A sample industrial system is used to reveal the complexities of scenario formulation for process and material alternatives in an LCI. The system includes 4 processes, each executable in 2 different ways, as well as 1 process able to use 2 different materials interchangeably. We formulate and evaluate scenarios for this system using three different methods and find advantages and disadvantages with each. First, the single branch decision tree method stays true to the typical construction of decision trees such that each branch of the tree represents a single scenario. Next, the process flow decision tree method strays from the typical construction of decision trees by following the process flow of the product system, such that multiple branches are needed to represent a single scenario. In the final method, disaggregating the demand vector, each scenario is represented by separate vectors which are combined into a matrix to allow the simultaneous solution of the inventory problem for all scenarios. Results  For both decision tree and matrix methods, scenario formulation, data collection, and scenario analysis are facilitated in two ways. First, process alternatives that cannot actually be chosen should be modeled as sub-inventories (or as a complete LCI within an LCI). Second, material alternatives (e.g., a choice between structural materials) must be maintained within the analysis to avoid the creation of artificial multi-functional processes. Further, in the same manner that decision trees can be used to estimate ‘expected value’ (the sum of the probability of each scenario multiplied by its ‘value’), we find that expected inventory and impact results can be defined for both decision tree and matrix methods. Discussion  For scenario formulation, naming scenarios in a way that differentiate them from other scenarios is complex and important in the continuing development of LCI data for use in databases or LCA software. In the formulation and assessment of scenarios, decision tree methods offer some level of visual appeal and the potential for using commercially available software/ traditional decision tree solution constructs for estimating expected values (for relatively small or highly aggregated product systems). However, solving decision tree systems requires the use of sequential process scaling which is difficult to formalize with mathematical notation. In contrast, preparation of a demand matrix does not require use of the sequential method to solve the inventory problem but requires careful scenario tracking efforts. Conclusions  Here, we recognize that improvements can be made within a product system. This recognition supports the greater use of LCA in supply chain formation and product research, development, and design. We further conclude that although both decision tree and matrix methods are formulated herein to reveal optimal life cycle scenarios, the use of demand matrices is preferred in the preparation of a formal mathematical construct. Further, for both methods, data collection and assessment are facilitated by the use of sub-inventories (or as a complete LCI within an LCI) for process alternatives and the full consideration of material alternatives to avoid the creation of artificial multi-functional processes. Recommendations and Perspectives  The methods described here are used in the assessment of forest management alternatives and are being further developed to form national commodity models considering technology alternatives, national production mixes and imports, and point-to-point transportation models. ESS-Submission Editor: Thomas Gloria, PhD (t.gloria@fivewinds.com)     

Features selection and architecture optimization in connectionist systems

In this paper, we propose a features selection measure and an architecture optimization procedure for Multi-Layer Perceptrons (MLP). The algorithm presented in this contribution employs a heuristic measure named HVS (Heuristic for Variable Selection). This new measure allows us to identify and select important variables in the features space. This can be achieved by eliminating redundant features and those which do not contain enough relevant information. The proposed measure is used in a new procedure aimed at selecting the "best" MLP architecture given an initial structure. Application results for two generic problems: regression and discrimination, demonstrates the proposed selection algorithm's effectiveness in identifying optimized connectionist models with higher accuracy. Finally, an extension of HVS, named epsilonHVS, is proposed for discriminative features detection and architecture optimization for Time Delay Neural Networks models (TDNN).     

Whole animal measurements of shear and adhesive forces in adult tree frogs: insights into underlying mechanisms of adhesion obtained from studying the effects of size and scale

This allometric study of adhesion in 15 Trinidadian tree frog species investigates how relationships between length, area and mass limit the ability of adult frog species of different sizes to adhere to inclined and overhanging surfaces. Our experiments show that hylid frogs possess an area-based wet adhesive system in which larger species are lighter than expected from isometry and adhere better than expected from their toe pad area. However, in spite of these adaptations, larger species adhere less well than smaller species. In addition to these adhesive forces, tree frogs also generate significant shear forces that scale with mass, suggesting that they are frictional forces. Toe pads detach by peeling and frogs have strategies to prevent peeling from taking place while they are adhering to surfaces, including orienting themselves head-up on slopes. The scaling of tree frog adhesion is also used to distinguish between different models for adhesion, including classic formulae for capillarity and Stefan adhesion. These classic equations grossly overestimate the adhesive forces that tree frogs produce. More promising are peeling models, designed to predict the pull-off forces of adhesive tape. However, more work is required before we can qualitatively and quantitatively describe the adhesive mechanism of tree frogs.     

An empirical approach to the analysis of forest stratification

Natural forest communities consist of different overlapping elementary subpopulations. Using the results of forest stratification in the preceding study, the properties of mean tree height for subpopulation in a stratified forest stand were examined. Mean tree height decreased as tree density per subpopulation increased. This relation was described by a simple mathematical model consisting of a power equation of tree density and two coefficients. The first coefficient or exponent of tree density was close to −1/2 in its expectation, while the other coefficient depended on life forms, especially in tropical forests. For tropical deciduous forests which suffered from seasonal forest fires, the latter coefficient was smaller than those for tropical evergreen and Japanese forests. This difference of the coefficient was not clear between tropical evergreen and Japanese forests and between deciduous and evergreen forests in Japan. In conclusion, the proposed model is similar to the 1/2 power law of tree height in man-made forests with simple architecture, and is designated the quasi-1/2 power law of tree height.     

Application of three independent consequential LCA approaches to the agricultural sector in Luxembourg

Purpose

Consequential Life Cycle Assessment (C-LCA) is a “system modelling approach in which activities in a product system are linked so that activities are included in the product system to the extent that they are expected to change as a consequence of a change in demand”. Hence, C-LCA focuses on micro-economic actions linked to macro-economic consequences, by identifying the (marginal) suppliers and technologies prone to be affected by variable scale changes in the demand of a product. Detecting the direct and indirect environmental effects due to changes in the production system is not an easy task. Hence, researchers have combined the consequential perspective with different econometric models. Therefore, the aim of this study is to assess an increase in biocrops cultivation in Luxembourg using three different consequential modelling approaches to understand the benefits, drawbacks and assumptions linked to each approach as applied to the case study selected.

Methods

Firstly, a partial equilibrium (PE) model is used to detect changes in land cultivation based on the farmers’ revenue maximisation. Secondly, another PE model is proposed, which considers a different perspective aiming at minimising a total adaptation cost (so-called opportunity cost) to satisfy a given new demand of domestically produced biofuel. Finally, the consequential system delimitation for agricultural LCA approach, as proposed by Schmidt (Int J Life Cycle Assess 13:350–364, 2008), is applied.

Results and discussion

The two PE models present complex shifts in crop rotation land use changes (LUCs), linked to the optimisation that is performed, while the remaining approach has limited consequential impact on changes in crop patterns since the expert opinion decision tree constitutes a simplification of the ongoing LUCs. However, environmental consequences in the latter were considerably higher due to intercontinental trade assumptions recommended by the experts that were not accounted for in the economic models. Environmental variations between the different scenarios due to LUCs vary based on the different expert- or computational-based assumptions. Finally, environmental consequences as compared with the current state-of-the-art are lame due to the limited impact of the shock within the global trade market.

Conclusions

The use of several consequential modelling approaches within the same study may help widen the interpretation of the advantages or risks of applying a specific change to a production system. In fact, different models may not only be good alternatives in terms of comparability of scenarios and assumptions, but there may also be room for complementing these within a unique framework to reduce uncertainties in an integrated way.     

A Software Architecture for Multi-Cellular System Simulations on Graphics Processing Units

The first aim of simulation in virtual environment is to help biologists to have a better understanding of the simulated system. The cost of such simulation is significantly reduced compared to that of in vivo simulation. However, the inherent complexity of biological system makes it hard to simulate these systems on non-parallel architectures: models might be made of sub-models and take several scales into account; the number of simulated entities may be quite large. Today, graphics cards are used for general purpose computing which has been made easier thanks to frameworks like CUDA or OpenCL. Parallelization of models may however not be easy: parallel computer programing skills are often required; several hardware architectures may be used to execute models. In this paper, we present the software architecture we built in order to implement various models able to simulate multi-cellular system. This architecture is modular and it implements data structures adapted for graphics processing units architectures. It allows efficient simulation of biological mechanisms.     

Rhamnaceae with multiple lateral buds: an architectural analysis

TOURN, G. M., TORTOSA, R. D. & MEDAN, D., 1992. Rhamnaceae with multiple lateral buds: an architectural analysis. A study was made of the morphology and architecture of three species of Rhamnaceae (Ziziphusjujuba, Zjziphus mistol and Paliurus spina-Christi) with multiple lateral buds. The developmental potential of individual meristems of bud complexes was studied and different kinds of shoots were recognized: vegetative long shoots (dominant and subordinate), flowering branches, short shoots and thorn-tipped branchlets. According to the different orders of branching and the patterns of growth, the architectural model for every species was determined. The architecture of the three species does not conform to that of known tree models. Ziziphus mistol and Paliurus spina-Christi have an architecture intermediate between Attim's and Roux's models; Ziziphusjujuba results in a combination of Koriba's and Roux's models.